BIOL 310: GENERAL

BIOLOGY (WADA)
BIOL 310: General Biology (Wada)
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TABLE OF CONTENTS
Licensing

1: Scientific Method and Designing Experiments

1.1: The Study of Life
1.1.1: Prelude to The Study of Life
1.1.2: The Science of Biology
1.1.3: Themes and Concepts of Biology
1.1.E: The Study of Life (Exercises)
1.2: The Scientific Process
1.3: Presenting Data - Graphs and Tables

2: Biological Macromolecules
2.1: The Building Blocks of Molecules
2.2: Water
2.3: Biological Molecules
2.E: Chemistry of Life (Exercises)

3: Cell Diversity, Structures, and Transport

3.1: Cell Structure and Function
3.1.1: How Cells Are Studied
3.1.2: Comparing Prokaryotic and Eukaryotic Cells
3.1.3: Eukaryotic Cells
3.1.4: The Cell Membrane
3.1.5: Passive Transport
3.1.6: Active Transport
3.1.E: Cell Structure and Function (Exercises)
3.2: Eukaryotic Origins
3.3: The Genome

4: Cell Division
4.1: Reproduction at the Cellular Level
4.1.1: The Genome
4.1.2: The Cell Cycle
4.1.3: Cancer and the Cell Cycle
4.1.4: Prokaryotic Cell Division
4.1.E: Reproduction at the Cellular Level (Exercises)
4.2: The Cellular Basis of Inheritance
4.2.1: Sexual Reproduction
4.2.2: Meiosis
4.2.3: Errors in Meiosis
4.2.E: The Cellular Basis of Inheritance (Exercises)

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5: DNA; DNA Technology
5.1: Molecular Biology
5.1.1: The Structure of DNA
5.1.2: DNA Replication
5.1.3: Transcription
5.1.4: Translation
5.1.5: How Genes Are Regulated
5.1.E: Molecular Biology (Exercises)
5.2: Biotechnology
5.2.1: Cloning and Genetic Engineering
5.2.2: Biotechnology in Medicine and Agriculture
5.2.3: Genomics and Proteomics
5.2.E: Biotechnology (Exercises)

6: Genetics
6.1: Patterns of Inheritance
6.1.1: Mendel’s Experiments
6.1.2: Laws of Inheritance
6.1.3: Extensions of the Laws of Inheritance
6.1.E: Patterns of Inheritance (Exercises)
6.2: Pedigrees review

7: Evolution
7.1: Discovering How Populations Change
7.2: Mechanisms of Evolution
7.3: Evidence of Evolution
7.4: Speciation
7.5: Common Misconceptions about Evolution
7.E: Evolution and Its Processes (Exercises)

8: Diversity of Life
8.1: Organizing Life on Earth
8.2: Determining Evolutionary Relationships
8.E: Diversity of Life (Exercises)

9: Ecology
9.1: Population and Community Ecology
9.1.1: Population Demographics and Dynamics
9.1.2: Population Growth and Regulation
9.1.3: The Human Population
9.1.4: Community Ecology
9.1.E: Population and Community Ecology (Exercises)
9.2: Ecosystems and the Biosphere
9.2.1: Energy Flow through Ecosystems
9.2.2: Biogeochemical Cycles
9.2.3: Terrestrial Biomes
9.2.4: Aquatic and Marine Biomes
9.2.E: Ecosystems and the Biosphere (Exercises)

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 9.3: Conservation and Biodiversity
9.3.1: Importance of Biodiversity
9.3.2: Threats to Biodiversity
9.3.3: Preserving Biodiversity
9.3.E: Conservation and Biodiversity (Exercises)

10: Energy and Enzymes

10.1: Free and Activation Energy
10.2: Enzymes
10.3: ATP in Living Systems

11: Photosynthesis
11.1: Photosynthesis
11.1.1: Overview of Photosynthesis
11.1.2: The Light-Dependent Reactions of Photosynthesis
11.1.3: The Calvin Cycle
11.1.E: Photosynthesis (Exercises)

12: Respiration
12.1: How Cells Obtain Energy
12.1.1: Glycolysis
12.1.2: Citric Acid Cycle and Oxidative Phosphorylation
12.1.3: Fermentation
12.1.4: Connections to Other Metabolic Pathways
12.1.E: How Cells Obtain Energy (Exercises)
12.2: Cellular Respiration Overview

13: Microbes; Immune System

13.1: Diversity of Microbes, Fungi, and Protists
13.1.1: Prokaryotic Diversity
13.1.2: Eukaryotic Origins
13.1.3: Protists
13.1.4: Fungi
13.1.E: Diversity of Microbes, Fungi, and Protists (Exercises)
13.2: The Immune System and Disease
13.2.1: Viruses
13.2.2: Innate Immunity
13.2.3: Adaptive Immunity
13.2.4: Disruptions in the Immune System
13.2.E: The Immune System and Desease (Exercises)

14: Reproductive System

14.1: How Animals Reproduce
14.2: Development and Organogenesis
14.3: Human Reproduction
14.E: Animal Reproduction and Development (Exercises)

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15: Skeletal System
15.1: The Animal Body - Basic Form and Function
15.1.1: Prelude to The Animal Body
15.1.2: Animal Form and Function
15.1.3: Animal Primary Tissues
15.1.4: Homeostasis
15.1.E: The Animal Body - Basic Form and Function (Exercises)
15.2: Types of Skeletal Systems
15.3: Bone

16: Circulatory System

16.1: Prelude to the Circulatory System
16.2: Overview of the Circulatory System
16.3: Components of the Blood
16.4: Mammalian Heart and Blood Vessels
16.5: Blood Flow and Blood Pressure Regulation
16.E: The Circulatory System (Exercises)

17: Nutrition and Digestion

17.1: Animal Nutrition and the Digestive System
17.1.1: Prelude to Animal Nutrition and the Digestive System
17.1.2: Digestive Systems
17.1.3: Nutrition and Energy Production
17.1.4: Digestive System Processes
17.1.5: Digestive System Regulation
17.1.E: Animal Nutrition and the Digestive System (Exercises)
17.2: Nervous System
17.3: Sensory Systems
17.3.1: Introduction
17.3.2: Sensory Processes
17.3.3: Somatosensation
17.3.4: Taste and Smell
17.3.5: Hearing and Vestibular Sensation
17.3.6: Vision
17.3.E: Sensory Systems (Exercises)

Index

Glossary

BIOL 307 Modules

18: Fungi and Protists
18.1: Prokaryotic Diversity
18.2: Eukaryotic Origins
18.3: Protists
18.4: Fungi
18.E: Diversity of Microbes, Fungi, and Protists (Exercises)
19: Plants
19.1: The Plant Kingdom

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 19.2: Seedless Plants
19.3: Seed Plants - Gymnosperms
19.4: Seed Plants- Angiosperms
19.E: Diversity of Plants (Exercises)
20: Animal Diversity
20.1: Features of the Animal Kingdom
20.2: Sponges and Cnidarians
20.3: Flatworms, Nematodes, and Arthropods
20.4: Mollusks and Annelids
20.5: Echinoderms and Chordates
20.6: Vertebrates
20.E: Diversity of Animals (Exercises)

Reference Material
A: The Periodic Table of Elements
B: Geological Time
C: Measurements and the Metric System

Detailed Licensing

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Licensing
A detailed breakdown of this resource's licensing can be found in Back Matter/Detailed Licensing.

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 CHAPTER OVERVIEW

1: Scientific Method and Designing Experiments

1.1: The Study of Life
1.1.1: Prelude to The Study of Life
1.1.2: The Science of Biology
1.1.3: Themes and Concepts of Biology
1.1.E: The Study of Life (Exercises)
1.2: The Scientific Process
1.3: Presenting Data - Graphs and Tables

Thumbnail: Person Holding Green-leafed Plant (Chokniti Khongchum via Pexels)

1: Scientific Method and Designing Experiments is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
 SECTION OVERVIEW

1.1: The Study of Life

1.1.1: Prelude to The Study of Life

1.1.2: The Science of Biology

1.1.3: Themes and Concepts of Biology

1.1.E: The Study of Life (Exercises)

Contributors and Attributions

Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski
(Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute
of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY
4.0; Download for free at [Link]

This page titled 1.1: The Study of Life is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.

Access for free at OpenStax 1.1.1 [Link]

1.1.1: Prelude to The Study of Life
Viewed from space, Earth offers no clues about the diversity of life forms that reside there. The first forms of life on Earth are
thought to have been microorganisms that existed for billions of years in the ocean before plants and animals appeared. The
mammals, birds, and flowers so familiar to us are all relatively recent, originating 130 to 200 million years ago. Humans have
inhabited this planet for only the last 2.5 million years, and only in the last 200,000 years have humans started looking like we do
today.

Figure [Link] : This NASA image is a composite of several satellite-based views of Earth. To make the whole-Earth image, NASA
scientists combine observations of different parts of the planet.

This page titled 1.1.1: Prelude to The Study of Life is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
1.0: Prelude to The Study of Life by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

1.1.2: The Science of Biology
Skills to Develop
Identify the shared characteristics of the natural sciences
Summarize the steps of the scientific method
Compare inductive reasoning with deductive reasoning
Describe the goals of basic science and applied science

(a) (b)
Figure [Link] : Formerly called blue-green algae, these (a) cyanobacteria, shown here at 300x magnification under a light
microscope, are some of Earth’s oldest life forms. These (b) stromatolites along the shores of Lake Thetis in Western Australia are
ancient structures formed by the layering of cyanobacteria in shallow waters. (credit a: modification of work by NASA; credit b:
modification of work by Ruth Ellison; scale-bar data from Matt Russell)
What is biology? In simple terms, biology is the study of living organisms and their interactions with one another and their
environments. This is a very broad definition because the scope of biology is vast. Biologists may study anything from the
microscopic or submicroscopic view of a cell to ecosystems and the whole living planet (Figure [Link]). Listening to the daily
news, you will quickly realize how many aspects of biology are discussed every day. For example, recent news topics include
Escherichia coli (Figure [Link]) outbreaks in spinach and Salmonella contamination in peanut butter. Other subjects include
efforts toward finding a cure for AIDS, Alzheimer’s disease, and cancer. On a global scale, many researchers are committed to
finding ways to protect the planet, solve environmental issues, and reduce the effects of climate change. All of these diverse
endeavors are related to different facets of the discipline of biology.

Figure [Link] : Escherichia coli (E. coli) bacteria, seen in this scanning electron micrograph, are normal residents of our digestive
tracts that aid in the absorption of vitamin K and other nutrients. However, virulent strains are sometimes responsible for disease
outbreaks. (credit: Eric Erbe, digital colorization by Christopher Pooley, both of USDA, ARS, EMU)

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The Process of Science
Biology is a science, but what exactly is science? What does the study of biology share with other scientific disciplines? Science
(from the Latin scientia, meaning “knowledge”) can be defined as knowledge that covers general truths or the operation of general
laws, especially when acquired and tested by the scientific method. It becomes clear from this definition that the application of the
scientific method plays a major role in science. The scientific method is a method of research with defined steps that include
experiments and careful observation.
The steps of the scientific method will be examined in detail later, but one of the most important aspects of this method is the
testing of hypotheses by means of repeatable experiments. A hypothesis is a suggested explanation for an event, which can be
tested. Although using the scientific method is inherent to science, it is inadequate in determining what science is. This is because it
is relatively easy to apply the scientific method to disciplines such as physics and chemistry, but when it comes to disciplines like
archaeology, psychology, and geology, the scientific method becomes less applicable as it becomes more difficult to repeat
experiments.
These areas of study are still sciences, however. Consider archeology—even though one cannot perform repeatable experiments,
hypotheses may still be supported. For instance, an archeologist can hypothesize that an ancient culture existed based on finding a
piece of pottery. Further hypotheses could be made about various characteristics of this culture, and these hypotheses may be found
to be correct or false through continued support or contradictions from other findings. A hypothesis may become a verified theory.
A theory is a tested and confirmed explanation for observations or phenomena. Science may be better defined as fields of study that
attempt to comprehend the nature of the universe.

Natural Sciences
What would you expect to see in a museum of natural sciences? Frogs? Plants? Dinosaur skeletons? Exhibits about how the brain
functions? A planetarium? Gems and minerals? Or, maybe all of the above? Science includes such diverse fields as astronomy,
biology, computer sciences, geology, logic, physics, chemistry, and mathematics (Figure [Link]). However, those fields of science
related to the physical world and its phenomena and processes are considered natural sciences. Thus, a museum of natural sciences
might contain any of the items listed above.

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 Figure [Link] : The diversity of scientific fields includes astronomy, biology, computer science, geology, logic, physics, chemistry,
mathematics, and many other fields. (credit: “Image Editor”/Flickr)
There is no complete agreement when it comes to defining what the natural sciences include, however. For some experts, the
natural sciences are astronomy, biology, chemistry, earth science, and physics. Other scholars choose to divide natural sciences into
life sciences, which study living things and include biology, and physical sciences, which study nonliving matter and include
astronomy, geology, physics, and chemistry. Some disciplines such as biophysics and biochemistry build on both life and physical
sciences and are interdisciplinary. Natural sciences are sometimes referred to as “hard science” because they rely on the use of
quantitative data; social sciences that study society and human behavior are more likely to use qualitative assessments to drive
investigations and findings.
Not surprisingly, the natural science of biology has many branches or subdisciplines. Cell biologists study cell structure and
function, while biologists who study anatomy investigate the structure of an entire organism. Those biologists studying physiology,
however, focus on the internal functioning of an organism. Some areas of biology focus on only particular types of living things.
For example, botanists explore plants, while zoologists specialize in animals.

Scientific Reasoning
One thing is common to all forms of science: an ultimate goal “to know.” Curiosity and inquiry are the driving forces for the
development of science. Scientists seek to understand the world and the way it operates. To do this, they use two methods of logical
thinking: inductive reasoning and deductive reasoning.
Inductive reasoning is a form of logical thinking that uses related observations to arrive at a general conclusion. This type of
reasoning is common in descriptive science. A life scientist such as a biologist makes observations and records them. These data
can be qualitative or quantitative, and the raw data can be supplemented with drawings, pictures, photos, or videos. From many
observations, the scientist can infer conclusions (inductions) based on evidence. Inductive reasoning involves formulating
generalizations inferred from careful observation and the analysis of a large amount of data. Brain studies provide an example. In

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this type of research, many live brains are observed while people are doing a specific activity, such as viewing images of food. The
part of the brain that “lights up” during this activity is then predicted to be the part controlling the response to the selected stimulus,
in this case, images of food. The “lighting up” of the various areas of the brain is caused by excess absorption of radioactive sugar
derivatives by active areas of the brain. The resultant increase in radioactivity is observed by a scanner. Then, researchers can
stimulate that part of the brain to see if similar responses result.
Deductive reasoning or deduction is the type of logic used in hypothesis-based science. In deductive reason, the pattern of thinking
moves in the opposite direction as compared to inductive reasoning. Deductive reasoning is a form of logical thinking that uses a
general principle or law to forecast specific results. From those general principles, a scientist can extrapolate and predict the
specific results that would be valid as long as the general principles are valid. Studies in climate change can illustrate this type of
reasoning. For example, scientists may predict that if the climate becomes warmer in a particular region, then the distribution of
plants and animals should change. These predictions have been made and tested, and many such changes have been found, such as
the modification of arable areas for agriculture, with change based on temperature averages.
Both types of logical thinking are related to the two main pathways of scientific study: descriptive science and hypothesis-based
science. Descriptive (or discovery) science, which is usually inductive, aims to observe, explore, and discover, while hypothesis-
based science, which is usually deductive, begins with a specific question or problem and a potential answer or solution that can be
tested. The boundary between these two forms of study is often blurred, and most scientific endeavors combine both approaches.
The fuzzy boundary becomes apparent when thinking about how easily observation can lead to specific questions. For example, a
gentleman in the 1940s observed that the burr seeds that stuck to his clothes and his dog’s fur had a tiny hook structure. On closer
inspection, he discovered that the burrs’ gripping device was more reliable than a zipper. He eventually developed a company and
produced the hook-and-loop fastener popularly known today as Velcro. Descriptive science and hypothesis-based science are in
continuous dialogue.

The Scientific Method

Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to
other sciences as well and is often referred to as the scientific method. The scientific method was used even in ancient times, but it
was first documented by England’s Sir Francis Bacon (1561–1626) (Figure [Link]), who set up inductive methods for scientific
inquiry. The scientific method is not exclusively used by biologists but can be applied to almost all fields of study as a logical,
rational problem-solving method.

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 Figure [Link] : Sir Francis Bacon (1561–1626) is credited with being the first to define the scientific method. (credit: Paul van
Somer)
The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Let’s think about a
simple problem that starts with an observation and apply the scientific method to solve the problem. One Monday morning, a
student arrives at class and quickly discovers that the classroom is too warm. That is an observation that also describes a problem:
the classroom is too warm. The student then asks a question: “Why is the classroom so warm?”

Proposing a Hypothesis
Recall that a hypothesis is a suggested explanation that can be tested. To solve a problem, several hypotheses may be proposed. For
example, one hypothesis might be, “The classroom is warm because no one turned on the air conditioning.” But there could be
other responses to the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The classroom is
warm because there is a power failure, and so the air conditioning doesn’t work.”
Once a hypothesis has been selected, the student can make a prediction. A prediction is similar to a hypothesis but it typically has
the format “If . . . then . . . .” For example, the prediction for the first hypothesis might be, “If the student turns on the air
conditioning, then the classroom will no longer be too warm.”

Testing a Hypothesis
A valid hypothesis must be testable. It should also be falsifiable, meaning that it can be disproven by experimental results.
Importantly, science does not claim to “prove” anything because scientific understandings are always subject to modification with
further information. This step—openness to disproving ideas—is what distinguishes sciences from non-sciences. The presence of
the supernatural, for instance, is neither testable nor falsifiable. To test a hypothesis, a researcher will conduct one or more

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experiments designed to eliminate one or more of the hypotheses. Each experiment will have one or more variables and one or
more controls. A variable is any part of the experiment that can vary or change during the experiment. The control group contains
every feature of the experimental group except it is not given the manipulation that is hypothesized about. Therefore, if the results
of the experimental group differ from the control group, the difference must be due to the hypothesized manipulation, rather than
some outside factor. Look for the variables and controls in the examples that follow. To test the first hypothesis, the student would
find out if the air conditioning is on. If the air conditioning is turned on but does not work, there should be another reason, and this
hypothesis should be rejected. To test the second hypothesis, the student could check if the lights in the classroom are functional. If
so, there is no power failure and this hypothesis should be rejected. Each hypothesis should be tested by carrying out appropriate
experiments. Be aware that rejecting one hypothesis does not determine whether or not the other hypotheses can be accepted; it
simply eliminates one hypothesis that is not valid (Figure [Link]). Using the scientific method, the hypotheses that are inconsistent
with experimental data are rejected.
While this “warm classroom” example is based on observational results, other hypotheses and experiments might have clearer
controls. For instance, a student might attend class on Monday and realize she had difficulty concentrating on the lecture. One
observation to explain this occurrence might be, “When I eat breakfast before class, I am better able to pay attention.” The student
could then design an experiment with a control to test this hypothesis.
In hypothesis-based science, specific results are predicted from a general premise. This type of reasoning is called deductive
reasoning: deduction proceeds from the general to the particular. But the reverse of the process is also possible: sometimes,
scientists reach a general conclusion from a number of specific observations. This type of reasoning is called inductive reasoning,
and it proceeds from the particular to the general. Inductive and deductive reasoning are often used in tandem to advance scientific
knowledge (Figure [Link]).

Art Connection

Figure [Link] : The scientific method consists of a series of well-defined steps. If a hypothesis is not supported by
experimental data, a new hypothesis can be proposed.

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In the example below, the scientific method is used to solve an everyday problem. Order the scientific method steps (numbered
items) with the process of solving the everyday problem (lettered items). Based on the results of the experiment, is the
hypothesis correct? If it is incorrect, propose some alternative hypotheses.
1. Observation
2. Question
3. Hypothesis (answer)
4. Prediction
5. Experiment
6. Result
A. There is something wrong with the electrical outlet.
B. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.
C. My toaster doesn’t toast my bread.
D. I plug my coffee maker into the outlet.
E. My coffeemaker works.
F. Why doesn’t my toaster work?

Art Connection

Figure [Link] : Scientists use two types of reasoning, inductive and deductive reasoning, to advance scientific knowledge. As
is the case in this example, the conclusion from inductive reasoning can often become the premise for inductive reasoning.
Decide if each of the following is an example of inductive or deductive reasoning.
1. All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings
enable flight.
2. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if
global temperatures increase.
3. Chromosomes, the carriers of DNA, separate into daughter cells during cell division. Therefore, DNA is the genetic
material.
4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an
evolutionary advantage.

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The scientific method may seem too rigid and structured. It is important to keep in mind that, although scientists often follow this
sequence, there is flexibility. Sometimes an experiment leads to conclusions that favor a change in approach; often, an experiment
brings entirely new scientific questions to the puzzle. Many times, science does not operate in a linear fashion; instead, scientists
continually draw inferences and make generalizations, finding patterns as their research proceeds. Scientific reasoning is more
complex than the scientific method alone suggests. Notice, too, that the scientific method can be applied to solving problems that
aren’t necessarily scientific in nature.

Two Types of Science: Basic Science and Applied Science

The scientific community has been debating for the last few decades about the value of different types of science. Is it valuable to
pursue science for the sake of simply gaining knowledge, or does scientific knowledge only have worth if we can apply it to
solving a specific problem or to bettering our lives? This question focuses on the differences between two types of science: basic
science and applied science.
Basic science or “pure” science seeks to expand knowledge regardless of the short-term application of that knowledge. It is not
focused on developing a product or a service of immediate public or commercial value. The immediate goal of basic science is
knowledge for knowledge’s sake, though this does not mean that, in the end, it may not result in a practical application.
In contrast, applied science or “technology,” aims to use science to solve real-world problems, making it possible, for example, to
improve a crop yield, find a cure for a particular disease, or save animals threatened by a natural disaster (Figure [Link]). In
applied science, the problem is usually defined for the researcher.

Figure [Link] : After Hurricane Ike struck the Gulf Coast in 2008, the U.S. Fish and Wildlife Service rescued this brown pelican.
Thanks to applied science, scientists knew how to rehabilitate the bird. (credit: FEMA)
Some individuals may perceive applied science as “useful” and basic science as “useless.” A question these people might pose to a
scientist advocating knowledge acquisition would be, “What for?” A careful look at the history of science, however, reveals that
basic knowledge has resulted in many remarkable applications of great value. Many scientists think that a basic understanding of
science is necessary before an application is developed; therefore, applied science relies on the results generated through basic
science. Other scientists think that it is time to move on from basic science and instead to find solutions to actual problems. Both
approaches are valid. It is true that there are problems that demand immediate attention; however, few solutions would be found
without the help of the wide knowledge foundation generated through basic science.
One example of how basic and applied science can work together to solve practical problems occurred after the discovery of DNA
structure led to an understanding of the molecular mechanisms governing DNA replication. Strands of DNA, unique in every
human, are found in our cells, where they provide the instructions necessary for life. During DNA replication, DNA makes new
copies of itself, shortly before a cell divides. Understanding the mechanisms of DNA replication enabled scientists to develop
laboratory techniques that are now used to identify genetic diseases, pinpoint individuals who were at a crime scene, and determine
paternity. Without basic science, it is unlikely that applied science would exist.
Another example of the link between basic and applied research is the Human Genome Project, a study in which each human
chromosome was analyzed and mapped to determine the precise sequence of DNA subunits and the exact location of each gene.
(The gene is the basic unit of heredity; an individual’s complete collection of genes is his or her genome.) Other less complex
organisms have also been studied as part of this project in order to gain a better understanding of human chromosomes. The Human

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Genome Project (Figure [Link]) relied on basic research carried out with simple organisms and, later, with the human genome. An
important end goal eventually became using the data for applied research, seeking cures and early diagnoses for genetically related
diseases.

Figure [Link] : The Human Genome Project was a 13-year collaborative effort among researchers working in several different
fields of science. The project, which sequenced the entire human genome, was completed in 2003. (credit: the U.S. Department of
Energy Genome Programs ([Link]
While research efforts in both basic science and applied science are usually carefully planned, it is important to note that some
discoveries are made by serendipity, that is, by means of a fortunate accident or a lucky surprise. Penicillin was discovered when
biologist Alexander Fleming accidentally left a petri dish of Staphylococcus bacteria open. An unwanted mold grew on the dish,
killing the bacteria. The mold turned out to be Penicillium, and a new antibiotic was discovered. Even in the highly organized
world of science, luck—when combined with an observant, curious mind—can lead to unexpected breakthroughs.

Reporting Scientific Work

Whether scientific research is basic science or applied science, scientists must share their findings in order for other researchers to
expand and build upon their discoveries. Collaboration with other scientists—when planning, conducting, and analyzing results—
are all important for scientific research. For this reason, important aspects of a scientist’s work are communicating with peers and
disseminating results to peers. Scientists can share results by presenting them at a scientific meeting or conference, but this
approach can reach only the select few who are present. Instead, most scientists present their results in peer-reviewed manuscripts
that are published in scientific journals. Peer-reviewed manuscripts are scientific papers that are reviewed by a scientist’s
colleagues, or peers. These colleagues are qualified individuals, often experts in the same research area, who judge whether or not
the scientist’s work is suitable for publication. The process of peer review helps to ensure that the research described in a scientific
paper or grant proposal is original, significant, logical, and thorough. Grant proposals, which are requests for research funding, are
also subject to peer review. Scientists publish their work so other scientists can reproduce their experiments under similar or
different conditions to expand on the findings. The experimental results must be consistent with the findings of other scientists.
A scientific paper is very different from creative writing. Although creativity is required to design experiments, there are fixed
guidelines when it comes to presenting scientific results. First, scientific writing must be brief, concise, and accurate. A scientific
paper needs to be succinct but detailed enough to allow peers to reproduce the experiments.
The scientific paper consists of several specific sections—introduction, materials and methods, results, and discussion. This
structure is sometimes called the “IMRaD” format. There are usually acknowledgment and reference sections as well as an abstract
(a concise summary) at the beginning of the paper. There might be additional sections depending on the type of paper and the
journal where it will be published; for example, some review papers require an outline.

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The introduction starts with brief, but broad, background information about what is known in the field. A good introduction also
gives the rationale of the work; it justifies the work carried out and also briefly mentions the end of the paper, where the hypothesis
or research question driving the research will be presented. The introduction refers to the published scientific work of others and
therefore requires citations following the style of the journal. Using the work or ideas of others without proper citation is
considered plagiarism.
The materials and methods section includes a complete and accurate description of the substances used, and the method and
techniques used by the researchers to gather data. The description should be thorough enough to allow another researcher to repeat
the experiment and obtain similar results, but it does not have to be verbose. This section will also include information on how
measurements were made and what types of calculations and statistical analyses were used to examine raw data. Although the
materials and methods section gives an accurate description of the experiments, it does not discuss them.
Some journals require a results section followed by a discussion section, but it is more common to combine both. If the journal
does not allow the combination of both sections, the results section simply narrates the findings without any further interpretation.
The results are presented by means of tables or graphs, but no duplicate information should be presented. In the discussion section,
the researcher will interpret the results, describe how variables may be related, and attempt to explain the observations. It is
indispensable to conduct an extensive literature search to put the results in the context of previously published scientific research.
Therefore, proper citations are included in this section as well.
Finally, the conclusion section summarizes the importance of the experimental findings. While the scientific paper almost certainly
answered one or more scientific questions that were stated, any good research should lead to more questions. Therefore, a well-
done scientific paper leaves doors open for the researcher and others to continue and expand on the findings.
Review articles do not follow the IMRAD format because they do not present original scientific findings, or primary literature;
instead, they summarize and comment on findings that were published as primary literature and typically include extensive
reference sections.

Summary
Biology is the science that studies living organisms and their interactions with one another and their environments. Science
attempts to describe and understand the nature of the universe in whole or in part by rational means. Science has many fields; those
fields related to the physical world and its phenomena are considered natural sciences.
Science can be basic or applied. The main goal of basic science is to expand knowledge without any expectation of short-term
practical application of that knowledge. The primary goal of applied research, however, is to solve practical problems.
Two types of logical reasoning are used in science. Inductive reasoning uses particular results to produce general scientific
principles. Deductive reasoning is a form of logical thinking that predicts results by applying general principles. The common
thread throughout scientific research is the use of the scientific method, a step-based process that consists of making observations,
defining a problem, posing hypotheses, testing these hypotheses, and drawing one or more conclusions. The testing uses proper
controls. Scientists present their results in peer-reviewed scientific papers published in scientific journals. A scientific research
paper consists of several well-defined sections: introduction, materials and methods, results, and, finally, a concluding discussion.
Review papers summarize the research done in a particular field over a period of time.

Art Connections
Figure [Link]: In the example below, the scientific method is used to solve an everyday problem. Order the scientific method
steps (numbered items) with the process of solving the everyday problem (lettered items). Based on the results of the
experiment, is the hypothesis correct? If it is incorrect, propose some alternative hypotheses.
1. Observation
2. Question
3. Hypothesis (answer)
4. Prediction
5. Experiment
6. Result
A. There is something wrong with the electrical outlet.
B. If something is wrong with the outlet, my coffeemaker also won’t work when plugged into it.

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 C. My toaster doesn’t toast my bread.
D. I plug my coffee maker into the outlet.
E. My coffeemaker works.
F. Why doesn’t my toaster work?

Answer
1: C; 2: F; 3: A; 4: B; 5: D; 6: E. The original hypothesis is incorrect, as the coffeemaker works when plugged into the outlet.
Alternative hypotheses include that the toaster might be broken or that the toaster wasn't turned on.

Figure [Link]: Decide if each of the following is an example of inductive or deductive reasoning.
1. All flying birds and insects have wings. Birds and insects flap their wings as they move through the air. Therefore, wings
enable flight.
2. Insects generally survive mild winters better than harsh ones. Therefore, insect pests will become more problematic if global
temperatures increase.
3. Chromosomes, the carriers of DNA, separate into daughter cells during cell division. Therefore, DNA is the genetic material.
4. Animals as diverse as humans, insects, and wolves all exhibit social behavior. Therefore, social behavior must have an
evolutionary advantage.

Answer
1: inductive; 2: deductive; 3: deductive; 4: inductive.

Glossary
abstract
opening section of a scientific paper that summarizes the research and conclusions

applied science
form of science that aims to solve real-world problems

basic science
science that seeks to expand knowledge and understanding regardless of the short-term application of that knowledge

biology
the study of living organisms and their interactions with one another and their environments

conclusion
section of a scientific paper that summarizes the importance of the experimental findings

control
part of an experiment that does not change during the experiment

deductive reasoning
form of logical thinking that uses a general inclusive statement to forecast specific results

descriptive science
(also, discovery science) form of science that aims to observe, explore, and investigate

discussion
section of a scientific paper in which the author interprets experimental results, describes how variables may be related, and
attempts to explain the phenomenon in question

falsifiable
able to be disproven by experimental results

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hypothesis
suggested explanation for an observation, which can be tested

hypothesis-based science
form of science that begins with a specific question and potential testable answers

inductive reasoning
form of logical thinking that uses related observations to arrive at a general conclusion

introduction
opening section of a scientific paper, which provides background information about what was known in the field prior to the
research reported in the paper

life science
field of science, such as biology, that studies living things

materials and methods

section of a scientific paper that includes a complete description of the substances, methods, and techniques used by the
researchers to gather data

natural science
field of science that is related to the physical world and its phenomena and processes

peer-reviewed manuscript
scientific paper that is reviewed by a scientist’s colleagues who are experts in the field of study

physical science
field of science, such as geology, astronomy, physics, and chemistry, that studies nonliving matter

plagiarism
using other people’s work or ideas without proper citation, creating the false impression that those are the author’s original ideas

results
section of a scientific paper in which the author narrates the experimental findings and presents relevant figures, pictures,
diagrams, graphs, and tables, without any further interpretation

review article
paper that summarizes and comments on findings that were published as primary literature

science
knowledge that covers general truths or the operation of general laws, especially when acquired and tested by the scientific
method

scientific method
method of research with defined steps that include observation, formulation of a hypothesis, testing, and confirming or
falsifying the hypothesis

serendipity
fortunate accident or a lucky surprise

theory
tested and confirmed explanation for observations or phenomena

variable
part of an experiment that the experimenter can vary or change

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This page titled 1.1.2: The Science of Biology is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
1.1: The Science of Biology by OpenStax is licensed CC BY 4.0.

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1.1.3: Themes and Concepts of Biology
Skills to Develop
Identify and describe the properties of life
Describe the levels of organization among living things
Recognize and interpret a phylogenetic tree
List examples of different sub disciplines in biology

Biology is the science that studies life, but what exactly is life? This may sound like a silly question with an obvious response, but
it is not always easy to define life. For example, a branch of biology called virology studies viruses, which exhibit some of the
characteristics of living entities but lack others. It turns out that although viruses can attack living organisms, cause diseases, and
even reproduce, they do not meet the criteria that biologists use to define life. Consequently, virologists are not biologists, strictly
speaking. Similarly, some biologists study the early molecular evolution that gave rise to life; since the events that preceded life are
not biological events, these scientists are also excluded from biology in the strict sense of the term.
From its earliest beginnings, biology has wrestled with three questions: What are the shared properties that make something
“alive”? And once we know something is alive, how do we find meaningful levels of organization in its structure? And, finally,
when faced with the remarkable diversity of life, how do we organize the different kinds of organisms so that we can better
understand them? As new organisms are discovered every day, biologists continue to seek answers to these and other questions.

Properties of Life
All living organisms share several key characteristics or functions: order, sensitivity or response to the environment, reproduction,
adaptation, growth and development, regulation, homeostasis, energy processing, and evolution. When viewed together, these nine
characteristics serve to define life.

Order
Organisms are highly organized, coordinated structures that consist of one or more cells. Even very simple, single-celled organisms
are remarkably complex: inside each cell, atoms make up molecules; these in turn make up cell organelles and other cellular
inclusions. In multicellular organisms (Figure [Link]), similar cells form tissues. Tissues, in turn, collaborate to create organs
(body structures with a distinct function). Organs work together to form organ systems.

Figure [Link] : A toad represents a highly organized structure consisting of cells, tissues, organs, and organ systems. (credit:
“Ivengo”/Wikimedia Commons)

Sensitivity or Response to Stimuli

Organisms respond to diverse stimuli. For example, plants can bend toward a source of light, climb on fences and walls, or respond
to touch (Figure [Link]). Even tiny bacteria can move toward or away from chemicals (a process called chemotaxis) or light
(phototaxis). Movement toward a stimulus is considered a positive response, while movement away from a stimulus is considered a
negative response.

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 Figure [Link] : The leaves of this sensitive plant (Mimosa pudica) will instantly droop and fold when touched. After a few minutes,
the plant returns to normal. (credit: Alex Lomas)

Link to Learning

How sun owers "track" movements o…

o…

Video: Watch this video to see how plants respond to a stimulus—from opening to light, to wrapping a tendril around a branch,
to capturing prey.

Reproduction
Single-celled organisms reproduce by first duplicating their DNA, and then dividing it equally as the cell prepares to divide to form
two new cells. Multicellular organisms often produce specialized reproductive germline cells that will form new individuals. When
reproduction occurs, genes containing DNA are passed along to an organism’s offspring. These genes ensure that the offspring will
belong to the same species and will have similar characteristics, such as size and shape.

Growth and Development

Organisms grow and develop following specific instructions coded for by their genes. These genes provide instructions that will
direct cellular growth and development, ensuring that a species’ young (Figure [Link]) will grow up to exhibit many of the same
characteristics as its parents.

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 Figure [Link] : Although no two look alike, these kittens have inherited genes from both parents and share many of the same
characteristics. (credit: Rocky Mountain Feline Rescue)

Regulation
Even the smallest organisms are complex and require multiple regulatory mechanisms to coordinate internal functions, respond to
stimuli, and cope with environmental stresses. Two examples of internal functions regulated in an organism are nutrient transport
and blood flow. Organs (groups of tissues working together) perform specific functions, such as carrying oxygen throughout the
body, removing wastes, delivering nutrients to every cell, and cooling the body.

Homeostasis
In order to function properly, cells need to have appropriate conditions such as proper temperature, pH, and appropriate
concentration of diverse chemicals. These conditions may, however, change from one moment to the next. Organisms are able to
maintain internal conditions within a narrow range almost constantly, despite environmental changes, through homeostasis
(literally, “steady state”)—the ability of an organism to maintain constant internal conditions. For example, an organism needs to
regulate body temperature through a process known as thermoregulation. Organisms that live in cold climates, such as the polar
bear (Figure [Link]), have body structures that help them withstand low temperatures and conserve body heat. Structures that aid
in this type of insulation include fur, feathers, blubber, and fat. In hot climates, organisms have methods (such as perspiration in
humans or panting in dogs) that help them to shed excess body heat.

Figure [Link] : Polar bears (Ursus maritimus) and other mammals living in ice-covered regions maintain their body temperature by
generating heat and reducing heat loss through thick fur and a dense layer of fat under their skin. (credit: “longhorndave”/Flickr)

Energy Processing
All organisms use a source of energy for their metabolic activities. Some organisms capture energy from the sun and convert it into
chemical energy in food; others use chemical energy in molecules they take in as food (Figure [Link]).

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 Figure [Link] : The California condor (Gymnogyps californianus) uses chemical energy derived from food to power flight.
California condors are an endangered species; this bird has a wing tag that helps biologists identify the individual. (credit: Pacific
Southwest Region U.S. Fish and Wildlife Service)

Levels of Organization of Living Things

Living things are highly organized and structured, following a hierarchy that can be examined on a scale from small to large. The
atom is the smallest and most fundamental unit of matter. It consists of a nucleus surrounded by electrons. Atoms form molecules.
A molecule is a chemical structure consisting of at least two atoms held together by one or more chemical bonds. Many molecules
that are biologically important are macromolecules, large molecules that are typically formed by polymerization (a polymer is a
large molecule that is made by combining smaller units called monomers, which are simpler than macromolecules). An example of
a macromolecule is deoxyribonucleic acid (DNA) (Figure [Link]), which contains the instructions for the structure and functioning
of all living organisms.

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 Figure [Link] : All molecules, including this DNA molecule, are composed of atoms. (credit: “brian0918”/Wikimedia Commons)

Link to Learning

Video: Watch this video that animates the three-dimensional structure of the DNA molecule shown in Figure [Link].

Some cells contain aggregates of macromolecules surrounded by membranes; these are called organelles. Organelles are small
structures that exist within cells. Examples of organelles include mitochondria and chloroplasts, which carry out indispensable
functions: mitochondria produce energy to power the cell, while chloroplasts enable green plants to utilize the energy in sunlight to
make sugars. All living things are made of cells; the cell itself is the smallest fundamental unit of structure and function in living
organisms. (This requirement is why viruses are not considered living: they are not made of cells. To make new viruses, they have
to invade and hijack the reproductive mechanism of a living cell; only then can they obtain the materials they need to reproduce.)

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Some organisms consist of a single cell and others are multicellular. Cells are classified as prokaryotic or eukaryotic. Prokaryotes
are single-celled or colonial organisms that do not have membrane-bound nuclei; in contrast, the cells of eukaryotes do have
membrane-bound organelles and a membrane-bound nucleus.
In larger organisms, cells combine to make tissues, which are groups of similar cells carrying out similar or related functions.
Organs are collections of tissues grouped together performing a common function. Organs are present not only in animals but also
in plants. An organ system is a higher level of organization that consists of functionally related organs. Mammals have many organ
systems. For instance, the circulatory system transports blood through the body and to and from the lungs; it includes organs such
as the heart and blood vessels. Organisms are individual living entities. For example, each tree in a forest is an organism. Single-
celled prokaryotes and single-celled eukaryotes are also considered organisms and are typically referred to as microorganisms.
All the individuals of a species living within a specific area are collectively called a population. For example, a forest may include
many pine trees. All of these pine trees represent the population of pine trees in this forest. Different populations may live in the
same specific area. For example, the forest with the pine trees includes populations of flowering plants and also insects and
microbial populations. A community is the sum of populations inhabiting a particular area. For instance, all of the trees, flowers,
insects, and other populations in a forest form the forest’s community. The forest itself is an ecosystem. An ecosystem consists of
all the living things in a particular area together with the abiotic, non-living parts of that environment such as nitrogen in the soil or
rain water. At the highest level of organization (Figure [Link]), the biosphere is the collection of all ecosystems, and it represents
the zones of life on earth. It includes land, water, and even the atmosphere to a certain extent.

Art Connection

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Figure [Link] : The biological levels of organization of living things are shown. From a single organelle to the entire
biosphere, living organisms are parts of a highly structured hierarchy. (credit “organelles”: modification of work by Umberto
Salvagnin; credit “cells”: modification of work by Bruce Wetzel, Harry Schaefer/ National Cancer Institute; credit “tissues”:
modification of work by Kilbad; Fama Clamosa; Mikael Häggström; credit “organs”: modification of work by Mariana Ruiz
Villareal; credit “organisms”: modification of work by "Crystal"/Flickr; credit “ecosystems”: modification of work by US Fish
and Wildlife Service Headquarters; credit “biosphere”: modification of work by NASA)

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 Which of the following statements is false?
A. Tissues exist within organs which exist within organ systems.
B. Communities exist within populations which exist within ecosystems.
C. Organelles exist within cells which exist within tissues.
D. Communities exist within ecosystems which exist in the biosphere.

The Diversity of Life

The fact that biology, as a science, has such a broad scope has to do with the tremendous diversity of life on earth. The source of
this diversity is evolution, the process of gradual change during which new species arise from older species. Evolutionary biologists
study the evolution of living things in everything from the microscopic world to ecosystems.
The evolution of various life forms on Earth can be summarized in a phylogenetic tree (Figure [Link]). A phylogenetic tree is a
diagram showing the evolutionary relationships among biological species based on similarities and differences in genetic or
physical traits or both. A phylogenetic tree is composed of nodes and branches. The internal nodes represent ancestors and are
points in evolution when, based on scientific evidence, an ancestor is thought to have diverged to form two new species. The length
of each branch is proportional to the time elapsed since the split.

Figure [Link] : This phylogenetic tree was constructed by microbiologist Carl Woese using data obtained from sequencing
ribosomal RNA genes. The tree shows the separation of living organisms into three domains: Bacteria, Archaea, and Eukarya.
Bacteria and Archaea are prokaryotes, single-celled organisms lacking intracellular organelles. (credit: Eric Gaba; NASA
Astrobiology Institute)

Evolution Connection: Carl Woese and the Phylogenetic Tree

In the past, biologists grouped living organisms into five kingdoms: animals, plants, fungi, protists, and bacteria. The
organizational scheme was based mainly on physical features, as opposed to physiology, biochemistry, or molecular biology,
all of which are used by modern systematics. The pioneering work of American microbiologist Carl Woese in the early 1970s
has shown, however, that life on Earth has evolved along three lineages, now called domains—Bacteria, Archaea, and Eukarya.
The first two are prokaryotic cells with microbes that lack membrane-enclosed nuclei and organelles. The third domain
contains the eukaryotes and includes unicellular microorganisms together with the four original kingdoms (excluding bacteria).
Woese defined Archaea as a new domain, and this resulted in a new taxonomic tree (Figure [Link]). Many organisms
belonging to the Archaea domain live under extreme conditions and are called extremophiles. To construct his tree, Woese
used genetic relationships rather than similarities based on morphology (shape).
Woese’s tree was constructed from comparative sequencing of the genes that are universally distributed, present in every
organism, and conserved (meaning that these genes have remained essentially unchanged throughout evolution). Woese’s

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 approach was revolutionary because comparisons of physical features are insufficient to differentiate between the prokaryotes
that appear fairly similar in spite of their tremendous biochemical diversity and genetic variability (Figure [Link]). The
comparison of homologous DNA and RNA sequences provided Woese with a sensitive device that revealed the extensive
variability of prokaryotes, and which justified the separation of the prokaryotes into two domains: bacteria and archaea.

Figure [Link] : These images represent different domains. The (a) bacteria in this micrograph belong to Domain Bacteria,
while the (b) extremophiles (not visible) living in this hot vent belong to Domain Archaea. Both the (c) sunflower and (d) lion
are part of Domain Eukarya. (credit a: modification of work by Drew March; credit b: modification of work by Steve
Jurvetson; credit c: modification of work by Michael Arrighi; credit d: modification of work by Leszek Leszcynski)

Branches of Biological Study

The scope of biology is broad and therefore contains many branches and subdisciplines. Biologists may pursue one of those
subdisciplines and work in a more focused field. For instance, molecular biology and biochemistry study biological processes at the
molecular and chemical level, including interactions among molecules such as DNA, RNA, and proteins, as well as the way they
are regulated. Microbiology, the study of microorganisms, is the study of the structure and function of single-celled organisms. It is
quite a broad branch itself, and depending on the subject of study, there are also microbial physiologists, ecologists, and geneticists,
among others.

Career Connection: Forensic Scientist

Forensic science is the application of science to answer questions related to the law. Biologists as well as chemists and
biochemists can be forensic scientists. Forensic scientists provide scientific evidence for use in courts, and their job involves
examining trace materials associated with crimes. Interest in forensic science has increased in the last few years, possibly
because of popular television shows that feature forensic scientists on the job. Also, the development of molecular techniques
and the establishment of DNA databases have expanded the types of work that forensic scientists can do. Their job activities
are primarily related to crimes against people such as murder, rape, and assault. Their work involves analyzing samples such as
hair, blood, and other body fluids and also processing DNA (Figure [Link]) found in many different environments and
materials. Forensic scientists also analyze other biological evidence left at crime scenes, such as insect larvae or pollen grains.
Students who want to pursue careers in forensic science will most likely be required to take chemistry and biology courses as
well as some intensive math courses.

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 Figure [Link] : This forensic scientist works in a DNA extraction room at the U.S. Army Criminal Investigation Laboratory at
Fort Gillem, GA. (credit: United States Army CID Command Public Affairs)

Another field of biological study, neurobiology, studies the biology of the nervous system, and although it is considered a branch of
biology, it is also recognized as an interdisciplinary field of study known as neuroscience. Because of its interdisciplinary nature,
this subdiscipline studies different functions of the nervous system using molecular, cellular, developmental, medical, and
computational approaches.

Figure [Link] : Researchers work on excavating dinosaur fossils at a site in Castellón, Spain. (credit: Mario Modesto)
Paleontology, another branch of biology, uses fossils to study life’s history (Figure [Link]). Zoology and botany are the study of
animals and plants, respectively. Biologists can also specialize as biotechnologists, ecologists, or physiologists, to name just a few
areas. This is just a small sample of the many fields that biologists can pursue.
Biology is the culmination of the achievements of the natural sciences from their inception to today. Excitingly, it is the cradle of
emerging sciences, such as the biology of brain activity, genetic engineering of custom organisms, and the biology of evolution that
uses the laboratory tools of molecular biology to retrace the earliest stages of life on earth. A scan of news headlines—whether
reporting on immunizations, a newly discovered species, sports doping, or a genetically-modified food—demonstrates the way
biology is active in and important to our everyday world.

Summary
Biology is the science of life. All living organisms share several key properties such as order, sensitivity or response to stimuli,
reproduction, growth and development, regulation, homeostasis, and energy processing. Living things are highly organized parts of
a hierarchy that includes atoms, molecules, organelles, cells, tissues, organs, and organ systems. Organisms, in turn, are grouped as
populations, communities, ecosystems, and the biosphere. The great diversity of life today evolved from less-diverse ancestral

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organisms over billions of years. A diagram called a phylogenetic tree can be used to show evolutionary relationships among
organisms.
Biology is very broad and includes many branches and subdisciplines. Examples include molecular biology, microbiology,
neurobiology, zoology, and botany, among others.

Art Connections
Figure [Link]: Which of the following statements is false?
A. Tissues exist within organs which exist within organ systems.
B. Communities exist within populations which exist within ecosystems.
C. Organelles exist within cells which exist within tissues.
D. Communities exist within ecosystems which exist in the biosphere.

Answer
Communities exist within populations which exist within ecosystems.

Glossary
atom
smallest and most fundamental unit of matter

biochemistry
study of the chemistry of biological organisms

biosphere
collection of all the ecosystems on Earth

botany
study of plants

cell
smallest fundamental unit of structure and function in living things

community
set of populations inhabiting a particular area

ecosystem
all the living things in a particular area together with the abiotic, nonliving parts of that environment

eukaryote
organism with cells that have nuclei and membrane-bound organelles

evolution
process of gradual change during which new species arise from older species and some species become extinct

homeostasis
ability of an organism to maintain constant internal conditions

macromolecule
large molecule, typically formed by the joining of smaller molecules

microbiology
study of the structure and function of microorganisms

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molecule
chemical structure consisting of at least two atoms held together by one or more chemical bonds

molecular biology
study of biological processes and their regulation at the molecular level, including interactions among molecules such as DNA,
RNA, and proteins

neurobiology
study of the biology of the nervous system

organ
collection of related tissues grouped together performing a common function

organ system
level of organization that consists of functionally related interacting organs

organelle
small structures that exist within cells and carry out cellular functions

organism
individual living entity

paleontology
study of life’s history by means of fossils

phylogenetic tree
diagram showing the evolutionary relationships among various biological species based on similarities and differences in
genetic or physical traits or both; in essence, a hypothesis concerning evolutionary connections

population
all of the individuals of a species living within a specific area

prokaryote
single-celled organism that lacks organelles and does not have nuclei surrounded by a nuclear membrane

tissue
group of similar cells carrying out related functions

zoology
study of animals

This page titled 1.1.3: Themes and Concepts of Biology is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
1.2: Themes and Concepts of Biology is licensed CC BY 4.0.

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1.1.E: The Study of Life (Exercises)
1.1: The Science of Biology
Review Questions
The first forms of life on Earth were ________.
A. plants
B. microorganisms
C. birds
D. dinosaurs

Answer
B

A suggested and testable explanation for an event is called a ________.

A. hypothesis
B. variable
C. theory
D. control

Answer
A

Which of the following sciences is not considered a natural science?

A. biology
B. astronomy
C. physics
D. computer science

Answer
D

The type of logical thinking that uses related observations to arrive at a general conclusion is called ________.
A. deductive reasoning
B. the scientific method
C. hypothesis-based science
D. inductive reasoning

Answer
D

The process of ________ helps to ensure that a scientist’s research is original, significant, logical, and thorough.
A. publication
B. public speaking
C. peer review
D. the scientific method

Answer

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 C

A person notices that her houseplants that are regularly exposed to music seem to grow more quickly than those in rooms with
no music. As a result, she determines that plants grow better when exposed to music. This example most closely resembles
which type of reasoning?
A. inductive reasoning
B. deductive reasoning
C. neither, because no hypothesis was made
D. both inductive and deductive reasoning

Answer
A

Free Response
Although the scientific method is used by most of the sciences, it can also be applied to everyday situations. Think about a
problem that you may have at home, at school, or with your car, and apply the scientific method to solve it.

Answer
Answers will vary, but should apply the steps of the scientific method. One possibility could be a car which doesn’t start.
The hypothesis could be that the car doesn’t start because the battery is dead. The experiment would be to change the
battery or to charge the battery and then check whether the car starts or not. If it starts, the problem was due to the battery,
and the hypothesis is accepted.

Give an example of how applied science has had a direct effect on your daily life.

Answer
Answers will vary. One example of how applied science has had a direct effect on daily life is the presence of vaccines.
Vaccines to prevent diseases such polio, measles, tetanus, and even influenza affect daily life by contributing to individual
and societal health.

Name two topics that are likely to be studied by biologists, and two areas of scientific study that would fall outside the realm of
biology.

Answer
Answers will vary. Topics that fall inside the area of biological study include how diseases affect human bodies, how
pollution impacts a species’ habitat, and how plants respond to their environments. Topics that fall outside of biology (the
“study of life”) include how metamorphic rock is formed and how planetary orbits function.

Thinking about the topic of cancer, write a basic science question and an applied science question that a researcher interested in
this topic might ask

Answer
Answers will vary. Basic science: What evolutionary purpose might cancer serve? Applied science: What strategies might
be found to prevent cancer from reproducing at the cellular level?

1.2: Themes and Concepts of Biology

Access for free at OpenStax 1.1.E.2 [Link]

Review Questions
The smallest unit of biological structure that meets the functional requirements of “living” is the ________.
A. organ
B. organelle
C. cell
D. macromolecule

Answer
C

Viruses are not considered living because they ________.

A. are not made of cells
B. lack cell nuclei
C. do not contain DNA or RNA
D. cannot reproduce

Answer
A

The presence of a membrane-enclosed nucleus is a characteristic of ________.

A. prokaryotic cells
B. eukaryotic cells
C. living organisms
D. bacteria

Answer
B

A group of individuals of the same species living in the same area is called a(n) ________.
A. family
B. community
C. population
D. ecosystem

Answer
C

Which of the following sequences represents the hierarchy of biological organization from the most inclusive to the least
complex level?
A. organelle, tissue, biosphere, ecosystem, population
B. organ, organism, tissue, organelle, molecule
C. organism, community, biosphere, molecule, tissue, organ
D. biosphere, ecosystem, community, population, organism

Answer
D

Where in a phylogenetic tree would you expect to find the organism that had evolved most recently?

Access for free at OpenStax 1.1.E.3 [Link]

 A. at the base
B. within the branches
C. at the nodes
D. at the branch tips

Answer
D

Free Response

Select two items that biologists agree are necessary in order to consider an organism “alive.” For each, give an example of a
non-living object that otherwise fits the definition of “alive.”

Answer
Answers will vary. Layers of sedimentary rock have order but are not alive. Technology is capable of regulation but is not,
of itself, alive.

Consider the levels of organization of the biological world, and place each of these items in order from smallest level of
organization to most encompassing: skin cell, elephant, water molecule, planet Earth, tropical rainforest, hydrogen atom, wolf
pack, liver.

Answer
Smallest level of organization to largest: hydrogen atom, water molecule, skin cell, liver, elephant, wolf pack, tropical
rainforest, planet Earth

You go for a long walk on a hot day. Give an example of a way in which homeostasis keeps your body healthy.

Answer
During your walk, you may begin to perspire, which cools your body and helps your body to maintain a constant internal
temperature. You might also become thirsty and pause long enough for a cool drink, which will help to restore the water
lost during perspiration.

Using examples, explain how biology can be studied from a microscopic approach to a global approach.

Answer
Researchers can approach biology from the smallest to the largest, and everything in between. For instance, an ecologist
may study a population of individuals, the population’s community, the community’s ecosystem, and the ecosystem’s part
in the biosphere. When studying an individual organism, a biologist could examine the cell and its organelles, the tissues
that the cells make up, the organs and their respective organ systems, and the sum total—the organism itself.

This page titled 1.1.E: The Study of Life (Exercises) is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
1.E: The Study of Life (Exercises) by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 1.1.E.4 [Link]

1.2: The Scientific Process
Biologists study the living world by posing questions about it and seeking science-based responses. This approach is common to
other sciences as well and is often referred to as the scientific method. The scientific process was used even in ancient times, but it
was first documented by England’s Sir Francis Bacon (1561–1626) (Figure 1.2.1 ), who set up inductive methods for scientific
inquiry. The scientific method is not exclusively used by biologists but can be applied to almost anything as a logical problem
solving method.

Figure 1.2.1: Sir Francis Bacon (1561–1626) is credited with being the first to define the scientific method. (credit: Paul van
Somer)

Question
The scientific process typically starts with an observation (often a problem to be solved) that leads to a question. Remember that
science is very good at answering questions having to do with observations about the natural world, but is very bad at answering
questions having to do with morals, ethics, or personal opinions.

Questions that can be answered using science Questions that cannot be answered using science

• What is the optimum temperature for the growth of E. coli bacteria? • How tall is Santa Claus?

• Do birds prefer bird feeders of a specific color? • Do angels exist?

• What is the cause of this disease? • Which is better: classical music or rock and roll?

• How effective is this drug in treating this disease? • What are the ethical implications of human cloning?

Let’s think about a simple problem that starts with an observation and apply the scientific method to solve the problem. Imagine
that one morning when you wake up and flip the switch to turn on your bedside lamp, the light won’t turn on. That is an
observation that also describes a problem: the lights won’t turn on. Of course, you would next ask the question: “Why won’t the
light turn on?”

Hypothesis
Recall that a hypothesis is a suggested explanation that can be tested. A hypothesis is NOT the question you are trying to answer –
it is what you think the answer to the question will be and why. To solve a problem, several hypotheses may be proposed. For
example, one hypothesis might be, “The light won’t turn on because the bulb is burned out.” But there could be other answers to
the question, and therefore other hypotheses may be proposed. A second hypothesis might be, “The light won’t turn on because the
lamp is unplugged” or “The light won’t turn on because the power is out.” A hypothesis should be based on credible background
information. A hypothesis is NOT just a guess (not even an educated one), although it can be based on your prior experience (such
as in the example where the light won’t turn on). In general, hypotheses in biology should be based on a credible, referenced source
of information.
A hypothesis must be testable to ensure that it is valid. For example, a hypothesis that depends on what a dog thinks is not testable,
because we can’t tell what a dog thinks. It should also be falsifiable, meaning that it can be disproven by experimental results. An
example of an unfalsifiable hypothesis is “Red is a better color than blue.” There is no experiment that might show this statement to

1.2.1 [Link]
be false. To test a hypothesis, a researcher will conduct one or more experiments designed to eliminate one or more of the
hypotheses. This is important: a hypothesis can be disproven, or eliminated, but it can never be proven. Science does not deal in
proofs like mathematics. If an experiment fails to disprove a hypothesis, then that explanation (the hypothesis) is supported as the
answer to the question. However, that doesn’t mean that later on, we won’t find a better explanation or design a better experiment
that will be found to falsify the first hypothesis and lead to a better one.

Variables
A variable is any part of the experiment that can vary or change during the experiment. Typically, an experiment only tests one
variable and all the other conditions in the experiment are held constant.
The variable that is tested is known as the independent variable.
The dependent variable is the thing (or things) that you are measuring as the outcome of your experiment.
A constant is a condition that is the same between all of the tested groups.
A confounding variable is a condition that is not held constant that could affect the experimental results.
A hypothesis often has the format “If [I change the independent variable in this way] then [I will observe that the dependent
variable does this] because [of some reason].” For example, the first hypothesis might be, “If you change the light bulb, then the
light will turn on because the bulb is burned out.” In this experiment, the independent variable (the thing that you are testing) would
be changing the light bulb and the dependent variable is whether or not the light turns on. It would be important to hold all the other
aspects of the environment constant, for example not messing with the lamp cord or trying to turn the lamp on using a different
light switch. If the entire house had lost power during the experiment because a car hit the power pole, that would be a confounding
variable.
You may have learned that a hypothesis can be phrased as an “If..then…” statement. Simple hypotheses can be phrased that way
(but they must also include a “because”), but more complicated hypotheses may require several sentences. It is also very easy to get
confused by trying to put your hypothesis into this format. Hypotheses do not have to be phrased as “if..then..” statements, it is just
sometimes a useful format.

Results
The results of your experiment are the data that you collect as the outcome. In the light experiment, your results are either that the
light turns on or the light doesn’t turn on. Based on your results, you can make a conclusion. Your conclusion uses the results to
answer your original question.

1.2.2 [Link]
 Figure 1.2.2: The basic process of the scientific method. This is what science looks like in a simplified world.
We can put the experiment with the light that won’t go in into the figure above:
1. Observation: the light won’t turn on.
2. Question: why won’t the light turn on?
3. Hypothesis: the lightbulb is burned out.
4. Prediction: if I change the lightbulb (independent variable), then the light will turn on (dependent variable).
5. Experiment: change the lightbulb while leaving all other variables the same.
6. Analyze the results: the light didn’t turn on.
7. Conclusion: The lightbulb isn’t burned out. The results do not support the hypothesis, time to develop a new one!
8. Hypothesis 2: the lamp is unplugged.
9. Prediction 2: if I plug in the lamp, then the light will turn on.
10. Experiment: plug in the lamp
11. Analyze the results: the light turned on!
12. Conclusion: The light wouldn’t turn on because the lamp was unplugged. The results support the hypothesis, it’s time to move
on to the next experiment!
In practice, the scientific method is not as rigid and structured as it might at first appear. Sometimes an experiment leads to
conclusions that favor a change in approach; often, an experiment brings entirely new scientific questions to the puzzle. Many
times, science does not operate in a linear fashion; instead, scientists continually draw inferences and make generalizations, finding
patterns as their research proceeds. Scientific reasoning is more complex than the scientific method alone suggests.

1.2.3 [Link]
 Figure 1.2.3: The actual process of using the scientific method. “The general process of scientific investigations” by Laura
Guerin, CK-12 Foundation is licensed under CC BY-NC 3.0

Control Groups
Another important aspect of designing an experiment is the presence of one or more control groups. A control group allows you to
make a comparison that is important for interpreting your results. Control groups are samples that help you to determine that
differences between your experimental groups are due to your treatment rather than a different variable – they eliminate alternate
explanations for your results (including experimental error and experimenter bias). They increase reliability, often through the
comparison of control measurements and measurements of the experimental groups. Often, the control group is a sample that is not
treated with the independent variable, but is otherwise treated the same way as your experimental sample. This type of control
group contains every feature of the experimental group except it is not given the manipulation that is hypothesized about (it does
not get treated with the independent variable). Therefore, if the results of the experimental group differ from the control group, the
difference must be due to the hypothesized manipulation, rather than some outside factor. It is common in complex experiments
(such as those published in scientific journals) to have more control groups than experimental groups.

Example 1.2.1

Question: Which fertilizer will produce the greatest number of tomatoes when applied to the plants?
Prediction and Hypothesis: If I apply different brands of fertilizer to tomato plants, the most tomatoes will be produced from
plants watered with Brand A because Brand A advertises that it produces twice as many tomatoes as other leading brands.
Experiment: Purchase 10 tomato plants of the same type from the same nursery. Pick plants that are similar in size and age.
Divide the plants into two groups of 5. Apply Brand A to the first group and Brand B to the second group according to the
instructions on the packages. After 10 weeks, count the number of tomatoes on each plant.
Independent Variable: Brand of fertilizer.
Dependent Variable: Number of tomatoes.
The number of tomatoes produced depends on the brand of fertilizer applied to the plants.
Constants: amount of water, type of soil, size of pot, amount of light, type of tomato plant, length of time plants were grown.
Confounding variables: any of the above that are not held constant, plant health, diseases present in the soil or plant before it
was purchased.
Results: Tomatoes fertilized with Brand A produced an average of 20 tomatoes per plant, while tomatoes fertilized with Brand
B produced an average of 10 tomatoes per plant.

1.2.4 [Link]
 You’d want to use Brand A next time you grow tomatoes, right? But what if I told you that plants grown without fertilizer
produced an average of 30 tomatoes per plant! Now what will you use on your tomatoes?

Results including control group: Tomatoes which received no fertilizer produced more tomatoes than either brand of
fertilizer.
Conclusion: Although Brand A fertilizer produced more tomatoes than Brand B, neither fertilizer should be used because
plants grown without fertilizer produced the most tomatoes!

Positive control groups are often used to show that the experiment is valid and that everything has worked correctly. You can
think of a positive control group as being a group where you should be able to observe the thing that you are measuring (“the thing”
should happen). The conditions in a positive control group should guarantee a positive result. If the positive control group doesn’t
work, there may be something wrong with the experimental procedure.
Negative control groups are used to show whether a treatment had any effect. If your treated sample is the same as your negative
control group, your treatment had no effect. You can also think of a negative control group as being a group where you should NOT
be able to observe the thing that you are measuring (“the thing” shouldn’t happen), or where you should not observe any change in
the thing that you are measuring (there is no difference between the treated and control group). The conditions in a negative control
group should guarantee a negative result. A placebo group is an example of a negative control group.
As a general rule, you need a positive control to validate a negative result, and a negative control to validate a positive result.
You read an article in the NY Times that says some spinach is contaminated with Salmonella. You want to test the spinach
you have at home in your fridge, so you wet a sterile swab and wipe it on the spinach, then wipe the swab on a nutrient plate
(petri plate).
You observe growth. Does this mean that your spinach is really contaminated? Consider an alternate explanation for growth:
the swab, the water, or the plate is contaminated with bacteria. You could use a negative control to determine which
explanation is true. If a swab is wet and wiped on a nutrient plate, do bacteria grow?
You don’t observe growth. Does this mean that your spinach is really safe? Consider an alternate explanation for no growth:
Salmonella isn’t able to grow on the type of nutrient you used in your plates. You could use a positive control to determine
which explanation is true. If you wipe a known sample of Salmonella bacteria on the plate, do bacteria grow?
In a drug trial, one group of subjects are given a new drug, while a second group is given a placebo drug (a sugar pill;
something which appears like the drug, but doesn’t contain the active ingredient). Reduction in disease symptoms are measured.
The second group receiving the placebo is a negative control group. You might expect a reduction in disease symptoms purely
because the person knows they are taking a drug so they should be getting better. If the group treated with the real drug does not
show more a reduction in disease symptoms than the placebo group, the drug doesn’t really work. The placebo group sets a
baseline against which the experimental group (treated with the drug) can be compared. A positive control group is not required
for this experiment.
In an experiment measuring the preference of birds for various types of food, a negative control group would be a “placebo
feeder”. This would be the same type of feeder, but with no food in it. Birds might visit a feeder just because they are interested
in it; an empty feeder would give a baseline level for bird visits. A positive control group might be a food that squirrels are
known to like. This would be useful because if no squirrels visited any of the feeders, you couldn’t tell if this was because there
were no squirrels around or because they didn’t like any of your food offerings!
To test the effect of pH on the function of an enzyme, you would want a positive control group where you knew the enzyme
would function (pH not changed) and a negative control group where you knew the enzyme would not function (no enzyme
added). You need the positive control group so you know your enzyme is working: if you didn’t see a reaction in any of the
tubes with the pH adjusted, you wouldn’t know if it was because the enzyme wasn’t working at all or because the enzyme just

1.2.5 [Link]
 didn’t work at any of your tested pH. You need the negative control group so you can ensure that there is no reaction taking
place in the absence of enzyme: if the reaction proceeds without the enzyme, your results are meaningless.

References
Text adapted from: OpenStax, Biology. OpenStax CNX. May 27,
2016 [Link]

1.2: The Scientific Process is shared under a CC BY license and was authored, remixed, and/or curated by LibreTexts.

1.2.6 [Link]
1.3: Presenting Data - Graphs and Tables
Types of Data
There are different types of data that can be collected in an experiment. Typically, we try to design experiments that collect
objective, quantitative data.
Objective data is fact-based, measurable, and observable. This means that if two people made the same measurement with the
same tool, they would get the same answer. The measurement is determined by the object that is being measured. The length of a
worm measured with a ruler is an objective measurement. The observation that a chemical reaction in a test tube changed color is
an objective measurement. Both of these are observable facts.
Subjective data is based on opinions, points of view, or emotional judgment. Subjective data might give two different answers
when collected by two different people. The measurement is determined by the subject who is doing the measuring. Surveying
people about which of two chemicals smells worse is a subjective measurement. Grading the quality of a presentation is a
subjective measurement. Rating your relative happiness on a scale of 1-5 is a subjective measurement. All of these depend on the
person who is making the observation – someone else might make these measurements differently.
Quantitative measurements gather numerical data. For example, measuring a worm as being 5cm in length is a quantitative
measurement.
Qualitative measurements describe a quality, rather than a numerical value. Saying that one worm is longer than another worm is a
qualitative measurement.

Quantitative Qualitative

The chemical reaction has produced 5cm of The chemical reaction has produced a lot of
Objective
bubbles. bubbles.

I give the amount of bubbles a score of 7 on a

Subjective I think the bubbles are pretty.
scale of 1-10.

After you have collected data in an experiment, you need to figure out the best way to present that data in a meaningful way.
Depending on the type of data, and the story that you are trying to tell using that data, you may present your data in different ways.

Data Tables
The easiest way to organize data is by putting it into a data table. In most data tables, the independent variable (the variable that
you are testing or changing on purpose) will be in the column to the left and the dependent variable(s) will be across the top of the
table.
Be sure to:
Label each row and column so that the table can be interpreted
Include the units that are being used
Add a descriptive caption for the table

Example 1.3.1

You are evaluating the effect of different types of fertilizers on plant growth. You plant 12 tomato plants and divide them into
three groups, where each group contains four plants. To the first group, you do not add fertilizer and the plants are watered
with plain water. The second and third groups are watered with two different brands of fertilizer. After three weeks, you
measure the growth of each plant in centimeters and calculate the average growth for each type of fertilizer.
The effect of different brands of fertilizer on tomato plant growth over three weeks
Plant Number
Treatment
1 2 3 4 Average

No treatment 10 12 8 9 9.75

Brand A 15 16 14 12 14.25

1.3.1 [Link]
 Brand B 22 25 21 27 23.75

Scientific Method Review: Can you identify the key parts of the scientific method from this experiment?
Independent variable – Type of treatment (brand of fertilizer)
Dependent variable – plant growth in cm
Control group(s) – Plants treated with no fertilizer
Experimental group(s) – Plants treated with different brands of fertilizer

Graphing data
Graphs are used to display data because it is easier to see trends in the data when it is displayed visually compared to when it is
displayed numerically in a table. Complicated data can often be displayed and interpreted more easily in a graph format than in a
data table.
In a graph, the X-axis runs horizontally (side to side) and the Y-axis runs vertically (up and down). Typically, the independent
variable will be shown on the X axis and the dependent variable will be shown on the Y axis (just like you learned in math class!).

Line Graph
Line graphs are the best type of graph to use when you are displaying a change in something over a continuous range. For example,
you could use a line graph to display a change in temperature over time. Time is a continuous variable because it can have any
value between two given measurements. It is measured along a continuum. Between 1 minute and 2 minutes are an infinite number
of values, such as 1.1 minute or 1.93456 minutes.
Changes in several different samples can be shown on the same graph by using lines that differ in color, symbol, etc.

Figure 1.3.1: Change in bubble height in centimeters over 120 seconds for three samples containing different amounts of enzyme.
Sample A contained no enzyme, sample B contained 1mL of enzyme, sample C contained 2 mL of enzyme.

Bar Graph
Bar graphs are used to compare measurements between different groups. Bar graphs should be used when your data is not
continuous, but rather is divided into different categories. If you counted the number of birds of different species, each species of
bird would be its own category. There is no value between “robin” and “eagle”, so this data is not continuous.

Figure 1.3.2: Final bubble height after 120 seconds for three samples containing different combinations of ingredients. Sample A
contained enzyme but no substrate, sample B contained substrate but no enzyme, sample C contained substrate and enzyme.

Scatter Plot
Scatter plots are used to evaluate the relationship between two different continuous variables. These graphs compare changes in
two different variables at once. For example, you could look at the relationship between height and weight. Both height and weight
are continuous variables. You could not use a scatter plot to look at the relationship between number of children in a family and
weight of each child because the number of children in a family is not a continuous variable: you can’t have 2.3 children in a
family.

1.3.2 [Link]
 Figure 1.3.3: The relationship between height (in meters) and weight (in kilograms) of members of the girls softball team. “OLS
example weight vs height scatterplot” by Stpasha is in the Public Domain

How to make a graph

1. Identify your independent and dependent variables.
2. Choose the correct type of graph by determining whether each variable is continuous or not.
3. Determine the values that are going to go on the X and Y axis. If the values are continuous, they need to be evenly spaced based
on the value.
4. Label the X and Y axis, including units.
5. Graph your data.
6. Add a descriptive caption to your graph. Note that data tables are titled above the figure and graphs are captioned below the
figure.

Example 1.3.2

Let’s go back to the data from our fertilizer experiment and use it to make a graph. I’ve decided to graph only the average
growth for the four plants because that is the most important piece of data. Including every single data point would make the
graph very confusing.
1. The independent variable is type of treatment and the dependent variable is plant growth (in cm).
2. Type of treatment is not a continuous variable. There is no midpoint value between fertilizer brands (Brand A 1/2 doesn’t
make sense). Plant growth is a continuous variable. It makes sense to sub-divide centimeters into smaller values. Since the
independent variable is categorical and the dependent variable is continuous, this graph should be a bar graph.
3. Plant growth (the dependent variable) should go on the Y axis and type of treatment (the independent variable) should go
on the X axis.
4. Notice that the values on the Y axis are continuous and evenly spaced. Each line represents an increase of 5cm.
5. Notice that both the X and the Y axis have labels that include units (when required).
6. Notice that the graph has a descriptive caption that allows the figure to stand alone without additional information given
from the procedure: you know that this graph shows the average of the measurements taken from four tomato plants.

Figure 1.3.4: Average growth (in cm) of tomato plants when treated with different brands of fertilizer. There were four
tomato plants in each group (n = 4).

Descriptive captions
All figures that present data should stand alone – this means that you should be able to interpret the information contained in the
figure without referring to anything else (such as the methods section of the paper). This means that all figures should have
a descriptive caption that gives information about the independent and dependent variable. Another way to state this is that the
caption should describe what you are testing and what you are measuring. A good starting point to developing a caption is “the
effect of [the independent variable] on the [dependent variable].”
Here are some examples of good caption for figures:

1.3.3 [Link]
 The effect of exercise on heart rate
Growth rates of E. coli at different temperatures
The relationship between heat shock time and transformation efficiency
Here are a few less effective captions:
Heart rate and exercise
Graph of E. coli temperature growth
Table for experiment 1

1.3: Presenting Data - Graphs and Tables is shared under a CC BY license and was authored, remixed, and/or curated by LibreTexts.

1.3.4 [Link]
 CHAPTER OVERVIEW

2: Biological Macromolecules
2.1: The Building Blocks of Molecules
2.2: Water
2.3: Biological Molecules
2.E: Chemistry of Life (Exercises)

Thumbnail: Fatty acid molecules with cis and trans configurations. (CC BY 4.0 / modified from original; OpenStax).

This page titled 2: Biological Macromolecules is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.

1
2.1: The Building Blocks of Molecules
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements,
substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with
a constant number of protons and unique properties. A total of 118 elements have been defined; however, only 92 occur naturally,
and fewer than 30 are found in living cells. The remaining 26 elements are unstable and, therefore, do not exist for very long or are
theoretical and have yet to be detected.
Each element is designated by its chemical symbol (such as H, N, O, C, and Na), and possesses unique properties. These unique
properties allow elements to combine and to bond with each other in specific ways.

Atoms
An atom is the smallest component of an element that retains all of the chemical properties of that element. For example, one
hydrogen atom has all of the properties of the element hydrogen, such as it exists as a gas at room temperature, and it bonds with
oxygen to create a water molecule. Hydrogen atoms cannot be broken down into anything smaller while still retaining the
properties of hydrogen. If a hydrogen atom were broken down into subatomic particles, it would no longer have the properties of
hydrogen.
At the most basic level, all organisms are made of a combination of elements. They contain atoms that combine together to form
molecules. In multicellular organisms, such as animals, molecules can interact to form cells that combine to form tissues, which
make up organs. These combinations continue until entire multicellular organisms are formed.
All atoms contain protons, electrons, and neutrons (Figure 2.1.1). The only exception is hydrogen (H), which is made of one proton
and one electron. A proton is a positively charged particle that resides in the nucleus (the core of the atom) of an atom and has a
mass of 1 and a charge of +1. An electron is a negatively charged particle that travels in the space around the nucleus. In other
words, it resides outside of the nucleus. It has a negligible mass and has a charge of –1.

Figure 2.1.1: Atoms are made up of protons and neutrons located within the nucleus, and electrons surrounding the nucleus.
Neutrons, like protons, reside in the nucleus of an atom. They have a mass of 1 and no charge. The positive (protons) and negative
(electrons) charges balance each other in a neutral atom, which has a net zero charge.
Because protons and neutrons each have a mass of 1, the mass of an atom is equal to the number of protons and neutrons of that
atom. The number of electrons does not factor into the overall mass, because their mass is so small.
As stated earlier, each element has its own unique properties. Each contains a different number of protons and neutrons, giving it its
own atomic number and mass number. The atomic number of an element is equal to the number of protons that element contains.
The mass number, or atomic mass, is the number of protons plus the number of neutrons of that element. Therefore, it is possible to
determine the number of neutrons by subtracting the atomic number from the mass number.
These numbers provide information about the elements and how they will react when combined. Different elements have different
melting and boiling points, and are in different states (liquid, solid, or gas) at room temperature. They also combine in different
ways. Some form specific types of bonds, whereas others do not. How they combine is based on the number of electrons present.
Because of these characteristics, the elements are arranged into the periodic table of elements, a chart of the elements that includes
the atomic number and relative atomic mass of each element. The periodic table also provides key information about the properties

Access for free at OpenStax 2.1.1 [Link]

of elements (Figure 2.1.2)—often indicated by color-coding. The arrangement of the table also shows how the electrons in each
element are organized and provides important details about how atoms will react with each other to form molecules.
Isotopes are different forms of the same element that have the same number of protons, but a different number of neutrons. Some
elements, such as carbon, potassium, and uranium, have naturally occurring isotopes. Carbon-12, the most common isotope of
carbon, contains six protons and six neutrons. Therefore, it has a mass number of 12 (six protons and six neutrons) and an atomic
number of 6 (which makes it carbon). Carbon-14 contains six protons and eight neutrons. Therefore, it has a mass number of 14
(six protons and eight neutrons) and an atomic number of 6, meaning it is still the element carbon. These two alternate forms of
carbon are isotopes. Some isotopes are unstable and will lose protons, other subatomic particles, or energy to form more stable
elements. These are called radioactive isotopes or radioisotopes.

ART CONNECTION

Figure 2.1.2: Arranged in columns and rows based on the characteristics of the elements, the periodic table provides key
information about the elements and how they might interact with each other to form molecules. Most periodic tables provide a
key or legend to the information they contain.
How many neutrons do (K) potassium-39 and potassium-40 have, respectively?

EVOLUTION IN ACTION: Carbon Dating

Carbon-14 (14C) is a naturally occurring radioisotope that is created in the atmosphere by cosmic rays. This is a continuous
process, so more 14C is always being created. As a living organism develops, the relative level of 14C in its body is equal to the
concentration of 14C in the atmosphere. When an organism dies, it is no longer ingesting 14C, so the ratio will decline. 14C
decays to 14N by a process called beta decay; it gives off energy in this slow process.

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 After approximately 5,730 years, only one-half of the starting concentration of 14C will have been converted to 14N. The time it
takes for half of the original concentration of an isotope to decay to its more stable form is called its half-life. Because the half-
life of 14C is long, it is used to age formerly living objects, such as fossils. Using the ratio of the 14C concentration found in an
object to the amount of 14C detected in the atmosphere, the amount of the isotope that has not yet decayed can be determined.
Based on this amount, the age of the fossil can be calculated to about 50,000 years (Figure 2.1.3). Isotopes with longer half-
lives, such as potassium-40, are used to calculate the ages of older fossils. Through the use of carbon dating, scientists can
reconstruct the ecology and biogeography of organisms living within the past 50,000 years.

Figure 2.1.3: The age of remains that contain carbon and are less than about 50,000 years old, such as this pygmy mammoth,
can be determined using carbon dating. (credit: Bill Faulkner/NPS)

CONCEPT IN ACTION

To learn more about atoms and isotopes, and how you can tell one isotope from another, visit this site and run the simulation.

Chemical Bonds
How elements interact with one another depends on how their electrons are arranged and how many openings for electrons exist at
the outermost region where electrons are present in an atom. Electrons exist at energy levels that form shells around the nucleus.
The closest shell can hold up to two electrons. The closest shell to the nucleus is always filled first, before any other shell can be
filled. Hydrogen has one electron; therefore, it has only one spot occupied within the lowest shell. Helium has two electrons;
therefore, it can completely fill the lowest shell with its two electrons. If you look at the periodic table, you will see that hydrogen
and helium are the only two elements in the first row. This is because they only have electrons in their first shell. Hydrogen and
helium are the only two elements that have the lowest shell and no other shells.
The second and third energy levels can hold up to eight electrons. The eight electrons are arranged in four pairs and one position in
each pair is filled with an electron before any pairs are completed.
Looking at the periodic table again (Figure 2.1.2), you will notice that there are seven rows. These rows correspond to the number
of shells that the elements within that row have. The elements within a particular row have increasing numbers of electrons as the
columns proceed from left to right. Although each element has the same number of shells, not all of the shells are completely filled
with electrons. If you look at the second row of the periodic table, you will find lithium (Li), beryllium (Be), boron (B), carbon (C),
nitrogen (N), oxygen (O), fluorine (F), and neon (Ne). These all have electrons that occupy only the first and second shells. Lithium
has only one electron in its outermost shell, beryllium has two electrons, boron has three, and so on, until the entire shell is filled
with eight electrons, as is the case with neon.
Not all elements have enough electrons to fill their outermost shells, but an atom is at its most stable when all of the electron
positions in the outermost shell are filled. Because of these vacancies in the outermost shells, we see the formation of chemical
bonds, or interactions between two or more of the same or different elements that result in the formation of molecules. To achieve
greater stability, atoms will tend to completely fill their outer shells and will bond with other elements to accomplish this goal by
sharing electrons, accepting electrons from another atom, or donating electrons to another atom. Because the outermost shells of

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the elements with low atomic numbers (up to calcium, with atomic number 20) can hold eight electrons, this is referred to as the
octet rule. An element can donate, accept, or share electrons with other elements to fill its outer shell and satisfy the octet rule.
When an atom does not contain equal numbers of protons and electrons, it is called an ion. Because the number of electrons does
not equal the number of protons, each ion has a net charge. Positive ions are formed by losing electrons and are called cations.
Negative ions are formed by gaining electrons and are called anions.
For example, sodium only has one electron in its outermost shell. It takes less energy for sodium to donate that one electron than it
does to accept seven more electrons to fill the outer shell. If sodium loses an electron, it now has 11 protons and only 10 electrons,
leaving it with an overall charge of +1. It is now called a sodium ion.
The chlorine atom has seven electrons in its outer shell. Again, it is more energy-efficient for chlorine to gain one electron than to
lose seven. Therefore, it tends to gain an electron to create an ion with 17 protons and 18 electrons, giving it a net negative (–1)
charge. It is now called a chloride ion. This movement of electrons from one element to another is referred to as electron transfer.
As Figure 2.1.4 illustrates, a sodium atom (Na) only has one electron in its outermost shell, whereas a chlorine atom (Cl) has seven
electrons in its outermost shell. A sodium atom will donate its one electron to empty its shell, and a chlorine atom will accept that
electron to fill its shell, becoming chloride. Both ions now satisfy the octet rule and have complete outermost shells. Because the
number of electrons is no longer equal to the number of protons, each is now an ion and has a +1 (sodium) or –1 (chloride) charge.

Figure 2.1.4: Elements tend to fill their outermost shells with electrons. To do this, they can either donate or accept electrons
from other elements.

Ionic Bonds
There are four types of bonds or interactions: ionic, covalent, hydrogen bonds, and van der Waals interactions. Ionic and covalent
bonds are strong interactions that require a larger energy input to break apart. When an element donates an electron from its outer
shell, as in the sodium atom example above, a positive ion is formed. The element accepting the electron is now negatively
charged. Because positive and negative charges attract, these ions stay together and form an ionic bond, or a bond between ions.
The elements bond together with the electron from one element staying predominantly with the other element. When Na+ and Cl–

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ions combine to produce NaCl, an electron from a sodium atom stays with the other seven from the chlorine atom, and the sodium
and chloride ions attract each other in a lattice of ions with a net zero charge.

Covalent Bonds
Another type of strong chemical bond between two or more atoms is a covalent bond. These bonds form when an electron is shared
between two elements and are the strongest and most common form of chemical bond in living organisms. Covalent bonds form
between the elements that make up the biological molecules in our cells. Unlike ionic bonds, covalent bonds do not dissociate in
water.
The hydrogen and oxygen atoms that combine to form water molecules are bound together by covalent bonds. The electron from
the hydrogen atom divides its time between the outer shell of the hydrogen atom and the incomplete outer shell of the oxygen atom.
To completely fill the outer shell of an oxygen atom, two electrons from two hydrogen atoms are needed, hence the subscript “2” in
H2O. The electrons are shared between the atoms, dividing their time between them to “fill” the outer shell of each. This sharing is
a lower energy state for all of the atoms involved than if they existed without their outer shells filled.
There are two types of covalent bonds: polar and nonpolar. Nonpolar covalent bonds form between two atoms of the same element
or between different elements that share the electrons equally. For example, an oxygen atom can bond with another oxygen atom to
fill their outer shells. This association is nonpolar because the electrons will be equally distributed between each oxygen atom. Two
covalent bonds form between the two oxygen atoms because oxygen requires two shared electrons to fill its outermost shell.
Nitrogen atoms will form three covalent bonds (also called triple covalent) between two atoms of nitrogen because each nitrogen
atom needs three electrons to fill its outermost shell. Another example of a nonpolar covalent bond is found in the methane (CH4)
molecule. The carbon atom has four electrons in its outermost shell and needs four more to fill it. It gets these four from four
hydrogen atoms, each atom providing one. These elements all share the electrons equally, creating four nonpolar covalent bonds
(Figure 2.1.5).
In a polar covalent bond, the electrons shared by the atoms spend more time closer to one nucleus than to the other nucleus.
Because of the unequal distribution of electrons between the different nuclei, a slightly positive (δ+) or slightly negative (δ–)
charge develops. The covalent bonds between hydrogen and oxygen atoms in water are polar covalent bonds. The shared electrons
spend more time near the oxygen nucleus, giving it a small negative charge, than they spend near the hydrogen nuclei, giving these
molecules a small positive charge.

Figure 2.1.5: The water molecule (left) depicts a polar bond with a slightly positive charge on the hydrogen atoms and a slightly
negative charge on the oxygen. Examples of nonpolar bonds include methane (middle) and oxygen (right).

Hydrogen Bonds
Ionic and covalent bonds are strong bonds that require considerable energy to break. However, not all bonds between elements are
ionic or covalent bonds. Weaker bonds can also form. These are attractions that occur between positive and negative charges that
do not require much energy to break. Two weak bonds that occur frequently are hydrogen bonds and van der Waals interactions.
These bonds give rise to the unique properties of water and the unique structures of DNA and proteins.
When polar covalent bonds containing a hydrogen atom form, the hydrogen atom in that bond has a slightly positive charge. This is
because the shared electron is pulled more strongly toward the other element and away from the hydrogen nucleus. Because the
hydrogen atom is slightly positive (δ+), it will be attracted to neighboring negative partial charges (δ–). When this happens, a weak

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interaction occurs between the δ+ charge of the hydrogen atom of one molecule and the δ– charge of the other molecule. This
interaction is called a hydrogen bond. This type of bond is common; for example, the liquid nature of water is caused by the
hydrogen bonds between water molecules (Figure 2.1.6). Hydrogen bonds give water the unique properties that sustain life. If it
were not for hydrogen bonding, water would be a gas rather than a liquid at room temperature.

Figure 2.1.6: Hydrogen bonds form between slightly positive (δ+) and slightly negative (δ–) charges of polar covalent molecules,
such as water.
Hydrogen bonds can form between different molecules and they do not always have to include a water molecule. Hydrogen atoms
in polar bonds within any molecule can form bonds with other adjacent molecules. For example, hydrogen bonds hold together two
long strands of DNA to give the DNA molecule its characteristic double-stranded structure. Hydrogen bonds are also responsible
for some of the three-dimensional structure of proteins.

van der Waals Interactions

Like hydrogen bonds, van der Waals interactions are weak attractions or interactions between molecules. They occur between
polar, covalently bound, atoms in different molecules. Some of these weak attractions are caused by temporary partial charges
formed when electrons move around a nucleus. These weak interactions between molecules are important in biological systems.

CAREERS IN ACTION: Radiography Technician

Have you or anyone you know ever had a magnetic resonance imaging (MRI) scan, a mammogram, or an X-ray? These tests
produce images of your soft tissues and organs (as with an MRI or mammogram) or your bones (as happens in an X-ray) by
using either radiowaves or special isotopes (radiolabeled or fluorescently labeled) that are ingested or injected into the body.
These tests provide data for disease diagnoses by creating images of your organs or skeletal system.
MRI imaging works by subjecting hydrogen nuclei, which are abundant in the water in soft tissues, to fluctuating magnetic
fields, which cause them to emit their own magnetic field. This signal is then read by sensors in the machine and interpreted by
a computer to form a detailed image.
Some radiography technologists and technicians specialize in computed tomography, MRI, and mammography. They produce
films or images of the body that help medical professionals examine and diagnose. Radiologists work directly with patients,
explaining machinery, preparing them for exams, and ensuring that their body or body parts are positioned correctly to produce
the needed images. Physicians or radiologists then analyze the test results.
Radiography technicians can work in hospitals, doctors’ offices, or specialized imaging centers. Training to become a
radiography technician happens at hospitals, colleges, and universities that offer certificates, associate’s degrees, or bachelor’s
degrees in radiography.

Summary
Matter is anything that occupies space and has mass. It is made up of atoms of different elements. All of the 92 elements that occur
naturally have unique qualities that allow them to combine in various ways to create compounds or molecules. Atoms, which
consist of protons, neutrons, and electrons, are the smallest units of an element that retain all of the properties of that element.
Electrons can be donated or shared between atoms to create bonds, including ionic, covalent, and hydrogen bonds, as well as van
der Waals interactions.

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Art Connections
Figure 2.1.2: How many neutrons do (K) potassium-39 and potassium-40 have, respectively?

Answer
Potassium-39 has twenty neutrons. Potassium-40 has twenty one neutrons.

Glossary

anion
a negative ion formed by gaining electrons

atomic number
the number of protons in an atom

cation
a positive ion formed by losing electrons

chemical bond
an interaction between two or more of the same or different elements that results in the formation of molecules

covalent bond
a type of strong bond between two or more of the same or different elements; forms when electrons are shared between
elements

electron
a negatively charged particle that resides outside of the nucleus in the electron orbital; lacks functional mass and has a charge of
–1

electron transfer
the movement of electrons from one element to another

element
one of 118 unique substances that cannot be broken down into smaller substances and retain the characteristic of that substance;
each element has a specified number of protons and unique properties

hydrogen bond
a weak bond between partially positively charged hydrogen atoms and partially negatively charged elements or molecules

ion
an atom or compound that does not contain equal numbers of protons and electrons, and therefore has a net charge

ionic bond
a chemical bond that forms between ions of opposite charges

isotope
one or more forms of an element that have different numbers of neutrons

mass number
the number of protons plus neutrons in an atom

matter
anything that has mass and occupies space

neutron
a particle with no charge that resides in the nucleus of an atom; has a mass of 1

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nonpolar covalent bond
a type of covalent bond that forms between atoms when electrons are shared equally between atoms, resulting in no regions
with partial charges as in polar covalent bonds

nucleus
(chemistry) the dense center of an atom made up of protons and (except in the case of a hydrogen atom) neutrons

octet rule
states that the outermost shell of an element with a low atomic number can hold eight electrons

periodic table of elements

an organizational chart of elements, indicating the atomic number and mass number of each element; also provides key
information about the properties of elements

polar covalent bond

a type of covalent bond in which electrons are pulled toward one atom and away from another, resulting in slightly positive and
slightly negative charged regions of the molecule

proton
a positively charged particle that resides in the nucleus of an atom; has a mass of 1 and a charge of +1

radioactive isotope
an isotope that spontaneously emits particles or energy to form a more stable element

van der Waals interaction

a weak attraction or interaction between molecules caused by slightly positively charged or slightly negatively charged atoms

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 2.1: The Building Blocks of Molecules is shared under a not declared license and was authored, remixed, and/or curated by
OpenStax.
2.1: The Building Blocks of Molecules by OpenStax is licensed CC BY 4.0.

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2.2: Water
Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even
minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant
molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of
water. Without it, life simply would not exist.

Water Is Polar
The hydrogen and oxygen atoms within water molecules form polar covalent bonds. The shared electrons spend more time
associated with the oxygen atom than they do with hydrogen atoms. There is no overall charge to a water molecule, but there is a
slight positive charge on each hydrogen atom and a slight negative charge on the oxygen atom. Because of these charges, the
slightly positive hydrogen atoms repel each other and form the unique shape seen in Figure 2.1.6. Each water molecule attracts
other water molecules because of the positive and negative charges in the different parts of the molecule. Water also attracts other
polar molecules (such as sugars), forming hydrogen bonds. When a substance readily forms hydrogen bonds with water, it can
dissolve in water and is referred to as hydrophilic (“water-loving”). Hydrogen bonds are not readily formed with nonpolar
substances like oils and fats (Figure 2.2.1). These nonpolar compounds are hydrophobic (“water-fearing”) and will not dissolve in
water.

Figure 2.2.1: As this macroscopic image of oil and water show, oil is a nonpolar compound and, hence, will not dissolve in water.
Oil and water do not mix. (credit: Gautam Dogra)

Water Stabilizes Temperature

The hydrogen bonds in water allow it to absorb and release heat energy more slowly than many other substances. Temperature is a
measure of the motion (kinetic energy) of molecules. As the motion increases, energy is higher and thus temperature is higher.
Water absorbs a great deal of energy before its temperature rises. Increased energy disrupts the hydrogen bonds between water
molecules. Because these bonds can be created and disrupted rapidly, water absorbs an increase in energy and temperature changes
only minimally. This means that water moderates temperature changes within organisms and in their environments. As energy input
continues, the balance between hydrogen-bond formation and destruction swings toward the destruction side. More bonds are
broken than are formed. This process results in the release of individual water molecules at the surface of the liquid (such as a body
of water, the leaves of a plant, or the skin of an organism) in a process called evaporation. Evaporation of sweat, which is 90
percent water, allows for cooling of an organism, because breaking hydrogen bonds requires an input of energy and takes heat away
from the body.
Conversely, as molecular motion decreases and temperatures drop, less energy is present to break the hydrogen bonds between
water molecules. These bonds remain intact and begin to form a rigid, lattice-like structure (e.g., ice) (Figure 2.2.2a). When frozen,
ice is less dense than liquid water (the molecules are farther apart). This means that ice floats on the surface of a body of water

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(Figure 2.2.2b). In lakes, ponds, and oceans, ice will form on the surface of the water, creating an insulating barrier to protect the
animal and plant life beneath from freezing in the water. If this did not happen, plants and animals living in water would freeze in a
block of ice and could not move freely, making life in cold temperatures difficult or impossible.

Figure 2.2.2: (a) The lattice structure of ice makes it less dense than the freely flowing molecules of liquid water. Ice's lower
density enables it to (b) float on water. (credit a: modification of work by Jane Whitney; credit b: modification of work by Carlos
Ponte)

CONCEPTS IN ACTION

Click here to see a 3-D animation of the structure of an ice lattice. (credit: image created by Jane Whitney using Visual
1
Molecular Dynamics (VMD) software )

Water Is an Excellent Solvent

Because water is polar, with slight positive and negative charges, ionic compounds and polar molecules can readily dissolve in it.
Water is, therefore, what is referred to as a solvent—a substance capable of dissolving another substance. The charged particles will
form hydrogen bonds with a surrounding layer of water molecules. This is referred to as a sphere of hydration and serves to keep
the particles separated or dispersed in the water. In the case of table salt (NaCl) mixed in water (Figure 2.2.3), the sodium and
chloride ions separate, or dissociate, in the water, and spheres of hydration are formed around the ions. A positively charged
sodium ion is surrounded by the partially negative charges of oxygen atoms in water molecules. A negatively charged chloride ion
is surrounded by the partially positive charges of hydrogen atoms in water molecules. These spheres of hydration are also referred
to as hydration shells. The polarity of the water molecule makes it an effective solvent and is important in its many roles in living
systems.

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 Figure 2.2.3: When table salt (NaCl) is mixed in water, spheres of hydration form around the ions.

Water Is Cohesive
Have you ever filled up a glass of water to the very top and then slowly added a few more drops? Before it overflows, the water
actually forms a dome-like shape above the rim of the glass. This water can stay above the glass because of the property of
cohesion. In cohesion, water molecules are attracted to each other (because of hydrogen bonding), keeping the molecules together
at the liquid-air (gas) interface, although there is no more room in the glass. Cohesion gives rise to surface tension, the capacity of a
substance to withstand rupture when placed under tension or stress. When you drop a small scrap of paper onto a droplet of water,
the paper floats on top of the water droplet, although the object is denser (heavier) than the water. This occurs because of the
surface tension that is created by the water molecules. Cohesion and surface tension keep the water molecules intact and the item
floating on the top. It is even possible to “float” a steel needle on top of a glass of water if you place it gently, without breaking the
surface tension (Figure 2.2.4).

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 Figure 2.2.4: The weight of a needle on top of water pulls the surface tension downward; at the same time, the surface tension of
the water is pulling it up, suspending the needle on the surface of the water and keeping it from sinking. Notice the indentation in
the water around the needle. (credit: Cory Zanker)
These cohesive forces are also related to the water’s property of adhesion, or the attraction between water molecules and other
molecules. This is observed when water “climbs” up a straw placed in a glass of water. You will notice that the water appears to be
higher on the sides of the straw than in the middle. This is because the water molecules are attracted to the straw and therefore
adhere to it.
Cohesive and adhesive forces are important for sustaining life. For example, because of these forces, water can flow up from the
roots to the tops of plants to feed the plant.

CONCEPT IN ACTION
To learn more about water, visit the U.S. Geological Survey Water Science for Schools: All About Water! website.

Buffers, pH, Acids, and Bases

The pH of a solution is a measure of its acidity or alkalinity. You have probably used litmus paper, paper that has been treated with
a natural water-soluble dye so it can be used as a pH indicator, to test how much acid or base (alkalinity) exists in a solution. You
might have even used some to make sure the water in an outdoor swimming pool is properly treated. In both cases, this pH test
measures the amount of hydrogen ions that exists in a given solution. High concentrations of hydrogen ions yield a low pH,
whereas low levels of hydrogen ions result in a high pH. The overall concentration of hydrogen ions is inversely related to its pH
and can be measured on the pH scale (Figure 2.2.5). Therefore, the more hydrogen ions present, the lower the pH; conversely, the
fewer hydrogen ions, the higher the pH.
The pH scale ranges from 0 to 14. A change of one unit on the pH scale represents a change in the concentration of hydrogen ions
by a factor of 10, a change in two units represents a change in the concentration of hydrogen ions by a factor of 100. Thus, small
changes in pH represent large changes in the concentrations of hydrogen ions. Pure water is neutral. It is neither acidic nor basic,
and has a pH of 7.0. Anything below 7.0 (ranging from 0.0 to 6.9) is acidic, and anything above 7.0 (from 7.1 to 14.0) is alkaline.
The blood in your veins is slightly alkaline (pH = 7.4). The environment in your stomach is highly acidic (pH = 1 to 2). Orange
juice is mildly acidic (pH = approximately 3.5), whereas baking soda is basic (pH = 9.0).

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 Figure 2.2.5: The pH scale measures the amount of hydrogen ions (H+) in a substance. (credit: modification of work by Edward
Stevens)
Acids are substances that provide hydrogen ions (H+) and lower pH, whereas bases provide hydroxide ions (OH–) and raise pH.
The stronger the acid, the more readily it donates H+. For example, hydrochloric acid and lemon juice are very acidic and readily
give up H+ when added to water. Conversely, bases are those substances that readily donate OH–. The OH– ions combine with H+
to produce water, which raises a substance’s pH. Sodium hydroxide and many household cleaners are very alkaline and give up
OH– rapidly when placed in water, thereby raising the pH.
Most cells in our bodies operate within a very narrow window of the pH scale, typically ranging only from 7.2 to 7.6. If the pH of
the body is outside of this range, the respiratory system malfunctions, as do other organs in the body. Cells no longer function
properly, and proteins will break down. Deviation outside of the pH range can induce coma or even cause death.
So how is it that we can ingest or inhale acidic or basic substances and not die? Buffers are the key. Buffersreadily absorb excess
H+ or OH–, keeping the pH of the body carefully maintained in the aforementioned narrow range. Carbon dioxide is part of a
prominent buffer system in the human body; it keeps the pH within the proper range. This buffer system involves carbonic acid
(H2CO3) and bicarbonate (HCO3–) anion. If too much H+ enters the body, bicarbonate will combine with the H+ to create carbonic
acid and limit the decrease in pH. Likewise, if too much OH– is introduced into the system, carbonic acid will rapidly dissociate
into bicarbonate and H+ ions. The H+ ions can combine with the OH– ions, limiting the increase in pH. While carbonic acid is an
important product in this reaction, its presence is fleeting because the carbonic acid is released from the body as carbon dioxide gas
each time we breathe. Without this buffer system, the pH in our bodies would fluctuate too much and we would fail to survive.

Summary
Water has many properties that are critical to maintaining life. It is polar, allowing for the formation of hydrogen bonds, which
allow ions and other polar molecules to dissolve in water. Therefore, water is an excellent solvent. The hydrogen bonds between
water molecules give water the ability to hold heat better than many other substances. As the temperature rises, the hydrogen bonds
between water continually break and reform, allowing for the overall temperature to remain stable, although increased energy is
added to the system. Water’s cohesive forces allow for the property of surface tension. All of these unique properties of water are
important in the chemistry of living organisms.
The pH of a solution is a measure of the concentration of hydrogen ions in the solution. A solution with a high number of hydrogen
ions is acidic and has a low pH value. A solution with a high number of hydroxide ions is basic and has a high pH value. The pH

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scale ranges from 0 to 14, with a pH of 7 being neutral. Buffers are solutions that moderate pH changes when an acid or base is
added to the buffer system. Buffers are important in biological systems because of their ability to maintain constant pH conditions.

Footnotes
1. 1 Humphrey, W., Dalke, A. and Schulten, K., "VMD—Visual Molecular Dynamics", J. Molec. Graphics, 1996, vol. 14, pp. 33-
38. [Link]

Glossary

acid
a substance that donates hydrogen ions and therefore lowers pH

adhesion
the attraction between water molecules and molecules of a different substance

base
a substance that absorbs hydrogen ions and therefore raises pH

buffer
a solution that resists a change in pH by absorbing or releasing hydrogen or hydroxide ions

cohesion
the intermolecular forces between water molecules caused by the polar nature of water; creates surface tension

evaporation
the release of water molecules from liquid water to form water vapor

hydrophilic
describes a substance that dissolves in water; water-loving

hydrophobic
describes a substance that does not dissolve in water; water-fearing

litmus paper
filter paper that has been treated with a natural water-soluble dye so it can be used as a pH indicator

pH scale
a scale ranging from 0 to 14 that measures the approximate concentration of hydrogen ions of a substance

solvent
a substance capable of dissolving another substance

surface tension
the cohesive force at the surface of a body of liquid that prevents the molecules from separating

temperature
a measure of molecular motion

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 2.2: Water is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
2.2: Water by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 2.2.6 [Link]

2.3: Biological Molecules
The large molecules necessary for life that are built from smaller organic molecules are called biological macromolecules. There
are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an important
component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a cell’s mass.
Biological macromolecules are organic, meaning that they contain carbon (with some exceptions, like carbon dioxide). In addition,
they may contain hydrogen, oxygen, nitrogen, phosphorus, sulfur, and additional minor elements.

Carbon
It is often said that life is “carbon-based.” This means that carbon atoms, bonded to other carbon atoms or other elements, form the
fundamental components of many, if not most, of the molecules found uniquely in living things. Other elements play important
roles in biological molecules, but carbon certainly qualifies as the “foundation” element for molecules in living things. It is the
bonding properties of carbon atoms that are responsible for its important role.

Carbon Bonding
Carbon contains four electrons in its outer shell. Therefore, it can form four covalent bonds with other atoms or molecules. The
simplest organic carbon molecule is methane (CH4), in which four hydrogen atoms bind to a carbon atom (Figure 2.3.1).

Figure 2.3.1: Carbon can form four covalent bonds to create an organic molecule. The simplest carbon molecule is methane
(CH4), depicted here.
However, structures that are more complex are made using carbon. Any of the hydrogen atoms can be replaced with another carbon
atom covalently bonded to the first carbon atom. In this way, long and branching chains of carbon compounds can be made (Figure
2.3.2a). The carbon atoms may bond with atoms of other elements, such as nitrogen, oxygen, and phosphorus (Figure 2.3.2b). The

molecules may also form rings, which themselves can link with other rings (Figure 2.3.2c). This diversity of molecular forms
accounts for the diversity of functions of the biological macromolecules and is based to a large degree on the ability of carbon to
form multiple bonds with itself and other atoms.

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 Figure 2.3.2: These examples show three molecules (found in living organisms) that contain carbon atoms bonded in various
ways to other carbon atoms and the atoms of other elements. (a) This molecule of stearic acid has a long chain of carbon atoms. (b)
Glycine, a component of proteins, contains carbon, nitrogen, oxygen, and hydrogen atoms. (c) Glucose, a sugar, has a ring of
carbon atoms and one oxygen atom.

Carbohydrates
Carbohydrates are macromolecules with which most consumers are somewhat familiar. To lose weight, some individuals adhere to
“low-carb” diets. Athletes, in contrast, often “carb-load” before important competitions to ensure that they have sufficient energy to
compete at a high level. Carbohydrates are, in fact, an essential part of our diet; grains, fruits, and vegetables are all natural sources
of carbohydrates. Carbohydrates provide energy to the body, particularly through glucose, a simple sugar. Carbohydrates also have
other important functions in humans, animals, and plants.
Carbohydrates can be represented by the formula (CH2O)n, where n is the number of carbon atoms in the molecule. In other words,
the ratio of carbon to hydrogen to oxygen is 1:2:1 in carbohydrate molecules. Carbohydrates are classified into three subtypes:
monosaccharides, disaccharides, and polysaccharides.
Monosaccharides (mono- = “one”; sacchar- = “sweet”) are simple sugars, the most common of which is glucose. In
monosaccharides, the number of carbon atoms usually ranges from three to six. Most monosaccharide names end with the suffix -
ose. Depending on the number of carbon atoms in the sugar, they may be known as trioses (three carbon atoms), pentoses (five
carbon atoms), and hexoses (six carbon atoms).
Monosaccharides may exist as a linear chain or as ring-shaped molecules; in aqueous solutions, they are usually found in the ring
form.
The chemical formula for glucose is C6H12O6. In most living species, glucose is an important source of energy. During cellular
respiration, energy is released from glucose, and that energy is used to help make adenosine triphosphate (ATP). Plants synthesize
glucose using carbon dioxide and water by the process of photosynthesis, and the glucose, in turn, is used for the energy
requirements of the plant. The excess synthesized glucose is often stored as starch that is broken down by other organisms that feed
on plants.
Galactose (part of lactose, or milk sugar) and fructose (found in fruit) are other common monosaccharides. Although glucose,
galactose, and fructose all have the same chemical formula (C6H12O6), they differ structurally and chemically (and are known as
isomers) because of differing arrangements of atoms in the carbon chain (Figure 2.3.3).

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 Figure 2.3.3: Glucose, galactose, and fructose are isomeric monosaccharides, meaning that they have the same chemical formula
but slightly different structures.
Disaccharides (di- = “two”) form when two monosaccharides undergo a dehydration reaction (a reaction in which the removal of a
water molecule occurs). During this process, the hydroxyl group (–OH) of one monosaccharide combines with a hydrogen atom of
another monosaccharide, releasing a molecule of water (H2O) and forming a covalent bond between atoms in the two sugar
molecules.
Common disaccharides include lactose, maltose, and sucrose. Lactose is a disaccharide consisting of the monomers glucose and
galactose. It is found naturally in milk. Maltose, or malt sugar, is a disaccharide formed from a dehydration reaction between two
glucose molecules. The most common disaccharide is sucrose, or table sugar, which is composed of the monomers glucose and
fructose.
A long chain of monosaccharides linked by covalent bonds is known as a polysaccharide (poly- = “many”). The chain may be
branched or unbranched, and it may contain different types of monosaccharides. Polysaccharides may be very large molecules.
Starch, glycogen, cellulose, and chitin are examples of polysaccharides.
Starch is the stored form of sugars in plants and is made up of amylose and amylopectin (both polymers of glucose). Plants are able
to synthesize glucose, and the excess glucose is stored as starch in different plant parts, including roots and seeds. The starch that is
consumed by animals is broken down into smaller molecules, such as glucose. The cells can then absorb the glucose.
Glycogen is the storage form of glucose in humans and other vertebrates, and is made up of monomers of glucose. Glycogen is the
animal equivalent of starch and is a highly branched molecule usually stored in liver and muscle cells. Whenever glucose levels
decrease, glycogen is broken down to release glucose.
Cellulose is one of the most abundant natural biopolymers. The cell walls of plants are mostly made of cellulose, which provides
structural support to the cell. Wood and paper are mostly cellulosic in nature. Cellulose is made up of glucose monomers that are
linked by bonds between particular carbon atoms in the glucose molecule.
Every other glucose monomer in cellulose is flipped over and packed tightly as extended long chains. This gives cellulose its
rigidity and high tensile strength—which is so important to plant cells. Cellulose passing through our digestive system is called
dietary fiber. While the glucose-glucose bonds in cellulose cannot be broken down by human digestive enzymes, herbivores such as
cows, buffalos, and horses are able to digest grass that is rich in cellulose and use it as a food source. In these animals, certain
species of bacteria reside in the rumen (part of the digestive system of herbivores) and secrete the enzyme cellulase. The appendix

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also contains bacteria that break down cellulose, giving it an important role in the digestive systems of ruminants. Cellulases can
break down cellulose into glucose monomers that can be used as an energy source by the animal.
Carbohydrates serve other functions in different animals. Arthropods, such as insects, spiders, and crabs, have an outer skeleton,
called the exoskeleton, which protects their internal body parts. This exoskeleton is made of the biological macromolecule chitin,
which is a nitrogenous carbohydrate. It is made of repeating units of a modified sugar containing nitrogen.
Thus, through differences in molecular structure, carbohydrates are able to serve the very different functions of energy storage
(starch and glycogen) and structural support and protection (cellulose and chitin) (Figure 2.3.4).

Figure 2.3.4: Although their structures and functions differ, all polysaccharide carbohydrates are made up of monosaccharides
and have the chemical formula (CH2O)n.

CAREERS IN ACTION: Registered Dietitian

Obesity is a worldwide health concern, and many diseases, such as diabetes and heart disease, are becoming more prevalent
because of obesity. This is one of the reasons why registered dietitians are increasingly sought after for advice. Registered
dietitians help plan food and nutrition programs for individuals in various settings. They often work with patients in health-care
facilities, designing nutrition plans to prevent and treat diseases. For example, dietitians may teach a patient with diabetes how
to manage blood-sugar levels by eating the correct types and amounts of carbohydrates. Dietitians may also work in nursing
homes, schools, and private practices.
To become a registered dietitian, one needs to earn at least a bachelor’s degree in dietetics, nutrition, food technology, or a
related field. In addition, registered dietitians must complete a supervised internship program and pass a national exam. Those
who pursue careers in dietetics take courses in nutrition, chemistry, biochemistry, biology, microbiology, and human
physiology. Dietitians must become experts in the chemistry and functions of food (proteins, carbohydrates, and fats).

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Lipids
Lipids include a diverse group of compounds that are united by a common feature. Lipids are hydrophobic (“water-fearing”), or
insoluble in water, because they are nonpolar molecules. This is because they are hydrocarbons that include only nonpolar carbon-
carbon or carbon-hydrogen bonds. Lipids perform many different functions in a cell. Cells store energy for long-term use in the
form of lipids called fats. Lipids also provide insulation from the environment for plants and animals (Figure 2.3.5). For example,
they help keep aquatic birds and mammals dry because of their water-repelling nature. Lipids are also the building blocks of many
hormones and are an important constituent of the plasma membrane. Lipids include fats, oils, waxes, phospholipids, and steroids.

Figure 2.3.5: Hydrophobic lipids in the fur of aquatic mammals, such as this river otter, protect them from the elements. (credit:
Ken Bosma)
A fat molecule, such as a triglyceride, consists of two main components—glycerol and fatty acids. Glycerol is an organic
compound with three carbon atoms, five hydrogen atoms, and three hydroxyl (–OH) groups. Fatty acids have a long chain of
hydrocarbons to which an acidic carboxyl group is attached, hence the name “fatty acid.” The number of carbons in the fatty acid
may range from 4 to 36; most common are those containing 12–18 carbons. In a fat molecule, a fatty acid is attached to each of the
three oxygen atoms in the –OH groups of the glycerol molecule with a covalent bond (Figure 2.3.6).

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 Figure 2.3.6: Lipids include fats, such as triglycerides, which are made up of fatty acids and glycerol, phospholipids, and steroids.
During this covalent bond formation, three water molecules are released. The three fatty acids in the fat may be similar or
dissimilar. These fats are also called triglycerides because they have three fatty acids. Some fatty acids have common names that
specify their origin. For example, palmitic acid, a saturated fatty acid, is derived from the palm tree. Arachidic acid is derived from
Arachis hypogaea, the scientific name for peanuts.
Fatty acids may be saturated or unsaturated. In a fatty acid chain, if there are only single bonds between neighboring carbons in the
hydrocarbon chain, the fatty acid is saturated. Saturated fatty acids are saturated with hydrogen; in other words, the number of
hydrogen atoms attached to the carbon skeleton is maximized.
When the hydrocarbon chain contains a double bond, the fatty acid is an unsaturated fatty acid.
Most unsaturated fats are liquid at room temperature and are called oils. If there is one double bond in the molecule, then it is
known as a monounsaturated fat (e.g., olive oil), and if there is more than one double bond, then it is known as a polyunsaturated
fat (e.g., canola oil).
Saturated fats tend to get packed tightly and are solid at room temperature. Animal fats with stearic acid and palmitic acid
contained in meat, and the fat with butyric acid contained in butter, are examples of saturated fats. Mammals store fats in
specialized cells called adipocytes, where globules of fat occupy most of the cell. In plants, fat or oil is stored in seeds and is used
as a source of energy during embryonic development.
Unsaturated fats or oils are usually of plant origin and contain unsaturated fatty acids. The double bond causes a bend or a “kink”
that prevents the fatty acids from packing tightly, keeping them liquid at room temperature. Olive oil, corn oil, canola oil, and cod

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liver oil are examples of unsaturated fats. Unsaturated fats help to improve blood cholesterol levels, whereas saturated fats
contribute to plaque formation in the arteries, which increases the risk of a heart attack.
In the food industry, oils are artificially hydrogenated to make them semi-solid, leading to less spoilage and increased shelf life.
Simply speaking, hydrogen gas is bubbled through oils to solidify them. During this hydrogenation process, double bonds of the
cis-conformation in the hydrocarbon chain may be converted to double bonds in the trans-conformation. This forms a trans-fat
from a cis-fat. The orientation of the double bonds affects the chemical properties of the fat (Figure 2.3.7).

Figure 2.3.7: During the hydrogenation process, the orientation around the double bonds is changed, making a trans-fat from a
cis-fat. This changes the chemical properties of the molecule.
Margarine, some types of peanut butter, and shortening are examples of artificially hydrogenated trans-fats. Recent studies have
shown that an increase in trans-fats in the human diet may lead to an increase in levels of low-density lipoprotein (LDL), or “bad”
cholesterol, which, in turn, may lead to plaque deposition in the arteries, resulting in heart disease. Many fast food restaurants have
recently eliminated the use of trans-fats, and U.S. food labels are now required to list their trans-fat content.
Essential fatty acids are fatty acids that are required but not synthesized by the human body. Consequently, they must be
supplemented through the diet. Omega-3 fatty acids fall into this category and are one of only two known essential fatty acids for
humans (the other being omega-6 fatty acids). They are a type of polyunsaturated fat and are called omega-3 fatty acids because the
third carbon from the end of the fatty acid participates in a double bond.
Salmon, trout, and tuna are good sources of omega-3 fatty acids. Omega-3 fatty acids are important in brain function and normal
growth and development. They may also prevent heart disease and reduce the risk of cancer.
Like carbohydrates, fats have received a lot of bad publicity. It is true that eating an excess of fried foods and other “fatty” foods
leads to weight gain. However, fats do have important functions. Fats serve as long-term energy storage. They also provide
insulation for the body. Therefore, “healthy” unsaturated fats in moderate amounts should be consumed on a regular basis.
Phospholipids are the major constituent of the plasma membrane. Like fats, they are composed of fatty acid chains attached to a
glycerol or similar backbone. Instead of three fatty acids attached, however, there are two fatty acids and the third carbon of the
glycerol backbone is bound to a phosphate group. The phosphate group is modified by the addition of an alcohol.
A phospholipid has both hydrophobic and hydrophilic regions. The fatty acid chains are hydrophobic and exclude themselves from
water, whereas the phosphate is hydrophilic and interacts with water.
Cells are surrounded by a membrane, which has a bilayer of phospholipids. The fatty acids of phospholipids face inside, away from
water, whereas the phosphate group can face either the outside environment or the inside of the cell, which are both aqueous.

Steroids and Waxes

Unlike the phospholipids and fats discussed earlier, steroids have a ring structure. Although they do not resemble other lipids, they
are grouped with them because they are also hydrophobic. All steroids have four, linked carbon rings and several of them, like
cholesterol, have a short tail.

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Cholesterol is a steroid. Cholesterol is mainly synthesized in the liver and is the precursor of many steroid hormones, such as
testosterone and estradiol. It is also the precursor of vitamins E and K. Cholesterol is the precursor of bile salts, which help in the
breakdown of fats and their subsequent absorption by cells. Although cholesterol is often spoken of in negative terms, it is
necessary for the proper functioning of the body. It is a key component of the plasma membranes of animal cells.
Waxes are made up of a hydrocarbon chain with an alcohol (–OH) group and a fatty acid. Examples of animal waxes include
beeswax and lanolin. Plants also have waxes, such as the coating on their leaves, that helps prevent them from drying out.

CONCEPT IN ACTION
For an additional perspective on lipids, explore “Biomolecules: The Lipids” through this interactive animation.

Proteins
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all
macromolecules. Proteins may be structural, regulatory, contractile, or protective; they may serve in transport, storage, or
membranes; or they may be toxins or enzymes. Each cell in a living system may contain thousands of different proteins, each with
a unique function. Their structures, like their functions, vary greatly. They are all, however, polymers of amino acids, arranged in a
linear sequence.
The functions of proteins are very diverse because there are 20 different chemically distinct amino acids that form long chains, and
the amino acids can be in any order. For example, proteins can function as enzymes or hormones. Enzymes, which are produced by
living cells, are catalysts in biochemical reactions (like digestion) and are usually proteins. Each enzyme is specific for the
substrate (a reactant that binds to an enzyme) upon which it acts. Enzymes can function to break molecular bonds, to rearrange
bonds, or to form new bonds. An example of an enzyme is salivary amylase, which breaks down amylose, a component of starch.
Hormones are chemical signaling molecules, usually proteins or steroids, secreted by an endocrine gland or group of endocrine
cells that act to control or regulate specific physiological processes, including growth, development, metabolism, and reproduction.
For example, insulin is a protein hormone that maintains blood glucose levels.
Proteins have different shapes and molecular weights; some proteins are globular in shape whereas others are fibrous in nature. For
example, hemoglobin is a globular protein, but collagen, found in our skin, is a fibrous protein. Protein shape is critical to its
function. Changes in temperature, pH, and exposure to chemicals may lead to permanent changes in the shape of the protein,
leading to a loss of function or denaturation (to be discussed in more detail later). All proteins are made up of different
arrangements of the same 20 kinds of amino acids.
Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental structure, which consists of a
central carbon atom bonded to an amino group (–NH2), a carboxyl group (–COOH), and a hydrogen atom. Every amino acid also
has another variable atom or group of atoms bonded to the central carbon atom known as the R group. The R group is the only
difference in structure between the 20 amino acids; otherwise, the amino acids are identical (Figure 2.3.8).

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 Figure 2.3.8: Amino acids are made up of a central carbon bonded to an amino group (–NH2), a carboxyl group (–COOH), and a
hydrogen atom. The central carbon’s fourth bond varies among the different amino acids, as seen in these examples of alanine,
valine, lysine, and aspartic acid.
The chemical nature of the R group determines the chemical nature of the amino acid within its protein (that is, whether it is acidic,
basic, polar, or nonpolar).
The sequence and number of amino acids ultimately determine a protein’s shape, size, and function. Each amino acid is attached to
another amino acid by a covalent bond, known as a peptide bond, which is formed by a dehydration reaction. The carboxyl group
of one amino acid and the amino group of a second amino acid combine, releasing a water molecule. The resulting bond is the
peptide bond.
The products formed by such a linkage are called polypeptides. While the terms polypeptide and protein are sometimes used
interchangeably, a polypeptide is technically a polymer of amino acids, whereas the term protein is used for a polypeptide or
polypeptides that have combined together, have a distinct shape, and have a unique function.

EVOLUTION IN ACTION: The Evolutionary Significance of Cytochrome c

Cytochrome c is an important component of the molecular machinery that harvests energy from glucose. Because this protein’s
role in producing cellular energy is crucial, it has changed very little over millions of years. Protein sequencing has shown that
there is a considerable amount of sequence similarity among cytochrome c molecules of different species; evolutionary
relationships can be assessed by measuring the similarities or differences among various species’ protein sequences.

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 For example, scientists have determined that human cytochrome c contains 104 amino acids. For each cytochrome c molecule
that has been sequenced to date from different organisms, 37 of these amino acids appear in the same position in each
cytochrome c. This indicates that all of these organisms are descended from a common ancestor. On comparing the human and
chimpanzee protein sequences, no sequence difference was found. When human and rhesus monkey sequences were compared,
a single difference was found in one amino acid. In contrast, human-to-yeast comparisons show a difference in 44 amino acids,
suggesting that humans and chimpanzees have a more recent common ancestor than humans and the rhesus monkey, or
humans and yeast.

Protein Structure
As discussed earlier, the shape of a protein is critical to its function. To understand how the protein gets its final shape or
conformation, we need to understand the four levels of protein structure: primary, secondary, tertiary, and quaternary (Figure
2.3.9).

The unique sequence and number of amino acids in a polypeptide chain is its primary structure. The unique sequence for every
protein is ultimately determined by the gene that encodes the protein. Any change in the gene sequence may lead to a different
amino acid being added to the polypeptide chain, causing a change in protein structure and function. In sickle cell anemia, the
hemoglobin β chain has a single amino acid substitution, causing a change in both the structure and function of the protein. What is
most remarkable to consider is that a hemoglobin molecule is made up of two alpha chains and two beta chains that each consist of
about 150 amino acids. The molecule, therefore, has about 600 amino acids. The structural difference between a normal
hemoglobin molecule and a sickle cell molecule—that dramatically decreases life expectancy in the affected individuals—is a
single amino acid of the 600.
Because of this change of one amino acid in the chain, the normally biconcave, or disc-shaped, red blood cells assume a crescent or
“sickle” shape, which clogs arteries. This can lead to a myriad of serious health problems, such as breathlessness, dizziness,
headaches, and abdominal pain for those who have this disease.
Folding patterns resulting from interactions between the non-R group portions of amino acids give rise to the secondary structure of
the protein. The most common are the alpha (α)-helix and beta (β)-pleated sheet structures. Both structures are held in shape by
hydrogen bonds. In the alpha helix, the bonds form between every fourth amino acid and cause a twist in the amino acid chain.
In the β-pleated sheet, the “pleats” are formed by hydrogen bonding between atoms on the backbone of the polypeptide chain. The
R groups are attached to the carbons, and extend above and below the folds of the pleat. The pleated segments align parallel to each
other, and hydrogen bonds form between the same pairs of atoms on each of the aligned amino acids. The α-helix and β-pleated
sheet structures are found in many globular and fibrous proteins.
The unique three-dimensional structure of a polypeptide is known as its tertiary structure. This structure is caused by chemical
interactions between various amino acids and regions of the polypeptide. Primarily, the interactions among R groups create the
complex three-dimensional tertiary structure of a protein. There may be ionic bonds formed between R groups on different amino
acids, or hydrogen bonding beyond that involved in the secondary structure. When protein folding takes place, the hydrophobic R
groups of nonpolar amino acids lay in the interior of the protein, whereas the hydrophilic R groups lay on the outside. The former
types of interactions are also known as hydrophobic interactions.
In nature, some proteins are formed from several polypeptides, also known as subunits, and the interaction of these subunits forms
the quaternary structure. Weak interactions between the subunits help to stabilize the overall structure. For example, hemoglobin is
a combination of four polypeptide subunits.

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 Figure 2.3.9: The four levels of protein structure can be observed in these illustrations. (credit: modification of work by National
Human Genome Research Institute)
Each protein has its own unique sequence and shape held together by chemical interactions. If the protein is subject to changes in
temperature, pH, or exposure to chemicals, the protein structure may change, losing its shape in what is known as denaturation as
discussed earlier. Denaturation is often reversible because the primary structure is preserved if the denaturing agent is removed,
allowing the protein to resume its function. Sometimes denaturation is irreversible, leading to a loss of function. One example of
protein denaturation can be seen when an egg is fried or boiled. The albumin protein in the liquid egg white is denatured when
placed in a hot pan, changing from a clear substance to an opaque white substance. Not all proteins are denatured at high
temperatures; for instance, bacteria that survive in hot springs have proteins that are adapted to function at those temperatures.

CONCEPT IN ACTION
For an additional perspective on proteins, explore “Biomolecules: The Proteins” through this interactive animation.

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Nucleic Acids
Nucleic acids are key macromolecules in the continuity of life. They carry the genetic blueprint of a cell and carry instructions for
the functioning of the cell.
The two main types of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the genetic material
found in all living organisms, ranging from single-celled bacteria to multicellular mammals.
The other type of nucleic acid, RNA, is mostly involved in protein synthesis. The DNA molecules never leave the nucleus, but
instead use an RNA intermediary to communicate with the rest of the cell. Other types of RNA are also involved in protein
synthesis and its regulation.
DNA and RNA are made up of monomers known as nucleotides. The nucleotides combine with each other to form a
polynucleotide, DNA or RNA. Each nucleotide is made up of three components: a nitrogenous base, a pentose (five-carbon) sugar,
and a phosphate group (Figure 2.3.10). Each nitrogenous base in a nucleotide is attached to a sugar molecule, which is attached to
a phosphate group.

Figure 2.3.10: A nucleotide is made up of three components: a nitrogenous base, a pentose sugar, and a phosphate group.

DNA Double-Helical Structure

DNA has a double-helical structure (Figure 2.3.11). It is composed of two strands, or polymers, of nucleotides. The strands are
formed with bonds between phosphate and sugar groups of adjacent nucleotides. The strands are bonded to each other at their bases
with hydrogen bonds, and the strands coil about each other along their length, hence the “double helix” description, which means a
double spiral.

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 Figure 2.3.11: The double-helix model shows DNA as two parallel strands of intertwining molecules. (credit: Jerome Walker,
Dennis Myts)
The alternating sugar and phosphate groups lie on the outside of each strand, forming the backbone of the DNA. The nitrogenous
bases are stacked in the interior, like the steps of a staircase, and these bases pair; the pairs are bound to each other by hydrogen
bonds. The bases pair in such a way that the distance between the backbones of the two strands is the same all along the molecule.

Summary
Living things are carbon-based because carbon plays such a prominent role in the chemistry of living things. The four covalent
bonding positions of the carbon atom can give rise to a wide diversity of compounds with many functions, accounting for the
importance of carbon in living things. Carbohydrates are a group of macromolecules that are a vital energy source for the cell,
provide structural support to many organisms, and can be found on the surface of the cell as receptors or for cell recognition.
Carbohydrates are classified as monosaccharides, disaccharides, and polysaccharides, depending on the number of monomers in the
molecule.
Lipids are a class of macromolecules that are nonpolar and hydrophobic in nature. Major types include fats and oils, waxes,
phospholipids, and steroids. Fats and oils are a stored form of energy and can include triglycerides. Fats and oils are usually made
up of fatty acids and glycerol.
Proteins are a class of macromolecules that can perform a diverse range of functions for the cell. They help in metabolism by
providing structural support and by acting as enzymes, carriers or as hormones. The building blocks of proteins are amino acids.
Proteins are organized at four levels: primary, secondary, tertiary, and quaternary. Protein shape and function are intricately linked;
any change in shape caused by changes in temperature, pH, or chemical exposure may lead to protein denaturation and a loss of
function.
Nucleic acids are molecules made up of repeating units of nucleotides that direct cellular activities such as cell division and protein
synthesis. Each nucleotide is made up of a pentose sugar, a nitrogenous base, and a phosphate group. There are two types of nucleic
acids: DNA and RNA.

Glossary

amino acid
a monomer of a protein

carbohydrate

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 a biological macromolecule in which the ratio of carbon to hydrogen to oxygen is 1:2:1; carbohydrates serve as energy sources
and structural support in cells

cellulose
a polysaccharide that makes up the cell walls of plants and provides structural support to the cell

chitin
a type of carbohydrate that forms the outer skeleton of arthropods, such as insects and crustaceans, and the cell walls of fungi

denaturation
the loss of shape in a protein as a result of changes in temperature, pH, or exposure to chemicals

deoxyribonucleic acid (DNA)

a double-stranded polymer of nucleotides that carries the hereditary information of the cell

disaccharide
two sugar monomers that are linked together by a peptide bond

enzyme
a catalyst in a biochemical reaction that is usually a complex or conjugated protein

fat
a lipid molecule composed of three fatty acids and a glycerol (triglyceride) that typically exists in a solid form at room
temperature

glycogen
a storage carbohydrate in animals

hormone
a chemical signaling molecule, usually a protein or steroid, secreted by an endocrine gland or group of endocrine cells; acts to
control or regulate specific physiological processes

lipids
a class of macromolecules that are nonpolar and insoluble in water

macromolecule
a large molecule, often formed by polymerization of smaller monomers

monosaccharide
a single unit or monomer of carbohydrates

nucleic acid
a biological macromolecule that carries the genetic information of a cell and carries instructions for the functioning of the cell

nucleotide
a monomer of nucleic acids; contains a pentose sugar, a phosphate group, and a nitrogenous base

oil
an unsaturated fat that is a liquid at room temperature

phospholipid
a major constituent of the membranes of cells; composed of two fatty acids and a phosphate group attached to the glycerol
backbone

polypeptide

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 a long chain of amino acids linked by peptide bonds

polysaccharide
a long chain of monosaccharides; may be branched or unbranched

protein
a biological macromolecule composed of one or more chains of amino acids

ribonucleic acid (RNA)

a single-stranded polymer of nucleotides that is involved in protein synthesis

saturated fatty acid

a long-chain hydrocarbon with single covalent bonds in the carbon chain; the number of hydrogen atoms attached to the carbon
skeleton is maximized

starch
a storage carbohydrate in plants

steroid
a type of lipid composed of four fused hydrocarbon rings

trans-fat
a form of unsaturated fat with the hydrogen atoms neighboring the double bond across from each other rather than on the same
side of the double bond

triglyceride
a fat molecule; consists of three fatty acids linked to a glycerol molecule

unsaturated fatty acid

a long-chain hydrocarbon that has one or more than one double bonds in the hydrocarbon chain

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 2.3: Biological Molecules is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
2.3: Biological Molecules by OpenStax is licensed CC BY 4.0.

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2.E: Chemistry of Life (Exercises)
2.1: The Building Blocks of Molecules
At its most fundamental level, life is made up of matter. Matter occupies space and has mass. All matter is composed of elements,
substances that cannot be broken down or transformed chemically into other substances. Each element is made of atoms, each with
a constant number of protons and unique properties. Each element is designated by its chemical symbol and possesses unique
properties. These unique properties allow elements to combine and to bond with each other in specific ways.

Multiple Choice
Magnesium has an atomic number of 12. Which of the following statements is true of a neutral magnesium atom?
A. It has 12 protons, 12 electrons, and 12 neutrons.
B. It has 12 protons, 12 electrons, and six neutrons.
C. It has six protons, six electrons, and no neutrons.
D. It has six protons, six electrons, and six neutrons.

Answer
A

Which type of bond represents a weak chemical bond?

A. hydrogen bond
B. ionic bond
C. covalent bond
D. polar covalent bond

Answer
A

An isotope of sodium (Na) has a mass number of 22. How many neutrons does it have?
A. 11
B. 12
C. 22
D. 44

Answer
A

Free Response
Why are hydrogen bonds and van der Waals interactions necessary for cells?

Answer
Hydrogen bonds and van der Waals interactions form weak associations between different molecules. They provide the
structure and shape necessary for proteins and DNA within cells so that they function properly. Hydrogen bonds also give water
its unique properties, which are necessary for life.

2.2: Water
Do you ever wonder why scientists spend time looking for water on other planets? It is because water is essential to life; even
minute traces of it on another planet can indicate that life could or did exist on that planet. Water is one of the more abundant
molecules in living cells and the one most critical to life as we know it. Approximately 60–70 percent of your body is made up of
water. Without it, life simply would not exist.

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Multiple Choice
Which of the following statements is not true?
A. Water is polar.
B. Water stabilizes temperature.
C. Water is essential for life.
D. Water is the most abundant atom in Earth’s atmosphere.

Answer
D

Using a pH meter, you find the pH of an unknown solution to be 8.0. How would you describe this solution?
A. weakly acidic
B. strongly acidic
C. weakly basic
D. strongly basic

Answer
C

The pH of lemon juice is about 2.0, whereas tomato juice's pH is about 4.0. Approximately how much of an increase in hydrogen
ion concentration is there between tomato juice and lemon juice?
A. 2 times
B. 10 times
C. 100 times
D. 1000 times

Answer
C

Free Response
Why can some insects walk on water?

Answer
Some insects can walk on water, although they are heavier (denser) than water, because of the surface tension of water. Surface
tension results from cohesion, or the attraction between water molecules at the surface of the body of water [the liquid-air (gas)
interface].

Explain why water is an excellent solvent.

Answer
Water molecules are polar, meaning they have separated partial positive and negative charges. Because of these charges, water
molecules are able to surround charged particles created when a substance dissociates. The surrounding layer of water
molecules stabilizes the ion and keeps differently charged ions from reassociating, so the substance stays dissolved.

2.3: Biological Molecules

There are four major classes of biological macromolecules (carbohydrates, lipids, proteins, and nucleic acids), and each is an
important component of the cell and performs a wide array of functions. Combined, these molecules make up the majority of a
cell’s mass. Biological macromolecules are organic, meaning that they contain carbon (with some exceptions, like carbon dioxide).

Multiple Choice
An example of a monosaccharide is ________.

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 A. fructose
B. glucose
C. galactose
D. all of the above

Answer
D

Cellulose and starch are examples of ________.

A. monosaccharides
B. disaccharides
C. lipids
D. polysaccharides

Answer
D

Phospholipids are important components of __________.

A. the plasma membrane of cells
B. the ring structure of steroids
C. the waxy covering on leaves
D. the double bond in hydrocarbon chains

Answer
A

The monomers that make up proteins are called _________.

A. nucleotides
B. disaccharides
C. amino acids
D. chaperones

Answer
C

Free Response
Explain at least three functions that lipids serve in plants and/or animals.

Answer
Fat serves as a valuable way for animals to store energy. It can also provide insulation. Phospholipids and steroids are important
components of cell membranes.

Explain what happens if even one amino acid is substituted for another in a polypeptide chain. Provide a specific example.

Answer
A change in gene sequence can lead to a different amino acid being added to a polypeptide chain instead of the normal one.
This causes a change in protein structure and function. For example, in sickle cell anemia, the hemoglobin β chain has a single
amino acid substitution. Because of this change, the disc-shaped red blood cells assume a crescent shape, which can result in
serious health problems.

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 CHAPTER OVERVIEW

3: Cell Diversity, Structures, and Transport

3.1: Cell Structure and Function
3.1.1: How Cells Are Studied
3.1.2: Comparing Prokaryotic and Eukaryotic Cells
3.1.3: Eukaryotic Cells
3.1.4: The Cell Membrane
3.1.5: Passive Transport
3.1.6: Active Transport
3.1.E: Cell Structure and Function (Exercises)
3.2: Eukaryotic Origins
3.3: The Genome

Thumbnail: Animal Cell (Public Domain; Kelvin Song via Wikimedia Commons)

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1
 SECTION OVERVIEW

3.1: Cell Structure and Function

3.1.1: How Cells Are Studied

3.1.2: Comparing Prokaryotic and Eukaryotic Cells

3.1.3: Eukaryotic Cells

3.1.4: The Cell Membrane

3.1.5: Passive Transport

3.1.6: Active Transport

3.1.E: Cell Structure and Function (Exercises)

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3.1.1: How Cells Are Studied
A cell is the smallest unit of a living thing. A living thing, like you, is called an organism. Thus, cells are the basic building blocks
of all organisms.
In multicellular organisms, several cells of one particular kind interconnect with each other and perform shared functions to form
tissues (for example, muscle tissue, connective tissue, and nervous tissue), several tissues combine to form an organ (for example,
stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous
system). Several systems functioning together form an organism (such as an elephant, for example).
There are many types of cells, and all are grouped into one of two broad categories: prokaryotic and eukaryotic. Animal cells, plant
cells, fungal cells, and protist cells are classified as eukaryotic, whereas bacteria and archaea cells are classified as prokaryotic.
Before discussing the criteria for determining whether a cell is prokaryotic or eukaryotic, let us first examine how biologists study
cells.

Microscopy
Cells vary in size. With few exceptions, individual cells are too small to be seen with the naked eye, so scientists use microscopes
to study them. A microscope is an instrument that magnifies an object. Most images of cells are taken with a microscope and are
called micrographs.

Light Microscopes
To give you a sense of the size of a cell, a typical human red blood cell is about eight millionths of a meter or eight micrometers
(abbreviated as µm) in diameter; the head of a pin is about two thousandths of a meter (millimeters, or mm) in diameter. That
means that approximately 250 red blood cells could fit on the head of a pin.
The optics of the lenses of a light microscope changes the orientation of the image. A specimen that is right-side up and facing right
on the microscope slide will appear upside-down and facing left when viewed through a microscope, and vice versa. Similarly, if
the slide is moved left while looking through the microscope, it will appear to move right, and if moved down, it will seem to move
up. This occurs because microscopes use two sets of lenses to magnify the image. Due to the manner in which light travels through
the lenses, this system of lenses produces an inverted image (binoculars and a dissecting microscope work in a similar manner, but
include an additional magnification system that makes the final image appear to be upright).
Most student microscopes are classified as light microscopes (Figure 3.1.1.1a). Visible light both passes through and is bent by the
lens system to enable the user to see the specimen. Light microscopes are advantageous for viewing living organisms, but since
individual cells are generally transparent, their components are not distinguishable unless they are colored with special stains.
Staining, however, usually kills the cells.
Light microscopes commonly used in the undergraduate college laboratory magnify up to approximately 400 times. Two
parameters that are important in microscopy are magnification and resolving power. Magnification is the degree of enlargement of
an object. Resolving power is the ability of a microscope to allow the eye to distinguish two adjacent structures as separate; the
higher the resolution, the closer those two objects can be, and the better the clarity and detail of the image. When oil immersion
lenses are used, magnification is usually increased to 1,000 times for the study of smaller cells, like most prokaryotic cells. Because
light entering a specimen from below is focused onto the eye of an observer, the specimen can be viewed using light microscopy.
For this reason, for light to pass through a specimen, the sample must be thin or translucent.

CONCEPT IN ACTION

For another perspective on cell size, try the HowBig interactive.

A second type of microscope used in laboratories is the dissecting microscope (Figure 3.1.1.1b). These microscopes have a lower
magnification (20 to 80 times the object size) than light microscopes and can provide a three-dimensional view of the specimen.

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Thick objects can be examined with many components in focus at the same time. These microscopes are designed to give a
magnified and clear view of tissue structure as well as the anatomy of the whole organism. Like light microscopes, most modern
dissecting microscopes are also binocular, meaning that they have two separate lens systems, one for each eye. The lens systems
are separated by a certain distance, and therefore provide a sense of depth in the view of their subject to make manipulations by
hand easier. Dissecting microscopes also have optics that correct the image so that it appears as if being seen by the naked eye and
not as an inverted image. The light illuminating a sample under a dissecting microscope typically comes from above the sample,
but may also be directed from below.

Figure [Link]: (a) Most light microscopes used in a college biology lab can magnify cells up to approximately 400 times. (b)
Dissecting microscopes have a lower magnification than light microscopes and are used to examine larger objects, such as tissues.

Electron Microscopes
In contrast to light microscopes, electron microscopes use a beam of electrons instead of a beam of light. Not only does this allow
for higher magnification and, thus, more detail (Figure [Link]), it also provides higher resolving power. Preparation of a specimen
for viewing under an electron microscope will kill it; therefore, live cells cannot be viewed using this type of microscopy. In
addition, the electron beam moves best in a vacuum, making it impossible to view living materials.
In a scanning electron microscope, a beam of electrons moves back and forth across a cell’s surface, rendering the details of cell
surface characteristics by reflection. Cells and other structures are usually coated with a metal like gold. In a transmission electron
microscope, the electron beam is transmitted through the cell and provides details of a cell’s internal structures. As you might
imagine, electron microscopes are significantly more bulky and expensive than are light microscopes.

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 Figure [Link]: (a) Salmonella bacteria are viewed with a light microscope. (b) This scanning electron micrograph shows
Salmonella bacteria (in red) invading human cells. (credit a: modification of work by CDC, Armed Forces Institute of Pathology,
Charles N. Farmer; credit b: modification of work by Rocky Mountain Laboratories, NIAID, NIH; scale-bar data from Matt
Russell)

CAREERS IN ACTION: Cytotechnologist

Have you ever heard of a medical test called a Pap smear (Figure [Link])? In this test, a doctor takes a small sample of cells
from the uterine cervix of a patient and sends it to a medical lab where a cytotechnologist stains the cells and examines them
for any changes that could indicate cervical cancer or a microbial infection.
Cytotechnologists (cyto- = cell) are professionals who study cells through microscopic examinations and other laboratory tests.
They are trained to determine which cellular changes are within normal limits or are abnormal. Their focus is not limited to
cervical cells; they study cellular specimens that come from all organs. When they notice abnormalities, they consult a
pathologist, who is a medical doctor who can make a clinical diagnosis.
Cytotechnologists play vital roles in saving people’s lives. When abnormalities are discovered early, a patient’s treatment can
begin sooner, which usually increases the chances of successful treatment.

Figure [Link]: These uterine cervix cells, viewed through a light microscope, were obtained from a Pap smear. Normal cells
are on the left. The cells on the right are infected with human papillomavirus. (credit: modification of work by Ed Uthman;
scale-bar data from Matt Russell)

Cell Theory
The microscopes we use today are far more complex than those used in the 1600s by Antony van Leeuwenhoek, a Dutch
shopkeeper who had great skill in crafting lenses. Despite the limitations of his now-ancient lenses, van Leeuwenhoek observed the
movements of protists (a type of single-celled organism) and sperm, which he collectively termed “animalcules.”

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In a 1665 publication called Micrographia, experimental scientist Robert Hooke coined the term “cell” (from the Latin cella,
meaning “small room”) for the box-like structures he observed when viewing cork tissue through a lens. In the 1670s, van
Leeuwenhoek discovered bacteria and protozoa. Later advances in lenses and microscope construction enabled other scientists to
see different components inside cells.
By the late 1830s, botanist Matthias Schleiden and zoologist Theodor Schwann were studying tissues and proposed the unified cell
theory, which states that all living things are composed of one or more cells, that the cell is the basic unit of life, and that all new
cells arise from existing cells. These principles still stand today.

Section Summary
A cell is the smallest unit of life. Most cells are so small that they cannot be viewed with the naked eye. Therefore, scientists must
use microscopes to study cells. Electron microscopes provide higher magnification, higher resolution, and more detail than light
microscopes. The unified cell theory states that all organisms are composed of one or more cells, the cell is the basic unit of life,
and new cells arise from existing cells.

Glossary

microscope
the instrument that magnifies an object

unified cell theory

the biological concept that states that all organisms are composed of one or more cells, the cell is the basic unit of life, and new
cells arise from existing cells

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 3.1.1: How Cells Are Studied is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
3.1: How Cells Are Studied by OpenStax is licensed CC BY 4.0.

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3.1.2: Comparing Prokaryotic and Eukaryotic Cells
Cells fall into one of two broad categories: prokaryotic and eukaryotic. The predominantly single-celled organisms of the domains
Bacteria and Archaea are classified as prokaryotes (pro- = before; -karyon- = nucleus). Animal cells, plant cells, fungi, and protists
are eukaryotes (eu- = true).

Components of Prokaryotic Cells

All cells share four common components: 1) a plasma membrane, an outer covering that separates the cell’s interior from its
surrounding environment; 2) cytoplasm, consisting of a jelly-like region within the cell in which other cellular components are
found; 3) DNA, the genetic material of the cell; and 4) ribosomes, particles that synthesize proteins. However, prokaryotes differ
from eukaryotic cells in several ways.
A prokaryotic cell is a simple, single-celled (unicellular) organism that lacks a nucleus, or any other membrane-bound organelle.
We will shortly come to see that this is significantly different in eukaryotes. Prokaryotic DNA is found in the central part of the
cell: a darkened region called the nucleoid (Figure [Link]).

Figure [Link]: This figure shows the generalized structure of a prokaryotic cell.
Unlike Archaea and eukaryotes, bacteria have a cell wall made of peptidoglycan, comprised of sugars and amino acids, and many
have a polysaccharide capsule (Figure [Link]). The cell wall acts as an extra layer of protection, helps the cell maintain its shape,
and prevents dehydration. The capsule enables the cell to attach to surfaces in its environment. Some prokaryotes have flagella,
pili, or fimbriae. Flagella are used for locomotion, while most pili are used to exchange genetic material during a type of
reproduction called conjugation.

Eukaryotic Cells
In nature, the relationship between form and function is apparent at all levels, including the level of the cell, and this will become
clear as we explore eukaryotic cells. The principle “form follows function” is found in many contexts. For example, birds and fish
have streamlined bodies that allow them to move quickly through the medium in which they live, be it air or water. It means that, in
general, one can deduce the function of a structure by looking at its form, because the two are matched.
A eukaryotic cell is a cell that has a membrane-bound nucleus and other membrane-bound compartments or sacs, called organelles,
which have specialized functions. The word eukaryotic means “true kernel” or “true nucleus,” alluding to the presence of the
membrane-bound nucleus in these cells. The word “organelle” means “little organ,” and, as already mentioned, organelles have
specialized cellular functions, just as the organs of your body have specialized functions.

Cell Size
At 0.1–5.0 µm in diameter, prokaryotic cells are significantly smaller than eukaryotic cells, which have diameters ranging from 10–
100 µm (Figure [Link]). The small size of prokaryotes allows ions and organic molecules that enter them to quickly spread to
other parts of the cell. Similarly, any wastes produced within a prokaryotic cell can quickly move out. However, larger eukaryotic
cells have evolved different structural adaptations to enhance cellular transport. Indeed, the large size of these cells would not be
possible without these adaptations. In general, cell size is limited because volume increases much more quickly than does cell

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surface area. As a cell becomes larger, it becomes more and more difficult for the cell to acquire sufficient materials to support the
processes inside the cell, because the relative size of the surface area across which materials must be transported declines.

Figure [Link]: This figure shows the relative sizes of different kinds of cells and cellular components. An adult human is shown
for comparison.

Section Summary
Prokaryotes are predominantly single-celled organisms of the domains Bacteria and Archaea. All prokaryotes have plasma
membranes, cytoplasm, ribosomes, a cell wall, DNA, and lack membrane-bound organelles. Many also have polysaccharide
capsules. Prokaryotic cells range in diameter from 0.1–5.0 µm.
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically
larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound
organelles that allow for compartmentalization of functions. Eukaryotic cells tend to be 10 to 100 times the size of prokaryotic
cells.

Glossary

eukaryotic cell
a cell that has a membrane-bound nucleus and several other membrane-bound compartments or sacs

organelle
a membrane-bound compartment or sac within a cell

prokaryotic cell
a unicellular organism that lacks a nucleus or any other membrane-bound organelle

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]

Access for free at OpenStax [Link] [Link]

 e119a8aafbdd).

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curated by OpenStax.
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3.1.3: Eukaryotic Cells
At this point, it should be clear that eukaryotic cells have a more complex structure than do prokaryotic cells. Organelles allow for
various functions to occur in the cell at the same time. Before discussing the functions of organelles within a eukaryotic cell, let us
first examine two important components of the cell: the plasma membrane and the cytoplasm.

ART CONNECTION

Figure [Link]: This figure shows (a) a typical animal cell and (b) a typical plant cell.
What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have that a plant
cell does not have?

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The Plasma Membrane
Like prokaryotes, eukaryotic cells have a plasma membrane (Figure [Link]) made up of a phospholipid bilayer with embedded
proteins that separates the internal contents of the cell from its surrounding environment. A phospholipid is a lipid molecule
composed of two fatty acid chains, a glycerol backbone, and a phosphate group. The plasma membrane regulates the passage of
some substances, such as organic molecules, ions, and water, preventing the passage of some to maintain internal conditions, while
actively bringing in or removing others. Other compounds move passively across the membrane.

Figure [Link]: The plasma membrane is a phospholipid bilayer with embedded proteins. There are other components, such as
cholesterol and carbohydrates, which can be found in the membrane in addition to phospholipids and protein.
The plasma membranes of cells that specialize in absorption are folded into fingerlike projections called microvilli (singular =
microvillus). This folding increases the surface area of the plasma membrane. Such cells are typically found lining the small
intestine, the organ that absorbs nutrients from digested food. This is an excellent example of form matching the function of a
structure.
People with celiac disease have an immune response to gluten, which is a protein found in wheat, barley, and rye. The immune
response damages microvilli, and thus, afflicted individuals cannot absorb nutrients. This leads to malnutrition, cramping, and
diarrhea. Patients suffering from celiac disease must follow a gluten-free diet.

The Cytoplasm
The cytoplasm comprises the contents of a cell between the plasma membrane and the nuclear envelope (a structure to be discussed
shortly). It is made up of organelles suspended in the gel-like cytosol, the cytoskeleton, and various chemicals (Figure [Link]).
Even though the cytoplasm consists of 70 to 80 percent water, it has a semi-solid consistency, which comes from the proteins
within it. However, proteins are not the only organic molecules found in the cytoplasm. Glucose and other simple sugars,
polysaccharides, amino acids, nucleic acids, fatty acids, and derivatives of glycerol are found there too. Ions of sodium, potassium,
calcium, and many other elements are also dissolved in the cytoplasm. Many metabolic reactions, including protein synthesis, take
place in the cytoplasm.

The Cytoskeleton
If you were to remove all the organelles from a cell, would the plasma membrane and the cytoplasm be the only components left?
No. Within the cytoplasm, there would still be ions and organic molecules, plus a network of protein fibers that helps to maintain
the shape of the cell, secures certain organelles in specific positions, allows cytoplasm and vesicles to move within the cell, and
enables unicellular organisms to move independently. Collectively, this network of protein fibers is known as the cytoskeleton.
There are three types of fibers within the cytoskeleton: microfilaments, also known as actin filaments, intermediate filaments, and
microtubules (Figure [Link]).

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 Figure [Link]: Microfilaments, intermediate filaments, and microtubules compose a cell’s cytoskeleton.
Microfilaments are the thinnest of the cytoskeletal fibers and function in moving cellular components, for example, during cell
division. They also maintain the structure of microvilli, the extensive folding of the plasma membrane found in cells dedicated to
absorption. These components are also common in muscle cells and are responsible for muscle cell contraction. Intermediate
filaments are of intermediate diameter and have structural functions, such as maintaining the shape of the cell and anchoring
organelles. Keratin, the compound that strengthens hair and nails, forms one type of intermediate filament. Microtubules are the
thickest of the cytoskeletal fibers. These are hollow tubes that can dissolve and reform quickly. Microtubules guide organelle
movement and are the structures that pull chromosomes to their poles during cell division. They are also the structural components
of flagella and cilia. In cilia and flagella, the microtubules are organized as a circle of nine double microtubules on the outside and
two microtubules in the center.
The centrosome is a region near the nucleus of animal cells that functions as a microtubule-organizing center. It contains a pair of
centrioles, two structures that lie perpendicular to each other. Each centriole is a cylinder of nine triplets of microtubules.
The centrosome replicates itself before a cell divides, and the centrioles play a role in pulling the duplicated chromosomes to
opposite ends of the dividing cell. However, the exact function of the centrioles in cell division is not clear, since cells that have the
centrioles removed can still divide, and plant cells, which lack centrioles, are capable of cell division.

Flagella and Cilia

Flagella (singular = flagellum) are long, hair-like structures that extend from the plasma membrane and are used to move an entire
cell, (for example, sperm, Euglena). When present, the cell has just one flagellum or a few flagella. When cilia (singular = cilium)
are present, however, they are many in number and extend along the entire surface of the plasma membrane. They are short, hair-
like structures that are used to move entire cells (such as paramecium) or move substances along the outer surface of the cell (for
example, the cilia of cells lining the fallopian tubes that move the ovum toward the uterus, or cilia lining the cells of the respiratory
tract that move particulate matter toward the throat that mucus has trapped).

The Endomembrane System

The endomembrane system (endo = within) is a group of membranes and organelles (Figure [Link]) in eukaryotic cells that work
together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, and vesicles, the

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endoplasmic reticulum and Golgi apparatus, which we will cover shortly. Although not technically within the cell, the plasma
membrane is included in the endomembrane system because, as you will see, it interacts with the other endomembranous
organelles.

The Nucleus
Typically, the nucleus is the most prominent organelle in a cell (Figure [Link]). The nucleus (plural = nuclei) houses the cell’s
DNA in the form of chromatin and directs the synthesis of ribosomes and proteins. Let us look at it in more detail (Figure [Link]).

Figure [Link]: The outermost boundary of the nucleus is the nuclear envelope. Notice that the nuclear envelope consists of two
phospholipid bilayers (membranes)—an outer membrane and an inner membrane—in contrast to the plasma membrane (Figure
[Link] ), which consists of only one phospholipid bilayer. (credit: modification of work by NIGMS, NIH)

The nuclear envelope is a double-membrane structure that constitutes the outermost portion of the nucleus (Figure [Link] ). Both
the inner and outer membranes of the nuclear envelope are phospholipid bilayers.
The nuclear envelope is punctuated with pores that control the passage of ions, molecules, and RNA between the nucleoplasm and
the cytoplasm.
To understand chromatin, it is helpful to first consider chromosomes. Chromosomes are structures within the nucleus that are made
up of DNA, the hereditary material, and proteins. This combination of DNA and proteins is called chromatin. In eukaryotes,
chromosomes are linear structures. Every species has a specific number of chromosomes in the nucleus of its body cells. For
example, in humans, the chromosome number is 46, whereas in fruit flies, the chromosome number is eight.
Chromosomes are only visible and distinguishable from one another when the cell is getting ready to divide. When the cell is in the
growth and maintenance phases of its life cycle, the chromosomes resemble an unwound, jumbled bunch of threads.
We already know that the nucleus directs the synthesis of ribosomes, but how does it do this? Some chromosomes have sections of
DNA that encode ribosomal RNA. A darkly staining area within the nucleus, called the nucleolus (plural = nucleoli), aggregates
the ribosomal RNA with associated proteins to assemble the ribosomal subunits that are then transported through the nuclear pores
into the cytoplasm.

The Endoplasmic Reticulum

The endoplasmic reticulum (ER) (Figure [Link]) is a series of interconnected membranous tubules that collectively modify
proteins and synthesize lipids. However, these two functions are performed in separate areas of the endoplasmic reticulum: the
rough endoplasmic reticulum and the smooth endoplasmic reticulum, respectively.
The hollow portion of the ER tubules is called the lumen or cisternal space. The membrane of the ER, which is a phospholipid
bilayer embedded with proteins, is continuous with the nuclear envelope.
The rough endoplasmic reticulum (RER) is so named because the ribosomes attached to its cytoplasmic surface give it a studded
appearance when viewed through an electron microscope.
The ribosomes synthesize proteins while attached to the ER, resulting in transfer of their newly synthesized proteins into the lumen
of the RER where they undergo modifications such as folding or addition of sugars. The RER also makes phospholipids for cell
membranes.

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If the phospholipids or modified proteins are not destined to stay in the RER, they will be packaged within vesicles and transported
from the RER by budding from the membrane (Figure [Link]). Since the RER is engaged in modifying proteins that will be
secreted from the cell, it is abundant in cells that secrete proteins, such as the liver.
The smooth endoplasmic reticulum (SER) is continuous with the RER but has few or no ribosomes on its cytoplasmic surface (see
Figure [Link]). The SER’s functions include synthesis of carbohydrates, lipids (including phospholipids), and steroid hormones;
detoxification of medications and poisons; alcohol metabolism; and storage of calcium ions.

The Golgi Apparatus

We have already mentioned that vesicles can bud from the ER, but where do the vesicles go? Before reaching their final
destination, the lipids or proteins within the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the
right place. The sorting, tagging, packaging, and distribution of lipids and proteins take place in the Golgi apparatus (also called the
Golgi body), a series of flattened membranous sacs (Figure [Link]).

Figure [Link]: The Golgi apparatus in this transmission electron micrograph of a white blood cell is visible as a stack of
semicircular flattened rings in the lower portion of this image. Several vesicles can be seen near the Golgi apparatus. (credit:
modification of work by Louisa Howard; scale-bar data from Matt Russell)
The Golgi apparatus has a receiving face near the endoplasmic reticulum and a releasing face on the side away from the ER, toward
the cell membrane. The transport vesicles that form from the ER travel to the receiving face, fuse with it, and empty their contents
into the lumen of the Golgi apparatus. As the proteins and lipids travel through the Golgi, they undergo further modifications. The
most frequent modification is the addition of short chains of sugar molecules. The newly modified proteins and lipids are then
tagged with small molecular groups to enable them to be routed to their proper destinations.
Finally, the modified and tagged proteins are packaged into vesicles that bud from the opposite face of the Golgi. While some of
these vesicles, transport vesicles, deposit their contents into other parts of the cell where they will be used, others, secretory
vesicles, fuse with the plasma membrane and release their contents outside the cell.
The amount of Golgi in different cell types again illustrates that form follows function within cells. Cells that engage in a great deal
of secretory activity (such as cells of the salivary glands that secrete digestive enzymes or cells of the immune system that secrete
antibodies) have an abundant number of Golgi.
In plant cells, the Golgi has an additional role of synthesizing polysaccharides, some of which are incorporated into the cell wall
and some of which are used in other parts of the cell.

Lysosomes
In animal cells, the lysosomes are the cell’s “garbage disposal.” Digestive enzymes within the lysosomes aid the breakdown of
proteins, polysaccharides, lipids, nucleic acids, and even worn-out organelles. In single-celled eukaryotes, lysosomes are important
for digestion of the food they ingest and the recycling of organelles. These enzymes are active at a much lower pH (more acidic)
than those located in the cytoplasm. Many reactions that take place in the cytoplasm could not occur at a low pH, thus the
advantage of compartmentalizing the eukaryotic cell into organelles is apparent.
Lysosomes also use their hydrolytic enzymes to destroy disease-causing organisms that might enter the cell. A good example of
this occurs in a group of white blood cells called macrophages, which are part of your body’s immune system. In a process known
as phagocytosis, a section of the plasma membrane of the macrophage invaginates (folds in) and engulfs a pathogen. The
invaginated section, with the pathogen inside, then pinches itself off from the plasma membrane and becomes a vesicle. The vesicle
fuses with a lysosome. The lysosome’s hydrolytic enzymes then destroy the pathogen (Figure [Link]).

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 Figure [Link]: A macrophage has phagocytized a potentially pathogenic bacterium into a vesicle, which then fuses with a
lysosome within the cell so that the pathogen can be destroyed. Other organelles are present in the cell, but for simplicity, are not
shown.

Vesicles and Vacuoles

Vesicles and vacuoles are membrane-bound sacs that function in storage and transport. Vacuoles are somewhat larger than vesicles,
and the membrane of a vacuole does not fuse with the membranes of other cellular components. Vesicles can fuse with other
membranes within the cell system. Additionally, enzymes within plant vacuoles can break down macromolecules.

ART CONNECTION

Figure [Link]: The endomembrane system works to modify, package, and transport lipids and proteins. (credit: modification
of work by Magnus Manske)

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 Why does the cis face of the Golgi not face the plasma membrane?

Ribosomes
Ribosomes are the cellular structures responsible for protein synthesis. When viewed through an electron microscope, free
ribosomes appear as either clusters or single tiny dots floating freely in the cytoplasm. Ribosomes may be attached to either the
cytoplasmic side of the plasma membrane or the cytoplasmic side of the endoplasmic reticulum (Figure [Link]). Electron
microscopy has shown that ribosomes consist of large and small subunits. Ribosomes are enzyme complexes that are responsible
for protein synthesis.
Because protein synthesis is essential for all cells, ribosomes are found in practically every cell, although they are smaller in
prokaryotic cells. They are particularly abundant in immature red blood cells for the synthesis of hemoglobin, which functions in
the transport of oxygen throughout the body.

Mitochondria
Mitochondria (singular = mitochondrion) are often called the “powerhouses” or “energy factories” of a cell because they are
responsible for making adenosine triphosphate (ATP), the cell’s main energy-carrying molecule. The formation of ATP from the
breakdown of glucose is known as cellular respiration. Mitochondria are oval-shaped, double-membrane organelles (Figure
[Link]) that have their own ribosomes and DNA. Each membrane is a phospholipid bilayer embedded with proteins. The inner

layer has folds called cristae, which increase the surface area of the inner membrane. The area surrounded by the folds is called the
mitochondrial matrix. The cristae and the matrix have different roles in cellular respiration.
In keeping with our theme of form following function, it is important to point out that muscle cells have a very high concentration
of mitochondria because muscle cells need a lot of energy to contract.

Figure [Link]: This transmission electron micrograph shows a mitochondrion as viewed with an electron microscope. Notice the
inner and outer membranes, the cristae, and the mitochondrial matrix. (credit: modification of work by Matthew Britton; scale-bar
data from Matt Russell)

Peroxisomes
Peroxisomes are small, round organelles enclosed by single membranes. They carry out oxidation reactions that break down fatty
acids and amino acids. They also detoxify many poisons that may enter the body. Alcohol is detoxified by peroxisomes in liver
cells. A byproduct of these oxidation reactions is hydrogen peroxide, H2O2, which is contained within the peroxisomes to prevent
the chemical from causing damage to cellular components outside of the organelle. Hydrogen peroxide is safely broken down by
peroxisomal enzymes into water and oxygen.

Animal Cells versus Plant Cells

Despite their fundamental similarities, there are some striking differences between animal and plant cells (see Table [Link]).
Animal cells have centrioles, centrosomes (discussed under the cytoskeleton), and lysosomes, whereas plant cells do not. Plant

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cells have a cell wall, chloroplasts, plasmodesmata, and plastids used for storage, and a large central vacuole, whereas animal cells
do not.

The Cell Wall

In Figure 3.1.3.1b, the diagram of a plant cell, you see a structure external to the plasma membrane called the cell wall. The cell
wall is a rigid covering that protects the cell, provides structural support, and gives shape to the cell. Fungal and protist cells also
have cell walls.
While the chief component of prokaryotic cell walls is peptidoglycan, the major organic molecule in the plant cell wall is cellulose,
a polysaccharide made up of long, straight chains of glucose units. When nutritional information refers to dietary fiber, it is
referring to the cellulose content of food.

Chloroplasts
Like mitochondria, chloroplasts also have their own DNA and ribosomes. Chloroplasts function in photosynthesis and can be found
in eukaryotic cells such as plants and algae. In photosynthesis, carbon dioxide, water, and light energy are used to make glucose
and oxygen. This is the major difference between plants and animals: Plants (autotrophs) are able to make their own food, like
glucose, whereas animals (heterotrophs) must rely on other organisms for their organic compounds or food source.
Like mitochondria, chloroplasts have outer and inner membranes, but within the space enclosed by a chloroplast’s inner membrane
is a set of interconnected and stacked, fluid-filled membrane sacs called thylakoids (Figure [Link]). Each stack of thylakoids is
called a granum (plural = grana). The fluid enclosed by the inner membrane and surrounding the grana is called the stroma.

Figure [Link]: This simplified diagram of a chloroplast shows the outer membrane, inner membrane, thylakoids, grana, and
stroma.
The chloroplasts contain a green pigment called chlorophyll, which captures the energy of sunlight for photosynthesis. Like plant
cells, photosynthetic protists also have chloroplasts. Some bacteria also perform photosynthesis, but they do not have chloroplasts.
Their photosynthetic pigments are located in the thylakoid membrane within the cell itself.

EVOLUTION IN ACTION: Endosymbiosis

We have mentioned that both mitochondria and chloroplasts contain DNA and ribosomes. Have you wondered why? Strong
evidence points to endosymbiosis as the explanation.
Symbiosis is a relationship in which organisms from two separate species live in close association and typically exhibit specific
adaptations to each other. Endosymbiosis (endo-= within) is a relationship in which one organism lives inside the other.
Endosymbiotic relationships abound in nature. Microbes that produce vitamin K live inside the human gut. This relationship is
beneficial for us because we are unable to synthesize vitamin K. It is also beneficial for the microbes because they are
protected from other organisms and are provided a stable habitat and abundant food by living within the large intestine.
Scientists have long noticed that bacteria, mitochondria, and chloroplasts are similar in size. We also know that mitochondria
and chloroplasts have DNA and ribosomes, just as bacteria do. Scientists believe that host cells and bacteria formed a mutually
beneficial endosymbiotic relationship when the host cells ingested aerobic bacteria and cyanobacteria but did not destroy them.
Through evolution, these ingested bacteria became more specialized in their functions, with the aerobic bacteria becoming
mitochondria and the photosynthetic bacteria becoming chloroplasts.

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The Central Vacuole
Previously, we mentioned vacuoles as essential components of plant cells. If you look at Figure [Link], you will see that plant cells
each have a large, central vacuole that occupies most of the cell. The central vacuole plays a key role in regulating the cell’s
concentration of water in changing environmental conditions. In plant cells, the liquid inside the central vacuole provides turgor
pressure, which is the outward pressure caused by the fluid inside the cell. Have you ever noticed that if you forget to water a plant
for a few days, it wilts? That is because as the water concentration in the soil becomes lower than the water concentration in the
plant, water moves out of the central vacuoles and cytoplasm and into the soil. As the central vacuole shrinks, it leaves the cell wall
unsupported. This loss of support to the cell walls of a plant results in the wilted appearance. Additionally, this fluid has a very
bitter taste, which discourages consumption by insects and animals. The central vacuole also functions to store proteins in
developing seed cells.

Extracellular Matrix of Animal Cells

Most animal cells release materials into the extracellular space. The primary components of these materials are glycoproteins and
the protein collagen. Collectively, these materials are called the extracellular matrix (Figure [Link]). Not only does the
extracellular matrix hold the cells together to form a tissue, but it also allows the cells within the tissue to communicate with each
other.

Figure [Link]: The extracellular matrix consists of a network of substances secreted by cells.
Blood clotting provides an example of the role of the extracellular matrix in cell communication. When the cells lining a blood
vessel are damaged, they display a protein receptor called tissue factor. When tissue factor binds with another factor in the
extracellular matrix, it causes platelets to adhere to the wall of the damaged blood vessel, stimulates adjacent smooth muscle cells
in the blood vessel to contract (thus constricting the blood vessel), and initiates a series of steps that stimulate the platelets to
produce clotting factors.

Intercellular Junctions
Cells can also communicate with each other by direct contact, referred to as intercellular junctions. There are some differences in
the ways that plant and animal cells do this. Plasmodesmata (singular = plasmodesma) are junctions between plant cells, whereas
animal cell contacts include tight and gap junctions, and desmosomes.
In general, long stretches of the plasma membranes of neighboring plant cells cannot touch one another because they are separated
by the cell walls surrounding each cell. Plasmodesmata are numerous channels that pass between the cell walls of adjacent plant

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cells, connecting their cytoplasm and enabling signal molecules and nutrients to be transported from cell to cell (Figure 3.1.3.11a).

Figure [Link]: There are four kinds of connections between cells. (a) A plasmodesma is a channel between the cell walls of
two adjacent plant cells. (b) Tight junctions join adjacent animal cells. (c) Desmosomes join two animal cells together. (d) Gap
junctions act as channels between animal cells. (credit b, c, d: modification of work by Mariana Ruiz Villareal)
A tight junction is a watertight seal between two adjacent animal cells (Figure 3.1.3.11b). Proteins hold the cells tightly against
each other. This tight adhesion prevents materials from leaking between the cells. Tight junctions are typically found in the
epithelial tissue that lines internal organs and cavities, and composes most of the skin. For example, the tight junctions of the
epithelial cells lining the urinary bladder prevent urine from leaking into the extracellular space.
Also found only in animal cells are desmosomes, which act like spot welds between adjacent epithelial cells (Figure [Link] c).
They keep cells together in a sheet-like formation in organs and tissues that stretch, like the skin, heart, and muscles.
Gap junctions in animal cells are like plasmodesmata in plant cells in that they are channels between adjacent cells that allow for
the transport of ions, nutrients, and other substances that enable cells to communicate (Figure 3.1.3.11d). Structurally, however,
gap junctions and plasmodesmata differ.
Table [Link]: This table provides the components of prokaryotic and eukaryotic cells and their respective functions.
Cell Component Function Present in Prokaryotes? Present in Animal Cells? Present in Plant Cells?

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 Cell Component Function Present in Prokaryotes? Present in Animal Cells? Present in Plant Cells?

Separates cell from

external environment;
controls passage of organic
Plasma membrane Yes Yes Yes
molecules, ions, water,
oxygen, and wastes into
and out of the cell

Provides structure to cell;

site of many metabolic
Cytoplasm Yes Yes Yes
reactions; medium in
which organelles are found

Nucleoid Location of DNA Yes No No

Cell organelle that houses

Nucleus DNA and directs synthesis No Yes Yes
of ribosomes and proteins

Ribosomes Protein synthesis Yes Yes Yes

ATP production/cellular
Mitochondria No Yes Yes
respiration

Oxidizes and breaks down

fatty acids and amino
Peroxisomes No Yes Yes
acids, and detoxifies
poisons

Storage and transport;

Vesicles and vacuoles digestive function in plant No Yes Yes
cells

Unspecified role in cell

division in animal cells;
Centrosome organizing center of No Yes No
microtubules in animal
cells

Digestion of
Lysosomes macromolecules; recycling No Yes No
of worn-out organelles

Protection, structural Yes, primarily

Cell wall support and maintenance peptidoglycan in bacteria No Yes, primarily cellulose
of cell shape but not Archaea

Chloroplasts Photosynthesis No No Yes

Modifies proteins and

Endoplasmic reticulum No Yes Yes
synthesizes lipids

Modifies, sorts, tags,

Golgi apparatus packages, and distributes No Yes Yes
lipids and proteins

Maintains cell’s shape,

secures organelles in
specific positions, allows
cytoplasm and vesicles to
Cytoskeleton Yes Yes Yes
move within the cell, and
enables unicellular
organisms to move
independently

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 Cell Component Function Present in Prokaryotes? Present in Animal Cells? Present in Plant Cells?

No, except for some plant

Flagella Cellular locomotion Some Some
sperm

Cellular locomotion,
movement of particles
Cilia along extracellular surface No Some No
of plasma membrane, and
filtration

Summary
Like a prokaryotic cell, a eukaryotic cell has a plasma membrane, cytoplasm, and ribosomes, but a eukaryotic cell is typically
larger than a prokaryotic cell, has a true nucleus (meaning its DNA is surrounded by a membrane), and has other membrane-bound
organelles that allow for compartmentalization of functions. The plasma membrane is a phospholipid bilayer embedded with
proteins. The nucleolus within the nucleus is the site for ribosome assembly. Ribosomes are found in the cytoplasm or are attached
to the cytoplasmic side of the plasma membrane or endoplasmic reticulum. They perform protein synthesis. Mitochondria perform
cellular respiration and produce ATP. Peroxisomes break down fatty acids, amino acids, and some toxins. Vesicles and vacuoles are
storage and transport compartments. In plant cells, vacuoles also help break down macromolecules.
Animal cells also have a centrosome and lysosomes. The centrosome has two bodies, the centrioles, with an unknown role in cell
division. Lysosomes are the digestive organelles of animal cells.
Plant cells have a cell wall, chloroplasts, and a central vacuole. The plant cell wall, whose primary component is cellulose, protects
the cell, provides structural support, and gives shape to the cell. Photosynthesis takes place in chloroplasts. The central vacuole
expands, enlarging the cell without the need to produce more cytoplasm.
The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, Golgi apparatus, lysosomes, vesicles, as well
as the plasma membrane. These cellular components work together to modify, package, tag, and transport membrane lipids and
proteins.
The cytoskeleton has three different types of protein elements. Microfilaments provide rigidity and shape to the cell, and facilitate
cellular movements. Intermediate filaments bear tension and anchor the nucleus and other organelles in place. Microtubules help
the cell resist compression, serve as tracks for motor proteins that move vesicles through the cell, and pull replicated chromosomes
to opposite ends of a dividing cell. They are also the structural elements of centrioles, flagella, and cilia.
Animal cells communicate through their extracellular matrices and are connected to each other by tight junctions, desmosomes, and
gap junctions. Plant cells are connected and communicate with each other by plasmodesmata.

Art Connections
Figure [Link]: What structures does a plant cell have that an animal cell does not have? What structures does an animal cell have
that a plant cell does not have?

Answer
Plant cells have plasmodesmata, a cell wall, a large central vacuole, chloroplasts, and plastids. Animal cells have lysosomes and
centrosomes.

Figure [Link]: Why does the cis face of the Golgi not face the plasma membrane?

Answer
Because that face receives chemicals from the ER, which is toward the center of the cell.

Glossary
cell wall
a rigid cell covering made of cellulose in plants, peptidoglycan in bacteria, non-peptidoglycan compounds in Archaea, and
chitin in fungi that protects the cell, provides structural support, and gives shape to the cell

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central vacuole
a large plant cell organelle that acts as a storage compartment, water reservoir, and site of macromolecule degradation

chloroplast
a plant cell organelle that carries out photosynthesis

cilium
(plural: cilia) a short, hair-like structure that extends from the plasma membrane in large numbers and is used to move an entire
cell or move substances along the outer surface of the cell

cytoplasm
the entire region between the plasma membrane and the nuclear envelope, consisting of organelles suspended in the gel-like
cytosol, the cytoskeleton, and various chemicals

cytoskeleton
the network of protein fibers that collectively maintains the shape of the cell, secures some organelles in specific positions,
allows cytoplasm and vesicles to move within the cell, and enables unicellular organisms to move

cytosol
the gel-like material of the cytoplasm in which cell structures are suspended

desmosome
a linkage between adjacent epithelial cells that forms when cadherins in the plasma membrane attach to intermediate filaments

endomembrane system
the group of organelles and membranes in eukaryotic cells that work together to modify, package, and transport lipids and
proteins

endoplasmic reticulum (ER)

a series of interconnected membranous structures within eukaryotic cells that collectively modify proteins and synthesize lipids

extracellular matrix
the material, primarily collagen, glycoproteins, and proteoglycans, secreted from animal cells that holds cells together as a
tissue, allows cells to communicate with each other, and provides mechanical protection and anchoring for cells in the tissue

flagellum
(plural: flagella) the long, hair-like structure that extends from the plasma membrane and is used to move the cell

gap junction
a channel between two adjacent animal cells that allows ions, nutrients, and other low-molecular weight substances to pass
between the cells, enabling the cells to communicate

Golgi apparatus
a eukaryotic organelle made up of a series of stacked membranes that sorts, tags, and packages lipids and proteins for
distribution

lysosome
an organelle in an animal cell that functions as the cell’s digestive component; it breaks down proteins, polysaccharides, lipids,
nucleic acids, and even worn-out organelles

mitochondria
(singular: mitochondrion) the cellular organelles responsible for carrying out cellular respiration, resulting in the production of
ATP, the cell’s main energy-carrying molecule

nuclear envelope

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 the double-membrane structure that constitutes the outermost portion of the nucleus

nucleolus
the darkly staining body within the nucleus that is responsible for assembling ribosomal subunits

nucleus
the cell organelle that houses the cell’s DNA and directs the synthesis of ribosomes and proteins

peroxisome
a small, round organelle that contains hydrogen peroxide, oxidizes fatty acids and amino acids, and detoxifies many poisons

plasma membrane
a phospholipid bilayer with embedded (integral) or attached (peripheral) proteins that separates the internal contents of the cell
from its surrounding environment

plasmodesma
(plural: plasmodesmata) a channel that passes between the cell walls of adjacent plant cells, connects their cytoplasm, and
allows materials to be transported from cell to cell

ribosome
a cellular structure that carries out protein synthesis

rough endoplasmic reticulum (RER)

the region of the endoplasmic reticulum that is studded with ribosomes and engages in protein modification

smooth endoplasmic reticulum (SER)

the region of the endoplasmic reticulum that has few or no ribosomes on its cytoplasmic surface and synthesizes carbohydrates,
lipids, and steroid hormones; detoxifies chemicals like pesticides, preservatives, medications, and environmental pollutants, and
stores calcium ions

tight junction
a firm seal between two adjacent animal cells created by protein adherence

vacuole
a membrane-bound sac, somewhat larger than a vesicle, that functions in cellular storage and transport

vesicle
a small, membrane-bound sac that functions in cellular storage and transport; its membrane is capable of fusing with the plasma
membrane and the membranes of the endoplasmic reticulum and Golgi apparatus

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 3.1.3: Eukaryotic Cells is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
3.3: Eukaryotic Cells by OpenStax is licensed CC BY 4.0.

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3.1.4: The Cell Membrane
A cell’s plasma membrane defines the boundary of the cell and determines the nature of its contact with the environment. Cells
exclude some substances, take in others, and excrete still others, all in controlled quantities. Plasma membranes enclose the borders
of cells, but rather than being a static bag, they are dynamic and constantly in flux. The plasma membrane must be sufficiently
flexible to allow certain cells, such as red blood cells and white blood cells, to change shape as they pass through narrow
capillaries. These are the more obvious functions of a plasma membrane. In addition, the surface of the plasma membrane carries
markers that allow cells to recognize one another, which is vital as tissues and organs form during early development, and which
later plays a role in the “self” versus “non-self” distinction of the immune response.
The plasma membrane also carries receptors, which are attachment sites for specific substances that interact with the cell. Each
receptor is structured to bind with a specific substance. For example, surface receptors of the membrane create changes in the
interior, such as changes in enzymes of metabolic pathways. These metabolic pathways might be vital for providing the cell with
energy, making specific substances for the cell, or breaking down cellular waste or toxins for disposal. Receptors on the plasma
membrane’s exterior surface interact with hormones or neurotransmitters, and allow their messages to be transmitted into the cell.
Some recognition sites are used by viruses as attachment points. Although they are highly specific, pathogens like viruses may
evolve to exploit receptors to gain entry to a cell by mimicking the specific substance that the receptor is meant to bind. This
specificity helps to explain why human immunodeficiency virus (HIV) or any of the five types of hepatitis viruses invade only
specific cells.

Fluid Mosaic Model

In 1972, S. J. Singer and Garth L. Nicolson proposed a new model of the plasma membrane that, compared to earlier
understanding, better explained both microscopic observations and the function of the plasma membrane. This was called the fluid
mosaic model. The model has evolved somewhat over time, but still best accounts for the structure and functions of the plasma
membrane as we now understand them. The fluid mosaic model describes the structure of the plasma membrane as a mosaic of
components—including phospholipids, cholesterol, proteins, and carbohydrates—in which the components are able to flow and
change position, while maintaining the basic integrity of the membrane. Both phospholipid molecules and embedded proteins are
able to diffuse rapidly and laterally in the membrane. The fluidity of the plasma membrane is necessary for the activities of certain
enzymes and transport molecules within the membrane. Plasma membranes range from 5–10 nm thick. As a comparison, human
red blood cells, visible via light microscopy, are approximately 8 µm thick, or approximately 1,000 times thicker than a plasma
membrane. (Figure [Link])

Figure [Link]: The fluid mosaic model of the plasma membrane structure describes the plasma membrane as a fluid combination
of phospholipids, cholesterol, proteins, and carbohydrates.
The plasma membrane is made up primarily of a bilayer of phospholipids with embedded proteins, carbohydrates, glycolipids, and
glycoproteins, and, in animal cells, cholesterol. The amount of cholesterol in animal plasma membranes regulates the fluidity of the
membrane and changes based on the temperature of the cell’s environment. In other words, cholesterol acts as antifreeze in the cell
membrane and is more abundant in animals that live in cold climates.
The main fabric of the membrane is composed of two layers of phospholipid molecules, and the polar ends of these molecules
(which look like a collection of balls in an artist’s rendition of the model) (Figure [Link]) are in contact with aqueous fluid both
inside and outside the cell. Thus, both surfaces of the plasma membrane are hydrophilic. In contrast, the interior of the membrane,

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between its two surfaces, is a hydrophobic or nonpolar region because of the fatty acid tails. This region has no attraction for water
or other polar molecules.
Proteins make up the second major chemical component of plasma membranes. Integral proteins are embedded in the plasma
membrane and may span all or part of the membrane. Integral proteins may serve as channels or pumps to move materials into or
out of the cell. Peripheral proteins are found on the exterior or interior surfaces of membranes, attached either to integral proteins or
to phospholipid molecules. Both integral and peripheral proteins may serve as enzymes, as structural attachments for the fibers of
the cytoskeleton, or as part of the cell’s recognition sites.
Carbohydrates are the third major component of plasma membranes. They are always found on the exterior surface of cells and are
bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). These carbohydrate chains may consist of 2–60
monosaccharide units and may be either straight or branched. Along with peripheral proteins, carbohydrates form specialized sites
on the cell surface that allow cells to recognize each other.

EVOLUTION IN ACTION: How Viruses Infect Specific Organs

Specific glycoprotein molecules exposed on the surface of the cell membranes of host cells are exploited by many viruses to
infect specific organs. For example, HIV is able to penetrate the plasma membranes of specific kinds of white blood cells
called T-helper cells and monocytes, as well as some cells of the central nervous system. The hepatitis virus attacks only liver
cells.
These viruses are able to invade these cells, because the cells have binding sites on their surfaces that the viruses have
exploited with equally specific glycoproteins in their coats (Figure [Link]). The cell is tricked by the mimicry of the virus coat
molecules, and the virus is able to enter the cell. Other recognition sites on the virus’s surface interact with the human immune
system, prompting the body to produce antibodies. Antibodies are made in response to the antigens (or proteins associated with
invasive pathogens). These same sites serve as places for antibodies to attach, and either destroy or inhibit the activity of the
virus. Unfortunately, these sites on HIV are encoded by genes that change quickly, making the production of an effective
vaccine against the virus very difficult. The virus population within an infected individual quickly evolves through mutation
into different populations, or variants, distinguished by differences in these recognition sites. This rapid change of viral surface
markers decreases the effectiveness of the person’s immune system in attacking the virus, because the antibodies will not
recognize the new variations of the surface patterns.

Figure [Link]: HIV docks at and binds to the CD4 receptor, a glycoprotein on the surface of T cells, before entering, or
infecting, the cell. (credit: modification of work by US National Institutes of Health/National Institute of Allergy and Infectious
Diseases).

Summary
The modern understanding of the plasma membrane is referred to as the fluid mosaic model. The plasma membrane is composed of
a bilayer of phospholipids, with their hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is
studded with proteins, some of which span the membrane. Some of these proteins serve to transport materials into or out of the cell.
Carbohydrates are attached to some of the proteins and lipids on the outward-facing surface of the membrane. These form
complexes that function to identify the cell to other cells. The fluid nature of the membrane owes itself to the configuration of the
fatty acid tails, the presence of cholesterol embedded in the membrane (in animal cells), and the mosaic nature of the proteins and

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protein-carbohydrate complexes, which are not firmly fixed in place. Plasma membranes enclose the borders of cells, but rather
than being a static bag, they are dynamic and constantly in flux.

Glossary

fluid mosaic model

a model of the structure of the plasma membrane as a mosaic of components, including phospholipids, cholesterol, proteins, and
glycolipids, resulting in a fluid rather than static character

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 3.1.4: The Cell Membrane is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
3.4: The Cell Membrane by OpenStax is licensed CC BY 4.0.

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3.1.5: Passive Transport
Plasma membranes must allow certain substances to enter and leave a cell, while preventing harmful material from entering and
essential material from leaving. In other words, plasma membranes are selectively permeable—they allow some substances through
but not others. If they were to lose this selectivity, the cell would no longer be able to sustain itself, and it would be destroyed.
Some cells require larger amounts of specific substances than do other cells; they must have a way of obtaining these materials
from the extracellular fluids. This may happen passively, as certain materials move back and forth, or the cell may have special
mechanisms that ensure transport. Most cells expend most of their energy, in the form of adenosine triphosphate (ATP), to create
and maintain an uneven distribution of ions on the opposite sides of their membranes. The structure of the plasma membrane
contributes to these functions, but it also presents some problems.
The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not
require the cell to expend energy to accomplish the movement. In passive transport, substances move from an area of higher
concentration to an area of lower concentration in a process called diffusion. A physical space in which there is a different
concentration of a single substance is said to have a concentration gradient.

Selective Permeability
Plasma membranes are asymmetric, meaning that despite the mirror image formed by the phospholipids, the interior of the
membrane is not identical to the exterior of the membrane. Integral proteins that act as channels or pumps work in one direction.
Carbohydrates, attached to lipids or proteins, are also found on the exterior surface of the plasma membrane. These carbohydrate
complexes help the cell bind substances that the cell needs in the extracellular fluid. This adds considerably to the selective nature
of plasma membranes.
Recall that plasma membranes have hydrophilic and hydrophobic regions. This characteristic helps the movement of certain
materials through the membrane and hinders the movement of others. Lipid-soluble material can easily slip through the
hydrophobic lipid core of the membrane. Substances such as the fat-soluble vitamins A, D, E, and K readily pass through the
plasma membranes in the digestive tract and other tissues. Fat-soluble drugs also gain easy entry into cells and are readily
transported into the body’s tissues and organs. Molecules of oxygen and carbon dioxide have no charge and pass through by simple
diffusion.
Polar substances, with the exception of water, present problems for the membrane. While some polar molecules connect easily with
the outside of a cell, they cannot readily pass through the lipid core of the plasma membrane. Additionally, whereas small ions
could easily slip through the spaces in the mosaic of the membrane, their charge prevents them from doing so. Ions such as sodium,
potassium, calcium, and chloride must have a special means of penetrating plasma membranes. Simple sugars and amino acids also
need help with transport across plasma membranes.

Diffusion
Diffusion is a passive process of transport. A single substance tends to move from an area of high concentration to an area of low
concentration until the concentration is equal across the space. You are familiar with diffusion of substances through the air. For
example, think about someone opening a bottle of perfume in a room filled with people. The perfume is at its highest concentration
in the bottle and is at its lowest at the edges of the room. The perfume vapor will diffuse, or spread away, from the bottle, and
gradually, more and more people will smell the perfume as it spreads. Materials move within the cell’s cytosol by diffusion, and
certain materials move through the plasma membrane by diffusion (Figure [Link]). Diffusion expends no energy. Rather the
different concentrations of materials in different areas are a form of potential energy, and diffusion is the dissipation of that
potential energy as materials move down their concentration gradients, from high to low.

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 Figure [Link]: Diffusion through a permeable membrane follows the concentration gradient of a substance, moving the
substance from an area of high concentration to one of low concentration. (credit: modification of work by Mariana Ruiz Villarreal)
Each separate substance in a medium, such as the extracellular fluid, has its own concentration gradient, independent of the
concentration gradients of other materials. Additionally, each substance will diffuse according to that gradient.
Several factors affect the rate of diffusion.
Extent of the concentration gradient: The greater the difference in concentration, the more rapid the diffusion. The closer the
distribution of the material gets to equilibrium, the slower the rate of diffusion becomes.
Mass of the molecules diffusing: More massive molecules move more slowly, because it is more difficult for them to move
between the molecules of the substance they are moving through; therefore, they diffuse more slowly.
Temperature: Higher temperatures increase the energy and therefore the movement of the molecules, increasing the rate of
diffusion.
Solvent density: As the density of the solvent increases, the rate of diffusion decreases. The molecules slow down because they
have a more difficult time getting through the denser medium.

CONCEPT IN ACTION

Cell Membrane Passive Transport | Ce…

Ce…

For an animation of the diffusion process in action, view this short video on cell membrane transport.

Facilitated transport
In facilitated transport, also called facilitated diffusion, material moves across the plasma membrane with the assistance of
transmembrane proteins down a concentration gradient (from high to low concentration) without the expenditure of cellular energy.
However, the substances that undergo facilitated transport would otherwise not diffuse easily or quickly across the plasma
membrane. The solution to moving polar substances and other substances across the plasma membrane rests in the proteins that
span its surface. The material being transported is first attached to protein or glycoprotein receptors on the exterior surface of the
plasma membrane. This allows the material that is needed by the cell to be removed from the extracellular fluid. The substances are
then passed to specific integral proteins that facilitate their passage, because they form channels or pores that allow certain

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substances to pass through the membrane. The integral proteins involved in facilitated transport are collectively referred to as
transport proteins, and they function as either channels for the material or carriers.

Osmosis
Osmosis is the diffusion of water through a semipermeable membrane according to the concentration gradient of water across the
membrane. Whereas diffusion transports material across membranes and within cells, osmosis transports only water across a
membrane and the membrane limits the diffusion of solutes in the water. Osmosis is a special case of diffusion. Water, like other
substances, moves from an area of higher concentration to one of lower concentration. Imagine a beaker with a semipermeable
membrane, separating the two sides or halves (Figure [Link]). On both sides of the membrane, the water level is the same, but
there are different concentrations on each side of a dissolved substance, or solute, that cannot cross the membrane. If the volume of
the water is the same, but the concentrations of solute are different, then there are also different concentrations of water, the solvent,
on either side of the membrane.

Figure [Link]: In osmosis, water always moves from an area of higher concentration (of water) to one of lower concentration (of
water). In this system, the solute cannot pass through the selectively permeable membrane.
A principle of diffusion is that the molecules move around and will spread evenly throughout the medium if they can. However,
only the material capable of getting through the membrane will diffuse through it. In this example, the solute cannot diffuse
through the membrane, but the water can. Water has a concentration gradient in this system. Therefore, water will diffuse down its
concentration gradient, crossing the membrane to the side where it is less concentrated. This diffusion of water through the
membrane—osmosis—will continue until the concentration gradient of water goes to zero. Osmosis proceeds constantly in living
systems.

Tonicity
Tonicity describes the amount of solute in a solution. The measure of the tonicity of a solution, or the total amount of solutes
dissolved in a specific amount of solution, is called its osmolarity. Three terms—hypotonic, isotonic, and hypertonic—are used to
relate the osmolarity of a cell to the osmolarity of the extracellular fluid that contains the cells. In a hypotonic solution, such as tap
water, the extracellular fluid has a lower concentration of solutes than the fluid inside the cell, and water enters the cell. (In living
systems, the point of reference is always the cytoplasm, so the prefix hypo- means that the extracellular fluid has a lower
concentration of solutes, or a lower osmolarity, than the cell cytoplasm.) It also means that the extracellular fluid has a higher
concentration of water than does the cell. In this situation, water will follow its concentration gradient and enter the cell. This may
cause an animal cell to burst, or lyse.
In a hypertonic solution (the prefix hyper- refers to the extracellular fluid having a higher concentration of solutes than the cell’s
cytoplasm), the fluid contains less water than the cell does, such as seawater. Because the cell has a lower concentration of solutes,
the water will leave the cell. In effect, the solute is drawing the water out of the cell. This may cause an animal cell to shrivel, or
crenate.
In an isotonic solution, the extracellular fluid has the same osmolarity as the cell. If the concentration of solutes of the cell matches
that of the extracellular fluid, there will be no net movement of water into or out of the cell. Blood cells in hypertonic, isotonic, and
hypotonic solutions take on characteristic appearances (Figure [Link]).

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 ART CONNECTION

Figure [Link]: Osmotic pressure changes the shape of red blood cells in hypertonic, isotonic, and hypotonic solutions.
(credit: modification of work by Mariana Ruiz Villarreal)
A doctor injects a patient with what the doctor thinks is isotonic saline solution. The patient dies, and autopsy reveals that
many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?

Some organisms, such as plants, fungi, bacteria, and some protists, have cell walls that surround the plasma membrane and prevent
cell lysis. The plasma membrane can only expand to the limit of the cell wall, so the cell will not lyse. In fact, the cytoplasm in
plants is always slightly hypertonic compared to the cellular environment, and water will always enter a cell if water is available.
This influx of water produces turgor pressure, which stiffens the cell walls of the plant (Figure [Link]). In nonwoody plants, turgor
pressure supports the plant. If the plant cells become hypertonic, as occurs in drought or if a plant is not watered adequately, water
will leave the cell. Plants lose turgor pressure in this condition and wilt.

Figure [Link]: The turgor pressure within a plant cell depends on the tonicity of the solution that it is bathed in. (credit:
modification of work by Mariana Ruiz Villarreal)

Section Summary
The passive forms of transport, diffusion and osmosis, move material of small molecular weight. Substances diffuse from areas of
high concentration to areas of low concentration, and this process continues until the substance is evenly distributed in a system. In
solutions of more than one substance, each type of molecule diffuses according to its own concentration gradient. Many factors can
affect the rate of diffusion, including concentration gradient, the sizes of the particles that are diffusing, and the temperature of the
system.
In living systems, diffusion of substances into and out of cells is mediated by the plasma membrane. Some materials diffuse readily
through the membrane, but others are hindered, and their passage is only made possible by protein channels and carriers. The
chemistry of living things occurs in aqueous solutions, and balancing the concentrations of those solutions is an ongoing problem.
In living systems, diffusion of some substances would be slow or difficult without membrane proteins.

Art Connections
Figure [Link]: A doctor injects a patient with what he thinks is isotonic saline solution. The patient dies, and autopsy reveals that
many red blood cells have been destroyed. Do you think the solution the doctor injected was really isotonic?

Answer
No, it must have been hypotonic, as a hypotonic solution would cause water to enter the cells, thereby making them burst.

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Glossary

concentration gradient
an area of high concentration across from an area of low concentration

diffusion
a passive process of transport of low-molecular weight material down its concentration gradient

facilitated transport
a process by which material moves down a concentration gradient (from high to low concentration) using integral membrane
proteins

hypertonic
describes a solution in which extracellular fluid has higher osmolarity than the fluid inside the cell

hypotonic
describes a solution in which extracellular fluid has lower osmolarity than the fluid inside the cell

isotonic
describes a solution in which the extracellular fluid has the same osmolarity as the fluid inside the cell

osmolarity
the total amount of substances dissolved in a specific amount of solution

osmosis
the transport of water through a semipermeable membrane from an area of high water concentration to an area of low water
concentration across a membrane

passive transport
a method of transporting material that does not require energy

selectively permeable
the characteristic of a membrane that allows some substances through but not others

solute
a substance dissolved in another to form a solution

tonicity
the amount of solute in a solution.

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 3.1.5: Passive Transport is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
3.5: Passive Transport by OpenStax is licensed CC BY 4.0.

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3.1.6: Active Transport
Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a
substance must move into the cell against its concentration gradient, that is, if the concentration of the substance inside the cell
must be greater than its concentration in the extracellular fluid, the cell must use energy to move the substance. Some active
transport mechanisms move small-molecular weight material, such as ions, through the membrane.
In addition to moving small ions and molecules through the membrane, cells also need to remove and take in larger molecules and
particles. Some cells are even capable of engulfing entire unicellular microorganisms. You might have correctly hypothesized that
the uptake and release of large particles by the cell requires energy. A large particle, however, cannot pass through the membrane,
even with energy supplied by the cell.

Electrochemical Gradient
We have discussed simple concentration gradients—differential concentrations of a substance across a space or a membrane—but
in living systems, gradients are more complex. Because cells contain proteins, most of which are negatively charged, and because
ions move into and out of cells, there is an electrical gradient, a difference of charge, across the plasma membrane. The interior of
living cells is electrically negative with respect to the extracellular fluid in which they are bathed; at the same time, cells have
higher concentrations of potassium (K+) and lower concentrations of sodium (Na+) than does the extracellular fluid. Thus, in a
living cell, the concentration gradient and electrical gradient of Na+ promotes diffusion of the ion into the cell, and the electrical
gradient of Na+ (a positive ion) tends to drive it inward to the negatively charged interior. The situation is more complex, however,
for other elements such as potassium. The electrical gradient of K+ promotes diffusion of the ion into the cell, but the concentration
gradient of K+ promotes diffusion out of the cell (Figure [Link]). The combined gradient that affects an ion is called its
electrochemical gradient, and it is especially important to muscle and nerve cells.

Figure [Link]: Electrochemical gradients arise from the combined effects of concentration gradients and electrical gradients.
(credit: modification of work by “Synaptitude”/Wikimedia Commons)

Moving Against a Gradient

To move substances against a concentration or an electrochemical gradient, the cell must use energy. This energy is harvested from
ATP that is generated through cellular metabolism. Active transport mechanisms, collectively called pumps or carrier proteins,
work against electrochemical gradients. With the exception of ions, small substances constantly pass through plasma membranes.
Active transport maintains concentrations of ions and other substances needed by living cells in the face of these passive changes.

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Much of a cell’s supply of metabolic energy may be spent maintaining these processes. Because active transport mechanisms
depend on cellular metabolism for energy, they are sensitive to many metabolic poisons that interfere with the supply of ATP.
Two mechanisms exist for the transport of small-molecular weight material and macromolecules. Primary active transport moves
ions across a membrane and creates a difference in charge across that membrane. The primary active transport system uses ATP to
move a substance, such as an ion, into the cell, and often at the same time, a second substance is moved out of the cell. The
sodium-potassium pump, an important pump in animal cells, expends energy to move potassium ions into the cell and a different
number of sodium ions out of the cell (Figure [Link]). The action of this pump results in a concentration and charge difference
across the membrane.

Figure [Link]: The sodium-potassium pump moves potassium and sodium ions across the plasma membrane. (credit:
modification of work by Mariana Ruiz Villarreal)
Secondary active transport describes the movement of material using the energy of the electrochemical gradient established by
primary active transport. Using the energy of the electrochemical gradient created by the primary active transport system, other
substances such as amino acids and glucose can be brought into the cell through membrane channels. ATP itself is formed through
secondary active transport using a hydrogen ion gradient in the mitochondrion.

Endocytosis
Endocytosis is a type of active transport that moves particles, such as large molecules, parts of cells, and even whole cells, into a
cell. There are different variations of endocytosis, but all share a common characteristic: The plasma membrane of the cell
invaginates, forming a pocket around the target particle. The pocket pinches off, resulting in the particle being contained in a newly
created vacuole that is formed from the plasma membrane.

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 Figure [Link]: Three variations of endocytosis are shown. (a) In one form of endocytosis, phagocytosis, the cell membrane
surrounds the particle and pinches off to form an intracellular vacuole. (b) In another type of endocytosis, pinocytosis, the cell
membrane surrounds a small volume of fluid and pinches off, forming a vesicle. (c) In receptor-mediated endocytosis, uptake of
substances by the cell is targeted to a single type of substance that binds at the receptor on the external cell membrane. (credit:
modification of work by Mariana Ruiz Villarreal)
Phagocytosis is the process by which large particles, such as cells, are taken in by a cell. For example, when microorganisms
invade the human body, a type of white blood cell called a neutrophil removes the invader through this process, surrounding and
engulfing the microorganism, which is then destroyed by the neutrophil (Figure [Link]).
A variation of endocytosis is called pinocytosis. This literally means “cell drinking” and was named at a time when the assumption
was that the cell was purposefully taking in extracellular fluid. In reality, this process takes in solutes that the cell needs from the
extracellular fluid (Figure [Link]).
A targeted variation of endocytosis employs binding proteins in the plasma membrane that are specific for certain substances
(Figure [Link]). The particles bind to the proteins and the plasma membrane invaginates, bringing the substance and the proteins
into the cell. If passage across the membrane of the target of receptor-mediated endocytosis is ineffective, it will not be removed
from the tissue fluids or blood. Instead, it will stay in those fluids and increase in concentration. Some human diseases are caused
by a failure of receptor-mediated endocytosis. For example, the form of cholesterol termed low-density lipoprotein or LDL (also
referred to as “bad” cholesterol) is removed from the blood by receptor-mediated endocytosis. In the human genetic disease
familial hypercholesterolemia, the LDL receptors are defective or missing entirely. People with this condition have life-threatening
levels of cholesterol in their blood, because their cells cannot clear the chemical from their blood.

CONCEPT IN ACTION

13 3 Receptor Mediated Endocytosis

See receptor-mediated endocytosis animation in action.

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Exocytosis
In contrast to these methods of moving material into a cell is the process of exocytosis. Exocytosis is the opposite of the processes
discussed above in that its purpose is to expel material from the cell into the extracellular fluid. A particle enveloped in membrane
fuses with the interior of the plasma membrane. This fusion opens the membranous envelope to the exterior of the cell, and the
particle is expelled into the extracellular space (Figure [Link]).

Figure [Link]: In exocytosis, a vesicle migrates to the plasma membrane, binds, and releases its contents to the outside of the
cell. (credit: modification of work by Mariana Ruiz Villarreal)

Section Summary
The combined gradient that affects an ion includes its concentration gradient and its electrical gradient. Living cells need certain
substances in concentrations greater than they exist in the extracellular space. Moving substances up their electrochemical gradients
requires energy from the cell. Active transport uses energy stored in ATP to fuel the transport. Active transport of small molecular-
size material uses integral proteins in the cell membrane to move the material—these proteins are analogous to pumps. Some
pumps, which carry out primary active transport, couple directly with ATP to drive their action. In secondary transport, energy
from primary transport can be used to move another substance into the cell and up its concentration gradient.
Endocytosis methods require the direct use of ATP to fuel the transport of large particles such as macromolecules; parts of cells or
whole cells can be engulfed by other cells in a process called phagocytosis. In phagocytosis, a portion of the membrane invaginates
and flows around the particle, eventually pinching off and leaving the particle wholly enclosed by an envelope of plasma
membrane. Vacuoles are broken down by the cell, with the particles used as food or dispatched in some other way. Pinocytosis is a
similar process on a smaller scale. The cell expels waste and other particles through the reverse process, exocytosis. Wastes are
moved outside the cell, pushing a membranous vesicle to the plasma membrane, allowing the vesicle to fuse with the membrane
and incorporating itself into the membrane structure, releasing its contents to the exterior of the cell.

Glossary

active transport
the method of transporting material that requires energy

electrochemical gradient
a gradient produced by the combined forces of the electrical gradient and the chemical gradient

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endocytosis
a type of active transport that moves substances, including fluids and particles, into a cell

exocytosis
a process of passing material out of a cell

phagocytosis
a process that takes macromolecules that the cell needs from the extracellular fluid; a variation of endocytosis

pinocytosis
a process that takes solutes that the cell needs from the extracellular fluid; a variation of endocytosis

receptor-mediated endocytosis
a variant of endocytosis that involves the use of specific binding proteins in the plasma membrane for specific molecules or
particles

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 3.1.6: Active Transport is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
3.6: Active Transport by OpenStax is licensed CC BY 4.0.

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3.1.E: Cell Structure and Function (Exercises)
3.1: How Cells Are Studied
In multicellular organisms, several cells of one particular kind interconnect with each other and perform shared functions to form
tissues (for example, muscle tissue, connective tissue, and nervous tissue), several tissues combine to form an organ (for example,
stomach, heart, or brain), and several organs make up an organ system (such as the digestive system, circulatory system, or nervous
system). Several systems functioning together form an organism (such as an elephant, for example).

Multiple Choice
When viewing a specimen through a light microscope, scientists use _________ to distinguish the individual components of cells.
A. a beam of electrons
B. radioactive isotopes
C. special stains
D. high temperatures

Answer
C

The ___________ is the basic unit of life.

A. organism
B. cell
C. tissue
D. organ

Answer
B

Free Response
What are the advantages and disadvantages of light, transmission, and scanning electron microscopes?

Answer
The advantages of light microscopes are that they are easily obtained, and the light beam does not kill the cells. However,
typical light microscopes are somewhat limited in the amount of detail that they can reveal. Electron microscopes are ideal
because you can view intricate details, but they are bulky and costly, and preparation for the microscopic examination kills the
specimen. Transmission electron microscopes are designed to examine the internal structures of a cell, whereas a scanning
electron microscope only allows visualization of the surface of a structure.

3.2: Comparing Prokaryotic and Eukaryotic Cells

Cells fall into one of two broad categories: prokaryotic and eukaryotic. The predominantly single-celled organisms of the domains
Bacteria and Archaea are classified as prokaryotes (pro- = before; -karyon- = nucleus). Animal cells, plant cells, fungi, and protists
are eukaryotes (eu- = true).

Multiple Choice
Which of these do all prokaryotes and eukaryotes share?
A. nuclear envelope
B. cell walls
C. organelles
D. plasma membrane

Answer

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 D

A typical prokaryotic cell __________________ compared to a eukaryotic cell.

A. is smaller in size by a factor of 100
B. is similar in size
C. is smaller in size by a factor of one million
D. is larger in size by a factor of 10

Answer
A

Free Response
Describe the structures that are characteristic of a prokaryote cell.

Answer
Prokaryotic cells are surrounded by a plasma membrane and have DNA, cytoplasm, and ribosomes, like eukaryotic cells. They
also have cell walls and may have a cell capsule. Prokaryotes have a single large chromosome that is not surrounded by a
nuclear membrane. Prokaryotes may have flagella or motility, pili for conjugation, and fimbriae for adhesion to surfaces.

3.3: Eukaryotic Cells

At this point, it should be clear that eukaryotic cells have a more complex structure than do prokaryotic cells. Organelles allow for
various functions to occur in the cell at the same time. Before discussing the functions of organelles within a eukaryotic cell, let us
first examine two important components of the cell: the plasma membrane and the cytoplasm.

Multiple Choice
Which of the following is found both in eukaryotic and prokaryotic cells?
A. nucleus
B. mitochondrion
C. vacuole
D. ribosome

Answer
D

Which of the following is not a component of the endomembrane system?

A. mitochondrion
B. Golgi apparatus
C. endoplasmic reticulum
D. lysosome

Answer
A

Free Response
In the context of cell biology, what do we mean by form follows function? What are at least two examples of this concept?

Answer
“Form follows function” refers to the idea that the function of a body part dictates the form of that body part. As an example,
organisms like birds or fish that fly or swim quickly through the air or water have streamlined bodies that reduce drag. At the
level of the cell, in tissues involved in secretory functions, such as the salivary glands, the cells have abundant Golgi.

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3.4: The Cell Membrane
The plasma membrane is referred to as the fluid mosaic model and is composed of a bilayer of phospholipids, with their
hydrophobic, fatty acid tails in contact with each other. The landscape of the membrane is studded with proteins, some of which
span the membrane. Some of these proteins serve to transport materials into or out of the cell. Carbohydrates are attached to some
of the proteins and lipids on the outward-facing surface of the membrane. These function to identify other cells.

Multiple Choice
Which plasma membrane component can be either found on its surface or embedded in the membrane structure?
A. protein
B. cholesterol
C. carbohydrate
D. phospholipid

Answer
A

The tails of the phospholipids of the plasma membrane are composed of _____ and are _______?
A. phosphate groups; hydrophobic
B. fatty acid groups; hydrophilic
C. phosphate groups; hydrophilic
D. fatty acid groups; hydrophobic

Answer
D

Free Response
Why is it advantageous for the cell membrane to be fluid in nature?

Answer
The fluidity of the cell membrane is necessary for the operation of some enzymes and transport mechanisms within the
membrane.

3.5: Passive Transport

The most direct forms of membrane transport are passive. Passive transport is a naturally occurring phenomenon and does not
require the cell to expend energy to accomplish the movement. In passive transport, substances move from an area of higher
concentration to an area of lower concentration in a process called diffusion. A physical space in which there is a different
concentration of a single substance is said to have a concentration gradient.

Multiple Choice
Water moves via osmosis _________.
A. throughout the cytoplasm
B. from an area with a high concentration of other solutes to a lower one
C. from an area with a low concentration of solutes to an area with a higher one
D. from an area with a low concentration of water to one of higher concentration

Answer
C

The principal force driving movement in diffusion is __________.

A. temperature
B. particle size

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 C. concentration gradient
D. membrane surface area

Answer
C

Free Response
Why does osmosis occur?

Answer
Water moves through a semipermeable membrane in osmosis because there is a concentration gradient across the membrane of
solute and solvent. The solute cannot effectively move to balance the concentration on both sides of the membrane, so water
moves to achieve this balance.

3.6: Active Transport

Active transport mechanisms require the use of the cell’s energy, usually in the form of adenosine triphosphate (ATP). If a
substance must move into the cell against its concentration gradient, that is, if the concentration of the substance inside the cell
must be greater than its concentration in the extracellular fluid, the cell must use energy to move the substance. Some active
transport mechanisms move small-molecular weight material, such as ions, through the membrane.

Multiple Choice
Active transport must function continuously because __________.
A. plasma membranes wear out
B. cells must be in constant motion
C. facilitated transport opposes active transport
D. diffusion is constantly moving the solutes in the other direction

Answer
D

Free Response
Where does the cell get energy for active transport processes?

Answer
The cell harvests energy from ATP produced by its own metabolism to power active transport processes, such as pumps.

This page titled 3.1.E: Cell Structure and Function (Exercises) is shared under a not declared license and was authored, remixed, and/or curated
by OpenStax.
3.E: Cell Structure and Function (Exercises) by OpenStax is licensed CC BY 4.0.

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3.2: Eukaryotic Origins
The fossil record and genetic evidence suggest that prokaryotic cells were the first organisms on Earth. These cells originated
approximately 3.5 billion years ago, which was about 1 billion years after Earth’s formation, and were the only life forms on the
planet until eukaryotic cells emerged approximately 2.1 billion years ago. During the prokaryotic reign, photosynthetic prokaryotes
evolved that were capable of applying the energy from sunlight to synthesize organic materials (like carbohydrates) from carbon
dioxide and an electron source (such as hydrogen, hydrogen sulfide, or water).
Photosynthesis using water as an electron donor consumes carbon dioxide and releases molecular oxygen (O2) as a byproduct. The
functioning of photosynthetic bacteria over millions of years progressively saturated Earth’s water with oxygen and then
oxygenated the atmosphere, which previously contained much greater concentrations of carbon dioxide and much lower
concentrations of oxygen. Older anaerobic prokaryotes of the era could not function in their new, aerobic environment. Some
species perished, while others survived in the remaining anaerobic environments left on Earth. Still other early prokaryotes evolved
mechanisms, such as aerobic respiration, to exploit the oxygenated atmosphere by using oxygen to store energy contained within
organic molecules. Aerobic respiration is a more efficient way of obtaining energy from organic molecules, which contributed to
the success of these species (as evidenced by the number and diversity of aerobic organisms living on Earth today). The evolution
of aerobic prokaryotes was an important step toward the evolution of the first eukaryote, but several other distinguishing features
had to evolve as well.

Endosymbiosis
The origin of eukaryotic cells was largely a mystery until a revolutionary hypothesis was comprehensively examined in the 1960s
by Lynn Margulis. The endosymbiotic theory states that eukaryotes are a product of one prokaryotic cell engulfing another, one
living within another, and evolving together over time until the separate cells were no longer recognizable as such. This once-
revolutionary hypothesis had immediate persuasiveness and is now widely accepted, with work progressing on uncovering the
steps involved in this evolutionary process as well as the key players. It has become clear that many nuclear eukaryotic genes and
the molecular machinery responsible for replicating and expressing those genes appear closely related to the Archaea. On the other
hand, the metabolic organelles and the genes responsible for many energy-harvesting processes had their origins in bacteria. Much
remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. Several
endosymbiotic events likely contributed to the origin of the eukaryotic cell.

Mitochondria
Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy
consumption. Each mitochondrion measures 1 to 10 micrometers in length and exists in the cell as a moving, fusing, and dividing
oblong spheroid (Figure 3.2.1). However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by
photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell engulfed and kept alive a
free-living, aerobic prokaryote. This gave the host cell the ability to use oxygen to release energy stored in nutrients. Several lines
of evidence support that mitochondria are derived from this endosymbiotic event. Mitochondria are shaped like a specific group of
bacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed by another
membrane-bound organism. The mitochondrial inner membrane involves substantial infoldings or cristae that resemble the textured
outer surface of certain bacteria.

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 Figure 3.2.1: In this transmission electron micrograph of mitochondria in a mammalian lung cell, the cristae, infoldings of the
mitochondrial inner membrane, can be seen in cross-section. (credit: modification of work by Louisa Howard; scale-bar data from
Matt Russell)
Mitochondria divide on their own by a process that resembles binary fission in prokaryotes. Mitochondria have their own circular
DNA chromosome that carries genes similar to those expressed by bacteria. Mitochondria also have special ribosomes and transfer
RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living
prokaryotes.

Chloroplasts
Chloroplasts are one type of plastid, a group of related organelles in plant cells that are involved in the storage of starches, fats,
proteins, and pigments. Chloroplasts contain the green pigment chlorophyll and play a role in photosynthesis. Genetic and
morphological studies suggest that plastids evolved from the endosymbiosis of an ancestral cell that engulfed a photosynthetic
cyanobacterium. Plastids are similar in size and shape to cyanobacteria and are enveloped by two or more membranes,
corresponding to the inner and outer membranes of cyanobacteria. Like mitochondria, plastids also contain circular genomes and
divide by a process reminiscent of prokaryotic cell division. The chloroplasts of red and green algae exhibit DNA sequences that
are closely related to photosynthetic cyanobacteria, suggesting that red and green algae are direct descendants of this
endosymbiotic event.
Mitochondria likely evolved before plastids because all eukaryotes have either functional mitochondria or mitochondria-like
organelles. In contrast, plastids are only found in a subset of eukaryotes, such as terrestrial plants and algae. One hypothesis of the
evolutionary steps leading to the first eukaryote is summarized in Figure 3.2.2.

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 Figure 3.2.2: The first eukaryote may have originated from an ancestral prokaryote that had undergone membrane proliferation,
compartmentalization of cellular function (into a nucleus, lysosomes, and an endoplasmic reticulum), and the establishment of
endosymbiotic relationships with an aerobic prokaryote and, in some cases, a photosynthetic prokaryote to form mitochondria and
chloroplasts, respectively.
The exact steps leading to the first eukaryotic cell can only be hypothesized, and some controversy exists regarding which events
actually took place and in what order. Spirochete bacteria have been hypothesized to have given rise to microtubules, and a
flagellated prokaryote may have contributed the raw materials for eukaryotic flagella and cilia. Other scientists suggest that
membrane proliferation and compartmentalization, not endosymbiotic events, led to the development of mitochondria and plastids.
However, the vast majority of studies support the endosymbiotic hypothesis of eukaryotic evolution.
The early eukaryotes were unicellular like most protists are today, but as eukaryotes became more complex, the evolution of
multicellularity allowed cells to remain small while still exhibiting specialized functions. The ancestors of today’s multicellular
eukaryotes are thought to have evolved about 1.5 billion years ago.

Section Summary
The first eukaryotes evolved from ancestral prokaryotes by a process that involved membrane proliferation, the loss of a cell wall,
the evolution of a cytoskeleton, and the acquisition and evolution of organelles. Nuclear eukaryotic genes appear to have had an
origin in the Archaea, whereas the energy machinery of eukaryotic cells appears to be bacterial in origin. The mitochondria and
plastids originated from endosymbiotic events when ancestral cells engulfed an aerobic bacterium (in the case of mitochondria) and
a photosynthetic bacterium (in the case of chloroplasts). The evolution of mitochondria likely preceded the evolution of
chloroplasts. There is evidence of secondary endosymbiotic events in which plastids appear to be the result of endosymbiosis after
a previous endosymbiotic event.

Glossary
endosymbiosis
the engulfment of one cell by another such that the engulfed cell survives and both cells benefit; the process responsible for the
evolution of mitochondria and chloroplasts in eukaryotes

plastid
one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments

Access for free at OpenStax 3.2.3 [Link]

Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 3.2: Eukaryotic Origins is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
13.2: Eukaryotic Origins by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 3.2.4 [Link]

3.3: The Genome
The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle
is an orderly sequence of events in the life of a cell from the division of a single parent cell to produce two new daughter cells, to
the subsequent division of those daughter cells. The mechanisms involved in the cell cycle are highly conserved across eukaryotes.
Organisms as diverse as protists, plants, and animals employ similar steps.

Genomic DNA
Before discussing the steps a cell undertakes to replicate, a deeper understanding of the structure and function of a cell’s genetic
information is necessary. A cell’s complete complement of DNA is called its genome. In prokaryotes, the genome is composed of a
single, double-stranded DNA molecule in the form of a loop or circle. The region in the cell containing this genetic material is
called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth.
In eukaryotes, the genome comprises several double-stranded, linear DNA molecules (Figure 3.3.1) bound with proteins to form
complexes called chromosomes. Each species of eukaryote has a characteristic number of chromosomes in the nuclei of its cells.
Human body cells (somatic cells) have 46 chromosomes. A somatic cell contains two matched sets of chromosomes, a
configuration known as diploid. The letter n is used to represent a single set of chromosomes; therefore a diploid organism is
designated 2n. Human cells that contain one set of 23 chromosomes are called gametes, or sex cells; these eggs and sperm are
designated n, or haploid.

Figure 3.3.1: There are 23 pairs of homologous chromosomes in a female human somatic cell. These chromosomes are viewed
within the nucleus (top), removed from a cell in mitosis (right), and arranged according to length (left) in an arrangement called a
karyotype. In this image, the chromosomes were exposed to fluorescent stains to distinguish them. (credit: “718 Bot”/Wikimedia
Commons, National Human Genome Research)
The matched pairs of chromosomes in a diploid organism are called homologous chromosomes. Homologous chromosomes are the
same length and have specific nucleotide segments called genes in exactly the same location, or locus. Genes, the functional units
of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the different forms of a characteristic.
For example, the shape of earlobes is a characteristic with traits of free or attached.
Each copy of the homologous pair of chromosomes originates from a different parent; therefore, the copies of each of the genes
themselves may not be identical. The variation of individuals within a species is caused by the specific combination of the genes
inherited from both parents. For example, there are three possible gene sequences on the human chromosome that codes for blood
type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that
determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible
to have two copies of the same gene sequence, one on each homologous chromosome (for example, AA, BB, or OO), or two
different sequences, such as AB.
Minor variations in traits such as those for blood type, eye color, and height contribute to the natural variation found within a
species. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosomes; other than a small
amount of homology that is necessary to reliably produce gametes, the genes found on the X and Y chromosomes are not the same.

Access for free at OpenStax 3.3.1 [Link]

Summary
Prokaryotes have a single loop chromosome, whereas eukaryotes have multiple, linear chromosomes surrounded by a nuclear
membrane. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of
nonhomologous sex chromosomes. This is the 2n, or diploid, state. Human gametes have 23 chromosomes or one complete set of
chromosomes. This is the n, or haploid, state. Genes are segments of DNA that code for a specific protein or RNA molecule. An
organism’s traits are determined in large part by the genes inherited from each parent, but also by the environment that they
experience. Genes are expressed as characteristics of the organism and each characteristic may have different variants called traits
that are caused by differences in the DNA sequence for a gene.

Glossary

diploid
describes a cell, nucleus, or organism containing two sets of chromosomes (2n)

gamete
a haploid reproductive cell or sex cell (sperm or egg)

gene
the physical and functional unit of heredity; a sequence of DNA that codes for a specific peptide or RNA molecule

genome
the entire genetic complement (DNA) of an organism

haploid
describes a cell, nucleus, or organism containing one set of chromosomes (n)

homologous chromosomes
chromosomes of the same length with genes in the same location; diploid organisms have pairs of homologous chromosomes,
and the members of each pair come from different parents

locus
the position of a gene on a chromosome

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 3.3: The Genome is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
6.1: The Genome by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 3.3.2 [Link]

 CHAPTER OVERVIEW

4: Cell Division
4.1: Reproduction at the Cellular Level
4.1.1: The Genome
4.1.2: The Cell Cycle
4.1.3: Cancer and the Cell Cycle
4.1.4: Prokaryotic Cell Division
4.1.E: Reproduction at the Cellular Level (Exercises)
4.2: The Cellular Basis of Inheritance
4.2.1: Sexual Reproduction
4.2.2: Meiosis
4.2.3: Errors in Meiosis
4.2.E: The Cellular Basis of Inheritance (Exercises)

Thumbnail: Meiosis (CC BY-SA 3.0; Josef Reischig via Wikimedia Commons)

4: Cell Division is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
 SECTION OVERVIEW

4.1: Reproduction at the Cellular Level

The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle
is an orderly sequence of events in the life of a cell from the division of a single parent cell to produce two new daughter cells, to
the subsequent division of those daughter cells. The mechanisms involved in the cell cycle are highly conserved across eukaryotes.
Organisms as diverse as protists, plants, and animals employ similar steps.

4.1.1: The Genome

4.1.2: The Cell Cycle

4.1.3: Cancer and the Cell Cycle

4.1.4: Prokaryotic Cell Division

4.1.E: Reproduction at the Cellular Level (Exercises)

This page titled 4.1: Reproduction at the Cellular Level is shared under a not declared license and was authored, remixed, and/or curated by
OpenStax.

Access for free at OpenStax 4.1.1 [Link]

4.1.1: The Genome
The continuity of life from one cell to another has its foundation in the reproduction of cells by way of the cell cycle. The cell cycle
is an orderly sequence of events in the life of a cell from the division of a single parent cell to produce two new daughter cells, to
the subsequent division of those daughter cells. The mechanisms involved in the cell cycle are highly conserved across eukaryotes.
Organisms as diverse as protists, plants, and animals employ similar steps.

Genomic DNA
Before discussing the steps a cell undertakes to replicate, a deeper understanding of the structure and function of a cell’s genetic
information is necessary. A cell’s complete complement of DNA is called its genome. In prokaryotes, the genome is composed of a
single, double-stranded DNA molecule in the form of a loop or circle. The region in the cell containing this genetic material is
called a nucleoid. Some prokaryotes also have smaller loops of DNA called plasmids that are not essential for normal growth.
In eukaryotes, the genome comprises several double-stranded, linear DNA molecules (Figure [Link]) bound with proteins to form
complexes called chromosomes. Each species of eukaryote has a characteristic number of chromosomes in the nuclei of its cells.
Human body cells (somatic cells) have 46 chromosomes. A somatic cell contains two matched sets of chromosomes, a
configuration known as diploid. The letter n is used to represent a single set of chromosomes; therefore a diploid organism is
designated 2n. Human cells that contain one set of 23 chromosomes are called gametes, or sex cells; these eggs and sperm are
designated n, or haploid.

Figure [Link]: There are 23 pairs of homologous chromosomes in a female human somatic cell. These chromosomes are viewed
within the nucleus (top), removed from a cell in mitosis (right), and arranged according to length (left) in an arrangement called a
karyotype. In this image, the chromosomes were exposed to fluorescent stains to distinguish them. (credit: “718 Bot”/Wikimedia
Commons, National Human Genome Research)
The matched pairs of chromosomes in a diploid organism are called homologous chromosomes. Homologous chromosomes are the
same length and have specific nucleotide segments called genes in exactly the same location, or locus. Genes, the functional units
of chromosomes, determine specific characteristics by coding for specific proteins. Traits are the different forms of a characteristic.
For example, the shape of earlobes is a characteristic with traits of free or attached.
Each copy of the homologous pair of chromosomes originates from a different parent; therefore, the copies of each of the genes
themselves may not be identical. The variation of individuals within a species is caused by the specific combination of the genes
inherited from both parents. For example, there are three possible gene sequences on the human chromosome that codes for blood
type: sequence A, sequence B, and sequence O. Because all diploid human cells have two copies of the chromosome that
determines blood type, the blood type (the trait) is determined by which two versions of the marker gene are inherited. It is possible
to have two copies of the same gene sequence, one on each homologous chromosome (for example, AA, BB, or OO), or two
different sequences, such as AB.
Minor variations in traits such as those for blood type, eye color, and height contribute to the natural variation found within a
species. The sex chromosomes, X and Y, are the single exception to the rule of homologous chromosomes; other than a small
amount of homology that is necessary to reliably produce gametes, the genes found on the X and Y chromosomes are not the same.

Access for free at OpenStax [Link] [Link]

Summary
Prokaryotes have a single loop chromosome, whereas eukaryotes have multiple, linear chromosomes surrounded by a nuclear
membrane. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of
nonhomologous sex chromosomes. This is the 2n, or diploid, state. Human gametes have 23 chromosomes or one complete set of
chromosomes. This is the n, or haploid, state. Genes are segments of DNA that code for a specific protein or RNA molecule. An
organism’s traits are determined in large part by the genes inherited from each parent, but also by the environment that they
experience. Genes are expressed as characteristics of the organism and each characteristic may have different variants called traits
that are caused by differences in the DNA sequence for a gene.

Glossary

diploid
describes a cell, nucleus, or organism containing two sets of chromosomes (2n)

gamete
a haploid reproductive cell or sex cell (sperm or egg)

gene
the physical and functional unit of heredity; a sequence of DNA that codes for a specific peptide or RNA molecule

genome
the entire genetic complement (DNA) of an organism

haploid
describes a cell, nucleus, or organism containing one set of chromosomes (n)

homologous chromosomes
chromosomes of the same length with genes in the same location; diploid organisms have pairs of homologous chromosomes,
and the members of each pair come from different parents

locus
the position of a gene on a chromosome

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 4.1.1: The Genome is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
6.1: The Genome by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

4.1.2: The Cell Cycle
The cell cycle is an ordered series of events involving cell growth and cell division that produces two new daughter cells. Cells on
the path to cell division proceed through a series of precisely timed and carefully regulated stages of growth, DNA replication, and
division that produce two genetically identical cells. The cell cycle has two major phases: interphase and the mitotic phase (Figure
[Link]). During interphase, the cell grows and DNA is replicated. During the mitotic phase, the replicated DNA and cytoplasmic

contents are separated and the cell divides.

Figure [Link]: A cell moves through a series of phases in an orderly manner. During interphase, G1 involves cell growth and
protein synthesis, the S phase involves DNA replication and the replication of the centrosome, and G2 involves further growth and
protein synthesis. The mitotic phase follows interphase. Mitosis is nuclear division during which duplicated chromosomes are
segregated and distributed into daughter nuclei. Usually the cell will divide after mitosis in a process called cytokinesis in which
the cytoplasm is divided and two daughter cells are formed.

Interphase
During interphase, the cell undergoes normal processes while also preparing for cell division. For a cell to move from interphase to
the mitotic phase, many internal and external conditions must be met. The three stages of interphase are called G1, S, and G2.

G1 Phase
The first stage of interphase is called the G1 phase, or first gap, because little change is visible. However, during the G1 stage, the
cell is quite active at the biochemical level. The cell is accumulating the building blocks of chromosomal DNA and the associated
proteins, as well as accumulating enough energy reserves to complete the task of replicating each chromosome in the nucleus.

S Phase
Throughout interphase, nuclear DNA remains in a semi-condensed chromatin configuration. In the S phase (synthesis phase), DNA
replication results in the formation of two identical copies of each chromosome—sister chromatids—that are firmly attached at the
centromere region. At this stage, each chromosome is made of two sister chromatids and is a duplicated chromosome. The
centrosome is duplicated during the S phase. The two centrosomes will give rise to the mitotic spindle, the apparatus that
orchestrates the movement of chromosomes during mitosis. The centrosome consists of a pair of rod-like centrioles at right angles
to each other. Centrioles help organize cell division. Centrioles are not present in the centrosomes of many eukaryotic species, such
as plants and most fungi.

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G2 Phase
In the G2 phase, or second gap, the cell replenishes its energy stores and synthesizes the proteins necessary for chromosome
manipulation. Some cell organelles are duplicated, and the cytoskeleton is dismantled to provide resources for the mitotic spindle.
There may be additional cell growth during G2. The final preparations for the mitotic phase must be completed before the cell is
able to enter the first stage of mitosis.

The Mitotic Phase

To make two daughter cells, the contents of the nucleus and the cytoplasm must be divided. The mitotic phase is a multistep
process during which the duplicated chromosomes are aligned, separated, and moved to opposite poles of the cell, and then the cell
is divided into two new identical daughter cells. The first portion of the mitotic phase, mitosis, is composed of five stages, which
accomplish nuclear division. The second portion of the mitotic phase, called cytokinesis, is the physical separation of the
cytoplasmic components into two daughter cells.

Mitosis
Mitosis is divided into a series of phases—prophase, prometaphase, metaphase, anaphase, and telophase—that result in the division
of the cell nucleus (Figure [Link]).

ART CONNECTION

Figure [Link]: Animal cell mitosis is divided into five stages—prophase, prometaphase, metaphase, anaphase, and telophase
—visualized here by light microscopy with fluorescence. Mitosis is usually accompanied by cytokinesis, shown here by a
transmission electron microscope. (credit "diagrams": modification of work by Mariana Ruiz Villareal; credit "mitosis
micrographs": modification of work by Roy van Heesbeen; credit "cytokinesis micrograph": modification of work by the
Wadsworth Center, NY State Department of Health; donated to the Wikimedia foundation; scale-bar data from Matt Russell)

Access for free at OpenStax [Link] [Link]

 Which of the following is the correct order of events in mitosis?
A. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus re-
forms and the cell divides. The sister chromatids separate.
B. The kinetochore becomes attached to the mitotic spindle. The sister chromatids separate. Sister chromatids line up at the
metaphase plate. The nucleus re-forms and the cell divides.
C. The kinetochore becomes attached to metaphase plate. Sister chromatids line up at the metaphase plate. The kinetochore
breaks down and the sister chromatids separate. The nucleus re-forms and the cell divides.
D. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore
breaks apart and the sister chromatids separate. The nucleus re-forms and the cell divides.

During prophase, the “first phase,” several events must occur to provide access to the chromosomes in the nucleus. The nuclear
envelope starts to break into small vesicles, and the Golgi apparatus and endoplasmic reticulum fragment and disperse to the
periphery of the cell. The nucleolus disappears. The centrosomes begin to move to opposite poles of the cell. The microtubules that
form the basis of the mitotic spindle extend between the centrosomes, pushing them farther apart as the microtubule fibers
lengthen. The sister chromatids begin to coil more tightly and become visible under a light microscope.
During prometaphase, many processes that were begun in prophase continue to advance and culminate in the formation of a
connection between the chromosomes and cytoskeleton. The remnants of the nuclear envelope disappear. The mitotic spindle
continues to develop as more microtubules assemble and stretch across the length of the former nuclear area. Chromosomes
become more condensed and visually discrete. Each sister chromatid attaches to spindle microtubules at the centromere via a
protein complex called the kinetochore.
During metaphase, all of the chromosomes are aligned in a plane called the metaphase plate, or the equatorial plane, midway
between the two poles of the cell. The sister chromatids are still tightly attached to each other. At this time, the chromosomes are
maximally condensed.
During anaphase, the sister chromatids at the equatorial plane are split apart at the centromere. Each chromatid, now called a
chromosome, is pulled rapidly toward the centrosome to which its microtubule was attached. The cell becomes visibly elongated as
the non-kinetochore microtubules slide against each other at the metaphase plate where they overlap.
During telophase, all of the events that set up the duplicated chromosomes for mitosis during the first three phases are reversed.
The chromosomes reach the opposite poles and begin to decondense (unravel). The mitotic spindles are broken down into
monomers that will be used to assemble cytoskeleton components for each daughter cell. Nuclear envelopes form around
chromosomes.

CONCEPT IN ACTION
This page of movies illustrates different aspects of mitosis. Watch the movie entitled “DIC microscopy of cell division in a
newt lung cell” and identify the phases of mitosis.

Cytokinesis
Cytokinesis is the second part of the mitotic phase during which cell division is completed by the physical separation of the
cytoplasmic components into two daughter cells. Although the stages of mitosis are similar for most eukaryotes, the process of
cytokinesis is quite different for eukaryotes that have cell walls, such as plant cells.
In cells such as animal cells that lack cell walls, cytokinesis begins following the onset of anaphase. A contractile ring composed of
actin filaments forms just inside the plasma membrane at the former metaphase plate. The actin filaments pull the equator of the
cell inward, forming a fissure. This fissure, or “crack,” is called the cleavage furrow. The furrow deepens as the actin ring
contracts, and eventually the membrane and cell are cleaved in two (Figure [Link]).
In plant cells, a cleavage furrow is not possible because of the rigid cell walls surrounding the plasma membrane. A new cell wall
must form between the daughter cells. During interphase, the Golgi apparatus accumulates enzymes, structural proteins, and
glucose molecules prior to breaking up into vesicles and dispersing throughout the dividing cell. During telophase, these Golgi
vesicles move on microtubules to collect at the metaphase plate. There, the vesicles fuse from the center toward the cell walls; this
structure is called a cell plate. As more vesicles fuse, the cell plate enlarges until it merges with the cell wall at the periphery of the

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cell. Enzymes use the glucose that has accumulated between the membrane layers to build a new cell wall of cellulose. The Golgi
membranes become the plasma membrane on either side of the new cell wall (Figure [Link]).

Figure [Link]: In part (a), a cleavage furrow forms at the former metaphase plate in the animal cell. The plasma membrane is
drawn in by a ring of actin fibers contracting just inside the membrane. The cleavage furrow deepens until the cells are pinched in
two. In part (b), Golgi vesicles coalesce at the former metaphase plate in a plant cell. The vesicles fuse and form the cell plate. The
cell plate grows from the center toward the cell walls. New cell walls are made from the vesicle contents.

G0 Phase
Not all cells adhere to the classic cell-cycle pattern in which a newly formed daughter cell immediately enters interphase, closely
followed by the mitotic phase. Cells in the G0 phase are not actively preparing to divide. The cell is in a quiescent (inactive) stage,
having exited the cell cycle. Some cells enter G0 temporarily until an external signal triggers the onset of G1. Other cells that never
or rarely divide, such as mature cardiac muscle and nerve cells, remain in G0 permanently (Figure [Link]).

Figure [Link]: Cells that are not actively preparing to divide enter an alternate phase called G0. In some cases, this is a temporary
condition until triggered to enter G1. In other cases, the cell will remain in G0 permanently.

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Control of the Cell Cycle
The length of the cell cycle is highly variable even within the cells of an individual organism. In humans, the frequency of cell
turnover ranges from a few hours in early embryonic development to an average of two to five days for epithelial cells, or to an
entire human lifetime spent in G0 by specialized cells such as cortical neurons or cardiac muscle cells. There is also variation in the
time that a cell spends in each phase of the cell cycle. When fast-dividing mammalian cells are grown in culture (outside the body
under optimal growing conditions), the length of the cycle is approximately 24 hours. In rapidly dividing human cells with a 24-
hour cell cycle, the G1 phase lasts approximately 11 hours. The timing of events in the cell cycle is controlled by mechanisms that
are both internal and external to the cell.

Regulation at Internal Checkpoints

It is essential that daughter cells be exact duplicates of the parent cell. Mistakes in the duplication or distribution of the
chromosomes lead to mutations that may be passed forward to every new cell produced from the abnormal cell. To prevent a
compromised cell from continuing to divide, there are internal control mechanisms that operate at three main cell cycle checkpoints
at which the cell cycle can be stopped until conditions are favorable. These checkpoints occur near the end of G1, at the G2–M
transition, and during metaphase (Figure [Link]).

Figure [Link]: The cell cycle is controlled at three checkpoints. Integrity of the DNA is assessed at the G1 checkpoint. Proper
chromosome duplication is assessed at the G2 checkpoint. Attachment of each kinetochore to a spindle fiber is assessed at the M
checkpoint.

The G1 Checkpoint
The G1 checkpoint determines whether all conditions are favorable for cell division to proceed. The G1 checkpoint, also called the
restriction point, is the point at which the cell irreversibly commits to the cell-division process. In addition to adequate reserves and
cell size, there is a check for damage to the genomic DNA at the G1 checkpoint. A cell that does not meet all the requirements will
not be released into the S phase.

The G2 Checkpoint
The G2 checkpoint bars the entry to the mitotic phase if certain conditions are not met. As in the G1 checkpoint, cell size and
protein reserves are assessed. However, the most important role of the G2 checkpoint is to ensure that all of the chromosomes have
been replicated and that the replicated DNA is not damaged.

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The M Checkpoint
The M checkpoint occurs near the end of the metaphase stage of mitosis. The M checkpoint is also known as the spindle
checkpoint because it determines if all the sister chromatids are correctly attached to the spindle microtubules. Because the
separation of the sister chromatids during anaphase is an irreversible step, the cycle will not proceed until the kinetochores of each
pair of sister chromatids are firmly anchored to spindle fibers arising from opposite poles of the cell.

CONCEPT IN ACTION
Watch what occurs at the G1, G2, and M checkpoints by visiting this animation of the cell cycle.

Summary
The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and
carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is
divided into G1, S, and G2 phases. Mitosis consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase.
Mitosis is usually accompanied by cytokinesis, during which the cytoplasmic components of the daughter cells are separated either
by an actin ring (animal cells) or by cell plate formation (plant cells).
Each step of the cell cycle is monitored by internal controls called checkpoints. There are three major checkpoints in the cell cycle:
one near the end of G1, a second at the G2–M transition, and the third during metaphase.

Art Connections
Figure [Link]: Which of the following is the correct order of events in mitosis?
A. Sister chromatids line up at the metaphase plate. The kinetochore becomes attached to the mitotic spindle. The nucleus re-forms
and the cell divides. The sister chromatids separate.
B. The kinetochore becomes attached to the mitotic spindle. The sister chromatids separate. Sister chromatids line up at the
metaphase plate. The nucleus re-forms and the cell divides.
C. The kinetochore becomes attached to metaphase plate. Sister chromatids line up at the metaphase plate. The kinetochore breaks
down and the sister chromatids separate. The nucleus re-forms and the cell divides.
D. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore
breaks apart and the sister chromatids separate. The nucleus re-forms and the cell divides.

Answer
D. The kinetochore becomes attached to the mitotic spindle. Sister chromatids line up at the metaphase plate. The kinetochore
breaks apart and the sister chromatids separate. The nucleus reforms and the cell divides.

Glossary

anaphase
the stage of mitosis during which sister chromatids are separated from each other

cell cycle
the ordered sequence of events that a cell passes through between one cell division and the next

cell cycle checkpoints

mechanisms that monitor the preparedness of a eukaryotic cell to advance through the various cell cycle stages

cell plate
a structure formed during plant-cell cytokinesis by Golgi vesicles fusing at the metaphase plate; will ultimately lead to
formation of a cell wall to separate the two daughter cells

centriole
a paired rod-like structure constructed of microtubules at the center of each animal cell centrosome

cleavage furrow

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 a constriction formed by the actin ring during animal-cell cytokinesis that leads to cytoplasmic division

cytokinesis
the division of the cytoplasm following mitosis to form two daughter cells

G0 phase
a cell-cycle phase distinct from the G1 phase of interphase; a cell in G0 is not preparing to divide

G1 phase
(also, first gap) a cell-cycle phase; first phase of interphase centered on cell growth during mitosis

G2 phase
(also, second gap) a cell-cycle phase; third phase of interphase where the cell undergoes the final preparations for mitosis

interphase
the period of the cell cycle leading up to mitosis; includes G1, S, and G2 phases; the interim between two consecutive cell
divisions

kinetochore
a protein structure in the centromere of each sister chromatid that attracts and binds spindle microtubules during prometaphase

metaphase plate
the equatorial plane midway between two poles of a cell where the chromosomes align during metaphase

metaphase
the stage of mitosis during which chromosomes are lined up at the metaphase plate

mitosis
the period of the cell cycle at which the duplicated chromosomes are separated into identical nuclei; includes prophase,
prometaphase, metaphase, anaphase, and telophase

mitotic phase
the period of the cell cycle when duplicated chromosomes are distributed into two nuclei and the cytoplasmic contents are
divided; includes mitosis and cytokinesis

mitotic spindle
the microtubule apparatus that orchestrates the movement of chromosomes during mitosis

prometaphase
the stage of mitosis during which mitotic spindle fibers attach to kinetochores

prophase
the stage of mitosis during which chromosomes condense and the mitotic spindle begins to form

quiescent
describes a cell that is performing normal cell functions and has not initiated preparations for cell division

S phase
the second, or synthesis phase, of interphase during which DNA replication occurs

telophase
the stage of mitosis during which chromosomes arrive at opposite poles, decondense, and are surrounded by new nuclear
envelopes

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 4.1.2: The Cell Cycle is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
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4.1.3: Cancer and the Cell Cycle
Cancer is a collective name for many different diseases caused by a common mechanism: uncontrolled cell division. Despite the
redundancy and overlapping levels of cell-cycle control, errors occur. One of the critical processes monitored by the cell-cycle
checkpoint surveillance mechanism is the proper replication of DNA during the S phase. Even when all of the cell-cycle controls
are fully functional, a small percentage of replication errors (mutations) will be passed on to the daughter cells. If one of these
changes to the DNA nucleotide sequence occurs within a gene, a gene mutation results. All cancers begin when a gene mutation
gives rise to a faulty protein that participates in the process of cell reproduction. The change in the cell that results from the
malformed protein may be minor. Even minor mistakes, however, may allow subsequent mistakes to occur more readily. Over and
over, small, uncorrected errors are passed from parent cell to daughter cells and accumulate as each generation of cells produces
more non-functional proteins from uncorrected DNA damage. Eventually, the pace of the cell cycle speeds up as the effectiveness
of the control and repair mechanisms decreases. Uncontrolled growth of the mutated cells outpaces the growth of normal cells in
the area, and a tumor can result.

Proto-oncogenes
The genes that code for the positive cell-cycle regulators are called proto-oncogenes. Proto-oncogenes are normal genes that, when
mutated, become oncogenes—genes that cause a cell to become cancerous. Consider what might happen to the cell cycle in a cell
with a recently acquired oncogene. In most instances, the alteration of the DNA sequence will result in a less functional (or non-
functional) protein. The result is detrimental to the cell and will likely prevent the cell from completing the cell cycle; however, the
organism is not harmed because the mutation will not be carried forward. If a cell cannot reproduce, the mutation is not propagated
and the damage is minimal. Occasionally, however, a gene mutation causes a change that increases the activity of a positive
regulator. For example, a mutation that allows Cdk, a protein involved in cell-cycle regulation, to be activated before it should be
could push the cell cycle past a checkpoint before all of the required conditions are met. If the resulting daughter cells are too
damaged to undertake further cell divisions, the mutation would not be propagated and no harm comes to the organism. However,
if the atypical daughter cells are able to divide further, the subsequent generation of cells will likely accumulate even more
mutations, some possibly in additional genes that regulate the cell cycle.
The Cdk example is only one of many genes that are considered proto-oncogenes. In addition to the cell-cycle regulatory proteins,
any protein that influences the cycle can be altered in such a way as to override cell-cycle checkpoints. Once a proto-oncogene has
been altered such that there is an increase in the rate of the cell cycle, it is then called an oncogene.

Tumor Suppressor Genes

Like proto-oncogenes, many of the negative cell-cycle regulatory proteins were discovered in cells that had become cancerous.
Tumor suppressor genes are genes that code for the negative regulator proteins, the type of regulator that—when activated—can
prevent the cell from undergoing uncontrolled division. The collective function of the best-understood tumor suppressor gene
proteins, retinoblastoma protein (RB1), p53, and p21, is to put up a roadblock to cell-cycle progress until certain events are
completed. A cell that carries a mutated form of a negative regulator might not be able to halt the cell cycle if there is a problem.
Mutated p53 genes have been identified in more than half of all human tumor cells. This discovery is not surprising in light of the
multiple roles that the p53 protein plays at the G1 checkpoint. The p53 protein activates other genes whose products halt the cell
cycle (allowing time for DNA repair), activates genes whose products participate in DNA repair, or activates genes that initiate cell
death when DNA damage cannot be repaired. A damaged p53 gene can result in the cell behaving as if there are no mutations
(Figure [Link]). This allows cells to divide, propagating the mutation in daughter cells and allowing the accumulation of new
mutations. In addition, the damaged version of p53 found in cancer cells cannot trigger cell death.

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 Figure [Link]: (a) The role of p53 is to monitor DNA. If damage is detected, p53 triggers repair mechanisms. If repairs are
unsuccessful, p53 signals apoptosis. (b) A cell with an abnormal p53 protein cannot repair damaged DNA and cannot signal
apoptosis. Cells with abnormal p53 can become cancerous. (credit: modification of work by Thierry Soussi)

CONCEPT IN ACTION

Cancer | Cells | MCAT | Khan Academy

Go to this website to watch an animation of how cancer results from errors in the cell cycle.

Summary
Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms regulating the cell cycle. The loss of
control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead
to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to
the daughter cells. Each successive cell division will give rise to daughter cells with even more accumulated damage. Eventually,
all checkpoints become nonfunctional, and rapidly reproducing cells crowd out normal cells, resulting in tumorous growth.
Glossary

oncogene
a mutated version of a proto-oncogene, which allows for uncontrolled progression of the cell cycle, or uncontrolled cell
reproduction

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proto-oncogene
a normal gene that controls cell division by regulating the cell cycle that becomes an oncogene if it is mutated

tumor suppressor gene

a gene that codes for regulator proteins that prevent the cell from undergoing uncontrolled division

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 4.1.3: Cancer and the Cell Cycle is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
6.3: Cancer and the Cell Cycle by OpenStax is licensed CC BY 4.0.

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4.1.4: Prokaryotic Cell Division
Prokaryotes such as bacteria propagate by binary fission. For unicellular organisms, cell division is the only method to produce
new individuals. In both prokaryotic and eukaryotic cells, the outcome of cell reproduction is a pair of daughter cells that are
genetically identical to the parent cell. In unicellular organisms, daughter cells are individuals.
To achieve the outcome of identical daughter cells, some steps are essential. The genomic DNA must be replicated and then
allocated into the daughter cells; the cytoplasmic contents must also be divided to give both new cells the machinery to sustain life.
In bacterial cells, the genome consists of a single, circular DNA chromosome; therefore, the process of cell division is simplified.
Mitosis is unnecessary because there is no nucleus or multiple chromosomes. This type of cell division is called binary fission.

Binary Fission
The cell division process of prokaryotes, called binary fission, is a less complicated and much quicker process than cell division in
eukaryotes. Because of the speed of bacterial cell division, populations of bacteria can grow very rapidly. The single, circular DNA
chromosome of bacteria is not enclosed in a nucleus, but instead occupies a specific location, the nucleoid, within the cell. As in
eukaryotes, the DNA of the nucleoid is associated with proteins that aid in packaging the molecule into a compact size. The
packing proteins of bacteria are, however, related to some of the proteins involved in the chromosome compaction of eukaryotes.
The starting point of replication, the origin, is close to the binding site of the chromosome to the plasma membrane (Figure
[Link]). Replication of the DNA is bidirectional—moving away from the origin on both strands of the DNA loop simultaneously.

As the new double strands are formed, each origin point moves away from the cell-wall attachment toward opposite ends of the
cell. As the cell elongates, the growing membrane aids in the transport of the chromosomes. After the chromosomes have cleared
the midpoint of the elongated cell, cytoplasmic separation begins. A septum is formed between the nucleoids from the periphery
toward the center of the cell. When the new cell walls are in place, the daughter cells separate.

Figure [Link]: The binary fission of a bacterium is outlined in five steps. (credit: modification of work by
“Mcstrother”/Wikimedia Commons)

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 EVOLUTION IN ACTION: Mitotic Spindle Apparatus
The precise timing and formation of the mitotic spindle is critical to the success of eukaryotic cell division. Prokaryotic cells,
on the other hand, do not undergo mitosis and therefore have no need for a mitotic spindle. However, the FtsZ protein that
plays such a vital role in prokaryotic cytokinesis is structurally and functionally very similar to tubulin, the building block of
the microtubules that make up the mitotic spindle fibers that are necessary for eukaryotes. The formation of a ring composed of
repeating units of a protein called FtsZ directs the partition between the nucleoids in prokaryotes. Formation of the FtsZ ring
triggers the accumulation of other proteins that work together to recruit new membrane and cell-wall materials to the site. FtsZ
proteins can form filaments, rings, and other three-dimensional structures resembling the way tubulin forms microtubules,
centrioles, and various cytoskeleton components. In addition, both FtsZ and tubulin employ the same energy source, GTP
(guanosine triphosphate), to rapidly assemble and disassemble complex structures.
FtsZ and tubulin are an example of homology, structures derived from the same evolutionary origins. In this example, FtsZ is
presumed to be similar to the ancestor protein to both the modern FtsZ and tubulin. While both proteins are found in extant
organisms, tubulin function has evolved and diversified tremendously since the evolution from its FtsZ-like prokaryotic origin.
A survey of cell-division machinery in present-day unicellular eukaryotes reveals crucial intermediary steps to the complex
mitotic machinery of multicellular eukaryotes (Table [Link]).
Table [Link]: Mitotic Spindle Evolution
Structure of genetic material Division of nuclear material Separation of daughter cells

Occurs through binary fission.

There is no nucleus. The single,
As the chromosome is replicated,
circular chromosome exists in a FtsZ proteins assemble into a ring
Prokaryotes the two copies move to opposite
region of cytoplasm called the that pinches the cell in two.
ends of the cell by an unknown
nucleoid.
mechanism.

Chromosomes attach to the

nuclear envelope, which remains
Microfilaments form a cleavage
Linear chromosomes exist in the intact. The mitotic spindle passes
Some protists furrow that pinches the cell in
nucleus. through the envelope and
two.
elongates the cell. No centrioles
exist.

A mitotic spindle forms from the

centrioles and passes through the
nuclear membrane, which
Microfilaments form a cleavage
Linear chromosomes exist in the remains intact. Chromosomes
Other protists furrow that pinches the cell in
nucleus. attach to the mitotic spindle. The
two.
mitotic spindle separates the
chromosomes and elongates the
cell.

A mitotic spindle forms from the

centrioles. The nuclear envelope
Microfilaments form a cleavage
Linear chromosomes exist in the dissolves. Chromosomes attach
Animal cells furrow that pinches the cell in
nucleus. to the mitotic spindle, which
two.
separates them and elongates the
cell.

Summary
In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and each copy is allocated into a daughter cell. The
cytoplasmic contents are also divided evenly to the new cells. However, there are many differences between prokaryotic and
eukaryotic cell division. Bacteria have a single, circular DNA chromosome and no nucleus. Therefore, mitosis is not necessary in
bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ. Ingrowth of membrane and
cell-wall material from the periphery of the cells results in a septum that eventually forms the separate cell walls of the daughter
cells.

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Glossary

binary fission
the process of prokaryotic cell division

FtsZ
a tubulin-like protein component of the prokaryotic cytoskeleton that is important in prokaryotic cytokinesis (name origin:
Filamenting temperature-sensitive mutant Z)

origin
the region of the prokaryotic chromosome at which replication begins

septum
a wall formed between bacterial daughter cells as a precursor to cell separation

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

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6.4: Prokaryotic Cell Division by OpenStax is licensed CC BY 4.0.

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4.1.E: Reproduction at the Cellular Level (Exercises)
6.1: The Genome
Prokaryotes have a single loop chromosome, whereas eukaryotes have multiple, linear chromosomes surrounded by a nuclear
membrane. Human somatic cells have 46 chromosomes consisting of two sets of 22 homologous chromosomes and a pair of
nonhomologous sex chromosomes. This is the 2n, or diploid, state. Human gametes have 23 chromosomes or one complete set of
chromosomes. This is the n, or haploid, state. Genes are segments of DNA that code for a specific protein or RNA molecule.

Multiple Choice
A diploid cell has ________ the number of chromosomes as a haploid cell.
A. one-fourth
B. one-half
C. twice
D. four times

Answer
C

An organism’s traits are determined by the specific combination of inherited ________.

A. cells
B. genes
C. proteins
D. chromatids

Answer
B

Free Response
Compare and contrast a human somatic cell to a human gamete.

Answer
Human somatic cells have 46 chromosomes, including 22 homologous pairs and one pair of nonhomologous sex chromosomes.
This is the 2n, or diploid, condition. Human gametes have 23 chromosomes, one each of 23 unique chromosomes. This is the n,
or haploid, condition.

6.2: The Cell Cycle

The cell cycle is an orderly sequence of events. Cells on the path to cell division proceed through a series of precisely timed and
carefully regulated stages. In eukaryotes, the cell cycle consists of a long preparatory period, called interphase. Interphase is
divided into G1, S, and G2 phases. Mitosis consists of five stages: prophase, prometaphase, metaphase, anaphase, and telophase.
Mitosis is usually accompanied by cytokinesis.

Multiple Choice
Chromosomes are duplicated during what portion of the cell cycle?
A. G1 phase
B. S phase
C. prophase
D. prometaphase

Answer
B

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Separation of the sister chromatids is a characteristic of which stage of mitosis?
A. prometaphase
B. metaphase
C. anaphase
D. telophase

Answer
C

The individual chromosomes become visible with a light microscope during which stage of mitosis?
A. prophase
B. prometaphase
C. metaphase
D. anaphase

Answer
A

What is necessary for a cell to pass the G2 checkpoint?

A. cell has reached a sufficient size
B. an adequate stockpile of nucleotides
C. accurate and complete DNA replication
D. proper attachment of mitotic spindle fibers to kinetochores

Answer
C

Free Response
Describe the similarities and differences between the cytokinesis mechanisms found in animal cells versus those in plant cells.

Answer
There are very few similarities between animal cell and plant cell cytokinesis. In animal cells, a ring of actin fibers is formed
around the periphery of the cell at the former metaphase plate. The actin ring contracts inward, pulling the plasma membrane
toward the center of the cell until the cell is pinched in two. In plant cells, a new cell wall must be formed between the daughter
cells. Because of the rigid cell walls of the parent cell, contraction of the middle of the cell is not possible. Instead, a cell plate is
formed in the center of the cell at the former metaphase plate. The cell plate is formed from Golgi vesicles that contain
enzymes, proteins, and glucose. The vesicles fuse and the enzymes build a new cell wall from the proteins and glucose. The cell
plate grows toward, and eventually fuses with, the cell wall of the parent cell.

6.3: Cancer and the Cell Cycle

Cancer is the result of unchecked cell division caused by a breakdown of the mechanisms regulating the cell cycle. The loss of
control begins with a change in the DNA sequence of a gene that codes for one of the regulatory molecules. Faulty instructions lead
to a protein that does not function as it should. Any disruption of the monitoring system can allow other mistakes to be passed on to
the daughter cells. Each successive cell division will give rise to daughter cells with even more damage.

Multiple Choice
________ are changes to the nucleotides in a segment of DNA that codes for a protein.
A. Proto-oncogenes
B. Tumor suppressor genes
C. Gene mutations
D. Negative regulators

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Answer
C

A gene that codes for a positive cell cycle regulator is called a(n) ________.
A. kinase inhibitor
B. tumor suppressor gene
C. proto-oncogene
D. oncogene

Answer
C

Free Response
Outline the steps that lead to a cell becoming cancerous.

Answer
If one of the genes that produce regulator proteins becomes mutated, it produces a malformed, possibly non-functional, cell-
cycle regulator. This increases the chance that more mutations will be left unrepaired in the cell. Each subsequent generation of
cells sustains more damage. The cell cycle can speed up as a result of loss of functional checkpoint proteins. The cells can lose
the ability to self-destruct.

Explain the difference between a proto-oncogene and a tumor suppressor gene.

Answer
A proto-oncogene is the segment of DNA that codes for one of the positive cell-cycle regulators. If that gene becomes mutated
to a form that is overactive, it is considered an oncogene. A tumor suppressor gene is a segment of DNA that codes for one of
the negative cell-cycle regulators. If that gene becomes mutated to a form that is underactive, the cell cycle will run unchecked.

6.4: Prokaryotic Cell Division

In both prokaryotic and eukaryotic cell division, the genomic DNA is replicated and each copy is allocated into a daughter cell. The
cytoplasmic contents are also divided evenly to the new cells. However, there are many differences between prokaryotic and
eukaryotic cell division. Bacteria have a single, circular DNA chromosome and no nucleus. Therefore, mitosis is not necessary in
bacterial cell division. Bacterial cytokinesis is directed by a ring composed of a protein called FtsZ.

Multiple Choice
Which eukaryotic cell-cycle event is missing in binary fission?
A. cell growth
B. DNA duplication
C. mitosis
D. cytokinesis

Answer
C

FtsZ proteins direct the formation of a ________ that will eventually form the new cell walls of the daughter cells.
A. contractile ring
B. cell plate
C. cytoskeleton
D. septum

Answer
D

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Free Response
Name the common components of eukaryotic cell division and binary fission.

Answer
The common components of eukaryotic cell division and binary fission are DNA duplication, segregation of duplicated
chromosomes, and the division of the cytoplasmic contents.

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 SECTION OVERVIEW

4.2: The Cellular Basis of Inheritance

4.2.1: Sexual Reproduction

4.2.2: Meiosis

4.2.3: Errors in Meiosis

4.2.E: The Cellular Basis of Inheritance (Exercises)

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4.2.1: Sexual Reproduction
Sexual reproduction was an early evolutionary innovation after the appearance of eukaryotic cells. The fact that most eukaryotes
reproduce sexually is evidence of its evolutionary success. In many animals, it is the only mode of reproduction. And yet, scientists
recognize some real disadvantages to sexual reproduction. On the surface, offspring that are genetically identical to the parent may
appear to be more advantageous. If the parent organism is successfully occupying a habitat, offspring with the same traits would be
similarly successful. There is also the obvious benefit to an organism that can produce offspring by asexual budding, fragmentation,
or asexual eggs. These methods of reproduction do not require another organism of the opposite sex. There is no need to expend
energy finding or attracting a mate. That energy can be spent on producing more offspring. Indeed, some organisms that lead a
solitary lifestyle have retained the ability to reproduce asexually. In addition, asexual populations only have female individuals, so
every individual is capable of reproduction. In contrast, the males in sexual populations (half the population) are not producing
offspring themselves. Because of this, an asexual population can grow twice as fast as a sexual population in theory. This means
that in competition, the asexual population would have the advantage. All of these advantages to asexual reproduction, which are
also disadvantages to sexual reproduction, should mean that the number of species with asexual reproduction should be more
common.
However, multicellular organisms that exclusively depend on asexual reproduction are exceedingly rare. Why is sexual
reproduction so common? This is one of the important questions in biology and has been the focus of much research from the latter
half of the twentieth century until now. A likely explanation is that the variation that sexual reproduction creates among offspring is
very important to the survival and reproduction of those offspring. The only source of variation in asexual organisms is mutation.
This is the ultimate source of variation in sexual organisms. In addition, those different mutations are continually reshuffled from
one generation to the next when different parents combine their unique genomes, and the genes are mixed into different
combinations by the process of meiosis. Meiosis is the division of the contents of the nucleus that divides the chromosomes among
gametes. Variation is introduced during meiosis, as well as when the gametes combine in fertilization.

EVOLUTION IN ACTION: The Red Queen Hypothesis

There is no question that sexual reproduction provides evolutionary advantages to organisms that employ this mechanism to
produce offspring. The problematic question is why, even in the face of fairly stable conditions, sexual reproduction persists
when it is more difficult and produces fewer offspring for individual organisms? Variation is the outcome of sexual
reproduction, but why are ongoing variations necessary? Enter the Red Queen hypothesis, first proposed by Leigh Van Valen in
1
1973. The concept was named in reference to the Red Queen's race in Lewis Carroll's book, Through the Looking-Glass, in
which the Red Queen says one must run at full speed just to stay where one is.
All species coevolve with other organisms. For example, predators coevolve with their prey, and parasites coevolve with their
hosts. A remarkable example of coevolution between predators and their prey is the unique coadaptation of night flying bats
and their moth prey. Bats find their prey by emitting high-pitched clicks, but moths have evolved simple ears to hear these
clicks so they can avoid the bats. The moths have also adapted behaviors, such as flying away from the bat when they first hear
it, or dropping suddenly to the ground when the bat is upon them. Bats have evolved “quiet” clicks in an attempt to evade the
moth’s hearing. Some moths have evolved the ability to respond to the bats’ clicks with their own clicks as a strategy to
confuse the bats echolocation abilities.
Each tiny advantage gained by favorable variation gives a species an edge over close competitors, predators, parasites, or even
prey. The only method that will allow a coevolving species to keep its own share of the resources is also to continually improve
its ability to survive and produce offspring. As one species gains an advantage, other species must also develop an advantage
or they will be outcompeted. No single species progresses too far ahead because genetic variation among progeny of sexual
reproduction provides all species with a mechanism to produce adapted individuals. Species whose individuals cannot keep up
become extinct. The Red Queen’s catchphrase was, “It takes all the running you can do to stay in the same place.” This is an
apt description of coevolution between competing species.

Life Cycles of Sexually Reproducing Organisms

Fertilization and meiosis alternate in sexual life cycles. What happens between these two events depends on the organism. The
process of meiosis reduces the resulting gamete’s chromosome number by half. Fertilization, the joining of two haploid gametes,
restores the diploid condition. There are three main categories of life cycles in multicellular organisms: diploid-dominant, in which

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the multicellular diploid stage is the most obvious life stage (and there is no multicellular haploid stage), as with most animals
including humans; haploid-dominant, in which the multicellular haploid stage is the most obvious life stage (and there is no
multicellular diploid stage), as with all fungi and some algae; and alternation of generations, in which the two stages, haploid and
diploid, are apparent to one degree or another depending on the group, as with plants and some algae.
Nearly all animals employ a diploid-dominant life-cycle strategy in which the only haploid cells produced by the organism are the
gametes. The gametes are produced from diploid germ cells, a special cell line that only produces gametes. Once the haploid
gametes are formed, they lose the ability to divide again. There is no multicellular haploid life stage. Fertilization occurs with the
fusion of two gametes, usually from different individuals, restoring the diploid state (Figure 4.2.1.1a).

ART CONNECTION

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Access for free at OpenStax [Link] [Link]
 Figure [Link]: (a) In animals, sexually reproducing adults form haploid gametes from diploid germ cells. (b) Fungi, such as
black bread mold (Rhizopus nigricans), have haploid-dominant life cycles. (c) Plants have a life cycle that alternates between a
multicellular haploid organism and a multicellular diploid organism. (credit c “fern”: modification of work by Cory Zanker;
credit c “gametophyte”: modification of work by “Vlmastra”/Wikimedia Commons)
If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to reproduce?

Most fungi and algae employ a life-cycle strategy in which the multicellular “body” of the organism is haploid. During sexual
reproduction, specialized haploid cells from two individuals join to form a diploid zygote. The zygote immediately undergoes
meiosis to form four haploid cells called spores (Figure 4.2.1.1b).
The third life-cycle type, employed by some algae and all plants, is called alternation of generations. These species have both
haploid and diploid multicellular organisms as part of their life cycle. The haploid multicellular plants are called gametophytes
because they produce gametes. Meiosis is not involved in the production of gametes in this case, as the organism that produces
gametes is already haploid. Fertilization between the gametes forms a diploid zygote. The zygote will undergo many rounds of
mitosis and give rise to a diploid multicellular plant called a sporophyte. Specialized cells of the sporophyte will undergo meiosis
and produce haploid spores. The spores will develop into the gametophytes (Figure 4.2.1.1c).

Section Summary
Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be
one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles.
The process of meiosis produces genetically unique reproductive cells called gametes, which have half the number of chromosomes
as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually
reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced
and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant,
demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and alternation of generations,
demonstrated by plants and some algae.

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Art Connections
Figure [Link]: If a mutation occurs so that a fungus is no longer able to produce a minus mating type, will it still be able to
reproduce?

Answer
Yes, it will be able to reproduce asexually.

Footnotes
1. 1 Leigh Van Valen, “A new evolutionary law,” Evolutionary Theory 1 (1973): 1–30.

Glossary
alternation of generations
a life-cycle type in which the diploid and haploid stages alternate

diploid-dominant
a life-cycle type in which the multicellular diploid stage is prevalent

haploid-dominant
a life-cycle type in which the multicellular haploid stage is prevalent

gametophyte
a multicellular haploid life-cycle stage that produces gametes

germ cell
a specialized cell that produces gametes, such as eggs or sperm

life cycle
the sequence of events in the development of an organism and the production of cells that produce offspring

meiosis
a nuclear division process that results in four haploid cells

sporophyte
a multicellular diploid life-cycle stage that produces spores

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 4.2.1: Sexual Reproduction is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
7.1: Sexual Reproduction by OpenStax is licensed CC BY 4.0.

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4.2.2: Meiosis
Sexual reproduction requires fertilization, a union of two cells from two individual organisms. If those two cells each contain one
set of chromosomes, then the resulting cell contains two sets of chromosomes. The number of sets of chromosomes in a cell is
called its ploidy level. Haploid cells contain one set of chromosomes. Cells containing two sets of chromosomes are called diploid.
If the reproductive cycle is to continue, the diploid cell must somehow reduce its number of chromosome sets before fertilization
can occur again, or there will be a continual doubling in the number of chromosome sets in every generation. So, in addition to
fertilization, sexual reproduction includes a nuclear division, known as meiosis, that reduces the number of chromosome sets.
Most animals and plants are diploid, containing two sets of chromosomes; in each somatic cell (the nonreproductive cells of a
multicellular organism), the nucleus contains two copies of each chromosome that are referred to as homologous chromosomes.
Somatic cells are sometimes referred to as “body” cells. Homologous chromosomes are matched pairs containing genes for the
same traits in identical locations along their length. Diploid organisms inherit one copy of each homologous chromosome from
each parent; all together, they are considered a full set of chromosomes. In animals, haploid cells containing a single copy of each
homologous chromosome are found only within gametes. Gametes fuse with another haploid gamete to produce a diploid cell.
The nuclear division that forms haploid cells, which is called meiosis, is related to mitosis. As you have learned, mitosis is part of a
cell reproduction cycle that results in identical daughter nuclei that are also genetically identical to the original parent nucleus. In
mitosis, both the parent and the daughter nuclei contain the same number of chromosome sets—diploid for most plants and
animals. Meiosis employs many of the same mechanisms as mitosis. However, the starting nucleus is always diploid and the nuclei
that result at the end of a meiotic cell division are haploid. To achieve the reduction in chromosome number, meiosis consists of
one round of chromosome duplication and two rounds of nuclear division. Because the events that occur during each of the division
stages are analogous to the events of mitosis, the same stage names are assigned. However, because there are two rounds of
division, the stages are designated with a “I” or “II.” Thus, meiosis I is the first round of meiotic division and consists of prophase
I, prometaphase I, and so on. Meiosis I reduces the number of chromosome sets from two to one. The genetic information is also
mixed during this division to create unique recombinant chromosomes. Meiosis II, in which the second round of meiotic division
takes place in a way that is similar to mitosis, includes prophase II, prometaphase II, and so on.

Interphase
Meiosis is preceded by an interphase consisting of the G1, S, and G2 phases, which are nearly identical to the phases preceding
mitosis. The G1 phase is the first phase of interphase and is focused on cell growth. In the S phase, the DNA of the chromosomes is
replicated. Finally, in the G2 phase, the cell undergoes the final preparations for meiosis.
During DNA duplication of the S phase, each chromosome becomes composed of two identical copies (called sister chromatids)
that are held together at the centromere until they are pulled apart during meiosis II. In an animal cell, the centrosomes that
organize the microtubules of the meiotic spindle also replicate. This prepares the cell for the first meiotic phase.

Meiosis I
Early in prophase I, the chromosomes can be seen clearly microscopically. As the nuclear envelope begins to break down, the
proteins associated with homologous chromosomes bring the pair close to each other. The tight pairing of the homologous
chromosomes is called synapsis. In synapsis, the genes on the chromatids of the homologous chromosomes are precisely aligned
with each other. An exchange of chromosome segments between non-sister homologous chromatids occurs and is called crossing
over. This process is revealed visually after the exchange as chiasmata (singular = chiasma) (Figure [Link]).
As prophase I progresses, the close association between homologous chromosomes begins to break down, and the chromosomes
continue to condense, although the homologous chromosomes remain attached to each other at chiasmata. The number of
chiasmata varies with the species and the length of the chromosome. At the end of prophase I, the pairs are held together only at
chiasmata (Figure [Link]) and are called tetrads because the four sister chromatids of each pair of homologous chromosomes are
now visible.
The crossover events are the first source of genetic variation produced by meiosis. A single crossover event between homologous
non-sister chromatids leads to a reciprocal exchange of equivalent DNA between a maternal chromosome and a paternal
chromosome. Now, when that sister chromatid is moved into a gamete, it will carry some DNA from one parent of the individual
and some DNA from the other parent. The recombinant sister chromatid has a combination of maternal and paternal genes that did
not exist before the crossover.

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 Figure [Link]: In this illustration of the effects of crossing over, the blue chromosome came from the individual’s father and the
red chromosome came from the individual’s mother. Crossover occurs between non-sister chromatids of homologous
chromosomes. The result is an exchange of genetic material between homologous chromosomes. The chromosomes that have a
mixture of maternal and paternal sequence are called recombinant and the chromosomes that are completely paternal or maternal
are called non-recombinant.

The key event in prometaphase I is the attachment of the spindle fiber microtubules to the kinetochore proteins at the centromeres.
The microtubules assembled from centrosomes at opposite poles of the cell grow toward the middle of the cell. At the end of
prometaphase I, each tetrad is attached to microtubules from both poles, with one homologous chromosome attached at one pole
and the other homologous chromosome attached to the other pole. The homologous chromosomes are still held together at
chiasmata. In addition, the nuclear membrane has broken down entirely.
During metaphase I, the homologous chromosomes are arranged in the center of the cell with the kinetochores facing opposite
poles. The orientation of each pair of homologous chromosomes at the center of the cell is random.

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This randomness, called independent assortment, is the physical basis for the generation of the second form of genetic variation in
offspring. Consider that the homologous chromosomes of a sexually reproducing organism are originally inherited as two separate
sets, one from each parent. Using humans as an example, one set of 23 chromosomes is present in the egg donated by the mother.
The father provides the other set of 23 chromosomes in the sperm that fertilizes the egg. In metaphase I, these pairs line up at the
midway point between the two poles of the cell. Because there is an equal chance that a microtubule fiber will encounter a
maternally or paternally inherited chromosome, the arrangement of the tetrads at the metaphase plate is random. Any maternally
inherited chromosome may face either pole. Any paternally inherited chromosome may also face either pole. The orientation of
each tetrad is independent of the orientation of the other 22 tetrads.
In each cell that undergoes meiosis, the arrangement of the tetrads is different. The number of variations depends on the number of
chromosomes making up a set. There are two possibilities for orientation (for each tetrad); thus, the possible number of alignments
equals 2n where n is the number of chromosomes per set. Humans have 23 chromosome pairs, which results in over eight million
(223) possibilities. This number does not include the variability previously created in the sister chromatids by crossover. Given
these two mechanisms, it is highly unlikely that any two haploid cells resulting from meiosis will have the same genetic
composition (Figure [Link]).
To summarize the genetic consequences of meiosis I: the maternal and paternal genes are recombined by crossover events
occurring on each homologous pair during prophase I; in addition, the random assortment of tetrads at metaphase produces a
unique combination of maternal and paternal chromosomes that will make their way into the gametes.

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 Figure [Link]: To demonstrate random, independent assortment at metaphase I, consider a cell with n = 2. In this case, there are
two possible arrangements at the equatorial plane in metaphase I, as shown in the upper cell of each panel. These two possible
orientations lead to the production of genetically different gametes. With more chromosomes, the number of possible arrangements
increases dramatically.
In anaphase I, the spindle fibers pull the linked chromosomes apart. The sister chromatids remain tightly bound together at the
centromere. It is the chiasma connections that are broken in anaphase I as the fibers attached to the fused kinetochores pull the
homologous chromosomes apart (Figure [Link]).
In telophase I, the separated chromosomes arrive at opposite poles. The remainder of the typical telophase events may or may not
occur depending on the species. In some organisms, the chromosomes decondense and nuclear envelopes form around the
chromatids in telophase I.
Cytokinesis, the physical separation of the cytoplasmic components into two daughter cells, occurs without reformation of the
nuclei in other organisms. In nearly all species, cytokinesis separates the cell contents by either a cleavage furrow (in animals and
some fungi), or a cell plate that will ultimately lead to formation of cell walls that separate the two daughter cells (in plants). At
each pole, there is just one member of each pair of the homologous chromosomes, so only one full set of the chromosomes is
present. This is why the cells are considered haploid—there is only one chromosome set, even though there are duplicate copies of
the set because each homolog still consists of two sister chromatids that are still attached to each other. However, although the
sister chromatids were once duplicates of the same chromosome, they are no longer identical at this stage because of crossovers.

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 CONCEPT IN ACTION

Review the process of meiosis, observing how chromosomes align and migrate, at this site.

Meiosis II
In meiosis II, the connected sister chromatids remaining in the haploid cells from meiosis I will be split to form four haploid cells.
In some species, cells enter a brief interphase, or interkinesis, that lacks an S phase, before entering meiosis II. Chromosomes are
not duplicated during interkinesis. The two cells produced in meiosis I go through the events of meiosis II in synchrony. Overall,
meiosis II resembles the mitotic division of a haploid cell.
In prophase II, if the chromosomes decondensed in telophase I, they condense again. If nuclear envelopes were formed, they
fragment into vesicles. The centrosomes duplicated during interkinesis move away from each other toward opposite poles, and new
spindles are formed. In prometaphase II, the nuclear envelopes are completely broken down, and the spindle is fully formed. Each
sister chromatid forms an individual kinetochore that attaches to microtubules from opposite poles. In metaphase II, the sister
chromatids are maximally condensed and aligned at the center of the cell. In anaphase II, the sister chromatids are pulled apart by
the spindle fibers and move toward opposite poles.

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 Figure [Link]: In prometaphase I, microtubules attach to the fused kinetochores of homologous chromosomes. In anaphase I, the
homologous chromosomes are separated. In prometaphase II, microtubules attach to individual kinetochores of sister chromatids.
In anaphase II, the sister chromatids are separated.
In telophase II, the chromosomes arrive at opposite poles and begin to decondense. Nuclear envelopes form around the
chromosomes. Cytokinesis separates the two cells into four genetically unique haploid cells. At this point, the nuclei in the newly
produced cells are both haploid and have only one copy of the single set of chromosomes. The cells produced are genetically
unique because of the random assortment of paternal and maternal homologs and because of the recombination of maternal and
paternal segments of chromosomes—with their sets of genes—that occurs during crossover.

Comparing Meiosis and Mitosis

Mitosis and meiosis, which are both forms of division of the nucleus in eukaryotic cells, share some similarities, but also exhibit
distinct differences that lead to their very different outcomes. Mitosis is a single nuclear division that results in two nuclei, usually
partitioned into two new cells. The nuclei resulting from a mitotic division are genetically identical to the original. They have the
same number of sets of chromosomes: one in the case of haploid cells, and two in the case of diploid cells. On the other hand,
meiosis is two nuclear divisions that result in four nuclei, usually partitioned into four new cells. The nuclei resulting from meiosis
are never genetically identical, and they contain one chromosome set only—this is half the number of the original cell, which was
diploid (Figure [Link]).
The differences in the outcomes of meiosis and mitosis occur because of differences in the behavior of the chromosomes during
each process. Most of these differences in the processes occur in meiosis I, which is a very different nuclear division than mitosis.
In meiosis I, the homologous chromosome pairs become associated with each other, are bound together, experience chiasmata and

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crossover between sister chromatids, and line up along the metaphase plate in tetrads with spindle fibers from opposite spindle
poles attached to each kinetochore of a homolog in a tetrad. All of these events occur only in meiosis I, never in mitosis.
Homologous chromosomes move to opposite poles during meiosis I so the number of sets of chromosomes in each nucleus-to-be is
reduced from two to one. For this reason, meiosis I is referred to as a reduction division. There is no such reduction in ploidy level
in mitosis.
Meiosis II is much more analogous to a mitotic division. In this case, duplicated chromosomes (only one set of them) line up at the
center of the cell with divided kinetochores attached to spindle fibers from opposite poles. During anaphase II, as in mitotic
anaphase, the kinetochores divide and one sister chromatid is pulled to one pole and the other sister chromatid is pulled to the other
pole. If it were not for the fact that there had been crossovers, the two products of each meiosis II division would be identical as in
mitosis; instead, they are different because there has always been at least one crossover per chromosome. Meiosis II is not a
reduction division because, although there are fewer copies of the genome in the resulting cells, there is still one set of
chromosomes, as there was at the end of meiosis I.
Cells produced by mitosis will function in different parts of the body as a part of growth or replacing dead or damaged cells. They
may even be involved in asexual reproduction in some organisms. Cells produced by meiosis in a diploid-dominant organism such
as an animal will only participate in sexual reproduction.

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 Figure [Link]: Meiosis and mitosis are both preceded by one round of DNA replication; however, meiosis includes two nuclear
divisions. The four daughter cells resulting from meiosis are haploid and genetically distinct. The daughter cells resulting from
mitosis are diploid and identical to the parent cell.

CONCEPT IN ACTION

For an animation comparing mitosis and meiosis, go to this website.

Section Summary
Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid
offspring. The process that results in haploid cells is called meiosis. Meiosis is a series of events that arrange and separate
chromosomes into daughter cells. During the interphase of meiosis, each chromosome is duplicated. In meiosis, there are two

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rounds of nuclear division resulting in four nuclei and usually four haploid daughter cells, each with half the number of
chromosomes as the parent cell. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I
and random alignment at metaphase I. The cells that are produced by meiosis are genetically unique.
Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce
daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions
are two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set rather than
the two sets the parent cell had. The main differences between the processes occur in the first division of meiosis. The homologous
chromosomes separate into different nuclei during meiosis I causing a reduction of ploidy level. The second division of meiosis is
much more similar to a mitotic division.

Glossary

chiasmata
(singular = chiasma) the structure that forms at the crossover points after genetic material is exchanged

crossing over
(also, recombination) the exchange of genetic material between homologous chromosomes resulting in chromosomes that
incorporate genes from both parents of the organism forming reproductive cells

fertilization
the union of two haploid cells typically from two individual organisms

interkinesis
a period of rest that may occur between meiosis I and meiosis II; there is no replication of DNA during interkinesis

meiosis I
the first round of meiotic cell division; referred to as reduction division because the resulting cells are haploid

meiosis II
the second round of meiotic cell division following meiosis I; sister chromatids are separated from each other, and the result is
four unique haploid cells

recombinant
describing something composed of genetic material from two sources, such as a chromosome with both maternal and paternal
segments of DNA

reduction division
a nuclear division that produces daughter nuclei each having one-half as many chromosome sets as the parental nucleus;
meiosis I is a reduction division

somatic cell
all the cells of a multicellular organism except the gamete-forming cells

synapsis
the formation of a close association between homologous chromosomes during prophase I

tetrad
two duplicated homologous chromosomes (four chromatids) bound together by chiasmata during prophase I

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

Access for free at OpenStax [Link] [Link]

This page titled 4.2.2: Meiosis is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
7.2: Meiosis by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

4.2.3: Errors in Meiosis
Inherited disorders can arise when chromosomes behave abnormally during meiosis. Chromosome disorders can be divided into
two categories: abnormalities in chromosome number and chromosome structural rearrangements. Because even small segments of
chromosomes can span many genes, chromosomal disorders are characteristically dramatic and often fatal.

Disorders in Chromosome Number

The isolation and microscopic observation of chromosomes forms the basis of cytogenetics and is the primary method by which
clinicians detect chromosomal abnormalities in humans. A karyotype is the number and appearance of chromosomes, including
their length, banding pattern, and centromere position. To obtain a view of an individual’s karyotype, cytologists photograph the
chromosomes and then cut and paste each chromosome into a chart, or karyogram (Figure [Link]).

Figure [Link]: This karyogram shows the chromosomes of a female human immune cell during mitosis. (credit: Andreas Bolzer,
et al)

CAREERS IN ACTION: Geneticists Use Karyograms to Identify Chromosomal Aberrations

The karyotype is a method by which traits characterized by chromosomal abnormalities can be identified from a single cell. To
observe an individual’s karyotype, a person’s cells (like white blood cells) are first collected from a blood sample or other
tissue. In the laboratory, the isolated cells are stimulated to begin actively dividing. A chemical is then applied to the cells to
arrest mitosis during metaphase. The cells are then fixed to a slide.
The geneticist then stains chromosomes with one of several dyes to better visualize the distinct and reproducible banding
patterns of each chromosome pair. Following staining, chromosomes are viewed using bright-field microscopy. An
experienced cytogeneticist can identify each band. In addition to the banding patterns, chromosomes are further identified on
the basis of size and centromere location. To obtain the classic depiction of the karyotype in which homologous pairs of
chromosomes are aligned in numerical order from longest to shortest, the geneticist obtains a digital image, identifies each
chromosome, and manually arranges the chromosomes into this pattern (Figure [Link]).
At its most basic, the karyogram may reveal genetic abnormalities in which an individual has too many or too few
chromosomes per cell. Examples of this are Down syndrome, which is identified by a third copy of chromosome 21, and
Turner syndrome, which is characterized by the presence of only one X chromosome in women instead of two. Geneticists can
also identify large deletions or insertions of DNA. For instance, Jacobsen syndrome, which involves distinctive facial features
as well as heart and bleeding defects, is identified by a deletion on chromosome 11. Finally, the karyotype can pinpoint
translocations, which occur when a segment of genetic material breaks from one chromosome and reattaches to another
chromosome or to a different part of the same chromosome. Translocations are implicated in certain cancers, including chronic
myelogenous leukemia.
By observing a karyogram, geneticists can actually visualize the chromosomal composition of an individual to confirm or
predict genetic abnormalities in offspring even before birth.

Nondisjunctions, Duplications, and Deletions

Of all the chromosomal disorders, abnormalities in chromosome number are the most easily identifiable from a karyogram.
Disorders of chromosome number include the duplication or loss of entire chromosomes, as well as changes in the number of
complete sets of chromosomes. They are caused by nondisjunction, which occurs when pairs of homologous chromosomes or sister
chromatids fail to separate during meiosis. The risk of nondisjunction increases with the age of the parents.

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Nondisjunction can occur during either meiosis I or II, with different results (Figure [Link]). If homologous chromosomes fail to
separate during meiosis I, the result is two gametes that lack that chromosome and two gametes with two copies of the
chromosome. If sister chromatids fail to separate during meiosis II, the result is one gamete that lacks that chromosome, two
normal gametes with one copy of the chromosome, and one gamete with two copies of the chromosome.

Figure [Link]: Following meiosis, each gamete has one copy of each chromosome. Nondisjunction occurs when homologous
chromosomes (meiosis I) or sister chromatids (meiosis II) fail to separate during meiosis.
An individual with the appropriate number of chromosomes for their species is called euploid; in humans, euploidy corresponds to
22 pairs of autosomes and one pair of sex chromosomes. An individual with an error in chromosome number is described as
aneuploid, a term that includes monosomy (loss of one chromosome) or trisomy (gain of an extraneous chromosome). Monosomic
human zygotes missing any one copy of an autosome invariably fail to develop to birth because they have only one copy of
essential genes. Most autosomal trisomies also fail to develop to birth; however, duplications of some of the smaller chromosomes
(13, 15, 18, 21, or 22) can result in offspring that survive for several weeks to many years. Trisomic individuals suffer from a
different type of genetic imbalance: an excess in gene dose. Cell functions are calibrated to the amount of gene product produced
by two copies (doses) of each gene; adding a third copy (dose) disrupts this balance. The most common trisomy is that of
chromosome 21, which leads to Down syndrome. Individuals with this inherited disorder have characteristic physical features and
developmental delays in growth and cognition. The incidence of Down syndrome is correlated with maternal age, such that older
women are more likely to give birth to children with Down syndrome (Figure [Link]).

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 Figure [Link]: The incidence of having a fetus with trisomy 21 increases dramatically with maternal age.

CONCEPT IN ACTION

Down syndrome (trisomy 21) - causes,…

causes,…

Visualize the addition of a chromosome that leads to Down syndrome in this video simulation.

Humans display dramatic deleterious effects with autosomal trisomies and monosomies. Therefore, it may seem counterintuitive
that human females and males can function normally, despite carrying different numbers of the X chromosome. In part, this occurs
because of a process called X inactivation. Early in development, when female mammalian embryos consist of just a few thousand
cells, one X chromosome in each cell inactivates by condensing into a structure called a Barr body. The genes on the inactive X
chromosome are not expressed. The particular X chromosome (maternally or paternally derived) that is inactivated in each cell is
random, but once the inactivation occurs, all cells descended from that cell will have the same inactive X chromosome. By this
process, females compensate for their double genetic dose of X chromosome.
In so-called “tortoiseshell” cats, X inactivation is observed as coat-color variegation (Figure [Link]). Females heterozygous for an
X-linked coat color gene will express one of two different coat colors over different regions of their body, corresponding to
whichever X chromosome is inactivated in the embryonic cell progenitor of that region. When you see a tortoiseshell cat, you will
know that it has to be a female.

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 Figure [Link]: Embryonic inactivation of one of two different X chromosomes encoding different coat colors gives rise to the
tortoiseshell phenotype in cats. (credit: Michael Bodega)
In an individual carrying an abnormal number of X chromosomes, cellular mechanisms will inactivate all but one X in each of her
cells. As a result, X-chromosomal abnormalities are typically associated with mild mental and physical defects, as well as sterility.
If the X chromosome is absent altogether, the individual will not develop.
Several errors in sex chromosome number have been characterized. Individuals with three X chromosomes, called triplo-X, appear
female but express developmental delays and reduced fertility. The XXY chromosome complement, corresponding to one type of
Klinefelter syndrome, corresponds to male individuals with small testes, enlarged breasts, and reduced body hair. The extra X
chromosome undergoes inactivation to compensate for the excess genetic dosage. Turner syndrome, characterized as an X0
chromosome complement (i.e., only a single sex chromosome), corresponds to a female individual with short stature, webbed skin
in the neck region, hearing and cardiac impairments, and sterility.
An individual with more than the correct number of chromosome sets (two for diploid species) is called polyploid. For instance,
fertilization of an abnormal diploid egg with a normal haploid sperm would yield a triploid zygote. Polyploid animals are extremely
rare, with only a few examples among the flatworms, crustaceans, amphibians, fish, and lizards. Triploid animals are sterile
because meiosis cannot proceed normally with an odd number of chromosome sets. In contrast, polyploidy is very common in the
plant kingdom, and polyploid plants tend to be larger and more robust than euploids of their species.

Chromosome Structural Rearrangements

Cytologists have characterized numerous structural rearrangements in chromosomes, including partial duplications, deletions,
inversions, and translocations. Duplications and deletions often produce offspring that survive but exhibit physical and mental
abnormalities. Cri-du-chat (from the French for “cry of the cat”) is a syndrome associated with nervous system abnormalities and
identifiable physical features that results from a deletion of most of the small arm of chromosome 5 (Figure [Link]). Infants with
this genotype emit a characteristic high-pitched cry upon which the disorder’s name is based.

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 Figure [Link]: This individual with cri-du-chat syndrome is shown at various ages: (A) age two, (B) age four, (C) age nine, and
(D) age 12. (credit: Paola Cerruti Mainardi)
Chromosome inversions and translocations can be identified by observing cells during meiosis because homologous chromosomes
with a rearrangement in one of the pair must contort to maintain appropriate gene alignment and pair effectively during prophase I.
A chromosome inversion is the detachment, 180° rotation, and reinsertion of part of a chromosome (Figure [Link]). Unless they
disrupt a gene sequence, inversions only change the orientation of genes and are likely to have more mild effects than aneuploid
errors.

EVOLUTION IN ACTION: The Chromosome 18 Inversion

Not all structural rearrangements of chromosomes produce nonviable, impaired, or infertile individuals. In rare instances, such
a change can result in the evolution of a new species. In fact, an inversion in chromosome 18 appears to have contributed to the
evolution of humans. This inversion is not present in our closest genetic relatives, the chimpanzees.
The chromosome 18 inversion is believed to have occurred in early humans following their divergence from a common
ancestor with chimpanzees approximately five million years ago. Researchers have suggested that a long stretch of DNA was
duplicated on chromosome 18 of an ancestor to humans, but that during the duplication it was inverted (inserted into the
chromosome in reverse orientation.
A comparison of human and chimpanzee genes in the region of this inversion indicates that two genes—ROCK1 and USP14—
are farther apart on human chromosome 18 than they are on the corresponding chimpanzee chromosome. This suggests that
one of the inversion breakpoints occurred between these two genes. Interestingly, humans and chimpanzees express USP14 at
distinct levels in specific cell types, including cortical cells and fibroblasts. Perhaps the chromosome 18 inversion in an
ancestral human repositioned specific genes and reset their expression levels in a useful way. Because both ROCK1 and USP14
code for enzymes, a change in their expression could alter cellular function. It is not known how this inversion contributed to
1
hominid evolution, but it appears to be a significant factor in the divergence of humans from other primates.

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A translocation occurs when a segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome.
Translocations can be benign or have devastating effects, depending on how the positions of genes are altered with respect to
regulatory sequences. Notably, specific translocations have been associated with several cancers and with schizophrenia.
Reciprocal translocations result from the exchange of chromosome segments between two nonhomologous chromosomes such that
there is no gain or loss of genetic information (Figure [Link]).

Figure [Link]: An (a) inversion occurs when a chromosome segment breaks from the chromosome, reverses its orientation, and
then reattaches in the original position. A (b) reciprocal translocation occurs between two nonhomologous chromosomes and does
not cause any genetic information to be lost or duplicated. (credit: modification of work by National Human Genome Research
Institute (USA)

Section Summary
The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allow for the
assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the
embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have
milder effects on an individual. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted.
Chromosome structures also may be rearranged, for example by inversion or translocation. Both of these aberrations can result in
negative effects on development, or death. Because they force chromosomes to assume contorted pairings during meiosis I,
inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction.

Footnotes
1. 1 V Goidts, et al., “Segmental duplication associated with the human-specific inversion of chromosome 18: a further example
of the impact of segmental duplications on karyotype and genome evolution in primates,” Human Genetics, 115 (2004):116–22.

Glossary

aneuploid
an individual with an error in chromosome number; includes deletions and duplications of chromosome segments

autosome
any of the non-sex chromosomes

chromosome inversion
the detachment, 180° rotation, and reinsertion of a chromosome arm

euploid
an individual with the appropriate number of chromosomes for their species

karyogram
the photographic image of a karyotype

Access for free at OpenStax [Link] [Link]

karyotype
the number and appearance of an individuals chromosomes, including the size, banding patterns, and centromere position

monosomy
an otherwise diploid genotype in which one chromosome is missing

nondisjunction
the failure of synapsed homologs to completely separate and migrate to separate poles during the first cell division of meiosis

polyploid
an individual with an incorrect number of chromosome sets

translocation
the process by which one segment of a chromosome dissociates and reattaches to a different, nonhomologous chromosome

trisomy
an otherwise diploid genotype in which one entire chromosome is duplicated

X inactivation
the condensation of X chromosomes into Barr bodies during embryonic development in females to compensate for the double
genetic dose

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 4.2.3: Errors in Meiosis is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
7.3: Errors in Meiosis by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

4.2.E: The Cellular Basis of Inheritance (Exercises)
7.1: Sexual Reproduction
Nearly all eukaryotes undergo sexual reproduction. The variation introduced into the reproductive cells by meiosis appears to be
one of the advantages of sexual reproduction that has made it so successful. Meiosis and fertilization alternate in sexual life cycles.
The process of meiosis produces genetically unique reproductive cells called gametes, which have half the number of chromosomes
as the parent cell. Fertilization, the fusion of haploid gametes from two individuals, restores the diploid condition. Thus, sexually
reproducing organisms alternate between haploid and diploid stages. However, the ways in which reproductive cells are produced
and the timing between meiosis and fertilization vary greatly. There are three main categories of life cycles: diploid-dominant,
demonstrated by most animals; haploid-dominant, demonstrated by all fungi and some algae; and alternation of generations,
demonstrated by plants and some algae.

Multiple Choice
What is a likely evolutionary advantage of sexual reproduction over asexual reproduction?
A. sexual reproduction involves fewer steps
B. less chance of using up the resources in a given environment
C. sexual reproduction results in greater variation in the offspring
D. sexual reproduction is more cost-effective

Answer
C

Which type of life cycle has both a haploid and diploid multicellular stage?
A. an asexual life cycle
B. diploid-dominant
C. haploid-dominant
D. alternation of generations

Answer
D

Which event leads to a diploid cell in a life cycle?

A. meiosis
B. fertilization
C. alternation of generations
D. mutation

Answer
B

Free Response
Explain the advantage that populations of sexually reproducing organisms have over asexually reproducing organisms?

Answer
The offspring of sexually reproducing organisms are all genetically unique. Because of this, sexually reproducing organisms
may have more successful survival of offspring in environments that change than asexually reproducing organisms, whose
offspring are all genetically identical. In addition, the rate of adaptation of sexually reproducing organisms is higher, because of
their increased variation. This may allow sexually reproducing organisms to adapt more quickly to competitors and parasites,
who are evolving new ways to exploit or outcompete them.

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Describe the two events that are common to all sexually reproducing organisms and how they fit into the different life cycles of
those organisms.

Answer
The two events common to all sexually reproducing organisms are meiosis and fertilization. Meiosis reduces a diploid cell to a
haploid state. The haploid cell may divide mitotically to produce an organism, some of whose cells will combine during
fertilization, or the haploid cells produced by meiosis may immediately combine in fertilization to produce a diploid cell that
divides to produce an organism.

7.2: Meiosis
Sexual reproduction requires that diploid organisms produce haploid cells that can fuse during fertilization to form diploid
offspring. The process that results in haploid cells is called meiosis. Meiosis is a series of events that arrange and separate
chromosomes into daughter cells. During the interphase of meiosis, each chromosome is duplicated. In meiosis, there are two
rounds of nuclear division resulting in four nuclei and usually four haploid daughter cells, each with half the number of
chromosomes as the parent cell. During meiosis, variation in the daughter nuclei is introduced because of crossover in prophase I
and random alignment at metaphase I. The cells that are produced by meiosis are genetically unique.
Meiosis and mitosis share similarities, but have distinct outcomes. Mitotic divisions are single nuclear divisions that produce
daughter nuclei that are genetically identical and have the same number of chromosome sets as the original cell. Meiotic divisions
are two nuclear divisions that produce four daughter nuclei that are genetically different and have one chromosome set rather than
the two sets the parent cell had. The main differences between the processes occur in the first division of meiosis. The homologous
chromosomes separate into different nuclei during meiosis I causing a reduction of ploidy level. The second division of meiosis is
much more similar to a mitotic division.

Multiple Choice
Meiosis produces ________ daughter cells.
A. two haploid
B. two diploid
C. four haploid
D. four diploid

Answer
C

At which stage of meiosis are sister chromatids separated from each other?
A. prophase I
B. prophase II
C. anaphase I
D. anaphase II

Answer
D

The part of meiosis that is similar to mitosis is ________.

A. meiosis I
B. anaphase I
C. meiosis II
D. interkinesis

Answer
C

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If a muscle cell of a typical organism has 32 chromosomes, how many chromosomes will be in a gamete of that same organism?
A. 8
B. 16
C. 32
D. 64

Answer
B

Free Response
Explain how the random alignment of homologous chromosomes during metaphase I contributes to variation in gametes produced
by meiosis.

Answer
Random alignment leads to new combinations of traits. The chromosomes that were originally inherited by the gamete-
producing individual came equally from the egg and the sperm. In metaphase I, the duplicated copies of these maternal and
paternal homologous chromosomes line up across the center of the cell to form a tetrad. The orientation of each tetrad is
random. There is an equal chance that the maternally derived chromosomes will be facing either pole. The same is true of the
paternally derived chromosomes. The alignment should occur differently in almost every meiosis. As the homologous
chromosomes are pulled apart in anaphase I, any combination of maternal and paternal chromosomes will move toward each
pole. The gametes formed from these two groups of chromosomes will have a mixture of traits from the individual’s parents.
Each gamete is unique.

In what ways is meiosis II similar to and different from mitosis of a diploid cell?

Answer
The two divisions are similar in that the chromosomes line up along the metaphase plate individually, meaning unpaired with
other chromosomes (as in meiosis I). In addition, each chromosome consists of two sister chromatids that will be pulled apart.
The two divisions are different because in meiosis II there are half the number of chromosomes that are present in a diploid cell
of the same species undergoing mitosis. This is because meiosis I reduced the number of chromosomes to a haploid state.

7.3: Errors in Meiosis

The number, size, shape, and banding pattern of chromosomes make them easily identifiable in a karyogram and allow for the
assessment of many chromosomal abnormalities. Disorders in chromosome number, or aneuploidies, are typically lethal to the
embryo, although a few trisomic genotypes are viable. Because of X inactivation, aberrations in sex chromosomes typically have
milder effects on an individual. Aneuploidies also include instances in which segments of a chromosome are duplicated or deleted.
Chromosome structures also may be rearranged, for example by inversion or translocation. Both of these aberrations can result in
negative effects on development, or death. Because they force chromosomes to assume contorted pairings during meiosis I,
inversions and translocations are often associated with reduced fertility because of the likelihood of nondisjunction.

Multiple Choice
The genotype XXY corresponds to:
A. Klinefelter syndrome
B. Turner syndrome
C. Triplo-X
D. Jacob syndrome

Answer
A

Abnormalities in the number of X chromosomes tend to be milder than the same abnormalities in autosomes because of ________.

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 A. deletions
B. nonhomologous recombination
C. synapsis
D. X inactivation

Answer
D

Aneuploidies are deleterious for the individual because of what phenomenon?

A. nondisjunction
B. gene dosage
C. meiotic errors
D. X inactivation

Answer
B

Free Response
Individuals with trisomy 21 are more likely to survive to adulthood than individuals with trisomy 18. Based on what you know
about aneuploidies from this module, what can you hypothesize about chromosomes 21 and 18?

Answer
The problems caused by trisomies arise because the genes on the chromosome that is present in three copies produce more
product than genes on chromosomes with only two copies. The cell does not have a way to adjust the amount of product, and
the lack of balance causes problems in development and the maintenance of the individual. Each chromosome is different, and
the differences in survivability could have to do with the numbers of genes on the two chromosomes. Chromosome 21 may be a
smaller chromosome, so there are fewer unbalanced gene products. It is also possible that chromosome 21 carries genes whose
products are less sensitive to differences in dosage than chromosome 18. The genes may be less involved in critical pathways,
or the differences in dosage may make less of a difference to those pathways.

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 CHAPTER OVERVIEW

5: DNA; DNA Technology

5.1: Molecular Biology
5.1.1: The Structure of DNA
5.1.2: DNA Replication
5.1.3: Transcription
5.1.4: Translation
5.1.5: How Genes Are Regulated
5.1.E: Molecular Biology (Exercises)
5.2: Biotechnology
5.2.1: Cloning and Genetic Engineering
5.2.2: Biotechnology in Medicine and Agriculture
5.2.3: Genomics and Proteomics
5.2.E: Biotechnology (Exercises)

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5: DNA; DNA Technology is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
 SECTION OVERVIEW

5.1: Molecular Biology

5.1.1: The Structure of DNA

5.1.2: DNA Replication

5.1.3: Transcription

5.1.4: Translation

5.1.5: How Genes Are Regulated

5.1.E: Molecular Biology (Exercises)

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5.1.1: The Structure of DNA
In the 1950s, Francis Crick and James Watson worked together at the University of Cambridge, England, to determine the structure
of DNA. Other scientists, such as Linus Pauling and Maurice Wilkins, were also actively exploring this field. Pauling had
discovered the secondary structure of proteins using X-ray crystallography. X-ray crystallography is a method for investigating
molecular structure by observing the patterns formed by X-rays shot through a crystal of the substance. The patterns give important
information about the structure of the molecule of interest. In Wilkins’ lab, researcher Rosalind Franklin was using X-ray
crystallography to understand the structure of DNA. Watson and Crick were able to piece together the puzzle of the DNA molecule
using Franklin's data (Figure [Link]). Watson and Crick also had key pieces of information available from other researchers such
as Chargaff’s rules. Chargaff had shown that of the four kinds of monomers (nucleotides) present in a DNA molecule, two types
were always present in equal amounts and the remaining two types were also always present in equal amounts. This meant they
were always paired in some way. In 1962, James Watson, Francis Crick, and Maurice Wilkins were awarded the Nobel Prize in
Medicine for their work in determining the structure of DNA.

Figure [Link]: Pioneering scientists (a) James Watson and Francis Crick are pictured here with American geneticist Maclyn
McCarty. Scientist Rosalind Franklin discovered (b) the X-ray diffraction pattern of DNA, which helped to elucidate its double
helix structure. (credit a: modification of work by Marjorie McCarty; b: modification of work by NIH)
Now let’s consider the structure of the two types of nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). The
building blocks of DNA are nucleotides, which are made up of three parts: a deoxyribose (5-carbon sugar), a phosphate group, and
a nitrogenous base (Figure [Link]). There are four types of nitrogenous bases in DNA. Adenine (A) and guanine (G) are double-
ringed purines, and cytosine (C) and thymine (T) are smaller, single-ringed pyrimidines. The nucleotide is named according to the
nitrogenous base it contains.

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 Figure [Link]: (a) Each DNA nucleotide is made up of a sugar, a phosphate group, and a base. (b) Cytosine and thymine are
pyrimidines. Guanine and adenine are purines.
The phosphate group of one nucleotide bonds covalently with the sugar molecule of the next nucleotide, and so on, forming a long
polymer of nucleotide monomers. The sugar–phosphate groups line up in a “backbone” for each single strand of DNA, and the
nucleotide bases stick out from this backbone. The carbon atoms of the five-carbon sugar are numbered clockwise from the oxygen
as 1', 2', 3', 4', and 5' (1' is read as “one prime”). The phosphate group is attached to the 5' carbon of one nucleotide and the 3'
carbon of the next nucleotide. In its natural state, each DNA molecule is actually composed of two single strands held together
along their length with hydrogen bonds between the bases.
Watson and Crick proposed that the DNA is made up of two strands that are twisted around each other to form a right-handed helix,
called a double helix. Base-pairing takes place between a purine and pyrimidine: namely, A pairs with T, and G pairs with C. In
other words, adenine and thymine are complementary base pairs, and cytosine and guanine are also complementary base pairs. This
is the basis for Chargaff’s rule; because of their complementarity, there is as much adenine as thymine in a DNA molecule and as
much guanine as cytosine. Adenine and thymine are connected by two hydrogen bonds, and cytosine and guanine are connected by
three hydrogen bonds. The two strands are anti-parallel in nature; that is, one strand will have the 3' carbon of the sugar in the
“upward” position, whereas the other strand will have the 5' carbon in the upward position. The diameter of the DNA double helix
is uniform throughout because a purine (two rings) always pairs with a pyrimidine (one ring) and their combined lengths are always
equal (Figure [Link]).

Figure [Link]: DNA (a) forms a double stranded helix, and (b) adenine pairs with thymine and cytosine pairs with guanine.
(credit a: modification of work by Jerome Walker, Dennis Myts)

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The Structure of RNA
There is a second nucleic acid in all cells called ribonucleic acid, or RNA. Like DNA, RNA is a polymer of nucleotides. Each of
the nucleotides in RNA is made up of a nitrogenous base, a five-carbon sugar, and a phosphate group. In the case of RNA, the five-
carbon sugar is ribose, not deoxyribose. Ribose has a hydroxyl group at the 2' carbon, unlike deoxyribose, which has only a
hydrogen atom (Figure [Link]).

Figure [Link]: The difference between the ribose found in RNA and the deoxyribose found in DNA is that ribose has a hydroxyl
group at the 2' carbon.
RNA nucleotides contain the nitrogenous bases adenine, cytosine, and guanine. However, they do not contain thymine, which is
instead replaced by uracil, symbolized by a “U.” RNA exists as a single-stranded molecule rather than a double-stranded helix.
Molecular biologists have named several kinds of RNA on the basis of their function. These include messenger RNA (mRNA),
transfer RNA (tRNA), and ribosomal RNA (rRNA)—molecules that are involved in the production of proteins from the DNA
code.

How DNA Is Arranged in the Cell

DNA is a working molecule; it must be replicated when a cell is ready to divide, and it must be “read” to produce the molecules,
such as proteins, to carry out the functions of the cell. For this reason, the DNA is protected and packaged in very specific ways. In
addition, DNA molecules can be very long. Stretched end-to-end, the DNA molecules in a single human cell would come to a
length of about 2 meters. Thus, the DNA for a cell must be packaged in a very ordered way to fit and function within a structure
(the cell) that is not visible to the naked eye. The chromosomes of prokaryotes are much simpler than those of eukaryotes in many
of their features (Figure [Link]). Most prokaryotes contain a single, circular chromosome that is found in an area in the cytoplasm
called the nucleoid.

Figure [Link]: A eukaryote contains a well-defined nucleus, whereas in prokaryotes, the chromosome lies in the cytoplasm in an
area called the nucleoid.
The size of the genome in one of the most well-studied prokaryotes, Escherichia coli, is 4.6 million base pairs, which would extend
a distance of about 1.6 mm if stretched out. So how does this fit inside a small bacterial cell? The DNA is twisted beyond the
double helix in what is known as supercoiling. Some proteins are known to be involved in the supercoiling; other proteins and
enzymes help in maintaining the supercoiled structure.
Eukaryotes, whose chromosomes each consist of a linear DNA molecule, employ a different type of packing strategy to fit their
DNA inside the nucleus (Figure [Link]). At the most basic level, DNA is wrapped around proteins known as histones to form
structures called nucleosomes. The DNA is wrapped tightly around the histone core. This nucleosome is linked to the next one by a
short strand of DNA that is free of histones. This is also known as the “beads on a string” structure; the nucleosomes are the

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“beads” and the short lengths of DNA between them are the “string.” The nucleosomes, with their DNA coiled around them, stack
compactly onto each other to form a 30-nm–wide fiber. This fiber is further coiled into a thicker and more compact structure. At the
metaphase stage of mitosis, when the chromosomes are lined up in the center of the cell, the chromosomes are at their most
compacted. They are approximately 700 nm in width, and are found in association with scaffold proteins.
In interphase, the phase of the cell cycle between mitoses at which the chromosomes are decondensed, eukaryotic chromosomes
have two distinct regions that can be distinguished by staining. There is a tightly packaged region that stains darkly, and a less
dense region. The darkly staining regions usually contain genes that are not active, and are found in the regions of the centromere
and telomeres. The lightly staining regions usually contain genes that are active, with DNA packaged around nucleosomes but not
further compacted.

Figure [Link]: These figures illustrate the compaction of the eukaryotic chromosome.

CONCEPT IN ACTION

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 How DNA is Packaged (Advanced)

Watch this animation of DNA packaging.

Summary

The model of the double-helix structure of DNA was proposed by Watson and Crick. The DNA molecule is a polymer of
nucleotides. Each nucleotide is composed of a nitrogenous base, a five-carbon sugar (deoxyribose), and a phosphate group. There
are four nitrogenous bases in DNA, two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). A DNA
molecule is composed of two strands. Each strand is composed of nucleotides bonded together covalently between the phosphate
group of one and the deoxyribose sugar of the next. From this backbone extend the bases. The bases of one strand bond to the bases
of the second strand with hydrogen bonds. Adenine always bonds with thymine, and cytosine always bonds with guanine. The
bonding causes the two strands to spiral around each other in a shape called a double helix. Ribonucleic acid (RNA) is a second
nucleic acid found in cells. RNA is a single-stranded polymer of nucleotides. It also differs from DNA in that it contains the sugar
ribose, rather than deoxyribose, and the nucleotide uracil rather than thymine. Various RNA molecules function in the process of
forming proteins from the genetic code in DNA.
Prokaryotes contain a single, double-stranded circular chromosome. Eukaryotes contain double-stranded linear DNA molecules
packaged into chromosomes. The DNA helix is wrapped around proteins to form nucleosomes. The protein coils are further coiled,
and during mitosis and meiosis, the chromosomes become even more greatly coiled to facilitate their movement. Chromosomes
have two distinct regions which can be distinguished by staining, reflecting different degrees of packaging and determined by
whether the DNA in a region is being expressed (euchromatin) or not (heterochromatin).

Glossary

deoxyribose
a five-carbon sugar molecule with a hydrogen atom rather than a hydroxyl group in the 2' position; the sugar component of
DNA nucleotides

double helix
the molecular shape of DNA in which two strands of nucleotides wind around each other in a spiral shape

nitrogenous base
a nitrogen-containing molecule that acts as a base; often referring to one of the purine or pyrimidine components of nucleic
acids

phosphate group
a molecular group consisting of a central phosphorus atom bound to four oxygen atoms

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]

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 e119a8aafbdd).

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9.1: The Structure of DNA by OpenStax is licensed CC BY 4.0.

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5.1.2: DNA Replication
When a cell divides, it is important that each daughter cell receives an identical copy of the DNA. This is accomplished by the
process of DNA replication. The replication of DNA occurs during the synthesis phase, or S phase, of the cell cycle, before the cell
enters mitosis or meiosis.
The elucidation of the structure of the double helix provided a hint as to how DNA is copied. Recall that adenine nucleotides pair
with thymine nucleotides, and cytosine with guanine. This means that the two strands are complementary to each other. For
example, a strand of DNA with a nucleotide sequence of AGTCATGA will have a complementary strand with the sequence
TCAGTACT (Figure [Link]).

Figure [Link]: The two strands of DNA are complementary, meaning the sequence of bases in one strand can be used to create
the correct sequence of bases in the other strand.
Because of the complementarity of the two strands, having one strand means that it is possible to recreate the other strand. This
model for replication suggests that the two strands of the double helix separate during replication, and each strand serves as a
template from which the new complementary strand is copied (Figure [Link]).

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 Figure [Link]: The semiconservative model of DNA replication is shown. Gray indicates the original DNA strands, and blue
indicates newly synthesized DNA.
During DNA replication, each of the two strands that make up the double helix serves as a template from which new strands are
copied. The new strand will be complementary to the parental or “old” strand. Each new double strand consists of one parental
strand and one new daughter strand. This is known as semiconservative replication. When two DNA copies are formed, they have
an identical sequence of nucleotide bases and are divided equally into two daughter cells.

DNA Replication in Eukaryotes

Because eukaryotic genomes are very complex, DNA replication is a very complicated process that involves several enzymes and
other proteins. It occurs in three main stages: initiation, elongation, and termination.
Recall that eukaryotic DNA is bound to proteins known as histones to form structures called nucleosomes. During initiation, the
DNA is made accessible to the proteins and enzymes involved in the replication process. How does the replication machinery know
where on the DNA double helix to begin? It turns out that there are specific nucleotide sequences called origins of replication at
which replication begins. Certain proteins bind to the origin of replication while an enzyme called helicase unwinds and opens up
the DNA helix. As the DNA opens up, Y-shaped structures called replication forks are formed (Figure [Link]). Two replication
forks are formed at the origin of replication, and these get extended in both directions as replication proceeds. There are multiple
origins of replication on the eukaryotic chromosome, such that replication can occur simultaneously from several places in the
genome.
During elongation, an enzyme called DNA polymerase adds DNA nucleotides to the 3' end of the template. Because DNA
polymerase can only add new nucleotides at the end of a backbone, a primer sequence, which provides this starting point, is added
with complementary RNA nucleotides. This primer is removed later, and the nucleotides are replaced with DNA nucleotides. One
strand, which is complementary to the parental DNA strand, is synthesized continuously toward the replication fork so the
polymerase can add nucleotides in this direction. This continuously synthesized strand is known as the leading strand. Because
DNA polymerase can only synthesize DNA in a 5' to 3' direction, the other new strand is put together in short pieces called
Okazaki fragments. The Okazaki fragments each require a primer made of RNA to start the synthesis. The strand with the Okazaki
fragments is known as the lagging strand. As synthesis proceeds, an enzyme removes the RNA primer, which is then replaced with
DNA nucleotides, and the gaps between fragments are sealed by an enzyme called DNA ligase.
The process of DNA replication can be summarized as follows:
1. DNA unwinds at the origin of replication.

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 2. New bases are added to the complementary parental strands. One new strand is made continuously, while the other strand is
made in pieces.
3. Primers are removed, new DNA nucleotides are put in place of the primers and the backbone is sealed by DNA ligase.

ART CONNECTION

Figure [Link]: A replication fork is formed by the opening of the origin of replication, and helicase separates the DNA
strands. An RNA primer is synthesized, and is elongated by the DNA polymerase. On the leading strand, DNA is synthesized
continuously, whereas on the lagging strand, DNA is synthesized in short stretches. The DNA fragments are joined by DNA
ligase (not shown).
You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation has
occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?

Telomere Replication
Because eukaryotic chromosomes are linear, DNA replication comes to the end of a line in eukaryotic chromosomes. As you have
learned, the DNA polymerase enzyme can add nucleotides in only one direction. In the leading strand, synthesis continues until the
end of the chromosome is reached; however, on the lagging strand there is no place for a primer to be made for the DNA fragment
to be copied at the end of the chromosome. This presents a problem for the cell because the ends remain unpaired, and over time
these ends get progressively shorter as cells continue to divide. The ends of the linear chromosomes are known as telomeres, which
have repetitive sequences that do not code for a particular gene. As a consequence, it is telomeres that are shortened with each
round of DNA replication instead of genes. For example, in humans, a six base-pair sequence, TTAGGG, is repeated 100 to 1000
times. The discovery of the enzyme telomerase (Figure [Link]) helped in the understanding of how chromosome ends are
maintained. The telomerase attaches to the end of the chromosome, and complementary bases to the RNA template are added on
the end of the DNA strand. Once the lagging strand template is sufficiently elongated, DNA polymerase can now add nucleotides
that are complementary to the ends of the chromosomes. Thus, the ends of the chromosomes are replicated.

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 Figure [Link]: The ends of linear chromosomes are maintained by the action of the telomerase enzyme.
Telomerase is typically found to be active in germ cells, adult stem cells, and some cancer cells. For her discovery of telomerase
and its action, Elizabeth Blackburn (Figure [Link]) received the Nobel Prize for Medicine and Physiology in 2009.

Figure [Link]: Elizabeth Blackburn, 2009 Nobel Laureate, was the scientist who discovered how telomerase works. (credit: U.S.
Embassy, Stockholm, Sweden)
Telomerase is not active in adult somatic cells. Adult somatic cells that undergo cell division continue to have their telomeres
shortened. This essentially means that telomere shortening is associated with aging. In 2010, scientists found that telomerase can
1
reverse some age-related conditions in mice, and this may have potential in regenerative medicine. Telomerase-deficient mice
were used in these studies; these mice have tissue atrophy, stem-cell depletion, organ system failure, and impaired tissue injury
responses. Telomerase reactivation in these mice caused extension of telomeres, reduced DNA damage, reversed
neurodegeneration, and improved functioning of the testes, spleen, and intestines. Thus, telomere reactivation may have potential
for treating age-related diseases in humans.

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DNA Replication in Prokaryotes
Recall that the prokaryotic chromosome is a circular molecule with a less extensive coiling structure than eukaryotic chromosomes.
The eukaryotic chromosome is linear and highly coiled around proteins. While there are many similarities in the DNA replication
process, these structural differences necessitate some differences in the DNA replication process in these two life forms.
DNA replication has been extremely well-studied in prokaryotes, primarily because of the small size of the genome and large
number of variants available. Escherichia coli has 4.6 million base pairs in a single circular chromosome, and all of it gets
replicated in approximately 42 minutes, starting from a single origin of replication and proceeding around the chromosome in both
directions. This means that approximately 1000 nucleotides are added per second. The process is much more rapid than in
eukaryotes. Table [Link] summarizes the differences between prokaryotic and eukaryotic replications.
Table [Link]: Differences between Prokaryotic and Eukaryotic Replications
Property Prokaryotes Eukaryotes

Origin of replication Single Multiple

Rate of replication 1000 nucleotides/s 50 to 100 nucleotides/s

Chromosome structure circular linear

Telomerase Not present Present

CONCEPT IN ACTION

DNA replication animation by interact …

Click through a tutorial on DNA replication.

DNA Repair
DNA polymerase can make mistakes while adding nucleotides. It edits the DNA by proofreading every newly added base.
Incorrect bases are removed and replaced by the correct base, and then polymerization continues (Figure 5.1.2.6a). Most mistakes
are corrected during replication, although when this does not happen, the mismatch repair mechanism is employed. Mismatch
repair enzymes recognize the wrongly incorporated base and excise it from the DNA, replacing it with the correct base (Figure
5.1.2.6b). In yet another type of repair, nucleotide excision repair, the DNA double strand is unwound and separated, the incorrect

bases are removed along with a few bases on the 5' and 3' end, and these are replaced by copying the template with the help of
DNA polymerase (Figure 5.1.2.6c). Nucleotide excision repair is particularly important in correcting thymine dimers, which are
primarily caused by ultraviolet light. In a thymine dimer, two thymine nucleotides adjacent to each other on one strand are
covalently bonded to each other rather than their complementary bases. If the dimer is not removed and repaired it will lead to a
mutation. Individuals with flaws in their nucleotide excision repair genes show extreme sensitivity to sunlight and develop skin
cancers early in life.

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 Figure [Link]: Proofreading by DNA polymerase (a) corrects errors during replication. In mismatch repair (b), the incorrectly
added base is detected after replication. The mismatch repair proteins detect this base and remove it from the newly synthesized
strand by nuclease action. The gap is now filled with the correctly paired base. Nucleotide excision (c) repairs thymine dimers.
When exposed to UV, thymines lying adjacent to each other can form thymine dimers. In normal cells, they are excised and
replaced.

Most mistakes are corrected; if they are not, they may result in a mutation—defined as a permanent change in the DNA sequence.
Mutations in repair genes may lead to serious consequences like cancer.

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Summary
DNA replicates by a semi-conservative method in which each of the two parental DNA strands act as a template for new DNA to
be synthesized. After replication, each DNA has one parental or “old” strand, and one daughter or “new” strand.
Replication in eukaryotes starts at multiple origins of replication, while replication in prokaryotes starts from a single origin of
replication. The DNA is opened with enzymes, resulting in the formation of the replication fork. Primase synthesizes an RNA
primer to initiate synthesis by DNA polymerase, which can add nucleotides in only one direction. One strand is synthesized
continuously in the direction of the replication fork; this is called the leading strand. The other strand is synthesized in a direction
away from the replication fork, in short stretches of DNA known as Okazaki fragments. This strand is known as the lagging strand.
Once replication is completed, the RNA primers are replaced by DNA nucleotides and the DNA is sealed with DNA ligase.
The ends of eukaryotic chromosomes pose a problem, as polymerase is unable to extend them without a primer. Telomerase, an
enzyme with an inbuilt RNA template, extends the ends by copying the RNA template and extending one end of the chromosome.
DNA polymerase can then extend the DNA using the primer. In this way, the ends of the chromosomes are protected. Cells have
mechanisms for repairing DNA when it becomes damaged or errors are made in replication. These mechanisms include mismatch
repair to replace nucleotides that are paired with a non-complementary base and nucleotide excision repair, which removes bases
that are damaged such as thymine dimers.

Art Connections
Figure [Link]: You isolate a cell strain in which the joining together of Okazaki fragments is impaired and suspect that a mutation
has occurred in an enzyme found at the replication fork. Which enzyme is most likely to be mutated?

Answer
Ligase, as this enzyme joins together Okazaki fragments.

Footnotes
1. 1 Mariella Jaskelioff, et al., “Telomerase reactivation reverses tissue degeneration in aged telomerase-deficient mice,” Nature,
469 (2011):102–7.

Glossary

DNA ligase
the enzyme that catalyzes the joining of DNA fragments together

DNA polymerase
an enzyme that synthesizes a new strand of DNA complementary to a template strand

helicase
an enzyme that helps to open up the DNA helix during DNA replication by breaking the hydrogen bonds

lagging strand
during replication of the 3' to 5' strand, the strand that is replicated in short fragments and away from the replication fork

leading strand
the strand that is synthesized continuously in the 5' to 3' direction that is synthesized in the direction of the replication fork

mismatch repair
a form of DNA repair in which non-complementary nucleotides are recognized, excised, and replaced with correct nucleotides

mutation
a permanent variation in the nucleotide sequence of a genome

nucleotide excision repair

a form of DNA repair in which the DNA molecule is unwound and separated in the region of the nucleotide damage, the
damaged nucleotides are removed and replaced with new nucleotides using the complementary strand, and the DNA strand is

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 resealed and allowed to rejoin its complement

Okazaki fragments
the DNA fragments that are synthesized in short stretches on the lagging strand

primer
a short stretch of RNA nucleotides that is required to initiate replication and allow DNA polymerase to bind and begin
replication

replication fork
the Y-shaped structure formed during the initiation of replication

semiconservative replication
the method used to replicate DNA in which the double-stranded molecule is separated and each strand acts as a template for a
new strand to be synthesized, so the resulting DNA molecules are composed of one new strand of nucleotides and one old
strand of nucleotides

telomerase
an enzyme that contains a catalytic part and an inbuilt RNA template; it functions to maintain telomeres at chromosome ends

telomere
the DNA at the end of linear chromosomes

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 5.1.2: DNA Replication is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
9.2: DNA Replication by OpenStax is licensed CC BY 4.0.

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5.1.3: Transcription
In both prokaryotes and eukaryotes, the second function of DNA (the first was replication) is to provide the information needed to
construct the proteins necessary so that the cell can perform all of its functions. To do this, the DNA is “read” or transcribed into an
mRNA molecule. The mRNA then provides the code to form a protein by a process called translation. Through the processes of
transcription and translation, a protein is built with a specific sequence of amino acids that was originally encoded in the DNA.
This module discusses the details of transcription.

The Central Dogma: DNA Encodes RNA; RNA Encodes Protein

The flow of genetic information in cells from DNA to mRNA to protein is described by the central dogma (Figure [Link]), which
states that genes specify the sequences of mRNAs, which in turn specify the sequences of proteins.

Figure [Link]: The central dogma states that DNA encodes RNA, which in turn encodes protein.
The copying of DNA to mRNA is relatively straightforward, with one nucleotide being added to the mRNA strand for every
complementary nucleotide read in the DNA strand. The translation to protein is more complex because groups of three mRNA
nucleotides correspond to one amino acid of the protein sequence. However, as we shall see in the next module, the translation to
protein is still systematic, such that nucleotides 1 to 3 correspond to amino acid 1, nucleotides 4 to 6 correspond to amino acid 2,
and so on.

Transcription: from DNA to mRNA

Both prokaryotes and eukaryotes perform fundamentally the same process of transcription, with the important difference of the
membrane-bound nucleus in eukaryotes. With the genes bound in the nucleus, transcription occurs in the nucleus of the cell and the
mRNA transcript must be transported to the cytoplasm. The prokaryotes, which include bacteria and archaea, lack membrane-
bound nuclei and other organelles, and transcription occurs in the cytoplasm of the cell. In both prokaryotes and eukaryotes,
transcription occurs in three main stages: initiation, elongation, and termination.

Initiation
Transcription requires the DNA double helix to partially unwind in the region of mRNA synthesis. The region of unwinding is
called a transcription bubble. The DNA sequence onto which the proteins and enzymes involved in transcription bind to initiate the
process is called a promoter. In most cases, promoters exist upstream of the genes they regulate. The specific sequence of a
promoter is very important because it determines whether the corresponding gene is transcribed all of the time, some of the time, or
hardly at all (Figure [Link]).

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 Figure [Link]: The initiation of transcription begins when DNA is unwound, forming a transcription bubble. Enzymes and other
proteins involved in transcription bind at the promoter.

Elongation
Transcription always proceeds from one of the two DNA strands, which is called the template strand. The mRNA product is
complementary to the template strand and is almost identical to the other DNA strand, called the nontemplate strand, with the
exception that RNA contains a uracil (U) in place of the thymine (T) found in DNA. During elongation, an enzyme called RNA
polymerase proceeds along the DNA template adding nucleotides by base pairing with the DNA template in a manner similar to
DNA replication, with the difference that an RNA strand is being synthesized that does not remain bound to the DNA template. As
elongation proceeds, the DNA is continuously unwound ahead of the core enzyme and rewound behind it (Figure [Link]).

Figure [Link]: During elongation, RNA polymerase tracks along the DNA template, synthesizes mRNA in the 5' to 3' direction,
and unwinds then rewinds the DNA as it is read.

Termination
Once a gene is transcribed, the prokaryotic polymerase needs to be instructed to dissociate from the DNA template and liberate the
newly made mRNA. Depending on the gene being transcribed, there are two kinds of termination signals, but both involve repeated
nucleotide sequences in the DNA template that result in RNA polymerase stalling, leaving the DNA template, and freeing the
mRNA transcript.
On termination, the process of transcription is complete. In a prokaryotic cell, by the time termination occurs, the transcript would
already have been used to partially synthesize numerous copies of the encoded protein because these processes can occur
concurrently using multiple ribosomes (polyribosomes) (Figure [Link]). In contrast, the presence of a nucleus in eukaryotic cells
precludes simultaneous transcription and translation.

Figure [Link]: Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the
mRNA transcripts into polypeptides. In this way, a specific protein can rapidly reach a high concentration in the bacterial cell.

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Eukaryotic RNA Processing
The newly transcribed eukaryotic mRNAs must undergo several processing steps before they can be transferred from the nucleus to
the cytoplasm and translated into a protein. The additional steps involved in eukaryotic mRNA maturation create a molecule that is
much more stable than a prokaryotic mRNA. For example, eukaryotic mRNAs last for several hours, whereas the typical
prokaryotic mRNA lasts no more than five seconds.
The mRNA transcript is first coated in RNA-stabilizing proteins to prevent it from degrading while it is processed and exported out
of the nucleus. This occurs while the pre-mRNA still is being synthesized by adding a special nucleotide “cap” to the 5' end of the
growing transcript. In addition to preventing degradation, factors involved in protein synthesis recognize the cap to help initiate
translation by ribosomes.
Once elongation is complete, an enzyme then adds a string of approximately 200 adenine residues to the 3' end, called the poly-A
tail. This modification further protects the pre-mRNA from degradation and signals to cellular factors that the transcript needs to be
exported to the cytoplasm.
Eukaryotic genes are composed of protein-coding sequences called exons (ex-on signifies that they are expressed) and intervening
sequences called introns (int-ron denotes their intervening role). Introns are removed from the pre-mRNA during processing. Intron
sequences in mRNA do not encode functional proteins. It is essential that all of a pre-mRNA’s introns be completely and precisely
removed before protein synthesis so that the exons join together to code for the correct amino acids. If the process errs by even a
single nucleotide, the sequence of the rejoined exons would be shifted, and the resulting protein would be nonfunctional. The
process of removing introns and reconnecting exons is called splicing (Figure [Link]). Introns are removed and degraded while the
pre-mRNA is still in the nucleus.

Figure [Link]: Eukaryotic mRNA contains introns that must be spliced out. A 5' cap and 3' tail are also added.
Summary
In prokaryotes, mRNA synthesis is initiated at a promoter sequence on the DNA template. Elongation synthesizes new mRNA.
Termination liberates the mRNA and occurs by mechanisms that stall the RNA polymerase and cause it to fall off the DNA
template. Newly transcribed eukaryotic mRNAs are modified with a cap and a poly-A tail. These structures protect the mature
mRNA from degradation and help export it from the nucleus. Eukaryotic mRNAs also undergo splicing, in which introns are
removed and exons are reconnected with single-nucleotide accuracy. Only finished mRNAs are exported from the nucleus to the
cytoplasm.
Glossary

exon
a sequence present in protein-coding mRNA after completion of pre-mRNA splicing

intron
non–protein-coding intervening sequences that are spliced from mRNA during processing

mRNA
messenger RNA; a form of RNA that carries the nucleotide sequence code for a protein sequence that is translated into a
polypeptide sequence

nontemplate strand

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 the strand of DNA that is not used to transcribe mRNA; this strand is identical to the mRNA except that T nucleotides in the
DNA are replaced by U nucleotides in the mRNA

promoter
a sequence on DNA to which RNA polymerase and associated factors bind and initiate transcription

RNA polymerase
an enzyme that synthesizes an RNA strand from a DNA template strand

splicing
the process of removing introns and reconnecting exons in a pre-mRNA

template strand
the strand of DNA that specifies the complementary mRNA molecule

transcription bubble
the region of locally unwound DNA that allows for transcription of mRNA

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 5.1.3: Transcription is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
9.3: Transcription by OpenStax is licensed CC BY 4.0.

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5.1.4: Translation
The synthesis of proteins is one of a cell’s most energy-consuming metabolic processes. In turn, proteins account for more mass
than any other component of living organisms (with the exception of water), and proteins perform a wide variety of the functions of
a cell. The process of translation, or protein synthesis, involves decoding an mRNA message into a polypeptide product. Amino
acids are covalently strung together in lengths ranging from approximately 50 amino acids to more than 1,000.

The Protein Synthesis Machinery

In addition to the mRNA template, many other molecules contribute to the process of translation. The composition of each
component may vary across species; for instance, ribosomes may consist of different numbers of ribosomal RNAs (rRNA) and
polypeptides depending on the organism. However, the general structures and functions of the protein synthesis machinery are
comparable from bacteria to human cells. Translation requires the input of an mRNA template, ribosomes, tRNAs, and various
enzymatic factors (Figure [Link]).

Figure [Link]: The protein synthesis machinery includes the large and small subunits of the ribosome, mRNA, and tRNA.
(credit: modification of work by NIGMS, NIH)
In E. coli, there are 200,000 ribosomes present in every cell at any given time. A ribosome is a complex macromolecule composed
of structural and catalytic rRNAs, and many distinct polypeptides. In eukaryotes, the nucleolus is completely specialized for the
synthesis and assembly of rRNAs.
Ribosomes are located in the cytoplasm in prokaryotes and in the cytoplasm and endoplasmic reticulum of eukaryotes. Ribosomes
are made up of a large and a small subunit that come together for translation. The small subunit is responsible for binding the
mRNA template, whereas the large subunit sequentially binds tRNAs, a type of RNA molecule that brings amino acids to the
growing chain of the polypeptide. Each mRNA molecule is simultaneously translated by many ribosomes, all synthesizing protein
in the same direction.
Depending on the species, 40 to 60 types of tRNA exist in the cytoplasm. Serving as adaptors, specific tRNAs bind to sequences on
the mRNA template and add the corresponding amino acid to the polypeptide chain. Therefore, tRNAs are the molecules that
actually “translate” the language of RNA into the language of proteins. For each tRNA to function, it must have its specific amino
acid bonded to it. In the process of tRNA “charging,” each tRNA molecule is bonded to its correct amino acid.

The Genetic Code

To summarize what we know to this point, the cellular process of transcription generates messenger RNA (mRNA), a mobile
molecular copy of one or more genes with an alphabet of A, C, G, and uracil (U). Translation of the mRNA template converts
nucleotide-based genetic information into a protein product. Protein sequences consist of 20 commonly occurring amino acids;
therefore, it can be said that the protein alphabet consists of 20 letters. Each amino acid is defined by a three-nucleotide sequence
called the triplet codon. The relationship between a nucleotide codon and its corresponding amino acid is called the genetic code.

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Given the different numbers of “letters” in the mRNA and protein “alphabets,” combinations of nucleotides corresponded to single
amino acids. Using a three-nucleotide code means that there are a total of 64 (4 × 4 × 4) possible combinations; therefore, a given
amino acid is encoded by more than one nucleotide triplet (Figure [Link]).

Figure [Link]: This figure shows the genetic code for translating each nucleotide triplet, or codon, in mRNA into an amino acid
or a termination signal in a nascent protein. (credit: modification of work by NIH)
Three of the 64 codons terminate protein synthesis and release the polypeptide from the translation machinery. These triplets are
called stop codons. Another codon, AUG, also has a special function. In addition to specifying the amino acid methionine, it also
serves as the start codon to initiate translation. The reading frame for translation is set by the AUG start codon near the 5' end of the
mRNA. The genetic code is universal. With a few exceptions, virtually all species use the same genetic code for protein synthesis,
which is powerful evidence that all life on Earth shares a common origin.

The Mechanism of Protein Synthesis

Just as with mRNA synthesis, protein synthesis can be divided into three phases: initiation, elongation, and termination. The
process of translation is similar in prokaryotes and eukaryotes. Here we will explore how translation occurs in E. coli, a
representative prokaryote, and specify any differences between prokaryotic and eukaryotic translation.
Protein synthesis begins with the formation of an initiation complex. In E. coli, this complex involves the small ribosome subunit,
the mRNA template, three initiation factors, and a special initiator tRNA. The initiator tRNA interacts with the AUG start codon,
and links to a special form of the amino acid methionine that is typically removed from the polypeptide after translation is
complete.
In prokaryotes and eukaryotes, the basics of polypeptide elongation are the same, so we will review elongation from the
perspective of E. coli. The large ribosomal subunit of E. coli consists of three compartments: the A site binds incoming charged
tRNAs (tRNAs with their attached specific amino acids). The P site binds charged tRNAs carrying amino acids that have formed
bonds with the growing polypeptide chain but have not yet dissociated from their corresponding tRNA. The E site releases
dissociated tRNAs so they can be recharged with free amino acids. The ribosome shifts one codon at a time, catalyzing each
process that occurs in the three sites. With each step, a charged tRNA enters the complex, the polypeptide becomes one amino acid
longer, and an uncharged tRNA departs. The energy for each bond between amino acids is derived from GTP, a molecule similar to
ATP (Figure [Link]). Amazingly, the E. coli translation apparatus takes only 0.05 seconds to add each amino acid, meaning that a
200-amino acid polypeptide could be translated in just 10 seconds.

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 Figure [Link]: Translation begins when a tRNA anticodon recognizes a codon on the mRNA. The large ribosomal subunit joins
the small subunit, and a second tRNA is recruited. As the mRNA moves relative to the ribosome, the polypeptide chain is formed.
Entry of a release factor into the A site terminates translation and the components dissociate.
Termination of translation occurs when a stop codon (UAA, UAG, or UGA) is encountered. When the ribosome encounters the
stop codon, the growing polypeptide is released and the ribosome subunits dissociate and leave the mRNA. After many ribosomes
have completed translation, the mRNA is degraded so the nucleotides can be reused in another transcription reaction.

CONCEPT IN ACTION

Transcribe a gene and translate it to protein using complementary pairing and the genetic code at this site.

Summary
The central dogma describes the flow of genetic information in the cell from genes to mRNA to proteins. Genes are used to make
mRNA by the process of transcription; mRNA is used to synthesize proteins by the process of translation. The genetic code is the
correspondence between the three-nucleotide mRNA codon and an amino acid. The genetic code is “translated” by the tRNA
molecules, which associate a specific codon with a specific amino acid. The genetic code is degenerate because 64 triplet codons in
mRNA specify only 20 amino acids and three stop codons. This means that more than one codon corresponds to an amino acid.
Almost every species on the planet uses the same genetic code.
The players in translation include the mRNA template, ribosomes, tRNAs, and various enzymatic factors. The small ribosomal
subunit binds to the mRNA template. Translation begins at the initiating AUG on the mRNA. The formation of bonds occurs

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between sequential amino acids specified by the mRNA template according to the genetic code. The ribosome accepts charged
tRNAs, and as it steps along the mRNA, it catalyzes bonding between the new amino acid and the end of the growing polypeptide.
The entire mRNA is translated in three-nucleotide “steps” of the ribosome. When a stop codon is encountered, a release factor
binds and dissociates the components and frees the new protein.

Glossary

codon
three consecutive nucleotides in mRNA that specify the addition of a specific amino acid or the release of a polypeptide chain
during translation

genetic code
the amino acids that correspond to three-nucleotide codons of mRNA

rRNA
ribosomal RNA; molecules of RNA that combine to form part of the ribosome

stop codon
one of the three mRNA codons that specifies termination of translation

start codon
the AUG (or, rarely GUG) on an mRNA from which translation begins; always specifies methionine

tRNA
transfer RNA; an RNA molecule that contains a specific three-nucleotide anticodon sequence to pair with the mRNA codon and
also binds to a specific amino acid

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 5.1.4: Translation is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
9.4: Translation by OpenStax is licensed CC BY 4.0.

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5.1.5: How Genes Are Regulated
For a cell to function properly, necessary proteins must be synthesized at the proper time. All organisms and cells control or
regulate the transcription and translation of their DNA into protein. The process of turning on a gene to produce RNA and protein
is called gene expression. Whether in a simple unicellular organism or in a complex multicellular organism, each cell controls when
and how its genes are expressed. For this to occur, there must be a mechanism to control when a gene is expressed to make RNA
and protein, how much of the protein is made, and when it is time to stop making that protein because it is no longer needed.
Cells in multicellular organisms are specialized; cells in different tissues look very different and perform different functions. For
example, a muscle cell is very different from a liver cell, which is very different from a skin cell. These differences are a
consequence of the expression of different sets of genes in each of these cells. All cells have certain basic functions they must
perform for themselves, such as converting the energy in sugar molecules into energy in ATP. Each cell also has many genes that
are not expressed, and expresses many that are not expressed by other cells, such that it can carry out its specialized functions. In
addition, cells will turn on or off certain genes at different times in response to changes in the environment or at different times
during the development of the organism. Unicellular organisms, both eukaryotic and prokaryotic, also turn on and off genes in
response to the demands of their environment so that they can respond to special conditions.
The control of gene expression is extremely complex. Malfunctions in this process are detrimental to the cell and can lead to the
development of many diseases, including cancer.

Prokaryotic versus Eukaryotic Gene Expression

To understand how gene expression is regulated, we must first understand how a gene becomes a functional protein in a cell. The
process occurs in both prokaryotic and eukaryotic cells, just in slightly different fashions.
Because prokaryotic organisms lack a cell nucleus, the processes of transcription and translation occur almost simultaneously.
When the protein is no longer needed, transcription stops. As a result, the primary method to control what type and how much
protein is expressed in a prokaryotic cell is through the regulation of DNA transcription into RNA. All the subsequent steps happen
automatically. When more protein is required, more transcription occurs. Therefore, in prokaryotic cells, the control of gene
expression is almost entirely at the transcriptional level.
The first example of such control was discovered using E. coli in the 1950s and 1960s by French researchers and is called the lac
operon. The lac operon is a stretch of DNA with three adjacent genes that code for proteins that participate in the absorption and
metabolism of lactose, a food source for E. coli. When lactose is not present in the bacterium’s environment, the lac genes are
transcribed in small amounts. When lactose is present, the genes are transcribed and the bacterium is able to use the lactose as a
food source. The operon also contains a promoter sequence to which the RNA polymerase binds to begin transcription; between the
promoter and the three genes is a region called the operator. When there is no lactose present, a protein known as a repressor binds
to the operator and prevents RNA polymerase from binding to the promoter, except in rare cases. Thus very little of the protein
products of the three genes is made. When lactose is present, an end product of lactose metabolism binds to the repressor protein
and prevents it from binding to the operator. This allows RNA polymerase to bind to the promoter and freely transcribe the three
genes, allowing the organism to metabolize the lactose.
Eukaryotic cells, in contrast, have intracellular organelles and are much more complex. Recall that in eukaryotic cells, the DNA is
contained inside the cell’s nucleus and it is transcribed into mRNA there. The newly synthesized mRNA is then transported out of
the nucleus into the cytoplasm, where ribosomes translate the mRNA into protein. The processes of transcription and translation are
physically separated by the nuclear membrane; transcription occurs only within the nucleus, and translation only occurs outside the
nucleus in the cytoplasm. The regulation of gene expression can occur at all stages of the process (Figure [Link]). Regulation may
occur when the DNA is uncoiled and loosened from nucleosomes to bind transcription factors (epigenetic level), when the RNA is
transcribed (transcriptional level), when RNA is processed and exported to the cytoplasm after it is transcribed (post-transcriptional
level), when the RNA is translated into protein (translational level), or after the protein has been made (post-translational level).

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 Figure [Link]: Eukaryotic gene expression is regulated during transcription and RNA processing, which take place in the
nucleus, as well as during protein translation, which takes place in the cytoplasm. Further regulation may occur through post-
translational modifications of proteins.
The differences in the regulation of gene expression between prokaryotes and eukaryotes are summarized in Table [Link].
Table [Link]: Differences in the Regulation of Gene Expression of Prokaryotic and Eukaryotic Organisms
Prokaryotic organisms Eukaryotic organisms

Lack nucleus Contain nucleus

RNA transcription occurs prior to protein translation, and it takes

place in the nucleus. RNA translation to protein occurs in the
RNA transcription and protein translation occur almost simultaneously cytoplasm.
RNA post-processing includes addition of a 5' cap, poly-A tail, and
excision of introns and splicing of exons.

Gene expression is regulated at many levels (epigenetic, transcriptional,

Gene expression is regulated primarily at the transcriptional level
post-transcriptional, translational, and post-translational)

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 EVOLUTION IN ACTION: Alternative RNA Splicing
In the 1970s, genes were first observed that exhibited alternative RNA splicing. Alternative RNA splicing is a mechanism that
allows different protein products to be produced from one gene when different combinations of introns (and sometimes exons)
are removed from the transcript (Figure [Link]). This alternative splicing can be haphazard, but more often it is controlled and
acts as a mechanism of gene regulation, with the frequency of different splicing alternatives controlled by the cell as a way to
control the production of different protein products in different cells, or at different stages of development. Alternative splicing
is now understood to be a common mechanism of gene regulation in eukaryotes; according to one estimate, 70% of genes in
humans are expressed as multiple proteins through alternative splicing.

Figure [Link]: There are five basic modes of alternative splicing. Segments of pre-mRNA with exons shown in blue, red,
orange, and pink can be spliced to produce a variety of new mature mRNA segments.
How could alternative splicing evolve? Introns have a beginning and ending recognition sequence, and it is easy to imagine the
failure of the splicing mechanism to identify the end of an intron and find the end of the next intron, thus removing two introns
and the intervening exon. In fact, there are mechanisms in place to prevent such exon skipping, but mutations are likely to lead
to their failure. Such “mistakes” would more than likely produce a nonfunctional protein. Indeed, the cause of many genetic
diseases is alternative splicing rather than mutations in a sequence. However, alternative splicing would create a protein variant
without the loss of the original protein, opening up possibilities for adaptation of the new variant to new functions. Gene
duplication has played an important role in the evolution of new functions in a similar way—by providing genes that may
evolve without eliminating the original functional protein.

Summary
While all somatic cells within an organism contain the same DNA, not all cells within that organism express the same proteins.
Prokaryotic organisms express the entire DNA they encode in every cell, but not necessarily all at the same time. Proteins are
expressed only when they are needed. Eukaryotic organisms express a subset of the DNA that is encoded in any given cell. In each
cell type, the type and amount of protein is regulated by controlling gene expression. To express a protein, the DNA is first

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transcribed into RNA, which is then translated into proteins. In prokaryotic cells, these processes occur almost simultaneously. In
eukaryotic cells, transcription occurs in the nucleus and is separate from the translation that occurs in the cytoplasm. Gene
expression in prokaryotes is regulated only at the transcriptional level, whereas in eukaryotic cells, gene expression is regulated at
the epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels.

Glossary

alternative RNA splicing

a post-transcriptional gene regulation mechanism in eukaryotes in which multiple protein products are produced by a single
gene through alternative splicing combinations of the RNA transcript

epigenetic
describing non-genetic regulatory factors, such as changes in modifications to histone proteins and DNA that control
accessibility to genes in chromosomes

gene expression
processes that control whether a gene is expressed

post-transcriptional
control of gene expression after the RNA molecule has been created but before it is translated into protein

post-translational
control of gene expression after a protein has been created

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 5.1.5: How Genes Are Regulated is shared under a not declared license and was authored, remixed, and/or curated by OpenStax.
9.5: How Genes Are Regulated by OpenStax is licensed CC BY 4.0.

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5.1.E: Molecular Biology (Exercises)
9.1: The Structure of DNA
Multiple Choice
Which of the following does cytosine pair with?
A. guanine
B. thymine
C. adenine
D. a pyrimidine

Answer
A

Prokaryotes contain a ________chromosome, and eukaryotes contain ________ chromosomes.

A. single-stranded circular; single-stranded linear
B. single-stranded linear; single-stranded circular
C. double-stranded circular; double-stranded linear
D. double-stranded linear; double-stranded circular

Answer
C

Free Response
Describe the organization of the eukaryotic chromosome.

Answer
The DNA is wound around proteins called histones. The histones then stack together in a compact form that creates a fiber that
is 30-nm thick. The fiber is further coiled for greater compactness. During metaphase of mitosis, the chromosome is at its most
compact to facilitate chromosome movement. During interphase, there are denser areas of chromatin, called heterochromatin,
that contain DNA that is not expressed, and less dense euchromatin that contains DNA that is expressed.

Describe the structure and complementary base pairing of DNA.

Answer
A single strand of DNA is a polymer of nucleic acids joined covalently between the phosphate group of one and the
deoxyribose sugar of the next to form a “backbone” from which the nitrogenous bases stick out. In its natural state, DNA has
two strands wound around each other in a double helix. The bases on each strand are bonded to each other with hydrogen
bonds. Only specific bases bond with each other; adenine bonds with thymine, and cytosine bonds with guanine.

9.2: DNA Replication

Multiple Choice
DNA replicates by which of the following models?
A. conservative
B. semiconservative
C. dispersive
D. none of the above

Answer
B

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The initial mechanism for repairing nucleotide errors in DNA is ________.
A. mismatch repair
B. DNA polymerase proofreading
C. nucleotide excision repair
D. thymine dimers

Answer
B

Free Response
How do the linear chromosomes in eukaryotes ensure that its ends are replicated completely?

Answer
Telomerase has an inbuilt RNA template that extends the 3' end, so a primer is synthesized and extended. Thus, the ends are
protected.

9.3: Transcription
Multiple Choice
A promoter is ________.
A. a specific sequence of DNA nucleotides
B. a specific sequence of RNA nucleotides
C. a protein that binds to DNA
D. an enzyme that synthesizes RNA

Answer
A

Portions of eukaryotic mRNA sequence that are removed during RNA processing are ________.
A. exons
B. caps
C. poly-A tails
D. introns

Answer
D

9.4: Translation
Multiple Choice
The RNA components of ribosomes are synthesized in the ________.
A. cytoplasm
B. nucleus
C. nucleolus
D. endoplasmic reticulum

Answer
C

How long would the peptide be that is translated from this MRNA sequence: 5'-AUGGGCUACCGA-3'?
A. 0
B. 2

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 C. 3
D. 4

Answer
D

Free Response
Transcribe and translate the following DNA sequence (nontemplate strand): 5'-ATGGCCGGTTATTAAGCA-3'

Answer
The mRNA would be: 5'-AUGGCCGGUUAUUAAGCA-3'. The protein would be: MAGY. Even though there are six codons,
the fifth codon corresponds to a stop, so the sixth codon would not be translated.

9.5: How Genes Are Regulated

Multiple Choice
Control of gene expression in eukaryotic cells occurs at which level(s)?
A. only the transcriptional level
B. epigenetic and transcriptional levels
C. epigenetic, transcriptional, and translational levels
D. epigenetic, transcriptional, post-transcriptional, translational, and post-translational levels

Answer
D

Post-translational control refers to:

A. regulation of gene expression after transcription
B. regulation of gene expression after translation
C. control of epigenetic activation
D. period between transcription and translation

Answer
B

Free Response
Describe how controlling gene expression will alter the overall protein levels in the cell.

Answer
The cell controls which protein is expressed, and to what level that protein is expressed, in the cell. Prokaryotic cells alter the
transcription rate to turn genes on or off. This method will increase or decrease protein levels in response to what is needed by
the cell. Eukaryotic cells change the accessibility (epigenetic), transcription, or translation of a gene. This will alter the amount
of RNA, and the lifespan of the RNA, to alter the amount of protein that exists. Eukaryotic cells also change the protein’s
translation to increase or decrease its overall levels. Eukaryotic organisms are much more complex and can manipulate protein
levels by changing many stages in the process.

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 SECTION OVERVIEW

5.2: Biotechnology
5.2.1: Cloning and Genetic Engineering

5.2.2: Biotechnology in Medicine and Agriculture

5.2.3: Genomics and Proteomics

5.2.E: Biotechnology (Exercises)

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5.2.1: Cloning and Genetic Engineering
Biotechnology is the use of artificial methods to modify the genetic material of living organisms or cells to produce novel
compounds or to perform new functions. Biotechnology has been used for improving livestock and crops since the beginning of
agriculture through selective breeding. Since the discovery of the structure of DNA in 1953, and particularly since the development
of tools and methods to manipulate DNA in the 1970s, biotechnology has become synonymous with the manipulation of
organisms’ DNA at the molecular level. The primary applications of this technology are in medicine (for the production of vaccines
and antibiotics) and in agriculture (for the genetic modification of crops). Biotechnology also has many industrial applications,
such as fermentation, the treatment of oil spills, and the production of biofuels, as well as many household applications such as the
use of enzymes in laundry detergent.

Manipulating Genetic Material

To accomplish the applications described above, biotechnologists must be able to extract, manipulate, and analyze nucleic acids.

Review of Nucleic Acid Structure

To understand the basic techniques used to work with nucleic acids, remember that nucleic acids are macromolecules made of
nucleotides (a sugar, a phosphate, and a nitrogenous base). The phosphate groups on these molecules each have a net negative
charge. An entire set of DNA molecules in the nucleus of eukaryotic organisms is called the genome. DNA has two complementary
strands linked by hydrogen bonds between the paired bases.
Unlike DNA in eukaryotic cells, RNA molecules leave the nucleus. Messenger RNA (mRNA) is analyzed most frequently because
it represents the protein-coding genes that are being expressed in the cell.

Isolation of Nucleic Acids

To study or manipulate nucleic acids, the DNA must first be extracted from cells. Various techniques are used to extract different
types of DNA (Figure [Link]). Most nucleic acid extraction techniques involve steps to break open the cell, and then the use of
enzymatic reactions to destroy all undesired macromolecules. Cells are broken open using a detergent solution containing buffering
compounds. To prevent degradation and contamination, macromolecules such as proteins and RNA are inactivated using enzymes.
The DNA is then brought out of solution using alcohol. The resulting DNA, because it is made up of long polymers, forms a
gelatinous mass.

Figure [Link]: This diagram shows the basic method used for the extraction of DNA.
RNA is studied to understand gene expression patterns in cells. RNA is naturally very unstable because enzymes that break down
RNA are commonly present in nature. Some are even secreted by our own skin and are very difficult to inactivate. Similar to DNA
extraction, RNA extraction involves the use of various buffers and enzymes to inactivate other macromolecules and preserve only
the RNA.

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Gel Electrophoresis
Because nucleic acids are negatively charged ions at neutral or alkaline pH in an aqueous environment, they can be moved by an
electric field. Gel electrophoresis is a technique used to separate charged molecules on the basis of size and charge. The nucleic
acids can be separated as whole chromosomes or as fragments. The nucleic acids are loaded into a slot at one end of a gel matrix,
an electric current is applied, and negatively charged molecules are pulled toward the opposite end of the gel (the end with the
positive electrode). Smaller molecules move through the pores in the gel faster than larger molecules; this difference in the rate of
migration separates the fragments on the basis of size. The nucleic acids in a gel matrix are invisible until they are stained with a
compound that allows them to be seen, such as a dye. Distinct fragments of nucleic acids appear as bands at specific distances from
the top of the gel (the negative electrode end) that are based on their size (Figure [Link]). A mixture of many fragments of varying
sizes appear as a long smear, whereas uncut genomic DNA is usually too large to run through the gel and forms a single large band
at the top of the gel.

Figure [Link]: Shown are DNA fragments from six samples run on a gel, stained with a fluorescent dye and viewed under UV
light. (credit: modification of work by James Jacob, Tompkins Cortland Community College)

Polymerase Chain Reaction

DNA analysis often requires focusing on one or more specific regions of the genome. It also frequently involves situations in which
only one or a few copies of a DNA molecule are available for further analysis. These amounts are insufficient for most procedures,
such as gel electrophoresis. Polymerase chain reaction (PCR)is a technique used to rapidly increase the number of copies of
specific regions of DNA for further analyses (Figure [Link]). PCR uses a special form of DNA polymerase, the enzyme that
replicates DNA, and other short nucleotide sequences called primers that base pair to a specific portion of the DNA being
replicated. PCR is used for many purposes in laboratories. These include: 1) the identification of the owner of a DNA sample left at
a crime scene; 2) paternity analysis; 3) the comparison of small amounts of ancient DNA with modern organisms; and 4)
determining the sequence of nucleotides in a specific region.

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 Figure [Link]: Polymerase chain reaction, or PCR, is used to produce many copies of a specific sequence of DNA using a
special form of DNA polymerase.

Cloning
In general, cloning means the creation of a perfect replica. Typically, the word is used to describe the creation of a genetically
identical copy. In biology, the re-creation of a whole organism is referred to as “reproductive cloning.” Long before attempts were
made to clone an entire organism, researchers learned how to copy short stretches of DNA—a process that is referred to as
molecular cloning.

Molecular Cloning
Cloning allows for the creation of multiple copies of genes, expression of genes, and study of specific genes. To get the DNA
fragment into a bacterial cell in a form that will be copied or expressed, the fragment is first inserted into a plasmid. A plasmid
(also called a vector in this context) is a small circular DNA molecule that replicates independently of the chromosomal DNA in
bacteria. In cloning, the plasmid molecules can be used to provide a "vehicle" in which to insert a desired DNA fragment. Modified
plasmids are usually reintroduced into a bacterial host for replication. As the bacteria divide, they copy their own DNA (including
the plasmids). The inserted DNA fragment is copied along with the rest of the bacterial DNA. In a bacterial cell, the fragment of
DNA from the human genome (or another organism that is being studied) is referred to as foreign DNA to differentiate it from the
DNA of the bacterium (the host DNA).
Plasmids occur naturally in bacterial populations (such as Escherichia coli) and have genes that can contribute favorable traits to
the organism, such as antibiotic resistance (the ability to be unaffected by antibiotics). Plasmids have been highly engineered as
vectors for molecular cloning and for the subsequent large-scale production of important molecules, such as insulin. A valuable
characteristic of plasmid vectors is the ease with which a foreign DNA fragment can be introduced. These plasmid vectors contain
many short DNA sequences that can be cut with different commonly available restriction enzymes. Restriction enzymes (also
called restriction endonucleases) recognize specific DNA sequences and cut them in a predictable manner; they are naturally
produced by bacteria as a defense mechanism against foreign DNA. Many restriction enzymes make staggered cuts in the two

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strands of DNA, such that the cut ends have a 2- to 4-nucleotide single-stranded overhang. The sequence that is recognized by the
restriction enzyme is a four- to eight-nucleotide sequence that is a palindrome. Like with a word palindrome, this means the
sequence reads the same forward and backward. In most cases, the sequence reads the same forward on one strand and backward
on the complementary strand. When a staggered cut is made in a sequence like this, the overhangs are complementary (Figure
[Link]).

Figure [Link]: In this (a) six-nucleotide restriction enzyme recognition site, notice that the sequence of six nucleotides reads the
same in the 5' to 3' direction on one strand as it does in the 5' to 3' direction on the complementary strand. This is known as a
palindrome. (b) The restriction enzyme makes breaks in the DNA strands, and (c) the cut in the DNA results in “sticky ends”.
Another piece of DNA cut on either end by the same restriction enzyme could attach to these sticky ends and be inserted into the
gap made by this cut.
Because these overhangs are capable of coming back together by hydrogen bonding with complementary overhangs on a piece of
DNA cut with the same restriction enzyme, these are called “sticky ends.” The process of forming hydrogen bonds between
complementary sequences on single strands to form double-stranded DNA is called annealing. Addition of an enzyme called DNA
ligase, which takes part in DNA replication in cells, permanently joins the DNA fragments when the sticky ends come together. In
this way, any DNA fragment can be spliced between the two ends of a plasmid DNA that has been cut with the same restriction
enzyme (Figure [Link]).

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 Figure [Link]: This diagram shows the steps involved in molecular cloning.
Plasmids with foreign DNA inserted into them are called recombinant DNA molecules because they contain new combinations of
genetic material. Proteins that are produced from recombinant DNA molecules are called recombinant proteins. Not all
recombinant plasmids are capable of expressing genes. Plasmids may also be engineered to express proteins only when stimulated
by certain environmental factors, so that scientists can control the expression of the recombinant proteins.

Reproductive Cloning
Reproductive cloning is a method used to make a clone or an identical copy of an entire multicellular organism. Most multicellular
organisms undergo reproduction by sexual means, which involves the contribution of DNA from two individuals (parents), making
it impossible to generate an identical copy or a clone of either parent. Recent advances in biotechnology have made it possible to
reproductively clone mammals in the laboratory.

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Natural sexual reproduction involves the union, during fertilization, of a sperm and an egg. Each of these gametes is haploid,
meaning they contain one set of chromosomes in their nuclei. The resulting cell, or zygote, is then diploid and contains two sets of
chromosomes. This cell divides mitotically to produce a multicellular organism. However, the union of just any two cells cannot
produce a viable zygote; there are components in the cytoplasm of the egg cell that are essential for the early development of the
embryo during its first few cell divisions. Without these provisions, there would be no subsequent development. Therefore, to
produce a new individual, both a diploid genetic complement and an egg cytoplasm are required. The approach to producing an
artificially cloned individual is to take the egg cell of one individual and to remove the haploid nucleus. Then a diploid nucleus
from a body cell of a second individual, the donor, is put into the egg cell. The egg is then stimulated to divide so that development
proceeds. This sounds simple, but in fact it takes many attempts before each of the steps is completed successfully.
The first cloned agricultural animal was Dolly, a sheep who was born in 1996. The success rate of reproductive cloning at the time
was very low. Dolly lived for six years and died of a lung tumor (Figure [Link]). There was speculation that because the cell DNA
that gave rise to Dolly came from an older individual, the age of the DNA may have affected her life expectancy. Since Dolly,
several species of animals (such as horses, bulls, and goats) have been successfully cloned.
There have been attempts at producing cloned human embryos as sources of embryonic stem cells. In the procedure, the DNA from
an adult human is introduced into a human egg cell, which is then stimulated to divide. The technology is similar to the technology
that was used to produce Dolly, but the embryo is never implanted into a surrogate mother. The cells produced are called
embryonic stem cells because they have the capacity to develop into many different kinds of cells, such as muscle or nerve cells.
The stem cells could be used to research and ultimately provide therapeutic applications, such as replacing damaged tissues. The
benefit of cloning in this instance is that the cells used to regenerate new tissues would be a perfect match to the donor of the
original DNA. For example, a leukemia patient would not require a sibling with a tissue match for a bone-marrow transplant.

ART CONNECTION

Figure [Link]: Dolly the sheep was the first agricultural animal to be cloned. To create Dolly, the nucleus was removed from
a donor egg cell. The enucleated egg was placed next to the other cell, then they were shocked to fuse. They were shocked
again to start division. The cells were allowed to divide for several days until an early embryonic stage was reached, before
being implanted in a surrogate mother.
Why was Dolly a Finn-Dorset and not a Scottish Blackface sheep?

Genetic Engineering
Using recombinant DNA technology to modify an organism’s DNA to achieve desirable traits is called genetic engineering.
Addition of foreign DNA in the form of recombinant DNA vectors that are generated by molecular cloning is the most common
method of genetic engineering. An organism that receives the recombinant DNA is called a genetically modified organism (GMO).
If the foreign DNA that is introduced comes from a different species, the host organism is called transgenic. Bacteria, plants, and
animals have been genetically modified since the early 1970s for academic, medical, agricultural, and industrial purposes. These
applications will be examined in more detail in the next module.

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 CONCEPT IN ACTION

Watch this short video explaining how scientists create a transgenic animal.

Although the classic methods of studying the function of genes began with a given phenotype and determined the genetic basis of
that phenotype, modern techniques allow researchers to start at the DNA sequence level and ask: "What does this gene or DNA
element do?" This technique, called reverse genetics, has resulted in reversing the classical genetic methodology. One example of
this method is analogous to damaging a body part to determine its function. An insect that loses a wing cannot fly, which means
that the wing’s function is flight. The classic genetic method compares insects that cannot fly with insects that can fly, and observes
that the non-flying insects have lost wings. Similarly in a reverse genetics approach, mutating or deleting genes provides
researchers with clues about gene function. Alternately, reverse genetics can be used to cause a gene to overexpress itself to
determine what phenotypic effects may occur.

Summary
Nucleic acids can be isolated from cells for the purposes of further analysis by breaking open the cells and enzymatically
destroying all other major macromolecules. Fragmented or whole chromosomes can be separated on the basis of size by gel
electrophoresis. Short stretches of DNA can be amplified by PCR. DNA can be cut (and subsequently re-spliced together) using
restriction enzymes. The molecular and cellular techniques of biotechnology allow researchers to genetically engineer organisms,
modifying them to achieve desirable traits.
Cloning may involve cloning small DNA fragments (molecular cloning), or cloning entire organisms (reproductive cloning). In
molecular cloning with bacteria, a desired DNA fragment is inserted into a bacterial plasmid using restriction enzymes and the
plasmid is taken up by a bacterium, which will then express the foreign DNA. Using other techniques, foreign genes can be
inserted into eukaryotic organisms. In each case, the organisms are called transgenic organisms. In reproductive cloning, a donor
nucleus is put into an enucleated egg cell, which is then stimulated to divide and develop into an organism.
In reverse genetics methods, a gene is mutated or removed in some way to identify its effect on the phenotype of the whole
organism as a way to determine its function.

Art Connections
Figure [Link]: Why was Dolly a Finn-Dorset and not a Scottish Blackface sheep?

Answer
Because even though the original cell came from a Scottish Blackface sheep and the surrogate mother was a Scottish Blackface,
the DNA came from a Finn-Dorset.

Glossary

anneal
in molecular biology, the process by which two single strands of DNA hydrogen bond at complementary nucleotides to form a
double-stranded molecule

biotechnology
the use of artificial methods to modify the genetic material of living organisms or cells to produce novel compounds or to
perform new functions

cloning
the production of an exact copy—specifically, an exact genetic copy—of a gene, cell, or organism

gel electrophoresis

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 a technique used to separate molecules on the basis of their ability to migrate through a semisolid gel in response to an electric
current

genetic engineering
alteration of the genetic makeup of an organism using the molecular methods of biotechnology

genetically modified organism (GMO)

an organism whose genome has been artificially changed

plasmid
a small circular molecule of DNA found in bacteria that replicates independently of the main bacterial chromosome; plasmids
code for some important traits for bacteria and can be used as vectors to transport DNA into bacteria in genetic engineering
applications

polymerase chain reaction (PCR)

a technique used to make multiple copies of DNA

recombinant DNA
a combination of DNA fragments generated by molecular cloning that does not exist in nature

recombinant protein
a protein that is expressed from recombinant DNA molecules

restriction enzyme
an enzyme that recognizes a specific nucleotide sequence in DNA and cuts the DNA double strand at that recognition site, often
with a staggered cut leaving short single strands or “sticky” ends

reverse genetics
a form of genetic analysis that manipulates DNA to disrupt or affect the product of a gene to analyze the gene’s function

reproductive cloning
cloning of entire organisms

transgenic
describing an organism that receives DNA from a different species

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 5.2.1: Cloning and Genetic Engineering is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
10.1: Cloning and Genetic Engineering by OpenStax is licensed CC BY 4.0.

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5.2.2: Biotechnology in Medicine and Agriculture
It is easy to see how biotechnology can be used for medicinal purposes. Knowledge of the genetic makeup of our species, the
genetic basis of heritable diseases, and the invention of technology to manipulate and fix mutant genes provides methods to treat
diseases. Biotechnology in agriculture can enhance resistance to disease, pests, and environmental stress to improve both crop yield
and quality.

Genetic Diagnosis and Gene Therapy

The process of testing for suspected genetic defects before administering treatment is called genetic diagnosis by genetic testing. In
some cases in which a genetic disease is present in an individual’s family, family members may be advised to undergo genetic
testing. For example, mutations in the BRCA genes may increase the likelihood of developing breast and ovarian cancers in women
and some other cancers in women and men. A woman with breast cancer can be screened for these mutations. If one of the high-
risk mutations is found, her female relatives may also wish to be screened for that particular mutation, or simply be more vigilant
for the occurrence of cancers. Genetic testing is also offered for fetuses (or embryos with in vitro fertilization) to determine the
presence or absence of disease-causing genes in families with specific debilitating diseases.

CONCEPT IN ACTION

See how human DNA is extracted for uses such as genetic testing.

Gene therapy is a genetic engineering technique that may one day be used to cure certain genetic diseases. In its simplest form, it
involves the introduction of a non-mutated gene at a random location in the genome to cure a disease by replacing a protein that
may be absent in these individuals because of a genetic mutation. The non-mutated gene is usually introduced into diseased cells as
part of a vector transmitted by a virus, such as an adenovirus, that can infect the host cell and deliver the foreign DNA into the
genome of the targeted cell (Figure [Link]). To date, gene therapies have been primarily experimental procedures in humans. A
few of these experimental treatments have been successful, but the methods may be important in the future as the factors limiting
its success are resolved.

Figure [Link]: This diagram shows the steps involved in curing disease with gene therapy using an adenovirus vector. (credit:
modification of work by NIH)

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Production of Vaccines, Antibiotics, and Hormones
Traditional vaccination strategies use weakened or inactive forms of microorganisms or viruses to stimulate the immune system.
Modern techniques use specific genes of microorganisms cloned into vectors and mass-produced in bacteria to make large
quantities of specific substances to stimulate the immune system. The substance is then used as a vaccine. In some cases, such as
the H1N1 flu vaccine, genes cloned from the virus have been used to combat the constantly changing strains of this virus.
Antibiotics kill bacteria and are naturally produced by microorganisms such as fungi; penicillin is perhaps the most well-known
example. Antibiotics are produced on a large scale by cultivating and manipulating fungal cells. The fungal cells have typically
been genetically modified to improve the yields of the antibiotic compound.
Recombinant DNA technology was used to produce large-scale quantities of the human hormone insulin in E. coli as early as 1978.
Previously, it was only possible to treat diabetes with pig insulin, which caused allergic reactions in many humans because of
differences in the insulin molecule. In addition, human growth hormone (HGH) is used to treat growth disorders in children. The
HGH gene was cloned from a cDNA (complementary DNA) library and inserted into E. coli cells by cloning it into a bacterial
vector.

Transgenic Animals
Although several recombinant proteins used in medicine are successfully produced in bacteria, some proteins need a eukaryotic
animal host for proper processing. For this reason, genes have been cloned and expressed in animals such as sheep, goats, chickens,
and mice. Animals that have been modified to express recombinant DNA are called transgenic animals (Figure [Link]).

Figure [Link]: It can be seen that two of these mice are transgenic because they have a gene that causes them to fluoresce under
a UV light. The non-transgenic mouse does not have the gene that causes fluorescence. (credit: Ingrid Moen et al.)
Several human proteins are expressed in the milk of transgenic sheep and goats. In one commercial example, the FDA has
approved a blood anticoagulant protein that is produced in the milk of transgenic goats for use in humans. Mice have been used
extensively for expressing and studying the effects of recombinant genes and mutations.

Transgenic Plants
Manipulating the DNA of plants (creating genetically modified organisms, or GMOs) has helped to create desirable traits such as
disease resistance, herbicide, and pest resistance, better nutritional value, and better shelf life (Figure [Link]). Plants are the most
important source of food for the human population. Farmers developed ways to select for plant varieties with desirable traits long
before modern-day biotechnology practices were established.

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 Figure [Link]: Corn, a major agricultural crop used to create products for a variety of industries, is often modified through plant
biotechnology. (credit: Keith Weller, USDA)
Transgenic plants have received DNA from other species. Because they contain unique combinations of genes and are not restricted
to the laboratory, transgenic plants and other GMOs are closely monitored by government agencies to ensure that they are fit for
human consumption and do not endanger other plant and animal life. Because foreign genes can spread to other species in the
environment, particularly in the pollen and seeds of plants, extensive testing is required to ensure ecological stability. Staples like
corn, potatoes, and tomatoes were the first crop plants to be genetically engineered.

Transformation of Plants Using Agrobacterium tumefaciens

In plants, tumors caused by the bacterium Agrobacterium tumefaciens occur by transfer of DNA from the bacterium to the plant.
The artificial introduction of DNA into plant cells is more challenging than in animal cells because of the thick plant cell wall.
Researchers used the natural transfer of DNA from Agrobacterium to a plant host to introduce DNA fragments of their choice into
plant hosts. In nature, the disease-causing A. tumefaciens have a set of plasmids that contain genes that integrate into the infected
plant cell’s genome. Researchers manipulate the plasmids to carry the desired DNA fragment and insert it into the plant genome.

The Organic Insecticide Bacillus thuringiensis

Bacillus thuringiensis (Bt) is a bacterium that produces protein crystals that are toxic to many insect species that feed on plants.
Insects that have eaten Bt toxin stop feeding on the plants within a few hours. After the toxin is activated in the intestines of the
insects, death occurs within a couple of days. The crystal toxin genes have been cloned from the bacterium and introduced into
plants, therefore allowing plants to produce their own crystal Bt toxin that acts against insects. Bt toxin is safe for the environment
and non-toxic to mammals (including humans). As a result, it has been approved for use by organic farmers as a natural insecticide.
There is some concern, however, that insects may evolve resistance to the Bt toxin in the same way that bacteria evolve resistance
to antibiotics.

FlavrSavr Tomato
The first GM crop to be introduced into the market was the FlavrSavr Tomato produced in 1994. Molecular genetic technology was
used to slow down the process of softening and rotting caused by fungal infections, which led to increased shelf life of the GM
tomatoes. Additional genetic modification improved the flavor of this tomato. The FlavrSavr tomato did not successfully stay in the
market because of problems maintaining and shipping the crop.

Summary
Genetic testing is performed to identify disease-causing genes, and can be used to benefit affected individuals and their relatives
who have not developed disease symptoms yet. Gene therapy—by which functioning genes are incorporated into the genomes of
individuals with a non-functioning mutant gene—has the potential to cure heritable diseases. Transgenic organisms possess DNA

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from a different species, usually generated by molecular cloning techniques. Vaccines, antibiotics, and hormones are examples of
products obtained by recombinant DNA technology. Transgenic animals have been created for experimental purposes and some are
used to produce some human proteins.
Genes are inserted into plants, using plasmids in the bacterium Agrobacterium tumefaciens, which infects plants. Transgenic plants
have been created to improve the characteristics of crop plants—for example, by giving them insect resistance by inserting a gene
for a bacterial toxin.

Glossary

gene therapy
the technique used to cure heritable diseases by replacing mutant genes with good genes

genetic testing
identifying gene variants in an individual that may lead to a genetic disease in that individual

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 5.2.2: Biotechnology in Medicine and Agriculture is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
10.2: Biotechnology in Medicine and Agriculture by OpenStax is licensed CC BY 4.0.

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5.2.3: Genomics and Proteomics
The study of nucleic acids began with the discovery of DNA, progressed to the study of genes and small fragments, and has now
exploded to the field of genomics. Genomics is the study of entire genomes, including the complete set of genes, their nucleotide
sequence and organization, and their interactions within a species and with other species. The advances in genomics have been
made possible by DNA sequencing technology. Just as information technology has led to Google Maps that enable us to get
detailed information about locations around the globe, genomic information is used to create similar maps of the DNA of different
organisms.

Mapping Genomes
Genome mapping is the process of finding the location of genes on each chromosome. The maps that are created are comparable to
the maps that we use to navigate streets. A genetic map is an illustration that lists genes and their location on a chromosome.
Genetic maps provide the big picture (similar to a map of interstate highways) and use genetic markers (similar to landmarks). A
genetic marker is a gene or sequence on a chromosome that shows genetic linkage with a trait of interest. The genetic marker tends
to be inherited with the gene of interest, and one measure of distance between them is the recombination frequency during meiosis.
Early geneticists called this linkage analysis.
Physical maps get into the intimate details of smaller regions of the chromosomes (similar to a detailed road map) (Figure [Link]).
A physical map is a representation of the physical distance, in nucleotides, between genes or genetic markers. Both genetic linkage
maps and physical maps are required to build a complete picture of the genome. Having a complete map of the genome makes it
easier for researchers to study individual genes. Human genome maps help researchers in their efforts to identify human disease-
causing genes related to illnesses such as cancer, heart disease, and cystic fibrosis, to name a few. In addition, genome mapping can
be used to help identify organisms with beneficial traits, such as microbes with the ability to clean up pollutants or even prevent
pollution. Research involving plant genome mapping may lead to methods that produce higher crop yields or to the development of
plants that adapt better to climate change.

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 Figure [Link]: This is a physical map of the human X chromosome. (credit: modification of work by NCBI, NIH)
Genetic maps provide the outline, and physical maps provide the details. It is easy to understand why both types of genome-
mapping techniques are important to show the big picture. Information obtained from each technique is used in combination to
study the genome. Genomic mapping is used with different model organisms that are used for research. Genome mapping is still an
ongoing process, and as more advanced techniques are developed, more advances are expected. Genome mapping is similar to
completing a complicated puzzle using every piece of available data. Mapping information generated in laboratories all over the
world is entered into central databases, such as the National Center for Biotechnology Information (NCBI). Efforts are made to
make the information more easily accessible to researchers and the general public. Just as we use global positioning systems
instead of paper maps to navigate through roadways, NCBI allows us to use a genome viewer tool to simplify the data mining
process.

CONCEPT IN ACTION

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 Online Mendelian Inheritance in Man (OMIM) is a searchable online catalog of human genes and genetic disorders. This
website shows genome mapping, and also details the history and research of each trait and disorder. Click the link to search for
traits (such as handedness) and genetic disorders (such as diabetes).

Whole Genome Sequencing

Although there have been significant advances in the medical sciences in recent years, doctors are still confounded by many
diseases and researchers are using whole genome sequencing to get to the bottom of the problem. Whole genome sequencing is a
process that determines the DNA sequence of an entire genome. Whole genome sequencing is a brute-force approach to problem
solving when there is a genetic basis at the core of a disease. Several laboratories now provide services to sequence, analyze, and
interpret entire genomes.
In 2010, whole genome sequencing was used to save a young boy whose intestines had multiple mysterious abscesses. The child
had several colon operations with no relief. Finally, a whole genome sequence revealed a defect in a pathway that controls
apoptosis (programmed cell death). A bone marrow transplant was used to overcome this genetic disorder, leading to a cure for the
boy. He was the first person to be successfully diagnosed using whole genome sequencing.
The first genomes to be sequenced, such as those belonging to viruses, bacteria, and yeast, were smaller in terms of the number of
nucleotides than the genomes of multicellular organisms. The genomes of other model organisms, such as the mouse (Mus
musculus), the fruit fly (Drosophila melanogaster), and the nematode (Caenorhabditis elegans) are now known. A great deal of
basic research is performed in model organismsbecause the information can be applied to other organisms. A model organism is a
species that is studied as a model to understand the biological processes in other species that can be represented by the model
organism. For example, fruit flies are able to metabolize alcohol like humans, so the genes affecting sensitivity to alcohol have
been studied in fruit flies in an effort to understand the variation in sensitivity to alcohol in humans. Having entire genomes
sequenced helps with the research efforts in these model organisms (Figure [Link]).

Figure [Link]: Much basic research is done with model organisms, such as the mouse, Mus musculus; the fruit fly, Drosophila
melanogaster; the nematode Caenorhabditis elegans; the yeast Saccharomyces cerevisiae; and the common weed, Arabidopsis
thaliana. (credit "mouse": modification of work by Florean Fortescue; credit "nematodes": modification of work by
"snickclunk"/Flickr; credit "common weed": modification of work by Peggy Greb, USDA; scale-bar data from Matt Russell)
The first human genome sequence was published in 2003. The number of whole genomes that have been sequenced steadily
increases and now includes hundreds of species and thousands of individual human genomes.

Applying Genomics
The introduction of DNA sequencing and whole genome sequencing projects, particularly the Human Genome Project, has
expanded the applicability of DNA sequence information. Genomics is now being used in a wide variety of fields, such as
metagenomics, pharmacogenomics, and mitochondrial genomics. The most commonly known application of genomics is to
understand and find cures for diseases.

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Predicting Disease Risk at the Individual Level
Predicting the risk of disease involves screening and identifying currently healthy individuals by genome analysis at the individual
level. Intervention with lifestyle changes and drugs can be recommended before disease onset. However, this approach is most
applicable when the problem arises from a single gene mutation. Such defects only account for about 5 percent of diseases found in
developed countries. Most of the common diseases, such as heart disease, are multifactorial or polygenic, which refers to a
phenotypic characteristic that is determined by two or more genes, and also environmental factors such as diet. In April 2010,
scientists at Stanford University published the genome analysis of a healthy individual (Stephen Quake, a scientist at Stanford
University, who had his genome sequenced); the analysis predicted his propensity to acquire various diseases. A risk assessment
was done to analyze Quake’s percentage of risk for 55 different medical conditions. A rare genetic mutation was found that showed
him to be at risk for sudden heart attack. He was also predicted to have a 23 percent risk of developing prostate cancer and a 1.4
percent risk of developing Alzheimer’s disease. The scientists used databases and several publications to analyze the genomic data.
Even though genomic sequencing is becoming more affordable and analytical tools are becoming more reliable, ethical issues
surrounding genomic analysis at a population level remain to be addressed. For example, could such data be legitimately used to
charge more or less for insurance or to affect credit ratings?

Genome-wide Association Studies

Since 2005, it has been possible to conduct a type of study called a genome-wide association study, or GWAS. A GWAS is a
method that identifies differences between individuals in single nucleotide polymorphisms (SNPs) that may be involved in causing
diseases. The method is particularly suited to diseases that may be affected by one or many genetic changes throughout the
genome. It is very difficult to identify the genes involved in such a disease using family history information. The GWAS method
relies on a genetic database that has been in development since 2002 called the International HapMap Project. The HapMap Project
sequenced the genomes of several hundred individuals from around the world and identified groups of SNPs. The groups include
SNPs that are located near to each other on chromosomes so they tend to stay together through recombination. The fact that the
group stays together means that identifying one marker SNP is all that is needed to identify all the SNPs in the group. There are
several million SNPs identified, but identifying them in other individuals who have not had their complete genome sequenced is
much easier because only the marker SNPs need to be identified.
In a common design for a GWAS, two groups of individuals are chosen; one group has the disease, and the other group does not.
The individuals in each group are matched in other characteristics to reduce the effect of confounding variables causing differences
between the two groups. For example, the genotypes may differ because the two groups are mostly taken from different parts of the
world. Once the individuals are chosen, and typically their numbers are a thousand or more for the study to work, samples of their
DNA are obtained. The DNA is analyzed using automated systems to identify large differences in the percentage of particular
SNPs between the two groups. Often the study examines a million or more SNPs in the DNA. The results of GWAS can be used in
two ways: the genetic differences may be used as markers for susceptibility to the disease in undiagnosed individuals, and the
particular genes identified can be targets for research into the molecular pathway of the disease and potential therapies. An offshoot
of the discovery of gene associations with disease has been the formation of companies that provide so-called “personal genomics”
that will identify risk levels for various diseases based on an individual’s SNP complement. The science behind these services is
controversial.
Because GWAS looks for associations between genes and disease, these studies provide data for other research into causes, rather
than answering specific questions themselves. An association between a gene difference and a disease does not necessarily mean
there is a cause-and-effect relationship. However, some studies have provided useful information about the genetic causes of
diseases. For example, three different studies in 2005 identified a gene for a protein involved in regulating inflammation in the
body that is associated with a disease-causing blindness called age-related macular degeneration. This opened up new possibilities
for research into the cause of this disease. A large number of genes have been identified to be associated with Crohn’s disease using
GWAS, and some of these have suggested new hypothetical mechanisms for the cause of the disease.

Pharmacogenomics
Pharmacogenomics involves evaluating the effectiveness and safety of drugs on the basis of information from an individual's
genomic sequence. Personal genome sequence information can be used to prescribe medications that will be most effective and
least toxic on the basis of the individual patient’s genotype. Studying changes in gene expression could provide information about
the gene transcription profile in the presence of the drug, which can be used as an early indicator of the potential for toxic effects.
For example, genes involved in cellular growth and controlled cell death, when disturbed, could lead to the growth of cancerous

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cells. Genome-wide studies can also help to find new genes involved in drug toxicity. The gene signatures may not be completely
accurate, but can be tested further before pathologic symptoms arise.

Metagenomics
Traditionally, microbiology has been taught with the view that microorganisms are best studied under pure culture conditions,
which involves isolating a single type of cell and culturing it in the laboratory. Because microorganisms can go through several
generations in a matter of hours, their gene expression profiles adapt to the new laboratory environment very quickly. On the other
hand, many species resist being cultured in isolation. Most microorganisms do not live as isolated entities, but in microbial
communities known as biofilms. For all of these reasons, pure culture is not always the best way to study microorganisms.
Metagenomics is the study of the collective genomes of multiple species that grow and interact in an environmental niche.
Metagenomics can be used to identify new species more rapidly and to analyze the effect of pollutants on the environment (Figure
[Link]). Metagenomics techniques can now also be applied to communities of higher eukaryotes, such as fish.

Figure [Link]: Metagenomics involves isolating DNA from multiple species within an environmental niche. The DNA is cut up
and sequenced, allowing entire genome sequences of multiple species to be reconstructed from the sequences of overlapping
pieces.

Creation of New Biofuels

Knowledge of the genomics of microorganisms is being used to find better ways to harness biofuels from algae and cyanobacteria.
The primary sources of fuel today are coal, oil, wood, and other plant products such as ethanol. Although plants are renewable
resources, there is still a need to find more alternative renewable sources of energy to meet our population’s energy demands. The
microbial world is one of the largest resources for genes that encode new enzymes and produce new organic compounds, and it
remains largely untapped. This vast genetic resource holds the potential to provide new sources of biofuels (Figure [Link]).

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 Figure [Link]: Renewable fuels were tested in Navy ships and aircraft at the first Naval Energy Forum. (credit: modification of
work by John F. Williams, US Navy)

Mitochondrial Genomics
Mitochondria are intracellular organelles that contain their own DNA. Mitochondrial DNA mutates at a rapid rate and is often used
to study evolutionary relationships. Another feature that makes studying the mitochondrial genome interesting is that in most
multicellular organisms, the mitochondrial DNA is passed on from the mother during the process of fertilization. For this reason,
mitochondrial genomics is often used to trace genealogy.

Genomics in Forensic Analysis

Information and clues obtained from DNA samples found at crime scenes have been used as evidence in court cases, and genetic
markers have been used in forensic analysis. Genomic analysis has also become useful in this field. In 2001, the first use of
genomics in forensics was published. It was a collaborative effort between academic research institutions and the FBI to solve the
mysterious cases of anthrax (Figure [Link]) that was transported by the US Postal Service. Anthrax bacteria were made into an
infectious powder and mailed to news media and two U.S. Senators. The powder infected the administrative staff and postal
workers who opened or handled the letters. Five people died, and 17 were sickened from the bacteria. Using microbial genomics,
researchers determined that a specific strain of anthrax was used in all the mailings; eventually, the source was traced to a scientist
at a national biodefense laboratory in Maryland.

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 Figure [Link]: Bacillus anthracis is the organism that causes anthrax. (credit: modification of work by CDC; scale-bar data from
Matt Russell)

Genomics in Agriculture
Genomics can reduce the trials and failures involved in scientific research to a certain extent, which could improve the quality and
quantity of crop yields in agriculture (Figure [Link]). Linking traits to genes or gene signatures helps to improve crop breeding to
generate hybrids with the most desirable qualities. Scientists use genomic data to identify desirable traits, and then transfer those
traits to a different organism to create a new genetically modified organism, as described in the previous module. Scientists are
discovering how genomics can improve the quality and quantity of agricultural production. For example, scientists could use
desirable traits to create a useful product or enhance an existing product, such as making a drought-sensitive crop more tolerant of
the dry season.

Figure [Link]: Transgenic agricultural plants can be made to resist disease. These transgenic plums are resistant to the plum pox
virus. (credit: Scott Bauer, USDA ARS)

Proteomics
Proteins are the final products of genes that perform the function encoded by the gene. Proteins are composed of amino acids and
play important roles in the cell. All enzymes (except ribozymes) are proteins and act as catalysts that affect the rate of reactions.
Proteins are also regulatory molecules, and some are hormones. Transport proteins, such as hemoglobin, help transport oxygen to
various organs. Antibodies that defend against foreign particles are also proteins. In the diseased state, protein function can be
impaired because of changes at the genetic level or because of direct impact on a specific protein.
A proteome is the entire set of proteins produced by a cell type. Proteomes can be studied using the knowledge of genomes because
genes code for mRNAs, and the mRNAs encode proteins. The study of the function of proteomes is called proteomics. Proteomics
complements genomics and is useful when scientists want to test their hypotheses that were based on genes. Even though all cells
in a multicellular organism have the same set of genes, the set of proteins produced in different tissues is different and dependent
on gene expression. Thus, the genome is constant, but the proteome varies and is dynamic within an organism. In addition, RNAs
can be alternatively spliced (cut and pasted to create novel combinations and novel proteins), and many proteins are modified after

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translation. Although the genome provides a blueprint, the final architecture depends on several factors that can change the
progression of events that generate the proteome.
Genomes and proteomes of patients suffering from specific diseases are being studied to understand the genetic basis of the
disease. The most prominent disease being studied with proteomic approaches is cancer (Figure [Link]). Proteomic approaches are
being used to improve the screening and early detection of cancer; this is achieved by identifying proteins whose expression is
affected by the disease process. An individual protein is called a biomarker, whereas a set of proteins with altered expression levels
is called a protein signature. For a biomarker or protein signature to be useful as a candidate for early screening and detection of a
cancer, it must be secreted in body fluids such as sweat, blood, or urine, so that large-scale screenings can be performed in a
noninvasive fashion. The current problem with using biomarkers for the early detection of cancer is the high rate of false-negative
results. A false-negative result is a negative test result that should have been positive. In other words, many cases of cancer go
undetected, which makes biomarkers unreliable. Some examples of protein biomarkers used in cancer detection are CA-125 for
ovarian cancer and PSA for prostate cancer. Protein signatures may be more reliable than biomarkers to detect cancer cells.
Proteomics is also being used to develop individualized treatment plans, which involves the prediction of whether or not an
individual will respond to specific drugs and the side effects that the individual may have. Proteomics is also being used to predict
the possibility of disease recurrence.

Figure [Link]: This machine is preparing to do a proteomic pattern analysis to identify specific cancers so that an accurate
cancer prognosis can be made. (credit: Dorie Hightower, NCI, NIH)
The National Cancer Institute has developed programs to improve the detection and treatment of cancer. The Clinical Proteomic
Technologies for Cancer and the Early Detection Research Network are efforts to identify protein signatures specific to different
types of cancers. The Biomedical Proteomics Program is designed to identify protein signatures and design effective therapies for
cancer patients.

Summary
Genome mapping is similar to solving a big, complicated puzzle with pieces of information coming from laboratories all over the
world. Genetic maps provide an outline for the location of genes within a genome, and they estimate the distance between genes
and genetic markers on the basis of the recombination frequency during meiosis. Physical maps provide detailed information about
the physical distance between the genes. The most detailed information is available through sequence mapping. Information from
all mapping and sequencing sources is combined to study an entire genome.
Whole genome sequencing is the latest available resource to treat genetic diseases. Some doctors are using whole genome
sequencing to save lives. Genomics has many industrial applications, including biofuel development, agriculture, pharmaceuticals,
and pollution control.
Imagination is the only barrier to the applicability of genomics. Genomics is being applied to most fields of biology; it can be used
for personalized medicine, prediction of disease risks at an individual level, the study of drug interactions before the conduction of
clinical trials, and the study of microorganisms in the environment as opposed to the laboratory. It is also being applied to the

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generation of new biofuels, genealogical assessment using mitochondria, advances in forensic science, and improvements in
agriculture.
Proteomics is the study of the entire set of proteins expressed by a given type of cell under certain environmental conditions. In a
multicellular organism, different cell types will have different proteomes, and these will vary with changes in the environment.
Unlike a genome, a proteome is dynamic and under constant flux, which makes it more complicated and more useful than the
knowledge of genomes alone.

Glossary

biomarker
an individual protein that is uniquely produced in a diseased state

genetic map
an outline of genes and their location on a chromosome that is based on recombination frequencies between markers

genomics
the study of entire genomes, including the complete set of genes, their nucleotide sequence and organization, and their
interactions within a species and with other species

metagenomics
the study of the collective genomes of multiple species that grow and interact in an environmental niche

model organism
a species that is studied and used as a model to understand the biological processes in other species represented by the model
organism

pharmacogenomics
the study of drug interactions with the genome or proteome; also called toxicogenomics

physical map
a representation of the physical distance between genes or genetic markers

protein signature
a set of over- or under-expressed proteins characteristic of cells in a particular diseased tissue

proteomics
study of the function of proteomes

whole genome sequencing

a process that determines the nucleotide sequence of an entire genome

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 5.2.3: Genomics and Proteomics is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
10.3: Genomics and Proteomics by OpenStax is licensed CC BY 4.0.

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5.2.E: Biotechnology (Exercises)
10.1: Cloning and Genetic Engineering
Multiple Choice
In gel electrophoresis of DNA, the different bands in the final gel form because the DNA molecules ________.
A. are from different organisms
B. have different lengths
C. have different nucleotide compositions
D. have different genes

Answer
B

In the reproductive cloning of an animal, the genome of the cloned individual comes from ________.
A. a sperm cell
B. an egg cell
C. any gamete cell
D. a body cell

Answer
D

What carries a gene from one organism into a bacteria cell?

A. a plasmid
B. an electrophoresis gel
C. a restriction enzyme
D. polymerase chain reaction

Answer
A

Free Response
What is the purpose and benefit of the polymerase chain reaction?

Answer
The polymerase chain reaction is used to quickly produce many copies of a specific segment of DNA when only one or a very
few copies are originally present. The benefit of PCR is that there are many instances in which we would like to know
something about a sample of DNA when only very small amounts are available. PCR allows us to increase the number of DNA
molecules so that other tests, such as sequencing, can be performed with it.

10.2: Biotechnology in Medicine and Agriculture

Multiple Choice
What is a genetically modified organism (GMO)?
A. a plant with certain genes removed
B. an organism with an artificially altered genome
C. a hybrid organism
D. any agricultural organism produced by breeding or biotechnology

Answer

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 B

What is the role of Agrobacterium tumefaciens in the production of transgenic plants?

A. Genes from A. tumefaciens are inserted into plant DNA to give the plant different traits.
B. Transgenic plants have been given resistance to the pest A. tumefaciens.
C. A. tumefaciens is used as a vector to move genes into plant cells.
D. Plant genes are incorporated into the genome of Agrobacterium tumefaciens.

Answer
C

Free Response
Today, it is possible for a diabetic patient to purchase human insulin from a pharmacist. What technology makes this possible and
why is it a benefit over how things used to be?

Answer
The human insulin comes from the gene that produces insulin in humans, which has been spliced into a bacterial genome using
recombinant DNA technology. The bacterium produces the insulin, which is then purified for human use. Before there was
genetically engineered human insulin, diabetics were given insulin extracted from pig pancreases, which was similar to, but not
exactly like, human insulin. Because it was not exactly like human insulin, the pig insulin caused complications in some
diabetic patients.

10.3: Genomics and Proteomics

Multiple Choice
What is the most challenging issue facing genome sequencing?
A. the inability to develop fast and accurate sequencing techniques
B. the ethics of using information from genomes at the individual level
C. the availability and stability of DNA
D. all of the above

Answer
B

Genomics can be used in agriculture to:

A. generate new hybrid strains
B. improve disease resistance
C. improve yield
D. all of the above

Answer
D

What kind of diseases are studied using genome-wide association studies?

A. viral diseases
B. single-gene inherited diseases
C. diseases caused by multiple genes
D. diseases caused by environmental factors

Answer
C

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Free Response
Describe two of the applications for genome mapping.

Answer
Genome mapping helps researchers to study disease-causing genes in humans. It also helps to identify traits of organisms that
can be used in applications such as cleaning up pollution.

Identify a possible advantage and a possible disadvantage of a genetic test that would identify genes in individuals that increase
their probability of having Alzheimer's disease later in life.

Answer
The benefit of such a test is that the individual can make preparations for having the disease including taking treatments that
slow the disease. The disadvantage of the test is that it might be used by insurance companies to deny coverage to the person.

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10.E: Biotechnology (Exercises) by OpenStax is licensed CC BY 4.0.

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 CHAPTER OVERVIEW

6: Genetics
6.1: Patterns of Inheritance
6.1.1: Mendel’s Experiments
6.1.2: Laws of Inheritance
6.1.3: Extensions of the Laws of Inheritance
6.1.E: Patterns of Inheritance (Exercises)
6.2: Pedigrees review

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6: Genetics is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
 SECTION OVERVIEW

6.1: Patterns of Inheritance

6.1.1: Mendel’s Experiments

6.1.2: Laws of Inheritance

6.1.3: Extensions of the Laws of Inheritance

6.1.E: Patterns of Inheritance (Exercises)

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6.1.1: Mendel’s Experiments
Johann Gregor Mendel (1822–1884) (Figure [Link]) was a lifelong learner, teacher, scientist, and man of faith. As a young adult,
he joined the Augustinian Abbey of St. Thomas in Brno in what is now the Czech Republic. Supported by the monastery, he taught
physics, botany, and natural science courses at the secondary and university levels. In 1856, he began a decade-long research
pursuit involving inheritance patterns in honeybees and plants, ultimately settling on pea plants as his primary model system (a
system with convenient characteristics that is used to study a specific biological phenomenon to gain understanding to be applied to
other systems). In 1865, Mendel presented the results of his experiments with nearly 30,000 pea plants to the local natural history
society. He demonstrated that traits are transmitted faithfully from parents to offspring in specific patterns. In 1866, he published
1
his work, Experiments in Plant Hybridization, in the proceedings of the Natural History Society of Brünn.

Figure [Link]: Johann Gregor Mendel set the framework for the study of genetics.
Mendel’s work went virtually unnoticed by the scientific community, which incorrectly believed that the process of inheritance
involved a blending of parental traits that produced an intermediate physical appearance in offspring. This hypothetical process
appeared to be correct because of what we know now as continuous variation. Continuous variation is the range of small
differences we see among individuals in a characteristic like human height. It does appear that offspring are a “blend” of their
parents’ traits when we look at characteristics that exhibit continuous variation. Mendel worked instead with traits that show
discontinuous variation. Discontinuous variation is the variation seen among individuals when each individual shows one of two—
or a very few—easily distinguishable traits, such as violet or white flowers. Mendel’s choice of these kinds of traits allowed him to
see experimentally that the traits were not blended in the offspring as would have been expected at the time, but that they were
inherited as distinct traits. In 1868, Mendel became abbot of the monastery and exchanged his scientific pursuits for his pastoral
duties. He was not recognized for his extraordinary scientific contributions during his lifetime; in fact, it was not until 1900 that his
work was rediscovered, reproduced, and revitalized by scientists on the brink of discovering the chromosomal basis of heredity.

Mendel’s Crosses
Mendel’s seminal work was accomplished using the garden pea, Pisum sativum, to study inheritance. This species naturally self-
fertilizes, meaning that pollen encounters ova within the same flower. The flower petals remain sealed tightly until pollination is
completed to prevent the pollination of other plants. The result is highly inbred, or “true-breeding,” pea plants. These are plants that
always produce offspring that look like the parent. By experimenting with true-breeding pea plants, Mendel avoided the appearance
of unexpected traits in offspring that might occur if the plants were not true breeding. The garden pea also grows to maturity within
one season, meaning that several generations could be evaluated over a relatively short time. Finally, large quantities of garden peas
could be cultivated simultaneously, allowing Mendel to conclude that his results did not come about simply by chance.
Mendel performed hybridizations, which involve mating two true-breeding individuals that have different traits. In the pea, which
is naturally self-pollinating, this is done by manually transferring pollen from the anther of a mature pea plant of one variety to the
stigma of a separate mature pea plant of the second variety.
Plants used in first-generation crosses were called P, or parental generation, plants (Figure [Link]). Mendel collected the seeds
produced by the P plants that resulted from each cross and grew them the following season. These offspring were called the F1, or
the first filial (filial = daughter or son), generation. Once Mendel examined the characteristics in the F1 generation of plants, he

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allowed them to self-fertilize naturally. He then collected and grew the seeds from the F1 plants to produce the F2, or second filial,
generation. Mendel’s experiments extended beyond the F2 generation to the F3 generation, F4 generation, and so on, but it was the
ratio of characteristics in the P, F1, and F2 generations that were the most intriguing and became the basis of Mendel’s postulates.

Figure [Link]: Mendel’s process for performing crosses included examining flower color.

Garden Pea Characteristics Revealed the Basics of Heredity

In his 1865 publication, Mendel reported the results of his crosses involving seven different characteristics, each with two
contrasting traits. A trait is defined as a variation in the physical appearance of a heritable characteristic. The characteristics
included plant height, seed texture, seed color, flower color, pea-pod size, pea-pod color, and flower position. For the characteristic
of flower color, for example, the two contrasting traits were white versus violet. To fully examine each characteristic, Mendel
generated large numbers of F1 and F2 plants and reported results from thousands of F2 plants.
What results did Mendel find in his crosses for flower color? First, Mendel confirmed that he was using plants that bred true for
white or violet flower color. Irrespective of the number of generations that Mendel examined, all self-crossed offspring of parents
with white flowers had white flowers, and all self-crossed offspring of parents with violet flowers had violet flowers. In addition,
Mendel confirmed that, other than flower color, the pea plants were physically identical. This was an important check to make sure
that the two varieties of pea plants only differed with respect to one trait, flower color.
Once these validations were complete, Mendel applied the pollen from a plant with violet flowers to the stigma of a plant with
white flowers. After gathering and sowing the seeds that resulted from this cross, Mendel found that 100 percent of the F1 hybrid

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generation had violet flowers. Conventional wisdom at that time would have predicted the hybrid flowers to be pale violet or for
hybrid plants to have equal numbers of white and violet flowers. In other words, the contrasting parental traits were expected to
blend in the offspring. Instead, Mendel’s results demonstrated that the white flower trait had completely disappeared in the F1
generation.
Importantly, Mendel did not stop his experimentation there. He allowed the F1 plants to self-fertilize and found that 705 plants in
the F2 generation had violet flowers and 224 had white flowers. This was a ratio of 3.15 violet flowers to one white flower, or
approximately 3:1. When Mendel transferred pollen from a plant with violet flowers to the stigma of a plant with white flowers and
vice versa, he obtained approximately the same ratio irrespective of which parent—male or female—contributed which trait. This
is called a reciprocal cross—a paired cross in which the respective traits of the male and female in one cross become the respective
traits of the female and male in the other cross. For the other six characteristics that Mendel examined, the F1 and F2 generations
behaved in the same way that they behaved for flower color. One of the two traits would disappear completely from the F1
generation, only to reappear in the F2 generation at a ratio of roughly 3:1 (Figure [Link]).

Figure [Link]: Mendel identified seven pea plant characteristics.

Upon compiling his results for many thousands of plants, Mendel concluded that the characteristics could be divided into expressed
and latent traits. He called these dominant and recessive traits, respectively. Dominanttraits are those that are inherited unchanged
in a hybridization. Recessive traits become latent, or disappear in the offspring of a hybridization. The recessive trait does,
however, reappear in the progeny of the hybrid offspring. An example of a dominant trait is the violet-colored flower trait. For this
same characteristic (flower color), white-colored flowers are a recessive trait. The fact that the recessive trait reappeared in the F2
generation meant that the traits remained separate (and were not blended) in the plants of the F1 generation. Mendel proposed that
this was because the plants possessed two copies of the trait for the flower-color characteristic, and that each parent transmitted one
of their two copies to their offspring, where they came together. Moreover, the physical observation of a dominant trait could mean
that the genetic composition of the organism included two dominant versions of the characteristic, or that it included one dominant
and one recessive version. Conversely, the observation of a recessive trait meant that the organism lacked any dominant versions of
this characteristic.

Section Summary
Working with garden pea plants, Mendel found that crosses between parents that differed for one trait produced F1 offspring that all
expressed one parent’s traits. The traits that were visible in the F1 generation are referred to as dominant, and traits that disappear in
the F1 generation are described as recessive. When the F1 plants in Mendel’s experiment were self-crossed, the F2 offspring
exhibited the dominant trait or the recessive trait in a 3:1 ratio, confirming that the recessive trait had been transmitted faithfully

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from the original P parent. Reciprocal crosses generated identical F1 and F2 offspring ratios. By examining sample sizes, Mendel
showed that traits were inherited as independent events.

Footnotes
1. 1 Johann Gregor Mendel, “Versuche über Pflanzenhybriden.” Verhandlungen des naturforschenden Vereines in Brünn, Bd. IV
für das Jahr, 1865 Abhandlungen (1866):3–47. [for English translation, see [Link]/[Link]]

Glossary
continuous variation
a variation in a characteristic in which individuals show a range of traits with small differences between them

discontinuous variation
a variation in a characteristic in which individuals show two, or a few, traits with large differences between them

dominant
describes a trait that masks the expression of another trait when both versions of the gene are present in an individual

F1
the first filial generation in a cross; the offspring of the parental generation

F2
the second filial generation produced when F1 individuals are self-crossed or fertilized with each other

hybridization
the process of mating two individuals that differ, with the goal of achieving a certain characteristic in their offspring

model system
a species or biological system used to study a specific biological phenomenon to gain understanding that will be applied to
other species

P
the parental generation in a cross

recessive
describes a trait whose expression is masked by another trait when the alleles for both traits are present in an individual

reciprocal cross
a paired cross in which the respective traits of the male and female in one cross become the respective traits of the female and
male in the other cross

trait
a variation in an inherited characteristic

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 6.1.1: Mendel’s Experiments is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
8.1: Mendel’s Experiments by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

6.1.2: Laws of Inheritance
The seven characteristics that Mendel evaluated in his pea plants were each expressed as one of two versions, or traits. Mendel
deduced from his results that each individual had two discrete copies of the characteristic that are passed individually to offspring.
We now call those two copies genes, which are carried on chromosomes. The reason we have two copies of each gene is that we
inherit one from each parent. In fact, it is the chromosomes we inherit and the two copies of each gene are located on paired
chromosomes. Recall that in meiosis these chromosomes are separated out into haploid gametes. This separation, or segregation, of
the homologous chromosomes means also that only one of the copies of the gene gets moved into a gamete. The offspring are
formed when that gamete unites with one from another parent and the two copies of each gene (and chromosome) are restored.
For cases in which a single gene controls a single characteristic, a diploid organism has two genetic copies that may or may not
encode the same version of that characteristic. For example, one individual may carry a gene that determines white flower color
and a gene that determines violet flower color. Gene variants that arise by mutation and exist at the same relative locations on
homologous chromosomes are called alleles. Mendel examined the inheritance of genes with just two allele forms, but it is
common to encounter more than two alleles for any given gene in a natural population.

Phenotypes and Genotypes

Two alleles for a given gene in a diploid organism are expressed and interact to produce physical characteristics. The observable
traits expressed by an organism are referred to as its phenotype. An organism’s underlying genetic makeup, consisting of both the
physically visible and the non-expressed alleles, is called its genotype. Mendel’s hybridization experiments demonstrate the
difference between phenotype and genotype. For example, the phenotypes that Mendel observed in his crosses between pea plants
with differing traits are connected to the diploid genotypes of the plants in the P, F1, and F2 generations. We will use a second trait
that Mendel investigated, seed color, as an example. Seed color is governed by a single gene with two alleles. The yellow-seed
allele is dominant and the green-seed allele is recessive. When true-breeding plants were cross-fertilized, in which one parent had
yellow seeds and one had green seeds, all of the F1hybrid offspring had yellow seeds. That is, the hybrid offspring were
phenotypically identical to the true-breeding parent with yellow seeds. However, we know that the allele donated by the parent with
green seeds was not simply lost because it reappeared in some of the F2 offspring (Figure [Link]). Therefore, the F1 plants must
have been genotypically different from the parent with yellow seeds.
The P plants that Mendel used in his experiments were each homozygous for the trait he was studying. Diploid organisms that are
homozygous for a gene have two identical alleles, one on each of their homologous chromosomes. The genotype is often written as
YY or yy, for which each letter represents one of the two alleles in the genotype. The dominant allele is capitalized and the recessive
allele is lower case. The letter used for the gene (seed color in this case) is usually related to the dominant trait (yellow allele, in
this case, or “Y”). Mendel’s parental pea plants always bred true because both produced gametes carried the same allele. When P
plants with contrasting traits were cross-fertilized, all of the offspring were heterozygous for the contrasting trait, meaning their
genotype had different alleles for the gene being examined. For example, the F1 yellow plants that received a Y allele from their
yellow parent and a y allele from their green parent had the genotype Yy.

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 Figure [Link]: Phenotypes are physical expressions of traits that are transmitted by alleles. Capital letters represent dominant
alleles and lowercase letters represent recessive alleles. The phenotypic ratios are the ratios of visible characteristics. The genotypic
ratios are the ratios of gene combinations in the offspring, and these are not always distinguishable in the phenotypes.

Law of Dominance
Our discussion of homozygous and heterozygous organisms brings us to why the F1 heterozygous offspring were identical to one of
the parents, rather than expressing both alleles. In all seven pea-plant characteristics, one of the two contrasting alleles was
dominant, and the other was recessive. Mendel called the dominant allele the expressed unit factor; the recessive allele was referred
to as the latent unit factor. We now know that these so-called unit factors are actually genes on homologous chromosomes. For a
gene that is expressed in a dominant and recessive pattern, homozygous dominant and heterozygous organisms will look identical
(that is, they will have different genotypes but the same phenotype), and the recessive allele will only be observed in homozygous
recessive individuals (Table [Link]).

Table [Link]: Correspondence between Genotype and Phenotype for a Dominant-Recessive Characteristic.

Homozygous Heterozygous Homozygous

Genotype YY Yy yy

Phenotype yellow yellow green

Mendel’s law of dominance states that in a heterozygote, one trait will conceal the presence of another trait for the same
characteristic. For example, when crossing true-breeding violet-flowered plants with true-breeding white-flowered plants, all of the
offspring were violet-flowered, even though they all had one allele for violet and one allele for white. Rather than both alleles
contributing to a phenotype, the dominant allele will be expressed exclusively. The recessive allele will remain latent, but will be
transmitted to offspring in the same manner as that by which the dominant allele is transmitted. The recessive trait will only be
expressed by offspring that have two copies of this allele (Figure [Link]), and these offspring will breed true when self-crossed.

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 Figure [Link]: The allele for albinism, expressed here in humans, is recessive. Both of this child’s parents carried the recessive
allele.

Monohybrid Cross and the Punnett Square

When fertilization occurs between two true-breeding parents that differ by only the characteristic being studied, the process is
called a monohybrid cross, and the resulting offspring are called monohybrids. Mendel performed seven types of monohybrid
crosses, each involving contrasting traits for different characteristics. Out of these crosses, all of the F1 offspring had the phenotype
of one parent, and the F2 offspring had a 3:1 phenotypic ratio. On the basis of these results, Mendel postulated that each parent in
the monohybrid cross contributed one of two paired unit factors to each offspring, and every possible combination of unit factors
was equally likely.
The results of Mendel’s research can be explained in terms of probabilities, which are mathematical measures of likelihood. The
probability of an event is calculated by the number of times the event occurs divided by the total number of opportunities for the
event to occur. A probability of one (100 percent) for some event indicates that it is guaranteed to occur, whereas a probability of
zero (0 percent) indicates that it is guaranteed to not occur, and a probability of 0.5 (50 percent) means it has an equal chance of
occurring or not occurring.
To demonstrate this with a monohybrid cross, consider the case of true-breeding pea plants with yellow versus green seeds. The
dominant seed color is yellow; therefore, the parental genotypes were YY for the plants with yellow seeds and yy for the plants with
green seeds. A Punnett square, devised by the British geneticist Reginald Punnett, is useful for determining probabilities because it
is drawn to predict all possible outcomes of all possible random fertilization events and their expected frequencies. Figure [Link]
shows a Punnett square for a cross between a plant with yellow peas and one with green peas. To prepare a Punnett square, all
possible combinations of the parental alleles (the genotypes of the gametes) are listed along the top (for one parent) and side (for
the other parent) of a grid. The combinations of egg and sperm gametes are then made in the boxes in the table on the basis of
which alleles are combining. Each box then represents the diploid genotype of a zygote, or fertilized egg. Because each possibility
is equally likely, genotypic ratios can be determined from a Punnett square. If the pattern of inheritance (dominant and recessive) is
known, the phenotypic ratios can be inferred as well. For a monohybrid cross of two true-breeding parents, each parent contributes
one type of allele. In this case, only one genotype is possible in the F1 offspring. All offspring are Yy and have yellow seeds.

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When the F1 offspring are crossed with each other, each has an equal probability of contributing either a Y or a y to the F2 offspring.
The result is a 1 in 4 (25 percent) probability of both parents contributing a Y, resulting in an offspring with a yellow phenotype; a
25 percent probability of parent A contributing a Y and parent B a y, resulting in offspring with a yellow phenotype; a 25 percent
probability of parent A contributing a y and parent B a Y, also resulting in a yellow phenotype; and a (25 percent) probability of
both parents contributing a y, resulting in a green phenotype. When counting all four possible outcomes, there is a 3 in 4 probability
of offspring having the yellow phenotype and a 1 in 4 probability of offspring having the green phenotype. This explains why the
results of Mendel’s F2 generation occurred in a 3:1 phenotypic ratio. Using large numbers of crosses, Mendel was able to calculate
probabilities, found that they fit the model of inheritance, and use these to predict the outcomes of other crosses.

Law of Segregation
Observing that true-breeding pea plants with contrasting traits gave rise to F1 generations that all expressed the dominant trait and
F2 generations that expressed the dominant and recessive traits in a 3:1 ratio, Mendel proposed the law of segregation. This law
states that paired unit factors (genes) must segregate equally into gametes such that offspring have an equal likelihood of inheriting
either factor. For the F2 generation of a monohybrid cross, the following three possible combinations of genotypes result:
homozygous dominant, heterozygous, or homozygous recessive. Because heterozygotes could arise from two different pathways
(receiving one dominant and one recessive allele from either parent), and because heterozygotes and homozygous dominant
individuals are phenotypically identical, the law supports Mendel’s observed 3:1 phenotypic ratio. The equal segregation of alleles
is the reason we can apply the Punnett square to accurately predict the offspring of parents with known genotypes. The physical
basis of Mendel’s law of segregation is the first division of meiosis in which the homologous chromosomes with their different
versions of each gene are segregated into daughter nuclei. This process was not understood by the scientific community during
Mendel’s lifetime (Figure [Link]).

Figure [Link]: The first division in meiosis is shown.

Test Cross
Beyond predicting the offspring of a cross between known homozygous or heterozygous parents, Mendel also developed a way to
determine whether an organism that expressed a dominant trait was a heterozygote or a homozygote. Called the test cross, this
technique is still used by plant and animal breeders. In a test cross, the dominant-expressing organism is crossed with an organism
that is homozygous recessive for the same characteristic. If the dominant-expressing organism is a homozygote, then all F1
offspring will be heterozygotes expressing the dominant trait (Figure [Link]). Alternatively, if the dominant-expressing organism
is a heterozygote, the F1 offspring will exhibit a 1:1 ratio of heterozygotes and recessive homozygotes (Figure [Link]). The test
cross further validates Mendel’s postulate that pairs of unit factors segregate equally.

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 Figure [Link]: A test cross can be performed to determine whether an organism expressing a dominant trait is a homozygote or a
heterozygote.

ART CONNECTION

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 Figure [Link]: This Punnett square shows the cross between plants with yellow seeds and green seeds. The cross between
the true-breeding P plants produces F1 heterozygotes that can be self-fertilized. The self-cross of the F1 generation can be
analyzed with a Punnett square to predict the genotypes of the F2 generation. Given an inheritance pattern of dominant–
recessive, the genotypic and phenotypic ratios can then be determined.
In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with wrinkled peas
(genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have round peas.
From this data, can you tell if the parent plant is homozygous dominant or heterozygous?

Law of Independent Assortment

Mendel’s law of independent assortment states that genes do not influence each other with regard to the sorting of alleles into
gametes, and every possible combination of alleles for every gene is equally likely to occur. Independent assortment of genes can
be illustrated by the dihybrid cross, a cross between two true-breeding parents that express different traits for two characteristics.
Consider the characteristics of seed color and seed texture for two pea plants, one that has wrinkled, green seeds (rryy) and another
that has round, yellow seeds (RRYY). Because each parent is homozygous, the law of segregation indicates that the gametes for the
wrinkled–green plant all are ry, and the gametes for the round–yellow plant are all RY. Therefore, the F1 generation of offspring all
are RrYy (Figure [Link]).

ART CONNECTION

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 Figure [Link]: A dihybrid cross in pea plants involves the genes for seed color and texture. The P cross produces F1
offspring that are all heterozygous for both characteristics. The resulting 9:3:3:1 F2 phenotypic ratio is obtained using a Punnett
square.
In pea plants, purple flowers (P) are dominant to white (p), and yellow peas (Y) are dominant to green (y). What are the
possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares would you need to
complete a Punnett square analysis of this cross?

The gametes produced by the F1 individuals must have one allele from each of the two genes. For example, a gamete could get an
R allele for the seed shape gene and either a Y or a y allele for the seed color gene. It cannot get both an R and an r allele; each
gamete can have only one allele per gene. The law of independent assortment states that a gamete into which an r allele is sorted
would be equally likely to contain either a Y or a y allele. Thus, there are four equally likely gametes that can be formed when the
RrYy heterozygote is self-crossed, as follows: RY, rY, Ry, and ry. Arranging these gametes along the top and left of a 4 × 4 Punnett
square (Figure [Link]) gives us 16 equally likely genotypic combinations. From these genotypes, we find a phenotypic ratio of 9
round–yellow:3 round–green:3 wrinkled–yellow:1 wrinkled–green (Figure [Link]). These are the offspring ratios we would
expect, assuming we performed the crosses with a large enough sample size.
The physical basis for the law of independent assortment also lies in meiosis I, in which the different homologous pairs line up in
random orientations. Each gamete can contain any combination of paternal and maternal chromosomes (and therefore the genes on
them) because the orientation of tetrads on the metaphase plane is random (Figure [Link]).

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 Figure [Link]: The random segregation into daughter nuclei that happens during the first division in meiosis can lead to a variety
of possible genetic arrangements.

Section Summary
When true-breeding, or homozygous, individuals that differ for a certain trait are crossed, all of the offspring will be heterozygous
for that trait. If the traits are inherited as dominant and recessive, the F1 offspring will all exhibit the same phenotype as the parent
homozygous for the dominant trait. If these heterozygous offspring are self-crossed, the resulting F2 offspring will be equally likely
to inherit gametes carrying the dominant or recessive trait, giving rise to offspring of which one quarter are homozygous dominant,
half are heterozygous, and one quarter are homozygous recessive. Because homozygous dominant and heterozygous individuals are
phenotypically identical, the observed traits in the F2 offspring will exhibit a ratio of three dominant to one recessive.
Mendel postulated that genes (characteristics) are inherited as pairs of alleles (traits) that behave in a dominant and recessive
pattern. Alleles segregate into gametes such that each gamete is equally likely to receive either one of the two alleles present in a
diploid individual. In addition, genes are assorted into gametes independently of one another. That is, in general, alleles are not
more likely to segregate into a gamete with a particular allele of another gene.

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Art Connections
Figure [Link]: In pea plants, round peas (R) are dominant to wrinkled peas (r). You do a test cross between a pea plant with
wrinkled peas (genotype rr) and a plant of unknown genotype that has round peas. You end up with three plants, all which have
round peas. From this data, can you tell if the parent plant is homozygous dominant or heterozygous?

Answer
You cannot be sure if the plant is homozygous or heterozygous as the data set is too small: by random chance, all three plants
might have acquired only the dominant gene even if the recessive one is present.

Figure [Link]: In pea plants, purple flowers (P) are dominant to white (p), and yellow peas (Y) are dominant to green (y). What are
the possible genotypes and phenotypes for a cross between PpYY and ppYy pea plants? How many squares would you need to
complete a Punnett square analysis of this cross?

Answer
The possible genotypes are PpYY, PpYy, ppYY, and ppYy. The former two genotypes would result in plants with purple flowers
and yellow peas, while the latter two genotypes would result in plants with white flowers with yellow peas, for a 1:1 ratio of
each phenotype. You only need a 2 × 2 Punnett square (four squares total) to do this analysis because two of the alleles are
homozygous.

Glossary

allele
one of two or more variants of a gene that determines a particular trait for a characteristic

dihybrid
the result of a cross between two true-breeding parents that express different traits for two characteristics

genotype
the underlying genetic makeup, consisting of both physically visible and non-expressed alleles, of an organism

heterozygous
having two different alleles for a given gene on the homologous chromosomes

homozygous
having two identical alleles for a given gene on the homologous chromosomes

law of dominance
in a heterozygote, one trait will conceal the presence of another trait for the same characteristic

law of independent assortment

genes do not influence each other with regard to sorting of alleles into gametes; every possible combination of alleles is equally
likely to occur

law of segregation
paired unit factors (i.e., genes) segregate equally into gametes such that offspring have an equal likelihood of inheriting any
combination of factors

monohybrid
the result of a cross between two true-breeding parents that express different traits for only one characteristic

phenotype
the observable traits expressed by an organism

Punnett square

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 a visual representation of a cross between two individuals in which the gametes of each individual are denoted along the top and
side of a grid, respectively, and the possible zygotic genotypes are recombined at each box in the grid

test cross
a cross between a dominant expressing individual with an unknown genotype and a homozygous recessive individual; the
offspring phenotypes indicate whether the unknown parent is heterozygous or homozygous for the dominant trait

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 6.1.2: Laws of Inheritance is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
8.2: Laws of Inheritance by OpenStax is licensed CC BY 4.0.

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6.1.3: Extensions of the Laws of Inheritance
Mendel studied traits with only one mode of inheritance in pea plants. The inheritance of the traits he studied all followed the
relatively simple pattern of dominant and recessive alleles for a single characteristic. There are several important modes of
inheritance, discovered after Mendel’s work, that do not follow the dominant and recessive, single-gene model.

Alternatives to Dominance and Recessiveness

Mendel’s experiments with pea plants suggested that: 1) two types of “units” or alleles exist for every gene; 2) alleles maintain
their integrity in each generation (no blending); and 3) in the presence of the dominant allele, the recessive allele is hidden, with no
contribution to the phenotype. Therefore, recessive alleles can be “carried” and not expressed by individuals. Such heterozygous
individuals are sometimes referred to as “carriers.” Since then, genetic studies in other organisms have shown that much more
complexity exists, but that the fundamental principles of Mendelian genetics still hold true. In the sections to follow, we consider
some of the extensions of Mendelism.

Incomplete Dominance
Mendel’s results, demonstrating that traits are inherited as dominant and recessive pairs, contradicted the view at that time that
offspring exhibited a blend of their parents’ traits. However, the heterozygote phenotype occasionally does appear to be
intermediate between the two parents. For example, in the snapdragon, Antirrhinum majus (Figure [Link]), a cross between a
homozygous parent with white flowers (CWCW) and a homozygous parent with red flowers (CRCR) will produce offspring with
pink flowers (CRCW). (Note that different genotypic abbreviations are used for Mendelian extensions to distinguish these patterns
from simple dominance and recessiveness.) This pattern of inheritance is described as incomplete dominance, meaning that one of
the alleles appears in the phenotype in the heterozygote, but not to the exclusion of the other, which can also be seen. The allele for
red flowers is incompletely dominant over the allele for white flowers. However, the results of a heterozygote self-cross can still be
predicted, just as with Mendelian dominant and recessive crosses. In this case, the genotypic ratio would be 1 CRCR:2 CRCW:1
CWCW, and the phenotypic ratio would be 1:2:1 for red:pink:white. The basis for the intermediate color in the heterozygote is
simply that the pigment produced by the red allele (anthocyanin) is diluted in the heterozygote and therefore appears pink because
of the white background of the flower petals.

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 Figure [Link]: These pink flowers of a heterozygote snapdragon result from incomplete dominance. (credit:
"storebukkebruse"/Flickr)

Codominance
A variation on incomplete dominance is codominance, in which both alleles for the same characteristic are simultaneously
expressed in the heterozygote. An example of codominance occurs in the ABO blood groups of humans. The A and B alleles are
expressed in the form of A or B molecules present on the surface of red blood cells. Homozygotes (IAIA and IBIB) express either the
A or the B phenotype, and heterozygotes (IAIB) express both phenotypes equally. The IAIB individual has blood type AB. In a self-
cross between heterozygotes expressing a codominant trait, the three possible offspring genotypes are phenotypically distinct.
However, the 1:2:1 genotypic ratio characteristic of a Mendelian monohybrid cross still applies (Figure [Link]).

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 Figure [Link]: This Punnet square shows an AB/AB blood type cross.

Multiple Alleles
Mendel implied that only two alleles, one dominant and one recessive, could exist for a given gene. We now know that this is an
oversimplification. Although individual humans (and all diploid organisms) can only have two alleles for a given gene, multiple
alleles may exist at the population level, such that many combinations of two alleles are observed. Note that when many alleles
exist for the same gene, the convention is to denote the most common phenotype or genotype in the natural population as the wild
type (often abbreviated “+”). All other phenotypes or genotypes are considered variants (mutants) of this typical form, meaning
they deviate from the wild type. The variant may be recessive or dominant to the wild-type allele.
An example of multiple alleles is the ABO blood-type system in humans. In this case, there are three alleles circulating in the
population. The IA allele codes for A molecules on the red blood cells, the IB allele codes for B molecules on the surface of red
blood cells, and the i allele codes for no molecules on the red blood cells. In this case, the IA and IB alleles are codominant with
each other and are both dominant over the i allele. Although there are three alleles present in a population, each individual only gets
two of the alleles from their parents. This produces the genotypes and phenotypes shown in Figure [Link]. Notice that instead of
three genotypes, there are six different genotypes when there are three alleles. The number of possible phenotypes depends on the
dominance relationships between the three alleles.

Figure [Link]: Inheritance of the ABO blood system in humans is shown.

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 EVOLUTION IN ACTION: Multiple Alleles Confer Drug Resistance in the Malaria Parasite
Malaria is a parasitic disease in humans that is transmitted by infected female mosquitoes, including Anopheles gambiae, and is
characterized by cyclic high fevers, chills, flu-like symptoms, and severe anemia. Plasmodium falciparum and P. vivax are the
most common causative agents of malaria, and P. falciparum is the most deadly. When promptly and correctly treated, P.
falciparum malaria has a mortality rate of 0.1 percent. However, in some parts of the world, the parasite has evolved resistance
to commonly used malaria treatments, so the most effective malarial treatments can vary by geographic region.
In Southeast Asia, Africa, and South America, P. falciparum has developed resistance to the anti-malarial drugs chloroquine,
mefloquine, and sulfadoxine-pyrimethamine. P. falciparum, which is haploid during the life stage in which it is infective to
humans, has evolved multiple drug-resistant mutant alleles of the dhps gene. Varying degrees of sulfadoxine resistance are
associated with each of these alleles. Being haploid, P. falciparum needs only one drug-resistant allele to express this trait.
In Southeast Asia, different sulfadoxine-resistant alleles of the dhps gene are localized to different geographic regions. This is a
common evolutionary phenomenon that comes about because drug-resistant mutants arise in a population and interbreed with
other P. falciparum isolates in close proximity. Sulfadoxine-resistant parasites cause considerable human hardship in regions in
which this drug is widely used as an over-the-counter malaria remedy. As is common with pathogens that multiply to large
numbers within an infection cycle, P. falciparum evolves relatively rapidly (over a decade or so) in response to the selective
pressure of commonly used anti-malarial drugs. For this reason, scientists must constantly work to develop new drugs or drug
1
combinations to combat the worldwide malaria burden.

Sex-Linked Traits
In humans, as well as in many other animals and some plants, the sex of the individual is determined by sex chromosomes—one
pair of non-homologous chromosomes. Until now, we have only considered inheritance patterns among non-sex chromosomes, or
autosomes. In addition to 22 homologous pairs of autosomes, human females have a homologous pair of X chromosomes, whereas
human males have an XY chromosome pair. Although the Y chromosome contains a small region of similarity to the X
chromosome so that they can pair during meiosis, the Y chromosome is much shorter and contains fewer genes. When a gene being
examined is present on the X, but not the Y, chromosome, it is X-linked.
Eye color in Drosophila, the common fruit fly, was the first X-linked trait to be identified. Thomas Hunt Morgan mapped this trait
to the X chromosome in 1910. Like humans, Drosophila males have an XY chromosome pair, and females are XX. In flies the
wild-type eye color is red (XW) and is dominant to white eye color (Xw) (Figure [Link]). Because of the location of the eye-color
gene, reciprocal crosses do not produce the same offspring ratios. Males are said to be hemizygous, in that they have only one
allele for any X-linked characteristic. Hemizygosity makes descriptions of dominance and recessiveness irrelevant for XY males.
Drosophila males lack the white gene on the Y chromosome; that is, their genotype can only be XWY or XwY. In contrast, females
have two allele copies of this gene and can be XWXW, XWXw, or XwXw.

Figure [Link]: In Drosophila, the gene for eye color is located on the X chromosome. Red eye color is wild-type and is dominant
to white eye color.

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In an X-linked cross, the genotypes of F1 and F2 offspring depend on whether the recessive trait was expressed by the male or the
female in the P generation. With respect to Drosophila eye color, when the P male expresses the white-eye phenotype and the
female is homozygously red-eyed, all members of the F1 generation exhibit red eyes (Figure [Link]). The F1 females are
heterozygous (XWXw), and the males are all XWY, having received their X chromosome from the homozygous dominant P female
and their Y chromosome from the P male. A subsequent cross between the XWXw female and the XWY male would produce only
red-eyed females (with XWXW or XWXw genotypes) and both red- and white-eyed males (with XWY or XwY genotypes). Now,
consider a cross between a homozygous white-eyed female and a male with red eyes. The F1 generation would exhibit only
heterozygous red-eyed females (XWXw) and only white-eyed males (XwY). Half of the F2 females would be red-eyed (XWXw) and
half would be white-eyed (XwXw). Similarly, half of the F2 males would be red-eyed (XWY) and half would be white-eyed (XwY).

ART CONNECTION

Figure [Link]: Crosses involving sex-linked traits often give rise to different phenotypes for the different sexes of offspring,
as is the case for this cross involving red and white eye color in Drosophila. In the diagram, w is the white-eye mutant allele
and W is the wild-type, red-eye allele.
What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for red eye
color?

Discoveries in fruit fly genetics can be applied to human genetics. When a female parent is homozygous for a recessive X-linked
trait, she will pass the trait on to 100 percent of her male offspring, because the males will receive the Y chromosome from the
male parent. In humans, the alleles for certain conditions (some color-blindness, hemophilia, and muscular dystrophy) are X-
linked. Females who are heterozygous for these diseases are said to be carriers and may not exhibit any phenotypic effects. These
females will pass the disease to half of their sons and will pass carrier status to half of their daughters; therefore, X-linked traits
appear more frequently in males than females.
In some groups of organisms with sex chromosomes, the sex with the non-homologous sex chromosomes is the female rather than
the male. This is the case for all birds. In this case, sex-linked traits will be more likely to appear in the female, in whom they are
hemizygous.

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 CONCEPT IN ACTION

Sex-linked traits | Biomolecules | MCA…

MCA…

Watch this video to learn more about sex-linked traits.

Linked Genes Violate the Law of Independent Assortment

Although all of Mendel’s pea plant characteristics behaved according to the law of independent assortment, we now know that
some allele combinations are not inherited independently of each other. Genes that are located on separate, non-homologous
chromosomes will always sort independently. However, each chromosome contains hundreds or thousands of genes, organized
linearly on chromosomes like beads on a string. The segregation of alleles into gametes can be influenced by linkage, in which
genes that are located physically close to each other on the same chromosome are more likely to be inherited as a pair. However,
because of the process of recombination, or “crossover,” it is possible for two genes on the same chromosome to behave
independently, or as if they are not linked. To understand this, let us consider the biological basis of gene linkage and
recombination.
Homologous chromosomes possess the same genes in the same order, though the specific alleles of the gene can be different on
each of the two chromosomes. Recall that during interphase and prophase I of meiosis, homologous chromosomes first replicate
and then synapse, with like genes on the homologs aligning with each other. At this stage, segments of homologous chromosomes
exchange linear segments of genetic material (Figure [Link]). This process is called recombination, or crossover, and it is a
common genetic process. Because the genes are aligned during recombination, the gene order is not altered. Instead, the result of
recombination is that maternal and paternal alleles are combined onto the same chromosome. Across a given chromosome, several
recombination events may occur, causing extensive shuffling of alleles.

Figure [Link]: The process of crossover, or recombination, occurs when two homologous chromosomes align and exchange a
segment of genetic material.

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When two genes are located on the same chromosome, they are considered linked, and their alleles tend to be transmitted through
meiosis together. To exemplify this, imagine a dihybrid cross involving flower color and plant height in which the genes are next to
each other on the chromosome. If one homologous chromosome has alleles for tall plants and red flowers, and the other
chromosome has genes for short plants and yellow flowers, then when the gametes are formed, the tall and red alleles will tend to
go together into a gamete and the short and yellow alleles will go into other gametes. These are called the parental genotypes
because they have been inherited intact from the parents of the individual producing gametes. But unlike if the genes were on
different chromosomes, there will be no gametes with tall and yellow alleles and no gametes with short and red alleles. If you
create a Punnett square with these gametes, you will see that the classical Mendelian prediction of a 9:3:3:1 outcome of a dihybrid
cross would not apply. As the distance between two genes increases, the probability of one or more crossovers between them
increases and the genes behave more like they are on separate chromosomes. Geneticists have used the proportion of recombinant
gametes (the ones not like the parents) as a measure of how far apart genes are on a chromosome. Using this information, they have
constructed linkage maps of genes on chromosomes for well-studied organisms, including humans.
Mendel’s seminal publication makes no mention of linkage, and many researchers have questioned whether he encountered linkage
but chose not to publish those crosses out of concern that they would invalidate his independent assortment postulate. The garden
pea has seven chromosomes, and some have suggested that his choice of seven characteristics was not a coincidence. However,
even if the genes he examined were not located on separate chromosomes, it is possible that he simply did not observe linkage
because of the extensive shuffling effects of recombination.

Epistasis
Mendel’s studies in pea plants implied that the sum of an individual’s phenotype was controlled by genes (or as he called them, unit
factors), such that every characteristic was distinctly and completely controlled by a single gene. In fact, single observable
characteristics are almost always under the influence of multiple genes (each with two or more alleles) acting in unison. For
example, at least eight genes contribute to eye color in humans.

CONCEPT IN ACTION

Eye color in humans is determined by multiple alleles. Use the Eye Color Calculator to predict the eye color of children from
parental eye color.

In some cases, several genes can contribute to aspects of a common phenotype without their gene products ever directly interacting.
In the case of organ development, for instance, genes may be expressed sequentially, with each gene adding to the complexity and
specificity of the organ. Genes may function in complementary or synergistic fashions, such that two or more genes expressed
simultaneously affect a phenotype. An apparent example of this occurs with human skin color, which appears to involve the action
of at least three (and probably more) genes. Cases in which inheritance for a characteristic like skin color or human height depend
on the combined effects of numerous genes are called polygenic inheritance.
Genes may also oppose each other, with one gene suppressing the expression of another. In epistasis, the interaction between genes
is antagonistic, such that one gene masks or interferes with the expression of another. “Epistasis” is a word composed of Greek
roots meaning “standing upon.” The alleles that are being masked or silenced are said to be hypostatic to the epistatic alleles that
are doing the masking. Often the biochemical basis of epistasis is a gene pathway in which expression of one gene is dependent on
the function of a gene that precedes or follows it in the pathway.
An example of epistasis is pigmentation in mice. The wild-type coat color, agouti (AA) is dominant to solid-colored fur (aa).
However, a separate gene C, when present as the recessive homozygote (cc), negates any expression of pigment from the A gene
and results in an albino mouse (Figure [Link]). Therefore, the genotypes AAcc, Aacc, and aacc all produce the same albino
phenotype. A cross between heterozygotes for both genes (AaCc x AaCc) would generate offspring with a phenotypic ratio of 9
agouti:3 black:4 albino (Figure [Link]). In this case, the C gene is epistatic to the A gene.

Access for free at OpenStax [Link] [Link]

 Figure [Link]: In this example of epistasis, one gene (C) masks the expression of another (A) for coat color. When the C allele is
present, coat color is expressed; when it is absent (cc), no coat color is expressed. Coat color depends on the A gene, which shows
dominance, with the recessive homozygote showing a different phenotype than the heterozygote or dominant homozygote.

Section Summary
Alleles do not always behave in dominant and recessive patterns. Incomplete dominance describes situations in which the
heterozygote exhibits a phenotype that is intermediate between the homozygous phenotypes. Codominance describes the
simultaneous expression of both of the alleles in the heterozygote. Although diploid organisms can only have two alleles for any
given gene, it is common for more than two alleles for a gene to exist in a population. In humans, as in many animals and some
plants, females have two X chromosomes and males have one X and one Y chromosome. Genes that are present on the X but not
the Y chromosome are said to be X-linked, such that males only inherit one allele for the gene, and females inherit two.
According to Mendel’s law of independent assortment, genes sort independently of each other into gametes during meiosis. This
occurs because chromosomes, on which the genes reside, assort independently during meiosis and crossovers cause most genes on
the same chromosomes to also behave independently. When genes are located in close proximity on the same chromosome, their
alleles tend to be inherited together. This results in offspring ratios that violate Mendel's law of independent assortment. However,
recombination serves to exchange genetic material on homologous chromosomes such that maternal and paternal alleles may be
recombined on the same chromosome. This is why alleles on a given chromosome are not always inherited together.
Recombination is a random event occurring anywhere on a chromosome. Therefore, genes that are far apart on the same

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chromosome are likely to still assort independently because of recombination events that occurred in the intervening chromosomal
space.
Whether or not they are sorting independently, genes may interact at the level of gene products, such that the expression of an allele
for one gene masks or modifies the expression of an allele for a different gene. This is called epistasis.

Art Connections
Figure [Link]: What ratio of offspring would result from a cross between a white-eyed male and a female that is heterozygous for
red eye color?

Answer
Half of the female offspring would be heterozygous (XWXw) with red eyes, and half would be homozygous recessive (XwXw)
with white eyes. Half of the male offspring would be hemizygous dominant (XWY) with red eyes, and half would be
hemizygous recessive (XwY) with white eyes.

Footnotes
1. 1 Sumiti Vinayak et al., “Origin and Evolution of Sulfadoxine Resistant Plasmodium falciparum,” PLoS Pathogens 6 (2010):
e1000830.

Glossary

codominance
in a heterozygote, complete and simultaneous expression of both alleles for the same characteristic

epistasis
an interaction between genes such that one gene masks or interferes with the expression of another

hemizygous
the presence of only one allele for a characteristic, as in X-linkage; hemizygosity makes descriptions of dominance and
recessiveness irrelevant

incomplete dominance
in a heterozygote, expression of two contrasting alleles such that the individual displays an intermediate phenotype

linkage
a phenomenon in which alleles that are located in close proximity to each other on the same chromosome are more likely to be
inherited together

recombination
the process during meiosis in which homologous chromosomes exchange linear segments of genetic material, thereby
dramatically increasing genetic variation in the offspring and separating linked genes

wild type
the most commonly occurring genotype or phenotype for a given characteristic found in a population

X-linked
a gene present on the X chromosome, but not the Y chromosome

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 6.1.3: Extensions of the Laws of Inheritance is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.

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8.3: Extensions of the Laws of Inheritance by OpenStax is licensed CC BY 4.0.

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6.1.E: Patterns of Inheritance (Exercises)
8.1: Mendel’s Experiments
Multiple Choice
Imagine that you are performing a cross involving seed color in garden pea plants. What traits would you expect to observe in the
F1 offspring if you cross true-breeding parents with green seeds and yellow seeds? Yellow seed color is dominant over green.
A. only yellow-green seeds
B. only yellow seeds
C. 1:1 yellow seeds:green seeds
D. 1:3 green seeds:yellow seeds

Answer
B

Imagine that you are performing a cross involving seed texture in garden pea plants. You cross true-breeding round and wrinkled
parents to obtain F1 offspring. Which of the following experimental results in terms of numbers of plants are closest to what you
expect in the F2 progeny?
A. 810 round seeds
B. 810 wrinkled seeds
C. 405:395 round seeds:wrinkled seeds
D. 610:190 round seeds:wrinkled seeds

Answer
D

Free Response
Describe one of the reasons that made the garden pea an excellent choice of model system for studying inheritance.

Answer
The garden pea has flowers that close tightly during self-pollination. This helps to prevent accidental or unintentional
fertilizations that could have diminished the accuracy of Mendel’s data.

8.2: Laws of Inheritance

Multiple Choice
The observable traits expressed by an organism are described as its ________.
A. phenotype
B. genotype
C. alleles
D. zygote

Answer
A

A recessive trait will be observed in individuals that are ________ for that trait.
A. heterozygous
B. homozygous or heterozygous
C. homozygousdiploid

Answer

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 C

What are the types of gametes that can be produced by an individual with the genotype AaBb?
A. Aa, Bb
B. AA, aa, BB, bb
C. AB, Ab, aB, ab
D. AB, ab

Answer
C

What is the reason for doing a test cross?

A. to identify heterozygous individuals with the dominant phenotype
B. to determine which allele is dominant and which is recessive
C. to identify homozygous recessive individuals in the F2
D. to determine if two genes assort independently

Answer
A

Free Response
Use a Punnett square to predict the offspring in a cross between a dwarf pea plant (homozygous recessive) and a tall pea plant
(heterozygous). What is the phenotypic ratio of the offspring?

Answer
The Punnett square would be 2 × 2 and will have T and T along the top and T and t along the left side. Clockwise from the top
left, the genotypes listed within the boxes will be Tt, Tt, tt, and tt. The phenotypic ratio will be 1 tall:1 dwarf.

Use a Punnett square to predict the offspring in a cross between a tall pea plant (heterozygous) and a tall pea plant (heterozygous).
What is the genotypic ratio of the offspring?

Answer
The Punnett square will be 2 × 2 and will have T and t along the top and T and t along the left side. Clockwise from the top left,
the genotypes listed within the boxes will be TT, Tt, Tt, and tt. The genotypic ratio will be 1TT:2Tt:1tt.

8.3: Extensions of the Laws of Inheritance

Multiple Choice
If black and white true-breeding mice are mated and the result is all gray offspring, what inheritance pattern would this be
indicative of?
A. dominance
B. codominance
C. multiple alleles
D. incomplete dominance

Answer
D

The ABO blood groups in humans are expressed as the IA, IB, and i alleles. The IA allele encodes the A blood group antigen, IB
encodes B, and i encodes O. Both A and B are dominant to O. If a heterozygous blood type A parent (IAi) and a heterozygous blood
type B parent (IBi) mate, one quarter of their offspring are expected to have the AB blood type (IAIB) in which both antigens are
expressed equally. Therefore, ABO blood groups are an example of:

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 A. multiple alleles and incomplete dominance
B. codominance and incomplete dominance
C. incomplete dominance only
D. multiple alleles and codominance

Answer
D

In a cross between a homozygous red-eyed female fruit fly and a white-eyed male fruit fly, what is the expected outcome?
A. all white-eyed male offspring
B. all white-eyed female offspring
C. all red-eyed offspring
D. half white-eyed make offspring

Answer
C

When a population has a gene with four alleles circulating, how many possible genotypes are there?
A. 3
B. 6
C. 10
D. 16

Answer
C

Free Response
Can a male be a carrier of red-green color blindness?

Answer
No, males can only express color blindness and cannot carry it because an individual needs two X chromosomes to be a carrier.

Could an individual with blood type O (genotype ii) be a legitimate child of parents in which one parent had blood type A and the
other parent had blood type B?

Answer
Yes this child could have come from these parents. The child would have inherited an i allele from each parent and for this to
happen the type A parent had to have genotype IAi and the type b parent had to have genotype IBi.

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OpenStax.
8.E: Patterns of Inheritance (Exercises) by OpenStax is licensed CC BY 4.0.

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6.2: Pedigrees review
Key terms
Term Meaning

Chart that shows the presence or absence of a trait within a family

Pedigree
across generations

Genotype The genetic makeup of an organism (ex: TT)

Phenotype The physical characteristics of an organism (ex: tall)

Dominant allele Allele that is phenotypically expressed over another allele

Recessive allele Allele that is only expressed in absence of a dominant allele

Autosomal trait Trait that is located on an autosome (non-sex chromosome)

Sex-linked trait Trait that is located on one of the two sex chromosomes

Homozygous Having two identical alleles for a particular gene

Heterozygous Having two different alleles for a particular gene

Pedigrees
Pedigrees are used to analyze the pattern of inheritance of a particular trait throughout a family. Pedigrees show the presence or
absence of a trait as it relates to the relationship among parents, offspring, and siblings.

Reading a pedigree

Common pedigree symbols.

Pedigrees represent family members and relationships using standardized symbols.
By analyzing a pedigree, we can determine genotypes, identify phenotypes, and predict how a trait will be passed on in the future.
The information from a pedigree makes it possible to determine how certain alleles are inherited: whether they are dominant,
recessive, autosomal, or sex-linked.
To start reading a pedigree:
1. Determine whether the trait is dominant or recessive. If the trait is dominant, one of the parents must have the trait.
Dominant traits will not skip a generation. If the trait is recessive, neither parent is required to have the trait since they can be
heterozygous.

6.2.1 [Link]
 2. Determine if the chart shows an autosomal or sex-linked (usually X-linked) trait. For example, in X-linked recessive traits,
males are much more commonly affected than females. In autosomal traits, both males and females are equally likely to be
affected (usually in equal proportions).

Example: Autosomal dominant trait

The diagram shows the inheritance of freckles in a family. The allele for freckles (F) is dominant to the allele for no freckles (f).
At the top of the pedigree is a grandmother (individual I-2) who has freckles. Two of her three children have the trait (individuals
II-3 and II-5) and three of her grandchildren have the trait (individuals III-3, III-4, and III-5).

[What is the genotype of individual I-2?]

Since freckles are dominant to no freckles, an affected individual such as I-2 must at least have one F allele.
The trait shows up in all generations and affects both males and females equally. This suggests that it is an autosomal dominant
trait.
Unaffected individuals must have two recessive alleles (ff) in order to not have freckles. If we notice, I-2 has some children
who do not have freckles. In order to produce children with a genotype of ff, I-2 must be able to donate a f allele.
We can therefore conclude that her genotype is Ff.

Example: X-linked recessive trait

The diagram shows the inheritance of colorblindness in a family. Colorblindness is a recessive and X-linked trait (X ) . The allele
b

for normal vision is dominant and is represented by X . B

In generation I, neither parent has the trait, but one of their children (II-3) is colorblind. Because there are unaffected parents that
have affected offspring, it can be assumed that the trait is recessive. In addition, the trait appears to affect males more than females

6.2.2 [Link]
(in this case, exclusively males are affected), suggesting that the trait may be X-linked.

[What is the genotype of individual III-2?]

We can determine the genotype of III-2 by looking at her children. Since she is an unaffected female, she must have at least one
normal vision allele (X ) . Her two genotype options are then X X or X X .
B B B B b

However, her son (IV-1) is colorblind, meaning that he has a genotype of X Y. Because males always get their X chromosome
b

from their mothers (and their Y from their fathers), his colorblind allele must come from III-2.
We can then determine that III-2's genotype is X B b
X , so she can pass the X on to her son.
b

Common mistakes and misconceptions

The presence of many affected individuals in a family does not always mean that the trait is dominant. The terms
dominant and recessive refer to the way that a trait is expressed, not by how often it shows up in a family. In fact, although it is
uncommon, a trait may be recessive but still show up in all generations of a pedigree.
You may not always be able to determine the genotype of an individual based on a pedigree. Sometimes an individual can
either be homozygous dominant or heterozygous for a trait. Often, we can use the relationships between an individual and their
parents, siblings, and offspring to determine genotypes. However, not all carriers are always explicitly indicated in a pedigree,
and it may not be possible to determine based on the information provided.

Contributors and Attributions

Khan Academy (CC BY-NC-SA 3.0; All Khan Academy content is available for free at [Link])

6.2: Pedigrees review is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by LibreTexts.

6.2.3 [Link]
 CHAPTER OVERVIEW

7: Evolution
7.1: Discovering How Populations Change
7.2: Mechanisms of Evolution
7.3: Evidence of Evolution
7.4: Speciation
7.5: Common Misconceptions about Evolution
7.E: Evolution and Its Processes (Exercises)

Thumbnail: The hominoids are descendants of a common ancestor. (Public Domain; Huxley - Mans Place in Nature).

This page titled 7: Evolution is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.

1
7.1: Discovering How Populations Change
The theory of evolution by natural selection describes a mechanism for species change over time. That species change had been
suggested and debated well before Darwin. The view that species were static and unchanging was grounded in the writings of
Plato, yet there were also ancient Greeks that expressed evolutionary ideas.
In the eighteenth century, ideas about the evolution of animals were reintroduced by the naturalist Georges-Louis Leclerc, Comte
de Buffon and even by Charles Darwin’s grandfather, Erasmus Darwin. During this time, it was also accepted that there were
extinct species. At the same time, James Hutton, the Scottish naturalist, proposed that geological change occurred gradually by the
accumulation of small changes from processes (over long periods of time) just like those happening today. This contrasted with the
predominant view that the geology of the planet was a consequence of catastrophic events occurring during a relatively brief past.
Hutton’s view was later popularized by the geologist Charles Lyell in the nineteenth century. Lyell became a friend to Darwin and
his ideas were very influential on Darwin’s thinking. Lyell argued that the greater age of Earth gave more time for gradual change
in species, and the process provided an analogy for gradual change in species.
In the early nineteenth century, Jean-Baptiste Lamarck published a book that detailed a mechanism for evolutionary change that is
now referred to as inheritance of acquired characteristics. In Lamarck’s theory, modifications in an individual caused by its
environment, or the use or disuse of a structure during its lifetime, could be inherited by its offspring and, thus, bring about change
in a species. While this mechanism for evolutionary change as described by Lamarck was discredited, Lamarck’s ideas were an
important influence on evolutionary thought. The inscription on the statue of Lamarck that stands at the gates of the Jardin des
Plantes in Paris describes him as the “founder of the doctrine of evolution.”

Charles Darwin and Natural Selection

The actual mechanism for evolution was independently conceived of and described by two naturalists, Charles Darwin and Alfred
Russell Wallace, in the mid-nineteenth century. Importantly, each spent time exploring the natural world on expeditions to the
tropics. From 1831 to 1836, Darwin traveled around the world on H.M.S. Beagle, visiting South America, Australia, and the
southern tip of Africa. Wallace traveled to Brazil to collect insects in the Amazon rainforest from 1848 to 1852 and to the Malay
Archipelago from 1854 to 1862. Darwin’s journey, like Wallace’s later journeys in the Malay Archipelago, included stops at several
island chains, the last being the Galápagos Islands (west of Ecuador). On these islands, Darwin observed species of organisms on
different islands that were clearly similar, yet had distinct differences. For example, the ground finches inhabiting the Galápagos
Islands comprised several species that each had a unique beak shape (Figure 7.1.1). He observed both that these finches closely
resembled another finch species on the mainland of South America and that the group of species in the Galápagos formed a graded
series of beak sizes and shapes, with very small differences between the most similar. Darwin imagined that the island species
might be all species modified from one original mainland species. In 1860, he wrote, “Seeing this gradation and diversity of
structure in one small, intimately related group of birds, one might really fancy that from an original paucity of birds in this
1
archipelago, one species had been taken and modified for different ends.”

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 Figure 7.1.1: Darwin observed that beak shape varies among finch species. He postulated that the beak of an ancestral species
had adapted over time to equip the finches to acquire different food sources. This illustration shows the beak shapes for four
species of ground finch: 1. Geospiza magnirostris (the large ground finch), 2. G. fortis (the medium ground finch), 3. G. parvula
(the small tree finch), and 4. Certhidea olivacea (the green-warbler finch).
Wallace and Darwin both observed similar patterns in other organisms and independently conceived a mechanism to explain how
and why such changes could take place. Darwin called this mechanism natural selection. Natural selection, Darwin argued, was an
inevitable outcome of three principles that operated in nature. First, the characteristics of organisms are inherited, or passed from
parent to offspring. Second, more offspring are produced than are able to survive; in other words, resources for survival and
reproduction are limited. The capacity for reproduction in all organisms outstrips the availability of resources to support their
numbers. Thus, there is a competition for those resources in each generation. Both Darwin and Wallace’s understanding of this
principle came from reading an essay by the economist Thomas Malthus, who discussed this principle in relation to human
populations. Third, offspring vary among each other in regard to their characteristics and those variations are inherited. Out of these
three principles, Darwin and Wallace reasoned that offspring with inherited characteristics that allow them to best compete for
limited resources will survive and have more offspring than those individuals with variations that are less able to compete. Because
characteristics are inherited, these traits will be better represented in the next generation. This will lead to change in populations
over generations in a process that Darwin called “descent with modification.”
Papers by Darwin and Wallace (Figure 7.1.2) presenting the idea of natural selection were read together in 1858 before the
Linnaean Society in London. The following year Darwin’s book, On the Origin of Species, was published, which outlined in
considerable detail his arguments for evolution by natural selection.

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 Figure 7.1.2: (a) Charles Darwin and (b) Alfred Wallace wrote scientific papers on natural selection that were presented together
before the Linnean Society in 1858.
Demonstrations of evolution by natural selection can be time consuming. One of the best demonstrations has been in the very birds
that helped to inspire the theory, the Galápagos finches. Peter and Rosemary Grant and their colleagues have studied Galápagos
finch populations every year since 1976 and have provided important demonstrations of the operation of natural selection. The
Grants found changes from one generation to the next in the beak shapes of the medium ground finches on the Galápagos island of
Daphne Major. The medium ground finch feeds on seeds. The birds have inherited variation in the bill shape with some individuals
having wide, deep bills and others having thinner bills. Large-billed birds feed more efficiently on large, hard seeds, whereas
smaller billed birds feed more efficiently on small, soft seeds. During 1977, a drought period altered vegetation on the island. After
this period, the number of seeds declined dramatically: the decline in small, soft seeds was greater than the decline in large, hard
seeds. The large-billed birds were able to survive better than the small-billed birds the following year. The year following the
drought when the Grants measured beak sizes in the much-reduced population, they found that the average bill size was larger
(Figure 7.1.3). This was clear evidence for natural selection (differences in survival) of bill size caused by the availability of seeds.
The Grants had studied the inheritance of bill sizes and knew that the surviving large-billed birds would tend to produce offspring
with larger bills, so the selection would lead to evolution of bill size. Subsequent studies by the Grants have demonstrated selection
on and evolution of bill size in this species in response to changing conditions on the island. The evolution has occurred both to
larger bills, as in this case, and to smaller bills when large seeds became rare.

Figure 7.1.3: A drought on the Galápagos island of Daphne Major in 1977 reduced the number of small seeds available to
finches, causing many of the small-beaked finches to die. This caused an increase in the finches’ average beak size between 1976
and 1978.

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Variation and Adaptation
Natural selection can only take place if there is variation, or differences, among individuals in a population. Importantly, these
differences must have some genetic basis; otherwise, selection will not lead to change in the next generation. This is critical
because variation among individuals can be caused by non-genetic reasons, such as an individual being taller because of better
nutrition rather than different genes.
Genetic diversity in a population comes from two main sources: mutation and sexual reproduction. Mutation, a change in DNA, is
the ultimate source of new alleles or new genetic variation in any population. An individual that has a mutated gene might have a
different trait than other individuals in the population. However, this is not always the case. A mutation can have one of three
outcomes on the organisms’ appearance (or phenotype):
A mutation may affect the phenotype of the organism in a way that gives it reduced fitness—lower likelihood of survival,
resulting in fewer offspring.
A mutation may produce a phenotype with a beneficial effect on fitness.
Many mutations, called neutral mutations, will have no effect on fitness.
Mutations may also have a whole range of effect sizes on the fitness of the organism that expresses them in their phenotype, from a
small effect to a great effect. Sexual reproduction and crossing over in meiosis also lead to genetic diversity: when two parents
reproduce, unique combinations of alleles assemble to produce unique genotypes and, thus, phenotypes in each of the offspring.
A heritable trait that aids the survival and reproduction of an organism in its present environment is called an adaptation. An
adaptation is a “match” of the organism to the environment. Adaptation to an environment comes about when a change in the range
of genetic variation occurs over time that increases or maintains the match of the population with its environment. The variations in
finch beaks shifted from generation to generation providing adaptation to food availability.
Whether or not a trait is favorable depends on the environment at the time. The same traits do not always have the same relative
benefit or disadvantage because environmental conditions can change. For example, finches with large bills were benefited in one
climate, while small bills were a disadvantage; in a different climate, the relationship reversed.

Patterns of Evolution
The evolution of species has resulted in enormous variation in form and function. When two species evolve in different directions
from a common point, it is called divergent evolution. Such divergent evolution can be seen in the forms of the reproductive organs
of flowering plants, which share the same basic anatomies; however, they can look very different as a result of selection in different
physical environments, and adaptation to different kinds of pollinators (Figure 7.1.4).

Figure 7.1.4: Flowering plants evolved from a common ancestor. Notice that the (a) dense blazing star and (b) purple coneflower
vary in appearance, yet both share a similar basic morphology. (credit a, b: modification of work by Cory Zanker)
In other cases, similar phenotypes evolve independently in distantly related species. For example, flight has evolved in both bats
and insects, and they both have structures we refer to as wings, which are adaptations to flight. The wings of bats and insects,
however, evolved from very different original structures. When similar structures arise through evolution independently in different
species it is called convergent evolution. The wings of bats and insects are called analogous structures; they are similar in function
and appearance, but do not share an origin in a common ancestor. Instead they evolved independently in the two lineages. The

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wings of a hummingbird and an ostrich are homologous structures, meaning they share similarities (despite their differences
resulting from evolutionary divergence). The wings of hummingbirds and ostriches did not evolve independently in the
hummingbird lineage and the ostrich lineage—they descended from a common ancestor with wings.

The Modern Synthesis

The mechanisms of inheritance, genetics, were not understood at the time Darwin and Wallace were developing their idea of
natural selection. This lack of understanding was a stumbling block to comprehending many aspects of evolution. In fact, blending
inheritance was the predominant (and incorrect) genetic theory of the time, which made it difficult to understand how natural
selection might operate. Darwin and Wallace were unaware of the genetics work by Austrian monk Gregor Mendel, which was
published in 1866, not long after publication of On the Origin of Species. Mendel’s work was rediscovered in the early twentieth
century at which time geneticists were rapidly coming to an understanding of the basics of inheritance. Initially, the newly
discovered particulate nature of genes made it difficult for biologists to understand how gradual evolution could occur. But over the
next few decades genetics and evolution were integrated in what became known as the modern synthesis—the coherent
understanding of the relationship between natural selection and genetics that took shape by the 1940s and is generally accepted
today. In sum, the modern synthesis describes how evolutionary pressures, such as natural selection, can affect a population’s
genetic makeup, and, in turn, how this can result in the gradual evolution of populations and species. The theory also connects this
gradual change of a population over time, called microevolution, with the processes that gave rise to new species and higher
taxonomic groups with widely divergent characters, called macroevolution.

Population Genetics
Recall that a gene for a particular character may have several variants, or alleles, that code for different traits associated with that
character. For example, in the ABO blood type system in humans, three alleles determine the particular blood-type protein on the
surface of red blood cells. Each individual in a population of diploid organisms can only carry two alleles for a particular gene, but
more than two may be present in the individuals that make up the population. Mendel followed alleles as they were inherited from
parent to offspring. In the early twentieth century, biologists began to study what happens to all the alleles in a population in a field
of study known as population genetics.
Until now, we have defined evolution as a change in the characteristics of a population of organisms, but behind that phenotypic
change is genetic change. In population genetic terms, evolution is defined as a change in the frequency of an allele in a population.
Using the ABO system as an example, the frequency of one of the alleles, IA, is the number of copies of that allele divided by all
2
the copies of the ABO gene in the population. For example, a study in Jordan found a frequency of IA to be 26.1 percent. The IB, I0
alleles made up 13.4 percent and 60.5 percent of the alleles respectively, and all of the frequencies add up to 100 percent. A change
in this frequency over time would constitute evolution in the population.
There are several ways the allele frequencies of a population can change. One of those ways is natural selection. If a given allele
confers a phenotype that allows an individual to have more offspring that survive and reproduce, that allele, by virtue of being
inherited by those offspring, will be in greater frequency in the next generation. Since allele frequencies always add up to 100
percent, an increase in the frequency of one allele always means a corresponding decrease in one or more of the other alleles.
Highly beneficial alleles may, over a very few generations, become “fixed” in this way, meaning that every individual of the
population will carry the allele. Similarly, detrimental alleles may be swiftly eliminated from the gene pool, the sum of all the
alleles in a population. Part of the study of population genetics is tracking how selective forces change the allele frequencies in a
population over time, which can give scientists clues regarding the selective forces that may be operating on a given population.
The studies of changes in wing coloration in the peppered moth from mottled white to dark in response to soot-covered tree trunks
and then back to mottled white when factories stopped producing so much soot is a classic example of studying evolution in natural
populations (Figure 7.1.5).

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 Figure 7.1.5: As the Industrial Revolution caused trees to darken from soot, darker colored peppered moths were better
camouflaged than the lighter colored ones, which caused there to be more of the darker colored moths in the population.
In the early twentieth century, English mathematician Godfrey Hardy and German physician Wilhelm Weinberg independently
provided an explanation for a somewhat counterintuitive concept. Hardy’s original explanation was in response to a
misunderstanding as to why a “dominant” allele, one that masks a recessive allele, should not increase in frequency in a population
until it eliminated all the other alleles. The question resulted from a common confusion about what “dominant” means, but it forced
Hardy, who was not even a biologist, to point out that if there are no factors that affect an allele frequency those frequencies will
remain constant from one generation to the next. This principle is now known as the Hardy-Weinberg equilibrium. The theory
states that a population’s allele and genotype frequencies are inherently stable—unless some kind of evolutionary force is acting on
the population, the population would carry the same alleles in the same proportions generation after generation. Individuals would,
as a whole, look essentially the same and this would be unrelated to whether the alleles were dominant or recessive. The four most
important evolutionary forces, which will disrupt the equilibrium, are natural selection, mutation, genetic drift, and migration into
or out of a population. A fifth factor, nonrandom mating, will also disrupt the Hardy-Weinberg equilibrium but only by shifting
genotype frequencies, not allele frequencies. In nonrandom mating, individuals are more likely to mate with like individuals (or
unlike individuals) rather than at random. Since nonrandom mating does not change allele frequencies, it does not cause evolution
directly. Natural selection has been described. Mutation creates one allele out of another one and changes an allele’s frequency by a
small, but continuous amount each generation. Each allele is generated by a low, constant mutation rate that will slowly increase
the allele’s frequency in a population if no other forces act on the allele. If natural selection acts against the allele, it will be
removed from the population at a low rate leading to a frequency that results from a balance between selection and mutation. This
is one reason that genetic diseases remain in the human population at very low frequencies. If the allele is favored by selection, it
will increase in frequency. Genetic drift causes random changes in allele frequencies when populations are small. Genetic drift can
often be important in evolution, as discussed in the next section. Finally, if two populations of a species have different allele
frequencies, migration of individuals between them will cause frequency changes in both populations. As it happens, there is no
population in which one or more of these processes are not operating, so populations are always evolving, and the Hardy-Weinberg
equilibrium will never be exactly observed. However, the Hardy-Weinberg principle gives scientists a baseline expectation for
allele frequencies in a non-evolving population to which they can compare evolving populations and thereby infer what
evolutionary forces might be at play. The population is evolving if the frequencies of alleles or genotypes deviate from the value
expected from the Hardy-Weinberg principle.
Darwin identified a special case of natural selection that he called sexual selection. Sexual selection affects an individual’s ability
to mate and thus produce offspring, and it leads to the evolution of dramatic traits that often appear maladaptive in terms of
survival but persist because they give their owners greater reproductive success. Sexual selection occurs in two ways: through
male–male competition for mates and through female selection of mates. Male–male competition takes the form of conflicts
between males, which are often ritualized, but may also pose significant threats to a male’s survival. Sometimes the competition is
for territory, with females more likely to mate with males with higher quality territories. Female choice occurs when females
choose a male based on a particular trait, such as feather colors, the performance of a mating dance, or the building of an elaborate
structure. In some cases male–male competition and female choice combine in the mating process. In each of these cases, the traits
selected for, such as fighting ability or feather color and length, become enhanced in the males. In general, it is thought that sexual
selection can proceed to a point at which natural selection against a character’s further enhancement prevents its further evolution
because it negatively impacts the male’s ability to survive. For example, colorful feathers or an elaborate display make the male
more obvious to predators.

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Summary
Evolution by natural selection arises from three conditions: individuals within a species vary, some of those variations are heritable,
and organisms have more offspring than resources can support. The consequence is that individuals with relatively advantageous
variations will be more likely to survive and have higher reproductive rates than those individuals with different traits. The
advantageous traits will be passed on to offspring in greater proportion. Thus, the trait will have higher representation in the next
and subsequent generations leading to genetic change in the population.
The modern synthesis of evolutionary theory grew out of the reconciliation of Darwin’s, Wallace’s, and Mendel’s thoughts on
evolution and heredity. Population genetics is a theoretical framework for describing evolutionary change in populations through
the change in allele frequencies. Population genetics defines evolution as a change in allele frequency over generations. In the
absence of evolutionary forces allele frequencies will not change in a population; this is known as Hardy-Weinberg equilibrium
principle. However, in all populations, mutation, natural selection, genetic drift, and migration act to change allele frequencies.

Footnotes
1. 1 Charles Darwin, Journal of Researches into the Natural History and Geology of the Countries Visited during the Voyage of
H.M.S. Beagle Round the World, under the Command of Capt. Fitz Roy, R.N, 2nd. ed. (London: John Murray, 1860),
[Link]
2. 2 Sahar S. Hanania, Dhia S. Hassawi, and Nidal M. Irshaid, “Allele Frequency and Molecular Genotypes of ABO Blood Group
System in a Jordanian Population,” Journal of Medical Sciences 7 (2007): 51-58, doi:10.3923/jms.2007.51.58

Glossary

adaptation
a heritable trait or behavior in an organism that aids in its survival in its present environment

analogous structure
a structure that is similar because of evolution in response to similar selection pressures resulting in convergent evolution, not
similar because of descent from a common ancestor

convergent evolution
an evolution that results in similar forms on different species

divergent evolution
an evolution that results in different forms in two species with a common ancestor

gene pool
all of the alleles carried by all of the individuals in the population

genetic drift
the effect of chance on a population’s gene pool

homologous structure
a structure that is similar because of descent from a common ancestor

inheritance of acquired characteristics

a phrase that describes the mechanism of evolution proposed by Lamarck in which traits acquired by individuals through use or
disuse could be passed on to their offspring thus leading to evolutionary change in the population

macroevolution
a broader scale of evolutionary changes seen over paleontological time

microevolution
the changes in a population’s genetic structure (i.e., allele frequency)

migration

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 the movement of individuals of a population to a new location; in population genetics it refers to the movement of individuals
and their alleles from one population to another, potentially changing allele frequencies in both the old and the new population

modern synthesis
the overarching evolutionary paradigm that took shape by the 1940s and is generally accepted today

natural selection
the greater relative survival and reproduction of individuals in a population that have favorable heritable traits, leading to
evolutionary change

population genetics
the study of how selective forces change the allele frequencies in a population over time

variation
the variety of alleles in a population

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 7.1: Discovering How Populations Change is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
11.1: Discovering How Populations Change by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 7.1.8 [Link]

7.2: Mechanisms of Evolution
The Hardy-Weinberg equilibrium principle says that allele frequencies in a population will remain constant in the absence of the
four factors that could change them. Those factors are natural selection, mutation, genetic drift, and migration (gene flow). In fact,
we know they are probably always affecting populations.

Natural Selection
Natural selection has already been discussed. Alleles are expressed in a phenotype. Depending on the environmental conditions, the
phenotype confers an advantage or disadvantage to the individual with the phenotype relative to the other phenotypes in the
population. If it is an advantage, then that individual will likely have more offspring than individuals with the other phenotypes,
and this will mean that the allele behind the phenotype will have greater representation in the next generation. If conditions remain
the same, those offspring, which are carrying the same allele, will also benefit. Over time, the allele will increase in frequency in
the population.

Mutation
Mutation is a source of new alleles in a population. Mutation is a change in the DNA sequence of the gene. A mutation can change
one allele into another, but the net effect is a change in frequency. The change in frequency resulting from mutation is small, so its
effect on evolution is small unless it interacts with one of the other factors, such as selection. A mutation may produce an allele that
is selected against, selected for, or selectively neutral. Harmful mutations are removed from the population by selection and will
generally only be found in very low frequencies equal to the mutation rate. Beneficial mutations will spread through the population
through selection, although that initial spread is slow. Whether or not a mutation is beneficial or harmful is determined by whether
it helps an organism survive to sexual maturity and reproduce. It should be noted that mutation is the ultimate source of genetic
variation in all populations—new alleles, and, therefore, new genetic variations arise through mutation.

Genetic Drift
Another way a population’s allele frequencies can change is genetic drift (Figure 7.2.1), which is simply the effect of chance.
Genetic drift is most important in small populations. Drift would be completely absent in a population with infinite individuals, but,
of course, no population is this large. Genetic drift occurs because the alleles in an offspring generation are a random sample of the
alleles in the parent generation. Alleles may or may not make it into the next generation due to chance events including mortality of
an individual, events affecting finding a mate, and even the events affecting which gametes end up in fertilizations. If one
individual in a population of ten individuals happens to die before it leaves any offspring to the next generation, all of its genes—a
tenth of the population’s gene pool—will be suddenly lost. In a population of 100, that 1 individual represents only 1 percent of the
overall gene pool; therefore, it has much less impact on the population’s genetic structure and is unlikely to remove all copies of
even a relatively rare allele.
Imagine a population of ten individuals, half with allele A and half with allele a (the individuals are haploid). In a stable population,
the next generation will also have ten individuals. Choose that generation randomly by flipping a coin ten times and let heads be A
and tails be a. It is unlikely that the next generation will have exactly half of each allele. There might be six of one and four of the
other, or some different set of frequencies. Thus, the allele frequencies have changed and evolution has occurred. A coin will no
longer work to choose the next generation (because the odds are no longer one half for each allele). The frequency in each
generation will drift up and down on what is known as a random walk until at one point either all A or all a are chosen and that
allele is fixed from that point on. This could take a very long time for a large population. This simplification is not very biological,
but it can be shown that real populations behave this way. The effect of drift on frequencies is greater the smaller a population is.
Its effect is also greater on an allele with a frequency far from one half. Drift will influence every allele, even those that are being
naturally selected.

ART CONNECTION

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 Figure 7.2.1: Genetic drift in a population can lead to the elimination of an allele from a population by chance. In each
generation, a random set of individuals reproduces to produce the next generation. The frequency of alleles in the next
generation is equal to the frequency of alleles among the individuals reproducing.
Do you think genetic drift would happen more quickly on an island or on the mainland?

Genetic drift can also be magnified by natural or human-caused events, such as a disaster that randomly kills a large portion of the
population, which is known as the bottleneck effectthat results in a large portion of the genome suddenly being wiped out (Figure
7.2.2). In one fell swoop, the genetic structure of the survivors becomes the genetic structure of the entire population, which may

be very different from the pre-disaster population. The disaster must be one that kills for reasons unrelated to the organism’s traits,
such as a hurricane or lava flow. A mass killing caused by unusually cold temperatures at night, is likely to affect individuals
differently depending on the alleles they possess that confer cold hardiness.

Figure 7.2.2: A chance event or catastrophe can reduce the genetic variability within a population.

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Another scenario in which populations might experience a strong influence of genetic drift is if some portion of the population
leaves to start a new population in a new location, or if a population gets divided by a physical barrier of some kind. In this
situation, those individuals are unlikely to be representative of the entire population which results in the founder effect. The
founder effect occurs when the genetic structure matches that of the new population’s founding fathers and mothers. The founder
effect is believed to have been a key factor in the genetic history of the Afrikaner population of Dutch settlers in South Africa, as
evidenced by mutations that are common in Afrikaners but rare in most other populations. This is likely due to a higher-than-
normal proportion of the founding colonists, which were a small sample of the original population, carried these mutations. As a
result, the population expresses unusually high incidences of Huntington’s disease (HD) and Fanconi anemia (FA), a genetic
1
disorder known to cause bone marrow and congenital abnormalities, and even cancer.

CONCEPT IN ACTION

Visit this site to learn more about genetic drift and to run simulations of allele changes caused by drift.

Gene Flow
Another important evolutionary force is gene flow, or the flow of alleles in and out of a population resulting from the migration of
individuals or gametes (Figure 7.2.3). While some populations are fairly stable, others experience more flux. Many plants, for
example, send their seeds far and wide, by wind or in the guts of animals; these seeds may introduce alleles common in the source
population to a new population in which they are rare.

Figure 7.2.3: Gene flow can occur when an individual travels from one geographic location to another and joins a different
population of the species. In the example shown here, the brown allele is introduced into the green population.

Summary
There are four factors that can change the allele frequencies of a population. Natural selection works by selecting for alleles that
confer beneficial traits or behaviors, while selecting against those for deleterious qualities. Mutations introduce new alleles into a
population. Genetic drift stems from the chance occurrence that some individuals have more offspring than others and results in
changes in allele frequencies that are random in direction. When individuals leave or join the population, allele frequencies can
change as a result of gene flow.

Art Connections
Figure 7.2.1: Do you think genetic drift would happen more quickly on an island or on the mainland?

Answer
Genetic drift is likely to occur more rapidly on an island, where smaller populations are expected to occur.

Footnotes
1. 1 A. J. Tipping et al., “Molecular and Genealogical Evidence for a Founder Effect in Fanconi Anemia Families of the Afrikaner
Population of South Africa,” PNAS 98, no. 10 (2001): 5734-5739, doi: 10.1073/pnas.091402398.

Glossary

bottleneck effect
the magnification of genetic drift as a result of natural events or catastrophes

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founder effect
a magnification of genetic drift in a small population that migrates away from a large parent population carrying with it an
unrepresentative set of alleles

gene flow
the flow of alleles in and out of a population due to the migration of individuals or gametes

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 7.2: Mechanisms of Evolution is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
11.2: Mechanisms of Evolution by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 7.2.4 [Link]

7.3: Evidence of Evolution
The evidence for evolution is compelling and extensive. Looking at every level of organization in living systems, biologists see the
signature of past and present evolution. Darwin dedicated a large portion of his book, On the Origin of Species, identifying patterns
in nature that were consistent with evolution and since Darwin our understanding has become clearer and broader.

Fossils
Fossils provide solid evidence that organisms from the past are not the same as those found today; fossils show a progression of
evolution. Scientists determine the age of fossils and categorize them all over the world to determine when the organisms lived
relative to each other. The resulting fossil record tells the story of the past, and shows the evolution of form over millions of years
(Figure 7.3.1). For example, highly detailed fossil records have been recovered for sequences of species in the evolution of whales
and modern horses. The fossil record of horses in North America is especially rich and many contain transition fossils: those
showing intermediate anatomy between earlier and later forms. The fossil record extends back to a dog-like ancestor some 55
million years ago that gave rise to the first horse-like species 55 to 42 million years ago in the genus Eohippus. The series of fossils
tracks the change in anatomy resulting from a gradual drying trend that changed the landscape from a forested one to a prairie.
Successive fossils show the evolution of teeth shapes and foot and leg anatomy to a grazing habit, with adaptations for escaping
predators, for example in species of Mesohippus found from 40 to 30 million years ago. Later species showed gains in size, such as
those of Hipparion, which existed from about 23 to 2 million years ago. The fossil record shows several adaptive radiations in the
horse lineage, which is now much reduced to only one genus, Equus, with several species.

Figure 7.3.1: This illustration shows an artist’s renderings of these species derived from fossils of the evolutionary history of the
horse and its ancestors. The species depicted are only four from a very diverse lineage that contains many branches, dead ends, and
adaptive radiations. One of the trends, depicted here is the evolutionary tracking of a drying climate and increase in prairie versus
forest habitat reflected in forms that are more adapted to grazing and predator escape through running. Przewalski's horse is one of
a few living species of horse.

Anatomy and Embryology

Another type of evidence for evolution is the presence of structures in organisms that share the same basic form. For example, the
bones in the appendages of a human, dog, bird, and whale all share the same overall construction (Figure 7.3.2). That similarity
results from their origin in the appendages of a common ancestor. Over time, evolution led to changes in the shapes and sizes of
these bones in different species, but they have maintained the same overall layout, evidence of descent from a common ancestor.
Scientists call these synonymous parts homologous structures. Some structures exist in organisms that have no apparent function at
all, and appear to be residual parts from a past ancestor. For example, some snakes have pelvic bones despite having no legs
because they descended from reptiles that did have legs. These unused structures without function are called vestigial structures.
Other examples of vestigial structures are wings on flightless birds (which may have other functions), leaves on some cacti, traces
of pelvic bones in whales, and the sightless eyes of cave animals.

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 Figure 7.3.2: The similar construction of these appendages indicates that these organisms share a common ancestor.
Another evidence of evolution is the convergence of form in organisms that share similar environments. For example, species of
unrelated animals, such as the arctic fox and ptarmigan (a bird), living in the arctic region have temporary white coverings during
winter to blend with the snow and ice (Figure 7.3.3). The similarity occurs not because of common ancestry, indeed one covering is
of fur and the other of feathers, but because of similar selection pressures—the benefits of not being seen by predators.

Figure 7.3.3: The white winter coat of (a) the arctic fox and (b) the ptarmigan’s plumage are adaptations to their environments.
(credit a: modification of work by Keith Morehouse)
Embryology, the study of the development of the anatomy of an organism to its adult form also provides evidence of relatedness
between now widely divergent groups of organisms. Structures that are absent in some groups often appear in their embryonic
forms and disappear by the time the adult or juvenile form is reached. For example, all vertebrate embryos, including humans,
exhibit gill slits at some point in their early development. These disappear in the adults of terrestrial groups, but are maintained in
adult forms of aquatic groups such as fish and some amphibians. Great ape embryos, including humans, have a tail structure during
their development that is lost by the time of birth. The reason embryos of unrelated species are often similar is that mutational
changes that affect the organism during embryonic development can cause amplified differences in the adult, even while the
embryonic similarities are preserved.

Biogeography
The geographic distribution of organisms on the planet follows patterns that are best explained by evolution in conjunction with the
movement of tectonic plates over geological time. Broad groups that evolved before the breakup of the supercontinent Pangaea
(about 200 million years ago) are distributed worldwide. Groups that evolved since the breakup appear uniquely in regions of the

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planet, for example the unique flora and fauna of northern continents that formed from the supercontinent Laurasia and of the
southern continents that formed from the supercontinent Gondwana. The presence of Proteaceae in Australia, southern Africa, and
South America is best explained by the plant family’s presence there prior to the southern supercontinent Gondwana breaking up
(Figure 7.3.4).

Figure 7.3.4: The Proteacea family of plants evolved before the supercontinent Gondwana broke up. Today, members of this plant
family are found throughout the southern hemisphere (shown in red). (credit “Proteacea flower”: modification of work by
“dorofofoto”/Flickr)
The great diversification of the marsupials in Australia and the absence of other mammals reflects that island continent’s long
isolation. Australia has an abundance of endemic species—species found nowhere else—which is typical of islands whose isolation
by expanses of water prevents migration of species to other regions. Over time, these species diverge evolutionarily into new
species that look very different from their ancestors that may exist on the mainland. The marsupials of Australia, the finches on the
Galápagos, and many species on the Hawaiian Islands are all found nowhere else but on their island, yet display distant
relationships to ancestral species on mainlands.

Molecular Biology
Like anatomical structures, the structures of the molecules of life reflect descent with modification. Evidence of a common ancestor
for all of life is reflected in the universality of DNA as the genetic material and of the near universality of the genetic code and the
machinery of DNA replication and expression. Fundamental divisions in life between the three domains are reflected in major
structural differences in otherwise conservative structures such as the components of ribosomes and the structures of membranes.
In general, the relatedness of groups of organisms is reflected in the similarity of their DNA sequences—exactly the pattern that
would be expected from descent and diversification from a common ancestor.
DNA sequences have also shed light on some of the mechanisms of evolution. For example, it is clear that the evolution of new
functions for proteins commonly occurs after gene duplication events. These duplications are a kind of mutation in which an entire
gene is added as an extra copy (or many copies) in the genome. These duplications allow the free modification of one copy by
mutation, selection, and drift, while the second copy continues to produce a functional protein. This allows the original function for
the protein to be kept, while evolutionary forces tweak the copy until it functions in a new way.

Section Summary
The evidence for evolution is found at all levels of organization in living things and in the extinct species we know about through
fossils. Fossils provide evidence for the evolutionary change through now extinct forms that led to modern species. For example,
there is a rich fossil record that shows the evolutionary transitions from horse ancestors to modern horses that document
intermediate forms and a gradual adaptation to changing ecosystems. The anatomy of species and the embryological development

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of that anatomy reveal common structures in divergent lineages that have been modified over time by evolution. The geographical
distribution of living species reflects the origins of species in particular geographic locations and the history of continental
movements. The structures of molecules, like anatomical structures, reflect the relationships of living species and match patterns of
similarity expected from descent with modification.

Glossary

vestigial structure
a physical structure present in an organism but that has no apparent function and appears to be from a functional structure in a
distant ancestor

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 7.3: Evidence of Evolution is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
11.3: Evidence of Evolution by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 7.3.4 [Link]

7.4: Speciation
The biological definition of species, which works for sexually reproducing organisms, is a group of actually or potentially
interbreeding individuals. According to this definition, one species is distinguished from another by the possibility of matings
between individuals from each species to produce fertile offspring. There are exceptions to this rule. Many species are similar
enough that hybrid offspring are possible and may often occur in nature, but for the majority of species this rule generally holds. In
fact, the presence of hybrids between similar species suggests that they may have descended from a single interbreeding species
and that the speciation process may not yet be completed.
Given the extraordinary diversity of life on the planet there must be mechanisms for speciation: the formation of two species from
one original species. Darwin envisioned this process as a branching event and diagrammed the process in the only illustration found
in On the Origin of Species (Figure 7.4.1a). For speciation to occur, two new populations must be formed from one original
population, and they must evolve in such a way that it becomes impossible for individuals from the two new populations to
interbreed. Biologists have proposed mechanisms by which this could occur that fall into two broad categories. Allopatric
speciation, meaning speciation in “other homelands,” involves a geographic separation of populations from a parent species and
subsequent evolution. Sympatric speciation, meaning speciation in the “same homeland,” involves speciation occurring within a
parent species while remaining in one location.
Biologists think of speciation events as the splitting of one ancestral species into two descendant species. There is no reason why
there might not be more than two species formed at one time except that it is less likely and such multiple events can also be
conceptualized as single splits occurring close in time.

Figure 7.4.1: The only illustration in Darwin’s On the Origin of Species is (a) a diagram showing speciation events leading to
biological diversity. The diagram shows similarities to phylogenetic charts that are drawn today to illustrate the relationships of
species. (b) Modern elephants evolved from the Palaeomastodon, a species that lived in Egypt 35–50 million years ago.

Speciation through Geographic Separation

A geographically continuous population has a gene pool that is relatively homogeneous. Gene flow, the movement of alleles across
the range of the species, is relatively free because individuals can move and then mate with individuals in their new location. Thus,
the frequency of an allele at one end of a distribution will be similar to the frequency of the allele at the other end. When
populations become geographically discontinuous that free-flow of alleles is prevented. When that separation lasts for a period of
time, the two populations are able to evolve along different trajectories. Thus, their allele frequencies at numerous genetic loci
gradually become more and more different as new alleles independently arise by mutation in each population. Typically,
environmental conditions, such as climate, resources, predators, and competitors, for the two populations will differ causing natural
selection to favor divergent adaptations in each group. Different histories of genetic drift, enhanced because the populations are
smaller than the parent population, will also lead to divergence.

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Given enough time, the genetic and phenotypic divergence between populations will likely affect characters that influence
reproduction enough that were individuals of the two populations brought together, mating would be less likely, or if a mating
occurred, offspring would be non-viable or infertile. Many types of diverging characters may affect the reproductive isolation
(inability to interbreed) of the two populations. These mechanisms of reproductive isolation can be divided into prezygotic
mechanisms (those that operate before fertilization) and postzygotic mechanisms (those that operate after fertilization). Prezygotic
mechanisms include traits that allow the individuals to find each other, such as the timing of mating, sensitivity to pheromones, or
choice of mating sites. If individuals are able to encounter each other, character divergence may prevent courtship rituals from
leading to a mating either because female preferences have changed or male behaviors have changed. Physiological changes may
interfere with successful fertilization if mating is able to occur. Postzygotic mechanisms include genetic incompatibilities that
prevent proper development of the offspring, or if the offspring live, they may be unable to produce viable gametes themselves as
in the example of the mule, the infertile offspring of a female horse and a male donkey.
If the two isolated populations are brought back together and the hybrid offspring that formed from matings between individuals of
the two populations have lower survivorship or reduced fertility, then selection will favor individuals that are able to discriminate
between potential mates of their own population and the other population. This selection will enhance the reproductive isolation.
Isolation of populations leading to allopatric speciation can occur in a variety of ways: from a river forming a new branch, erosion
forming a new valley, or a group of organisms traveling to a new location without the ability to return, such as seeds floating over
the ocean to an island. The nature of the geographic separation necessary to isolate populations depends entirely on the biology of
the organism and its potential for dispersal. If two flying insect populations took up residence in separate nearby valleys, chances
are that individuals from each population would fly back and forth, continuing gene flow. However, if two rodent populations
became divided by the formation of a new lake, continued gene flow would be unlikely; therefore, speciation would be more likely.
Biologists group allopatric processes into two categories. If a few members of a species move to a new geographical area, this is
called dispersal. If a natural situation arises to physically divide organisms, this is called vicariance.
Scientists have documented numerous cases of allopatric speciation taking place. For example, along the west coast of the United
States, two separate subspecies of spotted owls exist. The northern spotted owl has genetic and phenotypic differences from its
close relative, the Mexican spotted owl, which lives in the south (Figure 7.4.2). The cause of their initial separation is not clear, but
1
it may have been caused by the glaciers of the ice age dividing an initial population into two.

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 Figure 7.4.2: The northern spotted owl and the Mexican spotted owl inhabit geographically separate locations with different
climates and ecosystems. The owl is an example of incipient speciation. (credit “northern spotted owl”: modification of work by
John and Karen Hollingsworth, USFWS; credit “Mexican spotted owl”: modification of work by Bill Radke, USFWS)
Additionally, scientists have found that the further the distance between two groups that once were the same species, the more
likely for speciation to take place. This seems logical because as the distance increases, the various environmental factors would
likely have less in common than locations in close proximity. Consider the two owls; in the north, the climate is cooler than in the
south; the other types of organisms in each ecosystem differ, as do their behaviors and habits; also, the hunting habits and prey
choices of the owls in the south vary from the northern ones. These variances can lead to evolved differences in the owls, and over
time speciation will likely occur unless gene flow between the populations is restored.
In some cases, a population of one species disperses throughout an area, and each finds a distinct niche or isolated habitat. Over
time, the varied demands of their new lifestyles lead to multiple speciation events originating from a single species, which is called
adaptive radiation. From one point of origin, many adaptations evolve causing the species to radiate into several new ones. Island
archipelagos like the Hawaiian Islands provide an ideal context for adaptive radiation events because water surrounds each island,
which leads to geographical isolation for many organisms (Figure 7.4.3). The Hawaiian honeycreeper illustrates one example of
adaptive radiation. From a single species, called the founder species, numerous species have evolved, including the eight shown in
Figure 7.4.3.

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 Figure 7.4.3: The honeycreeper birds illustrate adaptive radiation. From one original species of bird, multiple others evolved,
each with its own distinctive characteristics.
Notice the differences in the species’ beaks in Figure 7.4.3. Change in the genetic variation for beaks in response to natural
selection based on specific food sources in each new habitat led to evolution of a different beak suited to the specific food source.
The fruit and seed-eating birds have thicker, stronger beaks which are suited to break hard nuts. The nectar-eating birds have long
beaks to dip into flowers to reach their nectar. The insect-eating birds have beaks like swords, appropriate for stabbing and
impaling insects. Darwin’s finches are another well-studied example of adaptive radiation in an archipelago.

Speciation without Geographic Separation

Can divergence occur if no physical barriers are in place to separate individuals who continue to live and reproduce in the same
habitat? A number of mechanisms for sympatric speciation have been proposed and studied.
One form of sympatric speciation can begin with a chromosomal error during meiosis or the formation of a hybrid individual with
too many chromosomes. Polyploidy is a condition in which a cell, or organism, has an extra set, or sets, of chromosomes. Scientists
have identified two main types of polyploidy that can lead to reproductive isolation of an individual in the polyploid state. In some
cases a polyploid individual will have two or more complete sets of chromosomes from its own species in a condition called
autopolyploidy (Figure 7.4.4). The prefix “auto” means self, so the term means multiple chromosomes from one’s own species.
Polyploidy results from an error in meiosis in which all of the chromosomes move into one cell instead of separating.

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 Figure 7.4.4: Autopolyploidy results when mitosis is not followed by cytokinesis.
For example, if a plant species with 2n = 6 produces autopolyploid gametes that are also diploid (2n = 6, when they should be n =
3), the gametes now have twice as many chromosomes as they should have. These new gametes will be incompatible with the
normal gametes produced by this plant species. But they could either self-pollinate or reproduce with other autopolyploid plants
with gametes having the same diploid number. In this way, sympatric speciation can occur quickly by forming offspring with 4n
called a tetraploid. These individuals would immediately be able to reproduce only with those of this new kind and not those of the
ancestral species. The other form of polyploidy occurs when individuals of two different species reproduce to form a viable
offspring called an allopolyploid. The prefix “allo” means “other” (recall from allopatric); therefore, an allopolyploid occurs when
gametes from two different species combine. Figure 7.4.5 illustrates one possible way an allopolyploidy can form. Notice how it
takes two generations, or two reproductive acts, before the viable fertile hybrid results.

Figure 7.4.5: Alloploidy results when two species mate to produce viable offspring. In the example shown, a normal gamete from
one species fuses with a polyploid gamete from another. Two matings are necessary to produce viable offspring.
The cultivated forms of wheat, cotton, and tobacco plants are all allopolyploids. Although polyploidy occurs occasionally in
animals, most chromosomal abnormalities in animals are lethal; it takes place most commonly in plants. Scientists have discovered
more than 1/2 of all plant species studied relate back to a species evolved through polyploidy.
Sympatric speciation may also take place in ways other than polyploidy. For example, imagine a species of fish that lived in a lake.
As the population grew, competition for food also grew. Under pressure to find food, suppose that a group of these fish had the
genetic flexibility to discover and feed off another resource that was unused by the other fish. What if this new food source was
found at a different depth of the lake? Over time, those feeding on the second food source would interact more with each other than
the other fish; therefore they would breed together as well. Offspring of these fish would likely behave as their parents and feed and
live in the same area, keeping them separate from the original population. If this group of fish continued to remain separate from
the first population, eventually sympatric speciation might occur as more genetic differences accumulated between them.
This scenario does play out in nature, as do others that lead to reproductive isolation. One such place is Lake Victoria in Africa,
famous for its sympatric speciation of cichlid fish. Researchers have found hundreds of sympatric speciation events in these fish,
which have not only happened in great number, but also over a short period of time. Figure 7.4.6 shows this type of speciation
among a cichlid fish population in Nicaragua. In this locale, two types of cichlids live in the same geographic location; however,
they have come to have different morphologies that allow them to eat various food sources.

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 Figure 7.4.6: Cichlid fish from Lake Apoyeque, Nicaragua, show evidence of sympatric speciation. Lake Apoyeque, a crater lake,
is 1800 years old, but genetic evidence indicates that the lake was populated only 100 years ago by a single population of cichlid
fish. Nevertheless, two populations with distinct morphologies and diets now exist in the lake, and scientists believe these
populations may be in an early stage of speciation.
Finally, a well-documented example of ongoing sympatric speciation occurred in the apple maggot fly, Rhagoletis pomonella,
which arose as an isolated population sometime after the introduction of the apple into North America. The native population of
flies fed on hawthorn species and is host-specific: it only infests hawthorn trees. Importantly, it also uses the trees as a location to
meet for mating. It is hypothesized that either through mutation or a behavioral mistake, flies jumped hosts and met and mated in
apple trees, subsequently laying their eggs in apple fruit. The offspring matured and kept their preference for the apple trees
effectively dividing the original population into two new populations separated by host species, not by geography. The host jump
took place in the nineteenth century, but there are now measureable differences between the two populations of fly. It seems likely
that host specificity of parasites in general is a common cause of sympatric speciation.

Section Summary
Speciation occurs along two main pathways: geographic separation (allopatric speciation) and through mechanisms that occur
within a shared habitat (sympatric speciation). Both pathways force reproductive isolation between populations. Sympatric
speciation can occur through errors in meiosis that form gametes with extra chromosomes, called polyploidy. Autopolyploidy
occurs within a single species, whereas allopolyploidy occurs because of a mating between closely related species. Once the
populations are isolated, evolutionary divergence can take place leading to the evolution of reproductive isolating traits that prevent
interbreeding should the two populations come together again. The reduced viability of hybrid offspring after a period of isolation
is expected to select for stronger inherent isolating mechanisms.

Footnotes
1. 1 Courtney, S.P., et al, “Scientific Evaluation of the Status of the Northern Spotted Owl,” Sustainable Ecosystems Institute
(2004), Portland, OR.

Glossary

adaptive radiation
a speciation when one species radiates out to form several other species

allopatric speciation
a speciation that occurs via a geographic separation

dispersal
an allopatric speciation that occurs when a few members of a species move to a new geographical area

speciation
a formation of a new species

sympatric speciation
a speciation that occurs in the same geographic space

vicariance

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 an allopatric speciation that occurs when something in the environment separates organisms of the same species into separate
groups

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 7.4: Speciation is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
11.4: Speciation by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 7.4.7 [Link]

7.5: Common Misconceptions about Evolution
Although the theory of evolution initially generated some controversy, by 20 years after the publication of On the Origin of Species
it was almost universally accepted by biologists, particularly younger biologists. Nevertheless, the theory of evolution is a difficult
concept and misconceptions about how it works abound. In addition, there are those that reject it as an explanation for the diversity
of life.

CONCEPT IN ACTION
This website addresses some of the main misconceptions associated with the theory of evolution.

Evolution Is Just a Theory

Critics of the theory of evolution dismiss its importance by purposefully confounding the everyday usage of the word “theory” with
the way scientists use the word. In science, a “theory” is understood to be a concept that has been extensively tested and supported
over time. We have a theory of the atom, a theory of gravity, and the theory of relativity, each of which describes what scientists
understand to be facts about the world. In the same way, the theory of evolution describes facts about the living world. As such, a
theory in science has survived significant efforts to discredit it by scientists, who are naturally skeptical. While theories can
sometimes be overturned or revised, this does not lessen their weight but simply reflects the constantly evolving state of scientific
knowledge. In contrast, a “theory” in common vernacular means a guess or suggested explanation for something. This meaning is
more akin to the concept of a “hypothesis” used by scientists, which is a tentative explanation for something that is proposed to
either be supported or disproved. When critics of evolution say evolution is “just a theory,” they are implying that there is little
evidence supporting it and that it is still in the process of being rigorously tested. This is a mischaracterization. If this were the case,
1
geneticist Theodosius Dobzhansky would not have said that “nothing in biology makes sense, except in the light of evolution.”

Individuals Evolve
An individual is born with the genes it has—these do not change as the individual ages. Therefore, an individual cannot evolve or
adapt through natural selection. Evolution is the change in genetic composition of a population over time, specifically over
generations, resulting from differential reproduction of individuals with certain alleles. Individuals do change over their lifetime,
but this is called development; it involves changes programmed by the set of genes the individual acquired at birth in coordination
with the individual’s environment. When thinking about the evolution of a characteristic, it is probably best to think about the
change of the average value of the characteristic in the population over time. For example, when natural selection leads to bill-size
change in medium ground finches in the Galápagos, this does not mean that individual bills on the finches are changing. If one
measures the average bill size among all individuals in the population at one time, and then measures the average bill size in the
population several years later after there has been a strong selective pressure, this average value may be different as a result of
evolution. Although some individuals may survive from the first time to the second, those individuals will still have the same bill
size. However, there may be enough new individuals with different bill sizes to change the average bill size.

Evolution Explains the Origin of Life

It is a common misunderstanding that evolution includes an explanation of life’s origins. Conversely, some of the theory’s critics
complain that it cannot explain the origin of life. The theory does not try to explain the origin of life. The theory of evolution
explains how populations change over time and how life diversifies—the origin of species. It does not shed light on the beginnings
of life including the origins of the first cells, which is how life is defined. The mechanisms of the origin of life on Earth are a
particularly difficult problem because it occurred a very long time ago, over a very long time, and presumably just occurred once.
Importantly, biologists believe that the presence of life on Earth precludes the possibility that the events that led to life on Earth can
be repeated because the intermediate stages would immediately become food for existing living things. The early stages of life
included the formation of organic molecules such as carbohydrates, amino acids, or nucleotides. If these were formed from
inorganic precursors today, they would simply be broken down by living things. The early stages of life also probably included
more complex aggregations of molecules into enclosed structures with an internal environment, a boundary layer of some form,
and the external environment. Such structures, if they were formed now, would be quickly consumed or broken down by living
organisms.
However, once a mechanism of inheritance was in place in the form of a molecule like DNA or RNA, either within a cell or within
a pre-cell, these entities would be subject to the principle of natural selection. More effective reproducers would increase in

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frequency at the expense of inefficient reproducers. So while evolution does not explain the origin of life, it may have something to
say about some of the processes operating once pre-living entities acquired certain properties.

Organisms Evolve on Purpose

Statements such as “organisms evolve in response to a change in an environment,” are quite common. There are two easy
misunderstandings possible with such a statement. First of all, the statement must not be understood to mean that individual
organisms evolve, as was discussed above. The statement is shorthand for “a population evolves in response to a changing
environment.” However, a second misunderstanding may arise by interpreting the statement to mean that the evolution is somehow
intentional. A changed environment results in some individuals in the population, those with particular phenotypes, benefiting and,
therefore, producing proportionately more offspring than other phenotypes. This results in change in the population if the
characters are genetically determined.
It is also important to understand that the variation that natural selection works on is already in a population and does not arise in
response to an environmental change. For example, applying antibiotics to a population of bacteria will, over time, select for a
population of bacteria that are resistant to antibiotics. The resistance, which is caused by a gene, did not arise by mutation because
of the application of the antibiotic. The gene for resistance was already present in the gene pool of the bacteria, likely at a low
frequency. The antibiotic, which kills the bacterial cells without the resistance gene, strongly selects for individuals that are
resistant, since these would be the only ones that survived and divided. Experiments have demonstrated that mutations for
antibiotic resistance do not arise as a result of antibiotic application.
In a larger sense, evolution is also not goal directed. Species do not become “better” over time; they simply track their changing
environment with adaptations that maximize their reproduction in a particular environment at a particular time. Evolution has no
goal of making faster, bigger, more complex, or even smarter species. This kind of language is common in popular literature.
Certain organisms, ourselves included, are described as the “pinnacle” of evolution, or “perfected” by evolution. What
characteristics evolve in a species are a function of the variation present and the environment, both of which are constantly
changing in a non-directional way. What trait is fit in one environment at one time may well be fatal at some point in the future.
This holds equally well for a species of insect as it does the human species.

Evolution Is Controversial among Scientists

The theory of evolution was controversial when it was first proposed in 1859, yet within 20 years virtually every working biologist
had accepted evolution as the explanation for the diversity of life. The rate of acceptance was extraordinarily rapid, partly because
Darwin had amassed an impressive body of evidence. The early controversies involved both scientific arguments against the theory
and the arguments of religious leaders. It was the arguments of the biologists that were resolved after a short time, while the
arguments of religious leaders have persisted to this day.
The theory of evolution replaced the predominant theory at the time that species had all been specially created within relatively
recent history. Despite the prevalence of this theory, it was becoming increasingly clear to naturalists during the nineteenth century
that it could no longer explain many observations of geology and the living world. The persuasiveness of the theory of evolution to
these naturalists lay in its ability to explain these phenomena, and it continues to hold extraordinary explanatory power to this day.
Its continued rejection by some religious leaders results from its replacement of special creation, a tenet of their religious belief.
These leaders cannot accept the replacement of special creation by a mechanistic process that excludes the actions of a deity as an
explanation for the diversity of life including the origins of the human species. It should be noted, however, that most of the major
denominations in the United States have statements supporting the acceptance of evidence for evolution as compatible with their
theologies.
The nature of the arguments against evolution by religious leaders has evolved over time. One current argument is that the theory is
still controversial among biologists. This claim is simply not true. The number of working scientists who reject the theory of
evolution, or question its validity and say so, is small. A Pew Research poll in 2009 found that 97 percent of the 2500 scientists
2
polled believe species evolve. The support for the theory is reflected in signed statements from many scientific societies such as
the American Association for the Advancement of Science, which includes working scientists as members. Many of the scientists
that reject or question the theory of evolution are non-biologists, such as engineers, physicians, and chemists. There are no
experimental results or research programs that contradict the theory. There are no papers published in peer-reviewed scientific
journals that appear to refute the theory. The latter observation might be considered a consequence of suppression of dissent, but it
must be remembered that scientists are skeptics and that there is a long history of published reports that challenged scientific
orthodoxy in unpopular ways. Examples include the endosymbiotic theory of eukaryotic origins, the theory of group selection, the

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microbial cause of stomach ulcers, the asteroid-impact theory of the Cretaceous extinction, and the theory of plate tectonics.
Research with evidence and ideas with scientific merit are considered by the scientific community. Research that does not meet
these standards is rejected.

Other Theories Should Be Taught

A common argument from some religious leaders is that alternative theories to evolution should be taught in public schools. Critics
of evolution use this strategy to create uncertainty about the validity of the theory without offering actual evidence. In fact, there
are no viable alternative scientific theories to evolution. The last such theory, proposed by Lamarck in the nineteenth century, was
replaced by the theory of natural selection. A single exception was a research program in the Soviet Union based on Lamarck’s
theory during the early twentieth century that set that country’s agricultural research back decades. Special creation is not a viable
alternative scientific theory because it is not a scientific theory, since it relies on an untestable explanation. Intelligent design,
despite the claims of its proponents, is also not a scientific explanation. This is because intelligent design posits the existence of an
unknown designer of living organisms and their systems. Whether the designer is unknown or supernatural, it is a cause that cannot
be measured; therefore, it is not a scientific explanation. There are two reasons not to teach nonscientific theories. First, these
explanations for the diversity of life lack scientific usefulness because they do not, and cannot, give rise to research programs that
promote our understanding of the natural world. Experiments cannot test non-material explanations for natural phenomena. For this
reason, teaching these explanations as science in public schools is not in the public interest. Second, in the United States, it is
illegal to teach them as science because the U.S. Supreme Court and lower courts have ruled that the teaching of religious belief,
such as special creation or intelligent design, violates the establishment clause of the First Amendment of the U.S. Constitution,
which prohibits government sponsorship of a particular religion.
The theory of evolution and science in general is, by definition, silent on the existence or non-existence of the spiritual world.
Science is only able to study and know the material world. Individual biologists have sometimes been vocal atheists, but it is
equally true that there are many deeply religious biologists. Nothing in biology precludes the existence of a god, indeed biology as
a science has nothing to say about it. The individual biologist is free to reconcile her or his personal and scientific knowledge as
they see fit. The Voices for Evolution project ([Link] developed through the National Center for Science
Education, works to gather the diversity of perspectives on evolution to advocate it being taught in public schools.

Section Summary
The theory of evolution is a difficult concept and misconceptions abound. The factual nature of evolution is often challenged by
wrongly associating the scientific meaning of a theory with the vernacular meaning. Evolution is sometimes mistakenly interpreted
to mean that individuals evolve, when in fact only populations can evolve as their gene frequencies change over time. Evolution is
often assumed to explain the origin of life, which it does not speak to. It is often spoken in goal-directed terms by which organisms
change through intention, and selection operates on mutations present in a population that have not arisen in response to a
particular environmental stress. Evolution is often characterized as being controversial among scientists; however, it is accepted by
the vast majority of working scientists. Critics of evolution often argue that alternative theories to evolution should be taught in
public schools; however, there are no viable alternative scientific theories to evolution. The alternative religious beliefs should not
be taught as science because it cannot be proven, and in the United States it is unconstitutional. Science is silent on the question of
the existence of a god while scientists are able to reconcile religious belief and scientific knowledge.

Footnotes
1. 1 Theodosius Dobzhansky. “Biology, Molecular and Organismic.” American Zoologist 4, no. 4 (1964): 449.
2. 2 Pew Research Center for the People & the Press, Public Praises Science; Scientists Fault Public, Media (Washington, DC,
2009), [Link]

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 7.5: Common Misconceptions about Evolution is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
11.5: Common Misconceptions about Evolution by OpenStax is licensed CC BY 4.0.

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7.E: Evolution and Its Processes (Exercises)
11.1: Discovering How Populations Change
Multiple Choice
Which scientific concept did Charles Darwin and Alfred Wallace independently discover?
A. mutation
B. natural selection
C. overbreeding
D. sexual reproduction

Answer
B

Which of the following situations will lead to natural selection?

A. The seeds of two plants land near each other and one grows larger than the other.
B. Two types of fish eat the same kind of food, and one is better able to gather food than the other.
C. Male lions compete for the right to mate with females, with only one possible winner.
D. all of the above

Answer
D

What is the difference between micro- and macroevolution?

A. Microevolution describes the evolution of small organisms, such as insects, while macroevolution describes the evolution
of large organisms, like people and elephants.
B. Microevolution describes the evolution of microscopic entities, such as molecules and proteins, while macroevolution
describes the evolution of whole organisms.
C. Microevolution describes the evolution of populations, while macroevolution describes the emergence of new species
over long periods of time.
D. Microevolution describes the evolution of organisms over their lifetimes, while macroevolution describes the evolution of
organisms over multiple generations.

Answer
C

Population genetics is the study of ________.

A. how allele frequencies in a population change over time
B. populations of cells in an individual
C. the rate of population growth
D. how genes affect embryological development

Answer
A

Free Response
If a person scatters a handful of plant seeds from one species in an area, how would natural selection work in this situation?

Answer
The plants that can best use the resources of the area, including competing with other individuals for those resources, will
produce more seeds themselves and those traits that allowed them to better use the resources will increase in the population of

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 the next generation.

Explain the Hardy-Weinberg principle of equilibrium.

Answer
The Hardy-Weinberg principle of equilibrium states that a population’s allele frequencies are inherently stable. Unless an
evolutionary force is acting upon the population, the population would carry the same genes at the same frequencies generation
after generation, and individuals would, as a whole, look essentially the same.

11.2: Mechanisms of Evolution

Multiple Choice
Galápagos medium ground finches are found on Santa Cruz and San Cristóbal islands, which are separated by about 100 km of
ocean. Occasionally, individuals from either island fly to the other island to stay. This can alter the allele frequencies of the
population through which of the following mechanisms?
A. natural selection
B. genetic drift
C. gene flow
D. mutation

Answer
C

In which of the following pairs do both evolutionary processes introduce new genetic variation into a population?
A. natural selection and genetic drift
B. mutation and gene flow
C. natural selection and gene flow
D. gene flow and genetic drift

Answer
B

Free Response
Describe natural selection and give an example of natural selection at work in a population.

Answer
The theory of natural selection stems from the observation that some individuals in a population survive longer and have more
offspring than others, thus passing on more of their genes to the next generation. For example, a big, powerful male gorilla is
much more likely than a smaller, weaker gorilla to become the population’s silverback, the pack’s leader who mates far more
than the other males of the group. The pack leader will, therefore, father more offspring, who share half of his genes, and are
thus likely to also grow bigger and stronger like their father. Over time, the genes for bigger size will increase in frequency in
the population, and the population will, as a result, grow larger on average.

11.3: Evidence of Evolution

Multiple Choice
The wing of a bird and the arm of a human are examples of ________.
A. vestigial structures
B. molecular structures
C. homologous structures
D. analogous structures

Answer

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 C

The fact that DNA sequences are more similar in more closely related organisms is evidence of what?
A. optimal design in organisms
B. adaptation
C. mutation
D. descent with modification

Answer
D

Free Response
Why do scientists consider vestigial structures evidence for evolution?

Answer
A vestigial structure is an example of a homologous structure that has apparently been reduced through evolution to a non-
functional state because its function is no longer utilized by the species exhibiting it; therefore, any mutations which might
reduce its structure are not selected against. The fact that the species has vestiges of the structure rather than no structure at all
is evidence that it was present in an ancestor and evolved to non-functionality through accumulation of random mutations.

11.4: Speciation
Multiple Choice
Which situation would most likely lead to allopatric speciation?
A. A flood causes the formation of a new lake.
B. A storm causes several large trees to fall down.
C. A mutation causes a new trait to develop.
D. An injury causes an organism to seek out a new food source.

Answer
A

What is the main difference between dispersal and vicariance?

A. One leads to allopatric speciation, whereas the other leads to sympatric speciation.
B. One involves the movement of the organism, whereas the other involves a change in the environment.
C. One depends on a genetic mutation occurring, whereas the other does not.
D. One involves closely related organisms, whereas the other involves only individuals of the same species.

Answer
B

Which variable increases the likelihood of allopatric speciation taking place more quickly?
A. lower rate of mutation
B. longer distance between divided groups
C. increased instances of hybrid formation
D. equivalent numbers of individuals in each population

Answer
B

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Free Response
Why do island chains provide ideal conditions for adaptive radiation to occur?

Answer
Organisms of one species can arrive to an island together and then disperse throughout the chain, each settling into different
niches, exploiting different food resources and, evolving independently with little gene flow between different islands.

Two species of fish had recently undergone sympatric speciation. The males of each species had a different coloring through which
females could identify and choose a partner from her own species. After some time, pollution made the lake so cloudy it was hard
for females to distinguish colors. What might take place in this situation?

Answer
It is likely the two species would start to reproduce with each other if hybridization is still possible. Depending on the viability
of their offspring, they may fuse back into one species.

11.5: Common Misconceptions about Evolution

Multiple Choice
The word “theory” in theory of evolution is best replaced by ________.
A. fact
B. hypothesis
C. idea
D. alternate explanation

Answer
A

Why are alternative scientific theories to evolution not taught in public school?
A. more theories would confuse students
B. there are no viable scientific alternatives
C. it is against the law
D. alternative scientific theories are suppressed by the science establishment

Answer
B

Free Response
How does the scientific meaning of “theory” differ from the common, everyday meaning of the word?

Answer
In science, a theory is a thoroughly tested and verified set of explanations for a body of observations of nature. It is the strongest
form of knowledge in science. In contrast, a theory in common usage can mean a guess or speculation about something,
meaning that the knowledge implied by the theory may be very weak.

Explain why the statement that a monkey is more evolved than a mouse is incorrect.

Answer
The statement implies that there is a goal to evolution and that the monkey represents greater progress to that goal than the
mouse. Both species are likely to be well adapted to their particular environment, which is the outcome of natural selection.

This page titled 7.E: Evolution and Its Processes (Exercises) is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.

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11.E: Evolution and Its Processes (Exercises) by OpenStax is licensed CC BY 4.0.

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 CHAPTER OVERVIEW

8: Diversity of Life
8.1: Organizing Life on Earth
8.2: Determining Evolutionary Relationships
8.E: Diversity of Life (Exercises)

Thumbnail: A sampling of fungi from Saskatchewan demonstrating biodiversity. (CC BY-SA 3.0/cropped from original; Sasata via
Wikimedia Commons).

This page titled 8: Diversity of Life is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.

1
8.1: Organizing Life on Earth
All life on Earth evolved from a common ancestor. Biologists map how organisms are related by constructing phylogenetic trees. In
other words, a “tree of life” can be constructed to illustrate when different organisms evolved and to show the relationships among
different organisms, as shown in Figure 8.1.1. Notice that from a single point, the three domains of Archaea, Bacteria, and Eukarya
diverge and then branch repeatedly. The small branch that plants and animals (including humans) occupy in this diagram shows
how recently these groups had their origin compared with other groups.

Figure 8.1.1: In the evolution of life on Earth, the three domains of life—Archaea, Bacteria, and Eukarya—branch from a single
point. (credit: modification of work by Eric Gaba)
The phylogenetic tree in Figure 8.1.1 illustrates the pathway of evolutionary history. The pathway can be traced from the origin of
life to any individual species by navigating through the evolutionary branches between the two points. Also, by starting with a
single species and tracing backward to any branch point, the organisms related to it by various degrees of closeness can be
identified.
A phylogeny is the evolutionary history and the relationships among a species or group of species. The study of organisms with the
purpose of deriving their relationships is called systematics.
Many disciplines within the study of biology contribute to understanding how past and present life evolved over time, and together
they contribute to building, updating, and maintaining the “tree of life.” Information gathered may include data collected from
fossils, from studying morphology, from the structure of body parts, or from molecular structure, such as the sequence of amino
acids in proteins or DNA nucleotides. By considering the trees generated by different sets of data scientists can put together the
phylogeny of a species.
Scientists continue to discover new species of life on Earth as well as new character information, thus trees change as new data
arrive.

The Levels of Classification

Taxonomy (which literally means “arrangement law”) is the science of naming and grouping species to construct an internationally
shared classification system. The taxonomic classification system (also called the Linnaean system after its inventor, Carl Linnaeus,
a Swedish naturalist) uses a hierarchical model. A hierarchical system has levels and each group at one of the levels includes
groups at the next lowest level, so that at the lowest level each member belongs to a series of nested groups. An analogy is the
nested series of directories on the main disk drive of a computer. For example, in the most inclusive grouping, scientists divide
organisms into three domains: Bacteria, Archaea, and Eukarya. Within each domain is a second level called a kingdom. Each

Access for free at OpenStax 8.1.1 [Link]

domain contains several kingdoms. Within kingdoms, the subsequent categories of increasing specificity are: phylum, class, order,
family, genus, and species.
As an example, the classification levels for the domestic dog are shown in Figure 8.1.2. The group at each level is called a taxon
(plural: taxa). In other words, for the dog, Carnivora is the taxon at the order level, Canidae is the taxon at the family level, and so
forth. Organisms also have a common name that people typically use, such as domestic dog, or wolf. Each taxon name is
capitalized except for species, and the genus and species names are italicized. Scientists refer to an organism by its genus and
species names together, commonly called a scientific name, or Latin name. This two-name system is called binomial nomenclature.
The scientific name of the wolf is therefore Canis lupus. Recent study of the DNA of domestic dogs and wolves suggest that the
domestic dog is a subspecies of the wolf, not its own species, thus it is given an extra name to indicate its subspecies status, Canis
lupus familiaris.
Figure 8.1.2 also shows how taxonomic levels move toward specificity. Notice how within the domain we find the dog grouped
with the widest diversity of organisms. These include plants and other organisms not pictured, such as fungi and protists. At each
sublevel, the organisms become more similar because they are more closely related. Before Darwin’s theory of evolution was
developed, naturalists sometimes classified organisms using arbitrary similarities, but since the theory of evolution was proposed in
the 19th century, biologists work to make the classification system reflect evolutionary relationships. This means that all of the
members of a taxon should have a common ancestor and be more closely related to each other than to members of other taxa.
Recent genetic analysis and other advancements have found that some earlier taxonomic classifications do not reflect actual
evolutionary relationships, and therefore, changes and updates must be made as new discoveries take place. One dramatic and
recent example was the breaking apart of prokaryotic species, which until the 1970s were all classified as bacteria. Their division
into Archaea and Bacteria came about after the recognition that their large genetic differences warranted their separation into two
of three fundamental branches of life.

ART CONNECTION

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 Figure 8.1.2: At each sublevel in the taxonomic classification system, organisms become more similar. Dogs and wolves are
the same species because they can breed and produce viable offspring, but they are different enough to be classified as different
subspecies. (credit “plant”: modification of work by "berduchwal"/Flickr; credit “insect”: modification of work by Jon
Sullivan; credit “fish”: modification of work by Christian Mehlführer; credit “rabbit”: modification of work by Aidan Wojtas;
credit “cat”: modification of work by Jonathan Lidbeck; credit “fox”: modification of work by Kevin Bacher, NPS; credit
“jackal”: modification of work by Thomas A. Hermann, NBII, USGS; credit “wolf” modification of work by Robert Dewar;
credit “dog”: modification of work by "digital_image_fan"/Flickr)
In what levels are cats and dogs considered to be part of the same group?

CONCEPT IN ACTION

Visit this site to learn more about taxonomy.

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Classification and Phylogeny
Scientists use a tool called a phylogenetic tree to show the evolutionary pathways and relationships between organisms. A
phylogenetic tree is a diagram used to reflect evolutionary relationships among organisms or groups of organisms. The hierarchical
classification of groups nested within more inclusive groups is reflected in diagrams. Scientists consider phylogenetic trees to be a
hypothesis of the evolutionary past because one cannot go back through time to confirm the proposed relationships.
Unlike with a taxonomic classification, a phylogenetic tree can be read like a map of evolutionary history, as shown in Figure
8.1.3. Shared characteristics are used to construct phylogenetic trees. The point where a split occurs in a tree, called a branch point,

represents where a single lineage evolved into distinct new ones. Many phylogenetic trees have a single branch point at the base
representing a common ancestor of all the branches in the tree. Scientists call such trees rooted, which means there is a single
ancestral taxon at the base of a phylogenetic tree to which all organisms represented in the diagram descend from. When two
lineages stem from the same branch point, they are called sister taxa, for example the two species of orangutans. A branch point
with more than two groups illustrates a situation for which scientists have not definitively determined relationships. An example is
illustrated by the three branches leading to the gorilla subspecies; their exact relationships are not yet understood. It is important to
note that sister taxa share an ancestor, which does not mean that one taxon evolved from the other. The branch point, or split,
represents a common ancestor that existed in the past, but that no longer exists. Humans did not evolve from chimpanzees (nor did
chimpanzees evolve from humans) although they are our closest living relatives. Both humans and chimpanzees evolved from a
common ancestor that lived, scientists believe, six million years ago and looked different from both modern chimpanzees and
modern humans.

Figure 8.1.3: A phylogenetic tree is rooted and shows how different organisms, in this case the species and subspecies of living
apes, evolved from a common ancestor.
The branch points and the branches in phylogenetic tree structure also imply evolutionary change. Sometimes the significant
character changes are identified on a branch or branch point. For example, in Figure 8.1.4, the branch point that gives rise to the
mammal and reptile lineage from the frog lineage shows the origin of the amniotic egg character. Also the branch point that gives
rise to organisms with legs is indicated at the common ancestor of mammals, reptiles, amphibians, and jawed fishes.

Figure 8.1.4: This phylogenetic tree is rooted by an organism that lacked a vertebral column. At each branch point, organisms
with different characters are placed in different groups.

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Limitations of Phylogenetic Trees
It is easy to assume that more closely related organisms look more alike, and while this is often the case, it is not always true. If
two closely related lineages evolved under significantly different surroundings or after the evolution of a major new adaptation,
they may look quite different from each other, even more so than other groups that are not as closely related. For example, the
phylogenetic tree in Figure 8.1.4 shows that lizards and rabbits both have amniotic eggs, whereas salamanders (within the frog
lineage) do not; yet on the surface, lizards and salamanders appear more similar than the lizards and rabbits.
Another aspect of phylogenetic trees is that, unless otherwise indicated, the branches do not show length of time, they show only
the order in time of evolutionary events. In other words, a long branch does not necessarily mean more time passed, nor does a
short branch mean less time passed— unless specified on the diagram. For example, in Figure 8.1.4, the tree does not indicate how
much time passed between the evolution of amniotic eggs and hair. What the tree does show is the order in which things took place.
Again using Figure 8.1.4, the tree shows that the oldest trait is the vertebral column, followed by hinged jaws, and so forth.
Remember that any phylogenetic tree is a part of the greater whole, and similar to a real tree, it does not grow in only one direction
after a new branch develops. So, for the organisms in Figure 8.1.4, just because a vertebral column evolved does not mean that
invertebrate evolution ceased, it only means that a new branch formed. Also, groups that are not closely related, but evolve under
similar conditions, may appear more similar to each other than to a close relative.

Section Summary
Scientists continually obtain new information that helps to understand the evolutionary history of life on Earth. Each group of
organisms went through its own evolutionary journey, called its phylogeny. Each organism shares relatedness with others, and
based on morphologic and genetic evidence scientists attempt to map the evolutionary pathways of all life on Earth. Historically,
organisms were organized into a taxonomic classification system. However, today many scientists build phylogenetic trees to
illustrate evolutionary relationships and the taxonomic classification system is expected to reflect evolutionary relationships.

Art Connections
Figure 8.1.2: In what levels are cats and dogs considered to be part of the same group?

Answer
Cats and dogs are part of the same group at five levels: both are in the domain Eukarya, the kingdom Animalia, the phylum
Chordata, the class Mammalia, and the order Carnivora.

Glossary

binomial nomenclature
a system of two-part scientific names for an organism, which includes genus and species names

branch point
a point on a phylogenetic tree where a single lineage splits to distinct new ones

class
the category in the taxonomic classification system that falls within phylum and includes orders

domain
the highest level category in the classification system and that includes all taxonomic classifications below it; it is the most
inclusive taxon

family
the category in the taxonomic classification system that falls within order and includes genera

genus
the category in the taxonomic classification system that falls within family and includes species; the first part of the scientific
name

kingdom

Access for free at OpenStax 8.1.5 [Link]

 the category in the taxonomic classification system that falls within domain and includes phyla

order
the category in the taxonomic classification system that falls within class and includes families

phylogenetic tree
diagram used to reflect the evolutionary relationships between organisms or groups of organisms

phylogeny
evolutionary history and relationship of an organism or group of organisms

phylum
the category in the taxonomic classification system that falls within kingdom and includes classes

rooted
describing a phylogenetic tree with a single ancestral lineage to which all organisms represented in the diagram relate

sister taxa
two lineages that diverged from the same branch point

species
the most specific category of classification

systematics
the science of determining the evolutionary relationships of organisms

taxon
a single level in the taxonomic classification system

taxonomy
the science of classifying organisms

Contributors
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 8.1: Organizing Life on Earth is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
12.1: Organizing Life on Earth by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 8.1.6 [Link]

8.2: Determining Evolutionary Relationships
Scientists collect information that allows them to make evolutionary connections between organisms. Similar to detective work,
scientists must use evidence to uncover the facts. In the case of phylogeny, evolutionary investigations focus on two types of
evidence: morphologic (form and function) and genetic.

Two Measures of Similarity

Organisms that share similar physical features and genetic sequences tend to be more closely related than those that do not.
Features that overlap both morphologically and genetically are referred to as homologous structures; the similarities stem from
common evolutionary paths. For example, as shown in Figure 8.2.1, the bones in the wings of bats and birds, the arms of humans,
and the foreleg of a horse are homologous structures. Notice the structure is not simply a single bone, but rather a grouping of
several bones arranged in a similar way in each organism even though the elements of the structure may have changed shape and
size.

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Figure 8.2.1: Bat and bird wings, the foreleg of a horse, the flipper of a whale, and the arm of a human are homologous
structures, indicating that bats, birds, horses, whales, and humans share a common evolutionary past. (credit a photo: modification

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 of work by Steve Hillebrand, USFWS; credit b photo: modification of work by U.S. BLM; credit c photo: modification of work by
Virendra Kankariya; credit d photo: modification of work by Russian Gov./Wikimedia Commons)
Misleading Appearances
Some organisms may be very closely related, even though a minor genetic change caused a major morphological difference to
make them look quite different. For example, chimpanzees and humans, the skulls of which are shown in Figure 8.2.2 are very
1
similar genetically, sharing 99 percent of their genes. However, chimpanzees and humans show considerable anatomical
differences, including the degree to which the jaw protrudes in the adult and the relative lengths of our arms and legs.

Figure 8.2.2: (a) The chimpanzee jaw protrudes to a much greater degree than (b) the human jaw. (credit a: modification of work
by "Pastorius"/Wikimedia Commons)
However, unrelated organisms may be distantly related yet appear very much alike, usually because common adaptations to similar
environmental conditions evolved in both. An example is the streamlined body shapes, the shapes of fins and appendages, and the
shape of the tails in fishes and whales, which are mammals. These structures bear superficial similarity because they are
adaptations to moving and maneuvering in the same environment—water. When a characteristic that is similar occurs by adaptive
convergence (convergent evolution), and not because of a close evolutionary relationship, it is called an analogous structure. In
another example, insects use wings to fly like bats and birds. We call them both wings because they perform the same function and
have a superficially similar form, but the embryonic origin of the two wings is completely different. The difference in the
development, or embryogenesis, of the wings in each case is a signal that insects and bats or birds do not share a common ancestor
that had a wing. The wing structures, shown in Figure 8.2.3 evolved independently in the two lineages.
Similar traits can be either homologous or analogous. Homologous traits share an evolutionary path that led to the development of
that trait, and analogous traits do not. Scientists must determine which type of similarity a feature exhibits to decipher the
phylogeny of the organisms being studied.

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 Figure 8.2.3: The wing of a honey bee is similar in shape to a bird wing and a bat wing and serves the same function (flight). The
bird and bat wings are homologous structures. However, the honey bee wing has a different structure (it is made of a chitinous
exoskeleton, not a boney endoskeleton) and embryonic origin. The bee and bird or bat wing types illustrate an analogy—similar
structures that do not share an evolutionary history. (credit a photo: modification of work by U.S. BLM; credit b: modification of
work by Steve Hillebrand, USFWS; credit c: modification of work by Jon Sullivan)

Molecular Comparisons
With the advancement of DNA technology, the area of molecular systematics, which describes the use of information on the
molecular level including DNA sequencing, has blossomed. New analysis of molecular characters not only confirms many earlier
classifications, but also uncovers previously made errors. Molecular characters can include differences in the amino-acid sequence
of a protein, differences in the individual nucleotide sequence of a gene, or differences in the arrangements of genes. Phylogenies
based on molecular characters assume that the more similar the sequences are in two organisms, the more closely related they are.
Different genes change evolutionarily at different rates and this affects the level at which they are useful at identifying
relationships. Rapidly evolving sequences are useful for determining the relationships among closely related species. More slowly
evolving sequences are useful for determining the relationships between distantly related species. To determine the relationships
between very different species such as Eukarya and Archaea, the genes used must be very ancient, slowly evolving genes that are
present in both groups, such as the genes for ribosomal RNA. Comparing phylogenetic trees using different sequences and finding
them similar helps to build confidence in the inferred relationships.
Sometimes two segments of DNA in distantly related organisms randomly share a high percentage of bases in the same locations,
causing these organisms to appear closely related when they are not. For example, the fruit fly shares 60 percent of its DNA with
2
humans. In this situation, computer-based statistical algorithms have been developed to help identify the actual relationships, and
ultimately, the coupled use of both morphologic and molecular information is more effective in determining phylogeny.

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 EVOLUTION IN ACTION: Why Does Phylogeny Matter?
In addition to enhancing our understanding of the evolutionary history of species, our own included, phylogenetic analysis has
numerous practical applications. Two of those applications include understanding the evolution and transmission of disease and
3
making decisions about conservation efforts. A 2010 study of MRSA (methicillin-resistant Staphylococcus aureus), an
antibiotic resistant pathogenic bacterium, traced the origin and spread of the strain throughout the past 40 years. The study
uncovered the timing and patterns in which the resistant strain moved from its point of origin in Europe to centers of infection
and evolution in South America, Asia, North America, and Australasia. The study suggested that introductions of the bacteria
to new populations occurred very few times, perhaps only once, and then spread from that limited number of individuals. This
is in contrast to the possibility that many individuals had carried the bacteria from one place to another. This result suggests
that public health officials should concentrate on quickly identifying the contacts of individuals infected with a new strain of
bacteria to control its spread.
A second area of usefulness for phylogenetic analysis is in conservation. Biologists have argued that it is important to protect
species throughout a phylogenetic tree rather than just those from one branch of the tree. Doing this will preserve more of the
variation produced by evolution. For example, conservation efforts should focus on a single species without sister species
rather than another species that has a cluster of close sister species that recently evolved. If the single evolutionarily distinct
species goes extinct a disproportionate amount of variation from the tree will be lost compared to one species in the cluster of
4
closely related species. A study published in 2007 made recommendations for conservation of mammal species worldwide
based on how evolutionarily distinct and at risk of extinction they are. The study found that their recommendations differed
from priorities based on simply the level of extinction threat to the species. The study recommended protecting some
threatened and valued large mammals such as the orangutans, the giant and lesser pandas, and the African and Asian elephants.
But they also found that some much lesser known species should be protected based on how evolutionary distinct they are.
These include a number of rodents, bats, shrews and hedgehogs. In addition there are some critically endangered species that
did not rate as very important in evolutionary distinctiveness including species of deer mice and gerbils. While many criteria
affect conservation decisions, preserving phylogenetic diversity provides an objective way to protect the full range of diversity
generated by evolution.

Building Phylogenetic Trees

How do scientists construct phylogenetic trees? Presently, the most accepted method for constructing phylogenetic trees is a
method called cladistics. This method sorts organisms into clades, groups of organisms that are most closely related to each other
and the ancestor from which they descended. For example, in Figure 8.2.4, all of the organisms in the shaded region evolved from
a single ancestor that had amniotic eggs. Consequently, all of these organisms also have amniotic eggs and make a single clade,
also called a monophyletic group. Clades must include the ancestral species and all of the descendants from a branch point.

ART CONNECTION

Figure 8.2.4: Lizards, rabbits, and humans all descend from a common ancestor in which the amniotic egg evolved. Thus,
lizards, rabbits, and humans all belong to the clade Amniota. Vertebrata is a larger clade that also includes fish and lamprey.
Which animals in this figure belong to a clade that includes animals with hair? Which evolved first: hair or the amniotic egg?

Clades can vary in size depending on which branch point is being referenced. The important factor is that all of the organisms in
the clade or monophyletic group stem from a single point on the tree. This can be remembered because monophyletic breaks down
into “mono,” meaning one, and “phyletic,” meaning evolutionary relationship.

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Shared Characteristics
Cladistics rests on three assumptions. The first is that living things are related by descent from a common ancestor, which is a
general assumption of evolution. The second is that speciation occurs by splits of one species into two, never more than two at a
time, and essentially at one point in time. This is somewhat controversial, but is acceptable to most biologists as a simplification.
The third assumption is that traits change enough over time to be considered to be in a different state .It is also assumed that one
can identify the actual direction of change for a state. In other words, we assume that an amniotic egg is a later character state than
non-amniotic eggs. This is called the polarity of the character change. We know this by reference to a group outside the clade: for
example, insects have non-amniotic eggs; therefore, this is the older or ancestral character state. Cladistics compares ingroups and
outgroups. An ingroup (lizard, rabbit and human in our example) is the group of taxa being analyzed. An outgroup (lancelet,
lamprey and fish in our example) is a species or group of species that diverged before the lineage containing the group(s) of
interest. By comparing ingroup members to each other and to the outgroup members, we can determine which characteristics are
evolutionary modifications determining the branch points of the ingroup’s phylogeny.
If a characteristic is found in all of the members of a group, it is a shared ancestral characterbecause there has been no change in the
trait during the descent of each of the members of the clade. Although these traits appear interesting because they unify the clade,
in cladistics they are considered not helpful when we are trying to determine the relationships of the members of the clade because
every member is the same. In contrast, consider the amniotic egg characteristic of Figure 8.2.4. Only some of the organisms have
this trait, and to those that do, it is called a shared derived character because this trait changed at some point during descent. This
character does tell us about the relationships among the members of the clade; it tells us that lizards, rabbits, and humans group
more closely together than any of these organisms do with fish, lampreys, and lancelets.
A sometimes confusing aspect of “ancestral” and “derived” characters is that these terms are relative. The same trait could be either
ancestral or derived depending on the diagram being used and the organisms being compared. Scientists find these terms useful
when distinguishing between clades during the building of phylogenetic trees, but it is important to remember that their meaning
depends on context.

Choosing the Right Relationships

Constructing a phylogenetic tree, or cladogram, from the character data is a monumental task that is usually left up to a computer.
The computer draws a tree such that all of the clades share the same list of derived characters. But there are other decisions to be
made, for example, what if a species presence in a clade is supported by all of the shared derived characters for that clade except
one? One conclusion is that the trait evolved in the ancestor, but then changed back in that one species. Also a character state that
appears in two clades must be assumed to have evolved independently in those clades. These inconsistencies are common in trees
drawn from character data and complicate the decision-making process about which tree most closely represents the real
relationships among the taxa.
To aid in the tremendous task of choosing the best tree, scientists often use a concept called maximum parsimony, which means
that events occurred in the simplest, most obvious way. This means that the “best” tree is the one with the fewest number of
character reversals, the fewest number of independent character changes, and the fewest number of character changes throughout
the tree. Computer programs search through all of the possible trees to find the small number of trees with the simplest
evolutionary pathways. Starting with all of the homologous traits in a group of organisms, scientists can determine the order of
evolutionary events of which those traits occurred that is the most obvious and simple.

CONCEPT IN ACTION

Practice Parsimony: Go to this website to learn how maximum parsimony is used to create phylogenetic trees (be sure to
continue to the second page).

These tools and concepts are only a few of the strategies scientists use to tackle the task of revealing the evolutionary history of life
on Earth. Recently, newer technologies have uncovered surprising discoveries with unexpected relationships, such as the fact that

Access for free at OpenStax 8.2.6 [Link]

people seem to be more closely related to fungi than fungi are to plants. Sound unbelievable? As the information about DNA
sequences grows, scientists will become closer to mapping the evolutionary history of all life on Earth.

Section Summary
To build phylogenetic trees, scientists must collect character information that allows them to make evolutionary connections
between organisms. Using morphologic and molecular data, scientists work to identify homologous characteristics and genes.
Similarities between organisms can stem either from shared evolutionary history (homologies) or from separate evolutionary paths
(analogies). After homologous information is identified, scientists use cladistics to organize these events as a means to determine
an evolutionary timeline. Scientists apply the concept of maximum parsimony, which states that the likeliest order of events is
probably the simplest shortest path. For evolutionary events, this would be the path with the least number of major divergences that
correlate with the evidence.

Art Connections
Figure 8.2.3: Which animals in this figure belong to a clade that includes animals with hair? Which evolved first: hair or the
amniotic egg?

Answer
Rabbits and humans belong in the clade that includes animals with hair. The amniotic egg evolved before hair, because the
Amniota clade branches off earlier than the clade that encompasses animals with hair.

Footnotes
1. 1 Gibbons, A. (2012, June 13). Science Now. Retrieved from [Link]/scienceno...[Link]
2. 2 Background on comparative genomic analysis. (2002, December). Retrieved from [Link]
3. 3 Harris, S.R. et al. 2010. Evolution of MRSA during hospital transmission and intercontinental spread. Science 327:469–474.
4. 4 Isaac NJ, Turvey ST, Collen B, Waterman C, Baillie JE (2007) Mammals on the EDGE: Conservation Priorities Based on
Threat and Phylogeny. PLoS ONE 2(3): e296. doi:10.1371/[Link].0000296

Glossary

analogous structure
a character found in two taxa that looks similar because of convergent evolution, not because of descent from a common
ancestor

clade
a group of taxa with the same set of shared derived characters, including an ancestral species and all its descendants

cladistics
a method used to organize homologous traits to describe phylogenies using common descendent as the primary criterion used to
classify organisms

maximum parsimony
applying the simplest, most obvious way with the least number of steps

molecular systematics
the methods of using molecular evidence to identify phylogenetic relationships

monophyletic group
(also, clade) organisms that share a single ancestor

shared ancestral character

a character on a phylogenetic branch that is shared by a particular clade

shared derived character

a character on a phylogenetic tree that is shared only by a certain clade of organisms

Access for free at OpenStax 8.2.7 [Link]

Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 8.2: Determining Evolutionary Relationships is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
12.2: Determining Evolutionary Relationships by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 8.2.8 [Link]

8.E: Diversity of Life (Exercises)
12.1: Organizing Life on Earth
Multiple Choice
What is a phylogeny a description of?
A. mutations
B. DNA
C. evolutionary history
D. organisms on Earth

Answer
C

What do scientists in the field of systematics accomplish?

A. discover new fossil sites
B. organize and classify organisms
C. name new species
D. communicate between field biologists

Answer
B

Which statement about the taxonomic classification system is correct?

A. There are more domains than kingdoms.
B. Kingdoms are the top category of classification.
C. A phylum may be represented in more than one kingdom.
D. Species are the most specific category of classification.

Answer
D

Which best describes the relationship between chimpanzees and humans?

A. chimpanzees evolved from humans
B. humans evolved from chimpanzees
C. chimpanzees and humans evolved from a common ancestor
D. chimpanzees and humans belong to the same species

Answer
C

Which best describes a branch point in a phylogenetic tree?

A. a hypothesis
B. new lineage
C. hybridization
D. a mating

Answer
B

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Free Response
How does a phylogenetic tree indicate major evolutionary events within a lineage?

Answer
The phylogenetic tree shows the order in which evolutionary events took place and in what order certain characteristics and
organisms evolved in relation to others. It does not generally indicate time durations.

List the different levels of the taxonomic classification system.

Answer
Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species.

12.2: Determining Evolutionary Relationships

Multiple Choice
Which statement about analogies is correct?
A. They occur only as errors.
B. They are synonymous with homologous traits.
C. They are derived by response to similar environmental pressures.
D. They are a form of mutation.

Answer
C

What kind of trait is important to cladistics?

A. shared derived traits
B. shared ancestral traits
C. analogous traits
D. parsimonious traits

Answer
A

What is true about organisms that are a part of the same clade?
A. They all share the same basic characteristics.
B. They evolved from a shared ancestor.
C. They all are on the same tree.
D. They have identical phylogenies.

Answer
B

Which assumption of cladistics is stated incorrectly?

A. Living things are related by descent from a common ancestor.
B. Speciation can produce one, two, or three new species.
C. Traits change from one state to another.
D. The polarity of a character state change can be determined.

Answer
B

A monophyletic group is a ________.

Access for free at OpenStax 8.E.2 [Link]

 A. phylogenetic tree
B. shared derived trait
C. character state
D. clade

Answer
D

Free Response
Dolphins and fish have similar body shapes. Is this feature more likely a homologous or analogous trait?

Answer
Dolphins are mammals and fish are not, which means that their evolutionary paths (phylogenies) are quite separate. Dolphins
probably adapted to have a similar body plan after returning to an aquatic lifestyle, and therefore this trait is probably
analogous.

Describe maximum parsimony.

Answer
Maximum parsimony hypothesizes that events occurred in the simplest, most obvious way, and the pathway of evolution
probably includes the fewest major events that coincide with the evidence at hand.

How does a biologist determine the polarity of a character change?

Answer
The biologist looks at the state of the character in an outgroup, an organism that is outside the clade for which the phylogeny is
being developed. The polarity of the character change is from the state of the character in the outgroup to the second state.

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 CHAPTER OVERVIEW

9: Ecology
9.1: Population and Community Ecology
9.1.1: Population Demographics and Dynamics
9.1.2: Population Growth and Regulation
9.1.3: The Human Population
9.1.4: Community Ecology
9.1.E: Population and Community Ecology (Exercises)
9.2: Ecosystems and the Biosphere
9.2.1: Energy Flow through Ecosystems
9.2.2: Biogeochemical Cycles
9.2.3: Terrestrial Biomes
9.2.4: Aquatic and Marine Biomes
9.2.E: Ecosystems and the Biosphere (Exercises)
9.3: Conservation and Biodiversity
9.3.1: Importance of Biodiversity
9.3.2: Threats to Biodiversity
9.3.3: Preserving Biodiversity
9.3.E: Conservation and Biodiversity (Exercises)

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1
 SECTION OVERVIEW

9.1: Population and Community Ecology

9.1.1: Population Demographics and Dynamics

9.1.2: Population Growth and Regulation

9.1.3: The Human Population

9.1.4: Community Ecology

9.1.E: Population and Community Ecology (Exercises)

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OpenStax.

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9.1.1: Population Demographics and Dynamics
Populations are dynamic entities. Their size and composition fluctuate in response to numerous factors, including seasonal and
yearly changes in the environment, natural disasters such as forest fires and volcanic eruptions, and competition for resources
between and within species. The statistical study of populations is called demography: a set of mathematical tools designed to
describe populations and investigate how they change. Many of these tools were actually designed to study human populations. For
example, life tables, which detail the life expectancy of individuals within a population, were initially developed by life insurance
companies to set insurance rates. In fact, while the term “demographics” is sometimes assumed to mean a study of human
populations, all living populations can be studied using this approach.

Population Size and Density

Populations are characterized by their population size (total number of individuals) and their population density (number of
individuals per unit area). A population may have a large number of individuals that are distributed densely, or sparsely. There are
also populations with small numbers of individuals that may be dense or very sparsely distributed in a local area. Population size
can affect potential for adaptation because it affects the amount of genetic variation present in the population. Density can have
effects on interactions within a population such as competition for food and the ability of individuals to find a mate. Smaller
organisms tend to be more densely distributed than larger organisms (Figure [Link]).

ART CONNECTION

Figure [Link]: Australian mammals show a typical inverse relationship between population density and body size.
As this graph shows, population density typically decreases with increasing body size. Why do you think this is the case?

Estimating Population Size

The most accurate way to determine population size is to count all of the individuals within the area. However, this method is
usually not logistically or economically feasible, especially when studying large areas. Thus, scientists usually study populations by
sampling a representative portion of each habitat and use this sample to make inferences about the population as a whole. The
methods used to sample populations to determine their size and density are typically tailored to the characteristics of the organism
being studied. For immobile organisms such as plants, or for very small and slow-moving organisms, a quadrat may be used. A
quadrat is a wood, plastic, or metal square that is randomly located on the ground and used to count the number of individuals that
lie within its boundaries. To obtain an accurate count using this method, the square must be placed at random locations within the
habitat enough times to produce an accurate estimate. This counting method will provide an estimate of both population size and
density. The number and size of quadrat samples depends on the type of organisms and the nature of their distribution.

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For smaller mobile organisms, such as mammals, a technique called mark and recapture is often used. This method involves
marking a sample of captured animals in some way and releasing them back into the environment to mix with the rest of the
population; then, a new sample is captured and scientists determine how many of the marked animals are in the new sample. This
method assumes that the larger the population, the lower the percentage of marked organisms that will be recaptured since they will
have mixed with more unmarked individuals. For example, if 80 field mice are captured, marked, and released into the forest, then
a second trapping 100 field mice are captured and 20 of them are marked, the population size (N) can be determined using the
following equation:
number marked first catch × total number second catch
=N
number marked second catch

Using our example, the population size would be 400.

80 × 100
= 400
20

These results give us an estimate of 400 total individuals in the original population. The true number usually will be a bit different
from this because of chance errors and possible bias caused by the sampling methods.

Species Distribution
In addition to measuring density, further information about a population can be obtained by looking at the distribution of the
individuals throughout their range. A species distribution pattern is the distribution of individuals within a habitat at a particular
point in time—broad categories of patterns are used to describe them.
Individuals within a population can be distributed at random, in groups, or equally spaced apart (more or less). These are known as
random, clumped, and uniform distribution patterns, respectively (Figure [Link]). Different distributions reflect important aspects
of the biology of the species; they also affect the mathematical methods required to estimate population sizes. An example of
random distribution occurs with dandelion and other plants that have wind-dispersed seeds that germinate wherever they happen to
fall in favorable environments. A clumped distribution, may be seen in plants that drop their seeds straight to the ground, such as
oak trees; it can also be seen in animals that live in social groups (schools of fish or herds of elephants). Uniform distribution is
observed in plants that secrete substances inhibiting the growth of nearby individuals (such as the release of toxic chemicals by
sage plants). It is also seen in territorial animal species, such as penguins that maintain a defined territory for nesting. The territorial
defensive behaviors of each individual create a regular pattern of distribution of similar-sized territories and individuals within
those territories. Thus, the distribution of the individuals within a population provides more information about how they interact
with each other than does a simple density measurement. Just as lower density species might have more difficulty finding a mate,
solitary species with a random distribution might have a similar difficulty when compared to social species clumped together in
groups.

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 Figure [Link]: Species may have a random, clumped, or uniform distribution. Plants such as (a) dandelions with wind-dispersed
seeds tend to be randomly distributed. Animals such as (b) elephants that travel in groups exhibit a clumped distribution. Territorial
birds such as (c) penguins tend to have a uniform distribution. (credit a: modification of work by Rosendahl; credit b: modification
of work by Rebecca Wood; credit c: modification of work by Ben Tubby)

Demography
While population size and density describe a population at one particular point in time, scientists must use demography to study the
dynamics of a population. Demography is the statistical study of population changes over time: birth rates, death rates, and life
expectancies. These population characteristics are often displayed in a life table.

Life Tables
Life tables provide important information about the life history of an organism and the life expectancy of individuals at each age.
They are modeled after actuarial tables used by the insurance industry for estimating human life expectancy. Life tables may
include the probability of each age group dying before their next birthday, the percentage of surviving individuals dying at a
particular age interval (their mortality rate, and their life expectancy at each interval. An example of a life table is shown in Table
[Link] from a study of Dall mountain sheep, a species native to northwestern North America. Notice that the population is divided

into age intervals (column A). The mortality rate (per 1000) shown in column D is based on the number of individuals dying during
the age interval (column B), divided by the number of individuals surviving at the beginning of the interval (Column C) multiplied
by 1000.
number of individuals dying
mortality rate = × 1000
number of individuals surviving

For example, between ages three and four, 12 individuals die out of the 776 that were remaining from the original 1000 sheep. This
number is then multiplied by 1000 to give the mortality rate per thousand.
12
mortality rate = × 1000 ≈ 15.5
776

As can be seen from the mortality rate data (column D), a high death rate occurred when the sheep were between six months and a
year old, and then increased even more from 8 to 12 years old, after which there were few survivors. The data indicate that if a
sheep in this population were to survive to age one, it could be expected to live another 7.7 years on average, as shown by the life-
expectancy numbers in column E.
This life table of Ovis dalli shows the number of deaths, number of survivors, mortality rate, and life expectancy at each age interval for Dall
mountain sheep.
1
Table [Link]: Life Table of Dall Mountain Sheep

A B C D E

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 1
Table [Link]: Life Table of Dall Mountain Sheep Number surviving at Mortality rate per 1000 Life expectancy or mean
Number dying in age
Age interval (years) beginning of age interval alive at beginning of age lifetime remaining to those
A interval out of 1000 born
B C D E
out of 1000 born interval attaining age interval

Number surviving at Mortality rate per 1000 Life expectancy or mean

Number dying in age
Age interval (years) beginning of age interval alive at beginning of age lifetime remaining to those
interval out of 1000 born
out of 1000 born interval attaining age interval

0–0.5 54 1000 54.0 7.06

0.5–1 145 946 153.3 —

1–2 12 801 15.0 7.7

2–3 13 789 16.5 6.8

3–4 12 776 15.5 5.9

4–5 30 764 39.3 5.0

5–6 46 734 62.7 4.2

6–7 48 688 69.8 3.4

7–8 69 640 107.8 2.6

8–9 132 571 231.2 1.9

9–10 187 439 426.0 1.3

10–11 156 252 619.0 0.9

11–12 90 96 937.5 0.6

12–13 3 6 500.0 1.2

13–14 3 3 1000 0.7

Survivorship Curves
Another tool used by population ecologists is a survivorship curve, which is a graph of the number of individuals surviving at each
age interval versus time. These curves allow us to compare the life histories of different populations (Figure [Link]). There are
three types of survivorship curves. In a type I curve, mortality is low in the early and middle years and occurs mostly in older
individuals. Organisms exhibiting a type I survivorship typically produce few offspring and provide good care to the offspring
increasing the likelihood of their survival. Humans and most mammals exhibit a type I survivorship curve. In type II curves,
mortality is relatively constant throughout the entire life span, and mortality is equally likely to occur at any point in the life span.
Many bird populations provide examples of an intermediate or type II survivorship curve. In type III survivorship curves, early
ages experience the highest mortality with much lower mortality rates for organisms that make it to advanced years. Type III
organisms typically produce large numbers of offspring, but provide very little or no care for them. Trees and marine invertebrates
exhibit a type III survivorship curve because very few of these organisms survive their younger years, but those that do make it to
an old age are more likely to survive for a relatively long period of time.

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 Figure [Link]: Survivorship curves show the distribution of individuals in a population according to age. Humans and most
mammals have a Type I survivorship curve, because death primarily occurs in the older years. Birds have a Type II survivorship
curve, as death at any age is equally probable. Trees have a Type III survivorship curve because very few survive the younger
years, but after a certain age, individuals are much more likely to survive.

Section Summary
Populations are individuals of a species that live in a particular habitat. Ecologists measure characteristics of populations: size,
density, and distribution pattern. Life tables are useful to calculate life expectancies of individual population members.
Survivorship curves show the number of individuals surviving at each age interval plotted versus time.

Art Connections
Figure [Link]: As this graph shows, population density typically decreases with increasing body size. Why do you think this is the
case?

Answer
Smaller animals require less food and others resources, so the environment can support more of them per unit area.

Footnotes
1. 1 Data Adapted from Edward S. Deevey, Jr., “Life Tables for Natural Populations of Animals,” The Quarterly Review of
Biology 22, no. 4 (December 1947): 283-314.

Glossary

demography
the statistical study of changes in populations over time

life table
a table showing the life expectancy of a population member based on its age

mark and recapture

a method used to determine population size in mobile organisms

mortality rate
the proportion of population surviving to the beginning of an age interval that dies during that age interval

population density
the number of population members divided by the area being measured

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population size
the number of individuals in a population

quadrat
a square within which a count of individuals is made that is combined with other such counts to determine population size and
density in slow moving or stationary organisms

species distribution pattern

the distribution of individuals within a habitat at a given point in time

survivorship curve
a graph of the number of surviving population members versus the relative age of the member

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

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OpenStax.
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9.1.2: Population Growth and Regulation
Population ecologists make use of a variety of methods to model population dynamics. An accurate model should be able to
describe the changes occurring in a population and predict future changes.

Population Growth
The two simplest models of population growth use deterministic equations (equations that do not account for random events) to
describe the rate of change in the size of a population over time. The first of these models, exponential growth, describes theoretical
populations that increase in numbers without any limits to their growth. The second model, logistic growth, introduces limits to
reproductive growth that become more intense as the population size increases. Neither model adequately describes natural
populations, but they provide points of comparison.

Exponential Growth
Charles Darwin, in developing his theory of natural selection, was influenced by the English clergyman Thomas Malthus. Malthus
published his book in 1798 stating that populations with abundant natural resources grow very rapidly; however, they limit further
growth by depleting their resources. The early pattern of accelerating population size is called exponential growth.
The best example of exponential growth in organisms is seen in bacteria. Bacteria are prokaryotes that reproduce largely by binary
fission. This division takes about an hour for many bacterial species. If 1000 bacteria are placed in a large flask with an abundant
supply of nutrients (so the nutrients will not become quickly depleted), the number of bacteria will have doubled from 1000 to 2000
after just an hour. In another hour, each of the 2000 bacteria will divide, producing 4000 bacteria. After the third hour, there should
be 8000 bacteria in the flask. The important concept of exponential growth is that the growth rate—the number of organisms added
in each reproductive generation—is itself increasing; that is, the population size is increasing at a greater and greater rate. After 24
of these cycles, the population would have increased from 1000 to more than 16 billion bacteria. When the population size, N, is
plotted over time, a J-shaped growth curve is produced (Figure 9.1.2.1a).
The bacteria-in-a-flask example is not truly representative of the real world where resources are usually limited. However, when a
species is introduced into a new habitat that it finds suitable, it may show exponential growth for a while. In the case of the bacteria
in the flask, some bacteria will die during the experiment and thus not reproduce; therefore, the growth rate is lowered from a
maximal rate in which there is no mortality. The growth rate of a population is largely determined by subtracting the death rate, D,
(number organisms that die during an interval) from the birth rate, B, (number organisms that are born during an interval). The
growth rate can be expressed in a simple equation that combines the birth and death rates into a single factor: r. This is shown in
the following formula:
Population growth = rN

The value of r can be positive, meaning the population is increasing in size (the rate of change is positive); or negative, meaning
the population is decreasing in size; or zero, in which case the population size is unchanging, a condition known as zero population
growth.

Logistic Growth
Extended exponential growth is possible only when infinite natural resources are available; this is not the case in the real world.
Charles Darwin recognized this fact in his description of the “struggle for existence,” which states that individuals will compete
(with members of their own or other species) for limited resources. The successful ones are more likely to survive and pass on the
traits that made them successful to the next generation at a greater rate (natural selection). To model the reality of limited resources,
population ecologists developed the logistic growth model.

Carrying Capacity and the Logistic Model

In the real world, with its limited resources, exponential growth cannot continue indefinitely. Exponential growth may occur in
environments where there are few individuals and plentiful resources, but when the number of individuals gets large enough,
resources will be depleted and the growth rate will slow down. Eventually, the growth rate will plateau or level off (Figure
9.1.2.1b). This population size, which is determined by the maximum population size that a particular environment can sustain, is

called the carrying capacity, or K. In real populations, a growing population often overshoots its carrying capacity, and the death

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rate increases beyond the birth rate causing the population size to decline back to the carrying capacity or below it. Most
populations usually fluctuate around the carrying capacity in an undulating fashion rather than existing right at it.
The formula used to calculate logistic growth adds the carrying capacity as a moderating force in the growth rate. The expression
“K – N” is equal to the number of individuals that may be added to a population at a given time, and “K – N” divided by “K” is the
fraction of the carrying capacity available for further growth. Thus, the exponential growth model is restricted by this factor to
generate the logistic growth equation:
K −N
Population growth = rN [ ]
K

Notice that when N is almost zero the quantity in brackets is almost equal to 1 (or K/K) and growth is close to exponential. When
the population size is equal to the carrying capacity, or N = K, the quantity in brackets is equal to zero and growth is equal to zero.
A graph of this equation (logistic growth) yields the S-shaped curve (Figure 9.1.2.1b). It is a more realistic model of population
growth than exponential growth. There are three different sections to an S-shaped curve. Initially, growth is exponential because
there are few individuals and ample resources available. Then, as resources begin to become limited, the growth rate decreases.
Finally, the growth rate levels off at the carrying capacity of the environment, with little change in population number over time.

Figure [Link]: When resources are unlimited, populations exhibit (a) exponential growth, shown in a J-shaped curve. When
resources are limited, populations exhibit (b) logistic growth. In logistic growth, population expansion decreases as resources
become scarce, and it levels off when the carrying capacity of the environment is reached. The logistic growth curve is S-shaped.

Role of Intraspecific Competition

The logistic model assumes that every individual within a population will have equal access to resources and, thus, an equal chance
for survival. For plants, the amount of water, sunlight, nutrients, and space to grow are the important resources, whereas in animals,
important resources include food, water, shelter, nesting space, and mates.
In the real world, phenotypic variation among individuals within a population means that some individuals will be better adapted to
their environment than others. The resulting competition for resources among population members of the same species is termed
intraspecific competition. Intraspecific competition may not affect populations that are well below their carrying capacity, as
resources are plentiful and all individuals can obtain what they need. However, as population size increases, this competition
intensifies. In addition, the accumulation of waste products can reduce carrying capacity in an environment.

Examples of Logistic Growth

Yeast, a microscopic fungus used to make bread and alcoholic beverages, exhibits the classical S-shaped curve when grown in a
test tube (Figure 9.1.2.2a). Its growth levels off as the population depletes the nutrients that are necessary for its growth. In the real
world, however, there are variations to this idealized curve. Examples in wild populations include sheep and harbor seals (Figure
9.1.2.2b). In both examples, the population size exceeds the carrying capacity for short periods of time and then falls below the

carrying capacity afterwards. This fluctuation in population size continues to occur as the population oscillates around its carrying
capacity. Still, even with this oscillation, the logistic model is confirmed.

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ART CONNECTION

Figure [Link]: (a) Yeast grown in ideal conditions in a test tube shows a classical S-shaped logistic growth curve, whereas
(b) a natural population of seals shows real-world fluctuation. The yeast is visualized using differential interference contrast
light micrography. (credit a: scale-bar data from Matt Russell)
If the major food source of seals declines due to pollution or overfishing, which of the following would likely occur?
A. The carrying capacity of seals would decrease, as would the seal population.
B. The carrying capacity of seals would decrease, but the seal population would remain the same.
C. The number of seal deaths would increase, but the number of births would also increase, so the population size would
remain the same.
D. The carrying capacity of seals would remain the same, but the population of seals would decrease.

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Population Dynamics and Regulation
The logistic model of population growth, while valid in many natural populations and a useful model, is a simplification of real-
world population dynamics. Implicit in the model is that the carrying capacity of the environment does not change, which is not the
case. The carrying capacity varies annually. For example, some summers are hot and dry whereas others are cold and wet; in many
areas, the carrying capacity during the winter is much lower than it is during the summer. Also, natural events such as earthquakes,
volcanoes, and fires can alter an environment and hence its carrying capacity. Additionally, populations do not usually exist in
isolation. They share the environment with other species, competing with them for the same resources (interspecific competition).
These factors are also important to understanding how a specific population will grow.
Population growth is regulated in a variety of ways. These are grouped into density-dependent factors, in which the density of the
population affects growth rate and mortality, and density-independent factors, which cause mortality in a population regardless of
population density. Wildlife biologists, in particular, want to understand both types because this helps them manage populations
and prevent extinction or overpopulation.

Density-dependent Regulation
Most density-dependent factors are biological in nature and include predation, inter- and intraspecific competition, and parasites.
Usually, the denser a population is, the greater its mortality rate. For example, during intra- and interspecific competition, the
reproductive rates of the species will usually be lower, reducing their populations’ rate of growth. In addition, low prey density
increases the mortality of its predator because it has more difficulty locating its food source. Also, when the population is denser,
diseases spread more rapidly among the members of the population, which affect the mortality rate.
1
Density dependent regulation was studied in a natural experiment with wild donkey populations on two sites in Australia. On one
site the population was reduced by a population control program; the population on the other site received no interference. The
high-density plot was twice as dense as the low-density plot. From 1986 to 1987 the high-density plot saw no change in donkey
density, while the low-density plot saw an increase in donkey density. The difference in the growth rates of the two populations was
caused by mortality, not by a difference in birth rates. The researchers found that numbers of offspring birthed by each mother was
unaffected by density. Growth rates in the two populations were different mostly because of juvenile mortality caused by the
mother’s malnutrition due to scarce high-quality food in the dense population. Figure [Link] shows the difference in age-specific
mortalities in the two populations.

Figure [Link]: This graph shows the age-specific mortality rates for wild donkeys from high- and low-density populations. The
juvenile mortality is much higher in the high-density population because of maternal malnutrition caused by a shortage of high-
quality food.

Density-independent Regulation and Interaction with Density-dependent Factors

Many factors that are typically physical in nature cause mortality of a population regardless of its density. These factors include
weather, natural disasters, and pollution. An individual deer will be killed in a forest fire regardless of how many deer happen to be
in that area. Its chances of survival are the same whether the population density is high or low. The same holds true for cold winter
weather.

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In real-life situations, population regulation is very complicated and density-dependent and independent factors can interact. A
dense population that suffers mortality from a density-independent cause will be able to recover differently than a sparse
population. For example, a population of deer affected by a harsh winter will recover faster if there are more deer remaining to
reproduce.

EVOLUTION IN ACTION: Why Did the Woolly Mammoth Go Extinct?

Figure [Link]: The three images include: (a) 1916 mural of a mammoth herd from the American Museum of Natural
History, (b) the only stuffed mammoth in the world is in the Museum of Zoology located in St. Petersburg, Russia, and (c) a
one-month-old baby mammoth, named Lyuba, discovered in Siberia in 2007. (credit a: modification of work by Charles R.
Knight; credit b: modification of work by “Tanapon”/Flickr; credit c: modification of work by Matt Howry)
Woolly mammoths began to go extinct about 10,000 years ago, soon after paleontologists believe humans able to hunt them
began to colonize North America and northern Eurasia (Figure [Link]). A mammoth population survived on Wrangel Island,
in the East Siberian Sea, and was isolated from human contact until as recently as 1700 BC. We know a lot about these animals
from carcasses found frozen in the ice of Siberia and other northern regions.
It is commonly thought that climate change and human hunting led to their extinction. A 2008 study estimated that climate
2
change reduced the mammoth’s range from 3,000,000 square miles 42,000 years ago to 310,000 square miles 6,000 years ago.
Through archaeological evidence of kill sites, it is also well documented that humans hunted these animals. A 2012 study
3
concluded that no single factor was exclusively responsible for the extinction of these magnificent creatures. In addition to
climate change and reduction of habitat, scientists demonstrated another important factor in the mammoth’s extinction was the
migration of human hunters across the Bering Strait to North America during the last ice age 20,000 years ago.
The maintenance of stable populations was and is very complex, with many interacting factors determining the outcome. It is
important to remember that humans are also part of nature. Once we contributed to a species’ decline using primitive hunting
technology only.

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Demographic-Based Population Models
Population ecologists have hypothesized that suites of characteristics may evolve in species that lead to particular adaptations to
their environments. These adaptations impact the kind of population growth their species experience. Life history characteristics
such as birth rates, age at first reproduction, the numbers of offspring, and even death rates evolve just like anatomy or behavior,
leading to adaptations that affect population growth. Population ecologists have described a continuum of life-history “strategies”
with K-selected species on one end and r-selected species on the other. K-selected species are adapted to stable, predictable
environments. Populations of K-selected species tend to exist close to their carrying capacity. These species tend to have larger, but
fewer, offspring and contribute large amounts of resources to each offspring. Elephants would be an example of a K-selected
species. r-selected species are adapted to unstable and unpredictable environments. They have large numbers of small offspring.
Animals that are r-selected do not provide a lot of resources or parental care to offspring, and the offspring are relatively self-
sufficient at birth. Examples of r-selected species are marine invertebrates such as jellyfish and plants such as the dandelion. The
two extreme strategies are at two ends of a continuum on which real species life histories will exist. In addition, life history
strategies do not need to evolve as suites, but can evolve independently of each other, so each species may have some
characteristics that trend toward one extreme or the other.

Section Summary
Populations with unlimited resources grow exponentially—with an accelerating growth rate. When resources become limiting,
populations follow a logistic growth curve in which population size will level off at the carrying capacity.
Populations are regulated by a variety of density-dependent and density-independent factors. Life-history characteristics, such as
age at first reproduction or numbers of offspring, are characteristics that evolve in populations just as anatomy or behavior can
evolve over time. The model of r- and K-selection suggests that characters, and possibly suites of characters, may evolve
adaptations to population stability near the carrying capacity (K-selection) or rapid population growth and collapse (r-selection).
Species will exhibit adaptations somewhere on a continuum between these two extremes.

Art Exercise
Figure [Link]: If the major food source of seals declines due to pollution or overfishing, which of the following would likely
occur?
A. The carrying capacity of seals would decrease, as would the seal population.
B. The carrying capacity of seals would decrease, but the seal population would remain the same.
C. The number of seal deaths would increase, but the number of births would also increase, so the population size would remain
the same.
D. The carrying capacity of seals would remain the same, but the population of seals would decrease.

Answer
A: The carrying capacity of seals would decrease, as would the seal population.

Footnotes
1. 1 David Choquenot, “Density-Dependent Growth, Body Condition, and Demography in Feral Donkeys: Testing the Food
Hypothesis,” Ecology 72, no. 3 (June 1991):805–813.
2. 2 David Nogués-Bravo et al., “Climate Change, Humans, and the Extinction of the Woolly Mammoth.” PLoS Biol 6 (April
2008): e79, doi:10.1371/[Link].0060079.
3. 3 G.M. MacDonald et al., “Pattern of Extinction of the Woolly Mammoth in Beringia.” Nature Communications 3, no. 893
(June 2012), doi:10.1038/ncomms1881.

Glossary

birth rate
the number of births within a population at a specific point in time

carrying capacity
the maximum number of individuals of a population that can be supported by the limited resources of a habitat

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death rate
the number of deaths within a population at a specific point in time

density-dependent regulation
the regulation of population in which birth and death rates are dependent on population size

density-independent regulation
the regulation of population in which the death rate is independent of the population size

exponential growth
an accelerating growth pattern seen in populations where resources are not limiting

intraspecific competition
the competition among members of the same species

J-shaped growth curve

the shape of an exponential growth curve

K-selected species
a species suited to stable environments that produce a few, relatively large offspring and provide parental care

logistic growth
the leveling off of exponential growth due to limiting resources

r-selected species
a species suited to changing environments that produce many offspring and provide little or no parental care

S-shaped growth curve

the shape of a logistic growth curve

zero population growth

the steady population size where birth rates and death rates are equal

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.1.2: Population Growth and Regulation is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
19.2: Population Growth and Regulation by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

9.1.3: The Human Population
Concepts of animal population dynamics can be applied to human population growth. Humans are not unique in their ability to
alter their environment. For example, beaver dams alter the stream environment where they are built. Humans, however, have the
ability to alter their environment to increase its carrying capacity, sometimes to the detriment of other species. Earth’s human
population and their use of resources are growing rapidly, to the extent that some worry about the ability of Earth’s environment to
sustain its human population. Long-term exponential growth carries with it the potential risks of famine, disease, and large-scale
death, as well as social consequences of crowding such as increased crime.
Human technology and particularly our harnessing of the energy contained in fossil fuels have caused unprecedented changes to
Earth’s environment, altering ecosystems to the point where some may be in danger of collapse. Changes on a global scale
including depletion of the ozone layer, desertification and topsoil loss, and global climate change are caused by human activities.
The world’s human population is presently growing exponentially (Figure [Link]).

Figure [Link]: Human population growth since 1000 AD is exponential.

A consequence of exponential growth rate is that the time that it takes to add a particular number of humans to the population is
becoming shorter. Figure [Link] shows that 123 years were necessary to add 1 billion humans between 1804 and 1930, but it only
took 24 years to add the two billion people between 1975 and 1999. This acceleration in growth rate will likely begin to decrease in
the coming decades. Despite this, the population will continue to increase and the threat of overpopulation remains, particularly
because the damage caused to ecosystems and biodiversity is lowering the human carrying capacity of the planet.

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 Figure [Link]: The time between the addition of each billion human beings to Earth decreases over time. (credit: modification of
work by Ryan T. Cragun)

CONCEPT IN ACTION

Human Population Through Time

Watch this video of how human populations have changed over time.

Overcoming Density-Dependent Regulation

Humans are unique in their ability to alter their environment in myriad ways. This ability is responsible for human population
growth because it resets the carrying capacity and overcomes density-dependent growth regulation. Much of this ability is related
to human intelligence, society, and communication. Humans construct shelters to protect themselves from the elements and have
developed agriculture and domesticated animals to increase their food supplies. In addition, humans use language to communicate
this technology to new generations, allowing them to improve upon previous accomplishments.
Other factors in human population growth are migration and public health. Humans originated in Africa, but we have since
migrated to nearly all inhabitable land on Earth, thus, increasing the area that we have colonized. Public health, sanitation, and the
use of antibiotics and vaccines have decreased the ability of infectious disease to limit human population growth in developed
countries. In the past, diseases such as the bubonic plaque of the fourteenth century killed between 30 and 60 percent of Europe’s
population and reduced the overall world population by as many as one hundred million people. Infectious disease continues to
have an impact on human population growth. For example, life expectancy in sub-Saharan Africa, which was increasing from 1950
to 1990, began to decline after 1985 largely as a result of HIV/AIDS mortality. The reduction in life expectancy caused by
1
HIV/AIDS was estimated to be 7 years for 2005.
Declining life expectancy is an indicator of higher mortality rates and leads to lower birth rates.

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The fundamental cause of the acceleration of growth rate for humans in the past 200 years has been the reduced death rate due to a
development of the technological advances of the industrial age, urbanization that supported those technologies, and especially the
exploitation of the energy in fossil fuels. Fossil fuels are responsible for dramatically increasing the resources available for human
population growth through agriculture (mechanization, pesticides, and fertilizers) and harvesting wild populations.

Age Structure, Population Growth, and Economic Development

The age structure of a population is an important factor in population dynamics. Age structure is the proportion of a population in
different age classes. Models that incorporate age structure allow better prediction of population growth, plus the ability to
associate this growth with the level of economic development in a region. Countries with rapid growth have a pyramidal shape in
their age structure diagrams, showing a preponderance of younger individuals, many of whom are of reproductive age (Figure
[Link]). This pattern is most often observed in underdeveloped countries where individuals do not live to old age because of less-

than-optimal living conditions, and there is a high birth rate. Age structures of areas with slow growth, including developed
countries such as the United States, still have a pyramidal structure, but with many fewer young and reproductive-aged individuals
and a greater proportion of older individuals. Other developed countries, such as Italy, have zero population growth. The age
structure of these populations is more conical, with an even greater percentage of middle-aged and older individuals. The actual
growth rates in different countries are shown in Figure [Link], with the highest rates tending to be in the less economically
developed countries of Africa and Asia.

ART CONNECTION

Figure [Link]: Typical age structure diagrams are shown. The rapid growth diagram narrows to a point, indicating that the
number of individuals decreases rapidly with age. In the slow growth model, the number of individuals decreases steadily with
age. Stable population diagrams are rounded on the top, showing that the number of individuals per age group decreases
gradually, and then increases for the older part of the population.
Age structure diagrams for rapidly growing, slow growing, and stable populations are shown in stages 1 through 3. What type
of population change do you think stage 4 represents?

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 Figure [Link]: The percent growth rate of population in different countries is shown. Notice that the highest growth is occurring
in less economically developed countries in Africa and Asia.

Long-Term Consequences of Exponential Human Population Growth

Many dire predictions have been made about the world’s population leading to a major crisis called the “population explosion.” In
the 1968 book The Population Bomb, biologist Dr. Paul R. Ehrlich wrote, “The battle to feed all of humanity is over. In the 1970s
hundreds of millions of people will starve to death in spite of any crash programs embarked upon now. At this late date nothing can
2
prevent a substantial increase in the world death rate.” While many critics view this statement as an exaggeration, the laws of
exponential population growth are still in effect, and unchecked human population growth cannot continue indefinitely.
Efforts to moderate population control led to the one-child policy in China, which imposes fines on urban couples who have more
than one child. Due to the fact that some couples wish to have a male heir, many Chinese couples continue to have more than one
child. The effectiveness of the policy in limiting overall population growth is controversial, as is the policy itself. Moreover, there
are stories of female infanticide having occurred in some of the more rural areas of the country. Family planning education
programs in other countries have had highly positive effects on limiting population growth rates and increasing standards of living.
In spite of population control policies, the human population continues to grow. Because of the subsequent need to produce more
and more food to feed our population, inequalities in access to food and other resources will continue to widen. The United Nations
estimates the future world population size could vary from 6 billion (a decrease) to 16 billion people by the year 2100. There is no
way to know whether human population growth will moderate to the point where the crisis described by Dr. Ehrlich will be
averted.
Another consequence of population growth is the change and degradation of the natural environment. Many countries have
attempted to reduce the human impact on climate change by limiting their emission of greenhouse gases. However, a global climate
change treaty remains elusive, and many underdeveloped countries trying to improve their economic condition may be less likely
to agree with such provisions without compensation if it means slowing their economic development. Furthermore, the role of
human activity in causing climate change has become a hotly debated socio-political issue in some developed countries, including
the United States. Thus, we enter the future with considerable uncertainty about our ability to curb human population growth and
protect our environment to maintain the carrying capacity for the human species.

CONCEPT IN ACTION

Visit this website and select “Launch the movie” for an animation discussing the global impacts of human population growth.

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Section Summary
Earth’s human population is growing exponentially. Humans have increased their carrying capacity through technology,
urbanization, and harnessing the energy of fossil fuels. The age structure of a population allows us to predict population growth.
Unchecked human population growth could have dire long-term effects on human welfare and Earth’s ecosystems.

Art Connections
Figure [Link]: Age structure diagrams for rapidly growing, slow growing, and stable populations are shown in stages 1 through 3.
What type of population change do you think stage 4 represents?

Answer
Stage 4 represents a population that is decreasing.

Footnotes
1. 1 Danny Dorling, Mary Shaw, and George Davey Smith, “Global Inequality of Life Expectancy due to AIDS,” BMJ 332, no.
7542 (March 2006): 662-664, doi: 10.1136/bmj.332.7542.662.
2. 2 Paul R. Erlich, prologue to The Population Bomb, (1968; repr., New York: Ballantine, 1970).

Glossary

age structure
the distribution of the proportion of population members in each age class

one-child policy
a policy in China to limit population growth by limiting urban couples to have only one child or face a penalty of a fine

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.1.3: The Human Population is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
19.3: The Human Population by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

9.1.4: Community Ecology
In general, populations of one species never live in isolation from populations of other species. The interacting populations
occupying a given habitat form an ecological community. The number of species occupying the same habitat and their relative
abundance is known as the diversity of the community. Areas with low species diversity, such as the glaciers of Antarctica, still
contain a wide variety of living organisms, whereas the diversity of tropical rainforests is so great that it cannot be accurately
assessed. Scientists study ecology at the community level to understand how species interact with each other and compete for the
same resources.

Predation and Herbivory

Perhaps the classical example of species interaction is the predator-prey relationship. The narrowest definition of the predator-prey
interaction describes individuals of one population that kill and then consume the individuals of another population. Population
sizes of predators and prey in a community are not constant over time, and they may vary in cycles that appear to be related. The
most often cited example of predator-prey population dynamics is seen in the cycling of the lynx (predator) and the snowshoe hare
(prey), using 100 years of trapping data from North America (Figure [Link]). This cycling of predator and prey population sizes
has a period of approximately ten years, with the predator population lagging one to two years behind the prey population. An
apparent explanation for this pattern is that as the hare numbers increase, there is more food available for the lynx, allowing the
lynx population to increase as well. When the lynx population grows to a threshold level, however, they kill so many hares that
hare numbers begin to decline, followed by a decline in the lynx population because of scarcity of food. When the lynx population
is low, the hare population size begins to increase due, in part, to low predation pressure, starting the cycle anew.

Figure [Link]: The cycling of snowshoe hare and lynx populations in Northern Ontario is an example of predator-prey dynamics.

Defense Mechanisms against Predation and Herbivory

Predation and predator avoidance are strong selective agents. Any heritable character that allows an individual of a prey population
to better evade its predators will be represented in greater numbers in later generations. Likewise, traits that allow a predator to
more efficiently locate and capture its prey will lead to a greater number of offspring and an increase in the commonness of the trait
within the population. Such ecological relationships between specific populations lead to adaptations that are driven by reciprocal
evolutionary responses in those populations. Species have evolved numerous mechanisms to escape predation and herbivory (the
consumption of plants for food). Defenses may be mechanical, chemical, physical, or behavioral.
Mechanical defenses, such as the presence of armor in animals or thorns in plants, discourage predation and herbivory by
discouraging physical contact (Figure 9.1.4.2a). Many animals produce or obtain chemical defenses from plants and store them to
prevent predation. Many plant species produce secondary plant compounds that serve no function for the plant except that they are
toxic to animals and discourage consumption. For example, the foxglove produces several compounds, including digitalis, that are
extremely toxic when eaten (Figure 9.1.4.2b). (Biomedical scientists have purposed the chemical produced by foxglove as a heart
medication, which has saved lives for many decades.)

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 Figure [Link]: The (a) honey locust tree uses thorns, a mechanical defense, against herbivores, while the (b) foxglove uses a
chemical defense: toxins produces by the plant can cause nausea, vomiting, hallucinations, convulsions, or death when consumed.
(credit a: modification of work by Huw Williams; credit b: modification of work by Philip Jägenstedt)
Many species use their body shape and coloration to avoid being detected by predators. The tropical walking stick is an insect with
the coloration and body shape of a twig, which makes it very hard to see when it is stationary against a background of real twigs
(Figure 9.1.4.3a). In another example, the chameleon can change its color to match its surroundings (Figure 9.1.4.3b).

Figure [Link]: (a) The tropical walking stick and (b) the chameleon use their body shape and/or coloration to prevent detection
by predators. (credit a: modification of work by Linda Tanner; credit b: modification of work by Frank Vassen)
Some species use coloration as a way of warning predators that they are distasteful or poisonous. For example, the monarch
butterfly caterpillar sequesters poisons from its food (plants and milkweeds) to make itself poisonous or distasteful to potential
predators. The caterpillar is bright yellow and black to advertise its toxicity. The caterpillar is also able to pass the sequestered
toxins on to the adult monarch, which is also dramatically colored black and red as a warning to potential predators. Fire-bellied
toads produce toxins that make them distasteful to their potential predators. They have bright red or orange coloration on their
bellies, which they display to a potential predator to advertise their poisonous nature and discourage an attack. These are only two
examples of warning coloration, which is a relatively common adaptation. Warning coloration only works if a predator uses
eyesight to locate prey and can learn—a naïve predator must experience the negative consequences of eating one before it will
avoid other similarly colored individuals (Figure [Link]).

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 Figure [Link]: The fire-bellied toad has bright coloration on its belly that serves to warn potential predators that it is toxic.
(credit: modification of work by Roberto Verzo)
While some predators learn to avoid eating certain potential prey because of their coloration, other species have evolved
mechanisms to mimic this coloration to avoid being eaten, even though they themselves may not be unpleasant to eat or contain
toxic chemicals. In some cases of mimicry, a harmless species imitates the warning coloration of a harmful species. Assuming they
share the same predators, this coloration then protects the harmless ones. Many insect species mimic the coloration of wasps, which
are stinging, venomous insects, thereby discouraging predation (Figure [Link]).

Figure [Link]: One form of mimicry is when a harmless species mimics the coloration of a harmful species, as is seen with the
(a) wasp (Polistes sp.) and the (b) hoverfly (Syrphus sp.). (credit: modification of work by Tom Ings)
In other cases of mimicry, multiple species share the same warning coloration, but all of them actually have defenses. The
commonness of the signal improves the compliance of all the potential predators. Figure [Link] shows a variety of foul-tasting
butterflies with similar coloration.

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 Figure [Link]: Several unpleasant-tasting Heliconius butterfly species share a similar color pattern with better-tasting varieties,
an example of mimicry. (credit: Joron M, Papa R, Beltrán M, Chamberlain N, Mavárez J, et al.)

Competitive Exclusion Principle

Resources are often limited within a habitat and multiple species may compete to obtain them. Ecologists have come to understand
that all species have an ecological niche. A niche is the unique set of resources used by a species, which includes its interactions
with other species. The competitive exclusion principle states that two species cannot occupy the same niche in a habitat: in other
words, different species cannot coexist in a community if they are competing for all the same resources. This principle works
because if there is an overlap in resource use and therefore competition between two species, then traits that lessen reliance on the
shared resource will be selected for leading to evolution that reduces the overlap. If either species is unable to evolve to reduce
competition, then the species that most efficiently exploits the resource will drive the other species to extinction. An experimental
example of this principle is shown in Figure [Link] with two protozoan species: Paramecium aurelia and Paramecium caudatum.
When grown individually in the laboratory, they both thrive. But when they are placed together in the same test tube (habitat), P.
aurelia outcompetes P. caudatum for food, leading to the latter’s eventual extinction.

Figure [Link]: Paramecium aurelia and Paramecium caudatum grow well individually, but when they compete for the same
resources, the P. aurelia outcompetes the P. caudatum.

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Symbiosis
Symbiotic relationships are close, long-term interactions between individuals of different species. Symbioses may be commensal,
in which one species benefits while the other is neither harmed nor benefited; mutualistic, in which both species benefit; or
parasitic, in which the interaction harms one species and benefits the other.

Commensalism
A commensal relationship occurs when one species benefits from a close prolonged interaction, while the other neither benefits nor
is harmed. Birds nesting in trees provide an example of a commensal relationship (Figure [Link]). The tree is not harmed by the
presence of the nest among its branches. The nests are light and produce little strain on the structural integrity of the branch, and
most of the leaves, which the tree uses to get energy by photosynthesis, are above the nest so they are unaffected. The bird, on the
other hand, benefits greatly. If the bird had to nest in the open, its eggs and young would be vulnerable to predators. Many potential
commensal relationships are difficult to identify because it is difficult to prove that one partner does not derive some benefit from
the presence of the other.

Figure [Link]: The southern masked-weaver is starting to make a nest in a tree in Zambezi Valley, Zambia. This is an example of
a commensal relationship, in which one species (the bird) benefits, while the other (the tree) neither benefits nor is harmed. (credit:
“Hanay”/Wikimedia Commons)

Mutualism
A second type of symbiotic relationship is called mutualism, in which two species benefit from their interaction. For example,
termites have a mutualistic relationship with protists that live in the insect’s gut (Figure 9.1.4.9a). The termite benefits from the
ability of the protists to digest cellulose. However, the protists are able to digest cellulose only because of the presence of symbiotic
bacteria within their cells that produce the cellulase enzyme. The termite itself cannot do this: without the protozoa, it would not be
able to obtain energy from its food (cellulose from the wood it chews and eats). The protozoa benefit by having a protective
environment and a constant supply of food from the wood chewing actions of the termite. In turn, the protists benefit from the
enzymes provided by their bacterial endosymbionts, while the bacteria benefit from a doubly protective environment and a constant
source of nutrients from two hosts. Lichen are a mutualistic relationship between a fungus and photosynthetic algae or
cyanobacteria (Figure 9.1.4.9b). The glucose produced by the algae provides nourishment for both organisms, whereas the physical
structure of the lichen protects the algae from the elements and makes certain nutrients in the atmosphere more available to the
algae. The algae of lichens can live independently given the right environment, but many of the fungal partners are unable to live
on their own.

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 Figure [Link]: (a) Termites form a mutualistic relationship with symbiotic protozoa in their guts, which allow both organisms to
obtain energy from the cellulose the termite consumes. (b) Lichen is a fungus that has symbiotic photosynthetic algae living in
close association. (credit a: modification of work by Scott Bauer, USDA; credit b: modification of work by Cory Zanker)

Parasitism
A parasite is an organism that feeds off another without immediately killing the organism it is feeding on. In this relationship, the
parasite benefits, but the organism being fed upon, the host, is harmed. The host is usually weakened by the parasite as it siphons
resources the host would normally use to maintain itself. Parasites may kill their hosts, but there is usually selection to slow down
this process to allow the parasite time to complete its reproductive cycle before it or its offspring are able to spread to another host.
The reproductive cycles of parasites are often very complex, sometimes requiring more than one host species. A tapeworm causes
disease in humans when contaminated, undercooked meat such as pork, fish, or beef is consumed (Figure [Link]). The tapeworm
can live inside the intestine of the host for several years, benefiting from the host’s food, and it may grow to be over 50 feet long by
adding segments. The parasite moves from one host species to a second host species in order to complete its life cycle. Plasmodium
falciparum is another parasite: the protists that cause malaria, a significant disease in many parts of the world. Living inside human
liver and red blood cells, the organism reproduces asexually in the human host and then sexually in the gut of blood-feeding
mosquitoes to complete its life cycle. Thus malaria is spread from human to mosquito and back to human, one of many arthropod-
borne infectious diseases of humans.

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 Figure [Link]: This diagram shows the life cycle of the tapeworm, a human worm parasite. (credit: modification of work by
CDC)

CONCEPT IN ACTION

Symbiosis In The Sea | JONATHAN BI…

BI…

To learn more about “Symbiosis in the Sea,” watch this webisode of Jonathan Bird’s Blue World.

Characteristics of Communities
Communities are complex systems that can be characterized by their structure (the number and size of populations and their
interactions) and dynamics (how the members and their interactions change over time). Understanding community structure and
dynamics allows us to minimize impacts on ecosystems and manage ecological communities we benefit from.

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Biodiversity
Ecologists have extensively studied one of the fundamental characteristics of communities: biodiversity. One measure of
biodiversity used by ecologists is the number of different species in a particular area and their relative abundance. The area in
question could be a habitat, a biome, or the entire biosphere. Species richness is the term used to describe the number of species
living in a habitat or other unit. Species richness varies across the globe (Figure [Link]). Ecologists have struggled to understand
the determinants of biodiversity. Species richness is related to latitude: the greatest species richness occurs near the equator and the
lowest richness occurs near the poles. Other factors influence species richness as well. Island biogeography attempts to explain the
great species richness found in isolated islands, and has found relationships between species richness, island size, and distance from
the mainland.
Relative species abundance is the number individuals in a species relative to the total number of individuals in all species within a
system. Foundation species, described below, often have the highest relative abundance of species.

Figure [Link]: The greatest species richness for mammals in North America is associated in the equatorial latitudes. (credit:
modification of work by NASA, CIESIN, Columbia University)

Foundation Species
Foundation species are considered the “base” or “bedrock” of a community, having the greatest influence on its overall structure.
They are often primary producers, and they are typically an abundant organism. For example, kelp, a species of brown algae, is a
foundation species that forms the basis of the kelp forests off the coast of California.
Foundation species may physically modify the environment to produce and maintain habitats that benefit the other organisms that
use them. Examples include the kelp described above or tree species found in a forest. The photosynthetic corals of the coral reef
also provide structure by physically modifying the environment (Figure [Link]). The exoskeletons of living and dead coral make
up most of the reef structure, which protects many other species from waves and ocean currents.

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 Figure [Link]: Coral is the foundation species of coral reef ecosystems. (credit: Jim E. Maragos, USFWS)

Keystone Species
A keystone species is one whose presence has inordinate influence in maintaining the prevalence of various species in an
ecosystem, the ecological community’s structure, and sometimes its biodiversity. Pisaster ochraceus, the intertidal sea star, is a
keystone species in the northwestern portion of the United States (Figure [Link]). Studies have shown that when this organism is
removed from communities, mussel populations (their natural prey) increase, which completely alters the species composition and
reduces biodiversity. Another keystone species is the banded tetra, a fish in tropical streams, which supplies nearly all of the
phosphorus, a necessary inorganic nutrient, to the rest of the community. The banded tetra feeds largely on insects from the
terrestrial ecosystem and then excretes phosphorus into the aquatic ecosystem. The relationships between populations in the
community, and possibly the biodiversity, would change dramatically if these fish were to become extinct.

Figure [Link]: The Pisaster ochraceus sea star is a keystone species. (credit: Jerry Kirkhart)

BIOLOGY IN ACTION: Invasive Species

Invasive species are non-native organisms that, when introduced to an area out of its native range, alter the community they
invade. In the United States, invasive species like the purple loosestrife (Lythrum salicaria) and the zebra mussel (Dreissena
polymorpha) have altered aquatic ecosystems, and some forests are threatened by the spread of common buckthorn (Rhamnus
cathartica) and garlic mustard (Alliaria petiolata). Some well-known invasive animals include the emerald ash borer (Agrilus
planipennis) and the European starling (Sturnus vulgaris). Whether enjoying a forest hike, taking a summer boat trip, or simply
walking down an urban street, you have likely encountered an invasive species.
One of the many recent proliferations of an invasive species concerns the Asian carp in the United States. Asian carp were
introduced to the United States in the 1970s by fisheries (commercial catfish ponds) and by sewage treatment facilities that
used the fish’s excellent filter feeding abilities to clean their ponds of excess plankton. Some of the fish escaped, and by the
1980s they had colonized many waterways of the Mississippi River basin, including the Illinois and Missouri Rivers.
Voracious feeders and rapid reproducers, Asian carp may outcompete native species for food and could lead to their extinction.
One species, the grass carp, feeds on phytoplankton and aquatic plants. It competes with native species for these resources and

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 alters nursery habitats for other fish by removing aquatic plants. Another species, the silver carp, competes with native fish that
feed on zooplankton. In some parts of the Illinois River, Asian carp constitute 95 percent of the community's biomass.
Although edible, the fish is bony and not desired in the United States. Moreover, their presence now threatens the native fish
and fisheries of the Great Lakes, which are important to local economies and recreational anglers. Asian carp have even injured
humans. The fish, frightened by the sound of approaching motorboats, thrust themselves into the air, often landing in the boat
or directly hitting boaters.
The Great Lakes and their prized salmon and lake trout fisheries are being threatened by Asian carp. The carp are not yet
present in the Great Lakes, and attempts are being made to prevent its access to the lakes through the Chicago Ship and
Sanitary Canal, which is the only connection between the Mississippi River and Great Lakes basins. To prevent the Asian carp
from leaving the canal, a series of electric barriers have been used to discourage their migration; however, the threat is
significant enough that several states and Canada have sued to have the Chicago channel permanently cut off from Lake
Michigan. Local and national politicians have weighed in on how to solve the problem. In general, governments have been
ineffective in preventing or slowing the introduction of invasive species.
The issues associated with Asian carp show how population and community ecology, fisheries management, and politics
intersect on issues of vital importance to the human food supply and economy. Socio-political issues like the Asian carp make
extensive use of the sciences of population ecology, the study of members of a particular species occupying a habitat; and
community ecology, the study of the interaction of all species within a habitat.

Community Dynamics
Community dynamics are the changes in community structure and composition over time, often following environmental
disturbances such as volcanoes, earthquakes, storms, fires, and climate change. Communities with a relatively constant number of
species are said to be at equilibrium. The equilibrium is dynamic with species identities and relationships changing over time, but
maintaining relatively constant numbers. Following a disturbance, the community may or may not return to the equilibrium state.
Succession describes the sequential appearance and disappearance of species in a community over time after a severe disturbance.
In primary succession, newly exposed or newly formed rock is colonized by living organisms; in secondary succession, a part of an
ecosystem is disturbed and remnants of the previous community remain. In both cases, there is a sequential change in species until
a more or less permanent community develops.

Primary Succession and Pioneer Species

Primary succession occurs when new land is formed, for example, following the eruption of volcanoes, such as those on the Big
Island of Hawaii. As lava flows into the ocean, new land is continually being formed. On the Big Island, approximately 32 acres of
land is added to it its size each year. Weathering and other natural forces break down the rock enough for the establishment of
hearty species such as lichens and some plants, known as pioneer species(Figure [Link]). These species help to further break
down the mineral-rich lava into soil where other, less hardy but more competitive species, such as grasses, shrubs, and trees, will
grow and eventually replace the pioneer species. Over time the area will reach an equilibrium state, with a set of organisms quite
different from the pioneer species.

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 Figure [Link]: During primary succession in lava on Maui, Hawaii, succulent plants are the pioneer species. (credit: Forest and
Kim Starr)

Secondary succession
A classic example of secondary succession occurs in oak and hickory forests cleared by wildfire (Figure [Link]). Wildfires will
burn most vegetation, and unless the animals can flee the area, they are killed. Their nutrients, however, are returned to the ground
in the form of ash. Thus, although the community has been dramatically altered, there is a soil ecosystem present that provides a
foundation for rapid recolonization.
Before the fire, the vegetation was dominated by tall trees with access to the major plant energy resource: sunlight. Their height
gave them access to sunlight while also shading the ground and other low-lying species. After the fire, though, these trees are no
longer dominant. Thus, the first plants to grow back are usually annual plants followed within a few years by quickly growing and
spreading grasses and other pioneer species. Due, at least in part, to changes in the environment brought on by the growth of
grasses and forbs, over many years, shrubs emerge along with small pine, oak, and hickory trees. These organisms are called
intermediate species. Eventually, over 150 years, the forest will reach its equilibrium point and resemble the community before the
fire. This equilibrium state is referred to as the climax community, which will remain until the next disturbance. The climax
community is typically characteristic of a given climate and geology. Although the community in equilibrium looks the same once
it is attained, the equilibrium is a dynamic one with constant changes in abundance and sometimes species identities. The return of
a natural ecosystem after agricultural activities is also a well-documented secondary succession process.

Figure [Link]: Secondary succession is seen in an oak and hickory forest after a forest fire. A sequence of the community
present at three successive times at the same location is depicted.

Section Summary
Communities include all the different species living in a given area. The variety of these species is referred to as biodiversity. Many
organisms have developed defenses against predation and herbivory, including mechanical defenses, warning coloration, and

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mimicry. Two species cannot exist indefinitely in the same habitat competing directly for the same resources. Species may form
symbiotic relationships such as commensalism, mutualism, or parasitism. Community structure is described by its foundation and
keystone species. Communities respond to environmental disturbances by succession: the predictable appearance of different types
of plant species, until a stable community structure is established.

Glossary

climax community
the final stage of succession, where a stable community is formed by a characteristic assortment of plant and animal species

competitive exclusion principle

no two species within a habitat can coexist indefinitely when they compete for the same resources at the same time and place

environmental disturbance
a change in the environment caused by natural disasters or human activities

foundation species
a species which often forms the major structural portion of the habitat

host
an organism a parasite lives on

island biogeography
the study of life on island chains and how their geography interacts with the diversity of species found there

keystone species
a species whose presence is key to maintaining biodiversity in an ecosystem and to upholding an ecological community’s
structure

mimicry
an adaptation in which an organism looks like another organism that is dangerous, toxic, or distasteful to its predators

mutualism
a symbiotic relationship between two species where both species benefit

parasite
an organism that uses resources from another species: the host

pioneer species
the first species to appear in primary and secondary succession

primary succession
the succession on land that previously has had no life

relative species abundance

the absolute population size of a particular species relative to the population size of other species within the community

secondary succession
the succession in response to environmental disturbances that move a community away from its equilibrium

species richness
the number of different species in a community

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.1.4: Community Ecology is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
19.4: Community Ecology by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

9.1.E: Population and Community Ecology (Exercises)
19.1: Population Demographics and Dynamics
Multiple Choice
Which of the following methods will provide information to an ecologist about both the size and density of a population?
A. mark and recapture
B. mark and release
C. quadrat
D. life table

Answer
C

Which of the following is best at showing the life expectancy of an individual within a population?
A. quadrat
B. mark and recapture
C. survivorship curve
D. life table

Answer
D

Human populations have which type of survivorship curve?

A. Type I
B. Type II
C. Type III
D. Type IV

Answer
A

Free Response
Describe how a researcher would determine the size of a penguin population in Antarctica using the mark and release method.

Answer
The researcher would mark a certain number of penguins with a tag, release them back into the population, and, at a later time,
recapture penguins to see what percentage was tagged. This percentage would allow an estimation of the size of the penguin
population.

19.2: Population Growth and Regulation

Multiple Choice
Species with limited resources usually exhibit a(n) ________ growth curve.
A. logistic
B. logical
C. experimental
D. exponential

Answer
A

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The maximum growth rate characteristic of a species is called its ________.
A. limit
B. carrying capacity
C. biotic potential
D. exponential growth pattern

Answer
C

The population size of a species capable of being supported by the environment is called its ________.
A. limit
B. carrying capacity
C. biotic potential
D. logistic growth pattern

Answer
B

Species that have many offspring at one time are usually:

A. r-selected
B. K-selected
C. both r- and K-selected
D. not selected

Answer
A

A forest fire is an example of ________ regulation.

A. density-dependent
B. density-independent
C. r-selected
D. K-selected

Answer
B

Free Response
Describe the growth at various parts of the S-shaped curve of logistic growth.

Answer
In the first part of the curve, when few individuals of the species are present and resources are plentiful, growth is exponential,
similar to a J-shaped curve. Later, growth slows due to the species using up resources. Finally, the population levels off at the
carrying capacity of the environment, and it is relatively stable over time.

Give an example of how density-dependent and density-independent factors might interact.

Answer
If a natural disaster such as a fire happened in the winter, when populations are low, it would have a greater effect on the overall
population and its recovery than if the same disaster occurred during the summer, when population levels are high.

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19.3: The Human Population
Multiple Choice
A country with zero population growth is likely to be ________.
A. in Africa
B. in Asia
C. economically developed
D. economically underdeveloped

Answer
C

Which type of country has the greatest proportion of young individuals?

A. economically developed
B. economically underdeveloped
C. countries with zero population growth
D. countries in Europe

Answer
B

Which of the following is not a way that humans have increased the carrying capacity of the environment?
A. agriculture
B. using large amounts of natural resources
C. domestication of animals
D. use of language

Answer
B

Free Response
Describe the age structures in rapidly growing countries, slowly growing countries, and countries with zero population growth.

Answer
Rapidly growing countries have a large segment of the population at reproductive age or younger. Slower growing populations
have a lower percentage of these individuals, and countries with zero population growth have an even lower percentage. On the
other hand, a high proportion of older individuals is seen mostly in countries with zero growth, and a low proportion is most
common in rapidly growing countries.

19.4: Community Ecology

Multiple Choice
The first species to live on new land, such as that formed from volcanic lava, are called________.
A. climax community
B. keystone species
C. foundation species
D. pioneer species

Answer
D

A symbiotic relationship where both of the co-existing species benefit from the interaction is called ________.

Access for free at OpenStax 9.1.E.3 [Link]

 A. commensalism
B. parasitism
C. mutualism
D. communism

Answer
C

When an invasive species alters the community structure it is introduced to, what can the consequence be?
A. extinction of economically important species
B. reduced predation on some native species
C. increased predation on some native species
D. all of the above

Answer
D

Free Response
Describe the competitive exclusion principle and its effects on competing species.

Answer
The competitive exclusion principles states that no two species competing for the same resources at the same time and place can
co-exist over time. Thus, one of the competing species will eventually dominate. On the other hand, if the species evolve such
that they use resources from different parts of the habitat or at different times of day, the two species can exist together
indefinitely.

Describe the potential effects when a keystone species is removed from a community.

Answer
Removing a keystone species will have dramatic effects on the abundance of individuals in other populations, increasing some
and decreasing others. This affects the interactions between populations such as competition and predator-prey relationships. In
addition, the community may show a loss of diversity.

This page titled 9.1.E: Population and Community Ecology (Exercises) is shared under a CC BY license and was authored, remixed, and/or
curated by OpenStax.
19.E: Population and Community Ecology (Exercises) by OpenStax is licensed CC BY 4.0.

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 SECTION OVERVIEW

9.2: Ecosystems and the Biosphere

9.2.1: Energy Flow through Ecosystems

9.2.2: Biogeochemical Cycles

9.2.3: Terrestrial Biomes

9.2.4: Aquatic and Marine Biomes

9.2.E: Ecosystems and the Biosphere (Exercises)

This page titled 9.2: Ecosystems and the Biosphere is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.

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9.2.1: Energy Flow through Ecosystems
An ecosystem is a community of living organisms and their abiotic (non-living) environment. Ecosystems can be small, such as the
tide pools found near the rocky shores of many oceans, or large, such as those found in the tropical rainforest of the Amazon in
Brazil (Figure [Link]).

Figure [Link]: A (a) tidal pool ecosystem in Matinicus Island, Maine, is a small ecosystem, while the (b) Amazon rainforest in
Brazil is a large ecosystem. (credit a: modification of work by Jim Kuhn; credit b: modification of work by Ivan Mlinaric)
There are three broad categories of ecosystems based on their general environment: freshwater, marine, and terrestrial. Within these
three categories are individual ecosystem types based on the environmental habitat and organisms present.

Ecology of Ecosystems
Life in an ecosystem often involves competition for limited resources, which occurs both within a single species and between
different species. Organisms compete for food, water, sunlight, space, and mineral nutrients. These resources provide the energy for
metabolic processes and the matter to make up organisms’ physical structures. Other critical factors influencing community
dynamics are the components of its physical environment: a habitat’s climate (seasons, sunlight, and rainfall), elevation, and
geology. These can all be important environmental variables that determine which organisms can exist within a particular area.
Freshwater ecosystems are the least common, occurring on only 1.8 percent of Earth's surface. These systems comprise lakes,
rivers, streams, and springs; they are quite diverse, and support a variety of animals, plants, fungi, protists and prokaryotes.
Marine ecosystems are the most common, comprising 75 percent of Earth's surface and consisting of three basic types: shallow
ocean, deep ocean water, and deep ocean bottom. Shallow ocean ecosystems include extremely biodiverse coral reef ecosystems,
yet the deep ocean water is known for large numbers of plankton and krill (small crustaceans) that support it. These two
environments are especially important to aerobic respirators worldwide, as the phytoplankton perform 40 percent of all
photosynthesis on Earth. Although not as diverse as the other two, deep ocean bottom ecosystems contain a wide variety of marine
organisms. Such ecosystems exist even at depths where light is unable to penetrate through the water.
Terrestrial ecosystems, also known for their diversity, are grouped into large categories called biomes. A biome is a large-scale
community of organisms, primarily defined on land by the dominant plant types that exist in geographic regions of the planet with
similar climatic conditions. Examples of biomes include tropical rainforests, savannas, deserts, grasslands, temperate forests, and
tundras. Grouping these ecosystems into just a few biome categories obscures the great diversity of the individual ecosystems
within them. For example, the saguaro cacti (Carnegiea gigantean) and other plant life in the Sonoran Desert, in the United States,
are relatively diverse compared with the desolate rocky desert of Boa Vista, an island off the coast of Western Africa (Figure
[Link]).

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 Figure [Link]: Desert ecosystems, like all ecosystems, can vary greatly. The desert in (a) Saguaro National Park, Arizona, has
abundant plant life, while the rocky desert of (b) Boa Vista island, Cape Verde, Africa, is devoid of plant life. (credit a:
modification of work by Jay Galvin; credit b: modification of work by Ingo Wölbern)

Ecosystems and Disturbance

Ecosystems are complex with many interacting parts. They are routinely exposed to various disturbances: changes in the
environment that affect their compositions, such as yearly variations in rainfall and temperature. Many disturbances are a result of
natural processes. For example, when lightning causes a forest fire and destroys part of a forest ecosystem, the ground is eventually
populated with grasses, followed by bushes and shrubs, and later mature trees: thus, the forest is restored to its former state. This
process is so universal that ecologists have given it a name—succession. The impact of environmental disturbances caused by
human activities is now as significant as the changes wrought by natural processes. Human agricultural practices, air pollution, acid
rain, global deforestation, overfishing, oil spills, and illegal dumping on land and into the ocean all have impacts on ecosystems.
Equilibrium is a dynamic state of an ecosystem in which, despite changes in species numbers and occurrence, biodiversity remains
somewhat constant. In ecology, two parameters are used to measure changes in ecosystems: resistance and resilience. The ability of
an ecosystem to remain at equilibrium in spite of disturbances is called resistance. The speed at which an ecosystem recovers
equilibrium after being disturbed is called resilience. Ecosystem resistance and resilience are especially important when
considering human impact. The nature of an ecosystem may change to such a degree that it can lose its resilience entirely. This
process can lead to the complete destruction or irreversible altering of the ecosystem.

Food Chains and Food Webs

A food chain is a linear sequence of organisms through which nutrients and energy pass as one organism eats another; the levels in
the food chain are producers, primary consumers, higher-level consumers, and finally decomposers. These levels are used to
describe ecosystem structure and dynamics. There is a single path through a food chain. Each organism in a food chain occupies a
specific trophic level (energy level), its position in the food chain or food web.
In many ecosystems, the base, or foundation, of the food chain consists of photosynthetic organisms (plants or phytoplankton),
which are called producers. The organisms that consume the producers are herbivores: the primary consumers. Secondary
consumers are usually carnivores that eat the primary consumers. Tertiary consumers are carnivores that eat other carnivores.
Higher-level consumers feed on the next lower trophic levels, and so on, up to the organisms at the top of the food chain: the apex
consumers. In the Lake Ontario food chain, shown in Figure [Link], the Chinook salmon is the apex consumer at the top of this
food chain.

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 Figure [Link]: These are the trophic levels of a food chain in Lake Ontario at the United States–Canada border. Energy and
nutrients flow from photosynthetic green algae at the base to the top of the food chain: the Chinook salmon. (credit: modification of
work by National Oceanic and Atmospheric Administration/NOAA)
One major factor that limits the number of steps in a food chain is energy. Energy is lost at each trophic level and between trophic
levels as heat and in the transfer to decomposers (Figure [Link]). Thus, after a limited number of trophic energy transfers, the
amount of energy remaining in the food chain may not be great enough to support viable populations at yet a higher trophic level.

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 Figure [Link]: The relative energy in trophic levels in a Silver Springs, Florida, ecosystem is shown. Each trophic level has less
energy available, and usually, but not always, supports a smaller mass of organisms at the next level.
There is a one problem when using food chains to describe most ecosystems. Even when all organisms are grouped into appropriate
trophic levels, some of these organisms can feed on more than one trophic level; likewise, some of these organisms can also be fed
on from multiple trophic levels. In addition, species feed on and are eaten by more than one species. In other words, the linear
model of ecosystems, the food chain, is a hypothetical, overly simplistic representation of ecosystem structure. A holistic model—
which includes all the interactions between different species and their complex interconnected relationships with each other and
with the environment—is a more accurate and descriptive model for ecosystems. A food web is a concept that accounts for the
multiple trophic (feeding) interactions between each species and the many species it may feed on, or that feed on it. In a food web,
the several trophic connections between each species and the other species that interact with it may cross multiple trophic levels.
The matter and energy movements of virtually all ecosystems are more accurately described by food webs (Figure [Link]).

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 Figure [Link]: This food web shows the interactions between organisms across trophic levels. Arrows point from an organism
that is consumed to the organism that consumes it. All the producers and consumers eventually become nourishment for the
decomposers (fungi, mold, earthworms, and bacteria in the soil). (credit "fox": modification of work by Kevin Bacher, NPS; credit
"owl": modification of work by John and Karen Hollingsworth, USFWS; credit "snake": modification of work by Steve Jurvetson;
credit "robin": modification of work by Alan Vernon; credit "frog": modification of work by Alessandro Catenazzi; credit "spider":
modification of work by "Sanba38"/Wikimedia Commons; credit "centipede": modification of work by “Bauerph”/Wikimedia
Commons; credit "squirrel": modification of work by Dawn Huczek; credit "mouse": modification of work by NIGMS, NIH; credit
"sparrow": modification of work by David Friel; credit "beetle": modification of work by Scott Bauer, USDA Agricultural
Research Service; credit "mushrooms": modification of work by Chris Wee; credit "mold": modification of work by Dr. Lucille
Georg, CDC; credit "earthworm": modification of work by Rob Hille; credit "bacteria": modification of work by Don Stalons,
CDC)

CONCEPT IN ACTION

Head to this online interactive simulator to investigate food web function. In the Interactive Labs box, under Food Web, click
Step 1. Read the instructions first, and then click Step 2 for additional instructions. When you are ready to create a simulation,
in the upper-right corner of the Interactive Labs box, click OPEN SIMULATOR.

Two general types of food webs are often shown interacting within a single ecosystem. A grazing food web has plants or other
photosynthetic organisms at its base, followed by herbivores and various carnivores. A detrital food web consists of a base of
organisms that feed on decaying organic matter (dead organisms), including decomposers (which break down dead and decaying

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organisms) and detritivores (which consume organic detritus). These organisms are usually bacteria, fungi, and invertebrate animals
that recycle organic material back into the biotic part of the ecosystem as they themselves are consumed by other organisms. As
ecosystems require a method to recycle material from dead organisms, grazing food webs have an associated detrital food web. For
example, in a meadow ecosystem, plants may support a grazing food web of different organisms, primary and other levels of
consumers, while at the same time supporting a detrital food web of bacteria and fungi feeding off dead plants and animals.
Simultaneously, a detrital food web can contribute energy to a grazing food web, as when a robin eats an earthworm.

How Organisms Acquire Energy in a Food Web

All living things require energy in one form or another. Energy is used by most complex metabolic pathways (usually in the form of
ATP), especially those responsible for building large molecules from smaller compounds. Living organisms would not be able to
assemble macromolecules (proteins, lipids, nucleic acids, and complex carbohydrates) from their monomers without a constant
energy input.
Food-web diagrams illustrate how energy flows directionally through ecosystems. They can also indicate how efficiently organisms
acquire energy, use it, and how much remains for use by other organisms of the food web. Energy is acquired by living things in
two ways: autotrophs harness light or chemical energy and heterotrophs acquire energy through the consumption and digestion of
other living or previously living organisms.
Photosynthetic and chemosynthetic organisms are autotrophs, which are organisms capable of synthesizing their own food (more
specifically, capable of using inorganic carbon as a carbon source). Photosynthetic autotrophs (photoautotrophs) use sunlight as an
energy source, and chemosynthetic autotrophs (chemoautotrophs) use inorganic molecules as an energy source. Autotrophs are
critical for most ecosystems: they are the producer trophic level. Without these organisms, energy would not be available to other
living organisms, and life itself would not be possible.
Photoautotrophs, such as plants, algae, and photosynthetic bacteria, are the energy source for a majority of the world’s ecosystems.
These ecosystems are often described by grazing and detrital food webs. Photoautotrophs harness the Sun’s solar energy by
converting it to chemical energy in the form of ATP (and NADP). The energy stored in ATP is used to synthesize complex organic
molecules, such as glucose. The rate at which photosynthetic producers incorporate energy from the Sun is called gross primary
productivity. However, not all of the energy incorporated by producers is available to the other organisms in the food web because
producers must also grow and reproduce, which consumes energy. Net primary productivity is the energy that remains in the
producers after accounting for these organisms’ respiration and heat loss. The net productivity is then available to the primary
consumers at the next trophic level.
Chemoautotrophs are primarily bacteria and archaea that are found in rare ecosystems where sunlight is not available, such as those
associated with dark caves or hydrothermal vents at the bottom of the ocean (Figure [Link]). Many chemoautotrophs in
hydrothermal vents use hydrogen sulfide (H2S), which is released from the vents as a source of chemical energy; this allows them
to synthesize complex organic molecules, such as glucose, for their own energy and, in turn, supplies energy to the rest of the
ecosystem.

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 Figure [Link]: Swimming shrimp, a few squat lobsters, and hundreds of vent mussels are seen at a hydrothermal vent at the
bottom of the ocean. As no sunlight penetrates to this depth, the ecosystem is supported by chemoautotrophic bacteria and organic
material that sinks from the ocean’s surface. This picture was taken in 2006 at the submerged NW Eifuku volcano off the coast of
Japan by the National Oceanic and Atmospheric Administration (NOAA). The summit of this highly active volcano lies 1535 m
below the surface.

Consequences of Food Webs: Biological Magnification

One of the most important consequences of ecosystem dynamics in terms of human impact is biomagnification. Biomagnification
is the increasing concentration of persistent, toxic substances in organisms at each successive trophic level. These are substances
that are fat soluble, not water soluble, and are stored in the fat reserves of each organism. Many substances have been shown to
biomagnify, including classical studies with the pesticide dichlorodiphenyltrichloroethane (DDT), which were described in the
1960s bestseller, Silent Spring by Rachel Carson. DDT was a commonly used pesticide before its dangers to apex consumers, such
as the bald eagle, became known. In aquatic ecosystems, organisms from each trophic level consumed many organisms in the lower
level, which caused DDT to increase in birds (apex consumers) that ate fish. Thus, the birds accumulated sufficient amounts of
DDT to cause fragility in their eggshells. This effect increased egg breakage during nesting and was shown to have devastating
effects on these bird populations. The use of DDT was banned in the United States in the 1970s.
Other substances that biomagnify are polychlorinated biphenyls (PCB), which were used as coolant liquids in the United States
until their use was banned in 1979, and heavy metals, such as mercury, lead, and cadmium. These substances are best studied in
aquatic ecosystems, where predatory fish species accumulate very high concentrations of toxic substances that are at quite low
concentrations in the environment and in producers. As illustrated in a study performed by the NOAA in the Saginaw Bay of Lake
Huron of the North American Great Lakes (Figure [Link]), PCB concentrations increased from the producers of the ecosystem
(phytoplankton) through the different trophic levels of fish species. The apex consumer, the walleye, has more than four times the
amount of PCBs compared to phytoplankton. Also, based on results from other studies, birds that eat these fish may have PCB
levels at least one order of magnitude higher than those found in the lake fish.

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 Figure [Link]: This chart shows the PCB concentrations found at the various trophic levels in the Saginaw Bay ecosystem of
Lake Huron. Notice that the fish in the higher trophic levels accumulate more PCBs than those in lower trophic levels. (credit:
Patricia Van Hoof, NOAA)
Other concerns have been raised by the biomagnification of heavy metals, such as mercury and cadmium, in certain types of
seafood. The United States Environmental Protection Agency recommends that pregnant women and young children should not
consume any swordfish, shark, king mackerel, or tilefish because of their high mercury content. These individuals are advised to
eat fish low in mercury: salmon, shrimp, pollock, and catfish. Biomagnification is a good example of how ecosystem dynamics can
affect our everyday lives, even influencing the food we eat.

Section Summary
Ecosystems exist underground, on land, at sea, and in the air. Organisms in an ecosystem acquire energy in a variety of ways,
which is transferred between trophic levels as the energy flows from the base to the top of the food web, with energy being lost at
each transfer. There is energy lost at each trophic level, so the lengths of food chains are limited because there is a point where not
enough energy remains to support a population of consumers. Fat soluble compounds biomagnify up a food chain causing damage
to top consumers. even when environmental concentrations of a toxin are low.

Glossary

autotroph
an organism capable of synthesizing its own food molecules from smaller inorganic molecules

apex consumer
an organism at the top of the food chain

biomagnification
an increasing concentration of persistent, toxic substances in organisms at each trophic level, from the producers to the apex
consumers

biome
a large-scale community of organisms, primarily defined on land by the dominant plant types that exist in geographic regions of
the planet with similar climatic conditions

chemoautotroph
an organism capable of synthesizing its own food using energy from inorganic molecules

detrital food web

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 a type of food web that is supported by dead or decaying organisms rather than by living autotrophs; these are often associated
with grazing food webs within the same ecosystem

ecosystem
a community of living organisms and their interactions with their abiotic environment

equilibrium
the steady state of a system in which the relationships between elements of the system do not change

food chain
a linear sequence of trophic (feeding) relationships of producers, primary consumers, and higher level consumers

food web
a web of trophic (feeding) relationships among producers, primary consumers, and higher level consumers in an ecosystem

grazing food web

a type of food web in which the producers are either plants on land or phytoplankton in the water; often associated with a
detrital food web within the same ecosystem

gross primary productivity

the rate at which photosynthetic producers incorporate energy from the Sun

net primary productivity

the energy that remains in the producers after accounting for the organisms’ respiration and heat loss

photoautotroph
an organism that uses sunlight as an energy source to synthesize its own food molecules

primary consumer
the trophic level that obtains its energy from the producers of an ecosystem

producer
the trophic level that obtains its energy from sunlight, inorganic chemicals, or dead or decaying organic material

resilience (ecological)
the speed at which an ecosystem recovers equilibrium after being disturbed

resistance (ecological)
the ability of an ecosystem to remain at equilibrium in spite of disturbances

secondary consumer
a trophic level in an ecosystem, usually a carnivore that eats a primary consumer

tertiary consumer
a trophic level in an ecosystem, usually carnivores that eat other carnivores

trophic level
the position of a species or group of species in a food chain or a food web

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

Access for free at OpenStax [Link] [Link]

This page titled 9.2.1: Energy Flow through Ecosystems is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
20.1: Energy Flow through Ecosystems by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

9.2.2: Biogeochemical Cycles
Energy flows directionally through ecosystems, entering as sunlight (or inorganic molecules for chemoautotrophs) and leaving as
heat during the transfers between trophic levels. Rather than flowing through an ecosystem, the matter that makes up living
organisms is conserved and recycled. The six most common elements associated with organic molecules—carbon, nitrogen,
hydrogen, oxygen, phosphorus, and sulfur—take a variety of chemical forms and may exist for long periods in the atmosphere, on
land, in water, or beneath Earth’s surface. Geologic processes, such as weathering, erosion, water drainage, and the subduction of
the continental plates, all play a role in the cycling of elements on Earth. Because geology and chemistry have major roles in the
study of this process, the recycling of inorganic matter between living organisms and their nonliving environment is called a
biogeochemical cycle.
Water, which contains hydrogen and oxygen, is essential to all living processes. The hydrosphere is the area of Earth where water
movement and storage occurs: as liquid water on the surface (rivers, lakes, oceans) and beneath the surface (groundwater) or ice,
(polar ice caps and glaciers), and as water vapor in the atmosphere. Carbon is found in all organic macromolecules and is an
important constituent of fossil fuels. Nitrogen is a major component of our nucleic acids and proteins and is critical to human
agriculture. Phosphorus, a major component of nucleic acids, is one of the main ingredients (along with nitrogen) in artificial
fertilizers used in agriculture, which has environmental impacts on our surface water. Sulfur, critical to the three-dimensional
folding of proteins (as in disulfide binding), is released into the atmosphere by the burning of fossil fuels.
The cycling of these elements is interconnected. For example, the movement of water is critical for the leaching of nitrogen and
phosphate into rivers, lakes, and oceans. The ocean is also a major reservoir for carbon. Thus, mineral nutrients are cycled, either
rapidly or slowly, through the entire biosphere between the biotic and abiotic world and from one living organism to another.

The Water Cycle

Water is essential for all living processes. The human body is more than one-half water and human cells are more than 70 percent
water. Thus, most land animals need a supply of fresh water to survive. Of the stores of water on Earth, 97.5 percent is salt water
(Figure [Link]). Of the remaining water, 99 percent is locked as underground water or ice. Thus, less than one percent of fresh
water is present in lakes and rivers. Many living things are dependent on this small amount of surface fresh water supply, a lack of
which can have important effects on ecosystem dynamics. Humans, of course, have developed technologies to increase water
availability, such as digging wells to harvest groundwater, storing rainwater, and using desalination to obtain drinkable water from
the ocean. Although this pursuit of drinkable water has been ongoing throughout human history, the supply of fresh water continues
to be a major issue in modern times.

Figure [Link]: Only 2.5 percent of water on Earth is fresh water, and less than 1 percent of fresh water is easily accessible to
living things.
The various processes that occur during the cycling of water are illustrated in Figure [Link]. The processes include the following:
evaporation and sublimation
condensation and precipitation
subsurface water flow
surface runoff and snowmelt
streamflow

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The water cycle is driven by the Sun’s energy as it warms the oceans and other surface waters. This leads to evaporation (water to
water vapor) of liquid surface water and sublimation (ice to water vapor) of frozen water, thus moving large amounts of water into
the atmosphere as water vapor. Over time, this water vapor condenses into clouds as liquid or frozen droplets and eventually leads
to precipitation (rain or snow), which returns water to Earth’s surface. Rain reaching Earth’s surface may evaporate again, flow
over the surface, or percolate into the ground. Most easily observed is surface runoff: the flow of fresh water either from rain or
melting ice. Runoff can make its way through streams and lakes to the oceans or flow directly to the oceans themselves.
In most natural terrestrial environments rain encounters vegetation before it reaches the soil surface. A significant percentage of
water evaporates immediately from the surfaces of plants. What is left reaches the soil and begins to move down. Surface runoff
will occur only if the soil becomes saturated with water in a heavy rainfall. Most water in the soil will be taken up by plant roots.
The plant will use some of this water for its own metabolism, and some of that will find its way into animals that eat the plants, but
much of it will be lost back to the atmosphere through a process known as evapotranspiration. Water enters the vascular system of
the plant through the roots and evaporates, or transpires, through the stomata of the leaves. Water in the soil that is not taken up by
a plant and that does not evaporate is able to percolate into the subsoil and bedrock. Here it forms groundwater.
Groundwater is a significant reservoir of fresh water. It exists in the pores between particles in sand and gravel, or in the fissures in
rocks. Shallow groundwater flows slowly through these pores and fissures and eventually finds its way to a stream or lake where it
becomes a part of the surface water again. Streams do not flow because they are replenished from rainwater directly; they flow
because there is a constant inflow from groundwater below. Some groundwater is found very deep in the bedrock and can persist
there for millennia. Most groundwater reservoirs, or aquifers, are the source of drinking or irrigation water drawn up through wells.
In many cases these aquifers are being depleted faster than they are being replenished by water percolating down from above.
Rain and surface runoff are major ways in which minerals, including carbon, nitrogen, phosphorus, and sulfur, are cycled from land
to water. The environmental effects of runoff will be discussed later as these cycles are described.

Figure [Link]: Water from the land and oceans enters the atmosphere by evaporation or sublimation, where it condenses into
clouds and falls as rain or snow. Precipitated water may enter freshwater bodies or infiltrate the soil. The cycle is complete when
surface or groundwater reenters the ocean. (credit: modification of work by John M. Evans and Howard Perlman, USGS)

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The Carbon Cycle
Carbon is the fourth most abundant element in living organisms. Carbon is present in all organic molecules, and its role in the
structure of macromolecules is of primary importance to living organisms. Carbon compounds contain energy, and many of these
compounds from plants and algae have remained stored as fossilized carbon, which humans use as fuel. Since the 1800s, the use of
fossil fuels has accelerated. As global demand for Earth’s limited fossil fuel supplies has risen since the beginning of the Industrial
Revolution, the amount of carbon dioxide in our atmosphere has increased as the fuels are burned. This increase in carbon dioxide
has been associated with climate change and is a major environmental concern worldwide.
The carbon cycle is most easily studied as two interconnected subcycles: one dealing with rapid carbon exchange among living
organisms and the other dealing with the long-term cycling of carbon through geologic processes. The entire carbon cycle is shown
in Figure [Link].

Figure [Link]: Carbon dioxide gas exists in the atmosphere and is dissolved in water. Photosynthesis converts carbon dioxide gas
to organic carbon, and respiration cycles the organic carbon back into carbon dioxide gas. Long-term storage of organic carbon
occurs when matter from living organisms is buried deep underground and becomes fossilized. Volcanic activity and, more
recently, human emissions bring this stored carbon back into the carbon cycle. (credit: modification of work by John M. Evans and
Howard Perlman, USGS)

The Biological Carbon Cycle

Living organisms are connected in many ways, even between ecosystems. A good example of this connection is the exchange of
carbon between heterotrophs and autotrophs within and between ecosystems by way of atmospheric carbon dioxide. Carbon
dioxide is the basic building block that autotrophs use to build multi-carbon, high-energy compounds, such as glucose. The energy
harnessed from the Sun is used by these organisms to form the covalent bonds that link carbon atoms together. These chemical
bonds store this energy for later use in the process of respiration. Most terrestrial autotrophs obtain their carbon dioxide directly
from the atmosphere, while marine autotrophs acquire it in the dissolved form (carbonic acid, HCO3–). However the carbon dioxide
is acquired, a byproduct of fixing carbon in organic compounds is oxygen. Photosynthetic organisms are responsible for
maintaining approximately 21 percent of the oxygen content of the atmosphere that we observe today.

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The partners in biological carbon exchange are the heterotrophs (especially the primary consumers, largely herbivores).
Heterotrophs acquire the high-energy carbon compounds from the autotrophs by consuming them and breaking them down by
respiration to obtain cellular energy, such as ATP. The most efficient type of respiration, aerobic respiration, requires oxygen
obtained from the atmosphere or dissolved in water. Thus, there is a constant exchange of oxygen and carbon dioxide between the
autotrophs (which need the carbon) and the heterotrophs (which need the oxygen). Autotrophs also respire and consume the
organic molecules they form: using oxygen and releasing carbon dioxide. They release more oxygen gas as a waste product of
photosynthesis than they use for their own respiration; therefore, there is excess available for the respiration of other aerobic
organisms. Gas exchange through the atmosphere and water is one way that the carbon cycle connects all living organisms on
Earth.

The Biogeochemical Carbon Cycle

The movement of carbon through land, water, and air is complex, and, in many cases, it occurs much more slowly geologically
than the movement between living organisms. Carbon is stored for long periods in what are known as carbon reservoirs, which
include the atmosphere, bodies of liquid water (mostly oceans), ocean sediment, soil, rocks (including fossil fuels), and Earth’s
interior.
As stated, the atmosphere is a major reservoir of carbon in the form of carbon dioxide that is essential to the process of
photosynthesis. The level of carbon dioxide in the atmosphere is greatly influenced by the reservoir of carbon in the oceans. The
exchange of carbon between the atmosphere and water reservoirs influences how much carbon is found in each, and each one
affects the other reciprocally. Carbon dioxide (CO2) from the atmosphere dissolves in water and, unlike oxygen and nitrogen gas,
reacts with water molecules to form ionic compounds. Some of these ions combine with calcium ions in the seawater to form
calcium carbonate (CaCO3), a major component of the shells of marine organisms. These organisms eventually form sediments on
the ocean floor. Over geologic time, the calcium carbonate forms limestone, which comprises the largest carbon reservoir on Earth.
On land, carbon is stored in soil as organic carbon as a result of the decomposition of living organisms or from weathering of
terrestrial rock and minerals. Deeper under the ground, at land and at sea, are fossil fuels, the anaerobically decomposed remains of
plants that take millions of years to form. Fossil fuels are considered a non-renewable resource because their use far exceeds their
rate of formation. A non-renewable resource is either regenerated very slowly or not at all. Another way for carbon to enter the
atmosphere is from land (including land beneath the surface of the ocean) by the eruption of volcanoes and other geothermal
systems. Carbon sediments from the ocean floor are taken deep within Earth by the process of subduction: the movement of one
tectonic plate beneath another. Carbon is released as carbon dioxide when a volcano erupts or from volcanic hydrothermal vents.
Carbon dioxide is also added to the atmosphere by the animal husbandry practices of humans. The large number of land animals
raised to feed Earth’s growing human population results in increased carbon-dioxide levels in the atmosphere caused by their
respiration. This is another example of how human activity indirectly affects biogeochemical cycles in a significant way. Although
much of the debate about the future effects of increasing atmospheric carbon on climate change focuses on fossils fuels, scientists
take natural processes, such as volcanoes, plant growth, soil carbon levels, and respiration, into account as they model and predict
the future impact of this increase.

The Nitrogen Cycle

Getting nitrogen into the living world is difficult. Plants and phytoplankton are not equipped to incorporate nitrogen from the
atmosphere (which exists as tightly bonded, triple covalent N2) even though this molecule comprises approximately 78 percent of
the atmosphere. Nitrogen enters the living world via free-living and symbiotic bacteria, which incorporate nitrogen into their
macromolecules through nitrogen fixation (conversion of N2). Cyanobacteria live in most aquatic ecosystems where sunlight is
present; they play a key role in nitrogen fixation. Cyanobacteria are able to use inorganic sources of nitrogen to “fix” nitrogen.
Rhizobium bacteria live symbiotically in the root nodules of legumes (such as peas, beans, and peanuts) and provide them with the
organic nitrogen they need. Free-living bacteria, such as Azotobacter, are also important nitrogen fixers.
Organic nitrogen is especially important to the study of ecosystem dynamics since many ecosystem processes, such as primary
production and decomposition, are limited by the available supply of nitrogen. As shown in Figure [Link], the nitrogen that enters
living systems by nitrogen fixation is eventually converted from organic nitrogen back into nitrogen gas by bacteria. This process
occurs in three steps in terrestrial systems: ammonification, nitrification, and denitrification. First, the ammonification process
converts nitrogenous waste from living animals or from the remains of dead animals into ammonium (NH4+ ) by certain bacteria
and fungi. Second, this ammonium is then converted to nitrites (NO2−) by nitrifying bacteria, such as Nitrosomonas, through
nitrification. Subsequently, nitrites are converted to nitrates (NO3−) by similar organisms. Lastly, the process of denitrification

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occurs, whereby bacteria, such as Pseudomonas and Clostridium, convert the nitrates into nitrogen gas, thus allowing it to re-enter
the atmosphere.

ART CONNECTION

Figure [Link]: Nitrogen enters the living world from the atmosphere through nitrogen-fixing bacteria. This nitrogen and
nitrogenous waste from animals is then processed back into gaseous nitrogen by soil bacteria, which also supply terrestrial
food webs with the organic nitrogen they need. (credit: modification of work by John M. Evans and Howard Perlman, USGS)
Which of the following statements about the nitrogen cycle is false?
A. Ammonification converts organic nitrogenous matter from living organisms into ammonium (NH4+).
B. Denitrification by bacteria converts nitrates (NO3−) to nitrogen gas (N2).
C. Nitrification by bacteria converts nitrates (NO3−) to nitrites (NO2−).
D. Nitrogen fixing bacteria convert nitrogen gas (N2) into organic compounds.

Human activity can release nitrogen into the environment by two primary means: the combustion of fossil fuels, which releases
different nitrogen oxides, and by the use of artificial fertilizers (which contain nitrogen and phosphorus compounds) in agriculture,
which are then washed into lakes, streams, and rivers by surface runoff. Atmospheric nitrogen (other than N2) is associated with
several effects on Earth’s ecosystems including the production of acid rain (as nitric acid, HNO3) and greenhouse gas effects (as
nitrous oxide, N2O), potentially causing climate change. A major effect from fertilizer runoff is saltwater and freshwater
eutrophication, a process whereby nutrient runoff causes the overgrowth of algae and a number of consequential problems.
A similar process occurs in the marine nitrogen cycle, where the ammonification, nitrification, and denitrification processes are
performed by marine bacteria and archaea. Some of this nitrogen falls to the ocean floor as sediment, which can then be moved to
land in geologic time by uplift of Earth’s surface, and thereby incorporated into terrestrial rock. Although the movement of nitrogen
from rock directly into living systems has been traditionally seen as insignificant compared with nitrogen fixed from the
atmosphere, a recent study showed that this process may indeed be significant and should be included in any study of the global
1
nitrogen cycle.

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The Phosphorus Cycle
Phosphorus is an essential nutrient for living processes; it is a major component of nucleic acids and phospholipids, and, as calcium
phosphate, makes up the supportive components of our bones. Phosphorus is often the limiting nutrient (necessary for growth) in
aquatic, particularly freshwater, ecosystems.
Phosphorus occurs in nature as the phosphate ion (PO43-). In addition to phosphate runoff as a result of human activity, natural
surface runoff occurs when it is leached from phosphate-containing rock by weathering, thus sending phosphates into rivers, lakes,
and the ocean. This rock has its origins in the ocean. Phosphate-containing ocean sediments form primarily from the bodies of
ocean organisms and from their excretions. However, volcanic ash, aerosols, and mineral dust may also be significant phosphate
sources. This sediment then is moved to land over geologic time by the uplifting of Earth’s surface. (Figure [Link])
Phosphorus is also reciprocally exchanged between phosphate dissolved in the ocean and marine organisms. The movement of
phosphate from the ocean to the land and through the soil is extremely slow, with the average phosphate ion having an oceanic
residence time between 20,000 and 100,000 years.

Figure [Link]: In nature, phosphorus exists as the phosphate ion (PO43-). Weathering of rocks and volcanic activity releases
phosphate into the soil, water, and air, where it becomes available to terrestrial food webs. Phosphate enters the oceans in surface
runoff, groundwater flow, and river flow. Phosphate dissolved in ocean water cycles into marine food webs. Some phosphate from
the marine food webs falls to the ocean floor, where it forms sediment. (credit: modification of work by John M. Evans and
Howard Perlman, USGS)
Excess phosphorus and nitrogen that enter these ecosystems from fertilizer runoff and from sewage cause excessive growth of
algae. The subsequent death and decay of these organisms depletes dissolved oxygen, which leads to the death of aquatic
organisms, such as shellfish and finfish. This process is responsible for dead zones in lakes and at the mouths of many major rivers
and for massive fish kills, which often occur during the summer months (see Figure [Link]).

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 Figure [Link]: Dead zones occur when phosphorus and nitrogen from fertilizers cause excessive growth of microorganisms,
which depletes oxygen and kills fauna. Worldwide, large dead zones are found in areas of high population density. (credit: Robert
Simmon, Jesse Allen, NASA Earth Observatory)
A dead zone is an area in lakes and oceans near the mouths of rivers where large areas are periodically depleted of their normal
flora and fauna; these zones can be caused by eutrophication, oil spills, dumping toxic chemicals, and other human activities. The
number of dead zones has increased for several years, and more than 400 of these zones were present as of 2008. One of the worst
dead zones is off the coast of the United States in the Gulf of Mexico: fertilizer runoff from the Mississippi River basin created a
dead zone of over 8,463 square miles. Phosphate and nitrate runoff from fertilizers also negatively affect several lake and bay
ecosystems including the Chesapeake Bay in the eastern United States.

CAREERS IN ACTION: Chesapeake Bay

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 Figure [Link]: This (a) satellite image shows the Chesapeake Bay, an ecosystem affected by phosphate and nitrate runoff. A
(b) member of the Army Corps of Engineers holds a clump of oysters being used as a part of the oyster restoration effort in the
bay. (credit a: modification of work by NASA/MODIS; credit b: modification of work by U.S. Army)
The Chesapeake Bay (Figure 9.2.2.7a) is one of the most scenic areas on Earth; it is now in distress and is recognized as a case
study of a declining ecosystem. In the 1970s, the Chesapeake Bay was one of the first aquatic ecosystems to have identified
dead zones, which continue to kill many fish and bottom-dwelling species such as clams, oysters, and worms. Several species
have declined in the Chesapeake Bay because surface water runoff contains excess nutrients from artificial fertilizer use on
land. The source of the fertilizers (with high nitrogen and phosphate content) is not limited to agricultural practices. There are
many nearby urban areas and more than 150 rivers and streams empty into the bay that are carrying fertilizer runoff from lawns
and gardens. Thus, the decline of the Chesapeake Bay is a complex issue and requires the cooperation of industry, agriculture,
and individual homeowners.
Of particular interest to conservationists is the oyster population (Figure 9.2.2.7b); it is estimated that more than 200,000 acres
of oyster reefs existed in the bay in the 1700s, but that number has now declined to only 36,000 acres. Oyster harvesting was
once a major industry for Chesapeake Bay, but it declined 88 percent between 1982 and 2007. This decline was caused not
only by fertilizer runoff and dead zones, but also because of overharvesting. Oysters require a certain minimum population
density because they must be in close proximity to reproduce. Human activity has altered the oyster population and locations,
thus greatly disrupting the ecosystem.
The restoration of the oyster population in the Chesapeake Bay has been ongoing for several years with mixed success. Not
only do many people find oysters good to eat, but the oysters also clean up the bay. They are filter feeders, and as they eat, they
clean the water around them. Filter feeders eat by pumping a continuous stream of water over finely divided appendages (gills
in the case of oysters) and capturing prokaryotes, plankton, and fine organic particles in their mucus. In the 1700s, it was
estimated that it took only a few days for the oyster population to filter the entire volume of the bay. Today, with the changed
water conditions, it is estimated that the present population would take nearly a year to do the same job.
Restoration efforts have been ongoing for several years by non-profit organizations such as the Chesapeake Bay Foundation.
The restoration goal is to find a way to increase population density so the oysters can reproduce more efficiently. Many
disease-resistant varieties (developed at the Virginia Institute of Marine Science for the College of William and Mary) are now
available and have been used in the construction of experimental oyster reefs. Efforts by Virginia and Delaware to clean and
restore the bay have been hampered because much of the pollution entering the bay comes from other states, which emphasizes
the need for interstate cooperation to gain successful restoration.
The new, hearty oyster strains have also spawned a new and economically viable industry—oyster aquaculture—which not
only supplies oysters for food and profit, but also has the added benefit of cleaning the bay.

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The Sulfur Cycle
Sulfur is an essential element for the macromolecules of living things. As part of the amino acid cysteine, it is involved in the
formation of proteins. As shown in Figure [Link], sulfur cycles between the oceans, land, and atmosphere. Atmospheric sulfur is
found in the form of sulfur dioxide (SO2), which enters the atmosphere in three ways: first, from the decomposition of organic
molecules; second, from volcanic activity and geothermal vents; and, third, from the burning of fossil fuels by humans.

Figure [Link]: Sulfur dioxide from the atmosphere becomes available to terrestrial and marine ecosystems when it is dissolved
in precipitation as weak sulfuric acid or when it falls directly to Earth as fallout. Weathering of rocks also makes sulfates available
to terrestrial ecosystems. Decomposition of living organisms returns sulfates to the ocean, soil, and atmosphere. (credit:
modification of work by John M. Evans and Howard Perlman, USGS)
On land, sulfur is deposited in four major ways: precipitation, direct fallout from the atmosphere, rock weathering, and geothermal
vents (Figure [Link]). Atmospheric sulfur is found in the form of sulfur dioxide (SO2), and as rain falls through the atmosphere,
sulfur is dissolved in the form of weak sulfuric acid (H2SO4). Sulfur can also fall directly from the atmosphere in a process called
fallout. Also, as sulfur-containing rocks weather, sulfur is released into the soil. These rocks originate from ocean sediments that
are moved to land by the geologic uplifting of ocean sediments. Terrestrial ecosystems can then make use of these soil sulfates
(SO42-), which enter the food web by being taken up by plant roots. When these plants decompose and die, sulfur is released back
into the atmosphere as hydrogen sulfide (H2S) gas.

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 Figure [Link]: At this sulfur vent in Lassen Volcanic National Park in northeastern California, the yellowish sulfur deposits are
visible near the mouth of the vent. (credit: “Calbear22”/Wikimedia Commons)
Sulfur enters the ocean in runoff from land, from atmospheric fallout, and from underwater geothermal vents. Some ecosystems
rely on chemoautotrophs using sulfur as a biological energy source. This sulfur then supports marine ecosystems in the form of
sulfates.
Human activities have played a major role in altering the balance of the global sulfur cycle. The burning of large quantities of fossil
fuels, especially from coal, releases larger amounts of hydrogen sulfide gas into the atmosphere. As rain falls through this gas, it
creates the phenomenon known as acid rain, which damages the natural environment by lowering the pH of lakes, thus killing
many of the resident plants and animals. Acid rain is corrosive rain caused by rainwater falling to the ground through sulfur dioxide
gas, turning it into weak sulfuric acid, which causes damage to aquatic ecosystems. Acid rain also affects the man-made
environment through the chemical degradation of buildings. For example, many marble monuments, such as the Lincoln Memorial
in Washington, DC, have suffered significant damage from acid rain over the years. These examples show the wide-ranging effects
of human activities on our environment and the challenges that remain for our future.

Section Summary
Mineral nutrients are cycled through ecosystems and their environment. Of particular importance are water, carbon, nitrogen,
phosphorus, and sulfur. All of these cycles have major impacts on ecosystem structure and function. As human activities have
caused major disturbances to these cycles, their study and modeling is especially important. Ecosystems have been damaged by a
variety of human activities that alter the natural biogeochemical cycles due to pollution, oil spills, and events causing global
climate change. The health of the biosphere depends on understanding these cycles and how to protect the environment from
irreversible damage.

Art Connections
Figure [Link]: Which of the following statements about the nitrogen cycle is false?
A. Ammonification converts organic nitrogenous matter from living organisms into ammonium (NH4+).
B. Denitrification by bacteria converts nitrates (NO3-) to nitrogen gas (N2).
C. Nitrification by bacteria converts nitrates (NO3-) to nitrites (NO2-).
D. Nitrogen fixing bacteria convert nitrogen gas (N2) into organic compounds.

Answer
C: Nitrification by bacteria converts nitrates (NO3-) to nitrites (NO2-).

Footnotes
1. 1 Scott L. Morford, Benjamin Z. Houlton, and Randy A. Dahlgren, “Increased Forest Ecosystem Carbon and Nitrogen Storage
from Nitrogen Rich Bedrock,” Nature 477, no. 7362 (2011): 78–81.

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Glossary

acid rain
a corrosive rain caused by rainwater mixing with sulfur dioxide gas as it fall through the atmosphere, turning it into weak
sulfuric acid, causing damage to aquatic ecosystems

biogeochemical cycle
the cycling of minerals and nutrients through the biotic and abiotic world

dead zone
an area in a lake and ocean near the mouths of rivers where large areas are depleted of their normal flora and fauna; these zones
can be caused by eutrophication, oil spills, dumping of toxic chemicals, and other human activities

eutrophication
the process whereby nutrient runoff causes the excess growth of microorganisms and plants in aquatic systems

fallout
the direct deposition of solid minerals on land or in the ocean from the atmosphere

hydrosphere
the region of the planet in which water exists, including the atmosphere that contains water vapor and the region beneath the
ground that contains groundwater

non-renewable resource
a resource, such as a fossil fuel, that is either regenerated very slowly or not at all

subduction
the movement of one tectonic plate beneath another

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.2.2: Biogeochemical Cycles is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
20.2: Biogeochemical Cycles by OpenStax is licensed CC BY 4.0.

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9.2.3: Terrestrial Biomes
Earth’s biomes can be either terrestrial or aquatic. Terrestrial biomes are based on land, while aquatic biomes include both ocean
and freshwater biomes. The eight major terrestrial biomes on Earth are each distinguished by characteristic temperatures and
amount of precipitation. Annual totals and fluctuations of precipitation affect the kinds of vegetation and animal life that can exist
in broad geographical regions. Temperature variation on a daily and seasonal basis is also important for predicting the geographic
distribution of a biome. Since a biome is defined by climate, the same biome can occur in geographically distinct areas with similar
climates (Figure [Link]). There are also large areas on Antarctica, Greenland, and in mountain ranges that are covered by
permanent glaciers and support very little life. Strictly speaking, these are not considered biomes and in addition to extremes of
cold, they are also often deserts with very low precipitation.

Figure [Link]: Each of the world’s eight major biomes is distinguished by characteristic temperatures and amount of
precipitation. Polar ice caps and mountains are also shown.

Tropical Forest
Tropical rainforests are also referred to as tropical wet forests. This biome is found in equatorial regions (Figure [Link]). Tropical
rainforests are the most diverse terrestrial biome. This biodiversity is still largely unknown to science and is under extraordinary
threat primarily through logging and deforestation for agriculture. Tropical rainforests have also been described as nature’s
pharmacy because of the potential for new drugs that is largely hidden in the chemicals produced by the huge diversity of plants,
animals, and other organisms. The vegetation is characterized by plants with spreading roots and broad leaves that fall off
throughout the year, unlike the trees of deciduous forests that lose their leaves in one season. These forests are “evergreen,” year-
round.
The temperature and sunlight profiles of tropical rainforests are stable in comparison to that of other terrestrial biomes, with
average temperatures ranging from 20oC to 34oC (68oF to 93oF). Month-to-month temperatures are relatively constant in tropical
rainforests, in contrast to forests further from the equator. This lack of temperature seasonality leads to year-round plant growth,
rather than the seasonal growth seen in other biomes. In contrast to other ecosystems, a more constant daily amount of sunlight
(11–12 hours per day) provides more solar radiation, thereby a longer period of time for plant growth.
The annual rainfall in tropical rainforests ranges from 250 cm to more than 450 cm (8.2–14.8 ft) with considerable seasonal
variation. Tropical rainforests have wet months in which there can be more than 30 cm (11–12 in) of precipitation, as well as dry
months in which there are fewer than 10 cm (3.5 in) of rainfall. However, the driest month of a tropical rainforest can still exceed
the annual rainfall of some other biomes, such as deserts.
Tropical rainforests have high net primary productivity because the annual temperatures and precipitation values support rapid
plant growth (Figure [Link]). However, the high rainfall quickly leaches nutrients from the soils of these forests, which are
typically low in nutrients. Tropical rainforests are characterized by vertical layering of vegetation and the formation of distinct
habitats for animals within each layer. On the forest floor is a sparse layer of plants and decaying plant matter. Above that is an

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understory of short, shrubby foliage. A layer of trees rises above this understory and is topped by a closed upper canopy—the
uppermost overhead layer of branches and leaves. Some additional trees emerge through this closed upper canopy. These layers
provide diverse and complex habitats for the variety of plants, animals, and other organisms within the tropical wet forests. Many
species of animals use the variety of plants and the complex structure of the tropical wet forests for food and shelter. Some
organisms live several meters above ground rarely ever descending to the forest floor.
Rainforests are not the only forest biome in the tropics; there are also tropical dry forests, which are characterized by a dry season
of varying lengths. These forests commonly experience leaf loss during the dry season to one degree or another. The loss of leaves
from taller trees during the dry season opens up the canopy and allows sunlight to the forest floor that allows the growth of thick
ground-level brush, which is absent in tropical rainforests. Extensive tropical dry forests occur in Africa (including Madagascar),
India, southern Mexico, and South America.

Figure [Link]: Species diversity is very high in tropical wet forests, such as these forests of Madre de Dios, Peru, near the
Amazon River. (credit: Roosevelt Garcia)

Savannas
Savannas are grasslands with scattered trees, and they are found in Africa, South America, and northern Australia (Figure [Link]).
Savannas are hot, tropical areas with temperatures averaging from 24oC –29oC (75oF –84oF) and an annual rainfall of 51–127 cm
(20–50 in). Savannas have an extensive dry season and consequent fires. As a result, scattered in the grasses and forbs (herbaceous
flowering plants) that dominate the savanna, there are relatively few trees (Figure [Link]). Since fire is an important source of
disturbance in this biome, plants have evolved well-developed root systems that allow them to quickly re-sprout after a fire.

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 Figure [Link]: Although savannas are dominated by grasses, small woodlands, such as this one in Mount Archer National Park
in Queensland, Australia, may dot the landscape. (credit: "Ethel Aardvark"/Wikimedia Commons)

Deserts
Subtropical deserts exist between 15o and 30o north and south latitude and are centered on the Tropic of Cancer and the Tropic of
Capricorn (Figure [Link]). Deserts are frequently located on the downwind or lee side of mountain ranges, which create a rain
shadow after prevailing winds drop their water content on the mountains. This is typical of the North American deserts, such as the
Mohave and Sonoran deserts. Deserts in other regions, such as the Sahara Desert in northern Africa or the Namib Desert in
southwestern Africa are dry because of the high-pressure, dry air descending at those latitudes. Subtropical deserts are very dry;
evaporation typically exceeds precipitation. Subtropical hot deserts can have daytime soil surface temperatures above 60oC (140oF)
and nighttime temperatures approaching 0oC (32oF). The temperature drops so far because there is little water vapor in the air to
prevent radiative cooling of the land surface. Subtropical deserts are characterized by low annual precipitation of fewer than 30 cm
(12 in) with little monthly variation and lack of predictability in rainfall. Some years may receive tiny amounts of rainfall, while
others receive more. In some cases, the annual rainfall can be as low as 2 cm (0.8 in) in subtropical deserts located in central
Australia (“the Outback”) and northern Africa.
The low species diversity of this biome is closely related to its low and unpredictable precipitation. Despite the relatively low
diversity, desert species exhibit fascinating adaptations to the harshness of their environment. Very dry deserts lack perennial
vegetation that lives from one year to the next; instead, many plants are annuals that grow quickly and reproduce when rainfall does
occur, then they die. Perennial plants in deserts are characterized by adaptations that conserve water: deep roots, reduced foliage,
and water-storing stems (Figure [Link]). Seed plants in the desert produce seeds that can lie dormant for extended periods between
rains. Most animal life in subtropical deserts has adapted to a nocturnal life, spending the hot daytime hours beneath the ground.
The Namib Desert is the oldest on the planet, and has probably been dry for more than 55 million years. It supports a number of
endemic species (species found only there) because of this great age. For example, the unusual gymnosperm Welwitschia mirabilis
is the only extant species of an entire order of plants. There are also five species of reptiles considered endemic to the Namib.
In addition to subtropical deserts there are cold deserts that experience freezing temperatures during the winter and any
precipitation is in the form of snowfall. The largest of these deserts are the Gobi Desert in northern China and southern Mongolia,
the Taklimakan Desert in western China, the Turkestan Desert, and the Great Basin Desert of the United States.

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 Figure [Link]: Many desert plants have tiny leaves or no leaves at all to reduce water loss. The leaves of ocotillo, shown here in
the Chihuahuan Desert in Big Bend National Park, Texas, appear only after rainfall and then are shed. (credit “bare ocotillo”:
"Leaflet"/Wikimedia Commons)

Chaparral
The chaparral is also called scrub forest and is found in California, along the Mediterranean Sea, and along the southern coast of
Australia (Figure [Link]). The annual rainfall in this biome ranges from 65 cm to 75 cm (25.6–29.5 in) and the majority of the rain
falls in the winter. Summers are very dry and many chaparral plants are dormant during the summertime. The chaparral vegetation
is dominated by shrubs and is adapted to periodic fires, with some plants producing seeds that germinate only after a hot fire. The
ashes left behind after a fire are rich in nutrients like nitrogen that fertilize the soil and promote plant regrowth. Fire is a natural part
of the maintenance of this biome and frequently threatens human habitation in this biome in the U.S. (Figure [Link]).

Figure [Link]: The chaparral is dominated by shrubs. (credit: Miguel Vieira)

Temperate Grasslands
Temperate grasslands are found throughout central North America, where they are also known as prairies, and in Eurasia, where
they are known as steppes (Figure [Link]). Temperate grasslands have pronounced annual fluctuations in temperature with hot

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summers and cold winters. The annual temperature variation produces specific growing seasons for plants. Plant growth is possible
when temperatures are warm enough to sustain plant growth, which occurs in the spring, summer, and fall.
Annual precipitation ranges from 25.4 cm to 88.9 cm (10–35 in). Temperate grasslands have few trees except for those found
growing along rivers or streams. The dominant vegetation tends to consist of grasses. The treeless condition is maintained by low
precipitation, frequent fires, and grazing (Figure [Link]). The vegetation is very dense and the soils are fertile because the
subsurface of the soil is packed with the roots and rhizomes (underground stems) of these grasses. The roots and rhizomes act to
anchor plants into the ground and replenish the organic material (humus) in the soil when they die and decay.

Figure [Link]: The American bison (Bison bison), more commonly called the buffalo, is a grazing mammal that once populated
American prairies in huge numbers. (credit: Jack Dykinga, USDA ARS)
Fires, which are a natural disturbance in temperate grasslands, can be ignited by lightning strikes. It also appears that the lightning-
caused fire regime in North American grasslands was enhanced by intentional burning by humans. When fire is suppressed in
temperate grasslands, the vegetation eventually converts to scrub and dense forests. Often, the restoration or management of
temperate grasslands requires the use of controlled burns to suppress the growth of trees and maintain the grasses.

Temperate Forests
Temperate forests are the most common biome in eastern North America, Western Europe, Eastern Asia, Chile, and New Zealand
(Figure [Link]). This biome is found throughout mid-latitude regions. Temperatures range between –30oC and 30oC (–22oF to
86oF) and drop to below freezing on an annual basis. These temperatures mean that temperate forests have defined growing seasons
during the spring, summer, and early fall. Precipitation is relatively constant throughout the year and ranges between 75 cm and
150 cm (29.5–59 in).
Deciduous trees are the dominant plant in this biome with fewer evergreen conifers. Deciduous trees lose their leaves each fall and
remain leafless in the winter. Thus, little photosynthesis occurs during the dormant winter period. Each spring, new leaves appear
as temperature increases. Because of the dormant period, the net primary productivity of temperate forests is less than that of
tropical rainforests. In addition, temperate forests show far less diversity of tree species than tropical rainforest biomes.
The trees of the temperate forests leaf out and shade much of the ground; however, more sunlight reaches the ground in this biome
than in tropical rainforests because trees in temperate forests do not grow as tall as the trees in tropical rainforests. The soils of the
temperate forests are rich in inorganic and organic nutrients compared to tropical rainforests. This is because of the thick layer of
leaf litter on forest floors and reduced leaching of nutrients by rainfall. As this leaf litter decays, nutrients are returned to the soil.
The leaf litter also protects soil from erosion, insulates the ground, and provides habitats for invertebrates and their predators
(Figure [Link]).

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 Figure [Link]: Deciduous trees are the dominant plant in the temperate forest. (credit: Oliver Herold)

Boreal Forests
The boreal forest, also known as taiga or coniferous forest, is found roughly between 50o and 60o north latitude across most of
Canada, Alaska, Russia, and northern Europe (Figure [Link]). Boreal forests are also found above a certain elevation (and below
high elevations where trees cannot grow) in mountain ranges throughout the Northern Hemisphere. This biome has cold, dry
winters and short, cool, wet summers. The annual precipitation is from 40 cm to 100 cm (15.7–39 in) and usually takes the form of
snow; little evaporation occurs because of the cold temperatures.
The long and cold winters in the boreal forest have led to the predominance of cold-tolerant cone-bearing plants. These are
evergreen coniferous trees like pines, spruce, and fir, which retain their needle-shaped leaves year-round. Evergreen trees can
photosynthesize earlier in the spring than deciduous trees because less energy from the Sun is required to warm a needle-like leaf
than a broad leaf. Evergreen trees grow faster than deciduous trees in the boreal forest. In addition, soils in boreal forest regions
tend to be acidic with little available nitrogen. Leaves are a nitrogen-rich structure and deciduous trees must produce a new set of
these nitrogen-rich structures each year. Therefore, coniferous trees that retain nitrogen-rich needles in a nitrogen limiting
environment may have had a competitive advantage over the broad-leafed deciduous trees.
The net primary productivity of boreal forests is lower than that of temperate forests and tropical wet forests. The aboveground
biomass of boreal forests is high because these slow-growing tree species are long-lived and accumulate standing biomass over
time. Species diversity is less than that seen in temperate forests and tropical rainforests. Boreal forests lack the layered forest
structure seen in tropical rainforests or, to a lesser degree, temperate forests. The structure of a boreal forest is often only a tree
layer and a ground layer. When conifer needles are dropped, they decompose more slowly than broad leaves; therefore, fewer
nutrients are returned to the soil to fuel plant growth (Figure [Link]).

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 Figure [Link]: The boreal forest (taiga) has low lying plants and conifer trees. (credit: L.B. Brubaker, NOAA)

Arctic Tundra
The Arctic tundra lies north of the subarctic boreal forests and is located throughout the Arctic regions of the Northern Hemisphere
(Figure [Link]). Tundra also exists at elevations above the tree line on mountains. The average winter temperature is –34°C (–
29.2°F) and the average summer temperature is 3°C–12°C (37°F –52°F). Plants in the Arctic tundra have a short growing season of
approximately 50–60 days. However, during this time, there are almost 24 hours of daylight and plant growth is rapid. The annual
precipitation of the Arctic tundra is low (15–25 cm or 6–10 in) with little annual variation in precipitation. And, as in the boreal
forests, there is little evaporation because of the cold temperatures.
Plants in the Arctic tundra are generally low to the ground and include low shrubs, grasses, lichens, and small flowering plants
(Figure [Link]). There is little species diversity, low net primary productivity, and low aboveground biomass. The soils of the
Arctic tundra may remain in a perennially frozen state referred to as permafrost. The permafrost makes it impossible for roots to
penetrate far into the soil and slows the decay of organic matter, which inhibits the release of nutrients from organic matter. The
melting of the permafrost in the brief summer provides water for a burst of productivity while temperatures and long days permit it.
During the growing season, the ground of the Arctic tundra can be completely covered with plants or lichens.

Figure [Link]: Low-growing plants such as shrub willow dominate the tundra landscape during the summer, shown here in the
Arctic National Wildlife Refuge. (credit: Arctic National Wildlife Refuge, USFWS)

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 CONCEPT IN ACTION

Visit this site to investigate different biomes.

Section Summary
Earth has terrestrial and aquatic biomes. Aquatic biomes include both freshwater and marine environments. There are eight major
terrestrial biomes: tropical rainforests, savannas, subtropical deserts, chaparral, temperate grasslands, temperate forests, boreal
forests, and Arctic tundra. The same biome can occur in different geographic locations with similar climates. Temperature and
precipitation, and variations in both, are key abiotic factors that shape the composition of animal and plant communities in
terrestrial biomes. Some biomes, such as temperate grasslands and temperate forests, have distinct seasons with cold and hot
weather alternating throughout the year. In warm, moist biomes, such as the tropical rainforest, net primary productivity is high as
warm temperatures, abundant water, and a year-round growing season fuel plant growth. Other biomes, such as deserts and tundra,
have low primary productivity due to extreme temperatures and a shortage of water.

Glossary

arctic tundra
a biome characterized by low average temperatures, brief growing seasons, the presence of permafrost, and limited precipitation
largely in the form of snow in which the dominant vegetation are low shrubs, lichens, mosses, and small herbaceous plants

boreal forest
a biome found in temperate and subarctic regions characterized by short growing seasons and dominated structurally by
coniferous trees

canopy
the branches and foliage of trees that form a layer of overhead coverage in a forest

chaparral
a biome found in temperate coastal regions characterized by low trees and dry-adapted shrubs and forbs

permafrost
a perennially frozen portion of the Arctic tundra soil

savanna
a biome located in the tropics with an extended dry season and characterized by a grassland with sparsely distributed trees

subtropical desert
a biome found in the subtropics with hot daily temperatures, very low and unpredictable precipitation, and characterized by a
limited dry-adapted vegetation

temperate forest
a biome found in temperate regions with moderate rainfall and dominated structurally by deciduous trees

temperate grassland
a biome dominated by grasses and herbaceous plants due to low precipitation, periodic fires, and grazing

tropical rainforest
a biome found near the equator characterized by stable temperatures with abundant and seasonal rainfall in which trees form the
structurally important vegetation

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.2.3: Terrestrial Biomes is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
20.3: Terrestrial Biomes by OpenStax is licensed CC BY 4.0.

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9.2.4: Aquatic and Marine Biomes
Like terrestrial biomes, aquatic biomes are influenced by abiotic factors. In the case of aquatic biomes the abiotic factors include
light, temperature, flow regime, and dissolved solids. The aquatic medium—water— has different physical and chemical properties
than air. Even if the water in a pond or other body of water is perfectly clear (there are no suspended particles), water, on its own,
absorbs light. As one descends deep enough into a body of water, eventually there will be a depth at which the sunlight cannot
reach. While there are some abiotic and biotic factors in a terrestrial ecosystem that shade light (like fog, dust, or insect swarms),
these are not usually permanent features of the environment. The importance of light in aquatic biomes is central to the
communities of organisms found in both freshwater and marine ecosystems because it controls productivity through
photosynthesis.
In addition to light, solar radiation warms bodies of water and many exhibit distinct layers of water at differing temperatures. The
water temperature affects the organisms’ rates of growth and the amount of dissolved oxygen available for respiration.
The movement of water is also important in many aquatic biomes. In rivers, the organisms must obviously be adapted to the
constant movement of the water around them, but even in larger bodies of water such as the oceans, regular currents and tides
impact availability of nutrients, food resources, and the presence of the water itself.
Finally, all natural water contains dissolved solids, or salts. Fresh water contains low levels of such dissolved substances because
the water is rapidly recycled through evaporation and precipitation. The oceans have a relatively constant high salt content. Aquatic
habitats at the interface of marine and freshwater ecosystems have complex and variable salt environments that range between
freshwater and marine levels. These are known as brackish water environments. Lakes located in closed drainage basins
concentrate salt in their waters and can have extremely high salt content that only a few and highly specialized species are able to
inhabit.

Marine Biomes
The ocean is a continuous body of salt water that is relatively uniform in chemical composition. It is a weak solution of mineral
salts and decayed biological matter. Within the ocean, coral reefs are a second type of marine biome. Estuaries, coastal areas where
salt water and fresh water mix, form a third unique marine biome.
The ocean is categorized by several zones (Figure [Link]). All of the ocean’s open water is referred to as the pelagic realm (or
zone). The benthic realm (or zone) extends along the ocean bottom from the shoreline to the deepest parts of the ocean floor. From
the surface to the bottom or the limit to which photosynthesis occurs is the photic zone (approximately 200 m or 650 ft). At depths
greater than 200 m, light cannot penetrate; thus, this is referred to as the aphotic zone. The majority of the ocean is aphotic and
lacks sufficient light for photosynthesis. The deepest part of the ocean, the Challenger Deep (in the Mariana Trench, located in the
western Pacific Ocean), is about 11,000 m (about 6.8 mi) deep. To give some perspective on the depth of this trench, the ocean is,
on average, 4267 m or 14,000 ft deep.

Ocean
The physical diversity of the ocean has a significant influence on the diversity of organisms that live within it. The ocean is
categorized into different zones based on how far light reaches into the water. Each zone has a distinct group of species adapted to
the biotic and abiotic conditions particular to that zone.
The intertidal zone (Figure [Link]) is the oceanic region that is closest to land. With each tidal cycle, the intertidal zone alternates
between being inundated with water and left high and dry. Generally, most people think of this portion of the ocean as a sandy
beach. In some cases, the intertidal zone is indeed a sandy beach, but it can also be rocky, muddy, or dense with tangled roots in
mangrove forests. The intertidal zone is an extremely variable environment because of tides. Organisms may be exposed to air at
low tide and are underwater during high tide. Therefore, living things that thrive in the intertidal zone are often adapted to being
dry for long periods of time. The shore of the intertidal zone is also repeatedly struck by waves and the organisms found there are
adapted to withstand damage from the pounding action of the waves (Figure [Link]). The exoskeletons of shoreline crustaceans
(such as the shore crab, Carcinus maenas) are tough and protect them from desiccation (drying out) and wave damage. Another
consequence of the pounding waves is that few algae and plants establish themselves in constantly moving sand or mud.

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 Figure [Link]: Sea stars, sea urchins, and mussel shells are often found in the intertidal zone, shown here in Kachemak Bay,
Alaska. (credit: NOAA)
The neritic zone (Figure [Link]) extends from the margin of the intertidal zone to depths of about 200 m (or 650 ft) at the edge of
the continental shelf. When the water is relatively clear, photosynthesis can occur in the neritic zone. The water contains silt and is
well-oxygenated, low in pressure, and stable in temperature. These factors all contribute to the neritic zone having the highest
productivity and biodiversity of the ocean. Phytoplankton, including photosynthetic bacteria and larger species of algae, are
responsible for the bulk of this primary productivity. Zooplankton, protists, small fishes, and shrimp feed on the producers and are
the primary food source for most of the world’s fisheries. The majority of these fisheries exist within the neritic zone.
Beyond the neritic zone is the open ocean area known as the oceanic zone (Figure [Link]). Within the oceanic zone there is
thermal stratification. Abundant phytoplankton and zooplankton support populations of fish and whales. Nutrients are scarce and
this is a relatively less productive part of the marine biome. When photosynthetic organisms and the organisms that feed on them
die, their bodies fall to the bottom of the ocean where they remain; the open ocean lacks a process for bringing the organic nutrients
back up to the surface.
Beneath the pelagic zone is the benthic realm, the deepwater region beyond the continental shelf (Figure [Link]). The bottom of
the benthic realm is comprised of sand, silt, and dead organisms. Temperature decreases as water depth increases. This is a nutrient-
rich portion of the ocean because of the dead organisms that fall from the upper layers of the ocean. Because of this high level of
nutrients, a diversity of fungi, sponges, sea anemones, marine worms, sea stars, fishes, and bacteria exists.
The deepest part of the ocean is the abyssal zone, which is at depths of 4000 m or greater. The abyssal zone (Figure [Link]) is very
cold and has very high pressure, high oxygen content, and low nutrient content. There are a variety of invertebrates and fishes
found in this zone, but the abyssal zone does not have photosynthetic organisms. Chemosynthetic bacteria use the hydrogen sulfide
and other minerals emitted from deep hydrothermal vents. These chemosynthetic bacteria use the hydrogen sulfide as an energy
source and serve as the base of the food chain found around the vents.

ART CONNECTION

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 Figure [Link]: The ocean is divided into different zones based on water depth, distance from the shoreline, and light
penetration.
In which of the following regions would you expect to find photosynthetic organisms?
A. The aphotic zone, the neritic zone, the oceanic zone, and the benthic realm.
B. The photic zone, the intertidal zone, the neritic zone, and the oceanic zone.
C. The photic zone, the abyssal zone, the neritic zone, and the oceanic zone.
D. The pelagic realm, the aphotic zone, the neritic zone, and the oceanic zone.

Coral Reefs
Coral reefs are ocean ridges formed by marine invertebrates living in warm shallow waters within the photic zone of the ocean.
They are found within 30˚ north and south of the equator. The Great Barrier Reef is a well-known reef system located several miles
off the northeastern coast of Australia. Other coral reefs are fringing islands, which are directly adjacent to land, or atolls, which
are circular reefs surrounding a former island that is now underwater. The coral-forming colonies of organisms (members of
phylum Cnidaria) secrete a calcium carbonate skeleton. These calcium-rich skeletons slowly accumulate, thus forming the
underwater reef (Figure [Link]). Corals found in shallower waters (at a depth of approximately 60 m or about 200 ft) have a
mutualistic relationship with photosynthetic unicellular protists. The relationship provides corals with the majority of the nutrition
and the energy they require. The waters in which these corals live are nutritionally poor and, without this mutualism, it would not
be possible for large corals to grow because there are few planktonic organisms for them to feed on. Some corals living in deeper
and colder water do not have a mutualistic relationship with protists; these corals must obtain their energy exclusively by feeding
on plankton using stinging cells on their tentacles.

CONCEPT IN ACTION

In this National Oceanic and Atmospheric Administration (NOAA) video, marine ecologist Dr. Peter Etnoyer discusses his
research on coral organisms.

Coral reefs are one of the most diverse biomes. It is estimated that more than 4000 fish species inhabit coral reefs. These fishes can
feed on coral, the cryptofauna (invertebrates found within the calcium carbonate structures of the coral reefs), or the seaweed and
algae that are associated with the coral. These species include predators, herbivores, or planktivores. Predators are animal species
that hunt and are carnivores or “flesh eaters.” Herbivores eat plant material, and planktivores eat plankton.

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 Figure [Link]: Coral reefs are formed by the calcium carbonate skeletons of coral organisms, which are marine invertebrates in
the phylum Cnidaria. (credit: Terry Hughes)

EVOLUTION IN ACTION: Global Decline of Coral Reefs

It takes a long time to build a coral reef. The animals that create coral reefs do so over thousands of years, continuing to slowly
deposit the calcium carbonate that forms their characteristic ocean homes. Bathed in warm tropical waters, the coral animals
and their symbiotic protist partners evolved to survive at the upper limit of ocean water temperature.
Together, climate change and human activity pose dual threats to the long-term survival of the world’s coral reefs. The main
cause of killing of coral reefs is warmer-than-usual surface water. As global warming raises ocean temperatures, coral reefs are
suffering. The excessive warmth causes the coral organisms to expel their endosymbiotic, food-producing protists, resulting in
a phenomenon known as bleaching. The colors of corals are a result of the particular protist endosymbiont, and when the
protists leave, the corals lose their color and turn white, hence the term “bleaching.”
Rising levels of atmospheric carbon dioxide further threaten the corals in other ways; as carbon dioxide dissolves in ocean
waters, it lowers pH, thus increasing ocean acidity. As acidity increases, it interferes with the calcification that normally occurs
as coral animals build their calcium carbonate homes.
When a coral reef begins to die, species diversity plummets as animals lose food and shelter. Coral reefs are also economically
important tourist destinations, so the decline of coral reefs poses a serious threat to coastal economies.
Human population growth has damaged corals in other ways, too. As human coastal populations increase, the runoff of
sediment and agricultural chemicals has increased, causing some of the once-clear tropical waters to become cloudy. At the
same time, overfishing of popular fish species has allowed the predator species that eat corals to go unchecked.
Although a rise in global temperatures of 1°C–2°C (a conservative scientific projection) in the coming decades may not seem
large, it is very significant to this biome. When change occurs rapidly, species can become extinct before evolution leads to
newly adapted species. Many scientists believe that global warming, with its rapid (in terms of evolutionary time) and
inexorable increases in temperature, is tipping the balance beyond the point at which many of the world’s coral reefs can
recover.

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Estuaries: Where the Ocean Meets Fresh Water
Estuaries are biomes that occur where a river, a source of fresh water, meets the ocean. Therefore, both fresh water and salt water
are found in the same vicinity; mixing results in a diluted (brackish) salt water. Estuaries form protected areas where many of the
offspring of crustaceans, mollusks, and fish begin their lives. Salinity is an important factor that influences the organisms and the
adaptations of the organisms found in estuaries. The salinity of estuaries varies and is based on the rate of flow of its freshwater
sources. Once or twice a day, high tides bring salt water into the estuary. Low tides occurring at the same frequency reverse the
current of salt water (Figure [Link]).

Figure [Link]: As estuary is where fresh water and salt water meet, such as the mouth of the Klamath River in California, shown
here. (credit: U.S. Army Corps of Engineers)
The daily mixing of fresh water and salt water is a physiological challenge for the plants and animals that inhabit estuaries. Many
estuarine plant species are halophytes, plants that can tolerate salty conditions. Halophytic plants are adapted to deal with salt water
spray and salt water on their roots. In some halophytes, filters in the roots remove the salt from the water that the plant absorbs.
Animals, such as mussels and clams (phylum Mollusca), have developed behavioral adaptations that expend a lot of energy to
function in this rapidly changing environment. When these animals are exposed to low salinity, they stop feeding, close their shells,
and switch from aerobic respiration (in which they use gills) to anaerobic respiration (a process that does not require oxygen).
When high tide returns to the estuary, the salinity and oxygen content of the water increases, and these animals open their shells,
begin feeding, and return to aerobic respiration.

Freshwater Biomes
Freshwater biomes include lakes, ponds, and wetlands (standing water) as well as rivers and streams (flowing water). Humans rely
on freshwater biomes to provide aquatic resources for drinking water, crop irrigation, sanitation, recreation, and industry. These
various roles and human benefits are referred to as ecosystem services. Lakes and ponds are found in terrestrial landscapes and are
therefore connected with abiotic and biotic factors influencing these terrestrial biomes.

Lakes and Ponds

Lakes and ponds can range in area from a few square meters to thousands of square kilometers. Temperature is an important abiotic
factor affecting living things found in lakes and ponds. During the summer in temperate regions, thermal stratification of deep lakes
occurs when the upper layer of water is warmed by the Sun and does not mix with deeper, cooler water. The process produces a
sharp transition between the warm water above and cold water beneath. The two layers do not mix until cooling temperatures and
winds break down the stratification and the water in the lake mixes from top to bottom. During the period of stratification, most of
the productivity occurs in the warm, well-illuminated, upper layer, while dead organisms slowly rain down into the cold, dark layer
below where decomposing bacteria and cold-adapted species such as lake trout exist. Like the ocean, lakes and ponds have a photic

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layer in which photosynthesis can occur. Phytoplankton (algae and cyanobacteria) are found here and provide the base of the food
web of lakes and ponds. Zooplankton, such as rotifers and small crustaceans, consume these phytoplankton. At the bottom of lakes
and ponds, bacteria in the aphotic zone break down dead organisms that sink to the bottom.
Nitrogen and particularly phosphorus are important limiting nutrients in lakes and ponds. Therefore, they are determining factors in
the amount of phytoplankton growth in lakes and ponds. When there is a large input of nitrogen and phosphorus (e.g., from sewage
and runoff from fertilized lawns and farms), the growth of algae skyrockets, resulting in a large accumulation of algae called an
algal bloom. Algal blooms (Figure [Link]) can become so extensive that they reduce light penetration in water. As a result, the
lake or pond becomes aphotic and photosynthetic plants cannot survive. When the algae die and decompose, severe oxygen
depletion of the water occurs. Fishes and other organisms that require oxygen are then more likely to die.

Figure [Link]: The uncontrolled growth of algae in this waterway has resulted in an algal bloom.

Rivers and Streams

Rivers and the narrower streams that feed into the rivers are continuously moving bodies of water that carry water from the source
or headwater to the mouth at a lake or ocean. The largest rivers include the Nile River in Africa, the Amazon River in South
America, and the Mississippi River in North America (Figure [Link]).

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 Figure [Link]: Rivers range from (a) narrow and shallow to (b) wide and slow moving. (credit a: modification of work by Cory
Zanker; credit b: modification of work by David DeHetre)
Abiotic features of rivers and streams vary along the length of the river or stream. Streams begin at a point of origin referred to as
source water. The source water is usually cold, low in nutrients, and clear. The channel (the width of the river or stream) is
narrower here than at any other place along the length of the river or stream. Headwater streams are of necessity at a higher
elevation than the mouth of the river and often originate in regions with steep grades leading to higher flow rates than lower
elevation stretches of the river.
Faster-moving water and the short distance from its origin results in minimal silt levels in headwater streams; therefore, the water is
clear. Photosynthesis here is mostly attributed to algae that are growing on rocks; the swift current inhibits the growth of
phytoplankton. Photosynthesis may be further reduced by tree cover reaching over the narrow stream. This shading also keeps
temperatures lower. An additional input of energy can come from leaves or other organic material that falls into a river or stream
from the trees and other plants that border the water. When the leaves decompose, the organic material and nutrients in the leaves
are returned to the water. The leaves also support a food chain of invertebrates that eat them and are in turn eaten by predatory
invertebrates and fish. Plants and animals have adapted to this fast-moving water. For instance, leeches (phylum Annelida) have
elongated bodies and suckers on both ends. These suckers attach to the substrate, keeping the leech anchored in place. In temperate
regions, freshwater trout species (phylum Chordata) may be an important predator in these fast-moving and colder river and
streams.
As the river or stream flows away from the source, the width of the channel gradually widens, the current slows, and the
temperature characteristically increases. The increasing width results from the increased volume of water from more and more
tributaries. Gradients are typically lower farther along the river, which accounts for the slowing flow. With increasing volume can
come increased silt, and as the flow rate slows, the silt may settle, thus increasing the deposition of sediment. Phytoplankton can
also be suspended in slow-moving water. Therefore, the water will not be as clear as it is near the source. The water is also warmer
as a result of longer exposure to sunlight and the absence of tree cover over wider expanses between banks. Worms (phylum
Annelida) and insects (phylum Arthropoda) can be found burrowing into the mud. Predatory vertebrates (phylum Chordata) include
waterfowl, frogs, and fishes. In heavily silt-laden rivers, these predators must find food in the murky waters, and, unlike the trout in
the clear waters at the source, these vertebrates cannot use vision as their primary sense to find food. Instead, they are more likely
to use taste or chemical cues to find prey.
When a river reaches the ocean or a large lake, the water typically slows dramatically and any silt in the river water will settle.
Rivers with high silt content discharging into oceans with minimal currents and wave action will build deltas, low-elevation areas
of sand and mud, as the silt settles onto the ocean bottom. Rivers with low silt content or in areas where ocean currents or wave
action are high create estuarine areas where the fresh water and salt water mix.

Wetlands
Wetlands are environments in which the soil is either permanently or periodically saturated with water. Wetlands are different from
lakes and ponds because wetlands exhibit a near continuous cover of emergent vegetation. Emergent vegetation consists of wetland
plants that are rooted in the soil but have portions of leaves, stems, and flowers extending above the water’s surface. There are
several types of wetlands including marshes, swamps, bogs, mudflats, and salt marshes (Figure [Link]).

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 Figure [Link]: Located in southern Florida, Everglades National Park is a vast array of wetland environments, including
sawgrass marshes, cypress swamps, and estuarine mangrove forests. Here, a great egret walks among cypress trees. (credit: NPS)

Freshwater marshes and swamps are characterized by slow and steady water flow. Bogs develop in depressions where water flow is
low or nonexistent. Bogs usually occur in areas where there is a clay bottom with poor percolation. Percolation is the movement of
water through the pores in the soil or rocks. The water found in a bog is stagnant and oxygen depleted because the oxygen that is
used during the decomposition of organic matter is not replaced. As the oxygen in the water is depleted, decomposition slows. This
leads to organic acids and other acids building up and lowering the pH of the water. At a lower pH, nitrogen becomes unavailable
to plants. This creates a challenge for plants because nitrogen is an important limiting resource. Some types of bog plants (such as
sundews, pitcher plants, and Venus flytraps) capture insects and extract the nitrogen from their bodies. Bogs have low net primary
productivity because the water found in bogs has low levels of nitrogen and oxygen.

Section Summary
Aquatic biomes include both saltwater and freshwater biomes. The abiotic factors important for the structuring of aquatic biomes
can be different than those seen in terrestrial biomes. Sunlight is an important factor in bodies of water, especially those that are
very deep, because of the role of photosynthesis in sustaining certain organisms. Other important factors include temperature, water
movement, and salt content. Oceans may be thought of as consisting of different zones based on water depth, distance from the
shoreline, and light penetrance. Different kinds of organisms are adapted to the conditions found in each zone. Coral reefs are
unique marine ecosystems that are home to a wide variety of species. Estuaries are found where rivers meet the ocean; their
shallow waters provide nourishment and shelter for young crustaceans, mollusks, fishes, and many other species. Freshwater
biomes include lakes, ponds, rivers, streams, and wetlands. Bogs are an interesting type of wetland characterized by standing water,
a lower pH, and a lack of nitrogen.

Art Connections
Figure [Link]: In which of the following regions would you expect to find photosynthetic organisms?
A. The aphotic zone, the neritic zone, the oceanic zone, and the benthic realm.
B. The photic zone, the intertidal zone, the neritic zone, and the oceanic zone.
C. The photic zone, the abyssal zone, the neritic zone, and the oceanic zone.
D. The pelagic realm, the aphotic zone, the neritic zone, and the oceanic zone.

Answer
B. The photic zone, the intertidal zone, the neritic zone, and the oceanic zone.

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Glossary

abyssal zone
the deepest part of the ocean at depths of 4000 m or greater

algal bloom
a rapid increase of algae in an aquatic system

aphotic zone
the part of the ocean where photosynthesis cannot occur

benthic realm
(also, benthic zone) the part of the ocean that extends along the ocean bottom from the shoreline to the deepest parts of the
ocean floor

channel
the bed and banks of a river or stream

coral reef
an ocean ridge formed by marine invertebrates living in warm shallow waters within the photic zone

cryptofauna
the invertebrates found within the calcium carbonate substrate of coral reefs

ecosystem services
the human benefits provided by natural ecosystems

emergent vegetation
the plants living in bodies of water that are rooted in the soil but have portions of leaves, stems, and flowers extending above
the water’s surface

estuary
a region where fresh water and salt water mix where a river discharges into an ocean or sea

intertidal zone
the part of the ocean that is closest to land; parts extend above the water at low tide

neritic zone
the part of the ocean that extends from low tide to the edge of the continental shelf

oceanic zone
the part of the ocean that begins offshore where the water measures 200 m deep or deeper

pelagic realm
(also, pelagic zone) the open ocean waters that are not close to the bottom or near the shore

photic zone
the upper layer of ocean water in which photosynthesis is able to take place

planktivore
an animal that eats plankton

source water
the point of origin of a river or stream

wetland

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 environment in which the soil is either permanently or periodically saturated with water

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.2.4: Aquatic and Marine Biomes is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
20.4: Aquatic and Marine Biomes by OpenStax is licensed CC BY 4.0.

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9.2.E: Ecosystems and the Biosphere (Exercises)
20.1: Energy Flow through Ecosystems
Multiple Choice
Decomposers are associated with which class of food web?
A. grazing
B. detrital
C. inverted
D. aquatic

Answer
B

The producer in an ocean grazing food web is usually a ________.

A. plant
B. animal
C. fungi
D. plankton

Answer
D

Which term describes the process whereby toxic substances increase along trophic levels of an ecosystem?
A. biomassification
B. biomagnification
C. bioentropy
D. heterotrophy

Answer
B

Free Response
Compare grazing and detrital food webs. Why would they both be present in the same ecosystem?

Answer
Grazing food webs have a producer at their base, which is either a plant for terrestrial ecosystems or a phytoplankton for aquatic
ecosystems. The producers pass their energy to the various trophic levels of consumers. At the base of detrital food webs are the
decomposers, which pass their energy to a variety of other consumers. Detrital food webs are important for the health of many
grazing food webs because they eliminate dead and decaying organic material, thus clearing space for new organisms and
removing potential causes of disease.

20.2: Biogeochemical Cycles

Multiple Choice
The majority of the water found on Earth is:
A. ice
B. water vapor
C. fresh water
D. salt water

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Answer
D

The process whereby oxygen is depleted by the growth of microorganisms due to excess nutrients in aquatic systems is called
________.
A. dead zoning
B. eutrophication
C. retrophication
D. depletion

Answer
B

Free Response
Why are drinking water supplies still a major concern for many countries?

Answer
Most of the water on Earth is salt water, which humans cannot drink unless the salt is removed. Some fresh water is locked in
glaciers and polar ice caps, or is present in the atmosphere. The earth’s water supplies are threatened by pollution and
exhaustion. The effort to supply fresh drinking water to the planet’s ever-expanding human population is seen as a major
challenge in this century.

20.3: Terrestrial Biomes

Multiple Choice
Which of the following biomes is characterized by abundant water resources?
A. deserts
B. boreal forests
C. savanna
D. tropical wet forests

Answer
D

Which of the following biomes is characterized by short growing seasons?

A. deserts
B. tropical wet forests
C. Arctic tundra
D. savanna

Answer
C

Why is the tundra treeless?

A. lack of sufficient water
B. permanently frozen ground
C. winters too harsh
D. too many fires

Answer
B

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Free Response
The extremely low precipitation of subtropical desert biomes might lead one to expect fire to be a major disturbance factor;
however, fire is more common in the temperate grassland biome than in the subtropical desert biome. Why is this?

Answer
Fire is less common in desert biomes than in temperate grasslands because deserts have low net primary productivity, thus very
little plant biomass to fuel a fire.

In what ways are the subtropical desert and the Arctic tundra similar?

Answer
Both the subtropical desert and the Arctic tundra have a low supply of water. In the desert, this is due to extremely low
precipitation, and in the Arctic tundra, much of the water is unavailable to plants because it is frozen. Both the subtropical
desert and the Arctic tundra have low net primary productivity.

20.4: Aquatic and Marine Biomes

Multiple Choice
Where would you expect to find the most photosynthesis in an ocean biome?
A. aphotic zone
B. abyssal zone
C. benthic realm
D. intertidal zone

Answer
D

A key feature of estuaries is

A. low light conditions and high productivity
B. salt water and fresh water
C. frequent algal blooms
D. little or no vegetation

Answer
B

Free Response
Describe the conditions and challenges facing organisms living in the intertidal zone.

Answer
Organisms living in the intertidal zone must tolerate periodic exposure to air and sunlight and must be able to be periodically
dry. They also must be able to endure the pounding waves; for this reason, some shoreline organisms have hard exoskeletons
that provide protection while also reducing the likelihood of drying out.

This page titled 9.2.E: Ecosystems and the Biosphere (Exercises) is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
20.E: Ecosystems and the Biosphere (Exercises) by OpenStax is licensed CC BY 4.0.

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 SECTION OVERVIEW

9.3: Conservation and Biodiversity

Biologists recognize that human populations are embedded in ecosystems and are dependent on them, just as is every other species
on the planet. Agriculture began after early hunter-gatherer societies first settled in one place and heavily modified their immediate
environment: the ecosystem in which they existed. This cultural transition has made it difficult for humans to recognize their
dependence on living things other than crops and domesticated animals on the planet. Today our technology smoothes out the
extremes of existence and allows many of us to live longer, more comfortable lives, but ultimately the human species cannot exist
without its surrounding ecosystems.

9.3.1: Importance of Biodiversity

9.3.2: Threats to Biodiversity

9.3.3: Preserving Biodiversity

9.3.E: Conservation and Biodiversity (Exercises)

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9.3.1: Importance of Biodiversity
Biodiversity is a broad term for biological variety, and it can be measured at a number of organizational levels. Traditionally,
ecologists have measured biodiversity by taking into account both the number of species and the number of individuals in each of
those species. However, biologists are using measures of biodiversity at several levels of biological organization (including genes,
populations, and ecosystems) to help focus efforts to preserve the biologically and technologically important elements of
biodiversity.
When biodiversity loss through extinction is thought of as the loss of the passenger pigeon, the dodo, or, even, the woolly
mammoth there seems to be no reason to care about it because these events happened long ago. How is the loss practically
important for the welfare of the human species? Would these species have made our lives any better? From the perspective of
evolution and ecology, the loss of a particular individual species, with some exceptions, may seem unimportant, but the current
accelerated extinction rate means the loss of tens of thousands of species within our lifetimes. Much of this loss is occurring in
tropical rainforests like the one pictured in Figure [Link], which are especially high-diversity ecosystems that are being cleared for
timber and agriculture. This is likely to have dramatic effects on human welfare through the collapse of ecosystems and in added
costs to maintain food production, clean air and water, and improve human health.

Figure [Link]: This tropical lowland rainforest in Madagascar is an example of a high biodiversity habitat. This particular
location is protected within a national forest, yet only 10 percent of the original coastal lowland forest remains, and research
suggests half the original biodiversity has been lost. (credit: Frank Vassen)
Biologists recognize that human populations are embedded in ecosystems and are dependent on them, just as is every other species
on the planet. Agriculture began after early hunter-gatherer societies first settled in one place and heavily modified their immediate
environment: the ecosystem in which they existed. This cultural transition has made it difficult for humans to recognize their
dependence on living things other than crops and domesticated animals on the planet. Today our technology smoothes out the
extremes of existence and allows many of us to live longer, more comfortable lives, but ultimately the human species cannot exist
without its surrounding ecosystems. Our ecosystems provide our food. This includes living plants that grow in soil ecosystems and
the animals that eat these plants (or other animals) as well as photosynthetic organisms in the oceans and the other organisms that
eat them. Our ecosystems have provided and will provide many of the medications that maintain our health, which are commonly
made from compounds found in living organisms. Ecosystems provide our clean water, which is held in lake and river ecosystems
or passes through terrestrial ecosystems on its way into groundwater.

Types of Biodiversity
A common meaning of biodiversity is simply the number of species in a location or on Earth; for example, the American
Ornithologists’ Union lists 2078 species of birds in North and Central America. This is one measure of the bird biodiversity on the
continent. More sophisticated measures of diversity take into account the relative abundances of species. For example, a forest with
10 equally common species of trees is more diverse than a forest that has 10 species of trees wherein just one of those species
makes up 95 percent of the trees rather than them being equally distributed. Biologists have also identified alternate measures of
biodiversity, some of which are important in planning how to preserve biodiversity.

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Genetic and Chemical Biodiversity
Genetic diversity is one alternate concept of biodiversity. Genetic diversity (or variation) is the raw material for adaptation in a
species. A species’ future potential for adaptation depends on the genetic diversity held in the genomes of the individuals in
populations that make up the species. The same is true for higher taxonomic categories. A genus with very different types of
species will have more genetic diversity than a genus with species that look alike and have similar ecologies. The genus with the
greatest potential for subsequent evolution is the most genetically diverse one.
Most genes code for proteins, which in turn carry out the metabolic processes that keep organisms alive and reproducing. Genetic
diversity can also be conceived of as chemical diversity in that species with different genetic makeups produce different
assortments of chemicals in their cells (proteins as well as the products and byproducts of metabolism). This chemical diversity is
important for humans because of the potential uses for these chemicals, such as medications. For example, the drug eptifibatide is
derived from rattlesnake venom and is used to prevent heart attacks in individuals with certain heart conditions.
At present, it is far cheaper to discover compounds made by an organism than to imagine them and then synthesize them in a
laboratory. Chemical diversity is one way to measure diversity that is important to human health and welfare. Through selective
breeding, humans have domesticated animals, plants, and fungi, but even this diversity is suffering losses because of market forces
and increasing globalism in human agriculture and migration. For example, international seed companies produce only a very few
varieties of a given crop and provide incentives around the world for farmers to buy these few varieties while abandoning their
traditional varieties, which are far more diverse. The human population depends on crop diversity directly as a stable food source
and its decline is troubling to biologists and agricultural scientists.

Ecosystems Diversity
It is also useful to define ecosystem diversity: the number of different ecosystems on Earth or in a geographical area. Whole
ecosystems can disappear even if some of the species might survive by adapting to other ecosystems. The loss of an ecosystem
means the loss of the interactions between species, the loss of unique features of coadaptation, and the loss of biological
productivity that an ecosystem is able to create. An example of a largely extinct ecosystem in North America is the prairie
ecosystem (Figure [Link]). Prairies once spanned central North America from the boreal forest in northern Canada down into
Mexico. They are now all but gone, replaced by crop fields, pasture lands, and suburban sprawl. Many of the species survive, but
the hugely productive ecosystem that was responsible for creating our most productive agricultural soils is now gone. As a
consequence, their soils are now being depleted unless they are maintained artificially at greater expense. The decline in soil
productivity occurs because the interactions in the original ecosystem have been lost; this was a far more important loss than the
relatively few species that were driven extinct when the prairie ecosystem was destroyed.

Figure [Link]: The variety of ecosystems on Earth—from coral reef to prairie—enables a great diversity of species to exist.
(credit “coral reef”: modification of work by Jim Maragos, USFWS; credit: “prairie”: modification of work by Jim Minnerath,
USFWS)

Current Species Diversity

Despite considerable effort, knowledge of the species that inhabit the planet is limited. A recent estimate suggests that the
eukaryote species for which science has names, about 1.5 million species, account for less than 20 percent of the total number of
eukaryote species present on the planet (8.7 million species, by one estimate). Estimates of numbers of prokaryotic species are
largely guesses, but biologists agree that science has only just begun to catalog their diversity. Even with what is known, there is no
centralized repository of names or samples of the described species; therefore, there is no way to be sure that the 1.5 million
descriptions is an accurate number. It is a best guess based on the opinions of experts on different taxonomic groups. Given that

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Earth is losing species at an accelerating pace, science knows little about what is being lost. Table [Link] presents recent estimates
of biodiversity in different groups.
Table [Link]: Estimated Numbers of Described and Predicted species
Source: Mora et al 2011 Source: Chapman 2009 Source: Groombridge and Jenkins 2002

Described Predicted Described Predicted Described Predicted

Animals 1,124,516 9,920,000 1,424,153 6,836,330 1,225,500 10,820,000

Photosynthetic
17,892 34,900 25,044 200,500 — —
protists

Fungi 44,368 616,320 98,998 1,500,000 72,000 1,500,000

Plants 224,244 314,600 310,129 390,800 270,000 320,000

Non-
photosynthetic 16,236 72,800 28,871 1,000,000 80,000 600,000
protists

Prokaryotes — — 10,307 1,000,000 10,175 —

Total 1,438,769 10,960,000 1,897,502 10,897,630 1,657,675 13,240,000

Table [Link] : This table shows the estimated number of species by taxonomic group—including both described (named and
studied) and predicted (yet to be named) species.
There are various initiatives to catalog described species in accessible and more organized ways, and the internet is facilitating that
1
effort. Nevertheless, at the current rate of species description, which according to the State of Observed Species reports is 17,000–
20,000 new species a year, it would take close to 500 years to describe all of the species currently in existence. The task, however,
is becoming increasingly impossible over time as extinctionremoves species from Earth faster than they can be described.
Naming and counting species may seem an unimportant pursuit given the other needs of humanity, but it is not simply an
accounting. Describing species is a complex process by which biologists determine an organism’s unique characteristics and
whether or not that organism belongs to any other described species. It allows biologists to find and recognize the species after the
initial discovery to follow up on questions about its biology. That subsequent research will produce the discoveries that make the
species valuable to humans and to our ecosystems. Without a name and description, a species cannot be studied in depth and in a
coordinated way by multiple scientists.

Patterns of Biodiversity
Biodiversity is not evenly distributed on the planet. Lake Victoria contained almost 500 species of cichlids (only one family of
fishes present in the lake) before the introduction of an exotic species in the 1980s and 1990s caused a mass extinction. All of these
species were found only in Lake Victoria, which is to say they were endemic. Endemic species are found in only one location. For
example, the blue jay is endemic to North America, while the Barton Springs salamander is endemic to the mouth of one spring in
Austin, Texas. Endemics with highly restricted distributions, like the Barton Springs salamander, are particularly vulnerable to
extinction. Higher taxonomic levels, such as genera and families, can also be endemic.
Lake Huron contains about 79 species of fish, all of which are found in many other lakes in North America. What accounts for the
difference in diversity between Lake Victoria and Lake Huron? Lake Victoria is a tropical lake, while Lake Huron is a temperate
lake. Lake Huron in its present form is only about 7,000 years old, while Lake Victoria in its present form is about 15,000 years
old. These two factors, latitude and age, are two of several hypotheses biogeographers have suggested to explain biodiversity
patterns on Earth.

CAREER IN ACTION: Biogeography

Biogeography is the study of the distribution of the world’s species both in the past and in the present. The work of
biogeographers is critical to understanding our physical environment, how the environment affects species, and how changes in
environment impact the distribution of a species.
There are three main fields of study under the heading of biogeography: ecological biogeography, historical biogeography
(called paleobiogeography), and conservation biogeography. Ecological biogeography studies the current factors affecting the

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 distribution of plants and animals. Historical biogeography, as the name implies, studies the past distribution of species.
Conservation biogeography, on the other hand, is focused on the protection and restoration of species based upon the known
historical and current ecological information. Each of these fields considers both zoogeography and phytogeography—the past
and present distribution of animals and plants.

One of the oldest observed patterns in ecology is that biodiversity in almost every taxonomic group of organism increases as
latitude declines. In other words, biodiversity increases closer to the equator (Figure [Link]).

Figure [Link]: This map illustrates the number of amphibian species across the globe and shows the trend toward higher
biodiversity at lower latitudes. A similar pattern is observed for most taxonomic groups.
It is not yet clear why biodiversity increases closer to the equator, but hypotheses include the greater age of the ecosystems in the
tropics versus temperate regions, which were largely devoid of life or drastically impoverished during the last ice age. The greater
age provides more time for speciation. Another possible explanation is the greater energy the tropics receive from the sun versus
the lesser energy input in temperate and polar regions. But scientists have not been able to explain how greater energy input could
translate into more species. The complexity of tropical ecosystems may promote speciation by increasing the habitat heterogeneity,
or number of ecological niches, in the tropics relative to higher latitudes. The greater heterogeneity provides more opportunities for
coevolution, specialization, and perhaps greater selection pressures leading to population differentiation. However, this hypothesis
suffers from some circularity—ecosystems with more species encourage speciation, but how did they get more species to begin
with? The tropics have been perceived as being more stable than temperate regions, which have a pronounced climate and day-
length seasonality. The tropics have their own forms of seasonality, such as rainfall, but they are generally assumed to be more
stable environments and this stability might promote speciation.
Regardless of the mechanisms, it is certainly true that biodiversity is greatest in the tropics. The number of endemic species is
higher in the tropics. The tropics also contain more biodiversity hotspots. At the same time, our knowledge of the species living in
the tropics is lowest and because of recent, heavy human activity the potential for biodiversity loss is greatest.

Importance of Biodiversity
Loss of biodiversity eventually threatens other species we do not impact directly because of their interconnectedness; as species
disappear from an ecosystem other species are threatened by the changes in available resources. Biodiversity is important to the
survival and welfare of human populations because it has impacts on our health and our ability to feed ourselves through
agriculture and harvesting populations of wild animals.

Human Health
Many medications are derived from natural chemicals made by a diverse group of organisms. For example, many plants produce
secondary plant compounds, which are toxins used to protect the plant from insects and other animals that eat them. Some of these
secondary plant compounds also work as human medicines. Contemporary societies that live close to the land often have a broad
knowledge of the medicinal uses of plants growing in their area. For centuries in Europe, older knowledge about the medical uses

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of plants was compiled in herbals—books that identified the plants and their uses. Humans are not the only animals to use plants
for medicinal reasons. The other great apes, orangutans, chimpanzees, bonobos, and gorillas have all been observed self-medicating
with plants.
Modern pharmaceutical science also recognizes the importance of these plant compounds. Examples of significant medicines
derived from plant compounds include aspirin, codeine, digoxin, atropine, and vincristine (Figure [Link]). Many medications were
once derived from plant extracts but are now synthesized. It is estimated that, at one time, 25 percent of modern drugs contained at
least one plant extract. That number has probably decreased to about 10 percent as natural plant ingredients are replaced by
synthetic versions of the plant compounds. Antibiotics, which are responsible for extraordinary improvements in health and
lifespans in developed countries, are compounds largely derived from fungi and bacteria.

Figure [Link]: Catharanthus roseus, the Madagascar periwinkle, has various medicinal properties. Among other uses, it is a
source of vincristine, a drug used in the treatment of lymphomas. (credit: Forest and Kim Starr)
In recent years, animal venoms and poisons have excited intense research for their medicinal potential. By 2007, the FDA had
approved five drugs based on animal toxins to treat diseases such as hypertension, chronic pain, and diabetes. Another five drugs
are undergoing clinical trials and at least six drugs are being used in other countries. Other toxins under investigation come from
mammals, snakes, lizards, various amphibians, fish, snails, octopuses, and scorpions.
Aside from representing billions of dollars in profits, these medications improve people’s lives. Pharmaceutical companies are
actively looking for new natural compounds that can function as medicines. It is estimated that one third of pharmaceutical research
and development is spent on natural compounds and that about 35 percent of new drugs brought to market between 1981 and 2002
were from natural compounds.
Finally, it has been argued that humans benefit psychologically from living in a biodiverse world. The chief proponent of this idea
is entomologist E. O. Wilson. He argues that human evolutionary history has adapted us to living in a natural environment and that
built environments generate stresses that affect human health and well-being. There is considerable research into the
psychologically regenerative benefits of natural landscapes that suggest the hypothesis may hold some truth.

Agricultural
Since the beginning of human agriculture more than 10,000 years ago, human groups have been breeding and selecting crop
varieties. This crop diversity matched the cultural diversity of highly subdivided populations of humans. For example, potatoes
were domesticated beginning around 7,000 years ago in the central Andes of Peru and Bolivia. The people in this region
traditionally lived in relatively isolated settlements separated by mountains. The potatoes grown in that region belong to seven
species and the number of varieties likely is in the thousands. Each variety has been bred to thrive at particular elevations and soil
and climate conditions. The diversity is driven by the diverse demands of the dramatic elevation changes, the limited movement of
people, and the demands created by crop rotation for different varieties that will do well in different fields.
Potatoes are only one example of agricultural diversity. Every plant, animal, and fungus that has been cultivated by humans has
been bred from original wild ancestor species into diverse varieties arising from the demands for food value, adaptation to growing
conditions, and resistance to pests. The potato demonstrates a well-known example of the risks of low crop diversity: during the
tragic Irish potato famine (1845–1852 AD), the single potato variety grown in Ireland became susceptible to a potato blight—

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wiping out the crop. The loss of the crop led to famine, death, and mass emigration. Resistance to disease is a chief benefit to
maintaining crop biodiversity and lack of diversity in contemporary crop species carries similar risks. Seed companies, which are
the source of most crop varieties in developed countries, must continually breed new varieties to keep up with evolving pest
organisms. These same seed companies, however, have participated in the decline of the number of varieties available as they focus
on selling fewer varieties in more areas of the world replacing traditional local varieties.
The ability to create new crop varieties relies on the diversity of varieties available and the availability of wild forms related to the
crop plant. These wild forms are often the source of new gene variants that can be bred with existing varieties to create varieties
with new attributes. Loss of wild species related to a crop will mean the loss of potential in crop improvement. Maintaining the
genetic diversity of wild species related to domesticated species ensures our continued supply of food.
Since the 1920s, government agriculture departments have maintained seed banks of crop varieties as a way to maintain crop
diversity. This system has flaws because over time seed varieties are lost through accidents and there is no way to replace them. In
2008, the Svalbard Global seed Vault, located on Spitsbergen island, Norway, (Figure [Link]) began storing seeds from around the
world as a backup system to the regional seed banks. If a regional seed bank stores varieties in Svalbard, losses can be replaced
from Svalbard should something happen to the regional seeds. The Svalbard seed vault is deep into the rock of the arctic island.
Conditions within the vault are maintained at ideal temperature and humidity for seed survival, but the deep underground location
of the vault in the arctic means that failure of the vault’s systems will not compromise the climatic conditions inside the vault.

ART CONNECTION

Figure [Link]: The Svalbard Global Seed Vault is a storage facility for seeds of Earth’s diverse crops. (credit: Mari Tefre,
Svalbard Global Seed Vault)
The Svalbard seed vault is located on Spitsbergen island in Norway, which has an arctic climate. Why might an arctic climate
be good for seed storage?

Although crops are largely under our control, our ability to grow them is dependent on the biodiversity of the ecosystems in which
they are grown. That biodiversity creates the conditions under which crops are able to grow through what are known as ecosystem
services—valuable conditions or processes that are carried out by an ecosystem. Crops are not grown, for the most part, in built
environments. They are grown in soil. Although some agricultural soils are rendered sterile using controversial pesticide
treatments, most contain a huge diversity of organisms that maintain nutrient cycles—breaking down organic matter into nutrient
compounds that crops need for growth. These organisms also maintain soil texture that affects water and oxygen dynamics in the
soil that are necessary for plant growth. Replacing the work of these organisms in forming arable soil is not practically possible.
These kinds of processes are called ecosystem services. They occur within ecosystems, such as soil ecosystems, as a result of the
diverse metabolic activities of the organisms living there, but they provide benefits to human food production, drinking water
availability, and breathable air.
Other key ecosystem services related to food production are plant pollination and crop pest control. It is estimated that honeybee
pollination within the United States brings in $1.6 billion per year; other pollinators contribute up to $6.7 billion. Over 150 crops in
the United States require pollination to produce. Many honeybee populations are managed by beekeepers who rent out their hives’
services to farmers. Honeybee populations in North America have been suffering large losses caused by a syndrome known as
colony collapse disorder, a new phenomenon with an unclear cause. Other pollinators include a diverse array of other bee species

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and various insects and birds. Loss of these species would make growing crops requiring pollination impossible, increasing
dependence on other crops.
Finally, humans compete for their food with crop pests, most of which are insects. Pesticides control these competitors, but these
are costly and lose their effectiveness over time as pest populations adapt. They also lead to collateral damage by killing non-pest
species as well as beneficial insects like honeybees, and risking the health of agricultural workers and consumers. Moreover, these
pesticides may migrate from the fields where they are applied and do damage to other ecosystems like streams, lakes, and even the
ocean. Ecologists believe that the bulk of the work in removing pests is actually done by predators and parasites of those pests, but
the impact has not been well studied. A review found that in 74 percent of studies that looked for an effect of landscape complexity
(forests and fallow fields near to crop fields) on natural enemies of pests, the greater the complexity, the greater the effect of pest-
suppressing organisms. Another experimental study found that introducing multiple enemies of pea aphids (an important alfalfa
pest) increased the yield of alfalfa significantly. This study shows that a diversity of pests is more effective at control than one
single pest. Loss of diversity in pest enemies will inevitably make it more difficult and costly to grow food. The world’s growing
human population faces significant challenges in the increasing costs and other difficulties associated with producing food.

Wild Food Sources

In addition to growing crops and raising food animals, humans obtain food resources from wild populations, primarily wild fish
populations. For about one billion people, aquatic resources provide the main source of animal protein. But since 1990, production
from global fisheries has declined. Despite considerable effort, few fisheries on Earth are managed sustainability.
Fishery extinctions rarely lead to complete extinction of the harvested species, but rather to a radical restructuring of the marine
ecosystem in which a dominant species is so over-harvested that it becomes a minor player, ecologically. In addition to humans
losing the food source, these alterations affect many other species in ways that are difficult or impossible to predict. The collapse of
fisheries has dramatic and long-lasting effects on local human populations that work in the fishery. In addition, the loss of an
inexpensive protein source to populations that cannot afford to replace it will increase the cost of living and limit societies in other
ways. In general, the fish taken from fisheries have shifted to smaller species and the larger species are overfished. The ultimate
outcome could clearly be the loss of aquatic systems as food sources.

Summary
Biodiversity exists at multiple levels of organization, and is measured in different ways depending on the goals of those taking the
measurements. These include numbers of species, genetic diversity, chemical diversity, and ecosystem diversity. The number of
described species is estimated to be 1.5 million with about 17,000 new species being described each year. Estimates for the total
number of eukaryotic species on Earth vary but are on the order of 10 million. Biodiversity is negatively correlated with latitude for
most taxa, meaning that biodiversity is higher in the tropics. The mechanism for this pattern is not known with certainty, but several
plausible hypotheses have been advanced.
Humans use many compounds that were first discovered or derived from living organisms as medicines: secondary plant
compounds, animal toxins, and antibiotics produced by bacteria and fungi. More medicines are expected to be discovered in nature.
Loss of biodiversity will impact the number of pharmaceuticals available to humans. Biodiversity may provide important
psychological benefits to humans.
Crop diversity is a requirement for food security, and it is being lost. The loss of wild relatives to crops also threatens breeders’
abilities to create new varieties. Ecosystems provide ecosystem services that support human agriculture: pollination, nutrient
cycling, pest control, and soil development and maintenance. Loss of biodiversity threatens these ecosystem services and risks
making food production more expensive or impossible. Wild food sources are mainly aquatic, but few are being managed for
sustainability. Fisheries’ ability to provide protein to human populations is threatened when extinction occurs.

Art Connections
Figure [Link]: The Svalbard seed vault is located on Spitsbergen island in Norway, which has an arctic climate. Why might an
arctic climate be good for seed storage?

Answer
The ground is permanently frozen so the seeds will keep, even if the electricity fails.

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Footnotes
1. 1 International Institute for Species Exploration (IISE), 2011 State of Observed Species (SOS). Tempe, AZ: IISE, 2011.
Accessed May, 20, 2012. [Link]/SOS.

Glossary

biodiversity
the variety of a biological system, typically conceived as the number of species, but also applying to genes, biochemistry, and
ecosystems

chemical diversity
the variety of metabolic compounds in an ecosystem

ecosystem diversity
the variety of ecosystems

endemic species
a species native to one place

extinction
the disappearance of a species from Earth; local extinction is the disappearance of a species from a region

genetic diversity
the variety of genes and alleles in a species or other taxonomic group or ecosystem; the term can refer to allelic diversity or
genome-wide diversity

habitat heterogeneity
the number of ecological niches

secondary plant compound

a compound produced as a byproduct of plant metabolic processes that is typically toxic, but is sequestered by the plant to
defend against herbivores

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.3.1: Importance of Biodiversity is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
21.1: Importance of Biodiversity by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

9.3.2: Threats to Biodiversity
The core threat to biodiversity on the planet, and therefore a threat to human welfare, is the combination of human population
growth and the resources used by that population. The human population requires resources to survive and grow, and those
resources are being removed unsustainably from the environment. The three greatest proximate threats to biodiversity are habitat
loss, overharvesting, and introduction of exotic species. The first two of these are a direct result of human population growth and
resource use. The third results from increased mobility and trade. A fourth major cause of extinction, anthropogenic (human-
caused) climate change, has not yet had a large impact, but it is predicted to become significant during this century. Global climate
change is also a consequence of human population needs for energy and the use of fossil fuels to meet those needs (Figure [Link]).
Environmental issues, such as toxic pollution, have specific targeted effects on species, but are not generally seen as threats at the
magnitude of the others.

Figure [Link]: Atmospheric carbon dioxide levels fluctuate in a cyclical manner. However, the burning of fossil fuels in recent
history has caused a dramatic increase in the levels of carbon dioxide in the Earth’s atmosphere, which have now reached levels
never before seen recently on Earth. Scientists predict that the addition of this “greenhouse gas” to the atmosphere is resulting in
climate change that will significantly impact biodiversity in the coming century.

Habitat Loss
Humans rely on technology to modify their environment and replace certain functions that were once performed by the natural
ecosystem. Other species cannot do this. Elimination of their habitat—whether it is a forest, coral reef, grassland, or flowing river
—will kill the individuals in the species. Remove the entire habitat within the range of a species and, unless they are one of the few
species that do well in human-built environments, the species will become extinct. Human destruction of habitats (habitats
generally refer to the part of the ecosystem required by a particular species) accelerated in the latter half of the twentieth century.
Consider the exceptional biodiversity of Sumatra: it is home to one species of orangutan, a species of critically endangered
elephant, and the Sumatran tiger, but half of Sumatra’s forest is now gone. The neighboring island of Borneo, home to the other
species of orangutan, has lost a similar area of forest. Forest loss continues in protected areas of Borneo. The orangutan in Borneo
is listed as endangered by the International Union for Conservation of Nature (IUCN), but it is simply the most visible of thousands
of species that will not survive the disappearance of the forests of Borneo. The forests are removed for timber and to plant palm oil
plantations (Figure [Link]). Palm oil is used in many products including food products, cosmetics, and biodiesel in Europe. A 5-
year estimate of global forest cover loss for the years from 2000 to 2005 was 3.1 percent. Much loss (2.4 percent) occurred in the
humid tropics where forest loss is primarily from timber extraction. These losses certainly also represent the extinction of species
unique to those areas.

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 Figure [Link]: An oil palm plantation in Sabah province Borneo, Malaysia, replaces native forest habitat that a variety of species
depended on to live. (credit: Lian Pin Koh)

BIOLOGY IN ACTION: Preventing Habitat Destruction with Wise Wood Choices

Most consumers do not imagine that the home improvement products they buy might be contributing to habitat loss and
species extinctions. Yet the market for illegally harvested tropical timber is huge, and the wood products often find themselves
in building supply stores in the United States. One estimate is that 10 percent of the imported timber stream in the United
States, which is the world’s largest consumer of wood products, is potentially illegally logged. In 2006, this amounted to $3.6
billion in wood products. Most of the illegal products are imported from countries that act as intermediaries and are not the
originators of the wood.
How is it possible to determine if a wood product, such as flooring, was harvested sustainably or even legally? The Forest
Stewardship Council (FSC) certifies sustainably harvested forest products; therefore, looking for their certification on flooring
and other hardwood products is one way to ensure that the wood has not been taken illegally from a tropical forest.
Certification applies to specific products, not to a producer; some producers’ products may not have certification while other
products are certified. There are certifications other than the FSC, but these are run by timber companies creating a conflict of
interest. Another approach is to buy domestic wood species. While it would be great if there was a list of legal versus illegal
woods, it is not that simple. Logging and forest management laws vary from country to country; what is illegal in one country
may be legal in another. Where and how a product is harvested and whether the forest from which it comes is being sustainably
maintained all factor into whether a wood product will be certified by the FSC. It is always a good idea to ask questions about
where a wood product came from and how the supplier knows that it was harvested legally.

Habitat destruction can affect ecosystems other than forests. Rivers and streams are important ecosystems and are frequently the
target of habitat modification through building and from damming or water removal. Damming of rivers affects flows and access to
all parts of a river. Altering a flow regime can reduce or eliminate populations that are adapted to seasonal changes in flow. For
example, an estimated 91 percent of river lengths in the United States have been modified with damming or bank modifications.
Many fish species in the United States, especially rare species or species with restricted distributions, have seen declines caused by
river damming and habitat loss. Research has confirmed that species of amphibians that must carry out parts of their life cycles in
both aquatic and terrestrial habitats are at greater risk of population declines and extinction because of the increased likelihood that
one of their habitats or access between them will be lost. This is of particular concern because amphibians have been declining in
numbers and going extinct more rapidly than many other groups for a variety of possible reasons.

Overharvesting
Overharvesting is a serious threat to many species, but particularly to aquatic species. There are many examples of regulated
fisheries (including hunting of marine mammals and harvesting of crustaceans and other species) monitored by fisheries scientists
that have nevertheless collapsed. The western Atlantic cod fishery is the most spectacular recent collapse. While it was a hugely
productive fishery for 400 years, the introduction of modern factory trawlers in the 1980s and the pressure on the fishery led to it
becoming unsustainable. The causes of fishery collapse are both economic and political in nature. Most fisheries are managed as a
common resource, available to anyone willing to fish, even when the fishing territory lies within a country’s territorial waters.

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Common resources are subject to an economic pressure known as the tragedy of the commons, in which fishers have little
motivation to exercise restraint in harvesting a fishery when they do not own the fishery. The general outcome of harvests of
resources held in common is their overexploitation. While large fisheries are regulated to attempt to avoid this pressure, it still
exists in the background. This overexploitation is exacerbated when access to the fishery is open and unregulated and when
technology gives fishers the ability to overfish. In a few fisheries, the biological growth of the resource is less than the potential
growth of the profits made from fishing if that time and money were invested elsewhere. In these cases—whales are an example—
economic forces will drive toward fishing the population to extinction.

CONCEPT IN ACTION

Explore a U.S. Fish & Wildlife Service interactive map of critical habitat for endangered and threatened species in the United
States. To begin, select “Visit the online mapper.”

For the most part, fishery extinction is not equivalent to biological extinction—the last fish of a species is rarely fished out of the
ocean. But there are some instances in which true extinction is a possibility. Whales have slow-growing populations and are at risk
of complete extinction through hunting. Also, there are some species of sharks with restricted distributions that are at risk of
extinction. The groupers are another population of generally slow-growing fishes that, in the Caribbean, includes a number of
species that are at risk of extinction from overfishing.
Coral reefs are extremely diverse marine ecosystems that face peril from several processes. Reefs are home to 1/3 of the world’s
marine fish species—about 4000 species—despite making up only one percent of marine habitat. Most home marine aquaria house
coral reef species that are wild-caught organisms—not cultured organisms. Although no marine species is known to have been
driven extinct by the pet trade, there are studies showing that populations of some species have declined in response to harvesting,
indicating that the harvest is not sustainable at those levels. There are also concerns about the effect of the pet trade on some
terrestrial species such as turtles, amphibians, birds, plants, and even the orangutans.
Bush meat is the generic term used for wild animals killed for food. Hunting is practiced throughout the world, but hunting
practices, particularly in equatorial Africa and parts of Asia, are believed to threaten several species with extinction. Traditionally,
bush meat in Africa was hunted to feed families directly; however, recent commercialization of the practice now has bush meat
available in grocery stores, which has increased harvest rates to the level of unsustainability. Additionally, human population
growth has increased the need for protein foods that are not being met from agriculture. Species threatened by the bush meat trade
are mostly mammals including many monkeys and the great apes living in the Congo basin.

Exotic Species
Exotic species are species that have been intentionally or unintentionally introduced by humans into an ecosystem in which they
did not evolve. Human transportation of people and goods, including the intentional transport of organisms for trade, has
dramatically increased the introduction of species into new ecosystems. These new introductions are sometimes at distances that
are well beyond the capacity of the species to ever travel itself and outside the range of the species’ natural predators.
Most exotic species introductions probably fail because of the low number of individuals introduced or poor adaptation to the
ecosystem they enter. Some species, however, have characteristics that can make them especially successful in a new ecosystem.
These exotic species often undergo dramatic population increases in their new habitat and reset the ecological conditions in the new
environment, threatening the species that exist there. When this happens, the exotic species also becomes an invasive species.
Invasive species can threaten other species through competition for resources, predation, or disease.

CONCEPT IN ACTION
Explore this interactive global database of exotic or invasive species.

Lakes and islands are particularly vulnerable to extinction threats from introduced species. In Lake Victoria, the intentional
introduction of the Nile perch was largely responsible for the extinction of about 200 species of cichlids. The accidental
introduction of the brown tree snake via aircraft (Figure [Link]) from the Solomon Islands to Guam in 1950 has led to the
extinction of three species of birds and three to five species of reptiles endemic to the island. Several other species are still
threatened. The brown tree snake is adept at exploiting human transportation as a means to migrate; one was even found on an
aircraft arriving in Corpus Christi, Texas. Constant vigilance on the part of airport, military, and commercial aircraft personnel is
required to prevent the snake from moving from Guam to other islands in the Pacific, especially Hawaii. Islands do not make up a

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large area of land on the globe, but they do contain a disproportionate number of endemic species because of their isolation from
mainland ancestors.

Figure [Link]: The brown tree snake, Boiga irregularis, is an exotic species that has caused numerous extinctions on the island of
Guam since its accidental introduction in 1950. (credit: NPS)
Many introductions of aquatic species, both marine and freshwater, have occurred when ships have dumped ballast water taken on
at a port of origin into waters at a destination port. Water from the port of origin is pumped into tanks on a ship empty of cargo to
increase stability. The water is drawn from the ocean or estuary of the port and typically contains living organisms such as plant
parts, microorganisms, eggs, larvae, or aquatic animals. The water is then pumped out before the ship takes on cargo at the
destination port, which may be on a different continent. The zebra mussel was introduced to the Great Lakes from Europe prior to
1988 in ship ballast. The zebra mussels in the Great Lakes have cost the industry millions of dollars in clean up costs to maintain
water intakes and other facilities. The mussels have also altered the ecology of the lakes dramatically. They threaten native mollusk
populations, but have also benefited some species, such as smallmouth bass. The mussels are filter feeders and have dramatically
improved water clarity, which in turn has allowed aquatic plants to grow along shorelines, providing shelter for young fish where it
did not exist before. The European green crab, Carcinus maenas, was introduced to San Francisco Bay in the late 1990s, likely in
ship ballast water, and has spread north along the coast to Washington. The crabs have been found to dramatically reduce the
abundance of native clams and crabs with resulting increases in the prey of native crabs.
Invading exotic species can also be disease organisms. It now appears that the global decline in amphibian species recognized in
the 1990s is, in some part, caused by the fungus Batrachochytrium dendrobatidis, which causes the disease chytridiomycosis
(Figure [Link]). There is evidence that the fungus is native to Africa and may have been spread throughout the world by transport
of a commonly used laboratory and pet species: the African clawed frog, Xenopus laevis. It may well be that biologists themselves
are responsible for spreading this disease worldwide. The North American bullfrog, Rana catesbeiana, which has also been widely
introduced as a food animal but which easily escapes captivity, survives most infections of B. dendrobatidis and can act as a
reservoir for the disease.

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 Figure [Link]: This Limosa harlequin frog (Atelopus limosus), an endangered species from Panama, died from a fungal disease
called chytridiomycosis. The red lesions are symptomatic of the disease. (credit: Brian Gratwicke)
Early evidence suggests that another fungal pathogen, Geomyces destructans, introduced from Europe is responsible for white-nose
syndrome, which infects cave-hibernating bats in eastern North America and has spread from a point of origin in western New
York State (Figure [Link]). The disease has decimated bat populations and threatens extinction of species already listed as
endangered: the Indiana bat, Myotis sodalis, and potentially the Virginia big-eared bat, Corynorhinus townsendii virginianus. How
the fungus was introduced is unknown, but one logical presumption would be that recreational cavers unintentionally brought the
fungus on clothes or equipment from Europe.

Figure [Link]: This little brown bat in Greeley Mine, Vermont, March 26, 2009, was found to have white-nose syndrome.
(credit: modification of work by Marvin Moriarty, USFWS)

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Climate Change
Climate change, and specifically the anthropogenic warming trend presently underway, is recognized as a major extinction threat,
particularly when combined with other threats such as habitat loss. Anthropogenic warming of the planet has been observed and is
hypothesized to continue due to past and continuing emission of greenhouse gases, primarily carbon dioxide and methane, into the
atmosphere caused by the burning of fossil fuels and deforestation. These gases decrease the degree to which Earth is able to
radiate heat energy created by the sunlight that enters the atmosphere. The changes in climate and energy balance caused by
increasing greenhouse gases are complex and our understanding of them depends on predictions generated from detailed computer
models. Scientists generally agree the present warming trend is caused by humans and some of the likely effects include dramatic
and dangerous climate changes in the coming decades. However, there is still debate and a lack of understanding about specific
outcomes. Scientists disagree about the likely magnitude of the effects on extinction rates, with estimates ranging from 15 to 40
percent of species committed to extinction by 2050. Scientists do agree that climate change will alter regional climates, including
rainfall and snowfall patterns, making habitats less hospitable to the species living in them. The warming trend will shift colder
climates toward the north and south poles, forcing species to move with their adapted climate norms, but also to face habitat gaps
along the way. The shifting ranges will impose new competitive regimes on species as they find themselves in contact with other
species not present in their historic range. One such unexpected species contact is between polar bears and grizzly bears.
Previously, these two species had separate ranges. Now, their ranges are overlapping and there are documented cases of these two
species mating and producing viable offspring. Changing climates also throw off the delicate timing adaptations that species have
to seasonal food resources and breeding times. Scientists have already documented many contemporary mismatches to shifts in
resource availability and timing.
Range shifts are already being observed: for example, on average, European bird species ranges have moved 91 km (56.5 mi)
northward. The same study suggested that the optimal shift based on warming trends was double that distance, suggesting that the
populations are not moving quickly enough. Range shifts have also been observed in plants, butterflies, other insects, freshwater
fishes, reptiles, amphibians, and mammals.
Climate gradients will also move up mountains, eventually crowding species higher in altitude and eliminating the habitat for those
species adapted to the highest elevations. Some climates will completely disappear. The rate of warming appears to be accelerated
in the arctic, which is recognized as a serious threat to polar bear populations that require sea ice to hunt seals during the winter
months: seals are the only source of protein available to polar bears. A trend to decreasing sea ice coverage has occurred since
observations began in the mid-twentieth century. The rate of decline observed in recent years is far greater than previously
predicted by climate models (Figure [Link]).

Figure [Link]: The effect of global warming can be seen in the continuing retreat of Grinnell Glacier. The mean annual
temperature in Glacier National Park has increased 1.33°C since 1900. The loss of a glacier results in the loss of summer
meltwaters, sharply reducing seasonal water supplies and severely affecting local ecosystems. (credit: USGS, GNP Archives)
Finally, global warming will raise ocean levels due to meltwater from glaciers and the greater volume occupied by warmer water.
Shorelines will be inundated, reducing island size, which will have an effect on some species, and a number of islands will
disappear entirely. Additionally, the gradual melting and subsequent refreezing of the poles, glaciers, and higher elevation

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mountains—a cycle that has provided freshwater to environments for centuries—will be altered. This could result in an
overabundance of salt water and a shortage of fresh water.

Summary
The core threats to biodiversity are human population growth and unsustainable resource use. To date, the most significant causes
of extinction are habitat loss, introduction of exotic species, and overharvesting. Climate change is predicted to be a significant
cause of extinction in the coming century. Habitat loss occurs through deforestation, damming of rivers, and other activities.
Overharvesting is a threat particularly to aquatic species, but the taking of bush meat in the humid tropics threatens many species in
Asia, Africa, and the Americas. Exotic species have been the cause of a number of extinctions and are especially damaging to
islands and lakes. Exotic species’ introductions are increasing because of the increased mobility of human populations and growing
global trade and transportation. Climate change is forcing range changes that may lead to extinction. It is also affecting adaptations
to the timing of resource availability that negatively affects species in seasonal environments. The impacts of climate change are
currently greatest in the arctic. Global warming will also raise sea levels, eliminating some islands and reducing the area of all
others.

Glossary

bush meat
a wild-caught animal used as food (typically mammals, birds, and reptiles); usually referring to hunting in the tropics of sub-
Saharan Africa, Asia, and the Americas

chytridiomycosis
a disease of amphibians caused by the fungus Batrachochytrium dendrobatidis; thought to be a major cause of the global
amphibian decline

exotic species
(also, invasive species) a species that has been introduced to an ecosystem in which it did not evolve

tragedy of the commons

an economic principle that resources held in common will inevitably be over-exploited

white-nose syndrome
a disease of cave-hibernating bats in the eastern United States and Canada associated with the fungus Geomyces destructans

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.3.2: Threats to Biodiversity is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
21.2: Threats to Biodiversity by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

9.3.3: Preserving Biodiversity
Preserving biodiversity is an extraordinary challenge that must be met by greater understanding of biodiversity itself, changes in
human behavior and beliefs, and various preservation strategies.

Change in Biodiversity through Time

The number of species on the planet, or in any geographical area, is the result of an equilibrium of two evolutionary processes that
are ongoing: speciation and extinction. Both are natural “birth” and “death” processes of macroevolution. When speciation rates
begin to outstrip extinction rates, the number of species will increase; likewise, the reverse is true when extinction rates begin to
overtake speciation rates. Throughout the history of life on Earth, as reflected in the fossil record, these two processes have
fluctuated to a greater or lesser extent, sometimes leading to dramatic changes in the number of species on the planet as reflected in
the fossil record (Figure [Link]).

Figure [Link]: Extinction intensity as reflected in the fossil record has fluctuated throughout Earth’s history. Sudden and
dramatic losses of biodiversity, called mass extinctions, have occurred five times.
Paleontologists have identified five strata in the fossil record that appear to show sudden and dramatic (greater than half of all
extant species disappearing from the fossil record) losses in biodiversity. These are called mass extinctions. There are many lesser,
yet still dramatic, extinction events, but the five mass extinctions have attracted the most research into their causes. An argument
can be made that the five mass extinctions are only the five most extreme events in a continuous series of large extinction events
throughout the fossil record (since 542 million years ago). In most cases, the hypothesized causes are still controversial; in one, the
most recent, the cause seems clear. The most recent extinction in geological time, about 65 million years ago, saw the
disappearance of the dinosaurs and many other species. Most scientists now agree the cause of this extinction was the impact of a
large asteroid in the present-day Yucatán Peninsula and the subsequent energy release and global climate changes caused by dust
ejected into the atmosphere.

Recent and Current Extinction Rates

A sixth, or Holocene, mass extinction has mostly to do with the activities of Homo sapiens. There are numerous recent extinctions
of individual species that are recorded in human writings. Most of these are coincident with the expansion of the European colonies
since the 1500s.
One of the earlier and popularly known examples is the dodo bird. The dodo bird lived in the forests of Mauritius, an island in the
Indian Ocean. The dodo bird became extinct around 1662. It was hunted for its meat by sailors and was easy prey because the
dodo, which did not evolve with humans, would approach people without fear. Introduced pigs, rats, and dogs brought to the island
by European ships also killed dodo young and eggs (Figure [Link]).

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 Figure [Link]: The dodo bird was hunted to extinction around 1662. (credit: Ed Uthman, taken in Natural History Museum,
London, England)
Steller’s sea cow became extinct in 1768; it was related to the manatee and probably once lived along the northwest coast of North
America. Steller’s sea cow was discovered by Europeans in 1741, and it was hunted for meat and oil. A total of 27 years elapsed
between the sea cow’s first contact with Europeans and extinction of the species. The last Steller’s sea cow was killed in 1768. In
another example, the last living passenger pigeon died in a zoo in Cincinnati, Ohio, in 1914. This species had once migrated in the
millions but declined in numbers because of overhunting and loss of habitat through the clearing of forests for farmland.
These are only a few of the recorded extinctions in the past 500 years. The International Union for Conservation of Nature (IUCN)
keeps a list of extinct and endangered species called the Red List. The list is not complete, but it describes 380 vertebrates that
became extinct after 1500 AD, 86 of which were driven extinct by overhunting or overfishing.

Estimates of Present-day Extinction Rates

Estimates of extinction rates are hampered by the fact that most extinctions are probably happening without being observed. The
extinction of a bird or mammal is often noticed by humans, especially if it has been hunted or used in some other way. But there are
many organisms that are less noticeable to humans (not necessarily of less value) and many that are undescribed.
The background extinction rate is estimated to be about 1 per million species years (E/MSY). One “species year” is one species in
existence for one year. One million species years could be one species persisting for one million years, or a million species
persisting for one year. If it is the latter, then one extinction per million species years would be one of those million species
becoming extinct in that year. For example, if there are 10 million species in existence, then we would expect 10 of those species to
become extinct in a year. This is the background rate.
One contemporary extinction-rate estimate uses the extinctions in the written record since the year 1500. For birds alone, this
method yields an estimate of 26 E/MSY, almost three times the background rate. However, this value may be underestimated for
three reasons. First, many existing species would not have been described until much later in the time period and so their loss
would have gone unnoticed. Second, we know the number is higher than the written record suggests because now extinct species
are being described from skeletal remains that were never mentioned in written history. And third, some species are probably
already extinct even though conservationists are reluctant to name them as such. Taking these factors into account raises the
estimated extinction rate to nearer 100 E/MSY. The predicted rate by the end of the century is 1500 E/MSY.
A second approach to estimating present-time extinction rates is to correlate species loss with habitat loss, and it is based on
measuring forest-area loss and understanding species–area relationships. The species-area relationship is the rate at which new
species are seen when the area surveyed is increased (Figure [Link]). Likewise, if the habitat area is reduced, the number of
species seen will also decline. This kind of relationship is also seen in the relationship between an island’s area and the number of
species present on the island: as one increases, so does the other, though not in a straight line. Estimates of extinction rates based on

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habitat loss and species–area relationships have suggested that with about 90 percent of habitat loss an expected 50 percent of
species would become extinct. Figure [Link] shows that reducing forest area from 100 km2 to 10 km2, a decline of 90 percent,
reduces the number of species by about 50 percent. Species–area estimates have led to estimates of present-day species extinction
rates of about 1000 E/MSY and higher. In general, actual observations do not show this amount of loss and one explanation put
forward is that there is a delay in extinction. According to this explanation, it takes some time for species to fully suffer the effects
of habitat loss and they linger on for some time after their habitat is destroyed, but eventually they will become extinct. Recent
work has also called into question the applicability of the species-area relationship when estimating the loss of species. This work
argues that the species–area relationship leads to an overestimate of extinction rates. Using an alternate method would bring
estimates down to around 500 E/MSY in the coming century. Note that this value is still 500 times the background rate.

Figure [Link]: A typical species-area curve shows the cumulative number of species found as more and more area is sampled.
The curve has also been interpreted to show the effect on species numbers of destroying habitat; a reduction in habitat of 90 percent
from 100 km2 to 10 km2 reduces the number of species supported by about 50 percent.

CONCEPT IN ACTION

Go to this website for an interactive exploration of endangered and extinct species, their ecosystems, and the causes of their
endangerment or extinction.

Conservation of Biodiversity
The threats to biodiversity at the genetic, species, and ecosystem levels have been recognized for some time. In the United States,
the first national park with land set aside to remain in a wilderness state was Yellowstone Park in 1890. However, attempts to
preserve nature for various reasons have occurred for centuries. Today, the main efforts to preserve biodiversity involve legislative
approaches to regulate human and corporate behavior, setting aside protected areas, and habitat restoration.

Changing Human Behavior

Legislation has been enacted to protect species throughout the world. The legislation includes international treaties as well as
national and state laws. The Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) treaty
came into force in 1975. The treaty, and the national legislation that supports it, provides a legal framework for preventing “listed”
species from being transported across nations’ borders, thus protecting them from being caught or killed in the first place when the
purpose involves international trade. The listed species that are protected to one degree or another by the treaty number some

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33,000. The treaty is limited in its reach because it only deals with international movement of organisms or their parts. It is also
limited by various countries’ ability or willingness to enforce the treaty and supporting legislation. The illegal trade in organisms
and their parts is probably a market in the hundreds of millions of dollars.
Within many countries there are laws that protect endangered species and that regulate hunting and fishing. In the United States,
the Endangered Species Act was enacted in 1973. When an at-risk species is listed by the Act, the U.S. Fish & Wildlife Service is
required by law to develop a management plan to protect the species and bring it back to sustainable numbers. The Act, and others
like it in other countries, is a useful tool, but it suffers because it is often difficult to get a species listed, or to get an effective
management plan in place once a species is listed. Additionally, species may be controversially taken off the list without
necessarily having had a change in their situation. More fundamentally, the approach to protecting individual species rather than
entire ecosystems (although the management plans commonly involve protection of the individual species’ habitat) is both
inefficient and focuses efforts on a few highly visible and often charismatic species, perhaps at the expense of other species that go
unprotected.
The Migratory Bird Treaty Act (MBTA) is an agreement between the United States and Canada that was signed into law in 1918 in
response to declines in North American bird species caused by hunting. The Act now lists over 800 protected species. It makes it
illegal to disturb or kill the protected species or distribute their parts (much of the hunting of birds in the past was for their
feathers). Examples of protected species include northern cardinals, the red-tailed hawk, and the American black vulture.
Global warming is expected to be a major driver of biodiversity loss. Many governments are concerned about the effects of
anthropogenic global warming, primarily on their economies and food resources. Since greenhouse gas emissions do not respect
national boundaries, the effort to curb them is an international one. The international response to global warming has been mixed.
The Kyoto Protocol, an international agreement that came out of the United Nations Framework Convention on Climate Change
that committed countries to reducing greenhouse gas emissions by 2012, was ratified by some countries, but spurned by others.
Two countries that were especially important in terms of their potential impact that did not ratify the Kyoto protocol were the
United States and China. Some goals for reduction in greenhouse gasses were met and exceeded by individual countries, but,
worldwide, the effort to limit greenhouse gas production is not succeeding. The intended replacement for the Kyoto Protocol has
not materialized because governments cannot agree on timelines and benchmarks. Meanwhile, the resulting costs to human
societies and biodiversity predicted by a majority of climate scientists will be high.
As already mentioned, the non-profit, non-governmental sector plays a large role in conservation effort both in North America and
around the world. The approaches range from species-specific organizations to the broadly focused IUCN and Trade Records
Analysis of Flora and Fauna in Commerce (TRAFFIC). The Nature Conservancy takes a novel approach. It purchases land and
protects it in an attempt to set up preserves for ecosystems. Ultimately, human behavior will change when human values change. At
present, the growing urbanization of the human population is a force that mitigates against valuing biodiversity, because many
people no longer come in contact with natural environments and the species that inhabit them.

Conservation in Preserves
Establishment of wildlife and ecosystem preserves is one of the key tools in conservation efforts (Figure [Link]). A preserve is an
area of land set aside with varying degrees of protection for the organisms that exist within the boundaries of the preserve.
Preserves can be effective for protecting both species and ecosystems, but they have some serious drawbacks.

Figure [Link]: National parks, such as Grand Teton National Park in Wyoming, help conserve biodiversity. (credit: Don DeBold)

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A simple measure of success in setting aside preserves for biodiversity protection is to set a target percentage of land or marine
habitat to protect. However, a more detailed preserve design and choice of location is usually necessary because of the way
protected lands are allocated and how biodiversity is distributed: protected lands tend to contain less economically valuable
resources rather than being set aside specifically for the species or ecosystems at risk. In 2003, the IUCN World Parks Congress
estimated that 11.5 percent of Earth’s land surface was covered by preserves of various kinds. This area is greater than previous
goals; however, it only represents 9 out of 14 recognized major biomes and research has shown that 12 percent of all species live
outside preserves; these percentages are much higher when threatened species are considered and when only high quality preserves
are considered. For example, high quality preserves include only about 50 percent of threatened amphibian species. The conclusion
must be that either the percentage of area protected must be increased, the percentage of high quality preserves must be increased,
or preserves must be targeted with greater attention to biodiversity protection. Researchers argue that more attention to the latter
solution is required.
A biodiversity hotspot is a conservation concept developed by Norman Myers in 1988. Hotspots are geographical areas that contain
high numbers of endemic species. The purpose of the concept was to identify important locations on the planet for conservation
efforts, a kind of conservation triage. By protecting hotspots, governments are able to protect a larger number of species. The
original criteria for a hotspot included the presence of 1500 or more species of endemic plants and 70 percent of the area disturbed
by human activity. There are now 34 biodiversity hotspots (Figure [Link]) that contain large numbers of endemic species, which
include half of Earth’s endemic plants.

Figure [Link]: Conservation International has identified 34 biodiversity hotspots. Although these cover only 2.3 percent of the
Earth’s surface, 42 percent of the terrestrial vertebrate species and 50 percent of the world’s plants are endemic to those hotspots.
There has been extensive research into optimal preserve designs for maintaining biodiversity. The fundamental principles behind
much of the research have come from the seminal theoretical work of Robert H. MacArthur and Edward O. Wilson published in
1
1967 on island biogeography. This work sought to understand the factors affecting biodiversity on islands. Conservation preserves
can be seen as “islands” of habitat within “an ocean” of non-habitat. In general, large preserves are better because they support
more species, including species with large home ranges; they have more core area of optimal habitat for individual species; they
have more niches to support more species; and they attract more species because they can be found and reached more easily.
Preserves perform better when there are partially protected buffer zones around them of suboptimal habitat. The buffer allows
organisms to exit the boundaries of the preserve without immediate negative consequences from hunting or lack of resources. One
large preserve is better than the same area of several smaller preserves because there is more core habitat unaffected by less
hospitable ecosystems outside the preserve boundary. For this same reason, preserves in the shape of a square or circle will be
better than a preserve with many thin “arms.” If preserves must be smaller, then providing wildlife corridors between them so that
species and their genes can move between the preserves; for example, preserves along rivers and streams will make the smaller
preserves behave more like a large one. All of these factors are taken into consideration when planning the nature of a preserve
before the land is set aside.

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In addition to the physical specifications of a preserve, there are a variety of regulations related to the use of a preserve. These can
include anything from timber extraction, mineral extraction, regulated hunting, human habitation, and nondestructive human
recreation. Many of the decisions to include these other uses are made based on political pressures rather than conservation
considerations. On the other hand, in some cases, wildlife protection policies have been so strict that subsistence-living indigenous
populations have been forced from ancestral lands that fell within a preserve. In other cases, even if a preserve is designed to
protect wildlife, if the protections are not or cannot be enforced, the preserve status will have little meaning in the face of illegal
poaching and timber extraction. This is a widespread problem with preserves in the tropics.
Some of the limitations on preserves as conservation tools are evident from the discussion of preserve design. Political and
economic pressures typically make preserves smaller, never larger, so setting aside areas that are large enough is difficult.
Enforcement of protections is also a significant issue in countries without the resources or political will to prevent poaching and
illegal resource extraction.
Climate change will create inevitable problems with the location of preserves as the species within them migrate to higher latitudes
as the habitat of the preserve becomes less favorable. Planning for the effects of global warming on future preserves, or adding new
preserves to accommodate the changes expected from global warming is in progress, but will only be as effective as the accuracy of
the predictions of the effects of global warming on future habitats.
Finally, an argument can be made that conservation preserves reinforce the cultural perception that humans are separate from
nature, can exist outside of it, and can only operate in ways that do damage to biodiversity. Creating preserves reduces the pressure
on human activities outside the preserves to be sustainable and non-damaging to biodiversity. Ultimately, the political, economic,
and human demographic pressures will degrade and reduce the size of conservation preserves if the activities outside them are not
altered to be less damaging to biodiversity.

CONCEPT IN ACTION

Check out this interactive global data system of protected areas. Review data about specific protected areas by location or
study statistics on protected areas by country or region.

Habitat Restoration
Habitat restoration holds considerable promise as a mechanism for maintaining or restoring biodiversity. Of course once a species
has become extinct, its restoration is impossible. However, restoration can improve the biodiversity of degraded ecosystems.
Reintroducing wolves, a top predator, to Yellowstone National Park in 1995 led to dramatic changes in the ecosystem that increased
biodiversity. The wolves (Figure [Link]) function to suppress elk and coyote populations and provide more abundant resources to
the guild of carrion eaters. Reducing elk populations has allowed revegetation of riparian (the areas along the banks of a stream or
river) areas, which has increased the diversity of species in that habitat. Suppression of coyotes has increased the species previously
suppressed by this predator. The number of species of carrion eaters has increased because of the predatory activities of the wolves.
In this habitat, the wolf is a keystone species, meaning a species that is instrumental in maintaining diversity within an ecosystem.
Removing a keystone species from an ecological community causes a collapse in diversity. The results from the Yellowstone
experiment suggest that restoring a keystone species effectively can have the effect of restoring biodiversity in the community.
Ecologists have argued for the identification of keystone species where possible and for focusing protection efforts on these
species. It makes sense to return the keystone species to the ecosystems where they have been removed.

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 Figure [Link]: This photograph shows the Gibbon wolf pack in Yellowstone National Park, March 1, 2007. Wolves have been
identified as a keystone species. (credit: Doug Smith, NPS)
Other large-scale restoration experiments underway involve dam removal. In the United States, since the mid-1980s, many aging
dams are being considered for removal rather than replacement because of shifting beliefs about the ecological value of free-
flowing rivers. The measured benefits of dam removal include restoration of naturally fluctuating water levels (often the purpose of
dams is to reduce variation in river flows), which leads to increased fish diversity and improved water quality. In the Pacific
Northwest, dam removal projects are expected to increase populations of salmon, which is considered a keystone species because it
transports nutrients to inland ecosystems during its annual spawning migrations. In other regions, such as the Atlantic coast, dam
removal has allowed the return of other spawning anadromous fish species (species that are born in fresh water, live most of their
lives in salt water, and return to fresh water to spawn). Some of the largest dam removal projects have yet to occur or have
happened too recently for the consequences to be measured. The large-scale ecological experiments that these removal projects
constitute will provide valuable data for other dam projects slated either for removal or construction.

The Role of Zoos and Captive Breeding

Zoos have sought to play a role in conservation efforts both through captive breeding programs and education (Figure [Link]). The
transformation of the missions of zoos from collection and exhibition facilities to organizations that are dedicated to conservation is
ongoing. In general, it has been recognized that, except in some specific targeted cases, captive breeding programs for endangered
species are inefficient and often prone to failure when the species are reintroduced to the wild. Zoo facilities are far too limited to
contemplate captive breeding programs for the numbers of species that are now at risk. Education, on the other hand, is a potential
positive impact of zoos on conservation efforts, particularly given the global trend to urbanization and the consequent reduction in
contacts between people and wildlife. A number of studies have been performed to look at the effectiveness of zoos on people’s
attitudes and actions regarding conservation; at present, the results tend to be mixed.

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 Figure [Link]: Zoos and captive breeding programs help preserve many endangered species, such as this golden lion tamarin.
(credit: Garrett Ziegler)

Summary
Five mass extinctions with losses of more than 50 percent of extant species are observable in the fossil record. Recent extinctions
are recorded in written history and are the basis for one method of estimating contemporary extinction rates. The other method uses
measures of habitat loss and species-area relationships. Estimates of contemporary extinction rates vary but are as high as 500
times the background rate, as determined from the fossil record, and are predicted to rise.
There is a legislative framework for biodiversity protection. International treaties such as CITES regulate the transportation of
endangered species across international borders. Legislation within individual countries protecting species and agreements on
global warming have had limited success; there is at present no international agreement on targets for greenhouse gas emissions. In
the United States, the Endangered Species Act protects listed species but is hampered by procedural difficulties and a focus on
individual species. The Migratory Bird Act is an agreement between Canada and the United States to protect migratory birds. The
non-profit sector is also very active in conservation efforts in a variety of ways.
Conservation preserves are a major tool in biodiversity protection. Presently, 11 percent of Earth’s land surface is protected in some
way. The science of island biogeography has informed the optimal design of preserves; however, preserves have limitations
imposed by political and economic forces. In addition, climate change will limit the effectiveness of present preserves in the future.
A downside of preserves is that they may lessen the pressure on human societies to function more sustainably outside the preserves.
Habitat restoration has the potential to restore ecosystems to previous biodiversity levels before species become extinct. Examples
of restoration include reintroduction of keystone species and removal of dams on rivers. Zoos have attempted to take a more active
role in conservation and can have a limited role in captive breeding programs. Zoos also have a useful role in education.

Footnotes
1. 1 Robert H. MacArthur and Edward O. Wilson, E. O., The Theory of Island Biogeography (Princeton, N.J.: Princeton
University Press, 1967).

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Glossary

biodiversity hotspot
a concept originated by Norman Myers to describe a geographical region with a large number of endemic species and a large
percentage of degraded habitat

extinction rate
the number of species becoming extinct over time, sometimes defined as extinctions per million species–years to make numbers
manageable (E/MSY)

species-area relationship
the relationship between area surveyed and number of species encountered; typically measured by incrementally increasing the
area of a survey and determining the cumulative numbers of species

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 9.3.3: Preserving Biodiversity is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
21.3: Preserving Biodiversity by OpenStax is licensed CC BY 4.0.

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9.3.E: Conservation and Biodiversity (Exercises)
21.1: Importance of Biodiversity
Biodiversity exists at multiple levels of organization, and is measured in different ways depending on the goals of those taking the
measurements. These include numbers of species, genetic diversity, chemical diversity, and ecosystem diversity. The number of
described species is estimated to be 1.5 million with about 17,000 new species being described each year. Estimates for the total
number of eukaryotic species on Earth vary but are on the order of 10 million.

Multiple Choice
The number of currently described species on the planet is about ________.
A. 17,000
B. 150,000
C. 1.5 million
D. 10 million

Answer
C

A secondary plant compound might be used for which of the following?

A. a new crop variety
B. a new drug
C. a soil nutrient
D. a crop pest

Answer
B

Pollination is an example of ________.

A. a possible source of new drugs
B. chemical diversity
C. an ecosystem service
D. crop pest control

Answer
C

Free Response
Explain how biodiversity loss can impact crop diversity.

Answer
Crop plants are derived from wild plants, and genes from wild relatives are frequently brought into crop varieties by plant
breeders to add valued characteristics to the crops. If the wild species are lost, then this genetic variation would no longer be
available.

Describe two types of compounds from living things that are used as medications.

Answer
Secondary plant compounds are toxins produced by plants to kill predators trying to eat them; some of these compounds can be
used as drugs. Animal toxins, such as snake venom, can be used as medicine. (Alternate answer: antibiotics are compounds
produced by bacteria and fungi which can be used to kill bacteria.)

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21.2: Threats to Biodiversity
The core threats to biodiversity are human population growth and unsustainable resource use. To date, the most significant causes
of extinction are habitat loss, introduction of exotic species, and overharvesting. Climate change is predicted to be a significant
cause of extinction in the coming century. Habitat loss occurs through deforestation, damming of rivers, and other activities.
Overharvesting is a threat particularly to aquatic species, but the taking of bush meat in the humid tropics threatens many species in
Asia, Africa, and the Americas.

Multiple Choice
Converting a prairie to a farm field is an example of ________.
A. overharvesting
B. habitat loss
C. exotic species
D. climate change

Answer
B

Which two extinction risks may be a direct result of the pet trade?
A. climate change and exotic species introduction
B. habitat loss and overharvesting
C. overharvesting and exotic species introduction
D. habitat loss and climate change

Answer
C

What kind of ecosystem are exotic species especially threatening to?

A. deserts
B. marine ecosystems
C. islands
D. tropical forests

Answer
C

Free Response
Describe the mechanisms by which human population growth and resource use causes increased extinction rates.

Answer
Human population growth leads to unsustainable resource use, which causes habitat destruction to build new human
settlements, create agricultural fields, and so on. Larger human populations have also led to unsustainable fishing and hunting
of wild animal populations. Excessive use of fossil fuels also leads to global warming.

Explain what extinction threats a frog living on a mountainside in Costa Rica might face.

Answer
The frog is at risk from global warming shifting its preferred habitat up the mountain. In addition, it will be at risk from exotic
species, either as a new predator or through the impact of transmitted diseases such as chytridiomycosis. It is also possible that
habitat destruction will threaten the species.

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21.3: Preserving Biodiversity
Five mass extinctions with losses of more than 50 percent of extant species are observable in the fossil record. Recent extinctions
are recorded in written history and are the basis for one method of estimating contemporary extinction rates. The other method uses
measures of habitat loss and species-area relationships. Estimates of contemporary extinction rates vary but are as high as 500
times the background rate, as determined from the fossil record, and are predicted to rise.

Multiple Choice
Certain species of parrot cannot be brought to the United States to be sold as pets. What is the name of the legislation that makes
this illegal?
A. Red List
B. Migratory Bird Act
C. CITES
D. Endangered Species Act (ESA)

Answer
C

What is the name of the first international agreement on climate change?

A. Red List
B. Montreal Protocol
C. International Union for the Conservation of Nature (IUCN)
D. Kyoto Protocol

Answer
D

Free Response
Describe two considerations in conservation preserve design.

Answer
Larger preserves will contain more species. Preserves should have a buffer around them to protect species from edge effects.
Preserves that are round or square are better than preserves with many thin arms.

Describe what happens to an ecosystem when a keystone species is removed.

Answer
Many species will disappear from the ecosystem when a keystone species is removed.

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OpenStax.
21.E: Conservation and Biodiversity (Exercises) by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 9.3.E.3 [Link]

 CHAPTER OVERVIEW

10: Energy and Enzymes

10.1: Free and Activation Energy
10.2: Enzymes
10.3: ATP in Living Systems

Thumbnail: Glucosidase enzyme. (CC BY-SA 4.0; Thomas Shafee via Wikimedia Commons).

10: Energy and Enzymes is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.

1
10.1: Free and Activation Energy
After learning that chemical reactions release energy when energy-storing bonds are broken, an important next question is the
following: How is the energy associated with these chemical reactions quantified and expressed? How can the energy released from
one reaction be compared to that of another reaction? A measurement of free energy is used to quantify these energy transfers.
Recall that according to the second law of thermodynamics, all energy transfers involve the loss of some amount of energy in an
unusable form such as heat. Free energy specifically refers to the energy associated with a chemical reaction that is available after
the losses are accounted for. In other words, free energy is usable energy, or energy that is available to do work. Looking at this
concept in a biological sense, free energy is the energy within a molecule that can be used to perform work. Glucose has a lot of
free energy because there is a lot of energy stored within the bonds of the glucose molecule. Carbon dioxide has a much lower free
energy because there is much less energy stored in its bonds.
If energy is released during a chemical reaction, then the change in free energy from the conversion of the reactants to the products,
signified as ΔG (delta G) will be a negative number. A negative change in free energy also means that the products of the reaction
have less free energy than the reactants, because they release some free energy during the reaction. Reactions that have a negative
change in free energy and consequently release free energy are called exergonic reactions. Think: exergonic means energy is
exiting the system. These reactions are also referred to as spontaneous reactions, and their products have less stored energy than the
reactants. An important distinction must be drawn between the term spontaneous and the idea of a chemical reaction occurring
immediately. Contrary to the everyday use of the term, a spontaneous reaction is not one that suddenly or quickly occurs. The
rusting of iron is an example of a spontaneous reaction that occurs slowly, little by little, over time.

Figure 10.1.1: Free energy of endergonic and exergonic reactions. In an exergonic reaction, the reactants have more free energy
than the products. Therefore, energy is released as the reaction proceeds. In an endergonic reaction, the reactants have more less
energy than the products. Therefore, energy must be added to make the reaction move take place.
If a chemical reaction absorbs energy rather than releases energy on balance, then the ΔG for that reaction will be a positive value.
In this case, the products have more free energy than the reactants. Thus, the products of these reactions can be thought of as
energy-storing molecules. These chemical reactions are called endergonic reactions and they are nonspontaneous.
An endergonic reaction will not take place on its own without the addition of free energy.

10.1.1 [Link]
 Figure 10.1.2: Shown are some examples of endergonic processes (ones that require energy) and exergonic processes (ones that
release energy). (credit a: modification of work by Natalie Maynor; credit b: modification of work by USDA; credit c: modification
of work by Cory Zanker; credit d: modification of work by Harry Malsch)
There is another important concept that must be considered regarding endergonic and exergonic reactions. Exergonic reactions
require a small amount of energy input to get going, before they can proceed with their energy-releasing steps.
These reactions have a net release of energy, but still require some energy input in the beginning. This small amount of energy
input necessary for all chemical reactions to occur is called the activation energy (Figure 10.1.3 ).

Figure 10.1.3: Activation energy is the small amount of energy that must be put into a system in order for the reaction to take
place. Photo credit Brazosport College; Wikimedia.

References
Unless otherwise noted, images on this page are licensed under CC-BY 4.0 by OpenStax.
Text adapted from: OpenStax, Concepts of Biology. OpenStax CNX. May 18, 2016 [Link]
839...9a8aafbdd@9.10

10.1: Free and Activation Energy is shared under a CC BY license and was authored, remixed, and/or curated by LibreTexts.

10.1.2 [Link]
10.2: Enzymes
A substance that helps a chemical reaction to occur is called a catalyst, and the molecules that catalyze biochemical reactions are
called enzymes. Most enzymes are proteins and perform the critical task of lowering the activation energies of chemical reactions
inside the cell. Most of the reactions critical to a living cell happen too slowly at normal temperatures to be of any use to the cell.
Without enzymes to speed up these reactions, life could not persist. Enzymes do this by binding to the reactant molecules and
holding them in such a way as to make the chemical bond-breaking and -forming processes take place more easily. It is important
to remember that enzymes do not change whether a reaction is exergonic (spontaneous) or endergonic. This is because they do not
change the free energy of the reactants or products. They only reduce the activation energy required for the reaction to go forward
(Figure 10.2.1 ). In addition, an enzyme itself is unchanged by the reaction it catalyzes. Once one reaction has been catalyzed, the
enzyme is able to participate in other reactions.

Figure 10.2.1: Enzymes lower the activation energy of the reaction but do not change the free energy of the reaction.
The chemical reactants to which an enzyme binds are called the enzyme’s substrates. There may be one or more substrates,
depending on the particular chemical reaction. In some reactions, a single reactant substrate is broken down into multiple products.
In others, two substrates may come together to create one larger molecule. Two reactants might also enter a reaction and both
become modified, but they leave the reaction as two products. The location within the enzyme where the substrate binds is called
the enzyme’s active site. The active site is where the “action” happens. Since enzymes are proteins, there is a unique combination
of amino acid side chains within the active site. Each side chain is characterized by different properties. They can be large or small,
weakly acidic or basic, hydrophilic or hydrophobic, positively or negatively charged, or neutral. The unique combination of side
chains creates a very specific chemical environment within the active site. This specific environment is suited to bind to one
specific chemical substrate (or substrates).
Active sites are subject to influences of the local environment. Increasing the environmental temperature generally increases
reaction rates, enzyme-catalyzed or otherwise. However, temperatures outside of an optimal range reduce the rate at which an
enzyme catalyzes a reaction. Hot temperatures will eventually cause enzymes to denature, an irreversible change in the three-
dimensional shape and therefore the function of the enzyme (Figure 10.2.2 ). Enzymes are also suited to function best within a
certain pH and salt concentration range, and, as with temperature, extreme pH and salt concentrations can cause enzymes to
denature.

10.2.1 [Link]
 Figure 10.2.2: Heat applied to an egg during cooking irreversibly denatures the proteins. (credit: “K-Wall”/Flickr)
Typically, enzymes function optimally in the environment where they are typically found and used. For example, the enzyme
amylase is found in saliva, where it functions to break down starch (a polysaccharide – carbohydrate chain) into smaller sugars.
Note that in this example, amylase is the enzyme, starch is the substrate, and smaller sugars are the product. The pH of saliva is
typically between 6.2 and 7.6, with roughly 6.7 being the average. The optimum pH of amylase is between 6.7 and 7.0, which is
close to neutral (Figure 10.2.3 ). The optimum temperature for amylase is close to 37ºC (which is human body temperature).

Figure 10.2.3: The effect of pH and temperature on the activity of an enzyme. Amylase is shown in blue in both graphs. (top)
Amylase (blue) has an optimum pH of about 7. The green enzyme, which has an optimum pH of about 2.3, might function in the
stomach where it is very acidic. (bottom) Amylase (blue) has an optimum temperature of about 37 degrees C. The orange enzyme,
which has an optimum temperature of about 15 degrees C (about 60F) might function in a plant found outdoors.
For many years, scientists thought that enzyme-substrate binding took place in a simple “lock and key” fashion. This model
asserted that the enzyme and substrate fit together perfectly in one instantaneous step. However, current research supports a model
called induced fit (Figure 10.2.4 ). The induced-fit model expands on the lock-and-key model by describing a more dynamic
binding between enzyme and substrate. As the enzyme and substrate come together, their interaction causes a mild shift in the
enzyme’s structure that forms an ideal binding arrangement between enzyme and substrate.
When an enzyme binds its substrate, an enzyme-substrate complex is formed. This complex lowers the activation energy of the
reaction and promotes its rapid progression in one of multiple possible ways.
On a basic level, enzymes promote chemical reactions that involve more than one substrate by bringing the substrates together
in an optimal orientation for reaction.
Enzymes promote the reaction of their substrates by creating an optimal environment within the active site for the reaction to
occur. The chemical properties that emerge from the particular arrangement of amino acid R groups (side chains) within an
active site create the perfect environment for an enzyme’s specific substrates to react.
The enzyme-substrate complex can also lower activation energy by compromising the bond structure so that it is easier to break.

10.2.2 [Link]
 Finally, enzymes can also lower activation energies by taking part in the chemical reaction itself. In these cases, it is important
to remember that the enzyme will always return to its original state by the completion of the reaction.
One of the hallmark properties of enzymes is that they remain ultimately unchanged by the reactions they catalyze. After an
enzyme has catalyzed a reaction, it releases its product(s) and can catalyze a new reaction.

Figure 10.2.4: The induced-fit model is an adjustment to the lock-and-key model and explains how enzymes and substrates
undergo dynamic modifications during the transition state to increase the affinity of the substrate for the active site.
It would seem ideal to have a scenario in which all of an organism’s enzymes existed in abundant supply and functioned optimally
under all cellular conditions, in all cells, at all times. However, a variety of mechanisms ensures that this does not happen. Cellular
needs and conditions constantly vary from cell to cell, and change within individual cells over time. The required enzymes of
stomach cells differ from those of fat storage cells, skin cells, blood cells, and nerve cells. Furthermore, a digestive organ cell
works much harder to process and break down nutrients during the time that closely follows a meal compared with many hours
after a meal. As these cellular demands and conditions vary, so must the amounts and functionality of different enzymes.
Since the rates of biochemical reactions are controlled by activation energy, and enzymes lower and determine activation energies
for chemical reactions, the relative amounts and functioning of the variety of enzymes within a cell ultimately determine which
reactions will proceed and at what rates. This determination is tightly controlled in cells. In certain cellular environments, enzyme
activity is partly controlled by environmental factors like pH, temperature, salt concentration, and, in some cases, cofactors or
coenzymes.
Enzymes can also be regulated in ways that either promote or reduce enzyme activity. There are many kinds of molecules that
inhibit or promote enzyme function, and various mechanisms by which they do so. In some cases of enzyme inhibition, an inhibitor
molecule is similar enough to a substrate that it can bind to the active site and simply block the substrate from binding. When this
happens, the enzyme is inhibited through competitive inhibition, because an inhibitor molecule competes with the substrate for
binding to the active site.
On the other hand, in noncompetitive inhibition, an inhibitor molecule binds to the enzyme in a location other than the active site,
called an allosteric site, but still manages to block substrate binding to the active site. Some inhibitor molecules bind to enzymes in
a location where their binding induces a conformational change that reduces the affinity of the enzyme for its substrate. This type
of inhibition is called allosteric inhibition (Figure 10.2.5 ). Most allosterically regulated enzymes are made up of more than one
polypeptide, meaning that they have more than one protein subunit. When an allosteric inhibitor binds to a region on an enzyme, all
active sites on the protein subunits are changed slightly such that they bind their substrates with less efficiency. There are allosteric
activators as well as inhibitors. Allosteric activators bind to locations on an enzyme away from the active site, inducing a
conformational change that increases the affinity of the enzyme’s active site(s) for its substrate(s) (Figure 10.2.5 ).

10.2.3 [Link]
 Figure 10.2.5: Allosteric inhibition works by indirectly inducing a conformational change to the active site such that the substrate
no longer fits. In contrast, in allosteric activation, the activator molecule modifies the shape of the active site to allow a better fit of
the substrate.
Many enzymes do not work optimally, or even at all, unless bound to other specific non-protein helper molecules. They may bond
either temporarily through ionic or hydrogen bonds, or permanently through stronger covalent bonds. Binding to these molecules
promotes optimal shape and function of their respective enzymes. Two examples of these types of helper molecules are cofactors
and coenzymes. Cofactors are inorganic ions such as ions of iron and magnesium. Coenzymes are organic helper molecules, those
with a basic atomic structure made up of carbon and hydrogen. Like enzymes, these molecules participate in reactions without
being changed themselves and are ultimately recycled and reused. Vitamins are the source of coenzymes. Some vitamins are the
precursors of coenzymes and others act directly as coenzymes. Vitamin C is a direct coenzyme for multiple enzymes that take part
in building the important connective tissue, collagen. Therefore, enzyme function is, in part, regulated by the abundance of various
cofactors and coenzymes, which may be supplied by an organism’s diet or, in some cases, produced by the organism.

References
Unless otherwise noted, images on this page are licensed under CC-BY 4.0 by OpenStax.
Text adapted from: OpenStax, Concepts of Biology. OpenStax CNX. May 18, 2016 [Link]
839...9a8aafbdd@9.10

10.2: Enzymes is shared under a CC BY license and was authored, remixed, and/or curated by LibreTexts.

10.2.4 [Link]
10.3: ATP in Living Systems
A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell,
which would denature enzymes and other proteins, and thus destroy the cell. Rather, a cell must be able to store energy safely and
release it for use only as needed. Living cells accomplish this using ATP, which can be used to fill any energy need of the cell.
How? It functions as a rechargeable battery.
When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. This energy is used to do
work by the cell, usually by the binding of the released phosphate to another molecule, thus activating it. For example, in the
mechanical work of muscle contraction, ATP supplies energy to move the contractile muscle proteins.

ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to both
a ribose molecule and a single phosphate group (Figure 10.3.1). Ribose is a five-carbon sugar found in RNA and AMP is one of
the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in adenosine diphosphate (ADP);
the addition of a third phosphate group forms adenosine triphosphate (ATP).

Figure 10.3.1: The structure of ATP shows the basic components of a two-ring adenine, five-carbon ribose, and three phosphate
groups.
The addition of a phosphate group to a molecule requires a high amount of energy and results in a high-energy bond. Phosphate
groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This
repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process
called hydrolysis, releases energy.

10.3: ATP in Living Systems is shared under a not declared license and was authored, remixed, and/or curated by LibreTexts.
4.2: Glycolysis by OpenStax is licensed CC BY 4.0.

10.3.1 [Link]
 CHAPTER OVERVIEW

11: Photosynthesis
11.1: Photosynthesis
11.1.1: Overview of Photosynthesis
11.1.2: The Light-Dependent Reactions of Photosynthesis
11.1.3: The Calvin Cycle
11.1.E: Photosynthesis (Exercises)

Thumbnail: Green leaf. (Photo by Anthony Lee on Unsplash).

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11.1 [Link]
 SECTION OVERVIEW

11.1: Photosynthesis
The energy that is harnessed from photosynthesis enters the ecosystems of our planet continuously and is transferred from one
organism to another. Therefore, directly or indirectly, the process of photosynthesis provides most of the energy required by living
things on earth. Photosynthesis also results in the release of oxygen into the atmosphere. In short, to eat and breathe, humans
depend almost entirely on the organisms that carry out photosynthesis.

11.1.1: Overview of Photosynthesis

11.1.2: The Light-Dependent Reactions of Photosynthesis

11.1.3: The Calvin Cycle

11.1.E: Photosynthesis (Exercises)

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11.1.1: Overview of Photosynthesis
All living organisms on earth consist of one or more cells. Each cell runs on the chemical energy found mainly in carbohydrate
molecules (food), and the majority of these molecules are produced by one process: photosynthesis. Through photosynthesis,
certain organisms convert solar energy (sunlight) into chemical energy, which is then used to build carbohydrate molecules. The
energy used to hold these molecules together is released when an organism breaks down food. Cells then use this energy to perform
work, such as cellular respiration.
The energy that is harnessed from photosynthesis enters the ecosystems of our planet continuously and is transferred from one
organism to another. Therefore, directly or indirectly, the process of photosynthesis provides most of the energy required by living
things on earth. Photosynthesis also results in the release of oxygen into the atmosphere. In short, to eat and breathe, humans
depend almost entirely on the organisms that carry out photosynthesis.

CONCEPT IN ACTION
Click the following link to learn more about photosynthesis.

Solar Dependence and Food Production

Some organisms can carry out photosynthesis, whereas others cannot. An autotroph is an organism that can produce its own food.
The Greek roots of the word autotroph mean “self” (auto) “feeder” (troph). Plants are the best-known autotrophs, but others exist,
including certain types of bacteria and algae (Figure [Link]). Oceanic algae contribute enormous quantities of food and oxygen to
global food chains. Plants are also photoautotrophs, a type of autotroph that uses sunlight and carbon from carbon dioxide to
synthesize chemical energy in the form of carbohydrates. All organisms carrying out photosynthesis require sunlight.

Figure [Link]: (a) Plants, (b) algae, and (c) certain bacteria, called cyanobacteria, are photoautotrophs that can carry out
photosynthesis. Algae can grow over enormous areas in water, at times completely covering the surface. (credit a: Steve Hillebrand,
U.S. Fish and Wildlife Service; credit b: "eutrophication&hypoxia"/Flickr; credit c: NASA; scale-bar data from Matt Russell)
Heterotrophs are organisms incapable of photosynthesis that must therefore obtain energy and carbon from food by consuming
other organisms. The Greek roots of the word heterotroph mean “other” (hetero) “feeder” (troph), meaning that their food comes
from other organisms. Even if the food organism is another animal, this food traces its origins back to autotrophs and the process of
photosynthesis. Humans are heterotrophs, as are all animals. Heterotrophs depend on autotrophs, either directly or indirectly. Deer
and wolves are heterotrophs. A deer obtains energy by eating plants. A wolf eating a deer obtains energy that originally came from
the plants eaten by that deer. The energy in the plant came from photosynthesis, and therefore it is the only autotroph in this
example (Figure [Link]). Using this reasoning, all food eaten by humans also links back to autotrophs that carry out
photosynthesis.

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 Figure [Link]: The energy stored in carbohydrate molecules from photosynthesis passes through the food chain. The predator
that eats these deer is getting energy that originated in the photosynthetic vegetation that the deer consumed. (credit: Steve
VanRiper, U.S. Fish and Wildlife Service)

BIOLOGY IN ACTION: Photosynthesis at the Grocery Store

Major grocery stores in the United States are organized into departments, such as dairy, meats, produce, bread, cereals, and so
forth. Each aisle contains hundreds, if not thousands, of different products for customers to buy and consume (Figure
[Link]).

Figure [Link]: Photosynthesis is the origin of the products that comprise the main elements of the human diet. (credit:
Associação Brasileira de Supermercados)
Although there is a large variety, each item links back to photosynthesis. Meats and dairy products link to photosynthesis
because the animals were fed plant-based foods. The breads, cereals, and pastas come largely from grains, which are the seeds
of photosynthetic plants. What about desserts and drinks? All of these products contain sugar—the basic carbohydrate
molecule produced directly from photosynthesis. The photosynthesis connection applies to every meal and every food a person
consumes.

Main Structures and Summary of Photosynthesis

Photosynthesis requires sunlight, carbon dioxide, and water as starting reactants (Figure [Link]). After the process is complete,
photosynthesis releases oxygen and produces carbohydrate molecules, most commonly glucose. These sugar molecules contain the
energy that living things need to survive.

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 Figure [Link]: Photosynthesis uses solar energy, carbon dioxide, and water to release oxygen and to produce energy-storing
sugar molecules.
The complex reactions of photosynthesis can be summarized by the chemical equation shown in Figure [Link].

Figure [Link]: The process of photosynthesis can be represented by an equation, wherein carbon dioxide and water produce
sugar and oxygen using energy from sunlight.
Although the equation looks simple, the many steps that take place during photosynthesis are actually quite complex, as in the way
that the reaction summarizing cellular respiration represented many individual reactions. Before learning the details of how
photoautotrophs turn sunlight into food, it is important to become familiar with the physical structures involved.
In plants, photosynthesis takes place primarily in leaves, which consist of many layers of cells and have differentiated top and
bottom sides. The process of photosynthesis occurs not on the surface layers of the leaf, but rather in a middle layer called the
mesophyll (Figure [Link]). The gas exchange of carbon dioxide and oxygen occurs through small, regulated openings called
stomata.
In all autotrophic eukaryotes, photosynthesis takes place inside an organelle called a chloroplast. In plants, chloroplast-containing
cells exist in the mesophyll. Chloroplasts have a double (inner and outer) membrane. Within the chloroplast is a third membrane
that forms stacked, disc-shaped structures called thylakoids. Embedded in the thylakoid membrane are molecules of chlorophyll, a
pigment (a molecule that absorbs light) through which the entire process of photosynthesis begins. Chlorophyll is responsible for
the green color of plants. The thylakoid membrane encloses an internal space called the thylakoid space. Other types of pigments
are also involved in photosynthesis, but chlorophyll is by far the most important. As shown in Figure [Link], a stack of

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thylakoids is called a granum, and the space surrounding the granum is called stroma (not to be confused with stomata, the
openings on the leaves).

ART CONNECTION

Figure [Link]: Not all cells of a leaf carry out photosynthesis. Cells within the middle layer of a leaf have chloroplasts,
which contain the photosynthetic apparatus. (credit "leaf": modification of work by Cory Zanker)
On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

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The Two Parts of Photosynthesis
Photosynthesis takes place in two stages: the light-dependent reactions and the Calvin cycle. In the light-dependent reactions,
which take place at the thylakoid membrane, chlorophyll absorbs energy from sunlight and then converts it into chemical energy
with the use of water. The light-dependent reactions release oxygen from the hydrolysis of water as a byproduct. In the Calvin
cycle, which takes place in the stroma, the chemical energy derived from the light-dependent reactions drives both the capture of
carbon in carbon dioxide molecules and the subsequent assembly of sugar molecules. The two reactions use carrier molecules to
transport the energy from one to the other. The carriers that move energy from the light-dependent reactions to the Calvin cycle
reactions can be thought of as “full” because they bring energy. After the energy is released, the “empty” energy carriers return to
the light-dependent reactions to obtain more energy.

Summary
The process of photosynthesis transformed life on earth. By harnessing energy from the sun, photosynthesis allowed living things
to access enormous amounts of energy. Because of photosynthesis, living things gained access to sufficient energy, allowing them
to evolve new structures and achieve the biodiversity that is evident today.
Only certain organisms, called autotrophs, can perform photosynthesis; they require the presence of chlorophyll, a specialized
pigment that can absorb light and convert light energy into chemical energy. Photosynthesis uses carbon dioxide and water to
assemble carbohydrate molecules (usually glucose) and releases oxygen into the air. Eukaryotic autotrophs, such as plants and
algae, have organelles called chloroplasts in which photosynthesis takes place.

Art Connections
Figure [Link]: On a hot, dry day, plants close their stomata to conserve water. What impact will this have on photosynthesis?

Answer
Levels of carbon dioxide (a reactant) will fall, and levels of oxygen (a product) will rise. As a result, the rate of photosynthesis
will slow down.

Glossary
autotroph
an organism capable of producing its own food

chlorophyll
the green pigment that captures the light energy that drives the reactions of photosynthesis

chloroplast
the organelle where photosynthesis takes place

granum
a stack of thylakoids located inside a chloroplast

heterotroph
an organism that consumes other organisms for food

light-dependent reaction
the first stage of photosynthesis where visible light is absorbed to form two energy-carrying molecules (ATP and NADPH)

mesophyll
the middle layer of cells in a leaf

photoautotroph
an organism capable of synthesizing its own food molecules (storing energy), using the energy of light

pigment

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 a molecule that is capable of absorbing light energy

stoma
the opening that regulates gas exchange and water regulation between leaves and the environment; plural: stomata

stroma
the fluid-filled space surrounding the grana inside a chloroplast where the Calvin cycle reactions of photosynthesis take place

thylakoid
a disc-shaped membranous structure inside a chloroplast where the light-dependent reactions of photosynthesis take place using
chlorophyll embedded in the membranes

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 11.1.1: Overview of Photosynthesis is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
5.1: Overview of Photosynthesis by OpenStax is licensed CC BY 4.0.

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11.1.2: The Light-Dependent Reactions of Photosynthesis
How can light be used to make food? It is easy to think of light as something that exists and allows living organisms, such as
humans, to see, but light is a form of energy. Like all energy, light can travel, change form, and be harnessed to do work. In the case
of photosynthesis, light energy is transformed into chemical energy, which autotrophs use to build carbohydrate molecules.
However, autotrophs only use a specific component of sunlight (Figure [Link]).

Figure [Link]: Autotrophs can capture light energy from the sun, converting it into chemical energy used to build food
molecules. (credit: modification of work by Gerry Atwell, U.S. Fish and Wildlife Service)

CONCEPT IN ACTION

Photosynthesis

Watch the process of photosynthesis within a leaf in this video.

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What Is Light Energy?
The sun emits an enormous amount of electromagnetic radiation (solar energy). Humans can see only a fraction of this energy,
which is referred to as “visible light.” The manner in which solar energy travels can be described and measured as waves. Scientists
can determine the amount of energy of a wave by measuring its wavelength, the distance between two consecutive, similar points
in a series of waves, such as from crest to crest or trough to trough (Figure [Link]).

Figure [Link]: The wavelength of a single wave is the distance between two consecutive points along the wave.
Visible light constitutes only one of many types of electromagnetic radiation emitted from the sun. The electromagnetic spectrum is
the range of all possible wavelengths of radiation (Figure [Link]). Each wavelength corresponds to a different amount of energy
carried.

Figure [Link]: The sun emits energy in the form of electromagnetic radiation. This radiation exists in different wavelengths,
each of which has its own characteristic energy. Visible light is one type of energy emitted from the sun.
Each type of electromagnetic radiation has a characteristic range of wavelengths. The longer the wavelength (or the more stretched
out it appears), the less energy is carried. Short, tight waves carry the most energy. This may seem illogical, but think of it in terms
of a piece of moving rope. It takes little effort by a person to move a rope in long, wide waves. To make a rope move in short, tight
waves, a person would need to apply significantly more energy.
The sun emits (Figure [Link]) a broad range of electromagnetic radiation, including X-rays and ultraviolet (UV) rays. The
higher-energy waves are dangerous to living things; for example, X-rays and UV rays can be harmful to humans.

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Absorption of Light
Light energy enters the process of photosynthesis when pigments absorb the light. In plants, pigment molecules absorb only visible
light for photosynthesis. The visible light seen by humans as white light actually exists in a rainbow of colors. Certain objects, such
as a prism or a drop of water, disperse white light to reveal these colors to the human eye. The visible light portion of the
electromagnetic spectrum is perceived by the human eye as a rainbow of colors, with violet and blue having shorter wavelengths
and, therefore, higher energy. At the other end of the spectrum toward red, the wavelengths are longer and have lower energy.

Understanding Pigments
Different kinds of pigments exist, and each absorbs only certain wavelengths (colors) of visible light. Pigments reflect the color of
the wavelengths that they cannot absorb.
All photosynthetic organisms contain a pigment called chlorophyll a, which humans see as the common green color associated with
plants. Chlorophyll a absorbs wavelengths from either end of the visible spectrum (blue and red), but not from green. Because
green is reflected, chlorophyll appears green.
Other pigment types include chlorophyll b (which absorbs blue and red-orange light) and the carotenoids. Each type of pigment can
be identified by the specific pattern of wavelengths it absorbs from visible light, which is its absorption spectrum.
Many photosynthetic organisms have a mixture of pigments; between them, the organism can absorb energy from a wider range of
visible-light wavelengths. Not all photosynthetic organisms have full access to sunlight. Some organisms grow underwater where
light intensity decreases with depth, and certain wavelengths are absorbed by the water. Other organisms grow in competition for
light. Plants on the rainforest floor must be able to absorb any bit of light that comes through, because the taller trees block most of
the sunlight (Figure [Link]).

Figure [Link]: Plants that commonly grow in the shade benefit from having a variety of light-absorbing pigments. Each
pigment can absorb different wavelengths of light, which allows the plant to absorb any light that passes through the taller trees.
(credit: Jason Hollinger)

How Light-Dependent Reactions Work

The overall purpose of the light-dependent reactions is to convert light energy into chemical energy. This chemical energy will be
used by the Calvin cycle to fuel the assembly of sugar molecules.
The light-dependent reactions begin in a grouping of pigment molecules and proteins called a photosystem. Photosystems exist in
the membranes of thylakoids. A pigment molecule in the photosystem absorbs one photon, a quantity or “packet” of light energy, at
a time.
A photon of light energy travels until it reaches a molecule of chlorophyll. The photon causes an electron in the chlorophyll to
become “excited.” The energy given to the electron allows it to break free from an atom of the chlorophyll molecule. Chlorophyll
is therefore said to “donate” an electron (Figure [Link]).
To replace the electron in the chlorophyll, a molecule of water is split. This splitting releases an electron and results in the
formation of oxygen (O2) and hydrogen ions (H+) in the thylakoid space. Technically, each breaking of a water molecule releases a
pair of electrons, and therefore can replace two donated electrons.

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 Figure [Link]: Light energy is absorbed by a chlorophyll molecule and is passed along a pathway to other chlorophyll
molecules. The energy culminates in a molecule of chlorophyll found in the reaction center. The energy “excites” one of its
electrons enough to leave the molecule and be transferred to a nearby primary electron acceptor. A molecule of water splits to
release an electron, which is needed to replace the one donated. Oxygen and hydrogen ions are also formed from the splitting of
water.

The replacing of the electron enables chlorophyll to respond to another photon. The oxygen molecules produced as byproducts find
their way to the surrounding environment. The hydrogen ions play critical roles in the remainder of the light-dependent reactions.
Keep in mind that the purpose of the light-dependent reactions is to convert solar energy into chemical carriers that will be used in
the Calvin cycle. In eukaryotes and some prokaryotes, two photosystems exist. The first is called photosystem II, which was named
for the order of its discovery rather than for the order of the function.
After the photon hits, photosystem II transfers the free electron to the first in a series of proteins inside the thylakoid membrane
called the electron transport chain. As the electron passes along these proteins, energy from the electron fuels membrane pumps
that actively move hydrogen ions against their concentration gradient from the stroma into the thylakoid space. This is quite
analogous to the process that occurs in the mitochondrion in which an electron transport chain pumps hydrogen ions from the
mitochondrial stroma across the inner membrane and into the intermembrane space, creating an electrochemical gradient. After the
energy is used, the electron is accepted by a pigment molecule in the next photosystem, which is called photosystem I (Figure
[Link]).

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 Figure [Link]: From photosystem II, the electron travels along a series of proteins. This electron transport system uses the
energy from the electron to pump hydrogen ions into the interior of the thylakoid. A pigment molecule in photosystem I accepts the
electron.

Generating an Energy Carrier: ATP

In the light-dependent reactions, energy absorbed by sunlight is stored by two types of energy-carrier molecules: ATP and NADPH.
The energy that these molecules carry is stored in a bond that holds a single atom to the molecule. For ATP, it is a phosphate atom,
and for NADPH, it is a hydrogen atom. Recall that NADH was a similar molecule that carried energy in the mitochondrion from
the citric acid cycle to the electron transport chain. When these molecules release energy into the Calvin cycle, they each lose
atoms to become the lower-energy molecules ADP and NADP+.
The buildup of hydrogen ions in the thylakoid space forms an electrochemical gradient because of the difference in the
concentration of protons (H+) and the difference in the charge across the membrane that they create. This potential energy is
harvested and stored as chemical energy in ATP through chemiosmosis, the movement of hydrogen ions down their
electrochemical gradient through the transmembrane enzyme ATP synthase, just as in the mitochondrion.
The hydrogen ions are allowed to pass through the thylakoid membrane through an embedded protein complex called ATP
synthase. This same protein generated ATP from ADP in the mitochondrion. The energy generated by the hydrogen ion stream
allows ATP synthase to attach a third phosphate to ADP, which forms a molecule of ATP in a process called photophosphorylation.
The flow of hydrogen ions through ATP synthase is called chemiosmosis, because the ions move from an area of high to low
concentration through a semi-permeable structure.

Generating Another Energy Carrier: NADPH

The remaining function of the light-dependent reaction is to generate the other energy-carrier molecule, NADPH. As the electron
from the electron transport chain arrives at photosystem I, it is re-energized with another photon captured by chlorophyll. The
energy from this electron drives the formation of NADPH from NADP+ and a hydrogen ion (H+). Now that the solar energy is
stored in energy carriers, it can be used to make a sugar molecule.

Summary
In the first part of photosynthesis, the light-dependent reaction, pigment molecules absorb energy from sunlight. The most common
and abundant pigment is chlorophyll a. A photon strikes photosystem II to initiate photosynthesis. Energy travels through the
electron transport chain, which pumps hydrogen ions into the thylakoid space. This forms an electrochemical gradient. The ions
flow through ATP synthase from the thylakoid space into the stroma in a process called chemiosmosis to form molecules of ATP,
which are used for the formation of sugar molecules in the second stage of photosynthesis. Photosystem I absorbs a second photon,
which results in the formation of an NADPH molecule, another energy carrier for the Calvin cycle reactions.

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Glossary

absorption spectrum
the specific pattern of absorption for a substance that absorbs electromagnetic radiation

chlorophyll a
the form of chlorophyll that absorbs violet-blue and red light

chlorophyll b
the form of chlorophyll that absorbs blue and red-orange light

electromagnetic spectrum
the range of all possible frequencies of radiation

photon
a distinct quantity or “packet” of light energy

photosystem
a group of proteins, chlorophyll, and other pigments that are used in the light-dependent reactions of photosynthesis to absorb
light energy and convert it into chemical energy

wavelength
the distance between consecutive points of a wave

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 11.1.2: The Light-Dependent Reactions of Photosynthesis is shared under a CC BY license and was authored, remixed, and/or
curated by OpenStax.
5.2: The Light-Dependent Reactions of Photosynthesis by OpenStax is licensed CC BY 4.0.

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11.1.3: The Calvin Cycle
After the energy from the sun is converted and packaged into ATP and NADPH, the cell has the fuel needed to build food in the
form of carbohydrate molecules. The carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon
come from? The carbon atoms used to build carbohydrate molecules come from carbon dioxide, the gas that animals exhale with
each breath. The Calvin cycle is the term used for the reactions of photosynthesis that use the energy stored by the light-dependent
reactions to form glucose and other carbohydrate molecules.

The Interworkings of the Calvin Cycle

In plants, carbon dioxide (CO2) enters the chloroplast through the stomata and diffuses into the stroma of the chloroplast—the site
of the Calvin cycle reactions where sugar is synthesized. The reactions are named after the scientist who discovered them, and
reference the fact that the reactions function as a cycle. Others call it the Calvin-Benson cycle to include the name of another
scientist involved in its discovery (Figure [Link]).

Figure [Link]: Light-dependent reactions harness energy from the sun to produce ATP and NADPH. These energy-carrying
molecules travel into the stroma where the Calvin cycle reactions take place.
The Calvin cycle reactions (Figure [Link]) can be organized into three basic stages: fixation, reduction, and regeneration. In the
stroma, in addition to CO2, two other chemicals are present to initiate the Calvin cycle: an enzyme abbreviated RuBisCO, and the
molecule ribulose bisphosphate (RuBP). RuBP has five atoms of carbon and a phosphate group on each end.
RuBisCO catalyzes a reaction between CO2 and RuBP, which forms a six-carbon compound that is immediately converted into two
three-carbon compounds. This process is called carbon fixation, because CO2 is “fixed” from its inorganic form into organic
molecules.
ATP and NADPH use their stored energy to convert the three-carbon compound, 3-PGA, into another three-carbon compound
called G3P. This type of reaction is called a reduction reaction, because it involves the gain of electrons. A reduction is the gain of
an electron by an atom or molecule. The molecules of ADP and NAD+, resulting from the reduction reaction, return to the light-
dependent reactions to be re-energized.

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One of the G3P molecules leaves the Calvin cycle to contribute to the formation of the carbohydrate molecule, which is commonly
glucose (C6H12O6). Because the carbohydrate molecule has six carbon atoms, it takes six turns of the Calvin cycle to make one
carbohydrate molecule (one for each carbon dioxide molecule fixed). The remaining G3P molecules regenerate RuBP, which
enables the system to prepare for the carbon-fixation step. ATP is also used in the regeneration of RuBP.

Figure [Link]: The Calvin cycle has three stages. In stage 1, the enzyme RuBisCO incorporates carbon dioxide into an organic
molecule. In stage 2, the organic molecule is reduced. In stage 3, RuBP, the molecule that starts the cycle, is regenerated so that the
cycle can continue.
In summary, it takes six turns of the Calvin cycle to fix six carbon atoms from CO2. These six turns require energy input from 12
ATP molecules and 12 NADPH molecules in the reduction step and 6 ATP molecules in the regeneration step.

CONCEPT IN ACTION
The following is a link to an animation of the Calvin cycle. Click Stage 1, Stage 2, and then Stage 3 to see G3P and ATP
regenerate to form RuBP.

EVOLUTION IN ACTION: Photosynthesis

The shared evolutionary history of all photosynthetic organisms is conspicuous, as the basic process has changed little over
eras of time. Even between the giant tropical leaves in the rainforest and tiny cyanobacteria, the process and components of
photosynthesis that use water as an electron donor remain largely the same. Photosystems function to absorb light and use
electron transport chains to convert energy. The Calvin cycle reactions assemble carbohydrate molecules with this energy.
However, as with all biochemical pathways, a variety of conditions leads to varied adaptations that affect the basic pattern.
Photosynthesis in dry-climate plants (Figure [Link]) has evolved with adaptations that conserve water. In the harsh dry heat,
every drop of water and precious energy must be used to survive. Two adaptations have evolved in such plants. In one form, a
more efficient use of CO2 allows plants to photosynthesize even when CO2 is in short supply, as when the stomata are closed
on hot days. The other adaptation performs preliminary reactions of the Calvin cycle at night, because opening the stomata at
this time conserves water due to cooler temperatures. In addition, this adaptation has allowed plants to carry out low levels of
photosynthesis without opening stomata at all, an extreme mechanism to face extremely dry periods.

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 Figure [Link]: Living in the harsh conditions of the desert has led plants like this cactus to evolve variations in reactions
outside the Calvin cycle. These variations increase efficiency and help conserve water and energy. (credit: Piotr Wojtkowski)

Photosynthesis in Prokaryotes
The two parts of photosynthesis—the light-dependent reactions and the Calvin cycle—have been described, as they take place in
chloroplasts. However, prokaryotes, such as cyanobacteria, lack membrane-bound organelles. Prokaryotic photosynthetic
autotrophic organisms have infoldings of the plasma membrane for chlorophyll attachment and photosynthesis (Figure [Link]). It
is here that organisms like cyanobacteria can carry out photosynthesis.

Figure [Link]: A photosynthetic prokaryote has infolded regions of the plasma membrane that function like thylakoids.
Although these are not contained in an organelle, such as a chloroplast, all of the necessary components are present to carry out
photosynthesis. (credit: scale-bar data from Matt Russell)

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The Energy Cycle
Living things access energy by breaking down carbohydrate molecules. However, if plants make carbohydrate molecules, why
would they need to break them down? Carbohydrates are storage molecules for energy in all living things. Although energy can be
stored in molecules like ATP, carbohydrates are much more stable and efficient reservoirs for chemical energy. Photosynthetic
organisms also carry out the reactions of respiration to harvest the energy that they have stored in carbohydrates, for example,
plants have mitochondria in addition to chloroplasts.
You may have noticed that the overall reaction for photosynthesis:

6 CO +6 H O → C H O +6 O
2 2 6 12 6 2

is the reverse of the overall reaction for cellular respiration:

6O +C H O → 6 CO +6 H O
2 6 12 6 2 2

Photosynthesis produces oxygen as a byproduct, and respiration produces carbon dioxide as a byproduct.
In nature, there is no such thing as waste. Every single atom of matter is conserved, recycling indefinitely. Substances change form
or move from one type of molecule to another, but never disappear (Figure [Link]).
CO2 is no more a form of waste produced by respiration than oxygen is a waste product of photosynthesis. Both are byproducts of
reactions that move on to other reactions. Photosynthesis absorbs energy to build carbohydrates in chloroplasts, and aerobic cellular
respiration releases energy by using oxygen to break down carbohydrates. Both organelles use electron transport chains to generate
the energy necessary to drive other reactions. Photosynthesis and cellular respiration function in a biological cycle, allowing
organisms to access life-sustaining energy that originates millions of miles away in a star.

Figure [Link]: In the carbon cycle, the reactions of photosynthesis and cellular respiration share reciprocal reactants and
products. (credit: modification of work by Stuart Bassil)

Summary
Using the energy carriers formed in the first stage of photosynthesis, the Calvin cycle reactions fix CO2 from the environment to
build carbohydrate molecules. An enzyme, RuBisCO, catalyzes the fixation reaction, by combining CO2 with RuBP. The resulting
six-carbon compound is broken down into two three-carbon compounds, and the energy in ATP and NADPH is used to convert

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these molecules into G3P. One of the three-carbon molecules of G3P leaves the cycle to become a part of a carbohydrate molecule.
The remaining G3P molecules stay in the cycle to be formed back into RuBP, which is ready to react with more CO2.
Photosynthesis forms a balanced energy cycle with the process of cellular respiration. Plants are capable of both photosynthesis and
cellular respiration, since they contain both chloroplasts and mitochondria.

Glossary

Calvin cycle
the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other
carbohydrate molecules

carbon fixation
the process of converting inorganic CO2 gas into organic compounds

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

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11.1.E: Photosynthesis (Exercises)
5.1: Overview of Photosynthesis
All living organisms on earth consist of one or more cells. Each cell runs on the chemical energy found mainly in carbohydrate
molecules (food), and the majority of these molecules are produced by one process: photosynthesis. Through photosynthesis,
certain organisms convert solar energy (sunlight) into chemical energy, which is then used to build carbohydrate molecules. The
energy used to hold these molecules together is released when an organism breaks down food.

Multiple Choice
What two products result from photosynthesis?
A. water and carbon dioxide
B. water and oxygen
C. glucose and oxygen
D. glucose and carbon dioxide

Answer
C

Which statement about thylakoids in eukaryotes is not correct?

A. Thylakoids are assembled into stacks.
B. Thylakoids exist as a maze of folded membranes.
C. The space surrounding thylakoids is called stroma.
D. Thylakoids contain chlorophyll.

Answer
B

From where does a heterotroph directly obtain its energy?

A. the sun
B. the sun and eating other organisms
C. eating other organisms
D. simple chemicals in the environment

Answer
C

Free Response
What is the overall purpose of the light reactions in photosynthesis?

Answer
To convert solar energy into chemical energy that cells can use to do work.

Why are carnivores, such as lions, dependent on photosynthesis to survive?

Answer
Because lions eat animals that eat plants.

5.2: The Light-Dependent Reactions of Photosynthesis

How can light be used to make food? It is easy to think of light as something that exists and allows living organisms, such as
humans, to see, but light is a form of energy. Like all energy, light can travel, change form, and be harnessed to do work. In the case

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of photosynthesis, light energy is transformed into chemical energy, which autotrophs use to build carbohydrate molecules.
However, autotrophs only use a specific component of sunlight .

Multiple Choice
What is the energy of a photon first used to do in photosynthesis?
A. split a water molecule
B. energize an electron
C. produce ATP
D. synthesize glucose

Answer
B

Which molecule absorbs the energy of a photon in photosynthesis?

A. ATP
B. glucose
C. chlorophyll
D. water

Answer
C

Plants produce oxygen when they photosynthesize. Where does the oxygen come from?
A. splitting water molecules
B. ATP synthesis
C. the electron transport chain
D. chlorophyll

Answer
A

Which color(s) of light does chlorophyll a reflect?

A. red and blue
B. green
C. red
D. blue

Answer
B

Free Response
Describe the pathway of energy in light-dependent reactions.

Answer
The energy is present initially as light. A photon of light hits chlorophyll, causing an electron to be energized. The free electron
travels through the electron transport chain, and the energy of the electron is used to pump hydrogen ions into the thylakoid
space, transferring the energy into the electrochemical gradient. The energy of the electrochemical gradient is used to power
ATP synthase, and the energy is transferred into a bond in the ATP molecule. In addition, energy from another photon can be
used to create a high-energy bond in the molecule NADPH.

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5.3: The Calvin Cycle
Carbohydrate molecules made will have a backbone of carbon atoms. Where does the carbon come from? The carbon atoms used
to build carbohydrate molecules comes from carbon dioxide, the gas that animals exhale with each breath. The Calvin cycle is the
term used for the reactions of photosynthesis that use the energy stored by the light-dependent reactions to form glucose and other
carbohydrate molecules.

Multiple Choice
Where in plant cells does the Calvin cycle take place?
A. thylakoid membrane
B. thylakoid space
C. stroma
D. granum

Answer
C

Which statement correctly describes carbon fixation?

A. the conversion of CO2 to an organic compound
B. the use of RuBisCO to form 3-PGA
C. the production of carbohydrate molecules from G3P
D. the formation of RuBP from G3P molecules
E. the use of ATP and NADPH to reduce CO2

Answer
A

What is the molecule that leaves the Calvin cycle to be converted into glucose?
A. ADP
B. G3P
C. RuBP
D. 3-PGA

Answer
B

Free Response
Which part of the Calvin cycle would be affected if a cell could not produce the enzyme RuBisCO?

Answer
None of the cycle could take place, because RuBisCO is essential in fixing carbon dioxide. Specifically, RuBisCO catalyzes the
reaction between carbon dioxide and RuBP at the start of the cycle.

Explain the reciprocal nature of the net chemical reactions for photosynthesis and respiration.

Answer
Photosynthesis takes the energy of sunlight and combines water and carbon dioxide to produce sugar and oxygen as a waste
product. The reactions of respiration take sugar and consume oxygen to break it down into carbon dioxide and water, releasing
energy. Thus, the reactants of photosynthesis are the products of respiration, and vice versa.

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 CHAPTER OVERVIEW

12: Respiration
12.1: How Cells Obtain Energy
12.1.1: Glycolysis
12.1.2: Citric Acid Cycle and Oxidative Phosphorylation
12.1.3: Fermentation
12.1.4: Connections to Other Metabolic Pathways
12.1.E: How Cells Obtain Energy (Exercises)
12.2: Cellular Respiration Overview

Thumbnail: Adenosine triphosphate. (Image by FreeCliparts from Pixabay).

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1
 SECTION OVERVIEW

12.1: How Cells Obtain Energy

12.1.1: Glycolysis

12.1.2: Citric Acid Cycle and Oxidative Phosphorylation

12.1.3: Fermentation

12.1.4: Connections to Other Metabolic Pathways

12.1.E: How Cells Obtain Energy (Exercises)

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12.1.1: Glycolysis
Even exergonic, energy-releasing reactions require a small amount of activation energy to proceed. However, consider endergonic
reactions, which require much more energy input because their products have more free energy than their reactants. Within the cell,
where does energy to power such reactions come from? The answer lies with an energy-supplying molecule called adenosine
triphosphate, or ATP. ATP is a small, relatively simple molecule, but within its bonds contains the potential for a quick burst of
energy that can be harnessed to perform cellular work. This molecule can be thought of as the primary energy currency of cells in
the same way that money is the currency that people exchange for things they need. ATP is used to power the majority of energy-
requiring cellular reactions.

ATP in Living Systems

A living cell cannot store significant amounts of free energy. Excess free energy would result in an increase of heat in the cell,
which would denature enzymes and other proteins, and thus destroy the cell. Rather, a cell must be able to store energy safely and
release it for use only as needed. Living cells accomplish this using ATP, which can be used to fill any energy need of the cell.
How? It functions as a rechargeable battery.
When ATP is broken down, usually by the removal of its terminal phosphate group, energy is released. This energy is used to do
work by the cell, usually by the binding of the released phosphate to another molecule, thus activating it. For example, in the
mechanical work of muscle contraction, ATP supplies energy to move the contractile muscle proteins.

ATP Structure and Function

At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to both
a ribose molecule and a single phosphate group (Figure [Link]). Ribose is a five-carbon sugar found in RNA and AMP is one of
the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in adenosine diphosphate (ADP);
the addition of a third phosphate group forms adenosine triphosphate (ATP).

Figure [Link]: The structure of ATP shows the basic components of a two-ring adenine, five-carbon ribose, and three
phosphate groups.
The addition of a phosphate group to a molecule requires a high amount of energy and results in a high-energy bond. Phosphate
groups are negatively charged and thus repel one another when they are arranged in series, as they are in ADP and ATP. This
repulsion makes the ADP and ATP molecules inherently unstable. The release of one or two phosphate groups from ATP, a process
called hydrolysis, releases energy.

Glycolysis
You have read that nearly all of the energy used by living things comes to them in the bonds of the sugar, glucose. Glycolysis is the
first step in the breakdown of glucose to extract energy for cell metabolism. Many living organisms carry out glycolysis as part of
their metabolism. Glycolysis takes place in the cytoplasm of most prokaryotic and all eukaryotic cells.
Glycolysis begins with the six-carbon, ring-shaped structure of a single glucose molecule and ends with two molecules of a three-
carbon sugar called pyruvate. Glycolysis consists of two distinct phases. In the first part of the glycolysis pathway, energy is used
to make adjustments so that the six-carbon sugar molecule can be split evenly into two three-carbon pyruvate molecules. In the
second part of glycolysis, ATP and nicotinamide-adenine dinucleotide (NADH) are produced (Figure [Link]).
If the cell cannot catabolize the pyruvate molecules further, it will harvest only two ATP molecules from one molecule of glucose.
For example, mature mammalian red blood cells are only capable of glycolysis, which is their sole source of ATP. If glycolysis is

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interrupted, these cells would eventually die.

Figure [Link]: In glycolysis, a glucose molecule is converted into two pyruvate molecules.

Summary
ATP functions as the energy currency for cells. It allows cells to store energy briefly and transport it within itself to support
endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphate groups attached. As ATP is
used for energy, a phosphate group is detached, and ADP is produced. Energy derived from glucose catabolism is used to recharge
ADP into ATP.
Glycolysis is the first pathway used in the breakdown of glucose to extract energy. Because it is used by nearly all organisms on
earth, it must have evolved early in the history of life. Glycolysis consists of two parts: The first part prepares the six-carbon ring of
glucose for separation into two three-carbon sugars. Energy from ATP is invested into the molecule during this step to energize the
separation. The second half of glycolysis extracts ATP and high-energy electrons from hydrogen atoms and attaches them to
NAD+. Two ATP molecules are invested in the first half and four ATP molecules are formed during the second half. This produces
a net gain of two ATP molecules per molecule of glucose for the cell.

Glossary

ATP
(also, adenosine triphosphate) the cell’s energy currency

glycolysis
the process of breaking glucose into two three-carbon molecules with the production of ATP and NADH

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 12.1.1: Glycolysis is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
4.2: Glycolysis by OpenStax is licensed CC BY 4.0.

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12.1.2: Citric Acid Cycle and Oxidative Phosphorylation
The Citric Acid Cycle
In eukaryotic cells, the pyruvate molecules produced at the end of glycolysis are transported into mitochondria, which are sites of
cellular respiration. If oxygen is available, aerobic respiration will go forward. In mitochondria, pyruvate will be transformed into a
two-carbon acetyl group (by removing a molecule of carbon dioxide) that will be picked up by a carrier compound called
coenzyme A (CoA), which is made from vitamin B5. The resulting compound is called acetyl CoA. (Figure [Link]). Acetyl CoA
can be used in a variety of ways by the cell, but its major function is to deliver the acetyl group derived from pyruvate to the next
pathway in glucose catabolism.

Figure [Link]: Pyruvate is converted into acetyl-CoA before entering the citric acid cycle.
Like the conversion of pyruvate to acetyl CoA, the citric acid cycle in eukaryotic cells takes place in the matrix of the
mitochondria. Unlike glycolysis, the citric acid cycle is a closed loop: The last part of the pathway regenerates the compound used
in the first step. The eight steps of the cycle are a series of chemical reactions that produces two carbon dioxide molecules, one
ATP molecule (or an equivalent), and reduced forms (NADH and FADH2) of NAD+ and FAD+, important coenzymes in the cell.
Part of this is considered an aerobic pathway (oxygen-requiring) because the NADH and FADH2 produced must transfer their
electrons to the next pathway in the system, which will use oxygen. If oxygen is not present, this transfer does not occur.
Two carbon atoms come into the citric acid cycle from each acetyl group. Two carbon dioxide molecules are released on each turn
of the cycle; however, these do not contain the same carbon atoms contributed by the acetyl group on that turn of the pathway. The
two acetyl-carbon atoms will eventually be released on later turns of the cycle; in this way, all six carbon atoms from the original
glucose molecule will be eventually released as carbon dioxide. It takes two turns of the cycle to process the equivalent of one
glucose molecule. Each turn of the cycle forms three high-energy NADH molecules and one high-energy FADH2 molecule. These
high-energy carriers will connect with the last portion of aerobic respiration to produce ATP molecules. One ATP (or an equivalent)
is also made in each cycle. Several of the intermediate compounds in the citric acid cycle can be used in synthesizing non-essential
amino acids; therefore, the cycle is both anabolic and catabolic.

Oxidative Phosphorylation
You have just read about two pathways in glucose catabolism—glycolysis and the citric acid cycle—that generate ATP. Most of the
ATP generated during the aerobic catabolism of glucose, however, is not generated directly from these pathways. Rather, it derives
from a process that begins with passing electrons through a series of chemical reactions to a final electron acceptor, oxygen. These
reactions take place in specialized protein complexes located in the inner membrane of the mitochondria of eukaryotic organisms
and on the inner part of the cell membrane of prokaryotic organisms. The energy of the electrons is harvested and used to generate
a electrochemical gradient across the inner mitochondrial membrane. The potential energy of this gradient is used to generate ATP.
The entirety of this process is called oxidative phosphorylation.
The electron transport chain (Figure 12.1.2.2a) is the last component of aerobic respiration and is the only part of metabolism that
uses atmospheric oxygen. Oxygen continuously diffuses into plants for this purpose. In animals, oxygen enters the body through
the respiratory system. Electron transport is a series of chemical reactions that resembles a bucket brigade in that electrons are
passed rapidly from one component to the next, to the endpoint of the chain where oxygen is the final electron acceptor and water
is produced. There are four complexes composed of proteins, labeled I through IV in Figure 12.1.2.2c, and the aggregation of these
four complexes, together with associated mobile, accessory electron carriers, is called the electron transport chain. The electron
transport chain is present in multiple copies in the inner mitochondrial membrane of eukaryotes and in the plasma membrane of

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prokaryotes. In each transfer of an electron through the electron transport chain, the electron loses energy, but with some transfers,
the energy is stored as potential energy by using it to pump hydrogen ions across the inner mitochondrial membrane into the
intermembrane space, creating an electrochemical gradient.

ART CONNECTION

Figure [Link]: (a) The electron transport chain is a set of molecules that supports a series of oxidation-reduction reactions.
(b) ATP synthase is a complex, molecular machine that uses an H+ gradient to regenerate ATP from ADP. (c) Chemiosmosis
relies on the potential energy provided by the H+ gradient across the membrane.
Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs, would you
expect the pH of the intermembrane space to increase or decrease? What affect would cyanide have on ATP synthesis?

Electrons from NADH and FADH2 are passed to protein complexes in the electron transport chain. As they are passed from one
complex to another (there are a total of four), the electrons lose energy, and some of that energy is used to pump hydrogen ions
from the mitochondrial matrix into the intermembrane space. In the fourth protein complex, the electrons are accepted by oxygen,
the terminal acceptor. The oxygen with its extra electrons then combines with two hydrogen ions, further enhancing the
electrochemical gradient, to form water. If there were no oxygen present in the mitochondrion, the electrons could not be removed
from the system, and the entire electron transport chain would back up and stop. The mitochondria would be unable to generate
new ATP in this way, and the cell would ultimately die from lack of energy. This is the reason we must breathe to draw in new
oxygen.
In the electron transport chain, the free energy from the series of reactions just described is used to pump hydrogen ions across the
membrane. The uneven distribution of H+ ions across the membrane establishes an electrochemical gradient, owing to the H+ ions’
positive charge and their higher concentration on one side of the membrane.

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Hydrogen ions diffuse through the inner membrane through an integral membrane protein called ATP synthase (Figure 12.1.2.2b).
This complex protein acts as a tiny generator, turned by the force of the hydrogen ions diffusing through it, down their
electrochemical gradient from the intermembrane space, where there are many mutually repelling hydrogen ions to the matrix,
where there are few. The turning of the parts of this molecular machine regenerate ATP from ADP. This flow of hydrogen ions
across the membrane through ATP synthase is called chemiosmosis.
Chemiosmosis (Figure 12.1.2.2c) is used to generate 90 percent of the ATP made during aerobic glucose catabolism. The result of
the reactions is the production of ATP from the energy of the electrons removed from hydrogen atoms. These atoms were originally
part of a glucose molecule. At the end of the electron transport system, the electrons are used to reduce an oxygen molecule to
oxygen ions. The extra electrons on the oxygen ions attract hydrogen ions (protons) from the surrounding medium, and water is
formed. The electron transport chain and the production of ATP through chemiosmosis are collectively called oxidative
phosphorylation.

ATP Yield
The number of ATP molecules generated from the catabolism of glucose varies. For example, the number of hydrogen ions that the
electron transport chain complexes can pump through the membrane varies between species. Another source of variance stems
from the shuttle of electrons across the mitochondrial membrane. The NADH generated from glycolysis cannot easily enter
mitochondria. Thus, electrons are picked up on the inside of the mitochondria by either NAD+ or FAD+. Fewer ATP molecules are
generated when FAD+ acts as a carrier. NAD+ is used as the electron transporter in the liver and FAD+ in the brain, so ATP yield
depends on the tissue being considered.
Another factor that affects the yield of ATP molecules generated from glucose is that intermediate compounds in these pathways
are used for other purposes. Glucose catabolism connects with the pathways that build or break down all other biochemical
compounds in cells, and the result is somewhat messier than the ideal situations described thus far. For example, sugars other than
glucose are fed into the glycolytic pathway for energy extraction. Other molecules that would otherwise be used to harvest energy
in glycolysis or the citric acid cycle may be removed to form nucleic acids, amino acids, lipids, or other compounds. Overall, in
living systems, these pathways of glucose catabolism extract about 34 percent of the energy contained in glucose.

CAREERS IN ACTION: Mitochondrial Disease Physician

What happens when the critical reactions of cellular respiration do not proceed correctly? Mitochondrial diseases are genetic
disorders of metabolism. Mitochondrial disorders can arise from mutations in nuclear or mitochondrial DNA, and they result in
the production of less energy than is normal in body cells. Symptoms of mitochondrial diseases can include muscle weakness,
lack of coordination, stroke-like episodes, and loss of vision and hearing. Most affected people are diagnosed in childhood,
although there are some adult-onset diseases. Identifying and treating mitochondrial disorders is a specialized medical field.
The educational preparation for this profession requires a college education, followed by medical school with a specialization
in medical genetics. Medical geneticists can be board certified by the American Board of Medical Genetics and go on to
become associated with professional organizations devoted to the study of mitochondrial disease, such as the Mitochondrial
Medicine Society and the Society for Inherited Metabolic Disease.

Summary
The citric acid cycle is a series of chemical reactions that removes high-energy electrons and uses them in the electron transport
chain to generate ATP. One molecule of ATP (or an equivalent) is produced per each turn of the cycle.
The electron transport chain is the portion of aerobic respiration that uses free oxygen as the final electron acceptor for electrons
removed from the intermediate compounds in glucose catabolism. The electrons are passed through a series of chemical reactions,
with a small amount of free energy used at three points to transport hydrogen ions across the membrane. This contributes to the
gradient used in chemiosmosis. As the electrons are passed from NADH or FADH2 down the electron transport chain, they lose
energy. The products of the electron transport chain are water and ATP. A number of intermediate compounds can be diverted into
the anabolism of other biochemical molecules, such as nucleic acids, non-essential amino acids, sugars, and lipids. These same
molecules, except nucleic acids, can serve as energy sources for the glucose pathway.

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Art Connections
Figure [Link]: Cyanide inhibits cytochrome c oxidase, a component of the electron transport chain. If cyanide poisoning occurs,
would you expect the pH of the intermembrane space to increase or decrease? What affect would cyanide have on ATP synthesis?

Answer
After cyanide poisoning, the electron transport chain can no longer pump electrons into the intermembrane space. The pH of the
intermembrane space would increase, and ATP synthesis would stop.

Glossary

acetyl CoA
the combination of an acetyl group derived from pyruvic acid and coenzyme A which is made from pantothenic acid (a B-group
vitamin)

ATP synthase
a membrane-embedded protein complex that regenerates ATP from ADP with energy from protons diffusing through it

chemiosmosis
the movement of hydrogen ions down their electrochemical gradient across a membrane through ATP synthase to generate ATP

citric acid cycle

a series of enzyme-catalyzed chemical reactions of central importance in all living cells that harvests the energy in carbon-
carbon bonds of sugar molecules to generate ATP; the citric acid cycle is an aerobic metabolic pathway because it requires
oxygen in later reactions to proceed

electron transport chain

a series of four large, multi-protein complexes embedded in the inner mitochondrial membrane that accepts electrons from
donor compounds and harvests energy from a series of chemical reactions to generate a hydrogen ion gradient across the
membrane

oxidative phosphorylation
the production of ATP by the transfer of electrons down the electron transport chain to create a proton gradient that is used by
ATP synthase to add phosphate groups to ADP molecules

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 12.1.2: Citric Acid Cycle and Oxidative Phosphorylation is shared under a CC BY license and was authored, remixed, and/or
curated by OpenStax.
4.3: Citric Acid Cycle and Oxidative Phosphorylation by OpenStax is licensed CC BY 4.0.

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12.1.3: Fermentation
In aerobic respiration, the final electron acceptor is an oxygen molecule, O2. If aerobic respiration occurs, then ATP will be
produced using the energy of the high-energy electrons carried by NADH or FADH2 to the electron transport chain. If aerobic
respiration does not occur, NADH must be reoxidized to NAD+ for reuse as an electron carrier for glycolysis to continue. How is
this done? Some living systems use an organic molecule as the final electron acceptor. Processes that use an organic molecule to
regenerate NAD+ from NADH are collectively referred to as fermentation. In contrast, some living systems use an inorganic
molecule (other than oxygen) as a final electron acceptor to regenerate NAD+; both methods are anaerobic (do not require oxygen)
to achieve NAD+ regeneration and enable organisms to convert energy for their use in the absence of oxygen.

Lactic Acid Fermentation

The fermentation method used by animals and some bacteria like those in yogurt is lactic acid fermentation (Figure [Link]). This
occurs routinely in mammalian red blood cells and in skeletal muscle that has insufficient oxygen supply to allow aerobic
respiration to continue (that is, in muscles used to the point of fatigue). In muscles, lactic acid produced by fermentation must be
removed by the blood circulation and brought to the liver for further metabolism. The chemical reaction of lactic acid fermentation
is the following:
+
Pyruvic acid + NADH ↔ lactic acid + NAD

The enzyme that catalyzes this reaction is lactate dehydrogenase. The reaction can proceed in either direction, but the left-to-right
reaction is inhibited by acidic conditions. This lactic acid build-up causes muscle stiffness and fatigue. Once the lactic acid has
been removed from the muscle and is circulated to the liver, it can be converted back to pyruvic acid and further catabolized for
energy.

ART CONNECTION

Figure [Link]: Lactic acid fermentation is common in muscles that have become exhausted by use.
Tremetol, a metabolic poison found in white snake root plant, prevents the metabolism of lactate. When cows eat this plant,
Tremetol is concentrated in the milk. Humans who consume the milk become ill. Symptoms of this disease, which include

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 vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

Alcohol Fermentation
Another familiar fermentation process is alcohol fermentation (Figure ), which produces ethanol, an alcohol. The alcohol
[Link]

fermentation reaction is the following:

Figure [Link]: The reaction resulting in alcohol fermentation is shown.

In the first reaction, a carboxyl group is removed from pyruvic acid, releasing carbon dioxide as a gas. The loss of carbon dioxide
reduces the molecule by one carbon atom, making acetaldehyde. The second reaction removes an electron from NADH, forming
NAD+ and producing ethanol from the acetaldehyde, which accepts the electron. The fermentation of pyruvic acid by yeast
produces the ethanol found in alcoholic beverages (Figure [Link]). If the carbon dioxide produced by the reaction is not vented
from the fermentation chamber, for example in beer and sparkling wines, it remains dissolved in the medium until the pressure is
released. Ethanol above 12 percent is toxic to yeast, so natural levels of alcohol in wine occur at a maximum of 12 percent.

Figure [Link]: Fermentation of grape juice to make wine produces CO2 as a byproduct. Fermentation tanks have valves so that
pressure inside the tanks can be released.

Anaerobic Cellular Respiration

Certain prokaryotes, including some species of bacteria and Archaea, use anaerobic respiration. For example, the group of Archaea
called methanogens reduces carbon dioxide to methane to oxidize NADH. These microorganisms are found in soil and in the
digestive tracts of ruminants, such as cows and sheep. Similarly, sulfate-reducing bacteria and Archaea, most of which are
anaerobic (Figure [Link]), reduce sulfate to hydrogen sulfide to regenerate NAD+ from NADH.

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 Figure [Link]: The green color seen in these coastal waters is from an eruption of hydrogen sulfide. Anaerobic, sulfate-
reducing bacteria release hydrogen sulfide gas as they decompose algae in the water. (credit: NASA image courtesy Jeff Schmaltz,
MODIS Land Rapid Response Team at NASA GSFC)

CONCEPT IN ACTION

Science – Yeast Experiment: measuri…

measuri…

Visit this site to see anaerobic cellular respiration in action.

Other fermentation methods occur in bacteria. Many prokaryotes are facultatively anaerobic. This means that they can switch
between aerobic respiration and fermentation, depending on the availability of oxygen. Certain prokaryotes, like Clostridia
bacteria, are obligate anaerobes. Obligate anaerobes live and grow in the absence of molecular oxygen. Oxygen is a poison to these
microorganisms and kills them upon exposure. It should be noted that all forms of fermentation, except lactic acid fermentation,
produce gas. The production of particular types of gas is used as an indicator of the fermentation of specific carbohydrates, which
plays a role in the laboratory identification of the bacteria. The various methods of fermentation are used by different organisms to
ensure an adequate supply of NAD+ for the sixth step in glycolysis. Without these pathways, that step would not occur, and no ATP
would be harvested from the breakdown of glucose.

Section Summary
If NADH cannot be metabolized through aerobic respiration, another electron acceptor is used. Most organisms will use some form
of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+ in
fermentation is not accompanied by ATP production; therefore, the potential for NADH to produce ATP using an electron transport
chain is not utilized.

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Art Connections
Figure [Link]: Tremetol, a metabolic poison found in white snake root plant, prevents the metabolism of lactate. When cows eat
this plant, Tremetol is concentrated in the milk. Humans who consume the milk become ill. Symptoms of this disease, which
include vomiting, abdominal pain, and tremors, become worse after exercise. Why do you think this is the case?

Answer
The illness is caused by lactic acid build-up. Lactic acid levels rise after exercise, making the symptoms worse. Milk sickness is
rare today, but was common in the Midwestern United States in the early 1800s.

Glossary

anaerobic cellular respiration

the use of an electron acceptor other than oxygen to complete metabolism using electron transport-based chemiosmosis

fermentation
the steps that follow the partial oxidation of glucose via glycolysis to regenerate NAD+; occurs in the absence of oxygen and
uses an organic compound as the final electron acceptor

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 12.1.3: Fermentation is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
4.4: Fermentation by OpenStax is licensed CC BY 4.0.

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12.1.4: Connections to Other Metabolic Pathways
You have learned about the catabolism of glucose, which provides energy to living cells. But living things consume more than just
glucose for food. How does a turkey sandwich, which contains protein, provide energy to your cells? This happens because all of
the catabolic pathways for carbohydrates, proteins, and lipids eventually connect into glycolysis and the citric acid cycle pathways
(Figure [Link]). Metabolic pathways should be thought of as porous—that is, substances enter from other pathways, and other
substances leave for other pathways. These pathways are not closed systems. Many of the products in a particular pathway are
reactants in other pathways.

Connections of Other Sugars to Glucose Metabolism

Glycogen, a polymer of glucose, is a short-term energy storage molecule in animals. When there is adequate ATP present, excess
glucose is converted into glycogen for storage. Glycogen is made and stored in the liver and muscle. Glycogen will be taken out of
storage if blood sugar levels drop. The presence of glycogen in muscle cells as a source of glucose allows ATP to be produced for a
longer time during exercise.
Sucrose is a disaccharide made from glucose and fructose bonded together. Sucrose is broken down in the small intestine, and the
glucose and fructose are absorbed separately. Fructose is one of the three dietary monosaccharides, along with glucose and
galactose (which is part of milk sugar, the disaccharide lactose), that are absorbed directly into the bloodstream during digestion.
The catabolism of both fructose and galactose produces the same number of ATP molecules as glucose.

Connections of Proteins to Glucose Metabolism

Proteins are broken down by a variety of enzymes in cells. Most of the time, amino acids are recycled into new proteins. If there
are excess amino acids, however, or if the body is in a state of famine, some amino acids will be shunted into pathways of glucose
catabolism. Each amino acid must have its amino group removed prior to entry into these pathways. The amino group is converted
into ammonia. In mammals, the liver synthesizes urea from two ammonia molecules and a carbon dioxide molecule. Thus, urea is
the principal waste product in mammals from the nitrogen originating in amino acids, and it leaves the body in urine.

Connections of Lipids to Glucose Metabolism

The lipids that are connected to the glucose pathways are cholesterol and triglycerides. Cholesterol is a lipid that contributes to cell
membrane flexibility and is a precursor of steroid hormones. The synthesis of cholesterol starts with acetyl CoA and proceeds in
only one direction. The process cannot be reversed, and ATP is not produced.
Triglycerides are a form of long-term energy storage in animals. Triglycerides store about twice as much energy as carbohydrates.
Triglycerides are made of glycerol and three fatty acids. Animals can make most of the fatty acids they need. Triglycerides can be
both made and broken down through parts of the glucose catabolism pathways. Glycerol can be phosphorylated and proceeds
through glycolysis. Fatty acids are broken into two-carbon units that enter the citric acid cycle.

Figure [Link]: Glycogen from the liver and muscles, together with fats, can feed into the catabolic pathways for carbohydrates.

EVOLUTION IN ACTION: Pathways of Photosynthesis and Cellular Metabolism

Photosynthesis and cellular metabolism consist of several very complex pathways. It is generally thought that the first cells
arose in an aqueous environment—a “soup” of nutrients. If these cells reproduced successfully and their numbers climbed
steadily, it follows that the cells would begin to deplete the nutrients from the medium in which they lived, as they shifted the
nutrients into their own cells. This hypothetical situation would have resulted in natural selection favoring those organisms that
could exist by using the nutrients that remained in their environment and by manipulating these nutrients into materials that

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 they could use to survive. Additionally, selection would favor those organisms that could extract maximal value from the
available nutrients.
An early form of photosynthesis developed that harnessed the sun’s energy using compounds other than water as a source of
hydrogen atoms, but this pathway did not produce free oxygen. It is thought that glycolysis developed prior to this time and
could take advantage of simple sugars being produced, but these reactions were not able to fully extract the energy stored in the
carbohydrates. A later form of photosynthesis used water as a source of hydrogen ions and generated free oxygen. Over time,
the atmosphere became oxygenated. Living things adapted to exploit this new atmosphere and allowed respiration as we know
it to evolve. When the full process of photosynthesis as we know it developed and the atmosphere became oxygenated, cells
were finally able to use the oxygen expelled by photosynthesis to extract more energy from the sugar molecules using the citric
acid cycle.

Summary
The breakdown and synthesis of carbohydrates, proteins, and lipids connect with the pathways of glucose catabolism. The
carbohydrates that can also feed into glucose catabolism include galactose, fructose, and glycogen. These connect with glycolysis.
The amino acids from proteins connect with glucose catabolism through pyruvate, acetyl CoA, and components of the citric acid
cycle. Cholesterol synthesis starts with acetyl CoA, and the components of triglycerides are picked up by acetyl CoA and enter the
citric acid cycle.

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

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OpenStax.
4.5: Connections to Other Metabolic Pathways by OpenStax is licensed CC BY 4.0.

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12.1.E: How Cells Obtain Energy (Exercises)
4.1: Energy and Metabolism
Cells perform the functions of life through various chemical reactions. A cell’s metabolism refers to the combination of chemical
reactions that take place within it. Catabolic reactions break down complex chemicals into simpler ones and are associated with
energy release. Anabolic processes build complex molecules out of simpler ones and require energy. In studying energy, the term
system refers to the matter and environment involved in energy transfers.

Review Questions
Which of the following is not an example of an energy transformation?
A. Heating up dinner in a microwave
B. Solar panels at work
C. Formation of static electricity
D. None of the above

Answer
D

Which of the following is not true about enzymes?

A. They are consumed by the reactions they catalyze.
B. They are usually made of amino acids.
C. They lower the activation energy of chemical reactions.
D. Each one is specific to the particular substrate(s) to which it binds.

Answer
A

Free Response
Does physical exercise to increase muscle mass involve anabolic and/or catabolic processes? Give evidence for your answer.

Answer
Physical exercise involves both anabolic and catabolic processes. Body cells break down sugars to provide ATP to do the work
necessary for exercise, such as muscle contractions. This is catabolism. Muscle cells also must repair muscle tissue damaged by
exercise by building new muscle. This is anabolism.

Explain in your own terms the difference between a spontaneous reaction and one that occurs instantaneously, and what causes this
difference.

Answer
A spontaneous reaction is one that has a negative ∆G and thus releases energy. However, a spontaneous reaction need not occur
quickly or suddenly like an instantaneous reaction. It may occur over long periods of time due to a large energy of activation,
which prevents the reaction from occurring quickly.

With regard to enzymes, why are vitamins and minerals necessary for good health? Give examples.

Answer
Most vitamins and minerals act as cofactors and coenzymes for enzyme action. Many enzymes require the binding of certain
cofactors or coenzymes to be able to catalyze their reactions. Since enzymes catalyze many important reactions, it is critical to
obtain sufficient vitamins and minerals from diet and supplements. Vitamin C (ascorbic acid) is a coenzyme necessary for the
action of enzymes that build collagen.

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4.2: Glycolysis
ATP functions as the energy currency for cells. It allows cells to store energy briefly and transport it within itself to support
endergonic chemical reactions. The structure of ATP is that of an RNA nucleotide with three phosphate groups attached. As ATP is
used for energy, a phosphate group is detached, and ADP is produced. Energy derived from glucose catabolism is used to recharge
ADP into ATP. Glycolysis is the first pathway used in the breakdown of glucose to extract energy.

Multiple Choice
Energy is stored long-term in the bonds of _____ and used short-term to perform work from a(n) _____ molecule.
A. ATP : glucose
B. an anabolic molecule : catabolic molecule
C. glucose : ATP
D. a catabolic molecule : anabolic molecule

Answer
C

The energy currency used by cells is _____.

A. ATP
B. ADP
C. AMP
D. adenosine

Answer
A

The glucose that enters the glycolysis pathway is split into two molecules of _________.
A. ATP
B. phosphate
C. NADH
D. pyruvate

Answer
D

Free Response
Both prokaryotic and eukaryotic organisms carry out some form of glycolysis. How does that fact support or not support the
assertion that glycolysis is one of the oldest metabolic pathways?

Answer
If glycolysis evolved relatively late, it likely would not be as universal in organisms as it is. It probably evolved in very
primitive organisms and persisted, with the addition of other pathways of carbohydrate metabolism that evolved later.

4.3: Citric Acid Cycle and Oxidative Phosphorylation

The citric acid cycle is a series of chemical reactions that removes high-energy electrons and uses them in the electron transport
chain to generate ATP. One molecule of ATP (or an equivalent) is produced per each turn of the cycle. The electron transport chain
is the portion of aerobic respiration that uses free oxygen as the final electron acceptor for electrons removed from the intermediate
compounds in glucose catabolism.

Multiple Choice
What do the electrons added to NAD+ do?

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 A. They become part of a fermentation pathway.
B. They go to another pathway for ATP production.
C. They energize the entry of the acetyl group into the citric acid cycle.
D. They are converted into NADP.

Answer
B

Chemiosmosis involves
A. the movement of electrons across the cell membrane
B. the movement of hydrogen atoms across a mitochondrial membrane
C. the movement of hydrogen ions across a mitochondrial membran
D. the movement of glucose through the cell membrane

Answer
C

Free Response
We inhale oxygen when we breathe and exhale carbon dioxide. What is the oxygen used for and where does the carbon dioxide
come from?

Answer
The oxygen we inhale is the final electron acceptor in the electron transport chain and allows aerobic respiration to proceed,
which is the most efficient pathway for harvesting energy in the form of ATP from food molecules. The carbon dioxide we
breathe out is formed during the citric acid cycle when the bonds in carbon compounds are broken.

4.4: Fermentation
If NADH cannot be metabolized through aerobic respiration, another electron acceptor is used. Most organisms will use some form
of fermentation to accomplish the regeneration of NAD+, ensuring the continuation of glycolysis. The regeneration of NAD+ in
fermentation is not accompanied by ATP production; therefore, the potential for NADH to produce ATP using an electron transport
chain is not utilized.

Review Questions
Which of the following fermentation methods can occur in animal skeletal muscles?
A. lactic acid fermentation
B. alcohol fermentation
C. mixed acid fermentation
D. propionic fermentation

Answer
A

Free Response
When muscle cells run out of oxygen, what happens to the potential for energy extraction from sugars and what pathways do the
cell use?

Answer
Without oxygen, oxidative phosphorylation and the citric acid cycle stop, so ATP is no longer generated through this
mechanism, which extracts the greatest amount of energy from a sugar molecule. In addition, NADH accumulates, preventing
glycolysis from going forward because of an absence of NAD+. Lactic acid fermentation uses the electrons in NADH to
generate lactic acid from pyruvate, which allows glycolysis to continue and thus a smaller amount of ATP can be generated by
the cell.

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4.5: Connections to Other Metabolic Pathways
Metabolic pathways should be thought of as porous—that is, substances enter from other pathways, and other substances leave for
other pathways. These pathways are not closed systems. Many of the products in a particular pathway are reactants in other
pathways.

Multiple Choice
The cholesterol synthesized by cells uses which component of the glycolytic pathway as a starting point?
A. glucose
B. acetyl CoA
C. pyruvate
D. carbon dioxide

Answer
B

Beta oxidation is ________.

A. the breakdown of sugars
B. the assembly of sugars
C. the breakdown of fatty acids
D. the removal of amino groups from amino acids

Answer
C

Free Response
Would you describe metabolic pathways as inherently wasteful or inherently economical, and why?

Answer
They are very economical. The substrates, intermediates, and products move between pathways and do so in response to finely
tuned feedback inhibition loops that keep metabolism overall on an even keel. Intermediates in one pathway may occur in
another, and they can move from one pathway to another fluidly in response to the needs of the cell.

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OpenStax.
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12.2: Cellular Respiration Overview

Figure 12.2.1: This illustration is an overview of cellular respiration connecting glycolysis to the Krebs (Citric Acid) Cycle and
Oxidative Phosphorylation. The energy yield (ATP) and electron carriers (NADH and FADH2) are also shown in this
overview. (CC BY-NC-SA 4.0; Eunice Laurent via OER Commons)

12.2: Cellular Respiration Overview is shared under a CC BY-NC-SA license and was authored, remixed, and/or curated by LibreTexts.

12.2.1 [Link]
 CHAPTER OVERVIEW

13: Microbes; Immune System

13.1: Diversity of Microbes, Fungi, and Protists
13.1.1: Prokaryotic Diversity
13.1.2: Eukaryotic Origins
13.1.3: Protists
13.1.4: Fungi
13.1.E: Diversity of Microbes, Fungi, and Protists (Exercises)
13.2: The Immune System and Disease
13.2.1: Viruses
13.2.2: Innate Immunity
13.2.3: Adaptive Immunity
13.2.4: Disruptions in the Immune System
13.2.E: The Immune System and Desease (Exercises)

Thumbnail: Scanning electron micrograph of neutrophil ingesting methicillin-resistant Staphylococcus aureus bacteria. (Public
domain; NIAID/NIH via Wikimedia Commons).

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1
 SECTION OVERVIEW

13.1: Diversity of Microbes, Fungi, and Protists

13.1.1: Prokaryotic Diversity

13.1.2: Eukaryotic Origins

13.1.3: Protists

13.1.4: Fungi

13.1.E: Diversity of Microbes, Fungi, and Protists (Exercises)

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OpenStax.

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13.1.1: Prokaryotic Diversity
Prokaryotes are present everywhere. They cover every imaginable surface where there is sufficient moisture, and they live on and
inside of other living things. There are more prokaryotes inside and on the exterior of the human body than there are human cells in
the body. Some prokaryotes thrive in environments that are inhospitable for most other living things. Prokaryotes recycle nutrients
—essential substances (such as carbon and nitrogen)—and they drive the evolution of new ecosystems, some of which are natural
while others are man-made. Prokaryotes have been on Earth since long before multicellular life appeared.

Prokaryotic Diversity
The advent of DNA sequencing provided immense insight into the relationships and origins of prokaryotes that were not possible
using traditional methods of classification. A major insight identified two groups of prokaryotes that were found to be as different
from each other as they were from eukaryotes. This recognition of prokaryotic diversity forced a new understanding of the
classification of all life and brought us closer to understanding the fundamental relationships of all living things, including
ourselves.

Early Life on Earth

When and where did life begin? What were the conditions on Earth when life began? Prokaryotes were the first forms of life on
Earth, and they existed for billions of years before plants and animals appeared. Earth is about 4.54 billion years old. This estimate
is based on evidence from the dating of meteorite material, since surface rocks on Earth are not as old as Earth itself. Most rocks
available on Earth have undergone geological changes that make them younger than Earth itself. Some meteorites are made of the
original material in the solar disk that formed the objects of the solar system, and they have not been altered by the processes that
altered rocks on Earth. Thus, the age of meteorites is a good indicator of the age of the formation of Earth. The original estimate of
4.54 billion years was obtained by Clare Patterson in 1956. His meticulous work has since been corroborated by ages determined
from other sources, all of which point to an Earth age of about 4.54 billion years.
Early Earth had a very different atmosphere than it does today. Evidence indicates that during the first 2 billion years of Earth’s
existence, the atmosphere was anoxic, meaning that there was no oxygen. Therefore, only those organisms that can grow without
oxygen—anaerobicorganisms—were able to live. Organisms that convert solar energy into chemical energy are called phototrophs.
Phototrophic organisms that required an organic source of carbon appeared within one billion years of the formation of Earth.
Then, cyanobacteria, also known as blue-green algae, evolved from these simple phototrophs one billion years later. Cyanobacteria
are able to use carbon dioxide as a source of carbon. Cyanobacteria (Figure [Link]) began the oxygenation of the atmosphere.
The increase in oxygen concentration allowed the evolution of other life forms.

Figure [Link]: This hot spring in Yellowstone National Park flows toward the foreground. Cyanobacteria in the spring are
green, and as water flows down the heat gradient, the intensity of the color increases because cell density increases. The water is
cooler at the edges of the stream than in the center, causing the edges to appear greener. (credit: Graciela Brelles-Mariño)
Before the atmosphere became oxygenated, the planet was subjected to strong radiation; thus, the first organisms would have
flourished where they were more protected, such as in ocean depths or beneath the surface of Earth. At this time, too, strong
volcanic activity was common on Earth, so it is likely that these first organisms—the first prokaryotes—were adapted to very high

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temperatures. These are not the typical temperate environments in which most life flourishes today; thus, we can conclude that the
first organisms that appeared on Earth likely were able to withstand harsh conditions.
Microbial mats may represent the earliest forms of life on Earth, and there is fossil evidence of their presence, starting about 3.5
billion years ago. A microbial mat is a large biofilm, a multi-layered sheet of prokaryotes (Figure 13.1.1.2a), including mostly
bacteria, but also archaea. Microbial mats are a few centimeters thick, and they typically grow on moist surfaces. Their various
types of prokaryotes carry out different metabolic pathways, and for this reason, they reflect various colors. Prokaryotes in a
microbial mat are held together by a gummy-like substance that they secrete.
The first microbial mats likely obtained their energy from hydrothermal vents. A hydrothermal vent is a fissure in Earth’s surface
that releases geothermally heated water. With the evolution of photosynthesis about 3 billion years ago, some prokaryotes in
microbial mats came to use a more widely available energy source—sunlight—whereas others were still dependent on chemicals
from hydrothermal vents for food.

Figure [Link]: (a) This microbial mat grows over a hydrothermal vent in the Pacific Ocean. Chimneys such as the one
indicated by the arrow allow gases to escape. (b) This photo shows stromatolites that are nearly 1.5 billion years old, found in
Glacier National Park, Montana. (credit a: modification of work by Dr. Bob Embley, NOAA PMEL; credit b: modification of work
by P. Carrara, NPS)
Fossilized microbial mats represent the earliest record of life on Earth. A stromatolite is a sedimentary structure formed when
minerals are precipitated from water by prokaryotes in a microbial mat (Figure 13.1.1.2b). Stromatolites form layered rocks made
of carbonate or silicate. Although most stromatolites are artifacts from the past, there are places on Earth where stromatolites are
still forming. For example, living stromatolites have been found in the Anza-Borrego Desert State Park in San Diego County,
California.
Some prokaryotes are able to thrive and grow under conditions that would kill a plant or animal. Bacteria and archaea that grow
under extreme conditions are called extremophiles, meaning “lovers of extremes.” Extremophiles have been found in extreme
environments of all kinds, including the depths of the oceans, hot springs, the Arctic and the Antarctic, very dry places, deep inside
Earth, harsh chemical environments, and high radiation environments. Extremophiles give us a better understanding of prokaryotic
diversity and open up the possibility of the discovery of new therapeutic drugs or industrial applications. They have also opened up
the possibility of finding life in other places in the solar system, which have harsher environments than those typically found on
Earth. Many of these extremophiles cannot survive in moderate environments.

Biofilms
Until a couple of decades ago, microbiologists thought of prokaryotes as isolated entities living apart. This model, however, does
not reflect the true ecology of prokaryotes, most of which prefer to live in communities where they can interact. A biofilm is a
microbial community held together in a gummy-textured matrix, consisting primarily of polysaccharides secreted by the organisms,
together with some proteins and nucleic acids. Biofilms grow attached to surfaces. Some of the best-studied biofilms are composed
of prokaryotes, although fungal biofilms have also been described.
Biofilms are present almost everywhere. They cause the clogging of pipes and readily colonize surfaces in industrial settings. They
have played roles in recent, large-scale outbreaks of bacterial contamination of food. Biofilms also colonize household surfaces,

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such as kitchen counters, cutting boards, sinks, and toilets.
Interactions among the organisms that populate a biofilm, together with their protective environment, make these communities
more robust than are free-living, or planktonic, prokaryotes. Overall, biofilms are very difficult to destroy, because they are
resistant to many of the common forms of sterilization.

Characteristics of Prokaryotes
There are many differences between prokaryotic and eukaryotic cells. However, all cells have four common structures: a plasma
membrane that functions as a barrier for the cell and separates the cell from its environment; cytoplasm, a jelly-like substance
inside the cell; genetic material (DNA and RNA); and ribosomes, where protein synthesis takes place. Prokaryotes come in various
shapes, but many fall into three categories: cocci (spherical), bacilli (rod-shaped), and spirilla (spiral-shaped) (Figure [Link]).

Figure [Link]: Many prokaryotes fall into three basic categories based on their shape: (a) cocci, or spherical; (b) bacilli, or rod-
shaped; and (c) spirilla, or spiral-shaped. (credit a: modification of work by Janice Haney Carr, Dr. Richard Facklam, CDC; credit
c: modification of work by Dr. David Cox, CDC; scale-bar data from Matt Russell)

The Prokaryotic Cell

Recall that prokaryotes (Figure [Link]) are unicellular organisms that lack organelles surrounded by membranes. Therefore, they
do not have a nucleus but instead have a single chromosome—a piece of circular DNA located in an area of the cell called the
nucleoid. Most prokaryotes have a cell wall lying outside the plasma membrane. The composition of the cell wall differs
significantly between the domains Bacteria and Archaea (and their cell walls also differ from the eukaryotic cell walls found in
plants and fungi.) The cell wall functions as a protective layer and is responsible for the organism’s shape. Some other structures
are present in some prokaryotic species, but not in others. For example, the capsule found in some species enables the organism to
attach to surfaces and protects it from dehydration. Some species may also have flagella (singular, flagellum) used for locomotion,
and pili (singular, pilus) used for attachment to surfaces and to other bacteria for conjugation. Plasmids, which consist of small,
circular pieces of DNA outside of the main chromosome, are also present in many species of bacteria.

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 Figure [Link]: The features of a typical bacterium cell are shown.
Both Bacteria and Archaea are types of prokaryotic cells. They differ in the lipid composition of their cell membranes and in the
characteristics of their cell walls. Both types of prokaryotes have the same basic structures, but these are built from different
chemical components that are evidence of an ancient separation of their lineages. The archaeal plasma membrane is chemically
different from the bacterial membrane; some archaeal membranes are lipid monolayers instead of phosopholipid bilayers.

The Cell Wall

The cell wall is a protective layer that surrounds some prokaryotic cells and gives them shape and rigidity. It is located outside the
cell membrane and prevents osmotic lysis (bursting caused by increasing volume). The chemical compositions of the cell walls
vary between Archaea and Bacteria, as well as between bacterial species. Bacterial cell walls contain peptidoglycan, composed of
polysaccharide chains cross-linked to peptides. Bacteria are divided into two major groups: Gram-positive and Gram-negative,
based on their reaction to a procedure called Gram staining. The different bacterial responses to the staining procedure are caused
by cell wall structure. Gram-positive organisms have a thick wall consisting of many layers of peptidoglycan. Gram-negative
bacteria have a thinner cell wall composed of a few layers of peptidoglycan and additional structures, surrounded by an outer
membrane (Figure [Link]).

ART CONNECTION

Figure [Link]: Bacteria are divided into two major groups: Gram-positive and Gram-negative. Both groups have a cell
wall composed of peptidoglycans: In Gram-positive bacteria, the wall is thick, whereas in Gram-negative bacteria, the wall is
thin. In Gram-negative bacteria, the cell wall is surrounded by an outer membrane.
Which of the following statements is true?
A. Gram-positive bacteria have a single cell wall formed from peptidoglycan.
B. Gram-positive bacteria have an outer membrane.
C. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
D. Gram-negative bacteria have a cell wall made of peptidoglycan, while Gram-positive bacteria have a cell wall made of
phospholipids.

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Archaeal cell walls do not contain peptidoglycan. There are four different types of archaeal cell walls. One type is composed of
pseudopeptidoglycan. The other three types of cell walls contain polysaccharides, glycoproteins, and surface-layer proteins known
as S-layers.

Reproduction
Reproduction in prokaryotes is primarily asexual and takes place by binary fission. Recall that the DNA of a prokaryote exists
usually as a single, circular chromosome. Prokaryotes do not undergo mitosis. Rather, the chromosome loop is replicated, and the
two resulting copies attached to the plasma membrane move apart as the cell grows in a process called binary fission. The
prokaryote, now enlarged, is pinched inward at its equator, and the two resulting cells, which are clones, separate. Binary fission
does not provide an opportunity for genetic recombination, but prokaryotes can alter their genetic makeup in three ways.
In a process called transformation, the cell takes in DNA found in its environment that is shed by other prokaryotes, alive or dead.
A pathogen is an organism that causes a disease. If a nonpathogenic bacterium takes up DNA from a pathogen and incorporates the
new DNA in its own chromosome, it too may become pathogenic. In transduction, bacteriophages, the viruses that infect bacteria,
move DNA from one bacterium to another. Archaea have a different set of viruses that infect them and translocate genetic material
from one individual to another. During conjugation, DNA is transferred from one prokaryote to another by means of a pilus that
brings the organisms into contact with one another. The DNA transferred is usually a plasmid, but parts of the chromosome can
also be moved.
Cycles of binary fission can be very rapid, on the order of minutes for some species. This short generation time coupled with
mechanisms of genetic recombination result in the rapid evolution of prokaryotes, allowing them to respond to environmental
changes (such as the introduction of an antibiotic) very quickly.

How Prokaryotes Obtain Energy and Carbon

Prokaryotes are metabolically diverse organisms. Prokaryotes fill many niches on Earth, including being involved in nutrient cycles
such as the nitrogen and carbon cycles, decomposing dead organisms, and growing and multiplying inside living organisms,
including humans. Different prokaryotes can use different sources of energy to assemble macromolecules from smaller molecules.
Phototrophs obtain their energy from sunlight. Chemotrophs obtain their energy from chemical compounds.

Bacterial Diseases in Humans

Devastating pathogen-borne diseases and plagues, both viral and bacterial in nature, have affected and continue to affect humans. It
is worth noting that all pathogenic prokaryotes are Bacteria; there are no known pathogenic Archaea in humans or any other
organism. Pathogenic organisms evolved alongside humans. In the past, the true cause of these diseases was not understood, and
some cultures thought that diseases were a spiritual punishment or were mistaken about material causes. Over time, people came to
realize that staying apart from afflicted persons, improving sanitation, and properly disposing of the corpses and personal
belongings of victims of illness reduced their own chances of getting sick.

Historical Perspective
There are records of infectious diseases as far back as 3,000 B.C. A number of significant pandemics caused by Bacteria have been
documented over several hundred years. Some of the largest pandemics led to the decline of cities and cultures. Many were
zoonoses that appeared with the domestication of animals, as in the case of tuberculosis. A zoonosis is a disease that infects
animals but can be transmitted from animals to humans.
Infectious diseases remain among the leading causes of death worldwide. Their impact is less significant in many developed
countries, but they are important determiners of mortality in developing countries. The development of antibiotics did much to
lessen the mortality rates from bacterial infections, but access to antibiotics is not universal, and the overuse of antibiotics has led
to the development of resistant strains of bacteria. Public sanitation efforts that dispose of sewage and provide clean drinking water
have done as much or more than medical advances to prevent deaths caused by bacterial infections.
In 430 B.C., the plague of Athens killed one-quarter of the Athenian troops that were fighting in the Great Peloponnesian War. The
disease killed a quarter of the population of Athens in over 4 years and weakened Athens’ dominance and power. The source of the
plague may have been identified recently when researchers from the University of Athens were able to analyze DNA from teeth
recovered from a mass grave. The scientists identified nucleotide sequences from a pathogenic bacterium that causes typhoid
1
fever.

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From 541 to 750 A.D., an outbreak called the plague of Justinian (likely a bubonic plague) eliminated, by some estimates, one-
quarter to one-half of the human population. The population in Europe declined by 50 percent during this outbreak. Bubonic plague
would decimate Europe more than once.
One of the most devastating pandemics was the Black Death (1346 to 1361), which is believed to have been another outbreak of
bubonic plague caused by the bacterium Yersinia pestis. This bacterium is carried by fleas living on black rats. The Black Death
reduced the world’s population from an estimated 450 million to about 350 to 375 million. Bubonic plague struck London hard
again in the mid-1600s. There are still approximately 1,000 to 3,000 cases of plague globally each year. Although contracting
bubonic plague before antibiotics meant almost certain death, the bacterium responds to several types of modern antibiotics, and
mortality rates from plague are now very low.

CONCEPT IN ACTION

Secrets of the Black Death - by Nature…

Nature…

Watch a video on the modern understanding of the Black Death (bubonic plague) in Europe during the fourteenth century.

Over the centuries, Europeans developed resistance to many infectious diseases. However, European conquerors brought disease-
causing bacteria and viruses with them when they reached the Western hemisphere, triggering epidemics that completely devastated
populations of Native Americans (who had no natural resistance to many European diseases).

The Antibiotic Crisis

The word antibiotic comes from the Greek anti, meaning “against,” and bios, meaning “life.” An antibiotic is an organism-
produced chemical that is hostile to the growth of other organisms. Today’s news and media often address concerns about an
antibiotic crisis. Are antibiotics that were used to treat bacterial infections easily treatable in the past becoming obsolete? Are there
new “superbugs”—bacteria that have evolved to become more resistant to our arsenal of antibiotics? Is this the beginning of the
end of antibiotics? All of these questions challenge the healthcare community.
One of the main reasons for resistant bacteria is the overuse and incorrect use of antibiotics, such as not completing a full course of
prescribed antibiotics. The incorrect use of an antibiotic results in the natural selection of resistant forms of bacteria. The antibiotic
kills most of the infecting bacteria, and therefore only the resistant forms remain. These resistant forms reproduce, resulting in an
increase in the proportion of resistant forms over non-resistant ones.
Another problem is the excessive use of antibiotics in livestock. The routine use of antibiotics in animal feed promotes bacterial
resistance as well. In the United States, 70 percent of the antibiotics produced are fed to animals. The antibiotics are not used to
prevent disease, but to enhance production of their products.
Staphylococcus aureus, often called “staph,” is a common bacterium that can live in and on the human body, which usually is
easily treatable with antibiotics. A very dangerous strain, however, has made the news over the past few years (Figure [Link]).
This strain, methicillin-resistant Staphylococcus aureus (MRSA), is resistant to many commonly used antibiotics, including
methicillin, amoxicillin, penicillin, and oxacillin. While MRSA infections have been common among people in healthcare
facilities, it is appearing more commonly in healthy people who live or work in dense groups (like military personnel and
prisoners). The Journal of the American Medical Association reported that, among MRSA-afflicted persons in healthcare facilities,
2
the average age is 68 years, while people with “community-associated MRSA” (CA-MRSA) have an average age of 23 years.

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 Figure [Link]: This scanning electron micrograph shows methicillin-resistant Staphylococcus aureus bacteria, commonly
known as MRSA. (credit: modification of work by Janice Haney Carr, CDC; scale-bar data from Matt Russell)

In summary, society is facing an antibiotic crisis. Some scientists believe that after years of being protected from bacterial
infections by antibiotics, we may be returning to a time in which a simple bacterial infection could again devastate the human
population. Researchers are working on developing new antibiotics, but few are in the drug development pipeline, and it takes
many years to generate an effective and approved drug.

Foodborne Diseases
Prokaryotes are everywhere: They readily colonize the surface of any type of material, and food is not an exception. Outbreaks of
bacterial infection related to food consumption are common. A foodborne disease (colloquially called “food poisoning”) is an
illness resulting from the consumption of food contaminated with pathogenic bacteria, viruses, or other parasites. Although the
United States has one of the safest food supplies in the world, the Center for Disease Control and Prevention (CDC) has reported
3
that “76 million people get sick, more than 300,000 are hospitalized, and 5,000 Americans die each year from foodborne illness.”
The characteristics of foodborne illnesses have changed over time. In the past, it was relatively common to hear about sporadic
cases of botulism, the potentially fatal disease produced by a toxin from the anaerobic bacterium Clostridium botulinum. A can, jar,
or package created a suitable anaerobic environment where Clostridium could grow. Proper sterilization and canning procedures
have reduced the incidence of this disease.
Most cases of foodborne illnesses are now linked to produce contaminated by animal waste. For example, there have been serious,
produce-related outbreaks associated with raw spinach in the United States and with vegetable sprouts in Germany (Figure
[Link]). The raw spinach outbreak in 2006 was produced by the bacterium E. coli strain O157:H7. Most E. coli strains are not

particularly dangerous to humans, (indeed, they live in our large intestine), but O157:H7 is potentially fatal.

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 Figure [Link]: (a) Locally grown vegetable sprouts were the cause of a European E. coli outbreak that killed 31 people and
sickened about 3,000 in 2010. (b) Escherichia coli are shown here in a scanning electron micrograph. The strain of E. coli that
caused a deadly outbreak in Germany is a new one not involved in any previous E. coli outbreaks. It has acquired several antibiotic
resistance genes and specific genetic sequences involved in aggregation ability and virulence. It has recently been sequenced.
(credit b: Rocky Mountain Laboratories, NIAID, NIH; scale-bar data from Matt Russell)
All types of food can potentially be contaminated with harmful bacteria of different species. Recent outbreaks of Salmonella
reported by the CDC occurred in foods as diverse as peanut butter, alfalfa sprouts, and eggs.

CAREERS IN ACTION: Epidemiologist

Epidemiology is the study of the occurrence, distribution, and determinants of health and disease in a population. It is,
therefore, related to public health. An epidemiologist studies the frequency and distribution of diseases within human
populations and environments.
Epidemiologists collect data about a particular disease and track its spread to identify the original mode of transmission. They
sometimes work in close collaboration with historians to try to understand the way a disease evolved geographically and over
time, tracking the natural history of pathogens. They gather information from clinical records, patient interviews, and any other
available means. That information is used to develop strategies and design public health policies to reduce the incidence of a
disease or to prevent its spread. Epidemiologists also conduct rapid investigations in case of an outbreak to recommend
immediate measures to control it.
Epidemiologists typically have a graduate-level education. An epidemiologist often has a bachelor’s degree in some field and a
master’s degree in public health (MPH). Many epidemiologists are also physicians (and have an MD) or they have a PhD in an
associated field, such as biology or epidemiology.

Beneficial Prokaryotes
Not all prokaryotes are pathogenic. On the contrary, pathogens represent only a very small percentage of the diversity of the
microbial world. In fact, our life and all life on this planet would not be possible without prokaryotes.

Prokaryotes, and Food and Beverages

According to the United Nations Convention on Biological Diversity, biotechnology is “any technological application that uses
4
biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use.” The
concept of “specific use” involves some sort of commercial application. Genetic engineering, artificial selection, antibiotic
production, and cell culture are current topics of study in biotechnology. However, humans have used prokaryotes to create
products before the term biotechnology was even coined. And some of the goods and services are as simple as cheese, yogurt, sour
cream, vinegar, cured sausage, sauerkraut, and fermented seafood that contains both bacteria and archaea (Figure [Link]).

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 Figure [Link]: Some of the products derived from the use of prokaryotes in early biotechnology include (a) cheese, (b) salami,
(c) yogurt, and (d) fish sauce. (credit b: modification of work by Alisdair McDiarmid; credit c: modification of work by Kris
Miller; credit d: modification of work by Jane Whitney)

Cheese production began around 4,000 years ago when humans started to breed animals and process their milk. Evidence suggests
that cultured milk products, like yogurt, have existed for at least 4,000 years.

Using Prokaryotes to Clean up Our Planet: Bioremediation

Microbial bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants. Bioremediation has been used
to remove agricultural chemicals (pesticides and fertilizers) that leach from soil into groundwater. Certain toxic metals, such as
selenium and arsenic compounds, can also be removed from water by bioremediation. The reduction of SeO to SeO
2 −

4
and to
2 −
3

Se0 (metallic selenium) is a method used to remove selenium ions from water. Mercury is an example of a toxic metal that can be
removed from an environment by bioremediation. Mercury is an active ingredient of some pesticides; it is used in industry and is
also a byproduct of certain industries, such as battery production. Mercury is usually present in very low concentrations in natural
environments but it is highly toxic because it accumulates in living tissues. Several species of bacteria can carry out the
biotransformation of toxic mercury into nontoxic forms. These bacteria, such as Pseudomonas aeruginosa, can convert Hg2+ to
Hg0, which is nontoxic to humans.
Probably one of the most useful and interesting examples of the use of prokaryotes for bioremediation purposes is the cleanup of
oil spills. The importance of prokaryotes to petroleum bioremediation has been demonstrated in several oil spills in recent years,
such as the Exxon Valdez spill in Alaska (1989) (Figure [Link]), the Prestige oil spill in Spain (2002), the spill into the
Mediterranean from a Lebanon power plant (2006,) and more recently, the BP oil spill in the Gulf of Mexico (2010). To clean up
these spills, bioremediation is promoted by adding inorganic nutrients that help bacteria already present in the environment to grow.
Hydrocarbon-degrading bacteria feed on the hydrocarbons in the oil droplet, breaking them into inorganic compounds. Some

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species, such as Alcanivorax borkumensis, produce surfactants that solubilize the oil, while other bacteria degrade the oil into
carbon dioxide. In the case of oil spills in the ocean, ongoing, natural bioremediation tends to occur, inasmuch as there are oil-
consuming bacteria in the ocean prior to the spill. Under ideal conditions, it has been reported that up to 80 percent of the
nonvolatile components in oil can be degraded within 1 year of the spill. Other oil fractions containing aromatic and highly
branched hydrocarbon chains are more difficult to remove and remain in the environment for longer periods of time. Researchers
have genetically engineered other bacteria to consume petroleum products; indeed, the first patent application for a bioremediation
application in the U.S. was for a genetically modified oil-eating bacterium.

Figure [Link]: (a) Cleaning up oil after the Valdez spill in Alaska, the workers hosed oil from beaches and then used a floating
boom to corral the oil, which was finally skimmed from the water surface. Some species of bacteria are able to solubilize and
degrade the oil. (b) One of the most catastrophic consequences of oil spills is the damage to fauna. (credit a: modification of work
by NOAA; credit b: modification of work by GOLUBENKOV, NGO: Saving Taman)

Prokaryotes in and on the Body

Humans are no exception when it comes to forming symbiotic relationships with prokaryotes. We are accustomed to thinking of
ourselves as single organisms, but in reality, we are walking ecosystems. There are 10 to 100 times as many bacterial and archaeal
cells inhabiting our bodies as we have cells in our bodies. Some of these are in mutually beneficial relationships with us, in which
both the human host and the bacterium benefit, while some of the relationships are classified as commensalism, a type of
relationship in which the bacterium benefits and the human host is neither benefited nor harmed.
Human gut flora lives in the large intestine and consists of hundreds of species of bacteria and archaea, with different individuals
containing different species mixes. The term “flora,” which is usually associated with plants, is traditionally used in this context
because bacteria were once classified as plants. The primary functions of these prokaryotes for humans appear to be metabolism of
food molecules that we cannot break down, assistance with the absorption of ions by the colon, synthesis of vitamin K, training of
the infant immune system, maintenance of the adult immune system, maintenance of the epithelium of the large intestine, and
formation of a protective barrier against pathogens.
The surface of the skin is also coated with prokaryotes. The different surfaces of the skin, such as the underarms, the head, and the
hands, provide different habitats for different communities of prokaryotes. Unlike with gut flora, the possible beneficial roles of
skin flora have not been well studied. However, the few studies conducted so far have identified bacteria that produce antimicrobial
compounds as probably responsible for preventing infections by pathogenic bacteria.
Researchers are actively studying the relationships between various diseases and alterations to the composition of human microbial
flora. Some of this work is being carried out by the Human Microbiome Project, funded in the United States by the National
Institutes of Health.

Section Summary
Prokaryotes existed for billions of years before plants and animals appeared. Microbial mats are thought to represent the earliest
forms of life on Earth, and there is fossil evidence, called stromatolites, of their presence about 3.5 billion years ago. During the
first 2 billion years, the atmosphere was anoxic and only anaerobic organisms were able to live. Cyanobacteria began the
oxygenation of the atmosphere. The increase in oxygen concentration allowed the evolution of other life forms.

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Prokaryotes (domains Archaea and Bacteria) are single-celled organisms lacking a nucleus. They have a single piece of circular
DNA in the nucleoid area of the cell. Most prokaryotes have cell wall outside the plasma membrane. Bacteria and Archaea differ in
the compositions of their cell membranes and the characteristics of their cell walls.
Bacterial cell walls contain peptidoglycan. Archaean cell walls do not have peptidoglycan. Bacteria can be divided into two major
groups: Gram-positive and Gram-negative. Gram-positive organisms have a thick cell wall. Gram-negative organisms have a thin
cell wall and an outer membrane. Prokaryotes use diverse sources of energy to assemble macromolecules from smaller molecules.
Phototrophs obtain their energy from sunlight, whereas chemotrophs obtain it from chemical compounds.
Infectious diseases caused by bacteria remain among the leading causes of death worldwide. The excessive use of antibiotics to
control bacterial infections has resulted in resistant forms of bacteria being selected. Foodborne diseases result from the
consumption of contaminated food, pathogenic bacteria, viruses, or parasites that contaminate food. Prokaryotes are used in human
food products. Microbial bioremediation is the use of microbial metabolism to remove pollutants. The human body contains a huge
community of prokaryotes, many of which provide beneficial services such as the development and maintenance of the immune
system, nutrition, and protection from pathogens.

Art Connections
Figure [Link]: Which of the following statements is true?
A. Gram-positive bacteria have a single cell wall formed from peptidoglycan.
B. Gram-positive bacteria have an outer membrane.
C. The cell wall of Gram-negative bacteria is thick, and the cell wall of Gram-positive bacteria is thin.
D. Gram-negative bacteria have a cell wall made of peptidoglycan, while Gram-positive bacteria have a cell wall made of
phospholipids.

Answer
A

Footnotes
1. 1 Papagrigorakis M. J., Synodinos P. N., Yapijakis C, “Ancient typhoid epidemic reveals possible ancestral strain of Salmonella
enterica serovar Typhi, Infect Genet Evol 7 (2007): 126-7.
2. 2 Naimi, T. S., LeDell, K. H., Como-Sabetti, K., et al., “Comparison of community- and health care-associated methicillin-
resistant Staphylococcus aureus infection,” JAMA 290 (2003): 2976-2984, doi: 10.1001/jama.290.22.2976.
3. 3 [Link] Centers for Disease Control and Prevention, “Multi-state outbreak of E. coli
O157:H7 infections from spinach,” September-October (2006).
4. 4 [Link] United Nations Convention on Biological Diversity, “Article 2: Use of
Terms.”

Glossary

anaerobic
refers to organisms that grow without oxygen

anoxic
without oxygen

biofilm
a microbial community that is held together by a gummy-textured matrix

bioremediation
the use of microbial metabolism to remove pollutants

Black Death
a devastating pandemic that is believed to have been an outbreak of bubonic plague caused by the bacterium Yersinia pestis

botulism

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 a disease produce by the toxin of the anaerobic bacterium Clostridium botulinum

capsule
an external structure that enables a prokaryote to attach to surfaces and protects it from dehydration

commensalism
a symbiotic relationship in which one member benefits while the other member is not affected

conjugation
the process by which prokaryotes move DNA from one individual to another using a pilus

cyanobacteria
bacteria that evolved from early phototrophs and oxygenated the atmosphere; also known as blue-green algae

epidemic
a disease that occurs in an unusually high number of individuals in a population at the same time

extremophile
an organism that grows under extreme or harsh conditions

foodborne disease
any illness resulting from the consumption of contaminated food, or of the pathogenic bacteria, viruses, or other parasites that
contaminate food

Gram-negative
describes a bacterium whose cell wall contains little peptidoglycan but has an outer membrane

Gram-positive
describes a bacterium that contains mainly peptidoglycan in its cell walls

hydrothermal vent
a fissure in Earth’s surface that releases geothermally heated water

microbial mat
a multi-layered sheet of prokaryotes that may include bacteria and archaea

MRSA
(methicillin-resistant Staphylococcus aureus) a very dangerous Staphylococcus aureus strain resistant to antibiotics

pandemic
a widespread, usually worldwide, epidemic disease

pathogen
an organism, or infectious agent, that causes a disease

peptidoglycan
a material composed of polysaccharide chains cross-linked to unusual peptides

phototroph
an organism that uses energy from sunlight

pseudopeptidoglycan
a component of some cell walls of Archaea

stromatolite
a layered sedimentary structure formed by precipitation of minerals by prokaryotes in microbial mats

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transduction
the process by which a bacteriophage moves DNA from one prokaryote to another

transformation
a mechanism of genetic change in prokaryotes in which DNA present in the environment is taken into the cell and incorporated
into the genome

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.1.1: Prokaryotic Diversity is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
13.1: Prokaryotic Diversity by OpenStax is licensed CC BY 4.0.

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13.1.2: Eukaryotic Origins
The fossil record and genetic evidence suggest that prokaryotic cells were the first organisms on Earth. These cells originated
approximately 3.5 billion years ago, which was about 1 billion years after Earth’s formation, and were the only life forms on the
planet until eukaryotic cells emerged approximately 2.1 billion years ago. During the prokaryotic reign, photosynthetic prokaryotes
evolved that were capable of applying the energy from sunlight to synthesize organic materials (like carbohydrates) from carbon
dioxide and an electron source (such as hydrogen, hydrogen sulfide, or water).
Photosynthesis using water as an electron donor consumes carbon dioxide and releases molecular oxygen (O2) as a byproduct. The
functioning of photosynthetic bacteria over millions of years progressively saturated Earth’s water with oxygen and then
oxygenated the atmosphere, which previously contained much greater concentrations of carbon dioxide and much lower
concentrations of oxygen. Older anaerobic prokaryotes of the era could not function in their new, aerobic environment. Some
species perished, while others survived in the remaining anaerobic environments left on Earth. Still other early prokaryotes evolved
mechanisms, such as aerobic respiration, to exploit the oxygenated atmosphere by using oxygen to store energy contained within
organic molecules. Aerobic respiration is a more efficient way of obtaining energy from organic molecules, which contributed to
the success of these species (as evidenced by the number and diversity of aerobic organisms living on Earth today). The evolution
of aerobic prokaryotes was an important step toward the evolution of the first eukaryote, but several other distinguishing features
had to evolve as well.

Endosymbiosis
The origin of eukaryotic cells was largely a mystery until a revolutionary hypothesis was comprehensively examined in the 1960s
by Lynn Margulis. The endosymbiotic theory states that eukaryotes are a product of one prokaryotic cell engulfing another, one
living within another, and evolving together over time until the separate cells were no longer recognizable as such. This once-
revolutionary hypothesis had immediate persuasiveness and is now widely accepted, with work progressing on uncovering the
steps involved in this evolutionary process as well as the key players. It has become clear that many nuclear eukaryotic genes and
the molecular machinery responsible for replicating and expressing those genes appear closely related to the Archaea. On the other
hand, the metabolic organelles and the genes responsible for many energy-harvesting processes had their origins in bacteria. Much
remains to be clarified about how this relationship occurred; this continues to be an exciting field of discovery in biology. Several
endosymbiotic events likely contributed to the origin of the eukaryotic cell.

Mitochondria
Eukaryotic cells may contain anywhere from one to several thousand mitochondria, depending on the cell’s level of energy
consumption. Each mitochondrion measures 1 to 10 micrometers in length and exists in the cell as a moving, fusing, and dividing
oblong spheroid (Figure [Link]). However, mitochondria cannot survive outside the cell. As the atmosphere was oxygenated by
photosynthesis, and as successful aerobic prokaryotes evolved, evidence suggests that an ancestral cell engulfed and kept alive a
free-living, aerobic prokaryote. This gave the host cell the ability to use oxygen to release energy stored in nutrients. Several lines
of evidence support that mitochondria are derived from this endosymbiotic event. Mitochondria are shaped like a specific group of
bacteria and are surrounded by two membranes, which would result when one membrane-bound organism was engulfed by another
membrane-bound organism. The mitochondrial inner membrane involves substantial infoldings or cristae that resemble the textured
outer surface of certain bacteria.

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 Figure [Link]: In this transmission electron micrograph of mitochondria in a mammalian lung cell, the cristae, infoldings of the
mitochondrial inner membrane, can be seen in cross-section. (credit: modification of work by Louisa Howard; scale-bar data from
Matt Russell)
Mitochondria divide on their own by a process that resembles binary fission in prokaryotes. Mitochondria have their own circular
DNA chromosome that carries genes similar to those expressed by bacteria. Mitochondria also have special ribosomes and transfer
RNAs that resemble these components in prokaryotes. These features all support that mitochondria were once free-living
prokaryotes.

Chloroplasts
Chloroplasts are one type of plastid, a group of related organelles in plant cells that are involved in the storage of starches, fats,
proteins, and pigments. Chloroplasts contain the green pigment chlorophyll and play a role in photosynthesis. Genetic and
morphological studies suggest that plastids evolved from the endosymbiosis of an ancestral cell that engulfed a photosynthetic
cyanobacterium. Plastids are similar in size and shape to cyanobacteria and are enveloped by two or more membranes,
corresponding to the inner and outer membranes of cyanobacteria. Like mitochondria, plastids also contain circular genomes and
divide by a process reminiscent of prokaryotic cell division. The chloroplasts of red and green algae exhibit DNA sequences that
are closely related to photosynthetic cyanobacteria, suggesting that red and green algae are direct descendants of this
endosymbiotic event.
Mitochondria likely evolved before plastids because all eukaryotes have either functional mitochondria or mitochondria-like
organelles. In contrast, plastids are only found in a subset of eukaryotes, such as terrestrial plants and algae. One hypothesis of the
evolutionary steps leading to the first eukaryote is summarized in Figure [Link].

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 Figure [Link]: The first eukaryote may have originated from an ancestral prokaryote that had undergone membrane
proliferation, compartmentalization of cellular function (into a nucleus, lysosomes, and an endoplasmic reticulum), and the
establishment of endosymbiotic relationships with an aerobic prokaryote and, in some cases, a photosynthetic prokaryote to form
mitochondria and chloroplasts, respectively.
The exact steps leading to the first eukaryotic cell can only be hypothesized, and some controversy exists regarding which events
actually took place and in what order. Spirochete bacteria have been hypothesized to have given rise to microtubules, and a
flagellated prokaryote may have contributed the raw materials for eukaryotic flagella and cilia. Other scientists suggest that
membrane proliferation and compartmentalization, not endosymbiotic events, led to the development of mitochondria and plastids.
However, the vast majority of studies support the endosymbiotic hypothesis of eukaryotic evolution.
The early eukaryotes were unicellular like most protists are today, but as eukaryotes became more complex, the evolution of
multicellularity allowed cells to remain small while still exhibiting specialized functions. The ancestors of today’s multicellular
eukaryotes are thought to have evolved about 1.5 billion years ago.

Section Summary
The first eukaryotes evolved from ancestral prokaryotes by a process that involved membrane proliferation, the loss of a cell wall,
the evolution of a cytoskeleton, and the acquisition and evolution of organelles. Nuclear eukaryotic genes appear to have had an
origin in the Archaea, whereas the energy machinery of eukaryotic cells appears to be bacterial in origin. The mitochondria and
plastids originated from endosymbiotic events when ancestral cells engulfed an aerobic bacterium (in the case of mitochondria) and
a photosynthetic bacterium (in the case of chloroplasts). The evolution of mitochondria likely preceded the evolution of
chloroplasts. There is evidence of secondary endosymbiotic events in which plastids appear to be the result of endosymbiosis after
a previous endosymbiotic event.

Glossary
endosymbiosis
the engulfment of one cell by another such that the engulfed cell survives and both cells benefit; the process responsible for the
evolution of mitochondria and chloroplasts in eukaryotes

plastid
one of a group of related organelles in plant cells that are involved in the storage of starches, fats, proteins, and pigments

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.1.2: Eukaryotic Origins is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
13.2: Eukaryotic Origins by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

13.1.3: Protists

Figure [Link]: Protists range from the microscopic, single-celled (a) Acanthocystis turfacea and the (b) ciliate Tetrahymena
thermophila to the enormous, multicellular (c) kelps (Chromalveolata) that extend for hundreds of feet in underwater “forests.”
(credit a: modification of work by Yuiuji Tsukii; credit b: modification of work by Richard Robinson, Public Library of Science;
credit c: modification of work by Kip Evans, NOAA; scale-bar data from Matt Russell)
Eukaryotic organisms that did not fit the criteria for the kingdoms Animalia, Fungi, or Plantae historically were called protists and
were classified into the kingdom Protista. Protists include the single-celled eukaryotes living in pond water (Figure [Link]),
although protist species live in a variety of other aquatic and terrestrial environments, and occupy many different niches. Not all
protists are microscopic and single-celled; there exist some very large multicellular species, such as the kelps. During the past two
decades, the field of molecular genetics has demonstrated that some protists are more related to animals, plants, or fungi than they
are to other protists. For this reason, protist lineages originally classified into the kingdom Protista have been reassigned into new
kingdoms or other existing kingdoms. The evolutionary lineages of the protists continue to be examined and debated. In the
meantime, the term “protist” still is used informally to describe this tremendously diverse group of eukaryotes. As a collective
group, protists display an astounding diversity of morphologies, physiologies, and ecologies.

Characteristics of Protists
There are over 100,000 described living species of protists, and it is unclear how many undescribed species may exist. Since many
protists live in symbiotic relationships with other organisms and these relationships are often species specific, there is a huge
potential for undescribed protist diversity that matches the diversity of the hosts. As the catchall term for eukaryotic organisms that
are not animals, plants, fungi, or any single phylogenetically related group, it is not surprising that few characteristics are common
to all protists.
Nearly all protists exist in some type of aquatic environment, including freshwater and marine environments, damp soil, and even
snow. Several protist species are parasites that infect animals or plants. A parasite is an organism that lives on or in another
organism and feeds on it, often without killing it. A few protist species live on dead organisms or their wastes, and contribute to
their decay.

Protist Structure
The cells of protists are among the most elaborate of all cells. Most protists are microscopic and unicellular, but some true
multicellular forms exist. A few protists live as colonies that behave in some ways as a group of free-living cells and in other ways
as a multicellular organism. Still other protists are composed of enormous, multinucleate, single cells that look like amorphous
blobs of slime or, in other cases, like ferns. In fact, many protist cells are multinucleated; in some species, the nuclei are different
sizes and have distinct roles in protist cell function.

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Single protist cells range in size from less than a micrometer to the 3-meter lengths of the multinucleate cells of the seaweed
Caulerpa. Protist cells may be enveloped by animal-like cell membranes or plant-like cell walls. Others are encased in glassy
silica-based shells or wound with pellicles of interlocking protein strips. The pellicle functions like a flexible coat of armor,
preventing the protist from being torn or pierced without compromising its range of motion.
The majority of protists are motile, but different types of protists have evolved varied modes of movement. Some protists have one
or more flagella, which they rotate or whip. Others are covered in rows or tufts of tiny cilia that they beat in coordination to swim.
Still others send out lobe-like pseudopodia from anywhere on the cell, anchor the pseudopodium to a substrate, and pull the rest of
the cell toward the anchor point. Some protists can move toward light by coupling their locomotion strategy with a light-sensing
organ.

How Protists Obtain Energy

Protists exhibit many forms of nutrition and may be aerobic or anaerobic. Photosynthetic protists (photoautotrophs) are
characterized by the presence of chloroplasts. Other protists are heterotrophs and consume organic materials (such as other
organisms) to obtain nutrition. Amoebas and some other heterotrophic protist species ingest particles by a process called
phagocytosis, in which the cell membrane engulfs a food particle and brings it inward, pinching off an intracellular membranous
sac, or vesicle, called a food vacuole (Figure [Link]). This vesicle then fuses with a lysosome, and the food particle is broken
down into small molecules that can diffuse into the cytoplasm and be used in cellular metabolism. Undigested remains ultimately
are expelled from the cell through exocytosis.

Figure [Link]: The stages of phagocytosis include the engulfment of a food particle, the digestion of the particle using
hydrolytic enzymes contained within a lysosome, and the expulsion of undigested material from the cell.
Some heterotrophs absorb nutrients from dead organisms or their organic wastes, and others are able to use photosynthesis or feed
on organic matter, depending on conditions.

Reproduction
Protists reproduce by a variety of mechanisms. Most are capable some form of asexual reproduction, such as binary fission to
produce two daughter cells, or multiple fission to divide simultaneously into many daughter cells. Others produce tiny buds that go
on to divide and grow to the size of the parental protist. Sexual reproduction, involving meiosis and fertilization, is common among
protists, and many protist species can switch from asexual to sexual reproduction when necessary. Sexual reproduction is often
associated with periods when nutrients are depleted or environmental changes occur. Sexual reproduction may allow the protist to
recombine genes and produce new variations of progeny that may be better suited to surviving in the new environment. However,
sexual reproduction is also often associated with cysts that are a protective, resting stage. Depending on their habitat, the cysts may
be particularly resistant to temperature extremes, desiccation, or low pH. This strategy also allows certain protists to “wait out”
stressors until their environment becomes more favorable for survival or until they are carried (such as by wind, water, or transport
on a larger organism) to a different environment because cysts exhibit virtually no cellular metabolism.

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Protist Diversity
With the advent of DNA sequencing, the relationships among protist groups and between protist groups and other eukaryotes are
beginning to become clearer. Many relationships that were based on morphological similarities are being replaced by new
relationships based on genetic similarities. Protists that exhibit similar morphological features may have evolved analogous
structures because of similar selective pressures—rather than because of recent common ancestry. This phenomenon is called
convergent evolution. It is one reason why protist classification is so challenging. The emerging classification scheme groups the
entire domain Eukaryota into six “supergroups” that contain all of the protists as well as animals, plants, and fungi (Figure
[Link]); these include the Excavata, Chromalveolata, Rhizaria, Archaeplastida, Amoebozoa, and Opisthokonta. The supergroups

are believed to be monophyletic; all organisms within each supergroup are believed to have evolved from a single common
ancestor, and thus all members are most closely related to each other than to organisms outside that group. There is still evidence
lacking for the monophyly of some groups.

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 Figure [Link]: Protists appear in all six eukaryotic supergroups.

Human Pathogens
Many protists are pathogenic parasites that must infect other organisms to survive and propagate. Protist parasites include the
causative agents of malaria, African sleeping sickness, and waterborne gastroenteritis in humans. Other protist pathogens prey on
plants, effecting massive destruction of food crops.

Plasmodium Species
Members of the genus Plasmodium must infect a mosquito and a vertebrate to complete their life cycle. In vertebrates, the parasite
develops in liver cells and goes on to infect red blood cells, bursting from and destroying the blood cells with each asexual
replication cycle (Figure [Link]). Of the four Plasmodium species known to infect humans, P. falciparum accounts for 50 percent
of all malaria cases and is the primary cause of disease-related fatalities in tropical regions of the world. In 2010, it was estimated

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that malaria caused between 0.5 and 1 million deaths, mostly in African children. During the course of malaria, P. falciparum can
infect and destroy more than one-half of a human’s circulating blood cells, leading to severe anemia. In response to waste products
released as the parasites burst from infected blood cells, the host immune system mounts a massive inflammatory response with
delirium-inducing fever episodes, as parasites destroy red blood cells, spilling parasite waste into the blood stream. P. falciparum is
transmitted to humans by the African malaria mosquito, Anopheles gambiae. Techniques to kill, sterilize, or avoid exposure to this
highly aggressive mosquito species are crucial to malaria control.

Figure [Link]: This light micrograph shows a 100× magnification of red blood cells infected with P. falciparum (seen as
purple). (credit: modification of work by Michael Zahniser; scale-bar data from Matt Russell)

Trypanosomes
T. brucei, the parasite that is responsible for African sleeping sickness, confounds the human immune system by changing its thick
layer of surface glycoproteins with each infectious cycle (Figure [Link]). The glycoproteins are identified by the immune system
as foreign matter, and a specific antibody defense is mounted against the parasite. However, T. brucei has thousands of possible
antigens, and with each subsequent generation, the protist switches to a glycoprotein coating with a different molecular structure. In
this way, T. brucei is capable of replicating continuously without the immune system ever succeeding in clearing the parasite.
Without treatment, African sleeping sickness leads invariably to death because of damage it does to the nervous system. During
epidemic periods, mortality from the disease can be high. Greater surveillance and control measures have led to a reduction in
reported cases; some of the lowest numbers reported in 50 years (fewer than 10,000 cases in all of sub-Saharan Africa) have
happened since 2009.
In Latin America, another species in the genus, T. cruzi, is responsible for Chagas disease. T. cruzi infections are mainly caused by
a blood-sucking bug. The parasite inhabits heart and digestive system tissues in the chronic phase of infection, leading to
malnutrition and heart failure caused by abnormal heart rhythms. An estimated 10 million people are infected with Chagas disease,
which caused 10,000 deaths in 2008.

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 Figure [Link]: Trypanosomes are shown in this light micrograph among red blood cells. (credit: modification of work by
Myron G. Schultz, CDC; scale-bar data from Matt Russell)

Plant Parasites
Protist parasites of terrestrial plants include agents that destroy food crops. The oomycete Plasmopara viticola parasitizes grape
plants, causing a disease called downy mildew (Figure 13.1.3.6a). Grape plants infected with P. viticola appear stunted and have
discolored withered leaves. The spread of downy mildew caused the near collapse of the French wine industry in the nineteenth
century.

Figure [Link]: (a) The downy and powdery mildews on this grape leaf are caused by an infection of P. viticola. (b) This potato
exhibits the results of an infection with P. infestans, the potato late blight. (credit a: modification of work by David B. Langston,
University of Georgia, USDA ARS; credit b: USDA ARS)
Phytophthora infestans is an oomycete responsible for potato late blight, which causes potato stalks and stems to decay into black
slime (Figure 13.1.3.6b). Widespread potato blight caused by P. infestans precipitated the well-known Irish potato famine in the
nineteenth century that claimed the lives of approximately 1 million people and led to the emigration from Ireland of at least 1
million more. Late blight continues to plague potato crops in certain parts of the United States and Russia, wiping out as much as
70 percent of crops when no pesticides are applied.

Beneficial Protists
Protists play critically important ecological roles as producers particularly in the world’s oceans. They are equally important on the
other end of food webs as decomposers.

Protists as Food Sources

Protists are essential sources of nutrition for many other organisms. In some cases, as in plankton, protists are consumed directly.
Alternatively, photosynthetic protists serve as producers of nutrition for other organisms by carbon fixation. For instance,

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photosynthetic dinoflagellates called zooxanthellae pass on most of their energy to the coral polyps that house them (Figure
[Link]). In this mutually beneficial relationship, the polyps provide a protective environment and nutrients for the zooxanthellae.

The polyps secrete the calcium carbonate that builds coral reefs. Without dinoflagellate symbionts, corals lose algal pigments in a
process called coral bleaching, and they eventually die. This explains why reef-building corals do not reside in waters deeper than
20 meters: Not enough light reaches those depths for dinoflagellates to photosynthesize.

Figure [Link]: Coral polyps obtain nutrition through a symbiotic relationship with dinoflagellates.
Protists themselves and their products of photosynthesis are essential—directly or indirectly—to the survival of organisms ranging
from bacteria to mammals. As primary producers, protists feed a large proportion of the world’s aquatic species. (On land,
terrestrial plants serve as primary producers.) In fact, approximately one-quarter of the world’s photosynthesis is conducted by
protists, particularly dinoflagellates, diatoms, and multicellular algae.
Protists do not create food sources only for sea-dwelling organisms. For instance, certain anaerobic species exist in the digestive
tracts of termites and wood-eating cockroaches, where they contribute to digesting cellulose ingested by these insects as they bore
through wood. The actual enzyme used to digest the cellulose is actually produced by bacteria living within the protist cells. The
termite provides the food source to the protist and its bacteria, and the protist and bacteria provide nutrients to the termite by
breaking down the cellulose.

Agents of Decomposition
Many fungus-like protists are saprobes, organisms that feed on dead organisms or the waste matter produced by organisms
(saprophyte is an equivalent term), and are specialized to absorb nutrients from nonliving organic matter. For instance, many types
of oomycetes grow on dead animals or algae. Saprobic protists have the essential function of returning inorganic nutrients to the
soil and water. This process allows for new plant growth, which in turn generates sustenance for other organisms along the food
chain. Indeed, without saprobic species, such as protists, fungi, and bacteria, life would cease to exist as all organic carbon became
“tied up” in dead organisms.

Section Summary
Protists are extremely diverse in terms of biological and ecological characteristics due in large part to the fact that they are an
artificial assemblage of phylogenetically unrelated groups. Protists display highly varied cell structures, several types of
reproductive strategies, virtually every possible type of nutrition, and varied habitats. Most single-celled protists are motile, but
these organisms use diverse structures for transportation.
The process of classifying protists into meaningful groups is ongoing, but genetic data in the past 20 years have clarified many
relationships that were previously unclear or mistaken. The majority view at present is to order all eukaryotes into six supergroups.
The goal of this classification scheme is to create clusters of species that all are derived from a common ancestor.

Glossary

Amoebozoa

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 the eukaryotic supergroup that contains the amoebas and slime molds

Archaeplastida
the eukaryotic supergroup that contains land plants, green algae, and red algae

Chromalveolata
the eukaryotic supergroup that contains the dinoflagellates, ciliates, the brown algae, diatoms, and water molds

Excavata
the eukaryotic supergroup that contains flagellated single-celled organisms with a feeding groove

Opisthokonta
the eukaryotic supergroup that contains the fungi, animals, and choanoflagellates

parasite
an organism that lives on or in another organism and feeds on it, often without killing it

pellicle
an outer cell covering composed of interlocking protein strips that function like a flexible coat of armor, preventing cells from
being torn or pierced without compromising their range of motion

Rhizaria
the eukaryotic supergroup that contains organisms that move by amoeboid movement

saprobe
an organism that feeds on dead organic material

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.1.3: Protists is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
13.3: Protists by OpenStax is licensed CC BY 4.0.

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13.1.4: Fungi

Figure [Link]: The (a) familiar mushroom is only one type of fungus. The brightly colored fruiting bodies of this (b) coral
fungus are displayed. This (c) electron micrograph shows the spore-bearing structures of Aspergillus, a type of toxic fungi found
mostly in soil and plants. (credit a: modification of work by Chris Wee; credit b: modification of work by Cory Zanker; credit c:
modification of work by Janice Haney Carr, Robert Simmons, CDC; scale-bar data from Matt Russell)
The word fungus comes from the Latin word for mushroom. Indeed, the familiar mushrooms are fungi, but there are many other
types of fungi as well (Figure [Link]). The kingdom Fungi includes an enormous variety of living organisms collectively referred
to as Eumycota, or true fungi. While scientists have identified about 100,000 species of fungi, this is only a fraction of the over 1
million species likely present on Earth. Edible mushrooms, yeasts, black mold, and Penicillium notatum (the producer of the
antibiotic penicillin) are all members of the kingdom Fungi, which belongs to the domain Eukarya. As eukaryotes, a typical fungal
cell contains a true nucleus and many membrane-bound organelles.
Fungi were once considered plant-like organisms; however, DNA comparisons have shown that fungi are more closely related to
animals than plants. Fungi are not capable of photosynthesis: They use complex organic compounds as sources of energy and
carbon. Some fungal organisms multiply only asexually, whereas others undergo both asexual reproduction and sexual
reproduction. Most fungi produce a large number of spores that are disseminated by the wind. Like bacteria, fungi play an essential
role in ecosystems, because they are decomposers and participate in the cycling of nutrients by breaking down organic materials
into simple molecules.
Fungi often interact with other organisms, forming mutually beneficial or mutualistic associations. Fungi also cause serious
infections in plants and animals. For example, Dutch elm disease is a particularly devastating fungal infection that destroys many
native species of elm (Ulmus spp.). The fungus infects the vascular system of the tree. It was accidentally introduced to North
America in the 1900s and decimated elm trees across the continent. Dutch elm disease is caused by the fungus Ophiostoma ulmi.
The elm bark beetle acts as a vector and transmits the disease from tree to tree. Many European and Asiatic elms are less
susceptible than American elms.
In humans, fungal infections are generally considered challenging to treat because, unlike bacteria, they do not respond to
traditional antibiotic therapy since they are also eukaryotes. These infections may prove deadly for individuals with a compromised
immune system.
Fungi have many commercial applications. The food industry uses yeasts in baking, brewing, and wine making. Many industrial
compounds are byproducts of fungal fermentation. Fungi are the source of many commercial enzymes and antibiotics.

Cell Structure and Function

Fungi are eukaryotes and as such have a complex cellular organization. As eukaryotes, fungal cells contain a membrane-bound
nucleus. A few types of fungi have structures comparable to the plasmids (loops of DNA) seen in bacteria. Fungal cells also

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contain mitochondria and a complex system of internal membranes, including the endoplasmic reticulum and Golgi apparatus.
Fungal cells do not have chloroplasts. Although the photosynthetic pigment chlorophyll is absent, many fungi display bright colors,
ranging from red to green to black. The poisonous Amanita muscaria (fly agaric) is recognizable by its bright red cap with white
patches (Figure [Link]). Pigments in fungi are associated with the cell wall and play a protective role against ultraviolet radiation.
Some pigments are toxic.

Figure [Link]: The poisonous Amanita muscaria is native to the temperate and boreal regions of North America. (credit:
Christine Majul)
Like plant cells, fungal cells are surrounded by a thick cell wall; however, the rigid layers contain the complex polysaccharides
chitin and glucan and not cellulose that is used by plants. Chitin, also found in the exoskeleton of insects, gives structural strength
to the cell walls of fungi. The cell wall protects the cell from desiccation and predators. Fungi have plasma membranes similar to
other eukaryotes, except that the structure is stabilized by ergosterol, a steroid molecule that functions like the cholesterol found in
animal cell membranes. Most members of the kingdom Fungi are nonmotile. Flagella are produced only by the gametes in the
primitive division Chytridiomycota.

Growth and Reproduction

The vegetative body of a fungus is called a thallus and can be unicellular or multicellular. Some fungi are dimorphic because they
can go from being unicellular to multicellular depending on environmental conditions. Unicellular fungi are generally referred to as
[Link] cerevisiae (baker’s yeast) and Candida species (the agents of thrush, a common fungal infection) are
examples of unicellular fungi.
Most fungi are multicellular organisms. They display two distinct morphological stages: vegetative and reproductive. The
vegetative stage is characterized by a tangle of slender thread-like structures called hyphae (singular, hypha), whereas the
reproductive stage can be more conspicuous. A mass of hyphae is called a mycelium (Figure [Link]). It can grow on a surface, in
soil or decaying material, in a liquid, or even in or on living tissue. Although individual hypha must be observed under a
microscope, the mycelium of a fungus can be very large with some species truly being “the fungus humongous.” The giant
Armillaria ostoyae (honey mushroom) is considered the largest organism on Earth, spreading across over 2,000 acres of
underground soil in eastern Oregon; it is estimated to be at least 2,400 years old.

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 Figure [Link]: The mycelium of the fungus Neotestudina rosati can be pathogenic to humans. The fungus enters through a cut
or scrape and develops into a mycetoma, a chronic subcutaneous infection. (credit: CDC)
Most fungal hyphae are divided into separate cells by end walls called septa (singular, septum). In most divisions (like plants,
fungal phyla are called divisions by tradition) of fungi, tiny holes in the septa allow for the rapid flow of nutrients and small
molecules from cell to cell along the hyphae. They are described as perforated septa. The hyphae in bread molds (which belong to
the division Zygomycota) are not separated by septa. They are formed of large cells containing many nuclei, an arrangement
described as coenocytic hyphae.
Fungi thrive in environments that are moist and slightly acidic, and can grow with or without light. They vary in their oxygen
requirements. Most fungi are obligate aerobes, requiring oxygen to survive. Other species, such as the Chytridiomycota that reside
in the rumen of cattle, are obligate anaerobes, meaning that they cannot grow and reproduce in an environment with oxygen. Yeasts
are intermediate: They grow best in the presence of oxygen but can use fermentation in the absence of oxygen. The alcohol
produced from yeast fermentation is used in wine and beer production, and the carbon dioxide they produce carbonates beer and
sparkling wine, and makes bread rise.
Fungi can reproduce sexually or asexually. In both sexual and asexual reproduction, fungi produce spores that disperse from the
parent organism by either floating in the wind or hitching a ride on an animal. Fungal spores are smaller and lighter than plant
seeds, but they are not usually released as high in the air. The giant puffball mushroom bursts open and releases trillions of spores:
The huge number of spores released increases the likelihood of spores landing in an environment that will support growth (Figure
[Link]).

Figure [Link]: The (a) giant puffball mushroom releases (b) a cloud of spores when it reaches maturity. (credit a: modification
of work by Roger Griffith; credit b: modification of work by Pearson Scott Foresman, donated to the Wikimedia Foundation)

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How Fungi Obtain Nutrition
Like animals, fungi are heterotrophs: They use complex organic compounds as a source of carbon rather than fixing carbon dioxide
from the atmosphere, as some bacteria and most plants do. In addition, fungi do not fix nitrogen from the atmosphere. Like
animals, they must obtain it from their diet. However, unlike most animals that ingest food and then digest it internally in
specialized organs, fungi perform these steps in the reverse order. Digestion precedes ingestion. First, exoenzymes, enzymes that
catalyze reactions on compounds outside of the cell, are transported out of the hyphae where they break down nutrients in the
environment. Then, the smaller molecules produced by the external digestion are absorbed through the large surface areas of the
mycelium. As with animal cells, the fungal storage polysaccharide is glycogen rather than starch, as found in plants.
Fungi are mostly saprobes, organisms that derive nutrients from decaying organic matter. They obtain their nutrients from dead or
decomposing organic matter, mainly plant material. Fungal exoenzymes are able to break down insoluble polysaccharides, such as
the cellulose and lignin of dead wood, into readily absorbable glucose molecules. Decomposers are important components of
ecosystems, because they return nutrients locked in dead bodies to a form that is usable for other organisms. This role is discussed
in more detail later. Because of their varied metabolic pathways, fungi fulfill an important ecological role and are being
investigated as potential tools in bioremediation. For example, some species of fungi can be used to break down diesel oil and
polycyclic aromatic hydrocarbons. Other species take up heavy metals such as cadmium and lead.

Fungal Diversity
The kingdom Fungi contains four major divisions that were established according to their mode of sexual reproduction.
Polyphyletic, unrelated fungi that reproduce without a sexual cycle, are placed for convenience in a fifth division, and a sixth major
fungal group that does not fit well with any of the previous five has recently been described. Not all mycologists agree with this
scheme. Rapid advances in molecular biology and the sequencing of 18S rRNA (a component of ribosomes) continue to reveal new
and different relationships between the various categories of fungi.
The traditional divisions of Fungi are the Chytridiomycota (chytrids), the Zygomycota(conjugated fungi), the Ascomycota (sac
fungi), and the Basidiomycota (club fungi). An older classification scheme grouped fungi that strictly use asexual reproduction into
Deuteromycota, a group that is no longer in use. The Glomeromycota belong to a newly described group (Figure [Link]).

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 Figure [Link]: Divisions of fungi include (a) chytrids, (b) conjugated fungi, (c) sac fungi, and (d) club fungi. (credit a:
modification of work by USDA APHIS PPQ; credit c: modification of work by "icelight"/Flickr; credit d: modification of work by
Cory Zanker.)

Pathogenic Fungi
Many fungi have negative impacts on other species, including humans and the organisms they depend on for food. Fungi may be
parasites, pathogens, and, in a very few cases, predators.

Plant Parasites and Pathogens

The production of enough good-quality crops is essential to our existence. Plant diseases have ruined crops, bringing widespread
famine. Most plant pathogens are fungi that cause tissue decay and eventual death of the host (Figure [Link]). In addition to
destroying plant tissue directly, some plant pathogens spoil crops by producing potent toxins. Fungi are also responsible for food
spoilage and the rotting of stored crops. For example, the fungus Claviceps purpurea causes ergot, a disease of cereal crops
(especially of rye). Although the fungus reduces the yield of cereals, the effects of the ergot’s alkaloid toxins on humans and
animals are of much greater significance: In animals, the disease is referred to as ergotism. The most common signs and symptoms
are convulsions, hallucination, gangrene, and loss of milk in cattle. The active ingredient of ergot is lysergic acid, which is a
precursor of the drug LSD. Smuts, rusts, and powdery or downy mildew are other examples of common fungal pathogens that
affect crops.

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 Figure [Link]: Some fungal pathogens include (a) green mold on grapefruit, (b) fungus on grapes, (c) powdery mildew on a
zinnia, and (d) stem rust on a sheaf of barley. Notice the brownish color of the fungus in (b) Botrytis cinerea, also referred to as the
“noble rot,” which grows on grapes and other fruit. Controlled infection of grapes by Botrytis is used to produce strong and much-
prized dessert wines. (credit a: modification of work by Scott Bauer, USDA ARS; credit b: modification of work by Stephen
Ausmus, USDA ARS; credit c: modification of work by David Marshall, USDA ARS; credit d: modification of work by Joseph
Smilanick, USDA ARS)
Aflatoxins are toxic and carcinogenic compounds released by fungi of the genus Aspergillus. Periodically, harvests of nuts and
grains are tainted by aflatoxins, leading to massive recall of produce, sometimes ruining producers, and causing food shortages in
developing countries.

Animal and Human Parasites and Pathogens

Fungi can affect animals, including humans, in several ways. Fungi attack animals directly by colonizing and destroying tissues.
Humans and other animals can be poisoned by eating toxic mushrooms or foods contaminated by fungi. In addition, individuals
who display hypersensitivity to molds and spores develop strong and dangerous allergic reactions. Fungal infections are generally
very difficult to treat because, unlike bacteria, fungi are eukaryotes. Antibiotics only target prokaryotic cells, whereas compounds
that kill fungi also adversely affect the eukaryotic animal host.
Many fungal infections (mycoses) are superficial and termed cutaneous (meaning “skin”) mycoses. They are usually visible on the
skin of the animal. Fungi that cause the superficial mycoses of the epidermis, hair, and nails rarely spread to the underlying tissue
(Figure [Link]). These fungi are often misnamed “dermatophytes” from the Greek dermis skin and phyte plant, but they are not
plants. Dermatophytes are also called “ringworms” because of the red ring that they cause on skin (although the ring is caused by
fungi, not a worm). These fungi secrete extracellular enzymes that break down keratin (a protein found in hair, skin, and nails),
causing a number of conditions such as athlete’s foot, jock itch, and other cutaneous fungal infections. These conditions are usually
treated with over-the-counter topical creams and powders, and are easily cleared. More persistent, superficial mycoses may require
prescription oral medications.

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 Figure [Link]: (a) Ringworm presents as a red ring on the skin. (b) Trichophyton violaceum is a fungus that causes superficial
mycoses on the scalp. (c) Histoplasma capsulatum, seen in this X-ray as speckling of light areas in the lung, is a species of
Ascomycota that infects airways and causes symptoms similar to the flu. (credit a, b: modification of work by Dr. Lucille K. Georg,
CDC; credit c: modification of work by M Renz, CDC; scale-bar data from Matt Russell)
Systemic mycoses spread to internal organs, most commonly entering the body through the respiratory system. For example,
coccidioidomycosis (valley fever) is commonly found in the southwestern United States, where the fungus resides in the dust. Once
inhaled, the spores develop in the lungs and cause signs and symptoms similar to those of tuberculosis. Histoplasmosis (Figure
13.1.4.7c) is caused by the dimorphic fungus Histoplasma capsulatum; it causes pulmonary infections and, in rare cases, swelling

of the membranes of the brain and spinal cord. Treatment of many fungal diseases requires the use of antifungal medications that
have serious side effects.
Opportunistic mycoses are fungal infections that are either common in all environments or part of the normal biota. They affect
mainly individuals who have a compromised immune system. Patients in the late stages of AIDS suffer from opportunistic
mycoses, such as Pneumocystis, which can be life threatening. The yeast Candida spp., which is a common member of the natural
biota, can grow unchecked if the pH, the immune defenses, or the normal population of bacteria is altered, causing yeast infections
of the vagina or mouth (oral thrush).
Fungi may even take on a predatory lifestyle. In soil environments that are poor in nitrogen, some fungi resort to predation of
nematodes (small roundworms). Species of Arthrobotrys fungi have a number of mechanisms to trap nematodes. For example, they
have constricting rings within their network of hyphae. The rings swell when the nematode touches it and closes around the body of
the nematode, thus trapping it. The fungus extends specialized hyphae that can penetrate the body of the worm and slowly digest
the hapless prey.

Beneficial Fungi
Fungi play a crucial role in the balance of ecosystems. They colonize most habitats on Earth, preferring dark, moist conditions.
They can thrive in seemingly hostile environments, such as the tundra, thanks to a most successful symbiosis with photosynthetic
organisms, like lichens. Fungi are not obvious in the way that large animals or tall trees are. Yet, like bacteria, they are major
decomposers of nature. With their versatile metabolism, fungi break down organic matter that is insoluble and would not be
recycled otherwise.

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Importance to Ecosystems
Food webs would be incomplete without organisms that decompose organic matter and fungi are key participants in this process.
Decomposition allows for cycling of nutrients such as carbon, nitrogen, and phosphorus back into the environment so they are
available to living things, rather than being trapped in dead organisms. Fungi are particularly important because they have evolved
enzymes to break down cellulose and lignin, components of plant cell walls that few other organisms are able to digest, releasing
their carbon content.
Fungi are also involved in ecologically important coevolved symbioses, both mutually beneficial and pathogenic with organisms
from the other kingdoms. Mycorrhiza, a term combining the Greek roots myco meaning fungus and rhizo meaning root, refers to
the association between vascular plant roots and their symbiotic fungi. Somewhere between 80–90 percent of all plant species have
mycorrhizal partners. In a mycorrhizal association, the fungal mycelia use their extensive network of hyphae and large surface area
in contact with the soil to channel water and minerals from the soil into the plant. In exchange, the plant supplies the products of
photosynthesis to fuel the metabolism of the fungus. Ectomycorrhizae (“outside” mycorrhiza) depend on fungi enveloping the roots
in a sheath (called a mantle) and a net of hyphae that extends into the roots between cells. In a second type, the Glomeromycota
fungi form arbuscular mycorrhiza. In these mycorrhiza, the fungi form arbuscles, a specialized highly branched hypha, which
penetrate root cells and are the sites of the metabolic exchanges between the fungus and the host plant. Orchids rely on a third type
of mycorrhiza. Orchids form small seeds without much storage to sustain germination and growth. Their seeds will not germinate
without a mycorrhizal partner (usually Basidiomycota). After nutrients in the seed are depleted, fungal symbionts support the
growth of the orchid by providing necessary carbohydrates and minerals. Some orchids continue to be mycorrhizal throughout their
lifecycle.
Lichens blanket many rocks and tree bark, displaying a range of colors and textures. Lichens are important pioneer organisms that
colonize rock surfaces in otherwise lifeless environments such as are created by glacial recession. The lichen is able to leach
nutrients from the rocks and break them down in the first step to creating soil. Lichens are also present in mature habitats on rock
surfaces or the trunks of trees. They are an important food source for caribou. Lichens are not a single organism, but rather a fungus
(usually an Ascomycota or Basidiomycota species) living in close contact with a photosynthetic organism (an alga or
cyanobacterium). The body of a lichen, referred to as a thallus, is formed of hyphae wrapped around the green partner. The
photosynthetic organism provides carbon and energy in the form of carbohydrates and receives protection from the elements by the
thallus of the fungal partner. Some cyanobacteria fix nitrogen from the atmosphere, contributing nitrogenous compounds to the
association. In return, the fungus supplies minerals and protection from dryness and excessive light by encasing the algae in its
mycelium. The fungus also attaches the symbiotic organism to the substrate.
Fungi have evolved mutualistic associations with numerous arthropods. The association between species of Basidiomycota and
scale insects is one example. The fungal mycelium covers and protects the insect colonies. The scale insects foster a flow of
nutrients from the parasitized plant to the fungus. In a second example, leaf-cutting ants of Central and South America literally
farm fungi. They cut disks of leaves from plants and pile them up in gardens. Fungi are cultivated in these gardens, digesting the
cellulose that the ants cannot break down. Once smaller sugar molecules are produced and consumed by the fungi, they in turn
become a meal for the ants. The insects also patrol their garden, preying on competing fungi. Both ants and fungi benefit from the
association. The fungus receives a steady supply of leaves and freedom from competition, while the ants feed on the fungi they
cultivate.

Importance to Humans
Although we often think of fungi as organisms that cause diseases and rot food, fungi are important to human life on many levels.
As we have seen, they influence the well-being of human populations on a large scale because they help nutrients cycle in
ecosystems. They have other ecosystem roles as well. For example, as animal pathogens, fungi help to control the population of
damaging pests. These fungi are very specific to the insects they attack and do not infect other animals or plants. The potential to
use fungi as microbial insecticides is being investigated, with several species already on the market. For example, the fungus
Beauveria bassiana is a pesticide that is currently being tested as a possible biological control for the recent spread of emerald ash
borer. It has been released in Michigan, Illinois, Indiana, Ohio, West Virginia, and Maryland.
The mycorrhizal relationship between fungi and plant roots is essential for the productivity of farmland. Without the fungal partner
in the root systems, 80–90% of trees and grasses would not survive. Mycorrhizal fungal inoculants are available as soil
amendments from gardening supply stores and promoted by supporters of organic agriculture.

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We also eat some types of fungi. Mushrooms figure prominently in the human diet. Morels, shiitake mushrooms, chanterelles, and
truffles are considered delicacies (Figure [Link]). The humble meadow mushroom, Agaricus campestris, appears in many dishes.
Molds of the genus Penicillium ripen many cheeses. They originate in the natural environment such as the caves of Roquefort,
France, where wheels of sheep milk cheese are stacked to capture the molds responsible for the blue veins and pungent taste of the
cheese.

Figure [Link]: The morel mushroom is an ascomycete that is much appreciated for its delicate taste. (credit: Jason Hollinger)
Fermentation—of grains to produce beer, and of fruits to produce wine—is an ancient art that humans in most cultures have
practiced for millennia. Wild yeasts are acquired from the environment and used to ferment sugars into CO2 and ethyl alcohol
under anaerobic conditions. It is now possible to purchase isolated strains of wild yeasts from different wine-making regions.
Pasteur was instrumental in developing a reliable strain of brewer’s yeast, Saccharomyces cerevisiae, for the French brewing
industry in the late 1850s. It was one of the first examples of biotechnology patenting. Yeast is also used to make breads that rise.
The carbon dioxide they produce is responsible for the bubbles produced in the dough that become the air pockets of the baked
bread.
Many secondary metabolites of fungi are of great commercial importance. Antibiotics are naturally produced by fungi to kill or
inhibit the growth of bacteria, and limit competition in the natural environment. Valuable drugs isolated from fungi include the
immunosuppressant drug cyclosporine (which reduces the risk of rejection after organ transplant), the precursors of steroid
hormones, and ergot alkaloids used to stop bleeding. In addition, as easily cultured eukaryotic organisms, some fungi are important
model research organisms including the red bread mold Neurospora crassa and the yeast, S. cerevisiae.

Section Summary
Fungi are eukaryotic organisms that appeared on land over 450 million years ago. They are heterotrophs and contain neither
photosynthetic pigments such as chlorophylls nor organelles such as chloroplasts. Because they feed on decaying and dead matter,
they are saprobes. Fungi are important decomposers and release essential elements into the environment. External enzymes digest
nutrients that are absorbed by the body of the fungus called a thallus. A thick cell wall made of chitin surrounds the cell. Fungi can
be unicellular as yeasts or develop a network of filaments called a mycelium, often described as mold. Most species multiply by
asexual and sexual reproductive cycles, and display an alternation of generations.

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The divisions of fungi are the Chytridiomycota, Zygomycota, Ascomycota, Basidiomycota, and Glomeromycota.
Fungi establish parasitic relationships with plants and animals. Fungal diseases can decimate crops and spoil food during storage.
Compounds produced by fungi can be toxic to humans and other animals. Mycoses are infections caused by fungi. Superficial
mycoses affect the skin, whereas systemic mycoses spread through the body. Fungal infections are difficult to cure.
Fungi have colonized all environments on Earth but are most often found in cool, dark, moist places with a supply of decaying
material. Fungi are important decomposers because they are saprobes. Many successful mutualistic relationships involve a fungus
and another organism. They establish complex mycorrhizal associations with the roots of plants. Lichens are a symbiotic
relationship between a fungus and a photosynthetic organism, usually an alga or cyanobacterium.
Fungi are important to everyday human life. Fungi are important decomposers in most ecosystems. Mycorrhizal fungi are essential
for the growth of most plants. Fungi, as food, play a role in human nutrition in the form of mushrooms and as agents of
fermentation in the production of bread, cheeses, alcoholic beverages, and numerous other food preparations. Secondary
metabolites of fungi are used in medicine as antibiotics and anticoagulants. Fungi are used in research as model organisms for the
study of eukaryotic genetics and metabolism.

Glossary

Ascomycota
(sac fungi) a division of fungi that store spores in a sac called ascus

basidiomycota
(club fungi) a division of fungi that produce club shaped structures, basidia, which contain spores

Chytridiomycota
(chytrids) a primitive division of fungi that live in water and produce gametes with flagella

Glomeromycota
a group of fungi that form symbiotic relationships with the roots of trees

hypha
a fungal filament composed of one or more cells

lichen
the close association of a fungus with a photosynthetic alga or bacterium that benefits both partners

mold
a tangle of visible mycelia with a fuzzy appearance

mycelium
a mass of fungal hyphae

mycorrhiza
a mutualistic association between fungi and vascular plant roots

mycosis
a fungal infection

septum
the cell wall division between hyphae

thallus
a vegetative body of a fungus

yeast
a general term used to describe unicellular fungi

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Zygomycota
(conjugated fungi) the division of fungi that form a zygote contained in a zygospore

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.1.4: Fungi is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
13.4: Fungi by OpenStax is licensed CC BY 4.0.

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13.1.E: Diversity of Microbes, Fungi, and Protists (Exercises)
13.1: Prokaryotic Diversity
Multiple Choice
The first forms of life on Earth were thought to be_______.
A. single-celled plants
B. prokaryotes
C. insects
D. large animals such as dinosaurs

Answer
B

The first organisms that oxygenated the atmosphere were _______.

A. cyanobacteria
B. phototrophic organisms
C. anaerobic organisms
D. all of the above

Answer
A

Which of the following consist of prokaryotic cells?

A. bacteria and fungi
B. archaea and fungi
C. protists and animals
D. bacteria and archaea

Answer
D

Prokaryotes stain as Gram-positive or Gram-negative because of differences in the _______.

A. cell wall
B. cytoplasm
C. nucleus
D. chromosome

Answer
A

Prokaryotes that obtain their energy from chemical compounds are called _____.
A. phototrophs
B. auxotrophs
C. chemotrophs
D. lithotrophs

Answer
C

Bioremediation includes _____.

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 A. the use of prokaryotes that can fix nitrogen
B. the use of prokaryotes to clean up pollutants
C. the use of prokaryotes as natural fertilizers
D. All of the above

Answer
B

Free Response
Explain the reason why the imprudent and excessive use of antibiotics has resulted in a major global problem.

Answer
Antibiotics kill bacteria that are sensitive to them; thus, only the resistant ones will survive. These resistant bacteria will
reproduce, and therefore, after a while, there will be only resistant bacteria, making it more difficult to treat the diseases they
may cause in humans.

Your friend believes that prokaryotes are always detrimental and pathogenic. How would you explain to them that they are wrong?

Answer
Remind them of the important roles prokaryotes play in decomposition and freeing up nutrients in biogeochemical cycles;
remind them of the many prokaryotes that are not human pathogens and that fill very specialized niches.

13.2: Eukaryotic Origins

Multiple Choice
What event is thought to have contributed to the evolution of eukaryotes?
A. global warming
B. glaciation
C. volcanic activity
D. oxygenation of the atmosphere

Answer
D

Mitochondria most likely evolved from _____________.

A. a photosynthetic cyanobacterium
B. cytoskeletal elements
C. aerobic bacteria
D. membrane proliferation

Answer
C

Free Response
Describe the hypothesized steps in the origin of eukaryote cells.

Answer
Eukaryote cells arose through endosymbiotic events that gave rise to energy-producing organelles within the eukaryotic cells,
such as mitochondria and plastids. The nuclear genome of eukaryotes is related most closely to the Archaea, so it may have
been an early archaean that engulfed a bacterial cell that evolved into a mitochondrion. Mitochondria appear to have originated
from an alpha-proteobacterium, whereas chloroplasts originated from a cyanobacterium. There is also evidence of secondary
endosymbiotic events. Other cell components may have resulted from endosymbiotic events.

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13.3: Protists
Multiple Choice
Protists with the capabilities to absorb nutrients from dead organisms are called_____________.
A. photoautotrophs
B. autotrophs
C. saprobes
D. heterotrophs

Answer
C

Which parasitic protist evades the host immune system by altering its surface proteins with each generation?
A. Paramecium caudatum
B. Trypanosoma brucei
C. Plasmodium falciparum
D. Phytophthora infestans

Answer
B

Free Response
How does killing Anopheles mosquitoes affect the Plasmodium protists?

Answer
Plasmodium parasites infect humans and cause malaria. However, they must complete part of their life cycle within Anopheles
mosquitoes, and they can only be transmitted to humans via the bite wound of a mosquito. If the mosquito population were
decreased, then fewer Plasmodium would be able to develop and be transmitted to humans, thereby reducing the incidence of
human infections with this parasite.

Without treatment, why does African sleeping sickness invariably lead to death?

Answer
The trypanosomes that cause this disease are capable of expressing a glycoprotein coat with a different molecular structure with
each generation. Because the immune system must respond to specific antigens to raise a meaningful defense, the changing
nature of trypanosome antigens prevents the immune system from ever clearing this infection. Massive trypanosome infection
eventually leads to host organ failure and death.

13.4: Fungi
Multiple Choice
Which polysaccharide is usually found in the cell walls of fungi?
A. starch
B. glycogen
C. chitin
D. cellulose

Answer
C

What term describes the close association of a fungus with the root of a tree?

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 A. a rhizoid
B. a lichen
C. a mycorrhiza
D. an endophyte

Answer
C

Free Response
Why can superficial mycoses in humans lead to bacterial infections?

Answer
Dermatophytes that colonize skin break down the keratinized layer of dead cells that protects tissues from bacterial invasion.
Once the integrity of the skin is breached, bacteria can enter the deeper layers of tissues and cause infections.

This page titled 13.1.E: Diversity of Microbes, Fungi, and Protists (Exercises) is shared under a CC BY license and was authored, remixed, and/or
curated by OpenStax.
13.E: Diversity of Microbes, Fungi, and Protists (Exercises) by OpenStax is licensed CC BY 4.0.

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 SECTION OVERVIEW

13.2: The Immune System and Disease

13.2.1: Viruses

13.2.2: Innate Immunity

13.2.3: Adaptive Immunity

13.2.4: Disruptions in the Immune System

13.2.E: The Immune System and Desease (Exercises)

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13.2.1: Viruses
No one knows exactly when viruses emerged or from where they came, since viruses do not leave historical footprints such as
fossils. Modern viruses are thought to be a mosaic of bits and pieces of nucleic acids picked up from various sources along their
respective evolutionary paths. Viruses are acellular, parasitic entities that are not classified within any domain because they are not
considered alive. They have no plasma membrane, internal organelles, or metabolic processes, and they do not divide. Instead, they
infect a host cell and use the host’s replication processes to produce progeny virus particles. Viruses infect all forms of organisms
including bacteria, archaea, fungi, plants, and animals. Living things grow, metabolize, and reproduce. Viruses replicate, but to do
so, they are entirely dependent on their host cells. They do not metabolize or grow, but are assembled in their mature form.

Figure [Link]: (a) The tobacco mosaic virus, seen by transmission electron microscopy, was the first virus to be discovered. (b)
The leaves of an infected plant are shown. (credit a: scale-bar data from Matt Russell; credit b: modification of work by USDA,
Department of Plant Pathology Archive, North Carolina State University)
Viruses are diverse. They vary in their structure, their replication methods, and in their target hosts or even host cells. While most
biological diversity can be understood through evolutionary history, such as how species have adapted to conditions and
environments, much about virus origins and evolution remains unknown.

How Viruses Replicate

Viruses were first discovered after the development of a porcelain filter, called the Chamberland-Pasteur filter, which could remove
all bacteria visible under the microscope from any liquid sample. In 1886, Adolph Meyer demonstrated that a disease of tobacco
plants, tobacco mosaic disease, could be transferred from a diseased plant to a healthy one through liquid plant extracts. In 1892,
Dmitri Ivanowski showed that this disease could be transmitted in this way even after the Chamberland-Pasteur filter had removed
all viable bacteria from the extract. Still, it was many years before it was proven that these “filterable” infectious agents were not
simply very small bacteria but were a new type of tiny, disease-causing particle.
Virions, single virus particles, are very small, about 20–250 nanometers (1 nanometer = 1/1,000,000 mm). These individual virus
particles are the infectious form of a virus outside the host cell. Unlike bacteria (which are about 100 times larger), we cannot see
viruses with a light microscope, with the exception of some large virions of the poxvirus family (Figure [Link]).

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 Figure [Link]: The size of a virus is very small relative to the size of cells and organelles.
It was not until the development of the electron microscope in the 1940s that scientists got their first good view of the structure of
the tobacco mosaic virus (Figure [Link]) and others. The surface structure of virions can be observed by both scanning and
transmission electron microscopy, whereas the internal structures of the virus can only be observed in images from a transmission
electron microscope (Figure [Link]).

Figure [Link]: The ebola virus is shown here as visualized through (a) a scanning electron micrograph and (b) a transmission
electron micrograph. (credit a: modification of work by Cynthia Goldsmith, CDC; credit b: modification of work by Thomas W.
Geisbert, Boston University School of Medicine; scale-bar data from Matt Russell)

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The use of this technology has allowed for the discovery of many viruses of all types of living organisms. They were initially
grouped by shared morphology, meaning their size, shape, and distinguishing structures. Later, groups of viruses were classified by
the type of nucleic acid they contained, DNA or RNA, and whether their nucleic acid was single- or double-stranded. More
recently, molecular analysis of viral replication cycles has further refined their classification.
A virion consists of a nucleic-acid core, an outer protein coating, and sometimes an outer envelope made of protein and
phospholipid membranes derived from the host cell. The most visible difference between members of viral families is their
morphology, which is quite diverse. An interesting feature of viral complexity is that the complexity of the host does not correlate
to the complexity of the virion. Some of the most complex virion structures are observed in bacteriophages, viruses that infect the
simplest living organisms, bacteria.
Viruses come in many shapes and sizes, but these are consistent and distinct for each viral family (Figure [Link]). All virions
have a nucleic-acid genome covered by a protective layer of protein, called a capsid. The capsid is made of protein subunits called
capsomeres. Some viral capsids are simple polyhedral “spheres,” whereas others are quite complex in structure. The outer structure
surrounding the capsid of some viruses is called the viral envelope. All viruses use some sort of glycoprotein to attach to their host
cells at molecules on the cell called viral receptors. The virus exploits these cell-surface molecules, which the cell uses for some
other purpose, as a way to recognize and infect specific cell types. For example, the measles virus uses a cell-surface glycoprotein
in humans that normally functions in immune reactions and possibly in the sperm-egg interaction at fertilization. Attachment is a
requirement for viruses to later penetrate the cell membrane, inject the viral genome, and complete their replication inside the cell.
The T4 bacteriophage, which infects the E. coli bacterium, is among the most complex virion known; T4 has a protein tail structure
that the virus uses to attach to the host cell and a head structure that houses its DNA.
Adenovirus, a nonenveloped animal virus that causes respiratory illnesses in humans, uses protein spikes protruding from its
capsomeres to attach to the host cell. Nonenveloped viruses also include those that cause polio (poliovirus), plantar warts
(papillomavirus), and hepatitis A (hepatitis A virus). Nonenveloped viruses tend to be more robust and more likely to survive under
harsh conditions, such as the gut.
Enveloped virions like HIV (human immunodeficiency virus), the causative agent in AIDS (acquired immune deficiency
syndrome), consist of nucleic acid (RNA in the case of HIV) and capsid proteins surrounded by a phospholipid bilayer envelope
and its associated proteins (Figure [Link]). Chicken pox, influenza, and mumps are examples of diseases caused by viruses with
envelopes. Because of the fragility of the envelope, nonenveloped viruses are more resistant to changes in temperature, pH, and
some disinfectants than enveloped viruses.
Overall, the shape of the virion and the presence or absence of an envelope tells us little about what diseases the viruses may cause
or what species they might infect, but is still a useful means to begin viral classification.

ART CONNECTION

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 Figure [Link]: Viruses can be complex in shape or relatively simple. This figure shows three relatively complex virions:
the bacteriophage T4, with its DNA-containing head group and tail fibers that attach to host cells; adenovirus, which uses
spikes from its capsid to bind to the host cells; and HIV, which uses glycoproteins embedded in its envelope to do so. Notice
that HIV has proteins called matrix proteins, internal to the envelope, which help stabilize virion shape. HIV is a retrovirus,
which means it reverse transcribes its RNA genome into DNA, which is then spliced into the host’s DNA. (credit
“bacteriophage, adenovirus”: modification of work by NCBI, NIH; credit “HIV retrovirus”: modification of work by NIAID,
NIH)
Which of the following statements about virus structure is true?
A. All viruses are encased in a viral membrane.
B. The capsomere is made up of small protein subunits called capsids.
C. DNA is the genetic material in all viruses.
D. Glycoproteins help the virus attach to the host cell.

Unlike all living organisms that use DNA as their genetic material, viruses may use either DNA or RNA as theirs. The virus core
contains the genome or total genetic content of the virus. Viral genomes tend to be small compared to bacteria or eukaryotes,
containing only those genes that code for proteins the virus cannot get from the host cell. This genetic material may be single-
stranded or double-stranded. It may also be linear or circular. While most viruses contain a single segment of nucleic acid, others
have genomes that consist of several segments.
DNA viruses have a DNA core. The viral DNA directs the host cell’s replication proteins to synthesize new copies of the viral
genome and to transcribe and translate that genome into viral proteins. DNA viruses cause human diseases such as chickenpox,
hepatitis B, and some venereal diseases like herpes and genital warts.
RNA viruses contain only RNA in their cores. To replicate their genomes in the host cell, the genomes of RNA viruses encode
enzymes not found in host cells. RNA polymerase enzymes are not as stable as DNA polymerases and often make mistakes during
transcription. For this reason, mutations, changes in the nucleotide sequence, in RNA viruses occur more frequently than in DNA
viruses. This leads to more rapid evolution and change in RNA viruses. For example, the fact that influenza is an RNA virus is one
reason a new flu vaccine is needed every year. Human diseases caused by RNA viruses include hepatitis C, measles, and rabies.
Viruses can be seen as obligate intracellular parasites. The virus must attach to a living cell, be taken inside, manufacture its
proteins and copy its genome, and find a way to escape the cell so the virus can infect other cells and ultimately other individuals.
Viruses can infect only certain species of hosts and only certain cells within that host. The molecular basis for this specificity is that
a particular surface molecule, known as the viral receptor, must be found on the host cell surface for the virus to attach. Also,
metabolic differences seen in different cell types based on differential gene expression are a likely factor in which cells a virus may
use to replicate. The cell must be making the substances the virus needs, such as enzymes the virus genome itself does not have
genes for, or the virus will not be able to replicate using that cell.

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Steps of Virus Infections
A virus must “take over” a cell to replicate. The viral replication cycle can produce dramatic biochemical and structural changes in
the host cell, which may cause cell damage. These changes, called cytopathic effects, can change cell functions or even destroy the
cell. Some infected cells, such as those infected by the common cold virus (rhinovirus), die through lysis (bursting) or apoptosis
(programmed cell death or “cell suicide”), releasing all the progeny virions at once. The symptoms of viral diseases result from the
immune response to the virus, which attempts to control and eliminate the virus from the body, and from cell damage caused by the
virus. Many animal viruses, such as HIV (human immunodeficiency virus), leave the infected cells of the immune system by a
process known as budding, where virions leave the cell individually. During the budding process, the cell does not undergo lysis
and is not immediately killed. However, the damage to the cells that HIV infects may make it impossible for the cells to function as
mediators of immunity, even though the cells remain alive for a period of time. Most productive viral infections follow similar
steps in the virus replication cycle: attachment, penetration, uncoating, replication, assembly, and release.
A virus attaches to a specific receptor site on the host-cell membrane through attachment proteins in the capsid or proteins
embedded in its envelope. The attachment is specific, and typically a virus will only attach to cells of one or a few species and only
certain cell types within those species with the appropriate receptors.

CONCEPT IN ACTION
View this video for a visual explanation of how influenza attacks the body.

Unlike animal viruses, the nucleic acid of bacteriophages is injected into the host cell naked, leaving the capsid outside the cell.
Plant and animal viruses can enter their cells through endocytosis, in which the cell membrane surrounds and engulfs the entire
virus. Some enveloped viruses enter the cell when the viral envelope fuses directly with the cell membrane. Once inside the cell,
the viral capsid is degraded and the viral nucleic acid is released, which then becomes available for replication and transcription.
The replication mechanism depends on the viral genome. DNA viruses usually use host cell proteins and enzymes to make
additional DNA that is used to copy the genome or be transcribed to messenger RNA (mRNA), which is then used in protein
synthesis. RNA viruses, such as the influenza virus, usually use the RNA core as a template for synthesis of viral genomic RNA
and mRNA. The viral mRNA is translated into viral enzymes and capsid proteins to assemble new virions (Figure [Link]). Of
course, there are exceptions to this pattern. If a host cell does not provide the enzymes necessary for viral replication, viral genes
supply the information to direct synthesis of the missing proteins. Retroviruses, such as HIV, have an RNA genome that must be
reverse transcribed to make DNA, which then is inserted into the host’s DNA. To convert RNA into DNA, retroviruses contain
genes that encode the virus-specific enzyme reverse transcriptase that transcribes an RNA template to DNA. The fact that HIV
produces some of its own enzymes, which are not found in the host, has allowed researchers to develop drugs that inhibit these
enzymes. These drugs, including the reverse transcriptase inhibitor AZT, inhibit HIV replication by reducing the activity of the
enzyme without affecting the host’s metabolism.
The last stage of viral replication is the release of the new virions into the host organism, where they are able to infect adjacent
cells and repeat the replication cycle. Some viruses are released when the host cell dies and other viruses can leave infected cells by
budding through the membrane without directly killing the cell.

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 Figure [Link]: In influenza virus infection, glycoproteins attach to a host epithelial cell. As a result, the virus is engulfed.
RNA and proteins are made and assembled into new virions.
Influenza virus is packaged in a viral envelope, which fuses with the plasma membrane. This way, the virus can exit the host
cell without killing it. What advantage does the virus gain by keeping the host cell alive?

CONCEPT IN ACTION

Viruses

Click through this tutorial on viruses to identify structures, modes of transmission, replication, and more.

Viruses and Disease

Viruses cause a variety of diseases in animals, including humans, ranging from the common cold to potentially fatal illnesses like
meningitis (Figure [Link]). These diseases can be treated by antiviral drugs or by vaccines, but some viruses, such as HIV, are

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capable of avoiding the immune response and mutating so as to become resistant to antiviral drugs.

Figure [Link]: Viruses are the cause of dozens of ailments in humans, ranging from mild illnesses to serious diseases. (credit:
modification of work by Mikael Häggström)

Vaccines for Prevention

While we do have limited numbers of effective antiviral drugs, such as those used to treat HIV and influenza, the primary method
of controlling viral disease is by vaccination, which is intended to prevent outbreaks by building immunity to a virus or virus
family. A vaccine may be prepared using weakened live viruses, killed viruses, or molecular subunits of the virus. In general, live
viruses lead to better immunity, but have the possibility of causing disease at some low frequency. Killed viral vaccine and the
subunit viruses are both incapable of causing disease, but in general lead to less effective or long-lasting immunity.
Weakened live viral vaccines are designed in the laboratory to cause few symptoms in recipients while giving them immunity
against future infections. Polio was one disease that represented a milestone in the use of vaccines. Mass immunization campaigns
in the U.S. in the 1950s (killed vaccine) and 1960s (live vaccine) essentially eradicated the disease, which caused muscle paralysis
in children and generated fear in the general population when regional epidemics occurred. The success of the polio vaccine paved
the way for the routine dispensation of childhood vaccines against measles, mumps, rubella, chickenpox, and other diseases.
Live vaccines are usually made by attenuation (weakening) of the “wild-type” (disease-causing) virus by growing it in the
laboratory in tissues or at temperatures different from what the virus is accustomed to in the host. For example, the virus may be
grown in cells in a test tube, in bird embryos, or in live animals. The adaptation to these new cells or temperature induces mutations
in the virus’ genomes, allowing them to grow better in the laboratory while inhibiting their ability to cause disease when
reintroduced into the conditions found in the host. These attenuated viruses thus still cause an infection, but they do not grow very
well, allowing the immune response to develop in time to prevent major disease. The danger of using live vaccines, which are
usually more effective than killed vaccines, is the low but significant risk that these viruses will revert back to their disease-causing
form by back mutations. Back mutations occur when the vaccine undergoes mutations in the host such that it readapts to the host
and can again cause disease, which can then be spread to other humans in an epidemic. This happened as recently as 2007 in
Nigeria where mutations in a polio vaccine led to an epidemic of polio in that country.

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Some vaccines are in continuous development because certain viruses, such as influenza and HIV, have a high mutation rate
compared to other viruses or host cells. With influenza, mutation in genes for the surface molecules helps the virus evade the
protective immunity that may have been obtained in a previous influenza season, making it necessary for individuals to get
vaccinated every year. Other viruses, such as those that cause the childhood diseases measles, mumps, and rubella, mutate so little
that the same vaccine is used year after year.

Vaccines and Antiviral Drugs for Treatment

In some cases, vaccines can be used to treat an active viral infection. In the case of rabies, a fatal neurological disease transmitted
in the saliva of rabies virus-infected animals, the progression of the disease from the time of the animal bite to the time it enters the
central nervous system may be two weeks or longer. This is enough time to vaccinate an individual who suspects being bitten by a
rabid animal, and the boosted immune response from the vaccination is enough to prevent the virus from entering nervous tissue.
Thus, the fatal neurological consequences of the disease are averted and the individual only has to recover from the infected bite.
This approach is also being used for the treatment of Ebola, one of the fastest and most deadly viruses affecting humans, though
usually infecting limited populations. Ebola is also a leading cause of death in gorillas. Transmitted by bats and great apes, this
virus can cause death in 70–90 percent of the infected within two weeks. Using newly developed vaccines that boost the immune
response, there is hope that immune systems of affected individuals will be better able to control the virus, potentially reducing
mortality rates.
Another way of treating viral infections is the use of antiviral drugs. These drugs often have limited ability to cure viral disease but
have been used to control and reduce symptoms for a wide variety of viral diseases. For most viruses, these drugs inhibit the virus
by blocking the actions of one or more of its proteins. It is important that the targeted proteins be encoded for by viral genes and
that these molecules are not present in a healthy host cell. In this way, viral growth is inhibited without damaging the host. There
are large numbers of antiviral drugs available to treat infections, some specific for a particular virus and others that can affect
multiple viruses.
Antivirals have been developed to treat genital herpes (herpes simplex II) and influenza. For genital herpes, drugs such as acyclovir
can reduce the number and duration of the episodes of active viral disease during which patients develop viral lesions in their skins
cells. As the virus remains latent in nervous tissue of the body for life, this drug is not a cure but can make the symptoms of the
disease more manageable. For influenza, drugs like Tamiflu can reduce the duration of “flu” symptoms by one or two days, but the
drug does not prevent symptoms entirely. Other antiviral drugs, such as Ribavirin, have been used to treat a variety of viral
infections.
By far the most successful use of antivirals has been in the treatment of the retrovirus HIV, which causes a disease that, if untreated,
is usually fatal within 10–12 years after being infected. Anti-HIV drugs have been able to control viral replication to the point that
individuals receiving these drugs survive for a significantly longer time than the untreated.
Anti-HIV drugs inhibit viral replication at many different phases of the HIV replicative cycle. Drugs have been developed that
inhibit the fusion of the HIV viral envelope with the plasma membrane of the host cell (fusion inhibitors), the conversion of its
RNA genome to double-stranded DNA (reverse transcriptase inhibitors), the integration of the viral DNA into the host genome
(integrase inhibitors), and the processing of viral proteins (protease inhibitors).
When any of these drugs are used individually, the virus’ high mutation rate allows the virus to rapidly evolve resistance to the
drug. The breakthrough in the treatment of HIV was the development of highly active anti-retroviral therapy (HAART), which
involves a mixture of different drugs, sometimes called a drug “cocktail.” By attacking the virus at different stages of its replication
cycle, it is difficult for the virus to develop resistance to multiple drugs at the same time. Still, even with the use of combination
HAART therapy, there is concern that, over time, the virus will evolve resistance to this therapy. Thus, new anti-HIV drugs are
constantly being developed with the hope of continuing the battle against this highly fatal virus.

Summary
Viruses are acellular entities that can usually only be seen with an electron microscope. Their genomes contain either DNA or
RNA, and they replicate using the replication proteins of a host cell. Viruses are diverse, infecting archaea, bacteria, fungi, plants,
and animals. Viruses consist of a nucleic-acid core surrounded by a protein capsid with or without an outer lipid envelope.
Viral replication within a living cell always produces changes in the cell, sometimes resulting in cell death and sometimes slowly
killing the infected cells. There are six basic stages in the virus replication cycle: attachment, penetration, uncoating, replication,

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assembly, and release. A viral infection may be productive, resulting in new virions, or nonproductive, meaning the virus remains
inside the cell without producing new virions.
Viruses cause a variety of diseases in humans. Many of these diseases can be prevented by the use of viral vaccines, which
stimulate protective immunity against the virus without causing major disease. Viral vaccines may also be used in active viral
infections, boosting the ability of the immune system to control or destroy the virus. Antiviral drugs that target enzymes and other
protein products of viral genes have been developed and used with mixed success. Combinations of anti-HIV drugs have been used
to effectively control the virus, extending the lifespan of infected individuals.

Art Connections
Figure [Link]: Which of the following statements about virus structure is true?
A. All viruses are encased in a viral membrane.
B. The capsomere is made up of small protein subunits called capsids.
C. DNA is the genetic material in all viruses.
D. Glycoproteins help the virus attach to the host cell.

Answer
D

Figure [Link]: Influenza virus is packaged in a viral envelope, which fuses with the plasma membrane. This way, the virus can
exit the host cell without killing it. What advantage does the virus gain by keeping the host cell alive?

Answer
The host cell can continue to make new virus particles.

Glossary

acellular
lacking cells

apoptosis
the cell death caused by induction of a cell’s own internal mechanisms either as a natural step in the development of a
multicellular organism or by other environmental factors such as signals from cells of the immune system

attenuation
the weakening of a virus during vaccine development

capsid
the protein coating of the viral core

cytopathic
causing cell damage

glycoprotein
a protein molecule with attached carbohydrate molecules

vaccine
a weakened solution of virus components, viruses, or other agents that produce an immune response

virion
an individual virus particle outside a host cell

viral envelope
a lipid bilayer that envelops some viruses

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.2.1: Viruses is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
17.1: Viruses by OpenStax is licensed CC BY 4.0.

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13.2.2: Innate Immunity
The vertebrate, including human, immune system is a complex multilayered system for defending against external and internal
threats to the integrity of the body. The system can be divided into two types of defense systems: the innate immune system, which
is nonspecific toward a particular kind of pathogen, and the adaptive immune system, which is specific (Figure [Link]). Innate
immunity is not caused by an infection or vaccination and depends initially on physical and chemical barriers that work on all
pathogens, sometimes called the first line of defense. The second line of defense of the innate system includes chemical signals that
produce inflammation and fever responses as well as mobilizing protective cells and other chemical defenses. The adaptive
immune system mounts a highly specific response to substances and organisms that do not belong in the body. The adaptive system
takes longer to respond and has a memory system that allows it to respond with greater intensity should the body reencounter a
pathogen even years later.

Figure [Link]: There are two main parts to the vertebrate immune system. The innate immune system, which is made up of
physical barriers and internal defenses, responds to all pathogens. The adaptive immune system is highly specific.

External and Chemical Barriers

The body has significant physical barriers to potential pathogens. The skin contains the protein keratin, which resists physical entry
into cells. Other body surfaces, particularly those associated with body openings, are protected by the mucous membranes. The
sticky mucus provides a physical trap for pathogens, preventing their movement deeper into the body. The openings of the body,
such as the nose and ears, are protected by hairs that catch pathogens, and the mucous membranes of the upper respiratory tract
have cilia that constantly move pathogens trapped in the mucus coat up to the mouth.
The skin and mucous membranes also create a chemical environment that is hostile to many microorganisms. The surface of the
skin is acidic, which prevents bacterial growth. Saliva, mucus, and the tears of the eye contain an enzyme that breaks down
bacterial cell walls. The stomach secretions create a highly acidic environment, which kills many pathogens entering the digestive
system.
Finally, the surface of the body and the lower digestive system have a community of microorganisms such as bacteria, archaea, and
fungi that coexist without harming the body. There is evidence that these organisms are highly beneficial to their host, combating
disease-causing organisms and outcompeting them for nutritional resources provided by the host body. Despite these defenses,
pathogens may enter the body through skin abrasions or punctures, or by collecting on mucosal surfaces in large numbers that
overcome the protections of mucus or cilia.

Internal Defenses
When pathogens enter the body, the innate immune system responds with a variety of internal defenses. These include the
inflammatory response, phagocytosis, natural killer cells, and the complement system. White blood cells in the blood and lymph
recognize pathogens as foreign to the body. A white blood cell is larger than a red blood cell, is nucleated, and is typically able to
move using amoeboid locomotion. Because they can move on their own, white blood cells can leave the blood to go to infected
tissues. For example, a monocyte is a type of white blood cell that circulates in the blood and lymph and develops into a
macrophage after it moves into infected tissue. A macrophage is a large cell that engulfs foreign particles and pathogens. Mast cells
are produced in the same way as white blood cells, but unlike circulating white blood cells, mast cells take up residence in

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connective tissues and especially mucosal tissues. They are responsible for releasing chemicals in response to physical injury. They
also play a role in the allergic response, which will be discussed later in the chapter.
When a pathogen is recognized as foreign, chemicals called cytokines are released. A cytokine is a chemical messenger that
regulates cell differentiation (form and function), proliferation (production), and gene expression to produce a variety of immune
responses. Approximately 40 types of cytokines exist in humans. In addition to being released from white blood cells after
pathogen recognition, cytokines are also released by the infected cells and bind to nearby uninfected cells, inducing those cells to
release cytokines. This positive feedback loop results in a burst of cytokine production.
One class of early-acting cytokines is the interferons, which are released by infected cells as a warning to nearby uninfected cells.
An interferon is a small protein that signals a viral infection to other cells. The interferons stimulate uninfected cells to produce
compounds that interfere with viral replication. Interferons also activate macrophages and other cells.

The Inflammatory Response and Phagocytosis

The first cytokines to be produced encourage inflammation, a localized redness, swelling, heat, and pain. Inflammation is a
response to physical trauma, such as a cut or a blow, chemical irritation, and infection by pathogens (viruses, bacteria, or fungi).
The chemical signals that trigger an inflammatory response enter the extracellular fluid and cause capillaries to dilate (expand) and
capillary walls to become more permeable, or leaky. The serum and other compounds leaking from capillaries cause swelling of the
area, which in turn causes pain. Various kinds of white blood cells are attracted to the area of inflammation. The types of white
blood cells that arrive at an inflamed site depend on the nature of the injury or infecting pathogen. For example, a neutrophil is an
early arriving white blood cell that engulfs and digests pathogens. Neutrophils are the most abundant white blood cells of the
immune system (Figure [Link]). Macrophages follow neutrophils and take over the phagocytosis function and are involved in the
resolution of an inflamed site, cleaning up cell debris and pathogens.

Figure [Link]: White blood cells (leukocytes) release chemicals to stimulate the inflammatory response following a cut in the
skin.
Cytokines also send feedback to cells of the nervous system to bring about the overall symptoms of feeling sick, which include
lethargy, muscle pain, and nausea. Cytokines also increase the core body temperature, causing a fever. The elevated temperatures of
a fever inhibit the growth of pathogens and speed up cellular repair processes. For these reasons, suppression of fevers should be
limited to those that are dangerously high.

CONCEPT IN ACTION

Check out this 23-second, stop-motion video showing a neutrophil that searches and engulfs fungus spores during an elapsed
time of 79 minutes.

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Natural Killer Cells
A lymphocyte is a white blood cell that contains a large nucleus (Figure [Link]). Most lymphocytes are associated with the
adaptive immune response, but infected cells are identified and destroyed by natural killer cells, the only lymphocytes of the innate
immune system. A natural killer (NK) cell is a lymphocyte that can kill cells infected with viruses (or cancerous cells). NK cells
identify intracellular infections, especially from viruses, by the altered expression of major histocompatibility class (MHC) I
molecules on the surface of infected cells. MHC class I molecules are proteins on the surfaces of all nucleated cells that provide a
sample of the cell’s internal environment at any given time. Unhealthy cells, whether infected or cancerous, display an altered
MHC class I complement on their cell surfaces.

Figure [Link]: Lymphocytes, such as NK cells, are characterized by their large nuclei that actively absorb Wright stain and
therefore appear dark colored under a microscope. (credit: scale-bar data from Matt Russell)
After the NK cell detects an infected or tumor cell, it induces programmed cell death, or apoptosis. Phagocytic cells then come
along and digest the cell debris left behind. NK cells are constantly patrolling the body and are an effective mechanism for
controlling potential infections and preventing cancer progression. The various types of immune cells are shown in Figure
[Link].

Figure [Link]: Cells involved in the innate immune response include mast cells, natural killer cells, and white blood cells, such
as monocytes, macrophages and neutrophils.

Complement
An array of approximately 20 types of proteins, called a complement system, is also activated by infection or the activity of the
cells of the adaptive immune system and functions to destroy extracellular pathogens. Liver cells and macrophages synthesize
inactive forms of complement proteins continuously; these proteins are abundant in the blood serum and are capable of responding
immediately to infecting microorganisms. The complement system is so named because it is complementary to the innate and
adaptive immune system. Complement proteins bind to the surfaces of microorganisms and are particularly attracted to pathogens
that are already tagged by the adaptive immune system. This “tagging” involves the attachment of specific proteins called
antibodies (discussed in detail later) to the pathogen. When they attach, the antibodies change shape providing a binding site for
one of the complement proteins. After the first few complement proteins bind, a cascade of binding in a specific sequence of
proteins follows in which the pathogen rapidly becomes coated in complement proteins.
Complement proteins perform several functions, one of which is to serve as a marker to indicate the presence of a pathogen to
phagocytic cells and enhance engulfment. Certain complement proteins can combine to open pores in microbial cell membranes
and cause lysis of the cells.

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Summary
The innate immune system consists first of physical and chemical barriers to infection including the skin and mucous membranes
and their secretions, ciliated surfaces, and body hairs. The second line of defense is an internal defense system designed to counter
pathogenic threats that bypass the physical and chemical barriers of the body. Using a combination of cellular and molecular
responses, the innate immune system identifies the nature of a pathogen and responds with inflammation, phagocytosis, cytokine
release, destruction by NK cells, or the complement system.

Glossary

complement system
an array of approximately 20 soluble proteins of the innate immune system that enhance phagocytosis, bore holes in pathogens,
and recruit lymphocytes

cytokine
a chemical messenger that regulates cell differentiation, proliferation, and gene expression to effect immune responses

inflammation
the localized redness, swelling, heat, and pain that results from the movement of leukocytes through opened capillaries to a site
of infection

innate immunity
an immunity that occurs naturally because of genetic factors or physiology, and is not caused by infection or vaccination

interferon
a cytokine that inhibits viral replication

lymphocyte
a type of white blood cell that includes natural killer cells of the innate immune system and B and T cells of the adaptive
immune system

macrophage
a large phagocytic cell that engulfs foreign particles and pathogens

major histocompatibility class (MHC) I

a group of proteins found on the surface of all nucleated cells that signals to immune cells whether the cell is normal or is
infected or cancerous; it also provides the appropriate sites into which antigens can be loaded for recognition by lymphocytes

mast cell
a leukocyte that produces inflammatory molecules, such as histamine, in response to large pathogens

monocyte
a type of white blood cell that circulates in the blood and lymph and differentiates into a macrophage after it moves into
infected tissue

natural killer (NK) cell

a lymphocyte that can kill cells infected with viruses or tumor cells

neutrophil
a phagocytic leukocyte that engulfs and digests pathogens

white blood cell

a nucleated cell found in the blood that is a part of the immune system; also called leukocytes

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.2.2: Innate Immunity is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
17.2: Innate Immunity by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

13.2.3: Adaptive Immunity
The adaptive, or acquired, immune response takes days or even weeks to become established—much longer than the innate
response; however, adaptive immunity is more specific to an invading pathogen. Adaptive immunity is an immunity that occurs
after exposure to an antigen either from a pathogen or a vaccination. An antigen is a molecule that stimulates a response in the
immune system. This part of the immune system is activated when the innate immune response is insufficient to control an
infection. In fact, without information from the innate immune system, the adaptive response could not be mobilized. There are two
types of adaptive responses: the cell-mediated immune response, which is controlled by activated T cells, and the humoral immune
response, which is controlled by activated B cells and antibodies. Activated T and B cells whose surface binding sites are specific
to the molecules on the pathogen greatly increase in numbers and attack the invading pathogen. Their attack can kill pathogens
directly or they can secrete antibodies that enhance the phagocytosis of pathogens and disrupt the infection. Adaptive immunity
also involves a memory to give the host long-term protection from reinfection with the same type of pathogen; on reexposure, this
host memory will facilitate a rapid and powerful response.

B and T Cells
Lymphocytes, which are white blood cells, are formed with other blood cells in the red bone marrow found in many flat bones,
such as the shoulder or pelvic bones. The two types of lymphocytes of the adaptive immune response are B and T cells (Figure
[Link]). Whether an immature lymphocyte becomes a B cell or T cell depends on where in the body it matures. The B cells

remain in the bone marrow to mature (hence the name “B” for “bone marrow”), while T cells migrate to the thymus, where they
mature (hence the name “T” for “thymus”).
Maturation of a B or T cell involves becoming immunocompetent, meaning that it can recognize, by binding, a specific molecule or
antigen (discussed below). During the maturation process, B and T cells that bind too strongly to the body’s own cells are
eliminated in order to minimize an immune response against the body’s own tissues. Those cells that react weakly to the body’s
own cells, but have highly specific receptors on their cell surfaces that allow them to recognize a foreign molecule, or antigen,
remain. This process occurs during fetal development and continues throughout life. The specificity of this receptor is determined
by the genetics of the individual and is present before a foreign molecule is introduced to the body or encountered. Thus, it is
genetics and not experience that initially provides a vast array of cells, each capable of binding to a different specific foreign
molecule. Once they are immunocompetent, the T and B cells will migrate to the spleen and lymph nodes where they will remain
until they are called on during an infection. B cells are involved in the humoral immune response, which targets pathogens loose in
blood and lymph, and T cells are involved in the cell-mediated immune response, which targets infected cells.

Figure [Link]: This scanning electron micrograph shows a T lymphocyte. T and B cells are indistinguishable by light
microscopy but can be differentiated experimentally by probing their surface receptors. (credit: modification of work by NCI;
scale-bar data from Matt Russell)

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Humoral Immune Response
As mentioned, an antigen is a molecule that stimulates a response in the immune system. Not every molecule is antigenic. B cells
participate in a chemical response to antigens present in the body by producing specific antibodies that circulate throughout the
body and bind with the antigen whenever it is encountered. This is known as the humoral immune response. As discussed, during
maturation of B cells, a set of highly specific B cells are produced that have many antigen receptor molecules in their membrane
(Figure [Link]).

Figure [Link]: B cell receptors are embedded in the membranes of B cells and bind a variety of antigens through their variable
regions.
Each B cell has only one kind of antigen receptor, which makes every B cell different. Once the B cells mature in the bone marrow,
they migrate to lymph nodes or other lymphatic organs. When a B cell encounters the antigen that binds to its receptor, the antigen
molecule is brought into the cell by endocytosis and reappears on the surface of the cell bound to an MHC class II molecule. When
this process is complete, the B cell is sensitized. In most cases, the sensitized B cell must then encounter a specific kind of T cell,
called a helper T cell, before it is activated. The helper T cell must already have been activated through an encounter with the
antigen (discussed below).
The helper T cell binds to the antigen-MHC class II complex and is induced to release cytokines that induce the B cell to divide
rapidly, which makes thousands of identical (clonal) cells. These daughter cells become either plasma cells or memory B cells. The
memory B cells remain inactive at this point, until another later encounter with the antigen, caused by a reinfection by the same
bacteria or virus, results in them dividing into a new population of plasma cells. The plasma cells, on the other hand, produce and
secrete large quantities, up to 100 million molecules per hour, of antibody molecules. An antibody, also known as an
immunoglobulin (Ig), is a protein that is produced by plasma cells after stimulation by an antigen. Antibodies are the agents of
humoral immunity. Antibodies occur in the blood, in gastric and mucus secretions, and in breast milk. Antibodies in these bodily
fluids can bind pathogens and mark them for destruction by phagocytes before they can infect cells.
These antibodies circulate in the blood stream and lymphatic system and bind with the antigen whenever it is encountered. The
binding can fight infection in several ways. Antibodies can bind to viruses or bacteria and interfere with the chemical interactions
required for them to infect or bind to other cells. The antibodies may create bridges between different particles containing antigenic
sites clumping them all together and preventing their proper functioning. The antigen-antibody complex stimulates the complement
system described previously, destroying the cell bearing the antigen. Phagocytic cells, such as those already described, are attracted
by the antigen-antibody complexes, and phagocytosis is enhanced when the complexes are present. Finally, antibodies stimulate
inflammation, and their presence in mucus and on the skin prevents pathogen attack.
Antibodies coat extracellular pathogens and neutralize them by blocking key sites on the pathogen that enhance their infectivity
(such as receptors that “dock” pathogens on host cells) (Figure [Link]). Antibody neutralization can prevent pathogens from
entering and infecting host cells. The neutralized antibody-coated pathogens can then be filtered by the spleen and eliminated in
urine or feces.

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Antibodies also mark pathogens for destruction by phagocytic cells, such as macrophages or neutrophils, in a process called
opsonization. In a process called complement fixation, some antibodies provide a place for complement proteins to bind. The
combination of antibodies and complement promotes rapid clearing of pathogens.
The production of antibodies by plasma cells in response to an antigen is called active immunity and describes the host’s active
response of the immune system to an infection or to a vaccination. There is also a passive immune response where antibodies come
from an outside source, instead of the individual’s own plasma cells, and are introduced into the host. For example, antibodies
circulating in a pregnant woman’s body move across the placenta into the developing fetus. The child benefits from the presence of
these antibodies for up to several months after birth. In addition, a passive immune response is possible by injecting antibodies into
an individual in the form of an antivenom to a snake-bite toxin or antibodies in blood serum to help fight a hepatitis infection. This
gives immediate protection since the body does not need the time required to mount its own response.

Figure [Link]: Antibodies may inhibit infection by (a) preventing the antigen from binding its target, (b) tagging a pathogen for
destruction by macrophages or neutrophils, or (c) activating the complement cascade.

Cell-Mediated Immunity
Unlike B cells, T lymphocytes are unable to recognize pathogens without assistance. Instead, dendritic cells and macrophages first
engulf and digest pathogens into hundreds or thousands of antigens. Then, an antigen-presenting cell (APC) detects, engulfs, and
informs the adaptive immune response about an infection. When a pathogen is detected, these APCs will engulf and break it down
through phagocytosis. Antigen fragments will then be transported to the surface of the APC, where they will serve as an indicator
to other immune cells. A dendritic cell is an immune cell that mops up antigenic materials in its surroundings and presents them on
its surface. Dendritic cells are located in the skin, the linings of the nose, lungs, stomach, and intestines. These positions are ideal
locations to encounter invading pathogens. Once they are activated by pathogens and mature to become APCs they migrate to the

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spleen or a lymph node. Macrophages also function as APCs. After phagocytosis by a macrophage, the phagocytic vesicle fuses
with an intracellular lysosome. Within the resulting phagolysosome, the components are broken down into fragments; the
fragments are then loaded onto MHC class II molecules and are transported to the cell surface for antigen presentation (Figure
[Link]). Helper T cells cannot properly respond to an antigen unless it is processed and embedded in an MHC class II molecule.

The APCs express MHC class II on their surfaces, and when combined with a foreign antigen, these complexes signal an invader.

Figure [Link]: An antigen-presenting cell (APC), such as a macrophage, engulfs a foreign antigen, partially digests it in a
lysosome, and then embeds it in an MHC class II molecule for presentation at the cell surface. Lymphocytes of the adaptive
immune response must interact with antigen-embedded MHC class II molecules to mature into functional immune cells.
T cells have many functions. Some respond to APCs of the innate immune system and indirectly induce immune responses by
releasing cytokines. Others stimulate B cells to start the humoral response as described previously. Another type of T cell detects
APC signals and directly kills the infected cells, while some are involved in suppressing inappropriate immune reactions to
harmless or “self” antigens.
There are two main types of T cells: helper T lymphocytes (TH) and the cytotoxic T lymphocytes (TC). The TH lymphocytes
function indirectly to tell other immune cells about potential pathogens. TH lymphocytes recognize specific antigens presented by
the MHC class II complexes of APCs. There are two populations of TH cells: TH1 and TH2. TH1 cells secrete cytokines to enhance
the activities of macrophages and other T cells. TH2 cells stimulate naïve B cells to secrete antibodies. Whether a TH1 or a TH2
immune response develops depends on the specific types of cytokines secreted by cells of the innate immune system, which in turn
depends on the nature of the invading pathogen.
Cytotoxic T cells (TC) are the key component of the cell-mediated part of the adaptive immune system and attack and destroy
infected cells. TC cells are particularly important in protecting against viral infections; this is because viruses replicate within cells
where they are shielded from extracellular contact with circulating antibodies. Once activated, the TC creates a large clone of cells
with one specific set of cell-surface receptors, as in the case with proliferation of activated B cells. As with B cells, the clone
includes active TC cells and inactive memory TCcells. The resulting active TC cells then identify infected host cells. Because of the
time required to generate a population of clonal T and B cells, there is a delay in the adaptive immune response compared to the
innate immune response.
TC cells attempt to identify and destroy infected cells before the pathogen can replicate and escape, thereby halting the progression
of intracellular infections. TC cells also support NK lymphocytes to destroy early cancers. Cytokines secreted by the TH1 response
that stimulates macrophages also stimulate TC cells and enhance their ability to identify and destroy infected cells and tumors. A
summary of how the humoral and cell-mediated immune responses are activated appears in Figure [Link].
B plasma cells and TC cells are collectively called effector cells because they are involved in “effecting” (bringing about) the
immune response of killing pathogens and infected host cells.

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 Figure [Link]: A helper T cell becomes activated by binding to an antigen presented by an APC via the MHCII receptor,
causing it to release cytokines. Depending on the cytokines released, this activates either the humoral or the cell-mediated immune
response.

Immunological Memory
The adaptive immune system has a memory component that allows for a rapid and large response upon reinvasion of the same
pathogen. During the adaptive immune response to a pathogen that has not been encountered before, known as the primary immune
response, plasma cells secreting antibodies and differentiated T cells increase, then plateau over time. As B and T cells mature into
effector cells, a subset of the naïve populations differentiates into B and T memory cells with the same antigen specificities (Figure
[Link]). A memory cell is an antigen-specific B or T lymphocyte that does not differentiate into an effector cell during the

primary immune response, but that can immediately become an effector cell on reexposure to the same pathogen. As the infection
is cleared and pathogenic stimuli subside, the effectors are no longer needed and they undergo apoptosis. In contrast, the memory
cells persist in the circulation.

ART CONNECTION

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 Figure [Link]: After initially binding an antigen to the B cell receptor, a B cell internalizes the antigen and presents it on
MHC class II. A helper T cell recognizes the MHC class II- antigen complex and activates the B cell. As a result, memory B
cells and plasma cells are made.
The Rh antigen is found on Rh-positive red blood cells. An Rh-negative female can usually carry an Rh-positive fetus to term
without difficulty. However, if she has a second Rh-positive fetus, her body may launch an immune attack that causes
hemolytic disease of the newborn. Why do you think hemolytic disease is only a problem during the second or subsequent
pregnancies?

If the pathogen is never encountered again during the individual’s lifetime, B and T memory cells will circulate for a few years or
even several decades and will gradually die off, having never functioned as effector cells. However, if the host is re-exposed to the
same pathogen type, circulating memory cells will immediately differentiate into plasma cells and TC cells without input from
APCs or TH cells. This is known as the secondary immune response. One reason why the adaptive immune response is delayed is
because it takes time for naïve B and T cells with the appropriate antigen specificities to be identified, activated, and proliferate. On
reinfection, this step is skipped, and the result is a more rapid production of immune defenses. Memory B cells that differentiate
into plasma cells output tens to hundreds-fold greater antibody amounts than were secreted during the primary response (Figure
[Link]). This rapid and dramatic antibody response may stop the infection before it can even become established, and the

individual may not realize they had been exposed.

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 Figure [Link]: In the primary response to infection, antibodies are secreted first from plasma cells. Upon re-exposure to the
same pathogen, memory cells differentiate into antibody-secreting plasma cells that output a greater amount of antibody for a
longer period of time.
Vaccination is based on the knowledge that exposure to noninfectious antigens, derived from known pathogens, generates a mild
primary immune response. The immune response to vaccination may not be perceived by the host as illness but still confers
immune memory. When exposed to the corresponding pathogen to which an individual was vaccinated, the reaction is similar to a
secondary exposure. Because each reinfection generates more memory cells and increased resistance to the pathogen, some vaccine
courses involve one or more booster vaccinations to mimic repeat exposures.

The Lymphatic System

Lymph is the watery fluid that bathes tissues and organs and contains protective white blood cells but does not contain
erythrocytes. Lymph moves about the body through the lymphatic system, which is made up of vessels, lymph ducts, lymph glands,
and organs, such as tonsils, adenoids, thymus, and spleen.
Although the immune system is characterized by circulating cells throughout the body, the regulation, maturation, and
intercommunication of immune factors occur at specific sites. The blood circulates immune cells, proteins, and other factors
through the body. Approximately 0.1 percent of all cells in the blood are leukocytes, which include monocytes (the precursor of
macrophages) and lymphocytes. Most cells in the blood are red blood cells. Cells of the immune system can travel between the
distinct lymphatic and blood circulatory systems, which are separated by interstitial space, by a process called extravasation
(passing through to surrounding tissue).
Recall that cells of the immune system originate from stem cells in the bone marrow. B cell maturation occurs in the bone marrow,
whereas progenitor cells migrate from the bone marrow and develop and mature into naïve T cells in the organ called the thymus.
On maturation, T and B lymphocytes circulate to various destinations. Lymph nodes scattered throughout the body house large
populations of T and B cells, dendritic cells, and macrophages (Figure [Link]). Lymph gathers antigens as it drains from tissues.
These antigens then are filtered through lymph nodes before the lymph is returned to circulation. APCs in the lymph nodes capture
and process antigens and inform nearby lymphocytes about potential pathogens.

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 Figure [Link]: (a) Lymphatic vessels carry a clear fluid called lymph throughout the body. The liquid passes through (b) lymph
nodes that filter the lymph that enters the node through afferent vessels and leaves through efferent vessels; lymph nodes are filled
with lymphocytes that purge infecting cells. (credit a: modification of work by NIH; credit b: modification of work by NCI, NIH)
The spleen houses B and T cells, macrophages, dendritic cells, and NK cells (Figure [Link]). The spleen is the site where APCs
that have trapped foreign particles in the blood can communicate with lymphocytes. Antibodies are synthesized and secreted by
activated plasma cells in the spleen, and the spleen filters foreign substances and antibody-complexed pathogens from the blood.
Functionally, the spleen is to the blood as lymph nodes are to the lymph.

Figure [Link]: The spleen functions to immunologically filter the blood and allow for communication between cells
corresponding to the innate and adaptive immune responses. (credit: modification of work by NCI, NIH)

Mucosal Immune System

The innate and adaptive immune responses compose the systemic immune system (affecting the whole body), which is distinct
from the mucosal immune system. Mucosa associated lymphoid tissue (MALT) is a crucial component of a functional immune
system because mucosal surfaces, such as the nasal passages, are the first tissues onto which inhaled or ingested pathogens are
deposited. The mucosal tissue includes the mouth, pharynx, and esophagus, and the gastrointestinal, respiratory, and urogenital
tracts.

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Mucosal immunity is formed by MALT, which functions independently of the systemic immune system, and which has its own
innate and adaptive components. MALT is a collection of lymphatic tissue that combines with epithelial tissue lining the mucosa
throughout the body. This tissue functions as the immune barrier and response in areas of the body with direct contact to the
external environment. The systemic and mucosal immune systems use many of the same cell types. Foreign particles that make
their way to MALT are taken up by absorptive epithelial cells and delivered to APCs located directly below the mucosal tissue.
APCs of the mucosal immune system are primarily dendritic cells, with B cells and macrophages having minor roles. Processed
antigens displayed on APCs are detected by T cells in the MALT and at the tonsils, adenoids, appendix, or the mesenteric lymph
nodes of the intestine. Activated T cells then migrate through the lymphatic system and into the circulatory system to mucosal sites
of infection.

Immune Tolerance
The immune system has to be regulated to prevent wasteful, unnecessary responses to harmless substances, and more importantly,
so that it does not attack “self.” The acquired ability to prevent an unnecessary or harmful immune response to a detected foreign
substance known not to cause disease, or self-antigens, is described as immune tolerance. The primary mechanism for developing
immune tolerance to self-antigens occurs during the selection for weakly self-binding cells during T and B lymphocyte maturation.
There are populations of T cells that suppress the immune response to self-antigens and that suppress the immune response after the
infection has cleared to minimize host cell damage induced by inflammation and cell lysis. Immune tolerance is especially well
developed in the mucosa of the upper digestive system because of the tremendous number of foreign substances (such as food
proteins) that APCs of the oral cavity, pharynx, and gastrointestinal mucosa encounter. Immune tolerance is brought about by
specialized APCs in the liver, lymph nodes, small intestine, and lung that present harmless antigens to a diverse population of
regulatory T (Treg) cells, specialized lymphocytes that suppress local inflammation and inhibit the secretion of stimulatory immune
factors. The combined result of Treg cells is to prevent immunologic activation and inflammation in undesired tissue compartments
and to allow the immune system to focus on pathogens instead.

Section Summary
The adaptive immune response is a slower-acting, longer-lasting, and more specific response than the innate response. However,
the adaptive response requires information from the innate immune system to function. APCs display antigens on MHC molecules
to naïve T cells. T cells with cell-surface receptors that bind a specific antigen will bind to that APC. In response, the T cells
differentiate and proliferate, becoming TH cells or TC cells. TH cells stimulate B cells that have engulfed and presented pathogen-
derived antigens. B cells differentiate into plasma cells that secrete antibodies, whereas TC cells destroy infected or cancerous cells.
Memory cells are produced by activated and proliferating B and T cells and persist after a primary exposure to a pathogen. If re-
exposure occurs, memory cells differentiate into effector cells without input from the innate immune system. The mucosal immune
system is largely independent of the systemic immune system but functions in parallel to protect the extensive mucosal surfaces of
the body. Immune tolerance is brought about by Treg cells to limit reactions to harmless antigens and the body’s own molecules.

Art Connections
Figure [Link]: The Rh antigen is found on Rh-positive red blood cells. An Rh-negative female can usually carry an Rh-positive
fetus to term without difficulty. However, if she has a second Rh-positive fetus, her body may launch an immune attack that causes
hemolytic disease of the newborn. Why do you think hemolytic disease is only a problem during the second or subsequent
pregnancies?

Answer
If the blood of the mother and fetus mixes, memory cells that recognize the Rh antigen of the fetus can form in the mother late
in the first pregnancy. During subsequent pregnancies, these memory cells launch an immune attack on the fetal blood cells of
an Rh-positive fetus. Injection of anti-Rh antibody during the first pregnancy prevents the immune response from occurring.

Glossary

active immunity
an immunity that occurs as a result of the activity of the body’s own cells rather than from antibodies acquired from an external
source

adaptive immunity

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 a specific immune response that occurs after exposure to an antigen either from a pathogen or a vaccination

antibody
a protein that is produced by plasma cells after stimulation by an antigen; also known as an immunoglobulin

antigen
a macromolecule that reacts with cells of the immune system and which may or may not have a stimulatory effect

antigen-presenting cell (APC)

an immune cell that detects, engulfs, and informs the adaptive immune response about an infection by presenting the processed
antigen on its cell surface

B cell
a lymphocyte that matures in the bone marrow

cell-mediated immune response

an adaptive immune response that is controlled by T cells

cytotoxic T lymphocyte (TC)

an adaptive immune cell that directly kills infected cells via enzymes, and that releases cytokines to enhance the immune
response

dendritic cell
an immune cell that processes antigen material and presents it on the surface of its cell in MHC class II molecules and induces
an immune response in other cells

effector cell
a lymphocyte that has differentiated, such as a B cell, plasma cell, or cytotoxic T cell

helper T lymphocyte (TH)

a cell of the adaptive immune system that binds APCs via MHC class II molecules and stimulates B cells or secretes cytokines
to initiate the immune response

humoral immune response

the adaptive immune response that is controlled by activated B cells and antibodies

immune tolerance
an acquired ability to prevent an unnecessary or harmful immune response to a detected foreign body known not to cause
disease

lymph
the watery fluid present in the lymphatic circulatory system that bathes tissues and organs with protective white blood cells and
does not contain erythrocytes

memory cell
an antigen-specific B or T lymphocyte that does not differentiate into an effector cell during the primary immune response but
that can immediately become an effector cell on reexposure to the same pathogen

major histocompatibility class (MHC) II molecule

a protein found on the surface of antigen-presenting cells that signals to immune cells whether the cell is normal or is infected
or cancerous; it provides the appropriate template into which antigens can be loaded for recognition by lymphocytes

passive immunity
an immunity that does not result from the activity of the body’s own immune cells but by transfer of antibodies from one
individual to another

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primary immune response
the response of the adaptive immune system to the first exposure to an antigen

secondary immune response

the response of the adaptive immune system to a second or later exposure to an antigen mediated by memory cells

T cell
a lymphocyte that matures in the thymus gland

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.2.3: Adaptive Immunity is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
17.3: Adaptive Immunity by OpenStax is licensed CC BY 4.0.

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13.2.4: Disruptions in the Immune System
A functioning immune system is essential for survival, but even the sophisticated cellular and molecular defenses of the
mammalian immune response can be defeated by pathogens at virtually every step. In the competition between immune protection
and pathogen evasion, pathogens have the advantage of more rapid evolution because of their shorter generation time, large
population sizes and often higher mutation rates. Thus pathogens have evolved a diverse array of immune escape mechanisms. For
instance, Streptococcus pneumoniae (the bacterium that causes pneumonia and meningitis) surrounds itself with a capsule that
inhibits phagocytes from engulfing it and displaying antigens to the adaptive immune system. Staphylococcus aureus (the
bacterium that can cause skin infections, abscesses, and meningitis) synthesizes a toxin called leukocidin that kills phagocytes after
they engulf the bacterium. Other pathogens can also hinder the adaptive immune system. HIV infects TH cells using their CD4
surface molecules, gradually depleting the number of TH cells in the body (Figure [Link]); this inhibits the adaptive immune
system’s capacity to generate sufficient responses to infection or tumors. As a result, HIV-infected individuals often suffer from
infections that would not cause illness in people with healthy immune systems but which can cause devastating illness to immune-
compromised individuals.

Figure [Link]: HIV (green) is shown budding from a lymphocyte cell (red) in culture. (credit: modification of work by C.
Goldsmith, CDC; scale-bar data from Matt Russell)
Inappropriate responses of immune cells and molecules themselves can also disrupt the proper functioning of the entire system,
leading to host-cell damage that can become fatal.

Immunodeficiency
Immunodeficiency is a failure, insufficiency, or delay in the response of the immune system, which may be acquired or inherited.
Immunodeficiency can allow pathogens or tumor cells to gain a foothold and replicate or proliferate to high enough levels so that
the immune system becomes overwhelmed. Immunodeficiency can be acquired as a result of infection with certain pathogens that
attack the cells of the immune system itself (such as HIV), chemical exposure (including certain medical treatments such as
chemotherapy), malnutrition, or extreme stress. For instance, radiation exposure can destroy populations of lymphocytes and
elevate an individual’s susceptibility to infections and cancer. Rarely, primary immunodeficiencies that are present from birth may
also occur. For example, severe combined immunodeficiency disease (SCID) is a condition in which children are born without
functioning B or T cells.

Hypersensitivities
A maladaptive immune response toward harmless foreign substances or self-antigens that occur after tissue sensitization is termed
a hypersensitivity. Types of hypersensitivities include immediate, delayed, and autoimmune. A large proportion of the human
population is affected by one or more types of hypersensitivity.

Allergies
The immune reaction that results from immediate hypersensitivities in which an antibody-mediated immune response occurs within
minutes of exposure to a usually harmless antigen is called an allergy. In the United States, 20 percent of the population exhibits
symptoms of allergy or asthma, whereas 55 percent test positive against one or more allergens. On initial exposure to a potential
allergen, an allergic individual synthesizes antibodies through the typical process of APCs presenting processed antigen to TH cells

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that stimulate B cells to produce the antibodies. The antibody molecules interact with mast cells embedded in connective tissues.
This process primes, or sensitizes, the tissue. On subsequent exposure to the same allergen, antibody molecules on mast cells bind
the antigen and stimulate the mast cell to release histamine and other inflammatory chemicals; these chemical mediators then
recruit eosinophils (a type of white blood cell), which also appear to be adapted to responding to parasitic worms (Figure [Link]).
Eosinophils release factors that enhance the inflammatory response and the secretions of mast cells. The effects of an allergic
reaction range from mild symptoms like sneezing and itchy, watery eyes to more severe or even life-threatening reactions involving
intensely itchy welts or hives, airway constriction with severe respiratory distress, and plummeting blood pressure caused by
dilating blood vessels and fluid loss from the circulatory system. This extreme reaction, typically in response to an allergen
introduced to the circulatory system, is known as anaphylactic shock. Antihistamines are an insufficient counter to anaphylactic
shock and if not treated with epinephrine to counter the blood pressure and breathing effects, this condition can be fatal.

Figure [Link]: On first exposure to an allergen, an antibody is synthesized by plasma cells in response to a harmless antigen.
The antibodies bind to mast cells, and on secondary exposure, the mast cells release histamines and other modulators that cause the
symptoms of allergy. (credit: modification of work by NIH)
Delayed hypersensitivity is a cell-mediated immune response that takes approximately one to two days after secondary exposure
for a maximal reaction. This type of hypersensitivity involves the TH1 cytokine-mediated inflammatory response and may cause
local tissue lesions or contact dermatitis (rash or skin irritation). Delayed hypersensitivity occurs in some individuals in response to
contact with certain types of jewelry or cosmetics. Delayed hypersensitivity facilitates the immune response to poison ivy and is

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also the reason why the skin test for tuberculosis results in a small region of inflammation on individuals who were previously
exposed to Mycobacterium tuberculosis, the organism that causes tuberculosis.

CONCEPT IN ACTION

Try your hand at diagnosing an allergic reaction by selecting one of the interactive case studies at the World Allergy
Organization website.

Autoimmunity
Autoimmunity is a type of hypersensitivity to self-antigens that affects approximately five percent of the population. Most types of
autoimmunity involve the humoral immune response. An antibody that inappropriately marks self-components as foreign is termed
an autoantibody. In patients with myasthenia gravis, an autoimmune disease, muscle-cell receptors that induce contraction in
response to acetylcholine are targeted by antibodies. The result is muscle weakness that may include marked difficultly with fine or
gross motor functions. In systemic lupus erythematosus, a diffuse autoantibody response to the individual’s own DNA and proteins
results in various systemic diseases (Figure [Link]). Systemic lupus erythematosus may affect the heart, joints, lungs, skin,
kidneys, central nervous system, or other tissues, causing tissue damage through antibody binding, complement recruitment, lysis,
and inflammation.

Figure [Link]: Systemic lupus erythematosus is characterized by autoimmunity to the individual’s own DNA and/or proteins,
which leads to varied dysfunction of the organs. (credit: modification of work by Mikael Häggström)
Autoimmunity can develop with time and its causes may be rooted in molecular mimicry, a situation in which one molecule is
similar enough in shape to another molecule that it binds the same immune receptors. Antibodies and T-cell receptors may bind
self-antigens that are structurally similar to pathogen antigens. As an example, infection with Streptococcus pyogenes (the
bacterium that causes strep throat) may generate antibodies or T cells that react with heart muscle, which has a similar structure to
the surface of S. pyogenes. These antibodies can damage heart muscle with autoimmune attacks, leading to rheumatic fever.
Insulin-dependent (Type 1) diabetes mellitus arises from a destructive inflammatory TH1 response against insulin-producing cells
of the pancreas. Patients with this autoimmunity must be treated with regular insulin injections.

Summary
Immune disruptions may involve insufficient immune responses or inappropriate immune responses. Immunodeficiency increases
an individual's susceptibility to infections and cancers. Hypersensitivities are misdirected responses either to harmless foreign

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particles, as in the case of allergies, or to the individual’s own tissues, as in the case of autoimmunity. Reactions to self-components
may be the result of molecular mimicry.

Glossary

allergy
an immune reaction that results from immediate hypersensitivities in which an antibody-mediated immune response occurs
within minutes of exposure to a harmless antigen

autoantibody
an antibody that incorrectly marks “self” components as foreign and stimulates the immune response

autoimmunity
a type of hypersensitivity to self-antigens

hypersensitivity
a spectrum of inappropriate immune responses toward harmless foreign particles or self-antigens; occurs after tissue
sensitization and includes immediate-type (allergy), delayed-type, and autoimmunity

immunodeficiency
a failure, insufficiency, or delay at any level of the immune system, which may be acquired or inherited

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 13.2.4: Disruptions in the Immune System is shared under a CC BY license and was authored, remixed, and/or curated by
OpenStax.
17.4: Disruptions in the Immune System by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax [Link] [Link]

13.2.E: The Immune System and Desease (Exercises)
17.1: Viruses
Viruses are acellular, parasitic entities that are not classified within any domain because they are not considered alive. They have
no plasma membrane, internal organelles, or metabolic processes, and they do not divide. Instead, they infect a host cell and use the
host’s replication processes to produce progeny virus particles. Viruses infect all forms of organisms including bacteria, archaea,
fungi, plants, and animals.

Review Questions
Which statement is true?
A. A virion contains DNA and RNA.
B. Viruses are acellular.
C. Viruses replicate outside of the cell.
D. Most viruses are easily visualized with a light microscope.

Answer
B

The viral ________ plays a role in attaching a virion to the host cell.
A. core
B. capsid
C. envelope
D. both b and c

Answer
D

Which statement is true of viral replication?

A. In the process of apoptosis, the cell survives.
B. During attachment, the virus attaches at specific sites on the cell surface.
C. The viral capsid helps the host cell produce more copies of the viral genome.
D. mRNA works outside of the host cell to produce enzymes and proteins.

Answer
B

Free Response
Why can’t dogs catch the measles?

Answer
The virus cannot attach to dog cells because dog cells do not express the receptors for the virus or there is no cell within the dog
that is permissive for viral replication.

Why is immunization after being bitten by a rabid animal so effective?

Answer
Rabies vaccine works after a bite because it takes two weeks for the virus to travel from the site of the bite to the central
nervous system, where the most severe symptoms of the disease occur. The vaccine is able to cause an immune response in the
body during this time that clears the infection before it reaches the nervous system.

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17.2: Innate Immunity
Innate immunity is not caused by an infection or vaccination and depends initially on physical and chemical barriers that work on
all pathogens, sometimes called the first line of defense. The second line of defense of the innate system includes chemical signals
that produce inflammation and fever responses as well as mobilizing protective cells and other chemical defenses.

Review Questions
Which of the following is a barrier against pathogens provided by the skin?
A. low pH
B. mucus
C. tears
D. cilia

Answer
A

Although interferons have several effects, they are particularly useful against infections with which type of pathogen?
A. bacteria
B. viruses
C. fungi
D. helminths

Answer
B

Which innate immune system component uses MHC class I molecules directly in its defense strategy?
A. macrophages
B. neutrophils
C. NK cells
D. interferon

Answer
C

Free Response
Different MHC class I molecules between donor and recipient cells can lead to rejection of a transplanted organ or tissue. Suggest a
reason for this.

Answer
If the MHC class I molecules expressed on donor cells differ from the MHC class I molecules expressed on recipient cells, NK
cells may identify the donor cells as not normal and produce enzymes to induce the donor cells to undergo apoptosis, which
would destroy the transplanted organ.

If a series of genetic mutations prevented some, but not all, of the complement proteins from binding antibodies or pathogens,
would the entire complement system be compromised?

Answer
The entire complement system would probably be affected even when only a few members were mutated such that they could
no longer bind. Because the complement involves the binding of activated proteins in a specific sequence, when one or more
proteins in the sequence is absent, the subsequent proteins would be incapable of binding to elicit the complement’s pathogen-
destructive effects.

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17.3: Adaptive Immunity
The adaptive immune response is a slower-acting, longer-lasting, and more specific response than the innate response. However,
the adaptive response requires information from the innate immune system to function. APCs display antigens on MHC molecules
to naïve T cells. T cells with cell-surface receptors that bind a specific antigen will bind to that APC. In response, the T cells
differentiate and proliferate.

Review Questions
The humoral immune response depends on which cells?
A. TC cells
B. B cells
C. B and TH cells
D. TC and TH cells

Answer
C

The fact that the body does not normally mount an immune response to the molecules in food is an example of _______.
A. secondary immune response
B. immunological memory
C. immune tolerance
D. passive immunity

Answer
C

Foreign particles circulating in the blood are filtered by the ____________.

A. spleen
B. lymph nodes
C. MALT
D. lymph

Answer
A

Free Response
How do B and T cells differ with respect to antigens that they bind?

Answer
T cells bind antigens that have been digested and embedded in MHC molecules by APCs. In contrast, B cells function as APCs
to bind intact, unprocessed antigens.

Why is the immune response after reinfection much faster than the adaptive immune response after the initial infection?

Answer
Upon reinfection, the memory cells will immediately differentiate into plasma cells and CTLs without input from APCs or TH
cells. In contrast, the adaptive immune response to the initial infection requires time for naïve B and T cells with the appropriate
antigen specificities to be identified and activated.

17.4: Disruptions in the Immune System

A functioning immune system is essential for survival, but even the sophisticated cellular and molecular defenses of the
mammalian immune response can be defeated by pathogens at virtually every step. In the competition between immune protection

Access for free at OpenStax 13.2.E.3 [Link]

and pathogen evasion, pathogens have the advantage of more rapid evolution because of their shorter generation time, large
population sizes and often higher mutation rates. Thus pathogens have evolved a diverse array of immune escape mechanisms.

Review Questions
Allergy to pollen is classified as ________.
A. an autoimmune reaction
B. immunodeficiency
C. delayed hypersensitivity
D. immediate hypersensitivity

Answer
D

A potential cause of acquired autoimmunity is ________.

A. tissue hypersensitivity
B. molecular mimicry
C. histamine release
D. radiation exposure

Answer
B

Autoantibodies are probably involved in ________.

A. reactions to poison ivy
B. pollen allergies
C. systemic lupus erythematosus
D. HIV/AIDS

Answer
C

Free Response
Some photographers develop a sensitivity to certain film developing chemicals leading to severe rashes on their hands such that
they are unable to work with them. Explain what is probably happening.

Answer
This is probably a delayed sensitivity reaction to one or more chemicals in the developer. An initial exposure would have
sensitized the individual to the chemical and then subsequent exposures will induce a delayed inflammation reaction a day or
two after exposure.

This page titled 13.2.E: The Immune System and Desease (Exercises) is shared under a CC BY license and was authored, remixed, and/or curated
by OpenStax.
17.E: The Immune System and Desease (Exercises) by OpenStax is licensed CC BY 4.0.

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 CHAPTER OVERVIEW

14: Reproductive System

14.1: How Animals Reproduce
14.2: Development and Organogenesis
14.3: Human Reproduction
14.E: Animal Reproduction and Development (Exercises)

Thumbnail: Blue-tailed damselfies (Ischnura elegans) mating. CC-SA-BY 4.0; Charlesjsharp).

This page titled 14: Reproductive System is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.

1
14.1: How Animals Reproduce
Some animals produce offspring through asexual reproduction while other animals produce offspring through sexual reproduction.
Both methods have advantages and disadvantages. Asexual reproduction produces offspring that are genetically identical to the
parent because the offspring are all clones of the original parent. A single individual can produce offspring asexually and large
numbers of offspring can be produced quickly; these are two advantages that asexually reproducing organisms have over sexually
reproducing organisms. In a stable or predictable environment, asexual reproduction is an effective means of reproduction because
all the offspring will be adapted to that environment. In an unstable or unpredictable environment, species that reproduce asexually
may be at a disadvantage because all the offspring are genetically identical and may not be adapted to different conditions.
During sexual reproduction, the genetic material of two individuals is combined to produce genetically diverse offspring that differ
from their parents. The genetic diversity of sexually produced offspring is thought to give sexually reproducing individuals greater
fitness because more of their offspring may survive and reproduce in an unpredictable or changing environment. Species that
reproduce sexually (and have separate sexes) must maintain two different types of individuals, males and females. Only half the
population (females) can produce the offspring, so fewer offspring will be produced when compared to asexual reproduction. This
is a disadvantage of sexual reproduction compared to asexual reproduction.

Asexual Reproduction
Asexual reproduction occurs in prokaryotic microorganisms (bacteria and archaea) and in many eukaryotic, single-celled and
multi-celled organisms. There are several ways that animals reproduce asexually, the details of which vary among individual
species.

Fission
Fission, also called binary fission, occurs in some invertebrate, multi-celled organisms. It is in some ways analogous to the process
of binary fission of single-celled prokaryotic organisms. The term fission is applied to instances in which an organism appears to
split itself into two parts and, if necessary, regenerate the missing parts of each new organism. For example, species of turbellarian
flatworms commonly called the planarians, such as Dugesia dorotocephala, are able to separate their bodies into head and tail
regions and then regenerate the missing half in each of the two new organisms. Sea anemones (Cnidaria), such as species of the
genus Anthopleura (Figure 14.1.1), will divide along the oral-aboral axis, and sea cucumbers (Echinodermata) of the genus
Holothuria, will divide into two halves across the oral-aboral axis and regenerate the other half in each of the resulting individuals.

Figure 14.1.1: The Anthopleura artemisia sea anemone can reproduce through fission.

Budding
Budding is a form of asexual reproduction that results from the outgrowth of a part of the body leading to a separation of the “bud”
from the original organism and the formation of two individuals, one smaller than the other. Budding occurs commonly in some

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invertebrate animals such as hydras and corals. In hydras, a bud forms that develops into an adult and breaks away from the main
body (Figure 14.1.2).

Figure 14.1.2: (a) Hydra reproduce asexually through budding: a bud forms on the tubular body of an adult hydra, develops a
mouth and tentacles, and then detaches from its parent. The new hydra is fully developed and will find its own location for
attachment. (b) Some coral, such as the Lophelia pertusa shown here, can reproduce through budding. (credit b: modification of
work by Ed Bowlby, NOAA/Olympic Coast NMS; NOAA/OAR/Office of Ocean Exploration)

CONCEPT IN ACTION

Budding In Hydra

View this video to see a hydra budding.

Fragmentation
Fragmentation is the breaking of an individual into parts followed by regeneration. If the animal is capable of fragmentation, and
the parts are big enough, a separate individual will regrow from each part. Fragmentation may occur through accidental damage,
damage from predators, or as a natural form of reproduction. Reproduction through fragmentation is observed in sponges, some
cnidarians, turbellarians, echinoderms, and annelids. In some sea stars, a new individual can be regenerated from a broken arm and
a piece of the central disc. This sea star (Figure 14.1.3) is in the process of growing a complete sea star from an arm that has been

Access for free at OpenStax 14.1.2 [Link]

cut off. Fisheries workers have been known to try to kill the sea stars eating their clam or oyster beds by cutting them in half and
throwing them back into the ocean. Unfortunately for the workers, the two parts can each regenerate a new half, resulting in twice
as many sea stars to prey upon the oysters and clams.

Figure 14.1.3: (a) Linckia multifora is a species of sea star that can reproduce asexually via fragmentation. In this process, (b) an
arm that has been shed grows into a new sea star. (credit a: modifiction of work by Dwayne Meadows, NOAA/NMFS/OPR)

Parthenogenesis
Parthenogenesis is a form of asexual reproduction in which an egg develops into an individual without being fertilized. The
resulting offspring can be either haploid or diploid, depending on the process in the species. Parthenogenesis occurs in invertebrates
such as water fleas, rotifers, aphids, stick insects, and ants, wasps, and bees. Ants, bees, and wasps use parthenogenesis to produce
haploid males (drones). The diploid females (workers and queens) are the result of a fertilized egg.
Some vertebrate animals—such as certain reptiles, amphibians, and fish—also reproduce through parthenogenesis. Parthenogenesis
has been observed in species in which the sexes were separated in terrestrial or marine zoos. Two female Komodo dragons, a
hammerhead shark, and a blacktop shark have produced parthenogenic young when the females have been isolated from males. It
is possible that the asexual reproduction observed occurred in response to unusual circumstances and would normally not occur.

Sexual Reproduction
Sexual reproduction is the combination of reproductive cells from two individuals to form genetically unique offspring. The nature
of the individuals that produce the two kinds of gametes can vary, having for example separate sexes or both sexes in each
individual. Sex determination, the mechanism that determines which sex an individual develops into, also can vary.

Hermaphroditism
Hermaphroditism occurs in animals in which one individual has both male and female reproductive systems. Invertebrates such as
earthworms, slugs, tapeworms, and snails (Figure 14.1.4) are often hermaphroditic. Hermaphrodites may self-fertilize, but typically
they will mate with another of their species, fertilizing each other and both producing offspring. Self-fertilization is more common
in animals that have limited mobility or are not motile, such as barnacles and clams. Many species have specific mechanisms in
place to prevent self-fertilization, because it is an extreme form of inbreeding and usually produces less fit offspring.

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 Figure 14.1.4: Many (a) snails are hermaphrodites. When two individuals (b) mate, they can produce up to 100 eggs each. (credit
a: modification of work by Assaf Shtilman; credit b: modification of work by "Schristia"/Flickr)

Sex Determination
Mammalian sex is determined genetically by the combination of X and Y chromosomes. Individuals homozygous for X (XX) are
female and heterozygous individuals (XY) are male. In mammals, the presence of a Y chromosome causes the development of
male characteristics and its absence results in female characteristics. The XY system is also found in some insects and plants.
Bird sex determination is dependent on the combination of Z and W chromosomes. Homozygous for Z (ZZ) results in a male and
heterozygous (ZW) results in a female. Notice that this system is the opposite of the mammalian system because in birds the female
is the sex with the different sex chromosomes. The W appears to be essential in determining the sex of the individual, similar to the
Y chromosome in mammals. Some fish, crustaceans, insects (such as butterflies and moths), and reptiles use the ZW system.
More complicated chromosomal sex determining systems also exist. For example, some swordtail fish have three sex chromosomes
in a population.
The sex of some other species is not determined by chromosomes, but by some aspect of the environment. Sex determination in
alligators, some turtles, and tuataras, for example, is dependent on the temperature during the middle third of egg development.
This is referred to as environmental sex determination, or more specifically, as temperature-dependent sex determination. In many
turtles, cooler temperatures during egg incubation produce males and warm temperatures produce females, while in many other
species of turtles, the reverse is true. In some crocodiles and some turtles, moderate temperatures produce males and both warm
and cool temperatures produce females.
Individuals of some species change their sex during their lives, switching from one to the other. If the individual is female first, it is
termed protogyny or “first female,” if it is male first, it is termed protandry or “first male.” Oysters are born male, grow in size, and
become female and lay eggs. The wrasses, a family of reef fishes, are all sequential hermaphrodites. Some of these species live in
closely coordinated schools with a dominant male and a large number of smaller females. If the male dies, a female increases in
size, changes sex, and becomes the new dominant male.

Fertilization
The fusion of a sperm and an egg is a process called fertilization. This can occur either inside (internal fertilization) or outside
(external fertilization) the body of the female. Humans provide an example of the former, whereas frog reproduction is an example
of the latter.

External Fertilization
External fertilization usually occurs in aquatic environments where both eggs and sperm are released into the water. After the
sperm reaches the egg, fertilization takes place. Most external fertilization happens during the process of spawning where one or

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several females release their eggs and the male(s) release sperm in the same area, at the same time. The spawning may be triggered
by environmental signals, such as water temperature or the length of daylight. Nearly all fish spawn, as do crustaceans (such as
crabs and shrimp), mollusks (such as oysters), squid, and echinoderms (such as sea urchins and sea cucumbers). Frogs, corals,
molluscs, and sea cucumbers also spawn (Figure 14.1.5).

Figure 14.1.5: During sexual reproduction in toads, the male grasps the female from behind and externally fertilizes the eggs as
they are deposited. (credit: Bernie Kohl)

Internal Fertilization
Internal fertilization occurs most often in terrestrial animals, although some aquatic animals also use this method. Internal
fertilization may occur by the male directly depositing sperm in the female during mating. It may also occur by the male depositing
sperm in the environment, usually in a protective structure, which a female picks up to deposit the sperm in her reproductive tract.
There are three ways that offspring are produced following internal fertilization. In oviparity, fertilized eggs are laid outside the
female’s body and develop there, receiving nourishment from the yolk that is a part of the egg (Figure 14.1.6a). This occurs in
some bony fish, some reptiles, a few cartilaginous fish, some amphibians, a few mammals, and all birds. Most non-avian reptiles
and insects produce leathery eggs, while birds and some turtles produce eggs with high concentrations of calcium carbonate in the
shell, making them hard. Chicken eggs are an example of a hard shell. The eggs of the egg-laying mammals such as the platypus
and echidna are leathery.
In ovoviparity, fertilized eggs are retained in the female, and the embryo obtains its nourishment from the egg’s yolk. The eggs are
retained in the female’s body until they hatch inside of her, or she lays the eggs right before they hatch. This process helps protect
the eggs until hatching. This occurs in some bony fish (like the platyfish Xiphophorus maculatus, Figure 14.1.6b), some sharks,
lizards, some snakes (garter snake Thamnophis sirtalis), some vipers, and some invertebrate animals (Madagascar hissing
cockroach Gromphadorhina portentosa).
In viviparity the young are born alive. They obtain their nourishment from the female and are born in varying states of maturity.
This occurs in most mammals (Figure 14.1.6c), some cartilaginous fish, and a few reptiles.

Figure 14.1.6: In (a) oviparity, young develop in eggs outside the female body, as with these Harmonia axydridis beetles
hatching. Some aquatic animals, like this (b) pregnant Xiphophorus maculatus are ovoviparous, with the egg developing inside the
female and nutrition supplied primarily from the yolk. In mammals, nutrition is supported by the placenta, as was the case with this
(c) newborn squirrel. (credit b: modification of work by Gourami Watcher; credit c: modification of work by
"audreyjm529"/Flickr)

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Section Summary
Reproduction may be asexual when one individual produces genetically identical offspring, or sexual when the genetic material
from two individuals is combined to produce genetically diverse offspring. Asexual reproduction in animals occurs through fission,
budding, fragmentation, and parthenogenesis. Sexual reproduction may involve fertilization inside the body or in the external
environment. A species may have separate sexes or combined sexes; when the sexes are combined they may be expressed at
different times in the life cycle. The sex of an individual may be determined by various chromosomal systems or environmental
factors such as temperature.
Sexual reproduction starts with the combination of a sperm and an egg in a process called fertilization. This can occur either
outside the bodies or inside the female. The method of fertilization varies among animals. Some species release the egg and sperm
into the environment, some species retain the egg and receive the sperm into the female body and then expel the developing
embryo covered with shell, while still other species retain the developing offspring throughout the gestation period.

Glossary

asexual reproduction
a mechanism that produces offspring that are genetically identical to the parent

budding
a form of asexual reproduction that results from the outgrowth of a part of an organism leading to a separation from the original
animal into two individuals

external fertilization
the fertilization of eggs by sperm outside an animal’s body, often during spawning

fission
(also, binary fission) a form of asexual reproduction in which an organism splits into two separate organisms or two parts that
regenerate the missing portions of the body

fragmentation
the breaking of an organism into parts and the growth of a separate individual from each part

hermaphroditism
the state of having both male and female reproductive structures within the same individual

internal fertilization
the fertilization of eggs by sperm inside the body of the female

oviparity
a process by which fertilized eggs are laid outside the female’s body and develop there, receiving nourishment from the yolk
that is a part of the egg

ovoviparity
a process by which fertilized eggs are retained within the female; the embryo obtains its nourishment from the egg’s yolk, and
the young are fully developed when they are hatched

parthenogenesis
a form of asexual reproduction in which an egg develops into a complete individual without being fertilized

sex determination
the mechanism by which the sex of individuals in sexually reproducing organisms is initially established

sexual reproduction
a form of reproduction in which cells containing genetic material from two individuals combines to produce genetically unique
offspring

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viviparity
a process in which the young develop within the female and are born in a nonembryonic state

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 14.1: How Animals Reproduce is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
18.1: How Animals Reproduce by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 14.1.7 [Link]

14.2: Development and Organogenesis
The process by which an organism develops from a single-celled zygote to a multi-cellular organism is complex and well regulated.
The regulation occurs through signaling between cells and tissues and responses in the form of differential gene expression.

Early Embryonic Development

Fertilization is the process in which gametes (an egg and sperm) fuse to form a zygote (Figure 14.2.1). To ensure that the offspring
has only one complete diploid set of chromosomes, only one sperm must fuse with one egg. In mammals, a layer called the zona
pellucida protects the egg. At the tip of the head of a sperm cell is a structure like a lysosome called the acrosome, which contains
enzymes. When a sperm binds to the zona pellucida, a series of events, called the acrosomal reactions, take place. These reactions,
involving enzymes from the acrosome, allow the sperm plasma membrane to fuse with the egg plasma membrane and permit the
sperm nucleus to transfer into the ovum. The nuclear membranes of the egg and sperm break down and the two haploid nuclei fuse
to form a diploid nucleus or genome.

Figure 14.2.1: Fertilization is the process in which sperm and egg fuse to form a zygote. (credit: scale-bar data from Matt
Russell)
To ensure that no more than one sperm fertilizes the egg, once the acrosomal reactions take place at one location of the egg
membrane, the egg releases proteins in other locations to prevent other sperm from fusing with the egg.
The development of multi-cellular organisms begins from this single-celled zygote, which undergoes rapid cell division, called
cleavage (Figure 14.2.2a), to form a hollow ball of cells called a blastula (Figure 14.2.2b).

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 Figure 14.2.2: (a) During cleavage, the zygote rapidly divides into multiple cells. (b) The cells rearrange themselves to form a
hollow ball called the blastula. (credit a: modification of work by Gray's Anatomy; credit b: modification of work by Pearson Scott
Foresman; donated to the Wikimedia Foundation)
In mammals, the blastula forms the blastocyst in the next stage of development. Here the cells in the blastula arrange themselves in
two layers: the inner cell mass, and an outer layer called the trophoblast. The inner cell mass will go on to form the embryo. The
trophoblast secretes enzymes that allow implantation of the blastocyst into the endometrium of the uterus. The trophoblast will
contribute to the placenta and nourish the embryo.

CONCEPT IN ACTION

Visit the Virtual Human Embryo project at the Endowment for Human Development site to click through an interactive of the
stages of embryo development, including micrographs and rotating 3-D images.

The cells in the blastula then rearrange themselves spatially to form three layers of cells. This process is called gastrulation. During
gastrulation, the blastula folds in on itself and cells migrate to form the three layers of cells (Figure 14.2.3) in a structure, the
gastrula, with a hollow space that will become the digestive tract. Each of the layers of cells is called a germ layer and will
differentiate into different organ systems.

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 Figure 14.2.3: Gastrulation is the process wherein the cells in the blastula rearrange themselves to form the germ layers. (credit:
modification of work by Abigail Pyne)
The three germ layers are the endoderm, the ectoderm, and the mesoderm. Cells in each germ layer differentiate into tissues and
embryonic organs. The ectoderm gives rise to the nervous system and the epidermis, among other tissues. The mesoderm gives rise
to the muscle cells and connective tissue in the body. The endoderm gives rise to the gut and many internal organs.

Organogenesis
Gastrulation leads to the formation of the three germ layers that give rise during further development to the different organs in the
animal body. This process is called organogenesis.
Organs develop from the germ layers through the process of differentiation. During differentiation, the embryonic stem cells
express specific sets of genes that will determine their ultimate cell type. For example, some cells in the ectoderm will express the
genes specific to skin cells. As a result, these cells will take on the shape and characteristics of epidermal cells. The process of
differentiation is regulated by location-specific chemical signals from the cell’s embryonic environment that sets in play a cascade
of events that regulates gene expression.

Summary
The early stages of embryonic development begin with fertilization. The process of fertilization is tightly controlled to ensure that
only one sperm fuses with one egg. After fertilization, the zygote undergoes cleavage to form the blastula. The blastula, which in
some species is a hollow ball of cells, undergoes a process called gastrulation, during which the three germ layers form. The
ectoderm gives rise to the nervous system and the epidermal skin cells, the mesoderm gives rise to the muscle cells and connective
tissue in the body, and the endoderm gives rise to the digestive system and other internal organs. Organogenesis is the formation of
organs from the germ layers. Each germ layer gives rise to specific tissue types.

Glossary

blastocyst
the structure formed when cells in the mammalian blastula separate into an inner and outer layer

gastrulation
the process in which the blastula folds over itself to form the three germ layers

inner cell mass

the inner layer of cells in the blastocyst, which becomes the embryo

organogenesis
the process of organ formation during development

trophoblast
the outer layer of cells in the blastocyst, which gives rise to the embryo’s contribution to the placenta

zona pellucida
the protective layer around the mammalian egg

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Contributors and Attributions
Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 14.2: Development and Organogenesis is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
18.2: Development and Organogenesis by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 14.2.4 [Link]

14.3: Human Reproduction
As in all animals, the adaptations for reproduction in humans are complex. They involve specialized and different anatomies in the
two sexes, a hormone regulation system, and specialized behaviors regulated by the brain and endocrine system.

Human Reproductive Anatomy

The reproductive tissues of male and female humans develop similarly in utero until about the seventh week of gestation when a
low level of the hormone testosterone is released from the gonads of the developing male. Testosterone causes the primitive gonads
to differentiate into male sexual organs. When testosterone is absent, the primitive gonads develop into ovaries. Tissues that
produce a penis in males produce a clitoris in females. The tissue that will become the scrotum in a male becomes the labia in a
female. Thus the male and female anatomies arise from a divergence in the development of what were once common embryonic
structures.

Male Reproductive Anatomy

Sperm are immobile at body temperature; therefore, the testes are external to the body so that a correct temperature is maintained
for motility. In land mammals, including humans, the pair of testes must be suspended outside the body so the environment of the
sperm is about 2 °C lower than body temperature to produce viable sperm. If the testes do not descend through the abdominal
cavity during fetal development, the individual has reduced fertility.
The scrotum houses the testicles or testes (singular: testis), and provides passage for blood vessels, nerves, and muscles related to
testicular function. The testes are a pair of male gonads that produce sperm and reproductive hormones. Each testis is
approximately 2.5 by 3.8 cm (1.5 by 1 inch) in size and divided into wedge-shaped lobes by septa. Coiled in each wedge are
seminiferous tubules that produce sperm.
The penis drains urine from the urinary bladder and is a copulatory organ during intercourse (Figure 14.3.2; Table 14.3.1). The
penis contains three tubes of erectile tissue that become engorged with blood, making the penis erect, in preparation for intercourse.
The organ is inserted into the vagina culminating with an ejaculation. During orgasm, the accessory organs and glands connected to
the testes contract and empty the semen (containing sperm) into the urethra and the fluid is expelled from the body by muscular
contractions causing ejaculation. After intercourse, the blood drains from the erectile tissue and the penis becomes flaccid.
Semen is a mixture of sperm (about five percent of the total) and fluids from accessory glands that contribute most of the semen’s
volume. Sperm are haploid cells, consisting of a flagellum for motility, a neck that contains the cell’s energy-producing
mitochondria, and a head that contains the genetic material (Figure 14.3.1). An acrosome (acrosomal vesicle) is found at the top of
the head of the sperm. This structure contains enzymes that can digest the protective coverings that surround the egg and allow the
sperm to fuse with the egg. An ejaculate will contain from two to five milliliters of fluid and from 50–120 million sperm per
milliliter.

Figure 14.3.1: As seen in this scanning electron micrograph, human sperm has a flagellum, neck, and head. (credit: scale-bar data
from Matt Russell)
Sperm form in the walls of seminiferous tubules that are coiled inside the testes (Figure 14.3.2; Table 14.3.1). The walls of the
seminiferous tubules are made up of the developing sperm cells, with the least developed sperm at the periphery of the tubule and

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the fully developed sperm next to the lumen. The sperm cells are associated with Sertoli cells that nourish and promote the
development of the sperm. Other cells present between the walls of the tubules are the interstitial cells of Leydig, which produce
testosterone once the male reaches adolescence.
When the sperm have developed flagella they leave the seminiferous tubules and enter the epididymis (Figure 14.3.2; Table
14.3.1). This structure lies along the top and posterior of the testes and is the site of sperm maturation. The sperm leave the

epididymis and enter the vas deferens, which carries the sperm behind the bladder, and forms the ejaculatory duct with the duct
from the seminal vesicles. During a vasectomy, a section of the vas deferens is removed, preventing sperm (but not the secretions
of the accessory glands) from being passed out of the body during ejaculation and preventing fertilization.
The bulk of the semen comes from the accessory glands associated with the male reproductive system. These are the seminal
vesicles, the prostate gland, and the bulbourethral gland (Figure 14.3.2; Table 14.3.1). The secretions from the accessory glands
provide important compounds for the sperm including nutrients, electrolytes, and pH buffering. There are also coagulation factors
that affect sperm delivery and motility.

ART CONNECTION

Figure 14.3.2: The reproductive structures of the human male are shown.
Which of the following statements about the male reproductive system is false?
A. The vas deferens carries sperm from the testes to the seminal vesicles.
B. The ejaculatory duct joins the urethra.
C. Both the prostate and the bulbourethral glands produce components of the semen.
D. The prostate gland is located in the testes.

Table 14.3.1: Male Reproductive Anatomy

Organ Location Function

Scrotum External Supports testes and regulates their temperature

Penis External Delivers urine, copulating organ

Testes Internal Produce sperm and male hormones

Seminal Vesicles Internal Contribute to semen production

Prostate Gland Internal Contributes to semen production

Bulbourethtral Glands Internal Neutralize urine in urethra

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Female Reproductive Anatomy
A number of female reproductive structures are exterior to the body. These include the breasts and the vulva, which consists of the
mons pubis, clitoris, labia majora, labia minora, and the vestibular glands (Figure 14.3.3; Table 14.3.2).

Figure 14.3.3: The reproductive structures of the human female are shown. (credit a: modification of work by Gray's Anatomy;
credit b: modification of work by CDC)
The breasts consist of mammary glands and fat. Each gland consists of 15 to 25 lobes that have ducts that empty at the nipple and
that supply the nursing child with nutrient- and antibody-rich milk to aid development and protect the child.
Internal female reproductive structures include ovaries, oviducts, the uterus, and the vagina (Figure 14.3.3; Table 14.3.2). The pair
of ovaries is held in place in the abdominal cavity by a system of ligaments. The outermost layer of the ovary is made up of
follicles, each consisting of one or more follicular cells that surround, nourish, and protect a single egg. During the menstrual
period, a batch of follicular cells develops and prepares their eggs for release. At ovulation, one follicle ruptures and one egg is
released. Following ovulation, the follicular tissue that surrounded the ovulated egg stays within the ovary and grows to form a
solid mass called the corpus luteum. The corpus luteum secretes additional estrogen and the hormone progesterone that helps
maintain the uterine lining during pregnancy. The ovaries also produce hormones, such as estrogen.
The oviducts, or fallopian tubes, extend from the uterus in the lower abdominal cavity to the ovaries, but they are not in contact
with the ovaries. The lateral ends of the oviducts flare out into a trumpet-like structure and have a fringe of finger-like projections
called fimbrae. When an egg is released at ovulation, the fimbrae help the nonmotile egg enter into the tube. The walls of the
oviducts have a ciliated epithelium over smooth muscle. The cilia beat, and the smooth muscle contracts, moving the egg toward
the uterus. Fertilization usually takes place within the oviduct and the developing embryo is moved toward the uterus. It usually
takes the egg or embryo a week to travel through the oviduct.
Sterilization in women is called a tubal ligation; it is analogous to a vasectomy in males in that the oviducts are severed and sealed,
preventing sperm from reaching the egg.
The uterus is a structure about the size of a woman’s fist. The uterus has a thick muscular wall and is lined with an endometrium
rich in blood vessels and mucus glands that develop and thicken during the female cycle. Thickening of the endometrium prepares
the uterus to receive the fertilized egg or zygote, which will then implant itself in the endometrium. The uterus supports the
developing embryo and fetus during gestation. Contractions of the smooth muscle in the uterus aid in forcing the baby through the
vagina during labor. If fertilization does not occur, a portion of the lining of the uterus sloughs off during each menstrual period.
The endometrium builds up again in preparation for implantation. Part of the uterus, called the cervix, protrudes into the top of the
vagina.
The vagina is a muscular tube that serves several purposes. It allows menstrual flow to leave the body. It is the receptacle for the
penis during intercourse and the pathway for the delivery of offspring.

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 Table 14.3.2: Female Reproductive Anatomy

Organ Location Function

Clitoris External Sensory organ

Mons pubis External Fatty area overlying pubic bone

Covers labia minora; contains sweat and

Labia majora External
sebaceous glands

Labia minora External Covers vestibule

Greater vestibular glands External Secrete mucus; lubricate vagina

Breast External Produces and delivers milk

Ovaries Internal Produce and develop eggs

Oviducts Internal Transport egg to uterus; site of fertilization

Uterus Internal Supports developing embryo

Common tube for intercourse, birth canal,

Vagina Internal
passing menstrual flow

Gametogenesis (Spermatogenesis and Oogenesis)

Gametogenesis, the production of sperm and eggs, involves the process of meiosis. During meiosis, two nuclear divisions separate
the paired chromosomes in the nucleus and then separate the chromatids that were made during an earlier stage of the cell’s life
cycle. Meiosis and its associated cell divisions produces haploid cells with half of each pair of chromosomes normally found in
diploid cells. The production of sperm is called spermatogenesis and the production of eggs is called oogenesis.

Spermatogenesis
Spermatogenesis occurs in the wall of the seminiferous tubules, with the most primitive cells at the periphery of the tube and the
most mature sperm at the lumen of the tube (Figure 14.3.4). Immediately under the capsule of the tubule are diploid,
undifferentiated cells. These stem cells, each called a spermatogonium (pl. spermatogonia), go through mitosis to produce one cell
that remains as a stem cell and a second cell called a primary spermatocyte that will undergo meiosis to produce sperm.
The diploid primary spermatocyte goes through meiosis I to produce two haploid cells called secondary spermatocytes. Each
secondary spermatocyte divides after meiosis II to produce two cells called spermatids. The spermatids eventually reach the lumen
of the tubule and grow a flagellum, becoming sperm cells. Four sperm result from each primary spermatocyte that goes through
meiosis.

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 Figure 14.3.4: During spermatogenesis, four sperm result from each primary spermatocyte. The process also maps onto the
physical structure of the wall of the seminiferous tubule, with the spermatogonia on the outer side of the tubule, and the sperm with
their developing tails extended into the lumen of the tubule.

CONCEPT IN ACTION

Spermatogenesis | Reproductive syst…

syst…

Visit this site to see the process of spermatogenesis.

Oogenesis
Oogenesis occurs in the outermost layers of the ovaries. As with sperm production, oogenesis starts with a germ cell. In oogenesis,
this germ cell is called an oogonium and forms during the embryological development of the individual. The oogonium undergoes
mitosis to produce about one to two million oocytes by the time of birth.

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 Figure 14.3.5: The process of oogenesis occurs in the ovary’s outermost layer.
The primary oocytes begin meiosis before birth (Figure 14.3.5). However, the meiotic division is arrested in its progress in the first
prophase stage. At the time of birth, all future eggs are in prophase I. This situation is in contrast with the male reproductive system
in which sperm are produced continuously throughout the life of the individual. Starting at adolescence, anterior pituitary hormones
cause the development of a few follicles in an ovary each month. This results in a primary oocyte finishing the first meiotic
division. The cell divides unequally, with most of the cytoplasm and organelles going to one cell, called a secondary oocyte, and
only one set of chromosomes and a small amount of cytoplasm going to the other cell. This second cell is called a polar body and
usually dies. Cell division is again arrested, this time at metaphase II. At ovulation, this secondary oocyte is released and travels
toward the uterus through the oviduct. If the secondary oocyte is fertilized, the cell continues through meiosis II, producing a
second polar body and haploid egg, which fuses with the haploid sperm to form a fertilized egg (zygote) containing all 46
chromosomes.

Hormonal Control of Reproduction

The human male and female reproductive cycles are controlled by the interaction of hormones from the hypothalamus and anterior
pituitary with hormones from reproductive tissues and organs. In both sexes, the hypothalamus monitors and causes the release of
hormones from the anterior pituitary gland. When the reproductive hormone is required, the hypothalamus sends a gonadotropin-
releasing hormone (GnRH) to the anterior pituitary. This causes the release of follicle stimulating hormone (FSH) and luteinizing
hormone (LH) from the anterior pituitary into the blood. Although these hormones are named after their functions in female
reproduction, they are produced in both sexes and play important roles in controlling reproduction. Other hormones have specific
functions in the male and female reproductive systems.

Male Hormones
At the onset of puberty, the hypothalamus causes the release of FSH and LH into the male system for the first time. FSH enters the
testes and stimulates the Sertoli cells located in the walls of the seminiferous tubules to begin promoting spermatogenesis (Figure
14.3.6). LH also enters the testes and stimulates the interstitial cells of Leydig, located in between the walls of the seminiferous

tubules, to make and release testosterone into the testes and the blood.
Testosterone stimulates spermatogenesis. This hormone is also responsible for the secondary sexual characteristics that develop in
the male during adolescence. The secondary sex characteristics in males include a deepening of the voice, the growth of facial,
axillary, and pubic hair, an increase in muscle bulk, and the beginnings of the sex drive.

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 Figure 14.3.6: Hormones control sperm production in a negative feedback system.
A negative feedback system occurs in the male with rising levels of testosterone acting on the hypothalamus and anterior pituitary
to inhibit the release of GnRH, FSH, and LH. In addition, the Sertoli cells produce the hormone inhibin, which is released into the
blood when the sperm count is too high. This inhibits the release of GnRH and FSH, which will cause spermatogenesis to slow
down. If the sperm count reaches a low of 20 million/mL, the Sertoli cells cease the release of inhibin, and the sperm count
increases.

Female Hormones
The control of reproduction in females is more complex. The female reproductive cycle is divided into the ovarian cycle and the
menstrual cycle. The ovarian cycle governs the preparation of endocrine tissues and release of eggs, while the menstrual cycle
governs the preparation and maintenance of the uterine lining (Figure 14.3.7). These cycles are coordinated over a 22–32 day
cycle, with an average length of 28 days.
As with the male, the GnRH from the hypothalamus causes the release of the hormones FSH and LH from the anterior pituitary. In
addition, estrogen and progesterone are released from the developing follicles. As with testosterone in males, estrogen is
responsible for the secondary sexual characteristics of females. These include breast development, flaring of the hips, and a shorter
period for bone growth.

The Ovarian Cycle and the Menstrual Cycle

The ovarian and menstrual cycles are regulated by hormones of the hypothalamus, pituitary, and ovaries (Figure 14.3.7). The ebb
and flow of the hormones causes the ovarian and menstrual cycles to advance. The ovarian and menstrual cycles occur
concurrently. The first half of the ovarian cycle is the follicular phase. Slowly rising levels of FSH cause the growth of follicles on
the surface of the ovary. This process prepares the egg for ovulation. As the follicles grow, they begin releasing estrogen. The first
few days of this cycle coincide with menstruation or the sloughing off of the functional layer of the endometrium in the uterus.
After about five days, estrogen levels rise and the menstrual cycle enters the proliferative phase. The endometrium begins to
regrow, replacing the blood vessels and glands that deteriorated during the end of the last cycle.

ART CONNECTION

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 Figure 14.3.7: The ovarian and menstrual cycles of female reproduction are regulated by hormones produced by the
hypothalamus, pituitary, and ovaries.
Which of the following statements about hormone regulation of the female reproductive cycle is false?
A. LH and FSH are produced in the pituitary, and estrogen and progesterone are produced in the ovaries.
B. Estradiol and progesterone secreted from the corpus luteum cause the endometrium to thicken.
C. Both progesterone and estrogen are produced by the follicles.
D. Secretion of GnRH by the hypothalamus is inhibited by low levels of estrogen but stimulated by high levels of estrogen.

Just prior to the middle of the cycle (approximately day 14), the high level of estrogen causes FSH and especially LH to rise rapidly
then fall. The spike in LH causes the most mature follicle to rupture and release its egg. This is ovulation. The follicles that did not
rupture degenerate and their eggs are lost. The level of estrogen decreases when the extra follicles degenerate.

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Following ovulation, the ovarian cycle enters its luteal phase and the menstrual cycle enters its secretory phase, both of which run
from about day 15 to 28. The luteal and secretory phases refer to changes in the ruptured follicle. The cells in the follicle undergo
physical changes and produce a structure called a corpus luteum. The corpus luteum produces estrogen and progesterone. The
progesterone facilitates the regrowth of the uterine lining and inhibits the release of further FSH and LH. The uterus is being
prepared to accept a fertilized egg, should it occur during this cycle. The inhibition of FSH and LH prevents any further eggs and
follicles from developing, while the progesterone is elevated. The level of estrogen produced by the corpus luteum increases to a
steady level for the next few days.
If no fertilized egg is implanted into the uterus, the corpus luteum degenerates and the levels of estrogen and progesterone decrease.
The endometrium begins to degenerate as the progesterone levels drop, initiating the next menstrual cycle. The decrease in
progesterone also allows the hypothalamus to send GnRH to the anterior pituitary, releasing FSH and LH and starting the cycles
again.

CAREER IN ACTION: Reproductive Endocrinologist

A reproductive endocrinologist is a physician who treats a variety of hormonal disorders related to reproduction and infertility
in both men and women. The disorders include menstrual problems, infertility, pregnancy loss, sexual dysfunction, and
menopause. Doctors may use fertility drugs, surgery, or assisted reproductive techniques (ART) in their therapy. ART involves
the use of procedures to manipulate the egg or sperm to facilitate reproduction, such as in vitro fertilization.
Reproductive endocrinologists undergo extensive medical training, first in a four-year residency in obstetrics and gynecology,
then in a three-year fellowship in reproductive endocrinology. To be board certified in this area, the physician must pass written
and oral exams in both areas.

Gestation
Pregnancy begins with the fertilization of an egg and continues through to the birth of the individual. The length of time of
gestation, or the gestation period, in humans is 266 days and is similar in other great apes.
Within 24 hours of fertilization, the egg nucleus has finished meiosis and the egg and sperm nuclei fuse. With fusion, the cell is
known as a zygote. The zygote initiates cleavage and the developing embryo travels through the oviduct to the uterus. The
developing embryo must implant into the wall of the uterus within seven days, or it will deteriorate and die. The outer layers of the
developing embryo or blastocyst grow into the endometrium by digesting the endometrial cells, and healing of the endometrium
closes up the blastocyst into the tissue. Another layer of the blastocyst, the chorion, begins releasing a hormone called human beta
chorionic gonadotropin (β-HCG), which makes its way to the corpus luteum and keeps that structure active. This ensures adequate
levels of progesterone that will maintain the endometrium of the uterus for the support of the developing embryo. Pregnancy tests
determine the level of β-HCG in urine or serum. If the hormone is present, the test is positive.
The gestation period is divided into three equal periods or trimesters. During the first two-to-four weeks of the first trimester,
nutrition and waste are handled by the endometrial lining through diffusion. As the trimester progresses, the outer layer of the
embryo begins to merge with the endometrium, and the placenta forms. The placenta takes over the nutrient and waste
requirements of the embryo and fetus, with the mother’s blood passing nutrients to the placenta and removing waste from it.
Chemicals from the fetus, such as bilirubin, are processed by the mother’s liver for elimination. Some of the mother’s
immunoglobulins will pass through the placenta, providing passive immunity against some potential infections.
Internal organs and body structures begin to develop during the first trimester. By five weeks, limb buds, eyes, the heart, and liver
have been basically formed. By eight weeks, the term fetus applies, and the body is essentially formed (Figure 14.3.8a). The
individual is about five centimeters (two inches) in length and many of the organs, such as the lungs and liver, are not yet
functioning. Exposure to any toxins is especially dangerous during the first trimester, as all of the body’s organs and structures are
going through initial development. Anything that interferes with chemical signaling during that development can have a severe
effect on the fetus’ survival.

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 Figure 14.3.8: (a) Fetal development is shown at nine weeks gestation. (b) This fetus is just entering the second trimester, when
the placenta takes over more of the functions performed as the baby develops. (c) There is rapid fetal growth during the third
trimester. (credit a: modification of work by Ed Uthman; credit b: modification of work by National Museum of Health and
Medicine; credit c: modification of work by Gray’s Anatomy)
During the second trimester, the fetus grows to about 30 cm (about 12 inches) (Figure 14.3.8b). It becomes active and the mother
usually feels the first movements. All organs and structures continue to develop. The placenta has taken over the functions of
nutrition and waste elimination and the production of estrogen and progesterone from the corpus luteum, which has degenerated.
The placenta will continue functioning up through the delivery of the baby. During the third trimester, the fetus grows to 3 to 4 kg
(6.5–8.5 lbs.) and about 50 cm (19–20 inches) long (Figure 14.3.8c). This is the period of the most rapid growth during the
pregnancy as all organ systems continue to grow and develop.

CONCEPT IN ACTION

Visit this website to see the stages of human fetal development.

Labor is the muscular contractions to expel the fetus and placenta from the uterus. Toward the end of the third trimester, estrogen
causes receptors on the uterine wall to develop and bind the hormone oxytocin. At this time, the baby reorients, facing forward and
down with the back or crown of the head engaging the cervix (uterine opening). This causes the cervix to stretch and nerve
impulses are sent to the hypothalamus, which signals the release of oxytocin from the posterior pituitary. Oxytocin causes smooth
muscle in the uterine wall to contract. At the same time, the placenta releases prostaglandins into the uterus, increasing the
contractions. A positive feedback relay occurs between the uterus, hypothalamus, and the posterior pituitary to assure an adequate
supply of oxytocin. As more smooth muscle cells are recruited, the contractions increase in intensity and force.
There are three stages to labor. During stage one, the cervix thins and dilates. This is necessary for the baby and placenta to be
expelled during birth. The cervix will eventually dilate to about 10 cm. During stage two, the baby is expelled from the uterus. The
uterus contracts and the mother pushes as she compresses her abdominal muscles to aid the delivery. The last stage is the passage
of the placenta after the baby has been born and the organ has completely disengaged from the uterine wall. If labor should stop
before stage two is reached, synthetic oxytocin, known as Pitocin, can be administered to restart and maintain labor.

Section Summary
The reproductive structures that evolved in land animals allow males and females to mate, fertilize internally, and support the
growth and development of offspring. Gametogenesis, the production of sperm (spermatogenesis) and eggs (oogenesis), takes place

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through the process of meiosis.
The male and female reproductive cycles are controlled by hormones released from the hypothalamus and anterior pituitary and
hormones from reproductive tissues and organs. The hypothalamus monitors the need for FSH and LH production and release from
the anterior pituitary. FSH and LH affect reproductive structures to cause the formation of sperm and the preparation of eggs for
release and possible fertilization. In the male, FSH and LH stimulate Sertoli cells and interstitial cells of Leydig in the testes to
facilitate sperm production. The Leydig cells produce testosterone, which also is responsible for the secondary sexual
characteristics of males. In females, FSH and LH cause estrogen and progesterone to be produced. They regulate the female
reproductive cycle, which is divided into the ovarian cycle and the menstrual cycle.
Human pregnancy begins with fertilization of an egg and proceeds through the three trimesters of gestation. The first trimester lays
down the basic structures of the body, including the limb buds, heart, eyes, and the liver. The second trimester continues the
development of all of the organs and systems. The third trimester exhibits the greatest growth of the fetus and culminates in labor
and delivery. The labor process has three stages (contractions, delivery of the fetus, and expulsion of the placenta), each propelled
by hormones.

Art Connections
Figure 14.3.2: Which of the following statements about the male reproductive system is false?
A. The vas deferens carries sperm from the testes to the seminal vesicles.
B. The ejaculatory duct joins the urethra.
C. Both the prostate and the bulbourethral glands produce components of the semen.
D. The prostate gland is located in the testes.

Answer
D

Figure 14.3.7: Which of the following statements about hormone regulation of the female reproductive cycle is false?
A. LH and FSH are produced in the pituitary, and estrogen and progesterone are produced in the ovaries.
B. Estradiol and progesterone secreted from the corpus luteum cause the endometrium to thicken.
C. Both progesterone and estrogen are produced by the follicles.
D. Secretion of GnRH by the hypothalamus is inhibited by low levels of estrogen but stimulated by high levels of estrogen.

Answer
C

Glossary

bulbourethral gland
the paired glands in the human male that produce a secretion that cleanses the urethra prior to ejaculation

corpus luteum
the endocrine tissue that develops from an ovarian follicle after ovulation; secretes progesterone and estrogen during pregnancy

clitoris
a sensory and erectile structure in female mammals, homologous to the male penis, stimulated during sexual arousal

estrogen
a reproductive hormone in females that assists in endometrial regrowth, ovulation, and calcium absorption

follicle stimulating hormone (FSH)

a reproductive hormone that causes sperm production in men and follicle development in women

gestation
the development before birth of a viviparous animal

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gestation period
the length of time of development, from conception to birth, of the young of a viviparous animal

gonadotropin-releasing hormone (GnRH)

a hormone from the hypothalamus that causes the release of FSH and LH from the anterior pituitary

human beta chorionic gonadotropin (β-HCG)

a hormone produced by the chorion of the zygote that helps to maintain the corpus luteum and elevated levels of progesterone

inhibin
a hormone made by Sertoli cells, provides negative feedback to hypothalamus in control of FSH and GnRH release

interstitial cell of Leydig

a cell type found next to the seminiferous tubules that makes testosterone

labia majora
the large folds of tissue covering inguinal area

labia minora
the smaller folds of tissue within labia majora

luteinizing hormone (LH)

a reproductive hormone in both men and women, causes testosterone production in men and ovulation and lactation in women

menstrual cycle
the cycle of the degradation and re-growth of the endometrium

oogenesis
the process of producing haploid eggs

ovarian cycle
the cycle of preparation of egg for ovulation and the conversion of the follicle to the corpus luteum

oviduct
(also, fallopian tube) the muscular tube connecting uterus with ovary area

ovulation
the release of an oocyte from a mature follicle in the ovary of a vertebrate

penis
the male reproductive structure for urine elimination and copulation

placenta
the organ that supports the transport of nutrients and waste between the mothers and fetus’ blood in eutherian mammals

progesterone
a reproductive hormone in women; assists in endometrial regrowth and inhibition of FSH and LH release

prostate gland
a structure that is a mixture of smooth muscle and glandular material and that contributes to semen

scrotum
a sac containing testes, exterior to body

semen

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 a fluid mixture of sperm and supporting materials

seminal vesicle
a secretory accessory gland in male; contributes to semen

seminiferous tubule
the structures within which sperm production occurs in the testes

Sertoli cell
a cell in the walls of the seminiferous tubules that assists developing sperm and secretes inhibin

spermatogenesis
the process of producing haploid sperm

testes
a pair of male reproductive organs

testosterone
a reproductive hormone in men that assists in sperm production and promoting secondary sexual characteristics

uterus
a female reproductive structure in which an embryo develops

vagina
a muscular tube for the passage of menstrual flow, copulation, and birth of offspring

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

This page titled 14.3: Human Reproduction is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
18.3: Human Reproduction by OpenStax is licensed CC BY 4.0.

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14.E: Animal Reproduction and Development (Exercises)
18.1: How Animals Reproduce
Review Questions
In which group is parthenogenesis a normal event?
A. chickens
B. bees
C. rabbits
D. sea stars

Answer
B

Genetically unique individuals are produced through ________.

A. sexual reproduction
B. parthenogenesis
C. budding
D. fragmentation

Answer
A

External fertilization occurs in which type of environment?

A. aquatic
B. forested
C. savanna
D. steppe

Answer
A

Free Response
What might be a disadvantage to temperature-dependent sex determination?

Answer
Temperatures can vary from year to year and an unusually cold or hot year might produce offspring all of one sex, making it
hard for individuals to find mates.

Compared to separate sexes and assuming self-fertilizing is not possible, what might be one advantage and one disadvantage to
hermaphroditism?

Answer
A possible advantage of hermaphroditism might be that anytime an individual of the same species is encountered a mating is
possible, unlike separate sexes that must find an individual of the right sex to mate. (Also, every individual in a hermaphrodite
population is able to produce offspring, which is not the case in populations with separate sexes.) A disadvantage might be that
hermaphrodite populations are less efficient because they do not specialize in one sex or another, which means a hermaphrodite
does not produce as many offspring through eggs or sperm as do species with separate sexes. (Other answers are possible.)

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18.2: Development and Organogenesis
Review Questions
The process of gastrulation forms the _______.
A. blastula
B. zygote
C. organs
D. germ layers

Answer
D

Which of the following gives rise to the skin cells?

A. ectoderm
B. endoderm
C. mesoderm
D. none of the above

Answer
A

Free Response
What do you think would happen if multiple sperm fused with one egg?

Answer
If multiple sperm fused with one egg, a zygote with a multiple ploidy level (multiple copies of the chromosomes) would form,
and then would die.

18.3: Human Reproduction

Review Questions
Sperm are produced in the ________.
A. scrotum
B. seminal vesicles
C. seminiferous tubules
D. prostate gland

Answer
C

Which female organ has an endometrial lining that will support a developing baby?
A. labia minora
B. breast
C. ovaries
D. uterus

Answer
D

Which hormone causes FSH and LH to be released?

A. testosterone
B. estrogen

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 C. GnRH
D. progesterone

Answer
C

Nutrient and waste requirements for the developing fetus are handled during the first few weeks by ________.
A. the placenta
B. diffusion through the endometrium
C. the chorion
D. the blastocyst

Answer
B

Which hormone is primarily responsible for the contractions during labor?

A. oxytocin
B. estrogen
C. β-HCG
D. progesterone

Answer
A

Free Response
Compare spermatogenesis and oogenesis as to timing of the processes, and the number and type of cells finally produced.

Answer
Stem cells are laid down in the male during gestation and lie dormant until adolescence. Stem cells in the female increase to one
to two million and enter the first meiotic division and are arrested in prophase. At adolescence, spermatogenesis begins and
continues until death, producing the maximum number of sperm with each meiotic division. Oogenesis continues again at
adolescence in batches of eggs with each menstrual cycle. These primary oocytes finish the first meiotic division, producing a
viable egg with most of the cytoplasm and its contents, and a second cell called a polar body containing 23 chromosomes. The
second meiotic division is initiated and arrested in metaphase. At ovulation, one egg is released. If this egg is fertilized, it
finishes the second meiotic division. This is a diploid, fertilized egg.

Describe the events in the ovarian cycle leading up to ovulation.

Answer
Low levels of progesterone allow the hypothalamus to send GnRH to the anterior pituitary and cause the release of FSH and
LH. FSH stimulates follicles on the ovary to grow and prepare the eggs for ovulation. As the follicles increase in size, they
begin to release estrogen and a low level of progesterone into the blood. The level of estrogen rises to a peak, causing a spike in
the concentration of LH. This causes the most mature follicle to rupture and ovulation occurs.

Describe the stages of labor.

Answer
Stage one of labor results in uterine contractions, which thin the cervix and dilate the cervical opening. Stage two delivers the
baby, and stage three delivers the placenta.

This page titled 14.E: Animal Reproduction and Development (Exercises) is shared under a CC BY license and was authored, remixed, and/or
curated by OpenStax.

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18.E: Animal Reproduction and Development (Exercises) by OpenStax is licensed CC BY 4.0.

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 CHAPTER OVERVIEW

15: Skeletal System

15.1: The Animal Body - Basic Form and Function
15.1.1: Prelude to The Animal Body
15.1.2: Animal Form and Function
15.1.3: Animal Primary Tissues
15.1.4: Homeostasis
15.1.E: The Animal Body - Basic Form and Function (Exercises)
15.2: Types of Skeletal Systems
15.3: Bone

Thumbnail: Image by WikiImages from Pixabay

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1
 SECTION OVERVIEW

15.1: The Animal Body - Basic Form and Function

The structures of animals consist of primary tissues that make up more complex organs and organ systems. Homeostasis allows an
animal to maintain a balance between its internal and external environments.

15.1.1: Prelude to The Animal Body

15.1.2: Animal Form and Function

15.1.3: Animal Primary Tissues

15.1.4: Homeostasis

15.1.E: The Animal Body - Basic Form and Function (Exercises)

Contributors and Attributions

Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski
(Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute
of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY
4.0; Download for free at [Link]

This page titled 15.1: The Animal Body - Basic Form and Function is shared under a CC BY license and was authored, remixed, and/or curated
by OpenStax.

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15.1.1: Prelude to The Animal Body
The arctic fox is an example of a complex animal that has adapted to its environment and illustrates the relationships between an
animal’s form and function. The structures of animals consist of primary tissues that make up more complex organs and organ
systems. Homeostasis allows an animal to maintain a balance between its internal and external environments.

Figure [Link] : An arctic fox is a complex animal, well adapted to its environment. It changes coat color with the seasons, and has
longer fur in winter to trap heat. (credit: modification of work by Keith Morehouse, USFWS)

This page titled 15.1.1: Prelude to The Animal Body is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
33.0: Prelude to The Animal Body by OpenStax is licensed CC BY 4.0.

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15.1.2: Animal Form and Function
Skills to Develop
Describe the various types of body plans that occur in animals
Describe limits on animal size and shape
Relate bioenergetics to body size, levels of activity, and the environment

Animals vary in form and function. From a sponge to a worm to a goat, an organism has a distinct body plan that limits its size and
shape. Animals’ bodies are also designed to interact with their environments, whether in the deep sea, a rainforest canopy, or the
desert. Therefore, a large amount of information about the structure of an organism's body (anatomy) and the function of its cells,
tissues and organs (physiology) can be learned by studying that organism's environment.

Body Plans
Animal body plans follow set patterns related to symmetry. They are asymmetrical, radial, or bilateral in form as illustrated in
Figure [Link]. Asymmetrical animals are animals with no pattern or symmetry; an example of an asymmetrical animal is a
sponge. Radial symmetry, as illustrated in Figure [Link], describes when an animal has an up-and-down orientation: any plane
cut along its longitudinal axis through the organism produces equal halves, but not a definite right or left side. This plan is found
mostly in aquatic animals, especially organisms that attach themselves to a base, like a rock or a boat, and extract their food from
the surrounding water as it flows around the organism. Bilateral symmetry is illustrated in the same figure by a goat. The goat also
has an upper and lower component to it, but a plane cut from front to back separates the animal into definite right and left sides.
Additional terms used when describing positions in the body are anterior (front), posterior (rear), dorsal (toward the back), and
ventral (toward the stomach). Bilateral symmetry is found in both land-based and aquatic animals; it enables a high level of
mobility.

Figure [Link] : Animals exhibit different types of body symmetry. The sponge is asymmetrical, the sea anemone has radial
symmetry, and the goat has bilateral symmetry.

Limits on Animal Size and Shape

Animals with bilateral symmetry that live in water tend to have a fusiform shape: this is a tubular shaped body that is tapered at
both ends. This shape decreases the drag on the body as it moves through water and allows the animal to swim at high speeds. The
table below lists the maximum speed of various animals. Certain types of sharks can swim at fifty kilometers an hour and some
dolphins at 32 to 40 kilometers per hour. Land animals frequently travel faster, although the tortoise and snail are significantly
slower than cheetahs. Another difference in the adaptations of aquatic and land-dwelling organisms is that aquatic organisms are
constrained in shape by the forces of drag in the water since water has higher viscosity than air. On the other hand, land-dwelling
organisms are constrained mainly by gravity, and drag is relatively unimportant. For example, most adaptations in birds are for
gravity not for drag.

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 Table [Link]: Maximum Speed of Assorted Land and Marine Animals
Animal Speed (kmh) Speed (mph)

Cheetah 113 70

Quarter horse 77 48

Fox 68 42

Shortfin mako shark 50 31

Domestic house cat 48 30

Human 45 28

Dolphin 32–40 20–25

Mouse 13 8

Snail 0.05 0.03

Most animals have an exoskeleton, including insects, spiders, scorpions, horseshoe crabs, centipedes, and crustaceans. Scientists
estimate that, of insects alone, there are over 30 million species on our planet. The exoskeleton is a hard covering or shell that
provides benefits to the animal, such as protection against damage from predators and from water loss (for land animals); it also
provides for the attachments of muscles.
As the tough and resistant outer cover of an arthropod, the exoskeleton may be constructed of a tough polymer such as chitin and is
often biomineralized with materials such as calcium carbonate. This is fused to the animal’s epidermis. Ingrowths of the
exoskeleton, called apodemes, function as attachment sites for muscles, similar to tendons in more advanced animals (Figure
[Link]). In order to grow, the animal must first synthesize a new exoskeleton underneath the old one and then shed or molt the

original covering. This limits the animal’s ability to grow continually, and may limit the individual’s ability to mature if molting
does not occur at the proper time. The thickness of the exoskeleton must be increased significantly to accommodate any increase in
weight. It is estimated that a doubling of body size increases body weight by a factor of eight. The increasing thickness of the chitin
necessary to support this weight limits most animals with an exoskeleton to a relatively small size. The same principles apply to
endoskeletons, but they are more efficient because muscles are attached on the outside, making it easier to compensate for
increased mass.

Figure [Link] : Apodemes are ingrowths on arthropod exoskeletons to which muscles attach. The apodemes on this crab leg are
located above and below the fulcrum of the claw. Contraction of muscles attached to the apodemes pulls the claw closed.
An animal with an endoskeleton has its size determined by the amount of skeletal system it needs in order to support the other
tissues and the amount of muscle it needs for movement. As the body size increases, both bone and muscle mass increase. The
speed achievable by the animal is a balance between its overall size and the bone and muscle that provide support and movement.

Limiting Effects of Diffusion on Size and Development

The exchange of nutrients and wastes between a cell and its watery environment occurs through the process of diffusion. All living
cells are bathed in liquid, whether they are in a single-celled organism or a multicellular one. Diffusion is effective over a specific
distance and limits the size that an individual cell can attain. If a cell is a single-celled microorganism, such as an amoeba, it can

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satisfy all of its nutrient and waste needs through diffusion. If the cell is too large, then diffusion is ineffective and the center of the
cell does not receive adequate nutrients nor is it able to effectively dispel its waste.
An important concept in understanding how efficient diffusion is as a means of transport is the surface to volume ratio. Recall that
any three-dimensional object has a surface area and volume; the ratio of these two quantities is the surface-to-volume ratio.
Consider a cell shaped like a perfect sphere: it has a surface area of 4πr2, and a volume of (4/3)πr3. The surface-to-volume ratio of a
sphere is 3/r; as the cell gets bigger, its surface to volume ratio decreases, making diffusion less efficient. The larger the size of the
sphere, or animal, the less surface area for diffusion it possesses.
The solution to producing larger organisms is for them to become multicellular. Specialization occurs in complex organisms,
allowing cells to become more efficient at doing fewer tasks. For example, circulatory systems bring nutrients and remove waste,
while respiratory systems provide oxygen for the cells and remove carbon dioxide from them. Other organ systems have developed
further specialization of cells and tissues and efficiently control body functions. Moreover, surface-to-volume ratio applies to other
areas of animal development, such as the relationship between muscle mass and cross-sectional surface area in supporting
skeletons, and in the relationship between muscle mass and the generation of dissipation of heat.

Animal Bioenergetics
All animals must obtain their energy from food they ingest or absorb. These nutrients are converted to adenosine triphosphate
(ATP) for short-term storage and use by all cells. Some animals store energy for slightly longer times as glycogen, and others store
energy for much longer times in the form of triglycerides housed in specialized adipose tissues. No energy system is one hundred
percent efficient, and an animal’s metabolism produces waste energy in the form of heat. If an animal can conserve that heat and
maintain a relatively constant body temperature, it is classified as a warm-blooded animal and called an endotherm. The insulation
used to conserve the body heat comes in the forms of fur, fat, or feathers. The absence of insulation in ectothermic animals
increases their dependence on the environment for body heat.
The amount of energy expended by an animal over a specific time is called its metabolic rate. The rate is measured variously in
joules, calories, or kilocalories (1000 calories). Carbohydrates and proteins contain about 4.5 to 5 kcal/g, and fat contains about 9
kcal/g. Metabolic rate is estimated as the basal metabolic rate (BMR) in endothermic animals at rest and as the standard metabolic
rate (SMR) in ectotherms. Human males have a BMR of 1600 to 1800 kcal/day, and human females have a BMR of 1300 to 1500
kcal/day. Even with insulation, endothermal animals require extensive amounts of energy to maintain a constant body temperature.
An ectotherm such as an alligator has an SMR of 60 kcal/day.

Energy Requirements Related to Body Size

Smaller endothermic animals have a greater surface area for their mass than larger ones (Figure [Link]). Therefore, smaller
animals lose heat at a faster rate than larger animals and require more energy to maintain a constant internal temperature. This
results in a smaller endothermic animal having a higher BMR, per body weight, than a larger endothermic animal.

Figure [Link] : The mouse has a much higher metabolic rate than the elephant. (credit “mouse”: modification of work by Magnus
Kjaergaard; credit “elephant”: modification of work by “TheLizardQueen”/Flickr)

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Energy Requirements Related to Levels of Activity
The more active an animal is, the more energy is needed to maintain that activity, and the higher its BMR or SMR. The average
daily rate of energy consumption is about two to four times an animal’s BMR or SMR. Humans are more sedentary than most
animals and have an average daily rate of only 1.5 times the BMR. The diet of an endothermic animal is determined by its BMR.
For example: the type of grasses, leaves, or shrubs that an herbivore eats affects the number of calories that it takes in. The relative
caloric content of herbivore foods, in descending order, is tall grasses > legumes > short grasses > forbs (any broad-leaved plant,
not a grass) > subshrubs > annuals/biennials.

Energy Requirements Related to Environment

Animals adapt to extremes of temperature or food availability through torpor. Torpor is a process that leads to a decrease in activity
and metabolism and allows animals to survive adverse conditions. Torpor can be used by animals for long periods, such as entering
a state of hibernation during the winter months, in which case it enables them to maintain a reduced body temperature. During
hibernation, ground squirrels can achieve an abdominal temperature of 0° C (32° F), while a bear’s internal temperature is
maintained higher at about 37° C (99° F).
If torpor occurs during the summer months with high temperatures and little water, it is called estivation. Some desert animals use
this to survive the harshest months of the year. Torpor can occur on a daily basis; this is seen in bats and hummingbirds. While
endothermy is limited in smaller animals by surface to volume ratio, some organisms can be smaller and still be endotherms
because they employ daily torpor during the part of the day that is coldest. This allows them to conserve energy during the colder
parts of the day, when they consume more energy to maintain their body temperature.

Animal Body Planes and Cavities

A standing vertebrate animal can be divided by several planes. A sagittal plane divides the body into right and left portions. A
midsagittal plane divides the body exactly in the middle, making two equal right and left halves. A frontal plane (also called a
coronal plane) separates the front from the back. A transverse plane (or, horizontal plane) divides the animal into upper and lower
portions. This is sometimes called a cross section, and, if the transverse cut is at an angle, it is called an oblique plane. Figure
[Link] illustrates these planes on a goat (a four-legged animal) and a human being.

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 Figure [Link] : Shown are the planes of a quadruped goat and a bipedal human. The midsagittal plane divides the body exactly in
half, into right and left portions. The frontal plane divides the front and back, and the transverse plane divides the body into upper
and lower portions.
Vertebrate animals have a number of defined body cavities, as illustrated in Figure [Link]. Two of these are major cavities that
contain smaller cavities within them. The dorsal cavity contains the cranial and the vertebral (or spinal) cavities. The ventral cavity
contains the thoracic cavity, which in turn contains the pleural cavity around the lungs and the pericardial cavity, which surrounds
the heart. The ventral cavity also contains the abdominopelvic cavity, which can be separated into the abdominal and the pelvic
cavities.

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 Figure [Link] : Vertebrate animals have two major body cavities. The dorsal cavity, indicated in green, contains the cranial and
the spinal cavity. The ventral cavity, indicated in yellow, contains the thoracic cavity and the abdominopelvic cavity. The thoracic
cavity is separated from the abdominopelvic cavity by the diaphragm. The thoracic cavity is separated into the abdominal cavity
and the pelvic cavity by an imaginary line parallel to the pelvis bones. (credit: modification of work by NCI)

Career Connections: Physical Anthropologist

Physical anthropologists study the adaption, variability, and evolution of human beings, plus their living and fossil relatives.
They can work in a variety of settings, although most will have an academic appointment at a university, usually in an
anthropology department or a biology, genetics, or zoology department.
Non-academic positions are available in the automotive and aerospace industries where the focus is on human size, shape, and
anatomy. Research by these professionals might range from studies of how the human body reacts to car crashes to exploring
how to make seats more comfortable. Other non-academic positions can be obtained in museums of natural history,
anthropology, archaeology, or science and technology. These positions involve educating students from grade school through
graduate school. Physical anthropologists serve as education coordinators, collection managers, writers for museum
publications, and as administrators. Zoos employ these professionals, especially if they have an expertise in primate biology;
they work in collection management and captive breeding programs for endangered species. Forensic science utilizes physical
anthropology expertise in identifying human and animal remains, assisting in determining the cause of death, and for expert
testimony in trials.

Summary
Animal bodies come in a variety of sizes and shapes. Limits on animal size and shape include impacts to their movement. Diffusion
affects their size and development. Bioenergetics describes how animals use and obtain energy in relation to their body size,
activity level, and environment.

Glossary
apodeme
ingrowth of an animal’s exoskeleton that functions as an attachment site for muscles

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asymmetrical
describes animals with no axis of symmetry in their body pattern

basal metabolic rate (BMR)

metabolic rate at rest in endothermic animals

dorsal cavity
body cavity on the posterior or back portion of an animal; includes the cranial and vertebral cavities

ectotherm
animal incapable of maintaining a relatively constant internal body temperature

endotherm
animal capable of maintaining a relatively constant internal body temperature

estivation
torpor in response to extremely high temperatures and low water availability

frontal (coronal) plane

plane cutting through an animal separating the individual into front and back portions

fusiform
animal body shape that is tubular and tapered at both ends

hibernation
torpor over a long period of time, such as a winter

midsagittal plane
plane cutting through an animal separating the individual into even right and left sides

sagittal plane
plane cutting through an animal separating the individual into right and left sides

standard metabolic rate (SMR)

metabolic rate at rest in ectothermic animals

torpor
decrease in activity and metabolism that allows an animal to survive adverse conditions

transverse (horizontal) plane

plane cutting through an animal separating the individual into upper and lower portions

ventral cavity
body cavity on the anterior or front portion of an animal that includes the thoracic cavities and the abdominopelvic cavities

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33.1: Animal Form and Function by OpenStax is licensed CC BY 4.0.

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15.1.3: Animal Primary Tissues
Skills to Develop
Describe epithelial tissues
Discuss the different types of connective tissues in animals
Describe three types of muscle tissues
Describe nervous tissue

The tissues of multicellular, complex animals are four primary types: epithelial, connective, muscle, and nervous. Recall that
tissues are groups of similar cells group of similar cells carrying out related functions. These tissues combine to form organs—like
the skin or kidney—that have specific, specialized functions within the body. Organs are organized into organ systems to perform
functions; examples include the circulatory system, which consists of the heart and blood vessels, and the digestive system,
consisting of several organs, including the stomach, intestines, liver, and pancreas. Organ systems come together to create an entire
organism.

Epithelial Tissues
Epithelial tissues cover the outside of organs and structures in the body and line the lumens of organs in a single layer or multiple
layers of cells. The types of epithelia are classified by the shapes of cells present and the number of layers of cells. Epithelia
composed of a single layer of cells is called simple epithelia; epithelial tissue composed of multiple layers is called stratified
epithelia. The table summarizes the different types of epithelial tissues.
Table [Link]: Different Types of Epithelial Tissues
Cell shape Description Location

simple: lung alveoli, capillaries stratified: skin,

squamous flat, irregular round shape
mouth, vagina

cuboidal cube shaped, central nucleus glands, renal tubules

tall, narrow, nucleus toward base tall, narrow, simple: digestive tract pseudostratified:
columnar
nucleus along cell respiratory tract

transitional round, simple but appear stratified urinary bladder

Squamous Epithelia
Squamous epithelial cells are generally round, flat, and have a small, centrally located nucleus. The cell outline is slightly irregular,
and cells fit together to form a covering or lining. When the cells are arranged in a single layer (simple epithelia), they facilitate
diffusion in tissues, such as the areas of gas exchange in the lungs and the exchange of nutrients and waste at blood capillaries.

Figure [Link] : Squamous epithelia cells (a) have a slightly irregular shape, and a small, centrally located nucleus. These cells can
be stratified into layers, as in (b) this human cervix specimen. (credit b: modification of work by Ed Uthman; scale-bar data from
Matt Russell)
Figure [Link] illustrates a layer of squamous cells with their membranes joined together to form an epithelium. Image Figure
[Link] illustrates squamous epithelial cells arranged in stratified layers, where protection is needed on the body from outside

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abrasion and damage. This is called a stratified squamous epithelium and occurs in the skin and in tissues lining the mouth and
vagina.

Cuboidal Epithelia
Cuboidal epithelial cells, shown in Figure [Link], are cube-shaped with a single, central nucleus. They are most commonly found
in a single layer representing a simple epithelia in glandular tissues throughout the body where they prepare and secrete glandular
material. They are also found in the walls of tubules and in the ducts of the kidney and liver.

Figure [Link] : Simple cuboidal epithelial cells line tubules in the mammalian kidney, where they are involved in filtering the
blood.

Columnar Epithelia
Columnar epithelial cells are taller than they are wide: they resemble a stack of columns in an epithelial layer, and are most
commonly found in a single-layer arrangement. The nuclei of columnar epithelial cells in the digestive tract appear to be lined up at
the base of the cells, as illustrated in Figure [Link]. These cells absorb material from the lumen of the digestive tract and prepare
it for entry into the body through the circulatory and lymphatic systems.

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 Figure [Link] : Simple columnar epithelial cells absorb material from the digestive tract. Goblet cells secret mucous into the
digestive tract lumen.
Columnar epithelial cells lining the respiratory tract appear to be stratified. However, each cell is attached to the base membrane of
the tissue and, therefore, they are simple tissues. The nuclei are arranged at different levels in the layer of cells, making it appear as
though there is more than one layer, as seen in Figure [Link]. This is called pseudostratified, columnar epithelia. This cellular
covering has cilia at the apical, or free, surface of the cells. The cilia enhance the movement of mucous and trapped particles out of
the respiratory tract, helping to protect the system from invasive microorganisms and harmful material that has been breathed into
the body. Goblet cells are interspersed in some tissues (such as the lining of the trachea). The goblet cells contain mucous that traps
irritants, which in the case of the trachea keep these irritants from getting into the lungs.

Figure [Link] : Pseudostratified columnar epithelia line the respiratory tract. They exist in one layer, but the arrangement of nuclei
at different levels makes it appear that there is more than one layer. Goblet cells interspersed between the columnar epithelial cells
secrete mucous into the respiratory tract.

Transitional Epithelia
Transitional or uroepithelial cells appear only in the urinary system, primarily in the bladder and ureter. These cells are arranged in
a stratified layer, but they have the capability of appearing to pile up on top of each other in a relaxed, empty bladder, as illustrated

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in Figure [Link]. As the urinary bladder fills, the epithelial layer unfolds and expands to hold the volume of urine introduced into
it. As the bladder fills, it expands and the lining becomes thinner. In other words, the tissue transitions from thick to thin.

Figure [Link] : Transitional epithelia of the urinary bladder undergo changes in thickness depending on how full the bladder is.

Exercise

Which of the following statements about types of epithelial cells is false?

A. Simple columnar epithelial cells line the tissue of the lung.
B. Simple cuboidal epithelial cells are involved in the filtering of blood in the kidney.
C. Pseudostratisfied columnar epithilia occur in a single layer, but the arrangement of nuclei makes it appear that more than
one layer is present.
D. Transitional epithelia change in thickness depending on how full the bladder is.

Answer
A

Connective Tissues
Connective tissues are made up of a matrix consisting of living cells and a non-living substance, called the ground substance. The
ground substance is made of an organic substance (usually a protein) and an inorganic substance (usually a mineral or water). The
principal cell of connective tissues is the fibroblast. This cell makes the fibers found in nearly all of the connective tissues.
Fibroblasts are motile, able to carry out mitosis, and can synthesize whichever connective tissue is needed. Macrophages,
lymphocytes, and, occasionally, leukocytes can be found in some of the tissues. Some tissues have specialized cells that are not
found in the others. The matrix in connective tissues gives the tissue its density. When a connective tissue has a high concentration
of cells or fibers, it has proportionally a less dense matrix.
The organic portion or protein fibers found in connective tissues are either collagen, elastic, or reticular fibers. Collagen fibers
provide strength to the tissue, preventing it from being torn or separated from the surrounding tissues. Elastic fibers are made of the
protein elastin; this fiber can stretch to one and one half of its length and return to its original size and shape. Elastic fibers provide
flexibility to the tissues. Reticular fibers are the third type of protein fiber found in connective tissues. This fiber consists of thin
strands of collagen that form a network of fibers to support the tissue and other organs to which it is connected. The various types
of connective tissues, the types of cells and fibers they are made of, and sample locations of the tissues is summarized in the table.
Table [Link]: Connective Tissues
Tissue Cells Fibers Location

fibroblasts, macrophages, some around blood vessels; anchors

loose/areolar few: collagen, elastic, reticular
lymphocytes, some neutrophils epithelia

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 Tissue Cells Fibers Location

irregular: skin regular: tendons,

dense, fibrous connective tissue fibroblasts, macrophages, mostly collagen
ligaments

hyaline: few collagen

shark skeleton, fetal bones, human
cartilage chondrocytes, chondroblasts fibrocartilage: large amount of
ears, intervertebral discs
collagen

bone osteoblasts, osteocytes, osteoclasts some: collagen, elastic vertebrate skeletons

adipose adipocytes few adipose (fat)

blood red blood cells, white blood cells none blood

Loose/Areolar Connective Tissue

Loose connective tissue, also called areolar connective tissue, has a sampling of all of the components of a connective tissue. As
illustrated in Figure [Link], loose connective tissue has some fibroblasts; macrophages are present as well. Collagen fibers are
relatively wide and stain a light pink, while elastic fibers are thin and stain dark blue to black. The space between the formed
elements of the tissue is filled with the matrix. The material in the connective tissue gives it a loose consistency similar to a cotton
ball that has been pulled apart. Loose connective tissue is found around every blood vessel and helps to keep the vessel in place.
The tissue is also found around and between most body organs. In summary, areolar tissue is tough, yet flexible, and comprises
membranes.

Figure [Link] : Loose connective tissue is composed of loosely woven collagen and elastic fibers. The fibers and other
components of the connective tissue matrix are secreted by fibroblasts.

Fibrous Connective Tissue

Fibrous connective tissues contain large amounts of collagen fibers and few cells or matrix material. The fibers can be arranged
irregularly or regularly with the strands lined up in parallel. Irregularly arranged fibrous connective tissues are found in areas of the
body where stress occurs from all directions, such as the dermis of the skin. Regular fibrous connective tissue, shown in Figure
[Link], is found in tendons (which connect muscles to bones) and ligaments (which connect bones to bones).

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 Figure [Link] : Fibrous connective tissue from the tendon has strands of collagen fibers lined up in parallel.

Cartilage
Cartilage is a connective tissue with a large amount of the matrix and variable amounts of fibers. The cells, called chondrocytes,
make the matrix and fibers of the tissue. Chondrocytes are found in spaces within the tissue called lacunae.
A cartilage with few collagen and elastic fibers is hyaline cartilage, illustrated in Figure [Link]. The lacunae are randomly
scattered throughout the tissue and the matrix takes on a milky or scrubbed appearance with routine histological stains. Sharks have
cartilaginous skeletons, as does nearly the entire human skeleton during a specific pre-birth developmental stage. A remnant of this
cartilage persists in the outer portion of the human nose. Hyaline cartilage is also found at the ends of long bones, reducing friction
and cushioning the articulations of these bones.

Figure [Link] : Hyaline cartilage consists of a matrix with cells called chondrocytes embedded in it. The chondrocytes exist in
cavities in the matrix called lacunae.

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Elastic cartilage has a large amount of elastic fibers, giving it tremendous flexibility. The ears of most vertebrate animals contain
this cartilage as do portions of the larynx, or voice box. Fibrocartilage contains a large amount of collagen fibers, giving the tissue
tremendous strength. Fibrocartilage comprises the intervertebral discs in vertebrate animals. Hyaline cartilage found in movable
joints such as the knee and shoulder becomes damaged as a result of age or trauma. Damaged hyaline cartilage is replaced by
fibrocartilage and results in the joints becoming “stiff.”

Bone
Bone, or osseous tissue, is a connective tissue that has a large amount of two different types of matrix material. The organic matrix
is similar to the matrix material found in other connective tissues, including some amount of collagen and elastic fibers. This gives
strength and flexibility to the tissue. The inorganic matrix consists of mineral salts—mostly calcium salts—that give the tissue
hardness. Without adequate organic material in the matrix, the tissue breaks; without adequate inorganic material in the matrix, the
tissue bends.
There are three types of cells in bone: osteoblasts, osteocytes, and osteoclasts. Osteoblasts are active in making bone for growth
and remodeling. Osteoblasts deposit bone material into the matrix and, after the matrix surrounds them, they continue to live, but in
a reduced metabolic state as osteocytes. Osteocytes are found in lacunae of the bone. Osteoclasts are active in breaking down bone
for bone remodeling, and they provide access to calcium stored in tissues. Osteoclasts are usually found on the surface of the tissue.
Bone can be divided into two types: compact and spongy. Compact bone is found in the shaft (or diaphysis) of a long bone and the
surface of the flat bones, while spongy bone is found in the end (or epiphysis) of a long bone. Compact bone is organized into
subunits called osteons, as illustrated in Figure [Link]. A blood vessel and a nerve are found in the center of the structure within
the Haversian canal, with radiating circles of lacunae around it known as lamellae. The wavy lines seen between the lacunae are
microchannels called canaliculi; they connect the lacunae to aid diffusion between the cells. Spongy bone is made of tiny plates
called trabeculae these plates serve as struts to give the spongy bone strength. Over time, these plates can break causing the bone to
become less resilient. Bone tissue forms the internal skeleton of vertebrate animals, providing structure to the animal and points of
attachment for tendons.

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 Figure [Link] : (a) Compact bone is a dense matrix on the outer surface of bone. Spongy bone, inside the compact bone, is porous
with web-like trabeculae. (b) Compact bone is organized into rings called osteons. Blood vessels, nerves, and lymphatic vessels are
found in the central Haversian canal. Rings of lamellae surround the Haversian canal. Between the lamellae are cavities called
lacunae. Canaliculi are microchannels connecting the lacunae together. (c) Osteoblasts surround the exterior of the bone.
Osteoclasts bore tunnels into the bone and osteocytes are found in the lacunae.

Adipose Tissue
Adipose tissue, or fat tissue, is considered a connective tissue even though it does not have fibroblasts or a real matrix and only has
a few fibers. Adipose tissue is made up of cells called adipocytes that collect and store fat in the form of triglycerides, for energy
metabolism. Adipose tissues additionally serve as insulation to help maintain body temperatures, allowing animals to be
endothermic, and they function as cushioning against damage to body organs. Under a microscope, adipose tissue cells appear

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empty due to the extraction of fat during the processing of the material for viewing, as seen in Figure [Link]. The thin lines in
the image are the cell membranes, and the nuclei are the small, black dots at the edges of the cells.

Figure [Link] : Adipose is a connective tissue is made up of cells called adipocytes. Adipocytes have small nuclei localized at
the cell edge.

Blood
Blood is considered a connective tissue because it has a matrix, as shown in Figure [Link]. The living cell types are red blood
cells (RBC), also called erythrocytes, and white blood cells (WBC), also called leukocytes. The fluid portion of whole blood, its
matrix, is commonly called plasma.

Figure [Link] : Blood is a connective tissue that has a fluid matrix, called plasma, and no fibers. Erythrocytes (red blood cells),
the predominant cell type, are involved in the transport of oxygen and carbon dioxide. Also present are various leukocytes (white
blood cells) involved in immune response.
The cell found in greatest abundance in blood is the erythrocyte. Erythrocytes are counted in millions in a blood sample: the
average number of red blood cells in primates is 4.7 to 5.5 million cells per microliter. Erythrocytes are consistently the same size
in a species, but vary in size between species. For example, the average diameter of a primate red blood cell is 7.5 µl, a dog is close
at 7.0 µl, but a cat’s RBC diameter is 5.9 µl. Sheep erythrocytes are even smaller at 4.6 µl. Mammalian erythrocytes lose their
nuclei and mitochondria when they are released from the bone marrow where they are made. Fish, amphibian, and avian red blood
cells maintain their nuclei and mitochondria throughout the cell’s life. The principal job of an erythrocyte is to carry and deliver
oxygen to the tissues.

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Leukocytes are the predominant white blood cells found in the peripheral blood. Leukocytes are counted in the thousands in the
blood with measurements expressed as ranges: primate counts range from 4,800 to 10,800 cells per µl, dogs from 5,600 to 19,200
cells per µl, cats from 8,000 to 25,000 cells per µl, cattle from 4,000 to 12,000 cells per µl, and pigs from 11,000 to 22,000 cells per
µl.
Lymphocytes function primarily in the immune response to foreign antigens or material. Different types of lymphocytes make
antibodies tailored to the foreign antigens and control the production of those antibodies. Neutrophils are phagocytic cells and they
participate in one of the early lines of defense against microbial invaders, aiding in the removal of bacteria that has entered the
body. Another leukocyte that is found in the peripheral blood is the monocyte. Monocytes give rise to phagocytic macrophages that
clean up dead and damaged cells in the body, whether they are foreign or from the host animal. Two additional leukocytes in the
blood are eosinophils and basophils—both help to facilitate the inflammatory response.
The slightly granular material among the cells is a cytoplasmic fragment of a cell in the bone marrow. This is called a platelet or
thrombocyte. Platelets participate in the stages leading up to coagulation of the blood to stop bleeding through damaged blood
vessels. Blood has a number of functions, but primarily it transports material through the body to bring nutrients to cells and
remove waste material from them.

Muscle Tissues
There are three types of muscle in animal bodies: smooth, skeletal, and cardiac. They differ by the presence or absence of striations
or bands, the number and location of nuclei, whether they are voluntarily or involuntarily controlled, and their location within the
body. The table summarizes these differences.
Table [Link]: Types of Muscles
Type of Muscle Striations Nuclei Control Location

smooth no single, in center involuntary visceral organs

skeletal yes many, at periphery voluntary skeletal muscles

cardiac yes single, in center involuntary heart

Smooth Muscle
Smooth muscle does not have striations in its cells. It has a single, centrally located nucleus, as shown in Figure [Link].
Constriction of smooth muscle occurs under involuntary, autonomic nervous control and in response to local conditions in the
tissues. Smooth muscle tissue is also called non-striated as it lacks the banded appearance of skeletal and cardiac muscle. The walls
of blood vessels, the tubes of the digestive system, and the tubes of the reproductive systems are composed of mostly smooth
muscle.

Figure [Link] : Smooth muscle cells do not have striations, while skeletal muscle cells do. Cardiac muscle cells have striations,
but, unlike the multinucleate skeletal cells, they have only one nucleus. Cardiac muscle tissue also has intercalated discs,
specialized regions running along the plasma membrane that join adjacent cardiac muscle cells and assist in passing an electrical
impulse from cell to cell.

Skeletal Muscle
Skeletal muscle has striations across its cells caused by the arrangement of the contractile proteins actin and myosin. These muscle
cells are relatively long and have multiple nuclei along the edge of the cell. Skeletal muscle is under voluntary, somatic nervous
system control and is found in the muscles that move bones. Figure 15.1.3.12illustrates the histology of skeletal muscle.

Cardiac Muscle
Cardiac muscle, shown in Figure [Link], is found only in the heart. Like skeletal muscle, it has cross striations in its cells, but
cardiac muscle has a single, centrally located nucleus. Cardiac muscle is not under voluntary control but can be influenced by the
autonomic nervous system to speed up or slow down. An added feature to cardiac muscle cells is a line than extends along the end

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of the cell as it abuts the next cardiac cell in the row. This line is called an intercalated disc: it assists in passing electrical impulse
efficiently from one cell to the next and maintains the strong connection between neighboring cardiac cells.

Nervous Tissues
Nervous tissues are made of cells specialized to receive and transmit electrical impulses from specific areas of the body and to send
them to specific locations in the body. The main cell of the nervous system is the neuron, illustrated in Figure [Link]. The large
structure with a central nucleus is the cell body of the neuron. Projections from the cell body are either dendrites specialized in
receiving input or a single axon specialized in transmitting impulses. Some glial cells are also shown. Astrocytes regulate the
chemical environment of the nerve cell, and oligodendrocytes insulate the axon so the electrical nerve impulse is transferred more
efficiently. Other glial cells that are not shown support the nutritional and waste requirements of the neuron. Some of the glial cells
are phagocytic and remove debris or damaged cells from the tissue. A nerve consists of neurons and glial cells.
Figure [Link] : The neuron has projections called dendrites that receive signals and projections called axons that send signals.
Also shown are two types of glial cells: astrocytes regulate the chemical environment of the nerve cell, and oligodendrocytes
insulate the axon so the electrical nerve impulse is transferred more efficiently.

Link to Learning

Click through the interactive review to learn more about epithelial tissues.

Career Connections: Pathologist

A pathologist is a medical doctor or veterinarian who has specialized in the laboratory detection of disease in animals,
including humans. These professionals complete medical school education and follow it with an extensive post-graduate
residency at a medical center. A pathologist may oversee clinical laboratories for the evaluation of body tissue and blood
samples for the detection of disease or infection. They examine tissue specimens through a microscope to identify cancers and
other diseases. Some pathologists perform autopsies to determine the cause of death and the progression of disease.

Summary
The basic building blocks of complex animals are four primary tissues. These are combined to form organs, which have a specific,
specialized function within the body, such as the skin or kidney. Organs are organized together to perform common functions in the
form of systems. The four primary tissues are epithelia, connective tissues, muscle tissues, and nervous tissues.

Glossary
canaliculus
microchannel that connects the lacunae and aids diffusion between cells

cartilage
type of connective tissue with a large amount of ground substance matrix, cells called chondrocytes, and some amount of fibers

chondrocyte
cell found in cartilage

columnar epithelia
epithelia made of cells taller than they are wide, specialized in absorption

connective tissue

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 type of tissue made of cells, ground substance matrix, and fibers

cuboidal epithelia
epithelia made of cube-shaped cells, specialized in glandular functions

epithelial tissue
tissue that either lines or covers organs or other tissues

fibrous connective tissue

type of connective tissue with a high concentration of fibers

lacuna
space in cartilage and bone that contains living cells

loose (areolar) connective tissue

type of connective tissue with small amounts of cells, matrix, and fibers; found around blood vessels

matrix
component of connective tissue made of both living and non-living (ground substances) cells

osteon
subunit of compact bone

pseudostratified
layer of epithelia that appears multilayered, but is a simple covering

simple epithelia
single layer of epithelial cells

squamous epithelia
type of epithelia made of flat cells, specialized in aiding diffusion or preventing abrasion

stratified epithelia
multiple layers of epithelial cells

trabecula
tiny plate that makes up spongy bone and gives it strength

transitional epithelia
epithelia that can transition for appearing multilayered to simple; also called uroepithelial

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15.1.4: Homeostasis
Skills to Develop
Define homeostasis
Describe the factors affecting homeostasis
Discuss positive and negative feedback mechanisms used in homeostasis
Describe thermoregulation of endothermic and ectothermic animals

Animal organs and organ systems constantly adjust to internal and external changes through a process called homeostasis (“steady
state”). These changes might be in the level of glucose or calcium in blood or in external temperatures. Homeostasis means to
maintain dynamic equilibrium in the body. It is dynamic because it is constantly adjusting to the changes that the body’s systems
encounter. It is equilibrium because body functions are kept within specific ranges. Even an animal that is apparently inactive is
maintaining this homeostatic equilibrium.

Homeostatic Process
The goal of homeostasis is the maintenance of equilibrium around a point or value called a set point. While there are normal
fluctuations from the set point, the body’s systems will usually attempt to go back to this point. A change in the internal or external
environment is called a stimulus and is detected by a receptor; the response of the system is to adjust the deviation parameter
toward the set point. For instance, if the body becomes too warm, adjustments are made to cool the animal. If the blood’s glucose
rises after a meal, adjustments are made to lower the blood glucose level by getting the nutrient into tissues that need it or to store it
for later use.

Control of Homeostasis
When a change occurs in an animal’s environment, an adjustment must be made. The receptor senses the change in the
environment, then sends a signal to the control center (in most cases, the brain) which in turn generates a response that is signaled
to an effector. The effector is a muscle (that contracts or relaxes) or a gland that secretes. Homeostatsis is maintained by negative
feedback loops. Positive feedback loops actually push the organism further out of homeostasis, but may be necessary for life to
occur. Homeostasis is controlled by the nervous and endocrine system of mammals.

Negative Feedback Mechanisms

Any homeostatic process that changes the direction of the stimulus is a negative feedback loop. It may either increase or decrease
the stimulus, but the stimulus is not allowed to continue as it did before the receptor sensed it. In other words, if a level is too high,
the body does something to bring it down, and conversely, if a level is too low, the body does something to make it go up. Hence
the term negative feedback. An example is animal maintenance of blood glucose levels. When an animal has eaten, blood glucose
levels rise. This is sensed by the nervous system. Specialized cells in the pancreas sense this, and the hormone insulin is released by
the endocrine system. Insulin causes blood glucose levels to decrease, as would be expected in a negative feedback system, as
illustrated in Figure [Link]. However, if an animal has not eaten and blood glucose levels decrease, this is sensed in another
group of cells in the pancreas, and the hormone glucagon is released causing glucose levels to increase. This is still a negative
feedback loop, but not in the direction expected by the use of the term “negative.” Another example of an increase as a result of the
feedback loop is the control of blood calcium. If calcium levels decrease, specialized cells in the parathyroid gland sense this and
release parathyroid hormone (PTH), causing an increased absorption of calcium through the intestines and kidneys and, possibly,
the breakdown of bone in order to liberate calcium. The effects of PTH are to raise blood levels of the element. Negative feedback
loops are the predominant mechanism used in homeostasis.

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 Figure [Link] : Blood sugar levels are controlled by a negative feedback loop. (credit: modification of work by Jon Sullivan)

Positive Feedback Loop

A positive feedback loop maintains the direction of the stimulus, possibly accelerating it. Few examples of positive feedback loops
exist in animal bodies, but one is found in the cascade of chemical reactions that result in blood clotting, or coagulation. As one
clotting factor is activated, it activates the next factor in sequence until a fibrin clot is achieved. The direction is maintained, not
changed, so this is positive feedback. Another example of positive feedback is uterine contractions during childbirth, as illustrated
in Figure [Link]. The hormone oxytocin, made by the endocrine system, stimulates the contraction of the uterus. This produces
pain sensed by the nervous system. Instead of lowering the oxytocin and causing the pain to subside, more oxytocin is produced
until the contractions are powerful enough to produce childbirth.

Figure [Link] : The birth of a human infant is the result of positive feedback.

Exercise
State whether each of the following processes is regulated by a positive feedback loop or a negative feedback loop.
A. A person feels satiated after eating a large meal.
B. The blood has plenty of red blood cells. As a result, erythropoietin, a hormone that stimulates the production of new red
blood cells, is no longer released from the kidney.

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 Answer
Both processes are the result of negative feedback loops. Negative feedback loops, which tend to keep a system at
equilibrium, are more common than positive feedback loops.

Set Point
It is possible to adjust a system’s set point. When this happens, the feedback loop works to maintain the new setting. An example of
this is blood pressure: over time, the normal or set point for blood pressure can increase as a result of continued increases in blood
pressure. The body no longer recognizes the elevation as abnormal and no attempt is made to return to the lower set point. The
result is the maintenance of an elevated blood pressure that can have harmful effects on the body. Medication can lower blood
pressure and lower the set point in the system to a more healthy level. This is called a process of alteration of the set point in a
feedback loop.
Changes can be made in a group of body organ systems in order to maintain a set point in another system. This is called
acclimatization. This occurs, for instance, when an animal migrates to a higher altitude than it is accustomed to. In order to adjust
to the lower oxygen levels at the new altitude, the body increases the number of red blood cells circulating in the blood to ensure
adequate oxygen delivery to the tissues. Another example of acclimatization is animals that have seasonal changes in their coats: a
heavier coat in the winter ensures adequate heat retention, and a light coat in summer assists in keeping body temperature from
rising to harmful levels.

Link to Learning

Feedback Loops

Feedback mechanisms can be understood in terms of driving a race car along a track: watch a short video lesson on positive
and negative feedback loops.

Homeostasis: Thermoregulation
Body temperature affects body activities. Generally, as body temperature rises, enzyme activity rises as well. For every ten degree
centigrade rise in temperature, enzyme activity doubles, up to a point. Body proteins, including enzymes, begin to denature and
lose their function with high heat (around 50oC for mammals). Enzyme activity will decrease by half for every ten degree
centigrade drop in temperature, to the point of freezing, with a few exceptions. Some fish can withstand freezing solid and return to
normal with thawing.

Link to Learning

Access for free at OpenStax [Link] [Link]

 Watch this Discovery Channel video on thermoregulation to see illustrations of this process in a variety of animals.

Endotherms and Ectotherms

Animals can be divided into two groups: some maintain a constant body temperature in the face of differing environmental
temperatures, while others have a body temperature that is the same as their environment and thus varies with the environment.
Animals that do not control their body temperature are ectotherms. This group has been called cold-blooded, but the term may not
apply to an animal in the desert with a very warm body temperature. In contrast to ectotherms, which rely on external temperatures
to set their body temperatures, poikilotherms are animals with constantly varying internal temperatures. An animal that maintains a
constant body temperature in the face of environmental changes is called a homeotherm. Endotherms are animals that rely on
internal sources for body temperature but which can exhibit extremes in temperature. These animals are able to maintain a level of
activity at cooler temperature, which an ectotherm cannot due to differing enzyme levels of activity.
Heat can be exchanged between an animal and its environment through four mechanisms: radiation, evaporation, convection, and
conduction (Figure [Link]). Radiation is the emission of electromagnetic “heat” waves. Heat comes from the sun in this manner
and radiates from dry skin the same way. Heat can be removed with liquid from a surface during evaporation. This occurs when a
mammal sweats. Convection currents of air remove heat from the surface of dry skin as the air passes over it. Heat will be
conducted from one surface to another during direct contact with the surfaces, such as an animal resting on a warm rock.

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 Figure [Link] : Heat can be exchanged by four mechanisms: (a) radiation, (b) evaporation, (c) convection, or (d) conduction.
(credit b: modification of work by “Kullez”/Flickr; credit c: modification of work by Chad Rosenthal; credit d: modification of
work by “stacey.d”/Flickr)

Heat Conservation and Dissipation

Animals conserve or dissipate heat in a variety of ways. In certain climates, endothermic animals have some form of insulation,
such as fur, fat, feathers, or some combination thereof. Animals with thick fur or feathers create an insulating layer of air between
their skin and internal organs. Polar bears and seals live and swim in a subfreezing environment and yet maintain a constant, warm,
body temperature. The arctic fox, for example, uses its fluffy tail as extra insulation when it curls up to sleep in cold weather.
Mammals have a residual effect from shivering and increased muscle activity: arrector pili muscles cause “goose bumps,” causing
small hairs to stand up when the individual is cold; this has the intended effect of increasing body temperature. Mammals use layers
of fat to achieve the same end. Loss of significant amounts of body fat will compromise an individual’s ability to conserve heat.
Endotherms use their circulatory systems to help maintain body temperature. Vasodilation brings more blood and heat to the body
surface, facilitating radiation and evaporative heat loss, which helps to cool the body. Vasoconstriction reduces blood flow in
peripheral blood vessels, forcing blood toward the core and the vital organs found there, and conserving heat. Some animals have
adaptions to their circulatory system that enable them to transfer heat from arteries to veins, warming blood returning to the heart.
This is called a countercurrent heat exchange; it prevents the cold venous blood from cooling the heart and other internal organs.
This adaption can be shut down in some animals to prevent overheating the internal organs. The countercurrent adaption is found in
many animals, including dolphins, sharks, bony fish, bees, and hummingbirds. In contrast, similar adaptations can help cool
endotherms when needed, such as dolphin flukes and elephant ears.
Some ectothermic animals use changes in their behavior to help regulate body temperature. For example, a desert ectothermic
animal may simply seek cooler areas during the hottest part of the day in the desert to keep from getting too warm. The same

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animals may climb onto rocks to capture heat during a cold desert night. Some animals seek water to aid evaporation in cooling
them, as seen with reptiles. Other ectotherms use group activity such as the activity of bees to warm a hive to survive winter.
Many animals, especially mammals, use metabolic waste heat as a heat source. When muscles are contracted, most of the energy
from the ATP used in muscle actions is wasted energy that translates into heat. Severe cold elicits a shivering reflex that generates
heat for the body. Many species also have a type of adipose tissue called brown fat that specializes in generating heat.

Neural Control of Thermoregulation

The nervous system is important to thermoregulation, as illustrated in Figure [Link] . The processes of homeostasis and
temperature control are centered in the hypothalamus of the advanced animal brain.

Figure [Link] : The body is able to regulate temperature in response to signals from the nervous system.

Exercise
When bacteria are destroyed by leuckocytes, pyrogens are released into the blood. Pyrogens reset the body’s thermostat to a
higher temperature, resulting in fever. How might pyrogens cause the body temperature to rise?

Answer
Pyrogens increase body temperature by causing the blood vessels to constrict, inducing shivering, and stopping sweat
glands from secreting fluid.

The hypothalamus maintains the set point for body temperature through reflexes that cause vasodilation and sweating when the
body is too warm, or vasoconstriction and shivering when the body is too cold. It responds to chemicals from the body. When a
bacterium is destroyed by phagocytic leukocytes, chemicals called endogenous pyrogens are released into the blood. These
pyrogens circulate to the hypothalamus and reset the thermostat. This allows the body’s temperature to increase in what is
commonly called a fever. An increase in body temperature causes iron to be conserved, which reduces a nutrient needed by
bacteria. An increase in body heat also increases the activity of the animal’s enzymes and protective cells while inhibiting the
enzymes and activity of the invading microorganisms. Finally, heat itself may also kill the pathogen. A fever that was once thought
to be a complication of an infection is now understood to be a normal defense mechanism.

Summary
Homeostasis is a dynamic equilibrium that is maintained in body tissues and organs. It is dynamic because it is constantly adjusting
to the changes that the systems encounter. It is in equilibrium because body functions are kept within a normal range, with some
fluctuations around a set point for the processes.

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Glossary
acclimatization
alteration in a body system in response to environmental change

alteration
change of the set point in a homeostatic system

homeostasis
dynamic equilibrium maintaining appropriate body functions

negative feedback loop

feedback to a control mechanism that increases or decreases a stimulus instead of maintaining it

positive feedback loop

feedback to a control mechanism that continues the direction of a stimulus

set point
midpoint or target point in homeostasis

thermoregulation
regulation of body temperature

This page titled 15.1.4: Homeostasis is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
33.3: Homeostasis by OpenStax is licensed CC BY 4.0.

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15.1.E: The Animal Body - Basic Form and Function (Exercises)
33.1: Animal Form and Function
Animals vary in form and function. From a sponge to a worm to a goat, an organism has a distinct body plan that limits its size and
shape. Animals’ bodies are also designed to interact with their environments, whether in the deep sea, a rainforest canopy, or the
desert. Therefore, a large amount of information about the structure of an organism's body (anatomy) and the function of its cells,
tissues and organs (physiology) can be learned by studying that organism's environment.

Review Questions
Which type of animal maintains a constant internal body temperature?
A. endotherm
B. ectotherm
C. coelomate
D. mesoderm

Answer
A

The symmetry found in animals that move swiftly is ________.

A. radial
B. bilateral
C. sequential
D. interrupted

Answer
B

What term describes the condition of a desert mouse that lowers its metabolic rate and “sleeps” during the hot day?
A. turgid
B. hibernation
C. estivation
D. normal sleep pattern

Answer
C

A plane that divides an animal into equal right and left portions is ________.
A. diagonal
B. midsagittal
C. coronal
D. transverse

Answer
B

A plane that divides an animal into dorsal and ventral portions is ________.
A. sagittal
B. midsagittal

15.1.E.1 [Link]
 C. coronal
D. transverse

Answer
D

The pleural cavity is a part of which cavity?

A. dorsal cavity
B. thoracic cavity
C. abdominal cavity
D. pericardial cavity

Answer
B

Free Response
How does diffusion limit the size of an organism? How is this counteracted?

Answer
Diffusion is effective over a very short distance. If a cell exceeds this distance in its size, the center of the cell cannot get
adequate nutrients nor can it expel enough waste to survive. To compensate for this, cells can loosely adhere to each other
in a liquid medium, or develop into multi-celled organisms that use circulatory and respiratory systems to deliver nutrients
and remove wastes.

What is the relationship between BMR and body size? Why?

Answer
Basal Metabolic Rate is an expression of the metabolic processes that occur to maintain an individual’s functioning and
body temperature. Smaller bodied animals have a relatively large surface area compared to a much larger animal. The large
animal’s large surface area leads to increased heat loss that the animal must compensate for, resulting in a higher BMR. A
small animal, having less relative surface area, does not lose as much heat and has a correspondingly lower BMR.

33.2: Animal Primary Tissues

The tissues of multicellular, complex animals are four primary types: epithelial, connective, muscle, and nervous. Recall that
tissues are groups of similar cells group of similar cells carrying out related functions. These tissues combine to form organs—like
the skin or kidney—that have specific, specialized functions within the body. Organs are organized into organ systems to perform
functions.

Review Questions
Which type of epithelial cell is best adapted to aid diffusion?
A. squamous
B. cuboidal
C. columnar
D. transitional

Answer
C

15.1.E.2 [Link]
Which type of epithelial cell is found in glands?
A. squamous
B. cuboidal
C. columnar
D. transitional

Answer
B

Which type of epithelial cell is found in the urinary bladder?

A. squamous
B. cuboidal
C. columnar
D. transitional

Answer
D

Which type of connective tissue has the most fibers?

A. loose connective tissue
B. fibrous connective tissue
C. cartilage
D. bone

Answer
B

Which type of connective tissue has a mineralized different matrix?

A. loose connective tissue
B. fibrous connective tissue
C. cartilage
D. bone

Answer
D

The cell found in bone that breaks it down is called an ________.

A. osteoblast
B. osteocyte
C. osteoclast
D. osteon

Answer
C

The cell found in bone that makes the bone is called an ________.
A. osteoblast
B. osteocyte

15.1.E.3 [Link]
 C. osteoclast
D. osteon

Answer
A

Plasma is the ________.

A. fibers in blood
B. matrix of blood
C. cell that phagocytizes bacteria
D. cell fragment found in the tissue

Answer
B

The type of muscle cell under voluntary control is the ________.

A. smooth muscle
B. skeletal muscle
C. cardiac muscle
D. visceral muscle

Answer
B

The part of a neuron that contains the nucleus is the

A. cell body
B. dendrite
C. axon
D. glial

Answer
B

Free Response
How can squamous epithelia both facilitate diffusion and prevent damage from abrasion?

Answer
Squamous epithelia can be either simple or stratified. As a single layer of cells, it presents a very thin epithelia that
minimally inhibits diffusion. As a stratified epithelia, the surface cells can be sloughed off and the cells in deeper layers
protect the underlying tissues from damage.

What are the similarities between cartilage and bone?

Answer
Both contain cells other than the traditional fibroblast. Both have cells that lodge in spaces within the tissue called lacunae.
Both collagen and elastic fibers are found in bone and cartilage. Both tissues participate in vertebrate skeletal development
and formation.

15.1.E.4 [Link]
33.3: Homeostasis
Animal organs and organ systems constantly adjust to internal and external changes through a process called homeostasis (“steady
state”). These changes might be in the level of glucose or calcium in blood or in external temperatures. Homeostasis means to
maintain dynamic equilibrium in the body. It is dynamic because it is constantly adjusting to the changes that the body’s systems
encounter. It is equilibrium because body functions are kept within specific ranges.

Review Questions
When faced with a sudden drop in environmental temperature, an endothermic animal will:
A. experience a drop in its body temperature
B. wait to see if it goes lower
C. increase muscle activity to generate heat
D. add fur or fat to increase insulation

Answer
C

Which is an example of negative feedback?

A. lowering of blood glucose after a meal
B. blood clotting after an injury
C. lactation during nursing
D. uterine contractions during labor

Answer
A

Which method of heat exchange occurs during direct contact between the source and animal?
A. radiation
B. evaporation
C. convection
D. conduction

Answer
D

The body’s thermostat is located in the ________.

A. homeostatic receptor
B. hypothalamus
C. medulla
D. vasodilation center

Answer
B

Free Response
Why are negative feedback loops used to control body homeostasis?

Answer

15.1.E.5 [Link]
 An adjustment to a change in the internal or external environment requires a change in the direction of the stimulus. A
negative feedback loop accomplishes this, while a positive feedback loop would continue the stimulus and result in harm to
the animal.

Why is a fever a “good thing” during a bacterial infection?

Answer
Mammalian enzymes increase activity to the point of denaturation, increasing the chemical activity of the cells involved.
Bacterial enzymes have a specific temperature for their most efficient activity and are inhibited at either higher or lower
temperatures. Fever results in an increase in the destruction of the invading bacteria by increasing the effectiveness of body
defenses and an inhibiting bacterial metabolism.

How is a condition such as diabetes a good example of the failure of a set point in humans?

Answer
Diabetes is often associated with a lack in production of insulin. Without insulin, blood glucose levels go up after a meal,
but never go back down to normal levels.

15.1.E: The Animal Body - Basic Form and Function (Exercises) is shared under a CC BY license and was authored, remixed, and/or curated by
LibreTexts.
33.E: The Animal Body - Basic Form and Function (Exercises) is licensed CC BY 4.0.

15.1.E.6 [Link]
15.2: Types of Skeletal Systems
Skills to Develop
Discuss the different types of skeletal systems
Explain the role of the human skeletal system
Compare and contrast different skeletal systems

A skeletal system is necessary to support the body, protect internal organs, and allow for the movement of an organism. There are
three different skeleton designs that fulfill these functions: hydrostatic skeleton, exoskeleton, and endoskeleton.

Hydrostatic Skeleton
A hydrostatic skeleton is a skeleton formed by a fluid-filled compartment within the body, called the coelom. The organs of the
coelom are supported by the aqueous fluid, which also resists external compression. This compartment is under hydrostatic
pressure because of the fluid and supports the other organs of the organism. This type of skeletal system is found in soft-bodied
animals such as sea anemones, earthworms, Cnidaria, and other invertebrates (Figure 15.2.1).

Figure 15.2.1 : The skeleton of the red-knobbed sea star (Protoreaster linckii) is an example of a hydrostatic skeleton. (credit:
“Amada44”/Wikimedia Commons)
Movement in a hydrostatic skeleton is provided by muscles that surround the coelom. The muscles in a hydrostatic skeleton
contract to change the shape of the coelom; the pressure of the fluid in the coelom produces movement. For example, earthworms
move by waves of muscular contractions of the skeletal muscle of the body wall hydrostatic skeleton, called peristalsis, which
alternately shorten and lengthen the body. Lengthening the body extends the anterior end of the organism. Most organisms have a
mechanism to fix themselves in the substrate. Shortening the muscles then draws the posterior portion of the body forward.
Although a hydrostatic skeleton is well-suited to invertebrate organisms such as earthworms and some aquatic organisms, it is not
an efficient skeleton for terrestrial animals.

Exoskeleton
An exoskeleton is an external skeleton that consists of a hard encasement on the surface of an organism. For example, the shells of
crabs and insects are exoskeletons (Figure 15.2.2). This skeleton type provides defence against predators, supports the body, and
allows for movement through the contraction of attached muscles. As with vertebrates, muscles must cross a joint inside the
exoskeleton. Shortening of the muscle changes the relationship of the two segments of the exoskeleton. Arthropods such as crabs
and lobsters have exoskeletons that consist of 30–50 percent chitin, a polysaccharide derivative of glucose that is a strong but
flexible material. Chitin is secreted by the epidermal cells. The exoskeleton is further strengthened by the addition of calcium
carbonate in organisms such as the lobster. Because the exoskeleton is acellular, arthropods must periodically shed their
exoskeletons because the exoskeleton does not grow as the organism grows.

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 Figure 15.2.2 : Muscles attached to the exoskeleton of the Halloween crab (Gecarcinus quadratus) allow it to move.

Endoskeleton
An endoskeleton is a skeleton that consists of hard, mineralized structures located within the soft tissue of organisms. An example
of a primitive endoskeletal structure is the spicules of sponges. The bones of vertebrates are composed of tissues, whereas sponges
have no true tissues (Figure 15.2.1). Endoskeletons provide support for the body, protect internal organs, and allow for movement
through contraction of muscles attached to the skeleton.

Figure 15.2.3 : The skeletons of humans and horses are examples of endoskeletons. (credit: Ross Murphy)
The human skeleton is an endoskeleton that consists of 206 bones in the adult. It has five main functions: providing support to the
body, storing minerals and lipids, producing blood cells, protecting internal organs, and allowing for movement. The skeletal
system in vertebrates is divided into the axial skeleton (which consists of the skull, vertebral column, and rib cage), and the
appendicular skeleton (which consists of the shoulders, limb bones, the pectoral girdle, and the pelvic girdle).

Access for free at OpenStax 15.2.2 [Link]

Human Axial Skeleton
The axial skeleton forms the central axis of the body and includes the bones of the skull, ossicles of the middle ear, hyoid bone of
the throat, vertebral column, and the thoracic cage (ribcage) (Figure 15.2.1). The function of the axial skeleton is to provide
support and protection for the brain, the spinal cord, and the organs in the ventral body cavity. It provides a surface for the
attachment of muscles that move the head, neck, and trunk, performs respiratory movements, and stabilizes parts of the
appendicular skeleton.

Figure 15.2.4 : The axial skeleton consists of the bones of the skull, ossicles of the middle ear, hyoid bone, vertebral column, and
rib cage. (credit: modification of work by Mariana Ruiz Villareal)

The Skull
The bones of the skull support the structures of the face and protect the brain. The skull consists of 22 bones, which are divided into
two categories: cranial bones and facial bones. The cranial bones are eight bones that form the cranial cavity, which encloses the
brain and serves as an attachment site for the muscles of the head and neck. The eight cranial bones are the frontal bone, two
parietal bones, two temporal bones, occipital bone, sphenoid bone, and the ethmoid bone. Although the bones developed separately
in the embryo and fetus, in the adult, they are tightly fused with connective tissue and adjoining bones do not move (Figure 15.2.5).

Access for free at OpenStax 15.2.3 [Link]

 Figure 15.2.5 : The bones of the skull support the structures of the face and protect the brain. (credit: modification of work by
Mariana Ruiz Villareal)
The auditory ossicles of the middle ear transmit sounds from the air as vibrations to the fluid-filled cochlea. The auditory ossicles
consist of six bones: two malleus bones, two incus bones, and two stapes on each side. These are the smallest bones in the body and
are unique to mammals.
Fourteen facial bones form the face, provide cavities for the sense organs (eyes, mouth, and nose), protect the entrances to the
digestive and respiratory tracts, and serve as attachment points for facial muscles. The 14 facial bones are the nasal bones, the
maxillary bones, zygomatic bones, palatine, vomer, lacrimal bones, the inferior nasal conchae, and the mandible. All of these bones
occur in pairs except for the mandible and the vomer (Figure 15.2.6).

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 Figure 15.2.6 : The cranial bones, including the frontal, parietal, and sphenoid bones, cover the top of the head. The facial bones of
the skull form the face and provide cavities for the eyes, nose, and mouth.
Although it is not found in the skull, the hyoid bone is considered a component of the axial skeleton. The hyoid bone lies below the
mandible in the front of the neck. It acts as a movable base for the tongue and is connected to muscles of the jaw, larynx, and
tongue. The mandible articulates with the base of the skull. The mandible controls the opening to the airway and gut. In animals
with teeth, the mandible brings the surfaces of the teeth in contact with the maxillary teeth.

The Vertebral Column

The vertebral column, or spinal column, surrounds and protects the spinal cord, supports the head, and acts as an attachment point
for the ribs and muscles of the back and neck. The adult vertebral column comprises 26 bones: the 24 vertebrae, the sacrum, and
the coccyx bones. In the adult, the sacrum is typically composed of five vertebrae that fuse into one. The coccyx is typically 3–4
vertebrae that fuse into one. Around the age of 70, the sacrum and the coccyx may fuse together. We begin life with approximately
33 vertebrae, but as we grow, several vertebrae fuse together. The adult vertebrae are further divided into the 7 cervical vertebrae,
12 thoracic vertebrae, and 5 lumbar vertebrae (Figure 15.2.7).

Access for free at OpenStax 15.2.5 [Link]

 Figure 15.2.7 : (a) The vertebral column consists of seven cervical vertebrae (C1–7) twelve thoracic vertebrae (Th1–12), five
lumbar vertebrae (L1–5), the os sacrum, and the coccyx. (b) Spinal curves increase the strength and flexibility of the spine. (credit
a: modification of work by Uwe Gille based on original work by Gray's Anatomy; credit b: modification of work by NCI, NIH)
Each vertebral body has a large hole in the center through which the nerves of the spinal cord pass. There is also a notch on each
side through which the spinal nerves, which serve the body at that level, can exit from the spinal cord. The vertebral column is
approximately 71 cm (28 inches) in adult male humans and is curved, which can be seen from a side view. The names of the spinal
curves correspond to the region of the spine in which they occur. The thoracic and sacral curves are concave (curve inwards relative
to the front of the body) and the cervical and lumbar curves are convex (curve outwards relative to the front of the body). The
arched curvature of the vertebral column increases its strength and flexibility, allowing it to absorb shocks like a spring (Figure
15.2.7).

Intervertebral discs composed of fibrous cartilage lie between adjacent vertebral bodies from the second cervical vertebra to the
sacrum. Each disc is part of a joint that allows for some movement of the spine and acts as a cushion to absorb shocks from
movements such as walking and running. Intervertebral discs also act as ligaments to bind vertebrae together. The inner part of
discs, the nucleus pulposus, hardens as people age and becomes less elastic. This loss of elasticity diminishes its ability to absorb
shocks.

The Thoracic Cage

The thoracic cage, also known as the ribcage, is the skeleton of the chest, and consists of the ribs, sternum, thoracic vertebrae, and
costal cartilages (Figure [Link]). The thoracic cage encloses and protects the organs of the thoracic cavity, including the heart and

Access for free at OpenStax 15.2.6 [Link]

lungs. It also provides support for the shoulder girdles and upper limbs, and serves as the attachment point for the diaphragm,
muscles of the back, chest, neck, and shoulders. Changes in the volume of the thorax enable breathing.
The sternum, or breastbone, is a long, flat bone located at the anterior of the chest. It is formed from three bones that fuse in the
adult. The ribs are 12 pairs of long, curved bones that attach to the thoracic vertebrae and curve toward the front of the body,
forming the ribcage. Costal cartilages connect the anterior ends of the ribs to the sternum, with the exception of rib pairs 11 and 12,
which are free-floating ribs.

Figure 15.2.8 : The thoracic cage, or rib cage, protects the heart and the lungs. (credit: modification of work by NCI, NIH)

Human Appendicular Skeleton

The appendicular skeleton is composed of the bones of the upper limbs (which function to grasp and manipulate objects) and the
lower limbs (which permit locomotion). It also includes the pectoral girdle, or shoulder girdle, that attaches the upper limbs to the
body, and the pelvic girdle that attaches the lower limbs to the body (Figure 15.2.9).

Access for free at OpenStax 15.2.7 [Link]

 Figure 15.2.9 : The appendicular skeleton is composed of the bones of the pectoral limbs (arm, forearm, hand), the pelvic limbs
(thigh, leg, foot), the pectoral girdle, and the pelvic girdle. (credit: modification of work by Mariana Ruiz Villareal)

The Pectoral Girdle

The pectoral girdle bones provide the points of attachment of the upper limbs to the axial skeleton. The human pectoral girdle
consists of the clavicle (or collarbone) in the anterior, and the scapula (or shoulder blades) in the posterior (Figure 15.2.10).

Access for free at OpenStax 15.2.8 [Link]

 Figure 15.2.10: (a) The pectoral girdle in primates consists of the clavicles and scapulae. (b) The posterior view reveals the spine
of the scapula to which muscle attaches.
The clavicles are S-shaped bones that position the arms on the body. The clavicles lie horizontally across the front of the thorax
(chest) just above the first rib. These bones are fairly fragile and are susceptible to fractures. For example, a fall with the arms
outstretched causes the force to be transmitted to the clavicles, which can break if the force is excessive. The clavicle articulates
with the sternum and the scapula.
The scapulae are flat, triangular bones that are located at the back of the pectoral girdle. They support the muscles crossing the
shoulder joint. A ridge, called the spine, runs across the back of the scapula and can easily be felt through the skin (Figure 15.2.10).
The spine of the scapula is a good example of a bony protrusion that facilitates a broad area of attachment for muscles to bone.

The Upper Limb

The upper limb contains 30 bones in three regions: the arm (shoulder to elbow), the forearm (ulna and radius), and the wrist and
hand (Figure 15.2.11).

Figure 15.2.11: The upper limb consists of the humerus of the upper arm, the radius and ulna of the forearm, eight bones of the
carpus, five bones of the metacarpus, and 14 bones of the phalanges.
An articulation is any place at which two bones are joined. The humerus is the largest and longest bone of the upper limb and the
only bone of the arm. It articulates with the scapula at the shoulder and with the forearm at the elbow. The forearm extends from
the elbow to the wrist and consists of two bones: the ulna and the radius. The radius is located along the lateral (thumb) side of the

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forearm and articulates with the humerus at the elbow. The ulna is located on the medial aspect (pinky-finger side) of the forearm.
It is longer than the radius. The ulna articulates with the humerus at the elbow. The radius and ulna also articulate with the carpal
bones and with each other, which in vertebrates enables a variable degree of rotation of the carpus with respect to the long axis of
the limb. The hand includes the eight bones of the carpus (wrist), the five bones of the metacarpus (palm), and the 14 bones of the
phalanges (digits). Each digit consists of three phalanges, except for the thumb, when present, which has only two.

The Pelvic Girdle

The pelvic girdle attaches to the lower limbs of the axial skeleton. Because it is responsible for bearing the weight of the body and
for locomotion, the pelvic girdle is securely attached to the axial skeleton by strong ligaments. It also has deep sockets with robust
ligaments to securely attach the femur to the body. The pelvic girdle is further strengthened by two large hip bones. In adults, the
hip bones, or coxal bones, are formed by the fusion of three pairs of bones: the ilium, ischium, and pubis. The pelvis joins together
in the anterior of the body at a joint called the pubic symphysis and with the bones of the sacrum at the posterior of the body.
The female pelvis is slightly different from the male pelvis. Over generations of evolution, females with a wider pubic angle and
larger diameter pelvic canal reproduced more successfully. Therefore, their offspring also had pelvic anatomy that enabled
successful childbirth (Figure 15.2.12).

Figure 15.2.12: To adapt to reproductive fitness, the (a) female pelvis is lighter, wider, shallower, and has a broader angle between
the pubic bones than (b) the male pelvis.

The Lower Limb

The lower limb consists of the thigh, the leg, and the foot. The bones of the lower limb are the femur (thigh bone), patella
(kneecap), tibia and fibula (bones of the leg), tarsals (bones of the ankle), and metatarsals and phalanges (bones of the foot) (Figure
15.2.13). The bones of the lower limbs are thicker and stronger than the bones of the upper limbs because of the need to support

the entire weight of the body and the resulting forces from locomotion. In addition to evolutionary fitness, the bones of an
individual will respond to forces exerted upon them.

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 Figure 15.2.13: The lower limb consists of the thigh (femur), kneecap (patella), leg (tibia and fibula), ankle (tarsals), and foot
(metatarsals and phalanges) bones.
The femur, or thighbone, is the longest, heaviest, and strongest bone in the body. The femur and pelvis form the hip joint at the
proximal end. At the distal end, the femur, tibia, and patella form the knee joint. The patella, or kneecap, is a triangular bone that
lies anterior to the knee joint. The patella is embedded in the tendon of the femoral extensors (quadriceps). It improves knee
extension by reducing friction. The tibia, or shinbone, is a large bone of the leg that is located directly below the knee. The tibia
articulates with the femur at its proximal end, with the fibula and the tarsal bones at its distal end. It is the second largest bone in
the human body and is responsible for transmitting the weight of the body from the femur to the foot. The fibula, or calf bone,
parallels and articulates with the tibia. It does not articulate with the femur and does not bear weight. The fibula acts as a site for
muscle attachment and forms the lateral part of the ankle joint.
The tarsals are the seven bones of the ankle. The ankle transmits the weight of the body from the tibia and the fibula to the foot.
The metatarsals are the five bones of the foot. The phalanges are the 14 bones of the toes. Each toe consists of three phalanges,
except for the big toe that has only two (Figure 15.2.14). Variations exist in other species; for example, the horse’s metacarpals and
metatarsals are oriented vertically and do not make contact with the substrate.

Figure 15.2.14: This drawing shows the bones of the human foot and ankle, including the metatarsals and the phalanges.

Access for free at OpenStax 15.2.11 [Link]

 Evolution Connection: Evolution of Body Design for Locomotion on Land
The transition of vertebrates onto land required a number of changes in body design, as movement on land presents a number
of challenges for animals that are adapted to movement in water. The buoyancy of water provides a certain amount of lift, and
a common form of movement by fish is lateral undulations of the entire body. This back and forth movement pushes the body
against the water, creating forward movement. In most fish, the muscles of paired fins attach to girdles within the body,
allowing for some control of locomotion. As certain fish began moving onto land, they retained their lateral undulation form of
locomotion (anguilliform). However, instead of pushing against water, their fins or flippers became points of contact with the
ground, around which they rotated their bodies.
The effect of gravity and the lack of buoyancy on land meant that body weight was suspended on the limbs, leading to
increased strengthening and ossification of the limbs. The effect of gravity also required changes to the axial skeleton. Lateral
undulations of land animal vertebral columns cause torsional strain. A firmer, more ossified vertebral column became common
in terrestrial tetrapods because it reduces strain while providing the strength needed to support the body’s weight. In later
tetrapods, the vertebrae began allowing for vertical motion rather than lateral flexion. Another change in the axial skeleton was
the loss of a direct attachment between the pectoral girdle and the head. This reduced the jarring to the head caused by the
impact of the limbs on the ground. The vertebrae of the neck also evolved to allow movement of the head independently of the
body.
The appendicular skeleton of land animals is also different from aquatic animals. The shoulders attach to the pectoral girdle
through muscles and connective tissue, thus reducing the jarring of the skull. Because of a lateral undulating vertebral column,
in early tetrapods, the limbs were splayed out to the side and movement occurred by performing “push-ups.” The vertebrae of
these animals had to move side-to-side in a similar manner to fish and reptiles. This type of motion requires large muscles to
move the limbs toward the midline; it was almost like walking while doing push-ups, and it is not an efficient use of energy.
Later tetrapods have their limbs placed under their bodies, so that each stride requires less force to move forward. This resulted
in decreased adductor muscle size and an increased range of motion of the scapulae. This also restricts movement primarily to
one plane, creating forward motion rather than moving the limbs upward as well as forward. The femur and humerus were also
rotated, so that the ends of the limbs and digits were pointed forward, in the direction of motion, rather than out to the side. By
placement underneath the body, limbs can swing forward like a pendulum to produce a stride that is more efficient for moving
over land.

Summary
The three types of skeleton designs are hydrostatic skeletons, exoskeletons, and endoskeletons. A hydrostatic skeleton is formed by
a fluid-filled compartment held under hydrostatic pressure; movement is created by the muscles producing pressure on the fluid.
An exoskeleton is a hard external skeleton that protects the outer surface of an organism and enables movement through muscles
attached on the inside. An endoskeleton is an internal skeleton composed of hard, mineralized tissue that also enables movement by
attachment to muscles. The human skeleton is an endoskeleton that is composed of the axial and appendicular skeleton. The axial
skeleton is composed of the bones of the skull, ossicles of the ear, hyoid bone, vertebral column, and ribcage. The skull consists of
eight cranial bones and 14 facial bones. Six bones make up the ossicles of the middle ear, while the hyoid bone is located in the
neck under the mandible. The vertebral column contains 26 bones, and it surrounds and protects the spinal cord. The thoracic cage
consists of the sternum, ribs, thoracic vertebrae, and costal cartilages. The appendicular skeleton is made up of the limbs of the
upper and lower limbs. The pectoral girdle is composed of the clavicles and the scapulae. The upper limb contains 30 bones in the
arm, the forearm, and the hand. The pelvic girdle attaches the lower limbs to the axial skeleton. The lower limb includes the bones
of the thigh, the leg, and the foot.

Glossary
appendicular skeleton
composed of the bones of the upper limbs, which function to grasp and manipulate objects, and the lower limbs, which permit
locomotion

articulation
any place where two bones are joined

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auditory ossicle
(also, middle ear) transduces sounds from the air into vibrations in the fluid-filled cochlea

axial skeleton
forms the central axis of the body and includes the bones of the skull, the ossicles of the middle ear, the hyoid bone of the
throat, the vertebral column, and the thoracic cage (ribcage)

carpus
eight bones that comprise the wrist

clavicle
S-shaped bone that positions the arms laterally

coxal bone
hip bone

cranial bone
one of eight bones that form the cranial cavity that encloses the brain and serves as an attachment site for the muscles of the
head and neck

endoskeleton
skeleton of living cells that produce a hard, mineralized tissue located within the soft tissue of organisms

exoskeleton
a secreted cellular product external skeleton that consists of a hard encasement on the surface of an organism

facial bone
one of the 14 bones that form the face; provides cavities for the sense organs (eyes, mouth, and nose) and attachment points for
facial muscles

femur
(also, thighbone) longest, heaviest, and strongest bone in the body

fibula
(also, calf bone) parallels and articulates with the tibia

forearm
extends from the elbow to the wrist and consists of two bones: the ulna and the radius

humerus
only bone of the arm

hydrostatic skeleton
skeleton that consists of aqueous fluid held under pressure in a closed body compartment

hyoid bone
lies below the mandible in the front of the neck

intervertebral disc
composed of fibrous cartilage; lies between adjacent vertebrae from the second cervical vertebra to the sacrum

lower limb
consists of the thigh, the leg, and the foot

metacarpus

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 five bones that comprise the palm

metatarsal
one of the five bones of the foot

patella
(also, kneecap) triangular bone that lies anterior to the knee joint

pectoral girdle
bones that transmit the force generated by the upper limbs to the axial skeleton

phalange
one of the bones of the fingers or toes

pelvic girdle
bones that transmit the force generated by the lower limbs to the axial skeleton

radius
bone located along the lateral (thumb) side of the forearm; articulates with the humerus at the elbow

rib
one of 12 pairs of long, curved bones that attach to the thoracic vertebrae and curve toward the front of the body to form the
ribcage

scapula
flat, triangular bone located at the posterior pectoral girdle

skull
bone that supports the structures of the face and protects the brain

sternum
(also, breastbone) long, flat bone located at the front of the chest

tarsal
one of the seven bones of the ankle

thoracic cage
(also, ribcage) skeleton of the chest, which consists of the ribs, thoracic vertebrae, sternum, and costal cartilages

tibia
(also, shinbone) large bone of the leg that is located directly below the knee

ulna
bone located on the medial aspect (pinky-finger side) of the forearm

vertebral column
(also, spine) surrounds and protects the spinal cord, supports the head, and acts as an attachment point for ribs and muscles of
the back and neck

This page titled 15.2: Types of Skeletal Systems is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
38.1: Types of Skeletal Systems by OpenStax is licensed CC BY 4.0.

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15.3: Bone
Skills to Develop
Classify the different types of bones in the skeleton
Explain the role of the different cell types in bone
Explain how bone forms during development

Bone, or osseous tissue, is a connective tissue that constitutes the endoskeleton. It contains specialized cells and a matrix of mineral
salts and collagen fibers.
The mineral salts primarily include hydroxyapatite, a mineral formed from calcium phosphate. Calcification is the process of
deposition of mineral salts on the collagen fiber matrix that crystallizes and hardens the tissue. The process of calcification only
occurs in the presence of collagen fibers.
The bones of the human skeleton are classified by their shape: long bones, short bones, flat bones, sutural bones, sesamoid bones,
and irregular bones (Figure 15.3.1).

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 Figure 15.3.1 : Shown are different types of bones: flat, irregular, long, short, and sesamoid.
Long bones are longer than they are wide and have a shaft and two ends. The diaphysis, or central shaft, contains bone marrow in a
marrow cavity. The rounded ends, the epiphyses, are covered with articular cartilage and are filled with red bone marrow, which
produces blood cells (Figure 15.3.2). Most of the limb bones are long bones—for example, the femur, tibia, ulna, and radius.
Exceptions to this include the patella and the bones of the wrist and ankle.

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 Figure 15.3.2 : The long bone is covered by articular cartilage at either end and contains bone marrow (shown in yellow in this
illustration) in the marrow cavity.
Short bones, or cuboidal bones, are bones that are the same width and length, giving them a cube-like shape. For example, the
bones of the wrist (carpals) and ankle (tarsals) are short bones (Figure 15.3.1).
Flat bones are thin and relatively broad bones that are found where extensive protection of organs is required or where broad
surfaces of muscle attachment are required. Examples of flat bones are the sternum (breast bone), ribs, scapulae (shoulder blades),
and the roof of the skull (Figure 15.3.1).
Irregular bones are bones with complex shapes. These bones may have short, flat, notched, or ridged surfaces. Examples of
irregular bones are the vertebrae, hip bones, and several skull bones.
Sesamoid bones are small, flat bones and are shaped similarly to a sesame seed. The patellae are sesamoid bones (Figure 15.3.3 ).
Sesamoid bones develop inside tendons and may be found near joints at the knees, hands, and feet.

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 Figure 15.3.3 : The patella of the knee is an example of a sesamoid bone.
Sutural bones are small, flat, irregularly shaped bones. They may be found between the flat bones of the skull. They vary in
number, shape, size, and position.

Bone Tissue
Bones are considered organs because they contain various types of tissue, such as blood, connective tissue, nerves, and bone tissue.
Osteocytes, the living cells of bone tissue, form the mineral matrix of bones. There are two types of bone tissue: compact and
spongy.

Compact Bone Tissue

Compact bone (or cortical bone) forms the hard external layer of all bones and surrounds the medullary cavity, or bone marrow. It
provides protection and strength to bones. Compact bone tissue consists of units called osteons or Haversian systems. Osteons are
cylindrical structures that contain a mineral matrix and living osteocytes connected by canaliculi, which transport blood. They are
aligned parallel to the long axis of the bone. Each osteon consists of lamellae, which are layers of compact matrix that surround a
central canal called the Haversian canal. The Haversian canal (osteonic canal) contains the bone’s blood vessels and nerve fibers
(Figure 15.3.4). Osteons in compact bone tissue are aligned in the same direction along lines of stress and help the bone resist
bending or fracturing. Therefore, compact bone tissue is prominent in areas of bone at which stresses are applied in only a few
directions.

Art Connection

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 Figure 15.3.4 : Compact bone tissue consists of osteons that are aligned parallel to the long axis of the bone, and the Haversian
canal that contains the bone’s blood vessels and nerve fibers. The inner layer of bones consists of spongy bone tissue. The
small dark ovals in the osteon represent the living osteocytes. (credit: modification of work by NCI, NIH)
Which of the following statements about bone tissue is false?
A. Compact bone tissue is made of cylindrical osteons that are aligned such that they travel the length of the bone.
B. Haversian canals contain blood vessels only.
C. Haversian canals contain blood vessels and nerve fibers.
D. Spongy tissue is found on the interior of the bone, and compact bone tissue is found on the exterior.

Spongy Bone Tissue

Whereas compact bone tissue forms the outer layer of all bones, spongy bone or cancellous bone forms the inner layer of all bones.
Spongy bone tissue does not contain osteons that constitute compact bone tissue. Instead, it consists of trabeculae, which are
lamellae that are arranged as rods or plates. Red bone marrow is found between the trabuculae. Blood vessels within this tissue
deliver nutrients to osteocytes and remove waste. The red bone marrow of the femur and the interior of other large bones, such as
the ileum, forms blood cells.
Spongy bone reduces the density of bone and allows the ends of long bones to compress as the result of stresses applied to the
bone. Spongy bone is prominent in areas of bones that are not heavily stressed or where stresses arrive from many directions. The
epiphyses of bones, such as the neck of the femur, are subject to stress from many directions. Imagine laying a heavy framed
picture flat on the floor. You could hold up one side of the picture with a toothpick if the toothpick was perpendicular to the floor
and the picture. Now drill a hole and stick the toothpick into the wall to hang up the picture. In this case, the function of the
toothpick is to transmit the downward pressure of the picture to the wall. The force on the picture is straight down to the floor, but
the force on the toothpick is both the picture wire pulling down and the bottom of the hole in the wall pushing up. The toothpick
will break off right at the wall.
The neck of the femur is horizontal like the toothpick in the wall. The weight of the body pushes it down near the joint, but the
vertical diaphysis of the femur pushes it up at the other end. The neck of the femur must be strong enough to transfer the downward
force of the body weight horizontally to the vertical shaft of the femur (Figure 15.3.5).

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 Figure 15.3.5 : Trabeculae in spongy bone are arranged such that one side of the bone bears tension and the other withstands
compression.

Link to Learning

View micrographs of musculoskeletal tissues as you review the anatomy.

Cell Types in Bones

Bone consists of four types of cells: osteoblasts, osteoclasts, osteocytes, and osteoprogenitor cells. Osteoblasts are bone cells that
are responsible for bone formation. Osteoblasts synthesize and secrete the organic part and inorganic part of the extracellular matrix
of bone tissue, and collagen fibers. Osteoblasts become trapped in these secretions and differentiate into less active osteocytes.
Osteoclasts are large bone cells with up to 50 nuclei. They remove bone structure by releasing lysosomal enzymes and acids that
dissolve the bony matrix. These minerals, released from bones into the blood, help regulate calcium concentrations in body fluids.
Bone may also be resorbed for remodeling, if the applied stresses have changed. Osteocytes are mature bone cells and are the main
cells in bony connective tissue; these cells cannot divide. Osteocytes maintain normal bone structure by recycling the mineral salts
in the bony matrix. Osteoprogenitor cells are squamous stem cells that divide to produce daughter cells that differentiate into
osteoblasts. Osteoprogenitor cells are important in the repair of fractures.

Development of Bone
Ossification, or osteogenesis, is the process of bone formation by osteoblasts. Ossification is distinct from the process of
calcification; whereas calcification takes place during the ossification of bones, it can also occur in other tissues. Ossification
begins approximately six weeks after fertilization in an embryo. Before this time, the embryonic skeleton consists entirely of
fibrous membranes and hyaline cartilage. The development of bone from fibrous membranes is called intramembranous
ossification; development from hyaline cartilage is called endochondral ossification. Bone growth continues until approximately
age 25. Bones can grow in thickness throughout life, but after age 25, ossification functions primarily in bone remodeling and
repair.

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Intramembranous Ossification
Intramembranous ossification is the process of bone development from fibrous membranes. It is involved in the formation of the
flat bones of the skull, the mandible, and the clavicles. Ossification begins as mesenchymal cells form a template of the future
bone. They then differentiate into osteoblasts at the ossification center. Osteoblasts secrete the extracellular matrix and deposit
calcium, which hardens the matrix. The non-mineralized portion of the bone or osteoid continues to form around blood vessels,
forming spongy bone. Connective tissue in the matrix differentiates into red bone marrow in the fetus. The spongy bone is
remodeled into a thin layer of compact bone on the surface of the spongy bone.

Endochondral Ossification
Endochondral ossification is the process of bone development from hyaline cartilage. All of the bones of the body, except for the
flat bones of the skull, mandible, and clavicles, are formed through endochondral ossification.
In long bones, chondrocytes form a template of the hyaline cartilage diaphysis. Responding to complex developmental signals, the
matrix begins to calcify. This calcification prevents diffusion of nutrients into the matrix, resulting in chondrocytes dying and the
opening up of cavities in the diaphysis cartilage. Blood vessels invade the cavities, and osteoblasts and osteoclasts modify the
calcified cartilage matrix into spongy bone. Osteoclasts then break down some of the spongy bone to create a marrow, or
medullary, cavity in the center of the diaphysis. Dense, irregular connective tissue forms a sheath (periosteum) around the bones.
The periosteum assists in attaching the bone to surrounding tissues, tendons, and ligaments. The bone continues to grow and
elongate as the cartilage cells at the epiphyses divide.
In the last stage of prenatal bone development, the centers of the epiphyses begin to calcify. Secondary ossification centers form in
the epiphyses as blood vessels and osteoblasts enter these areas and convert hyaline cartilage into spongy bone. Until adolescence,
hyaline cartilage persists at the epiphyseal plate (growth plate), which is the region between the diaphysis and epiphysis that is
responsible for the lengthwise growth of long bones (Figure 15.3.6).

Figure 15.3.6 : Endochondral ossification is the process of bone development from hyaline cartilage. The periosteum is the
connective tissue on the outside of bone that acts as the interface between bone, blood vessels, tendons, and ligaments.

Growth of Bone
Long bones continue to lengthen, potentially until adolescence, through the addition of bone tissue at the epiphyseal plate. They
also increase in width through appositional growth.

Lengthening of Long Bones

Chondrocytes on the epiphyseal side of the epiphyseal plate divide; one cell remains undifferentiated near the epiphysis, and one
cell moves toward the diaphysis. The cells, which are pushed from the epiphysis, mature and are destroyed by calcification. This
process replaces cartilage with bone on the diaphyseal side of the plate, resulting in a lengthening of the bone.
Long bones stop growing at around the age of 18 in females and the age of 21 in males in a process called epiphyseal plate closure.
During this process, cartilage cells stop dividing and all of the cartilage is replaced by bone. The epiphyseal plate fades, leaving a
structure called the epiphyseal line or epiphyseal remnant, and the epiphysis and diaphysis fuse.

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Thickening of Long Bones
Appositional growth is the increase in the diameter of bones by the addition of bony tissue at the surface of bones. Osteoblasts at
the bone surface secrete bone matrix, and osteoclasts on the inner surface break down bone. The osteoblasts differentiate into
osteocytes. A balance between these two processes allows the bone to thicken without becoming too heavy.

Bone Remodeling and Repair

Bone renewal continues after birth into adulthood. Bone remodeling is the replacement of old bone tissue by new bone tissue. It
involves the processes of bone deposition by osteoblasts and bone resorption by osteoclasts. Normal bone growth requires vitamins
D, C, and A, plus minerals such as calcium, phosphorous, and magnesium. Hormones such as parathyroid hormone, growth
hormone, and calcitonin are also required for proper bone growth and maintenance.
Bone turnover rates are quite high, with five to seven percent of bone mass being recycled every week. Differences in turnover rate
exist in different areas of the skeleton and in different areas of a bone. For example, the bone in the head of the femur may be fully
replaced every six months, whereas the bone along the shaft is altered much more slowly.
Bone remodeling allows bones to adapt to stresses by becoming thicker and stronger when subjected to stress. Bones that are not
subject to normal stress, for example when a limb is in a cast, will begin to lose mass. A fractured or broken bone undergoes repair
through four stages:
1. Blood vessels in the broken bone tear and hemorrhage, resulting in the formation of clotted blood, or a hematoma, at the site of
the break. The severed blood vessels at the broken ends of the bone are sealed by the clotting process, and bone cells that are
deprived of nutrients begin to die.
2. Within days of the fracture, capillaries grow into the hematoma, and phagocytic cells begin to clear away the dead cells. Though
fragments of the blood clot may remain, fibroblasts and osteoblasts enter the area and begin to reform bone. Fibroblasts produce
collagen fibers that connect the broken bone ends, and osteoblasts start to form spongy bone. The repair tissue between the
broken bone ends is called the fibrocartilaginous callus, as it is composed of both hyaline and fibrocartilage (Figure 15.3.7).
Some bone spicules may also appear at this point.
3. The fibrocartilaginous callus is converted into a bony callus of spongy bone. It takes about two months for the broken bone
ends to be firmly joined together after the fracture. This is similar to the endochondral formation of bone, as cartilage becomes
ossified; osteoblasts, osteoclasts, and bone matrix are present.
4. The bony callus is then remodelled by osteoclasts and osteoblasts, with excess material on the exterior of the bone and within
the medullary cavity being removed. Compact bone is added to create bone tissue that is similar to the original, unbroken bone.
This remodeling can take many months, and the bone may remain uneven for years.

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 Figure 15.3.7 : After this bone is set, a callus will knit the two ends together. (credit: Bill Rhodes)

Scientific Method Connection: Decalcification of Bones

Question: What effect does the removal of calcium and collagen have on bone structure?
Background: Conduct a literature search on the role of calcium and collagen in maintaining bone structure. Conduct a
literature search on diseases in which bone structure is compromised.
Hypothesis: Develop a hypothesis that states predictions of the flexibility, strength, and mass of bones that have had the
calcium and collagen components removed. Develop a hypothesis regarding the attempt to add calcium back to decalcified
bones.
Test the hypothesis: Test the prediction by removing calcium from chicken bones by placing them in a jar of vinegar for seven
days. Test the hypothesis regarding adding calcium back to decalcified bone by placing the decalcified chicken bones into a jar
of water with calcium supplements added. Test the prediction by denaturing the collagen from the bones by baking them at
250°C for three hours.
Analyze the data: Create a table showing the changes in bone flexibility, strength, and mass in the three different
environments.
Report the results: Under which conditions was the bone most flexible? Under which conditions was the bone the strongest?
Draw a conclusion: Did the results support or refute the hypothesis? How do the results observed in this experiment
correspond to diseases that destroy bone tissue?

Summary
Bone, or osseous tissue, is connective tissue that includes specialized cells, mineral salts, and collagen fibers. The human skeleton
can be divided into long bones, short bones, flat bones, and irregular bones. Compact bone tissue is composed of osteons and forms
the external layer of all bones. Spongy bone tissue is composed of trabeculae and forms the inner part of all bones. Four types of

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cells compose bony tissue: osteocytes, osteoclasts, osteoprogenitor cells, and osteoblasts. Ossification is the process of bone
formation by osteoblasts. Intramembranous ossification is the process of bone development from fibrous membranes.
Endochondral ossification is the process of bone development from hyaline cartilage. Long bones lengthen as chondrocytes divide
and secrete hyaline cartilage. Osteoblasts replace cartilage with bone. Appositional growth is the increase in the diameter of bones
by the addition of bone tissue at the surface of bones. Bone remodeling involves the processes of bone deposition by osteoblasts
and bone resorption by osteoclasts. Bone repair occurs in four stages and can take several months.

Art Exercise
Figure 15.3.4: Which of the following statements about bone tissue is false?
A. Compact bone tissue is made of cylindrical osteons that are aligned such that they travel the length of the bone.
B. Haversian canals contain blood vessels only.
C. Haversian canals contain blood vessels and nerve fibers.
D. Spongy tissue is found on the interior of the bone, and compact bone tissue is found on the exterior.

Answer
B

Glossary
appositional growth
increase in the diameter of bones by the addition of bone tissue at the surface of bones

bone
(also, osseous tissue) connective tissue that constitutes the endoskeleton

bone remodeling
replacement of old bone tissue by new bone tissue

calcification
process of deposition of mineral salts in the collagen fiber matrix that crystallizes and hardens the tissue

compact bone
forms the hard external layer of all bones

diaphysis
central shaft of bone, contains bone marrow in a marrow cavity

endochondral ossification
process of bone development from hyaline cartilage

epiphyseal plate
region between the diaphysis and epiphysis that is responsible for the lengthwise growth of long bones

epiphysis
rounded end of bone, covered with articular cartilage and filled with red bone marrow, which produces blood cells

flat bone
thin and relatively broad bone found where extensive protection of organs is required or where broad surfaces of muscle
attachment are required

Haversian canal
contains the bone’s blood vessels and nerve fibers

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intramembranous ossification
process of bone development from fibrous membranes

irregular bone
bone with complex shapes; examples include vertebrae and hip bones

lamella
layer of compact tissue that surrounds a central canal called the Haversian canal

long bone
bone that is longer than wide, and has a shaft and two ends

osteoblast
bone cell responsible for bone formation

osteoclast
large bone cells with up to 50 nuclei, responsible for bone remodeling

osteocyte
mature bone cells and the main cell in bone tissue

osseous tissue
connective tissue that constitutes the endoskeleton

ossification
(also, osteogenesis) process of bone formation by osteoblasts

osteon
cylindrical structure aligned parallel to the long axis of the bone

resorption
process by which osteoclasts release minerals stored in bones

sesamoid bone
small, flat bone shaped like a sesame seed; develops inside tendons

short bone
bone that has the same width and length, giving it a cube-like shape

spongy bone tissue

forms the inner layer of all bones

suture bone
small, flat, irregularly shaped bone that forms between the flat bones of the cranium

trabeculae
lamellae that are arranged as rods or plates

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 CHAPTER OVERVIEW

16: Circulatory System

Most animals are complex multicellular organisms that require a mechanism for transporting nutrients throughout their bodies and
removing waste products. The circulatory system has evolved over time from simple diffusion through cells in the early evolution
of animals to a complex network of blood vessels that reach all parts of the human body. This extensive network supplies the cells,
tissues, and organs with oxygen and nutrients, and removes carbon dioxide and waste, which are byproducts of respiration.
16.1: Prelude to the Circulatory System
16.2: Overview of the Circulatory System
16.3: Components of the Blood
16.4: Mammalian Heart and Blood Vessels
16.5: Blood Flow and Blood Pressure Regulation
16.E: The Circulatory System (Exercises)

Thumbnail: The human heart. (CC-BY 4.0 / modified from original; OpenStax).

Contributors and Attributions

Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski
(Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute
of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY
4.0; Download for free at [Link]

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1
16.1: Prelude to the Circulatory System
Most animals are complex multicellular organisms that require a mechanism for transporting nutrients throughout their bodies and
removing waste products. The circulatory system has evolved over time from simple diffusion through cells in the early evolution
of animals to a complex network of blood vessels that reach all parts of the human body. This extensive network supplies the cells,
tissues, and organs with oxygen and nutrients, and removes carbon dioxide and waste, which are byproducts of respiration.

Figure 16.1.1 : Just as highway systems transport people and goods through a complex network, the circulatory system transports
nutrients, gases, and wastes throughout the animal body. (credit: modification of work by Andrey Belenko)
At the core of the human circulatory system is the heart. The size of a clenched fist, the human heart is protected beneath the rib
cage. Made of specialized and unique cardiac muscle, it pumps blood throughout the body and to the heart itself. Heart contractions
are driven by intrinsic electrical impulses that the brain and endocrine hormones help to regulate. Understanding the heart’s basic
anatomy and function is important to understanding the body’s circulatory and respiratory systems.
Gas exchange is one essential function of the circulatory system. A circulatory system is not needed in organisms with no
specialized respiratory organs because oxygen and carbon dioxide diffuse directly between their body tissues and the external
environment. However, in organisms that possess lungs and gills, oxygen must be transported from these specialized respiratory
organs to the body tissues via a circulatory system. Therefore, circulatory systems have had to evolve to accommodate the great
diversity of body sizes and body types present among animals.

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16.2: Overview of the Circulatory System
Skills to Develop
Describe an open and closed circulatory system
Describe interstitial fluid and hemolymph
Compare and contrast the organization and evolution of the vertebrate circulatory system.

In all animals, except a few simple types, the circulatory system is used to transport nutrients and gases through the body. Simple
diffusion allows some water, nutrient, waste, and gas exchange into primitive animals that are only a few cell layers thick; however,
bulk flow is the only method by which the entire body of larger more complex organisms is accessed.

Circulatory System Architecture

The circulatory system is effectively a network of cylindrical vessels: the arteries, veins, and capillaries that emanate from a pump,
the heart. In all vertebrate organisms, as well as some invertebrates, this is a closed-loop system, in which the blood is not free in a
cavity. In a closed circulatory system, blood is contained inside blood vessels and circulates unidirectionally from the heart around
the systemic circulatory route, then returns to the heart again, as illustrated in Figure 16.2.1a. As opposed to a closed system,
arthropods—including insects, crustaceans, and most mollusks—have an open circulatory system, as illustrated in Figure 16.2.1b.
In an open circulatory system, the blood is not enclosed in the blood vessels but is pumped into a cavity called a hemocoel and is
called hemolymph because the blood mixes with the interstitial fluid. As the heart beats and the animal moves, the hemolymph
circulates around the organs within the body cavity and then reenters the hearts through openings called ostia. This movement
allows for gas and nutrient exchange. An open circulatory system does not use as much energy as a closed system to operate or to
maintain; however, there is a trade-off with the amount of blood that can be moved to metabolically active organs and tissues that
require high levels of oxygen. In fact, one reason that insects with wing spans of up to two feet wide (70 cm) are not around today
is probably because they were outcompeted by the arrival of birds 150 million years ago. Birds, having a closed circulatory system,
are thought to have moved more agilely, allowing them to get food faster and possibly to prey on the insects.

Figure 16.2.1 : In (a) closed circulatory systems, the heart pumps blood through vessels that are separate from the interstitial fluid
of the body. Most vertebrates and some invertebrates, like this annelid earthworm, have a closed circulatory system. In (b) open
circulatory systems, a fluid called hemolymph is pumped through a blood vessel that empties into the body cavity. Hemolymph
returns to the blood vessel through openings called ostia. Arthropods like this bee and most mollusks have open circulatory
systems.

Circulatory System Variation in Animals

The circulatory system varies from simple systems in invertebrates to more complex systems in vertebrates. The simplest animals,
such as the sponges (Porifera) and rotifers (Rotifera), do not need a circulatory system because diffusion allows adequate exchange
of water, nutrients, and waste, as well as dissolved gases, as shown in Figure 16.2.2a. Organisms that are more complex but still
only have two layers of cells in their body plan, such as jellies (Cnidaria) and comb jellies (Ctenophora) also use diffusion through
their epidermis and internally through the gastrovascular compartment. Both their internal and external tissues are bathed in an

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aqueous environment and exchange fluids by diffusion on both sides, as illustrated in Figure 16.2.2b. Exchange of fluids is assisted
by the pulsing of the jellyfish body.

Figure 16.2.2 : Simple animals consisting of a single cell layer such as the (a) sponge or only a few cell layers such as the (b)
jellyfish do not have a circulatory system. Instead, gases, nutrients, and wastes are exchanged by diffusion.
For more complex organisms, diffusion is not efficient for cycling gases, nutrients, and waste effectively through the body;
therefore, more complex circulatory systems evolved. Most arthropods and many mollusks have open circulatory systems. In an
open system, an elongated beating heart pushes the hemolymph through the body and muscle contractions help to move fluids. The
larger more complex crustaceans, including lobsters, have developed arterial-like vessels to push blood through their bodies, and
the most active mollusks, such as squids, have evolved a closed circulatory system and are able to move rapidly to catch prey.
Closed circulatory systems are a characteristic of vertebrates; however, there are significant differences in the structure of the heart
and the circulation of blood between the different vertebrate groups due to adaptation during evolution and associated differences
in anatomy. Figure 16.2.3 illustrates the basic circulatory systems of some vertebrates: fish, amphibians, reptiles, and mammals.

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Figure 16.2.3 : (a) Fish have the simplest circulatory systems of the vertebrates: blood flows unidirectionally from the two-
chambered heart through the gills and then the rest of the body. (b) Amphibians have two circulatory routes: one for oxygenation of
the blood through the lungs and skin, and the other to take oxygen to the rest of the body. The blood is pumped from a three-
chambered heart with two atria and a single ventricle. (c) Reptiles also have two circulatory routes; however, blood is only
oxygenated through the lungs. The heart is three chambered, but the ventricles are partially separated so some mixing of
oxygenated and deoxygenated blood occurs except in crocodilians and birds. (d) Mammals and birds have the most efficient heart

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 with four chambers that completely separate the oxygenated and deoxygenated blood; it pumps only oxygenated blood through the
As illustrated
body andindeoxygenated
Figure 16.2.3 a Fish
blood have
to the a single circuit for blood flow and a two-chambered heart that has only a single atrium
lungs.
and a single ventricle. The atrium collects blood that has returned from the body and the ventricle pumps the blood to the gills
where gas exchange occurs and the blood is re-oxygenated; this is called gill circulation. The blood then continues through the rest
of the body before arriving back at the atrium; this is called systemic circulation. This unidirectional flow of blood produces a
gradient of oxygenated to deoxygenated blood around the fish’s systemic circuit. The result is a limit in the amount of oxygen that
can reach some of the organs and tissues of the body, reducing the overall metabolic capacity of fish.
In amphibians, reptiles, birds, and mammals, blood flow is directed in two circuits: one through the lungs and back to the heart,
which is called pulmonary circulation, and the other throughout the rest of the body and its organs including the brain (systemic
circulation). In amphibians, gas exchange also occurs through the skin during pulmonary circulation and is referred to as
pulmocutaneous circulation.
As shown in Figure 16.2.3b, amphibians have a three-chambered heart that has two atria and one ventricle rather than the two-
chambered heart of fish. The two atria (superior heart chambers) receive blood from the two different circuits (the lungs and the
systems), and then there is some mixing of the blood in the heart’s ventricle (inferior heart chamber), which reduces the efficiency
of oxygenation. The advantage to this arrangement is that high pressure in the vessels pushes blood to the lungs and body. The
mixing is mitigated by a ridge within the ventricle that diverts oxygen-rich blood through the systemic circulatory system and
deoxygenated blood to the pulmocutaneous circuit. For this reason, amphibians are often described as having double circulation.
Most reptiles also have a three-chambered heart similar to the amphibian heart that directs blood to the pulmonary and systemic
circuits, as shown in Figure 16.2.3c. The ventricle is divided more effectively by a partial septum, which results in less mixing of
oxygenated and deoxygenated blood. Some reptiles (alligators and crocodiles) are the most primitive animals to exhibit a four-
chambered heart. Crocodilians have a unique circulatory mechanism where the heart shunts blood from the lungs toward the
stomach and other organs during long periods of submergence, for instance, while the animal waits for prey or stays underwater
waiting for prey to rot. One adaptation includes two main arteries that leave the same part of the heart: one takes blood to the lungs
and the other provides an alternate route to the stomach and other parts of the body. Two other adaptations include a hole in the
heart between the two ventricles, called the foramen of Panizza, which allows blood to move from one side of the heart to the other,
and specialized connective tissue that slows the blood flow to the lungs. Together these adaptations have made crocodiles and
alligators one of the most evolutionarily successful animal groups on earth.
In mammals and birds, the heart is also divided into four chambers: two atria and two ventricles, as illustrated in Figure 40.1.3d.
The oxygenated blood is separated from the deoxygenated blood, which improves the efficiency of double circulation and is
probably required for the warm-blooded lifestyle of mammals and birds. The four-chambered heart of birds and mammals evolved
independently from a three-chambered heart. The independent evolution of the same or a similar biological trait is referred to as
convergent evolution.

Summary
In most animals, the circulatory system is used to transport blood through the body. Some primitive animals use diffusion for the
exchange of water, nutrients, and gases. However, complex organisms use the circulatory system to carry gases, nutrients, and
waste through the body. Circulatory systems may be open (mixed with the interstitial fluid) or closed (separated from the interstitial
fluid). Closed circulatory systems are a characteristic of vertebrates; however, there are significant differences in the structure of
the heart and the circulation of blood between the different vertebrate groups due to adaptions during evolution and associated
differences in anatomy. Fish have a two-chambered heart with unidirectional circulation. Amphibians have a three-chambered
heart, which has some mixing of the blood, and they have double circulation. Most non-avian reptiles have a three-chambered
heart, but have little mixing of the blood; they have double circulation. Mammals and birds have a four-chambered heart with no
mixing of the blood and double circulation.

Glossary
atrium
(plural: atria) chamber of the heart that receives blood from the veins and sends blood to the ventricles

closed circulatory system

system in which the blood is separated from the bodily interstitial fluid and contained in blood vessels

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double circulation
flow of blood in two circuits: the pulmonary circuit through the lungs and the systemic circuit through the organs and body

gill circulation
circulatory system that is specific to animals with gills for gas exchange; the blood flows through the gills for oxygenation

hemocoel
cavity into which blood is pumped in an open circulatory system

hemolymph
mixture of blood and interstitial fluid that is found in insects and other arthropods as well as most mollusks

interstitial fluid
fluid between cells

open circulatory system

system in which the blood is mixed with interstitial fluid and directly covers the organs

ostium
(plural: ostia) holes between blood vessels that allow the movement of hemolymph through the body of insects, arthropods, and
mollusks with open circulatory systems

pulmocutaneous circulation
circulatory system in amphibians; the flow of blood to the lungs and the moist skin for gas exchange

pulmonary circulation
flow of blood away from the heart through the lungs where oxygenation occurs and then returns to the heart again

systemic circulation
flow of blood away from the heart to the brain, liver, kidneys, stomach, and other organs, the limbs, and the muscles of the
body, and then the return of this blood to the heart

unidirectional circulation
flow of blood in a single circuit; occurs in fish where the blood flows through the gills, then past the organs and the rest of the
body, before returning to the heart

ventricle
(heart) large inferior chamber of the heart that pumps blood into arteries

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16.3: Components of the Blood
Skills to Develop
List the basic components of the blood
Compare red and white blood cells
Describe blood plasma and serum

Hemoglobin is responsible for distributing oxygen, and to a lesser extent, carbon dioxide, throughout the circulatory systems of
humans, vertebrates, and many invertebrates. The blood is more than the proteins, though. Blood is actually a term used to describe
the liquid that moves through the vessels and includes plasma (the liquid portion, which contains water, proteins, salts, lipids, and
glucose) and the cells (red and white cells) and cell fragments called platelets. Blood plasma is actually the dominant component of
blood and contains the water, proteins, electrolytes, lipids, and glucose. The cells are responsible for carrying the gases (red cells)
and immune the response (white). The platelets are responsible for blood clotting. Interstitial fluid that surrounds cells is separate
from the blood, but in hemolymph, they are combined. In humans, cellular components make up approximately 45 percent of the
blood and the liquid plasma 55 percent. Blood is 20 percent of a person’s extracellular fluid and eight percent of weight.

The Role of Blood in the Body

Blood, like the human blood illustrated in Figure 16.3.1 is important for regulation of the body’s systems and homeostasis. Blood
helps maintain homeostasis by stabilizing pH, temperature, osmotic pressure, and by eliminating excess heat. Blood supports
growth by distributing nutrients and hormones, and by removing waste. Blood plays a protective role by transporting clotting
factors and platelets to prevent blood loss and transporting the disease-fighting agents or white blood cells to sites of infection.

Figure 16.3.1 : The cells and cellular components of human blood are shown. Red blood cells deliver oxygen to the cells and
remove carbon dioxide. White blood cells—including neutrophils, monocytes, lymphocytes, eosinophils, and basophils—are
involved in the immune response. Platelets form clots that prevent blood loss after injury.

Red Blood Cells

Red blood cells, or erythrocytes (erythro- = “red”; -cyte = “cell”), are specialized cells that circulate through the body delivering
oxygen to cells; they are formed from stem cells in the bone marrow. In mammals, red blood cells are small biconcave cells that at
maturity do not contain a nucleus or mitochondria and are only 7–8 µm in size. In birds and non-avian reptiles, a nucleus is still
maintained in red blood cells.

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The red coloring of blood comes from the iron-containing protein hemoglobin, illustrated in Figure 16.3.2a. The principal job of
this protein is to carry oxygen, but it also transports carbon dioxide as well. Hemoglobin is packed into red blood cells at a rate of
about 250 million molecules of hemoglobin per cell. Each hemoglobin molecule binds four oxygen molecules so that each red
blood cell carries one billion molecules of oxygen. There are approximately 25 trillion red blood cells in the five liters of blood in
the human body, which could carry up to 25 sextillion (25 × 1021) molecules of oxygen in the body at any time. In mammals, the
lack of organelles in erythrocytes leaves more room for the hemoglobin molecules, and the lack of mitochondria also prevents use
of the oxygen for metabolic respiration. Only mammals have anucleated red blood cells, and some mammals (camels, for instance)
even have nucleated red blood cells. The advantage of nucleated red blood cells is that these cells can undergo mitosis. Anucleated
red blood cells metabolize anaerobically (without oxygen), making use of a primitive metabolic pathway to produce ATP and
increase the efficiency of oxygen transport.
Not all organisms use hemoglobin as the method of oxygen transport. Invertebrates that utilize hemolymph rather than blood use
different pigments to bind to the oxygen. These pigments use copper or iron to the oxygen. Invertebrates have a variety of other
respiratory pigments. Hemocyanin, a blue-green, copper-containing protein, illustrated in Figure 16.3.2b is found in mollusks,
crustaceans, and some of the arthropods. Chlorocruorin, a green-colored, iron-containing pigment is found in four families of
polychaete tubeworms. Hemerythrin, a red, iron-containing protein is found in some polychaete worms and annelids and is
illustrated in Figure 16.3.2c. Despite the name, hemerythrin does not contain a heme group and its oxygen-carrying capacity is
poor compared to hemoglobin.

Figure 16.3.2 : In most vertebrates, (a) hemoglobin delivers oxygen to the body and removes some carbon dioxide. Hemoglobin is
composed of four protein subunits, two alpha chains and two beta chains, and a heme group that has iron associated with it. The
iron reversibly associates with oxygen, and in so doing is oxidized from Fe2+ to Fe3+. In most mollusks and some arthropods, (b)
hemocyanin delivers oxygen. Unlike hemoglobin, hemolymph is not carried in blood cells, but floats free in the hemolymph.
Copper instead of iron binds the oxygen, giving the hemolymph a blue-green color. In annelids, such as the earthworm, and some
other invertebrates, (c) hemerythrin carries oxygen. Like hemoglobin, hemerythrin is carried in blood cells and has iron associated
with it, but despite its name, hemerythrin does not contain heme.
The small size and large surface area of red blood cells allows for rapid diffusion of oxygen and carbon dioxide across the plasma
membrane. In the lungs, carbon dioxide is released and oxygen is taken in by the blood. In the tissues, oxygen is released from the
blood and carbon dioxide is bound for transport back to the lungs. Studies have found that hemoglobin also binds nitrous oxide
(NO). NO is a vasodilator that relaxes the blood vessels and capillaries and may help with gas exchange and the passage of red
blood cells through narrow vessels. Nitroglycerin, a heart medication for angina and heart attacks, is converted to NO to help relax
the blood vessels and increase oxygen flow through the body.
A characteristic of red blood cells is their glycolipid and glycoprotein coating; these are lipids and proteins that have carbohydrate
molecules attached. In humans, the surface glycoproteins and glycolipids on red blood cells vary between individuals, producing

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the different blood types, such as A, B, and O. Red blood cells have an average life span of 120 days, at which time they are broken
down and recycled in the liver and spleen by phagocytic macrophages, a type of white blood cell.

White Blood Cells

White blood cells, also called leukocytes (leuko = white), make up approximately one percent by volume of the cells in blood. The
role of white blood cells is very different than that of red blood cells: they are primarily involved in the immune response to
identify and target pathogens, such as invading bacteria, viruses, and other foreign organisms. White blood cells are formed
continually; some only live for hours or days, but some live for years.
The morphology of white blood cells differs significantly from red blood cells. They have nuclei and do not contain hemoglobin.
The different types of white blood cells are identified by their microscopic appearance after histologic staining, and each has a
different specialized function. The two main groups, both illustrated in Figure 16.3.3 are the granulocytes, which include the
neutrophils, eosinophils, and basophils, and the agranulocytes, which include the monocytes and lymphocytes.

Figure 16.3.3 : (a) Granulocytes—including neutrophils, eosinophils and basophils—are characterized by a lobed nucleus and
granular inclusions in the cytoplasm. Granulocytes are typically first-responders during injury or infection. (b) Agranulocytes
include lymphocytes and monocytes. Lymphocytes, including B and T cells, are responsible for adaptive immune response.
Monocytes differentiate into macrophages and dendritic cells, which in turn respond to infection or injury.
Granulocytes contain granules in their cytoplasm; the agranulocytes are so named because of the lack of granules in their
cytoplasm. Some leukocytes become macrophages that either stay at the same site or move through the blood stream and gather at
sites of infection or inflammation where they are attracted by chemical signals from foreign particles and damaged cells.
Lymphocytes are the primary cells of the immune system and include B cells, T cells, and natural killer cells. B cells destroy
bacteria and inactivate their toxins. They also produce antibodies. T cells attack viruses, fungi, some bacteria, transplanted cells,
and cancer cells. T cells attack viruses by releasing toxins that kill the viruses. Natural killer cells attack a variety of infectious
microbes and certain tumor cells.
One reason that HIV poses significant management challenges is because the virus directly targets T cells by gaining entry through
a receptor. Once inside the cell, HIV then multiplies using the T cell’s own genetic machinery. After the HIV virus replicates, it is
transmitted directly from the infected T cell to macrophages. The presence of HIV can remain unrecognized for an extensive period
of time before full disease symptoms develop.

Platelets and Coagulation Factors

Blood must clot to heal wounds and prevent excess blood loss. Small cell fragments called platelets (thrombocytes) are attracted to
the wound site where they adhere by extending many projections and releasing their contents. These contents activate other
platelets and also interact with other coagulation factors, which convert fibrinogen, a water-soluble protein present in blood serum
into fibrin (a non-water soluble protein), causing the blood to clot. Many of the clotting factors require vitamin K to work, and
vitamin K deficiency can lead to problems with blood clotting. Many platelets converge and stick together at the wound site
forming a platelet plug (also called a fibrin clot), as illustrated in Figure 16.3.4b. The plug or clot lasts for a number of days and
stops the loss of blood. Platelets are formed from the disintegration of larger cells called megakaryocytes, like that shown in Figure
16.3.4a. For each megakaryocyte, 2000–3000 platelets are formed with 150,000 to 400,000 platelets present in each cubic

millimeter of blood. Each platelet is disc shaped and 2–4 μm in diameter. They contain many small vesicles but do not contain a
nucleus.

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 Figure 16.3.4 : (a) Platelets are formed from large cells called megakaryocytes. The megakaryocyte breaks up into thousands of
fragments that become platelets. (b) Platelets are required for clotting of the blood. The platelets collect at a wound site in
conjunction with other clotting factors, such as fibrinogen, to form a fibrin clot that prevents blood loss and allows the wound to
heal.

Plasma and Serum

The liquid component of blood is called plasma, and it is separated by spinning or centrifuging the blood at high rotations (3000
rpm or higher). The blood cells and platelets are separated by centrifugal forces to the bottom of a specimen tube. The upper liquid
layer, the plasma, consists of 90 percent water along with various substances required for maintaining the body’s pH, osmotic load,
and for protecting the body. The plasma also contains the coagulation factors and antibodies.
The plasma component of blood without the coagulation factors is called the serum. Serum is similar to interstitial fluid in which
the correct composition of key ions acting as electrolytes is essential for normal functioning of muscles and nerves. Other
components in the serum include proteins that assist with maintaining pH and osmotic balance while giving viscosity to the blood.
The serum also contains antibodies, specialized proteins that are important for defense against viruses and bacteria. Lipids,
including cholesterol, are also transported in the serum, along with various other substances including nutrients, hormones,
metabolic waste, plus external substances, such as, drugs, viruses, and bacteria.
Human serum albumin is the most abundant protein in human blood plasma and is synthesized in the liver. Albumin, which
constitutes about half of the blood serum protein, transports hormones and fatty acids, buffers pH, and maintains osmotic pressures.
Immunoglobin is a protein antibody produced in the mucosal lining and plays an important role in antibody mediated immunity.

Evolution Connection: Blood Types

Related to Proteins on the Surface of the Red Blood Cells Red blood cells are coated in antigens made of glycolipids and
glycoproteins. The composition of these molecules is determined by genetics, which have evolved over time. In humans, the
different surface antigens are grouped into 24 different blood groups with more than 100 different antigens on each red blood
cell. The two most well known blood groups are the ABO, shown in Figure 16.3.5, and Rh systems. The surface antigens in
the ABO blood group are glycolipids, called antigen A and antigen B. People with blood type A have antigen A, those with
blood type B have antigen B, those with blood type AB have both antigens, and people with blood type O have neither antigen.
Antibodies called agglutinougens are found in the blood plasma and react with the A or B antigens, if the two are mixed. When
type A and type B blood are combined, agglutination (clumping) of the blood occurs because of antibodies in the plasma that
bind with the opposing antigen; this causes clots that coagulate in the kidney causing kidney failure. Type O blood has neither
A or B antigens, and therefore, type O blood can be given to all blood types. Type O negative blood is the universal donor.

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 Type AB positive blood is the universal acceptor because it has both A and B antigen. The ABO blood groups were discovered
in 1900 and 1901 by Karl Landsteiner at the University of Vienna.
The Rh blood group was first discovered in Rhesus monkeys. Most people have the Rh antigen (Rh+) and do not have anti-Rh
antibodies in their blood. The few people who do not have the Rh antigen and are Rh– can develop anti-Rh antibodies if
exposed to Rh+ blood. This can happen after a blood transfusion or after an Rh– woman has an Rh+ baby. The first exposure
does not usually cause a reaction; however, at the second exposure, enough antibodies have built up in the blood to produce a
reaction that causes agglutination and breakdown of red blood cells. An injection can prevent this reaction.

Figure 16.3.5 : Human red blood cells may have either type A or B glycoproteins on their surface, both glycoproteins combined
(AB), or neither (O). The glycoproteins serve as antigens and can elicit an immune response in a person who receives a
transfusion containing unfamiliar antigens. Type O blood, which has no A or B antigens, does not elicit an immune response
when injected into a person of any blood type. Thus, O is considered the universal donor. Persons with type AB blood can
accept blood from any blood type, and type AB is considered the universal acceptor.

Summary
Specific components of the blood include red blood cells, white blood cells, platelets, and the plasma, which contains coagulation
factors and serum. Blood is important for regulation of the body’s pH, temperature, osmotic pressure, the circulation of nutrients
and removal of waste, the distribution of hormones from endocrine glands, and the elimination of excess heat; it also contains
components for blood clotting. Red blood cells are specialized cells that contain hemoglobin and circulate through the body
delivering oxygen to cells. White blood cells are involved in the immune response to identify and target invading bacteria, viruses,
and other foreign organisms; they also recycle waste components, such as old red blood cells. Platelets and blood clotting factors
cause the change of the soluble protein fibrinogen to the insoluble protein fibrin at a wound site forming a plug. Plasma consists of
90 percent water along with various substances, such as coagulation factors and antibodies. The serum is the plasma component of
the blood without the coagulation factors.

Glossary
plasma
liquid component of blood that is left after the cells are removed

platelet
(also, thrombocyte) small cellular fragment that collects at wounds, cross-reacts with clotting factors, and forms a plug to
prevent blood loss

red blood cell

small (7–8 μm) biconcave cell without mitochondria (and in mammals without nuclei) that is packed with hemoglobin, giving
the cell its red color; transports oxygen through the body

serum
plasma without the coagulation factors

white blood cell

large (30 μm) cell with nuclei of which there are many types with different roles including the protection of the body from
viruses and bacteria, and cleaning up dead cells and other waste

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40.2: Components of the Blood by OpenStax is licensed CC BY 4.0.

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16.4: Mammalian Heart and Blood Vessels
Skills to Develop
Describe the structure of the heart and explain how cardiac muscle is different from other muscles
Describe the cardiac cycle
Explain the structure of arteries, veins, and capillaries, and how blood flows through the body

The heart is a complex muscle that pumps blood through the three divisions of the circulatory system: the coronary (vessels that
serve the heart), pulmonary (heart and lungs), and systemic (systems of the body), as shown in Figure 16.4.1. Coronary circulation
intrinsic to the heart takes blood directly from the main artery (aorta) coming from the heart. For pulmonary and systemic
circulation, the heart has to pump blood to the lungs or the rest of the body, respectively. In vertebrates, the lungs are relatively
close to the heart in the thoracic cavity. The shorter distance to pump means that the muscle wall on the right side of the heart is not
as thick as the left side which must have enough pressure to pump blood all the way to your big toe.

Figure 16.4.1 : The mammalian circulatory system is divided into three circuits: the systemic circuit, the pulmonary circuit, and the
coronary circuit. Blood is pumped from veins of the systemic circuit into the right atrium of the heart, then into the right ventricle.
Blood then enters the pulmonary circuit, and is oxygenated by the lungs. From the pulmonary circuit, blood re-enters the heart
through the left atrium. From the left ventricle, blood re-enters the systemic circuit through the aorta and is distributed to the rest of
the body. The coronary circuit, which provides blood to the heart, is not shown.

Exercise
Which of the following statements about the circulatory system is false?
A. Blood in the pulmonary vein is deoxygenated.
B. Blood in the inferior vena cava is deoxygenated.
C. Blood in the pulmonary artery is deoxygenated.
D. Blood in the aorta is oxygenated.

Answer
C

Structure of the Heart

The heart muscle is asymmetrical as a result of the distance blood must travel in the pulmonary and systemic circuits. Since the
right side of the heart sends blood to the pulmonary circuit it is smaller than the left side which must send blood out to the whole
body in the systemic circuit, as shown in Figure 16.4.2. In humans, the heart is about the size of a clenched fist; it is divided into

Access for free at OpenStax 16.4.1 [Link]

four chambers: two atria and two ventricles. There is one atrium and one ventricle on the right side and one atrium and one
ventricle on the left side. The atria are the chambers that receive blood, and the ventricles are the chambers that pump blood. The
right atrium receives deoxygenated blood from the superior vena cava, which drains blood from the jugular vein that comes from
the brain and from the veins that come from the arms, as well as from the inferior vena cava which drains blood from the veins that
come from the lower organs and the legs. In addition, the right atrium receives blood from the coronary sinus which drains
deoxygenated blood from the heart itself. This deoxygenated blood then passes to the right ventricle through the atrioventricular
valve or the tricuspid valve, a flap of connective tissue that opens in only one direction to prevent the backflow of blood.
The valve separating the chambers on the left side of the heart valve is called the biscuspid or mitral valve. After it is filled, the
right ventricle pumps the blood through the pulmonary arteries, by-passing the semilunar valve (or pulmonic valve) to the lungs for
re-oxygenation. After blood passes through the pulmonary arteries, the right semilunar valves close preventing the blood from
flowing backwards into the right ventricle. The left atrium then receives the oxygen-rich blood from the lungs via the pulmonary
veins. This blood passes through the bicuspid valve or mitral valve (the atrioventricular valve on the left side of the heart) to the left
ventricle where the blood is pumped out through aorta, the major artery of the body, taking oxygenated blood to the organs and
muscles of the body. Once blood is pumped out of the left ventricle and into the aorta, the aortic semilunar valve (or aortic valve)
closes preventing blood from flowing backward into the left ventricle. This pattern of pumping is referred to as double circulation
and is found in all mammals.

Access for free at OpenStax 16.4.2 [Link]

Figure 16.4.2 : (a) The heart is primarily made of a thick muscle layer, called the myocardium, surrounded by membranes. One-way
valves separate the four chambers. (b) Blood vessels of the coronary system, including the coronary arteries and veins, keep the
heart musculature oxygenated.

Access for free at OpenStax 16.4.3 [Link]

 Exercise
Which of the following statements about the heart is false?
A. The mitral valve separates the left ventricle from the left atrium.
B. Blood travels through the bicuspid valve to the left atrium.
C. Both the aortic and the pulmonary valves are semilunar valves.
D. The mitral valve is an atrioventricular valve.

Answer
B

The heart is composed of three layers; the epicardium, the myocardium, and the endocardium, illustrated in Figure 16.4.2. The
inner wall of the heart has a lining called the endocardium. The myocardium consists of the heart muscle cells that make up the
middle layer and the bulk of the heart wall. The outer layer of cells is called the epicardium, of which the second layer is a
membranous layered structure called the pericardium that surrounds and protects the heart; it allows enough room for vigorous
pumping but also keeps the heart in place to reduce friction between the heart and other structures.
The heart has its own blood vessels that supply the heart muscle with blood. The coronary arteries branch from the aorta and
surround the outer surface of the heart like a crown. They diverge into capillaries where the heart muscle is supplied with oxygen
before converging again into the coronary veins to take the deoxygenated blood back to the right atrium where the blood will be re-
oxygenated through the pulmonary circuit. The heart muscle will die without a steady supply of blood. Atherosclerosis is the
blockage of an artery by the buildup of fatty plaques. Because of the size (narrow) of the coronary arteries and their function in
serving the heart itself, atherosclerosis can be deadly in these arteries. The slowdown of blood flow and subsequent oxygen
deprivation that results from atherosclerosis causes severe pain, known as angina, and complete blockage of the arteries will cause
myocardial infarction: the death of cardiac muscle tissue, commonly known as a heart attack.

The Cardiac Cycle

The main purpose of the heart is to pump blood through the body; it does so in a repeating sequence called the cardiac cycle. The
cardiac cycle is the coordination of the filling and emptying of the heart of blood by electrical signals that cause the heart muscles
to contract and relax. The human heart beats over 100,000 times per day. In each cardiac cycle, the heart contracts (systole),
pushing out the blood and pumping it through the body; this is followed by a relaxation phase (diastole), where the heart fills with
blood, as illustrated in Figure 16.4.3. The atria contract at the same time, forcing blood through the atrioventricular valves into the
ventricles. Closing of the atrioventricular valves produces a monosyllabic “lup” sound. Following a brief delay, the ventricles
contract at the same time forcing blood through the semilunar valves into the aorta and the artery transporting blood to the lungs
(via the pulmonary artery). Closing of the semilunar valves produces a monosyllabic “dup” sound.

Access for free at OpenStax 16.4.4 [Link]

 Figure 16.4.3 : During (a) cardiac diastole, the heart muscle is relaxed and blood flows into the heart. During (b) atrial systole, the
atria contract, pushing blood into the ventricles. During (c) atrial diastole, the ventricles contract, forcing blood out of the heart.
The pumping of the heart is a function of the cardiac muscle cells, or cardiomyocytes, that make up the heart muscle.
Cardiomyocytes, shown in Figure 16.4.4, are distinctive muscle cells that are striated like skeletal muscle but pump rhythmically
and involuntarily like smooth muscle; they are connected by intercalated disks exclusive to cardiac muscle. They are self-
stimulated for a period of time and isolated cardiomyocytes will beat if given the correct balance of nutrients and electrolytes.

Figure 16.4.4 : Cardiomyocytes are striated muscle cells found in cardiac tissue. (credit: modification of work by Dr. S. Girod,
Anton Becker; scale-bar data from Matt Russell)

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The autonomous beating of cardiac muscle cells is regulated by the heart’s internal pacemaker that uses electrical signals to time
the beating of the heart. The electrical signals and mechanical actions, illustrated in Figure 16.4.5, are intimately intertwined. The
internal pacemaker starts at the sinoatrial (SA) node, which is located near the wall of the right atrium. Electrical charges
spontaneously pulse from the SA node causing the two atria to contract in unison. The pulse reaches a second node, called the
atrioventricular (AV) node, between the right atrium and right ventricle where it pauses for approximately 0.1 second before
spreading to the walls of the ventricles. From the AV node, the electrical impulse enters the bundle of His, then to the left and right
bundle branches extending through the interventricular septum. Finally, the Purkinje fibers conduct the impulse from the apex of
the heart up the ventricular myocardium, and then the ventricles contract. This pause allows the atria to empty completely into the
ventricles before the ventricles pump out the blood. The electrical impulses in the heart produce electrical currents that flow
through the body and can be measured on the skin using electrodes. This information can be observed as an electrocardiogram
(ECG)—a recording of the electrical impulses of the cardiac muscle.

Figure 16.4.5 : The beating of the heart is regulated by an electrical impulse that causes the characteristic reading of an ECG. The
signal is initiated at the sinoatrial valve. The signal then (a) spreads to the atria, causing them to contract. The signal is (b) delayed
at the atrioventricular node before it is passed on to the (c) heart apex. The delay allows the atria to relax before the (d) ventricles
contract. The final part of the ECG cycle prepares the heart for the next beat.

Link to Learning

Access for free at OpenStax 16.4.6 [Link]

 Your Heart's Conduction System

Visit this site and select the dropdown “Your Heart’s Electrical System” to see the heart’s “pacemaker” in action.

Arteries, Veins, and Capillaries

The blood from the heart is carried through the body by a complex network of blood vessels (Figure 16.4.6). Arteries take blood
away from the heart. The main artery is the aorta that branches into major arteries that take blood to different limbs and organs.
These major arteries include the carotid artery that takes blood to the brain, the brachial arteries that take blood to the arms, and the
thoracic artery that takes blood to the thorax and then into the hepatic, renal, and gastric arteries for the liver, kidney, and stomach,
respectively. The iliac artery takes blood to the lower limbs. The major arteries diverge into minor arteries, and then smaller vessels
called arterioles, to reach more deeply into the muscles and organs of the body.

Figure 16.4.6 : The major human arteries and veins are shown. (credit: modification of work by Mariana Ruiz Villareal)

Access for free at OpenStax 16.4.7 [Link]

Arterioles diverge into capillary beds. Capillary beds contain a large number (10 to 100) of capillaries that branch among the cells
and tissues of the body. Capillaries are narrow-diameter tubes that can fit red blood cells through in single file and are the sites for
the exchange of nutrients, waste, and oxygen with tissues at the cellular level. Fluid also crosses into the interstitial space from the
capillaries. The capillaries converge again into venules that connect to minor veins that finally connect to major veins that take
blood high in carbon dioxide back to the heart. Veins are blood vessels that bring blood back to the heart. The major veins drain
blood from the same organs and limbs that the major arteries supply. Fluid is also brought back to the heart via the lymphatic
system.
The structure of the different types of blood vessels reflects their function or layers. There are three distinct layers, or tunics, that
form the walls of blood vessels (Figure 16.4.7). The first tunic is a smooth, inner lining of endothelial cells that are in contact with
the red blood cells. The endothelial tunic is continuous with the endocardium of the heart. In capillaries, this single layer of cells is
the location of diffusion of oxygen and carbon dioxide between the endothelial cells and red blood cells, as well as the exchange
site via endocytosis and exocytosis. The movement of materials at the site of capillaries is regulated by vasoconstriction, narrowing
of the blood vessels, and vasodilation, widening of the blood vessels; this is important in the overall regulation of blood pressure.
Veins and arteries both have two further tunics that surround the endothelium: the middle tunic is composed of smooth muscle and
the outermost layer is connective tissue (collagen and elastic fibers). The elastic connective tissue stretches and supports the blood
vessels, and the smooth muscle layer helps regulate blood flow by altering vascular resistance through vasoconstriction and
vasodilation. The arteries have thicker smooth muscle and connective tissue than the veins to accommodate the higher pressure and
speed of freshly pumped blood. The veins are thinner walled as the pressure and rate of flow are much lower. In addition, veins are
structurally different than arteries in that veins have valves to prevent the backflow of blood. Because veins have to work against
gravity to get blood back to the heart, contraction of skeletal muscle assists with the flow of blood back to the heart.

Figure 16.4.7 : Arteries and veins consist of three layers: an outer tunica externa, a middle tunica media, and an inner tunica intima.
Capillaries consist of a single layer of epithelial cells, the tunica intima. (credit: modification of work by NCI, NIH)

Summary
The heart muscle pumps blood through three divisions of the circulatory system: coronary, pulmonary, and systemic. There is one
atrium and one ventricle on the right side and one atrium and one ventricle on the left side. The pumping of the heart is a function
of cardiomyocytes, distinctive muscle cells that are striated like skeletal muscle but pump rhythmically and involuntarily like
smooth muscle. The internal pacemaker starts at the sinoatrial node, which is located near the wall of the right atrium. Electrical
charges pulse from the SA node causing the two atria to contract in unison; then the pulse reaches the atrioventricular node
between the right atrium and right ventricle. A pause in the electric signal allows the atria to empty completely into the ventricles
before the ventricles pump out the blood. The blood from the heart is carried through the body by a complex network of blood
vessels; arteries take blood away from the heart, and veins bring blood back to the heart.

Access for free at OpenStax 16.4.8 [Link]

Glossary
angina
pain caused by partial blockage of the coronary arteries by the buildup of plaque and lack of oxygen to the heart muscle

aorta
major artery of the body that takes blood away from the heart

arteriole
small vessel that connects an artery to a capillary bed

artery
blood vessel that takes blood away from the heart

atherosclerosis
buildup of fatty plaques in the coronary arteries in the heart

atrioventricular valve
one-way membranous flap of connective tissue between the atrium and the ventricle in the right side of the heart; also known as
tricuspid valve

bicuspid valve
(also, mitral valve; left atrioventricular valve) one-way membranous flap between the atrium and the ventricle in the left side of
the heart

capillary
smallest blood vessel that allows the passage of individual blood cells and the site of diffusion of oxygen and nutrient exchange

capillary bed
large number of capillaries that converge to take blood to a particular organ or tissue

cardiac cycle
filling and emptying the heart of blood by electrical signals that cause the heart muscles to contract and relax

cardiomyocyte
specialized heart muscle cell that is striated but contracts involuntarily like smooth muscle

coronary artery
vessel that supplies the heart tissue with blood

coronary vein
vessel that takes blood away from the heart tissue back to the chambers in the heart

diastole
relaxation phase of the cardiac cycle when the heart is relaxed and the ventricles are filling with blood

electrocardiogram (ECG)
recording of the electrical impulses of the cardiac muscle

endocardium
innermost layer of tissue in the heart

epicardium
outermost tissue layer of the heart

inferior vena cava

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 drains blood from the veins that come from the lower organs and the legs

myocardial infarction
(also, heart attack) complete blockage of the coronary arteries and death of the cardiac muscle tissue

myocardium
heart muscle cells that make up the middle layer and the bulk of the heart wall

pericardium
membrane layer protecting the heart; also part of the epicardium

semilunar valve
membranous flap of connective tissue between the aorta and a ventricle of the heart (the aortic or pulmonary semilunar valves)

sinoatrial (SA) node

the heart’s internal pacemaker; located near the wall of the right atrium

superior vena cava

drains blood from the jugular vein that comes from the brain and from the veins that come from the arms

systole
contraction phase of cardiac cycle when the ventricles are pumping blood into the arteries

tricuspid valve
one-way membranous flap of connective tissue between the atrium and the ventricle in the right side of the heart; also known as
atrioventricular valve

vasoconstriction
narrowing of a blood vessel

vasodilation
widening of a blood vessel

vein
blood vessel that brings blood back to the heart

vena cava
major vein of the body returning blood from the upper and lower parts of the body; see the superior vena cava and inferior vena
cava

venule
blood vessel that connects a capillary bed to a vein

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16.5: Blood Flow and Blood Pressure Regulation
Skills to Develop
Describe the system of blood flow through the body
Describe how blood pressure is regulated

Blood pressure (BP) is the pressure exerted by blood on the walls of a blood vessel that helps to push blood through the body.
Systolic blood pressure measures the amount of pressure that blood exerts on vessels while the heart is beating. The optimal
systolic blood pressure is 120 mmHg. Diastolic blood pressure measures the pressure in the vessels between heartbeats. The
optimal diastolic blood pressure is 80 mmHg. Many factors can affect blood pressure, such as hormones, stress, exercise, eating,
sitting, and standing. Blood flow through the body is regulated by the size of blood vessels, by the action of smooth muscle, by
one-way valves, and by the fluid pressure of the blood itself.

How Blood Flows Through the Body

Blood is pushed through the body by the action of the pumping heart. With each rhythmic pump, blood is pushed under high
pressure and velocity away from the heart, initially along the main artery, the aorta. In the aorta, the blood travels at 30 cm/sec. As
blood moves into the arteries, arterioles, and ultimately to the capillary beds, the rate of movement slows dramatically to about
0.026 cm/sec, one-thousand times slower than the rate of movement in the aorta. While the diameter of each individual arteriole
and capillary is far narrower than the diameter of the aorta, and according to the law of continuity, fluid should travel faster through
a narrower diameter tube, the rate is actually slower due to the overall diameter of all the combined capillaries being far greater
than the diameter of the individual aorta.
The slow rate of travel through the capillary beds, which reach almost every cell in the body, assists with gas and nutrient exchange
and also promotes the diffusion of fluid into the interstitial space. After the blood has passed through the capillary beds to the
venules, veins, and finally to the main venae cavae, the rate of flow increases again but is still much slower than the initial rate in
the aorta. Blood primarily moves in the veins by the rhythmic movement of smooth muscle in the vessel wall and by the action of
the skeletal muscle as the body moves. Because most veins must move blood against the pull of gravity, blood is prevented from
flowing backward in the veins by one-way valves. Because skeletal muscle contraction aids in venous blood flow, it is important to
get up and move frequently after long periods of sitting so that blood will not pool in the extremities.
Blood flow through the capillary beds is regulated depending on the body’s needs and is directed by nerve and hormone signals.
For example, after a large meal, most of the blood is diverted to the stomach by vasodilation of vessels of the digestive system and
vasoconstriction of other vessels. During exercise, blood is diverted to the skeletal muscles through vasodilation while blood to the
digestive system would be lessened through vasoconstriction. The blood entering some capillary beds is controlled by small
muscles, called precapillary sphincters, illustrated in Figure 16.5.1. If the sphincters are open, the blood will flow into the
associated branches of the capillary blood. If all of the sphincters are closed, then the blood will flow directly from the arteriole to
the venule through the thoroughfare channel (see Figure 16.5.1). These muscles allow the body to precisely control when capillary
beds receive blood flow. At any given moment only about 5-10% of our capillary beds actually have blood flowing through them.

Figure 16.5.1 : (a) Precapillary sphincters are rings of smooth muscle that regulate the flow of blood through capillaries; they help
control the location of blood flow to where it is needed. (b) Valves in the veins prevent blood from moving backward. (credit a:
modification of work by NCI)

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 Exercise
Varicose veins are veins that become enlarged because the valves no longer close properly, allowing blood to flow backward.
Varicose veins are often most prominent on the legs. Why do you think this is the case?

Answer
Blood in the legs is farthest away from the heart and has to flow up to reach it.

Link to Learning

CIRCULATION

The circulatory system consisting of the heart, arteries, capillaries, and veins, is the pumping mechanism that transports blood
throughout the body. Watch this video to see the circulatory system’s blood flow.

Proteins and other large solutes cannot leave the capillaries. The loss of the watery plasma creates a hyperosmotic solution within
the capillaries, especially near the venules. This causes about 85% of the plasma that leaves the capillaries to eventually diffuses
back into the capillaries near the venules. The remaining 15% of blood plasma drains out from the interstitial fluid into nearby
lymphatic vessels (Figure 16.5.2). The fluid in the lymph is similar in composition to the interstitial fluid. The lymph fluid passes
through lymph nodes before it returns to the heart via the vena cava. Lymph nodes are specialized organs that filter the lymph by
percolation through a maze of connective tissue filled with white blood cells. The white blood cells remove infectious agents, such
as bacteria and viruses, to clean the lymph before it returns to the bloodstream. After it is cleaned, the lymph returns to the heart by
the action of smooth muscle pumping, skeletal muscle action, and one-way valves joining the returning blood near the junction of
the venae cavae entering the right atrium of the heart.

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 Figure 16.5.2 : Fluid from the capillaries moves into the interstitial space and lymph capillaries by diffusion down a pressure
gradient and also by osmosis. Out of 7,200 liters of fluid pumped by the average heart in a day, over 1,500 liters is filtered. (credit:
modification of work by NCI, NIH)

Evolution Connection: Vertebrate Diversity in Blood Circulation

Blood circulation has evolved differently in vertebrates and may show variation in different animals for the required amount of
pressure, organ and vessel location, and organ size. Animals with longs necks and those that live in cold environments have
distinct blood pressure adaptations.
Long necked animals, such as giraffes, need to pump blood upward from the heart against gravity. The blood pressure required
from the pumping of the left ventricle would be equivalent to 250 mm Hg (mm Hg = millimeters of mercury, a unit of
pressure) to reach the height of a giraffe’s head, which is 2.5 meters higher than the heart. However, if checks and balances
were not in place, this blood pressure would damage the giraffe’s brain, particularly if it was bending down to drink. These
checks and balances include valves and feedback mechanisms that reduce the rate of cardiac output. Long-necked dinosaurs
such as the sauropods had to pump blood even higher, up to ten meters above the heart. This would have required a blood
pressure of more than 600 mm Hg, which could only have been achieved by an enormous heart. Evidence for such an
enormous heart does not exist and mechanisms to reduce the blood pressure required include the slowing of metabolism as
these animals grew larger. It is likely that they did not routinely feed on tree tops but grazed on the ground.
Living in cold water, whales need to maintain the temperature in their blood. This is achieved by the veins and arteries being
close together so that heat exchange can occur. This mechanism is called a countercurrent heat exchanger. The blood vessels
and the whole body are also protected by thick layers of blubber to prevent heat loss. In land animals that live in cold
environments, thick fur and hibernation are used to retain heat and slow metabolism.

Blood Pressure
The pressure of the blood flow in the body is produced by the hydrostatic pressure of the fluid (blood) against the walls of the
blood vessels. Fluid will move from areas of high to low hydrostatic pressures. In the arteries, the hydrostatic pressure near the
heart is very high and blood flows to the arterioles where the rate of flow is slowed by the narrow openings of the arterioles. During
systole, when new blood is entering the arteries, the artery walls stretch to accommodate the increase of pressure of the extra blood;
during diastole, the walls return to normal because of their elastic properties. The blood pressure of the systole phase and the
diastole phase, graphed in Figure 16.5.3, gives the two pressure readings for blood pressure. For example, 120/80 indicates a
reading of 120 mm Hg during the systole and 80 mm Hg during diastole. Throughout the cardiac cycle, the blood continues to
empty into the arterioles at a relatively even rate. This resistance to blood flow is called peripheral resistance.

Access for free at OpenStax 16.5.3 [Link]

 Figure 16.5.3 : Blood pressure is related to the blood velocity in the arteries and arterioles. In the capillaries and veins, the blood
pressure continues to decease but velocity increases.

Blood Pressure Regulation

Cardiac output is the volume of blood pumped by the heart in one minute. It is calculated by multiplying the number of heart
contractions that occur per minute (heart rate) times the stroke volume (the volume of blood pumped into the aorta per contraction
of the left ventricle). Therefore, cardiac output can be increased by increasing heart rate, as when exercising. However, cardiac
output can also be increased by increasing stroke volume, such as if the heart contracts with greater strength. Stroke volume can
also be increased by speeding blood circulation through the body so that more blood enters the heart between contractions. During
heavy exertion, the blood vessels relax and increase in diameter, offsetting the increased heart rate and ensuring adequate
oxygenated blood gets to the muscles. Stress triggers a decrease in the diameter of the blood vessels, consequently increasing blood
pressure. These changes can also be caused by nerve signals or hormones, and even standing up or lying down can have a great
effect on blood pressure.

Summary
Blood primarily moves through the body by the rhythmic movement of smooth muscle in the vessel wall and by the action of the
skeletal muscle as the body moves. Blood is prevented from flowing backward in the veins by one-way valves. Blood flow through
the capillary beds is controlled by precapillary sphincters to increase and decrease flow depending on the body’s needs and is
directed by nerve and hormone signals. Lymph vessels take fluid that has leaked out of the blood to the lymph nodes where it is
cleaned before returning to the heart. During systole, blood enters the arteries, and the artery walls stretch to accommodate the
extra blood. During diastole, the artery walls return to normal. The blood pressure of the systole phase and the diastole phase gives
the two pressure readings for blood pressure.

Glossary
blood pressure (BP)
pressure of blood in the arteries that helps to push blood through the body

cardiac output
the volume of blood pumped by the heart in one minute as a product of heart rate multiplied by stroke volume

lymph node
specialized organ that contains a large number of macrophages that clean the lymph before the fluid is returned to the heart

peripheral resistance

Access for free at OpenStax 16.5.4 [Link]

 resistance of the artery and blood vessel walls to the pressure placed on them by the force of the heart pumping

precapillary sphincter
small muscle that controls blood circulation in the capillary beds

stroke volume
the volume of blood pumped into the aorta per contraction of the left ventricle

This page titled 16.5: Blood Flow and Blood Pressure Regulation is shared under a CC BY license and was authored, remixed, and/or curated by
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40.4: Blood Flow and Blood Pressure Regulation by OpenStax is licensed CC BY 4.0.

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16.E: The Circulatory System (Exercises)
40.1: Overview of the Circulatory System
In all animals, except a few simple types, the circulatory system is used to transport nutrients and gases through the body. Simple
diffusion allows some water, nutrient, waste, and gas exchange into primitive animals that are only a few cell layers thick; however,
bulk flow is the only method by which the entire body of larger more complex organisms is accessed.

Review Questions
Why are open circulatory systems advantageous to some animals?
A. They use less metabolic energy.
B. They help the animal move faster.
C. They do not need a heart.
D. They help large insects develop.

Answer
A

Some animals use diffusion instead of a circulatory system. Examples include:

A. birds and jellyfish
B. flatworms and arthropods
C. mollusks and jellyfish
D. None of the above

Answer
D

Blood flow that is directed through the lungs and back to the heart is called ________.
A. unidirectional circulation
B. gill circulation
C. pulmonary circulation
D. pulmocutaneous circulation

Answer
C

Free Response
Describe a closed circulatory system.

Answer
A closed circulatory system is a closed-loop system, in which blood is not free in a cavity. Blood is separate from the bodily
interstitial fluid and contained within blood vessels. In this type of system, blood circulates unidirectionally from the heart
around the systemic circulatory route, and then returns to the heart.

Describe systemic circulation.

Answer
Systemic circulation flows through the systems of the body. The blood flows away from the heart to the brain, liver,
kidneys, stomach, and other organs, the limbs, and the muscles of the body; it then returns to the heart.

16.E.1 [Link]
40.2: Components of the Blood
Blood is the liquid that moves through the vessels and includes plasma (the liquid portion, which contains water, proteins, salts,
lipids, and glucose) and the cells (red and white cells) and cell fragments called platelets. Blood plasma is actually the dominant
component of blood and contains the water, proteins, electrolytes, lipids, and glucose. The cells are responsible for carrying the
gases (red cells) and immune the response (white). The platelets are responsible for blood clotting.

Review Questions
White blood cells:
A. can be classified as granulocytes or agranulocytes
B. defend the body against bacteria and viruses
C. are also called leucocytes
D. All of the above

Answer
D

Platelet plug formation occurs at which point?

A. when large megakaryocytes break up into thousands of smaller fragments
B. when platelets are dispersed through the blood stream
C. when platelets are attracted to a site of blood vessel damage
D. none of the above

Answer
C

In humans, the plasma comprises what percentage of the blood?

A. 45 percent
B. 55 percent
C. 25 percent
D. 90 percent

Answer
B

The red blood cells of birds differ from mammalian red blood cells because:
A. they are white and have nuclei
B. they do not have nuclei
C. they have nuclei
D. they fight disease

Answer
C

Free Response
Describe the cause of different blood type groups.

Answer

16.E.2 [Link]
 Red blood cells are coated with proteins called antigens made of glycolipids and glycoproteins. When type A and type B
blood are mixed, the blood agglutinates because of antibodies in the plasma that bind with the opposing antigen. Type O
blood has no antigens. The Rh blood group has either the Rh antigen (Rh+) or no Rh antigen (Rh–).

List some of the functions of blood in the body.

Answer
Blood is important for regulation of the body’s pH, temperature, and osmotic pressure, the circulation of nutrients and
removal of wastes, the distribution of hormones from endocrine glands, the elimination of excess heat; it also contains
components for the clotting of blood to prevent blood loss. Blood also transports clotting factors and disease-fighting
agents.

How does the lymphatic system work with blood flow?

Answer
Lymph capillaries take fluid from the blood to the lymph nodes. The lymph nodes filter the lymph by percolation through
connective tissue filled with white blood cells. The white blood cells remove infectious agents, such as bacteria and viruses,
to clean the lymph before it returns to the bloodstream.

40.3: Mammalian Heart and Blood Vessels

The heart is a complex muscle that pumps blood through the three divisions of the circulatory system: the coronary (vessels that
serve the heart), pulmonary (heart and lungs), and systemic (systems of the body). Coronary circulation intrinsic to the heart takes
blood directly from the main artery (aorta) coming from the heart.

Review Questions
The heart’s internal pacemaker beats by:
A. an internal implant that sends an electrical impulse through the heart
B. the excitation of cardiac muscle cells at the sinoatrial node followed by the atrioventricular node
C. the excitation of cardiac muscle cells at the atrioventricular node followed by the sinoatrial node
D. the action of the sinus

Answer
B

During the systolic phase of the cardiac cycle, the heart is ________.
A. contracting
B. relaxing
C. contracting and relaxing
D. filling with blood

Answer
A

Cardiomyocytes are similar to skeletal muscle because:

A. they beat involuntarily
B. they are used for weight lifting
C. they pulse rhythmically
D. they are striated

16.E.3 [Link]
 Answer
D

How do arteries differ from veins?

A. Arteries have thicker smooth muscle layers to accommodate the changes in pressure from the heart.
B. Arteries carry blood.
C. Arteries have thinner smooth muscle layers and valves and move blood by the action of skeletal muscle.
D. Arteries are thin walled and are used for gas exchange.

Answer
A

Free Response
Describe the cardiac cycle.

Answer
The heart receives an electrical signal from the sinoatrial node triggering the cardiac muscle cells in the atria to contract.
The signal pauses at the atrioventricular node before spreading to the walls of the ventricles so the blood is pumped through
the body. This is the systolic phase. The heart then relaxes in the diastole and fills again with blood.

What happens in capillaries?

Answer
The capillaries basically exchange materials with their surroundings. Their walls are very thin and are made of one or two
layers of cells, where gases, nutrients, and waste are diffused. They are distributed as beds, complex networks that link
arteries as well as veins.

40.4: Blood Flow and Blood Pressure Regulation

Blood pressure is the pressure exerted by blood on the walls of a blood vessel that helps to push blood through the body. Systolic
blood pressure measures the amount of pressure that blood exerts on vessels while the heart is beating. The optimal systolic blood
pressure is 120 mmHg. Diastolic blood pressure measures the pressure in the vessels between heartbeats. The optimal diastolic
blood pressure is 80 mmHg.

Review Questions

High blood pressure would be a result of ________.

A. a high cardiac output and high peripheral resistance
B. a high cardiac output and low peripheral resistance
C. a low cardiac output and high peripheral resistance
D. a low cardiac output and low peripheral resistance

Answer
A

Free Response
How does blood pressure change during heavy exercise?

Answer

16.E.4 [Link]
 The heart rate increases, which increases the hydrostatic pressure against the artery walls. At the same time, the arterioles
dilate in response to the increased exercise, which reduces peripheral resistance.

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16.E.5 [Link]
 CHAPTER OVERVIEW

17: Nutrition and Digestion

17.1: Animal Nutrition and the Digestive System
17.1.1: Prelude to Animal Nutrition and the Digestive System
17.1.2: Digestive Systems
17.1.3: Nutrition and Energy Production
17.1.4: Digestive System Processes
17.1.5: Digestive System Regulation
17.1.E: Animal Nutrition and the Digestive System (Exercises)
17.2: Nervous System
17.3: Sensory Systems
17.3.1: Introduction
17.3.2: Sensory Processes
17.3.3: Somatosensation
17.3.4: Taste and Smell
17.3.5: Hearing and Vestibular Sensation
17.3.6: Vision
17.3.E: Sensory Systems (Exercises)

Thumbnail: Intestine. (Image by JimCoote from Pixabay).

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1
 SECTION OVERVIEW

17.1: Animal Nutrition and the Digestive System

All living organisms need nutrients to survive. While plants can obtain the molecules required for cellular function through the
process of photosynthesis, most animals obtain their nutrients by the consumption of other organisms. At the cellular level, the
biological molecules necessary for animal function are amino acids, lipid molecules, nucleotides, and simple sugars. However, the
food consumed consists of protein, fat, and complex carbohydrates. Animals must convert these macromolecules into the simple
molecules required for maintaining cellular functions, such as assembling new molecules, cells, and tissues. The conversion of the
food consumed to the nutrients required is a multi-step process involving digestion and absorption. During digestion, food particles
are broken down to smaller components, and later, they are absorbed by the body.

17.1.1: Prelude to Animal Nutrition and the Digestive System

17.1.2: Digestive Systems

17.1.3: Nutrition and Energy Production

17.1.4: Digestive System Processes

17.1.5: Digestive System Regulation

17.1.E: Animal Nutrition and the Digestive System (Exercises)

Contributors and Attributions

Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski
(Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute
of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY
4.0; Download for free at [Link]

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OpenStax.

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17.1.1: Prelude to Animal Nutrition and the Digestive System
All living organisms need nutrients to survive. While plants can obtain the molecules required for cellular function through the
process of photosynthesis, most animals obtain their nutrients by the consumption of other organisms. At the cellular level, the
biological molecules necessary for animal function are amino acids, lipid molecules, nucleotides, and simple sugars. However, the
food consumed consists of protein, fat, and complex carbohydrates. Animals must convert these macromolecules into the simple
molecules required for maintaining cellular functions, such as assembling new molecules, cells, and tissues. The conversion of the
food consumed to the nutrients required is a multi-step process involving digestion and absorption. During digestion, food particles
are broken down to smaller components, and later, they are absorbed by the body.

Figure [Link] : For humans, fruits and vegetables are important in maintaining a balanced diet. (credit: modification of work by
Julie Rybarczyk)
One of the challenges in human nutrition is maintaining a balance between food intake, storage, and energy expenditure.
Imbalances can have serious health consequences. For example, eating too much food while not expending much energy leads to
obesity, which in turn will increase the risk of developing illnesses such as type-2 diabetes and cardiovascular disease. The recent
rise in obesity and related diseases makes understanding the role of diet and nutrition in maintaining good health all the more
important.

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curated by OpenStax.
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17.1.2: Digestive Systems
Skills to Develop
Explain the processes of digestion and absorption
Compare and contrast different types of digestive systems
Explain the specialized functions of the organs involved in processing food in the body
Describe the ways in which organs work together to digest food and absorb nutrients

Animals obtain their nutrition from the consumption of other organisms. Depending on their diet, animals can be classified into the
following categories: plant eaters (herbivores), meat eaters (carnivores), and those that eat both plants and animals (omnivores).
The nutrients and macromolecules present in food are not immediately accessible to the cells. There are a number of processes that
modify food within the animal body in order to make the nutrients and organic molecules accessible for cellular function. As
animals evolved in complexity of form and function, their digestive systems have also evolved to accommodate their various
dietary needs.

Herbivores, Omnivores, and Carnivores

Herbivores are animals whose primary food source is plant-based. Examples of herbivores, as shown in Figure [Link] include
vertebrates like deer, koalas, and some bird species, as well as invertebrates such as crickets and caterpillars. These animals have
evolved digestive systems capable of handling large amounts of plant material. Herbivores can be further classified into frugivores
(fruit-eaters), granivores (seed eaters), nectivores (nectar feeders), and folivores (leaf eaters).

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 Figure [Link] : Herbivores, like this (a) mule deer and (b) monarch caterpillar, eat primarily plant material. (credit a: modification
of work by Bill Ebbesen; credit b: modification of work by Doug Bowman)
Carnivores are animals that eat other animals. The word carnivore is derived from Latin and literally means “meat eater.” Wild cats
such as lions, shown in Figure 17.1.2.2a and tigers are examples of vertebrate carnivores, as are snakes and sharks, while
invertebrate carnivores include sea stars, spiders, and ladybugs, shown in Figure 17.1.2.2b. Obligate carnivores are those that rely
entirely on animal flesh to obtain their nutrients; examples of obligate carnivores are members of the cat family, such as lions and
cheetahs. Facultative carnivores are those that also eat non-animal food in addition to animal food. Note that there is no clear line
that differentiates facultative carnivores from omnivores; dogs would be considered facultative carnivores.

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 Figure [Link] : Carnivores like the (a) lion eat primarily meat. The (b) ladybug is also a carnivore that consumes small insects
called aphids. (credit a: modification of work by Kevin Pluck; credit b: modification of work by Jon Sullivan)
Omnivores are animals that eat both plant- and animal-derived food. In Latin, omnivore means to eat everything. Humans, bears
(shown in Figure 17.1.2.3a), and chickens are example of vertebrate omnivores; invertebrate omnivores include cockroaches and
crayfish (shown in Figure 17.1.2.3b).

Figure [Link] : Omnivores like the (a) bear and (b) crayfish eat both plant and animal based food. (credit a: modification of work
by Dave Menke; credit b: modification of work by Jon Sullivan)

Invertebrate Digestive Systems

Animals have evolved different types of digestive systems to aid in the digestion of the different foods they consume. The simplest
example is that of a gastrovascular cavity and is found in organisms with only one opening for digestion. Platyhelminthes
(flatworms), Ctenophora (comb jellies), and Cnidaria (coral, jelly fish, and sea anemones) use this type of digestion. Gastrovascular
cavities, as shown in Figure 17.1.2.4a, are typically a blind tube or cavity with only one opening, the “mouth”, which also serves
as an “anus”. Ingested material enters the mouth and passes through a hollow, tubular cavity. Cells within the cavity secrete
digestive enzymes that break down the food. The food particles are engulfed by the cells lining the gastrovascular cavity.
The alimentary canal, shown in Figure 17.1.2.4b, is a more advanced system: it consists of one tube with a mouth at one end and
an anus at the other. Earthworms are an example of an animal with an alimentary canal. Once the food is ingested through the
mouth, it passes through the esophagus and is stored in an organ called the crop; then it passes into the gizzard where it is churned
and digested. From the gizzard, the food passes through the intestine, the nutrients are absorbed, and the waste is eliminated as
feces, called castings, through the anus.

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 Figure [Link] : (a) A gastrovascular cavity has a single opening through which food is ingested and waste is excreted, as shown in
this hydra and in this jellyfish medusa. (b) An alimentary canal has two openings: a mouth for ingesting food, and an anus for
eliminating waste, as shown in this nematode.

Vertebrate Digestive Systems

Vertebrates have evolved more complex digestive systems to adapt to their dietary needs. Some animals have a single stomach,
while others have multi-chambered stomachs. Birds have developed a digestive system adapted to eating unmasticated food.

Monogastric: Single-chambered Stomach

As the word monogastric suggests, this type of digestive system consists of one (“mono”) stomach chamber (“gastric”). Humans
and many animals have a monogastric digestive system as illustrated in Figure [Link]. The process of digestion begins with the
mouth and the intake of food. The teeth play an important role in masticating (chewing) or physically breaking down food into
smaller particles. The enzymes present in saliva also begin to chemically break down food. The esophagus is a long tube that
connects the mouth to the stomach. Using peristalsis, or wave-like smooth muscle contractions, the muscles of the esophagus push
the food towards the stomach. In order to speed up the actions of enzymes in the stomach, the stomach is an extremely acidic
environment, with a pH between 1.5 and 2.5. The gastric juices, which include enzymes in the stomach, act on the food particles
and continue the process of digestion. Further breakdown of food takes place in the small intestine where enzymes produced by the
liver, the small intestine, and the pancreas continue the process of digestion. The nutrients are absorbed into the blood stream across
the epithelial cells lining the walls of the small intestines. The waste material travels on to the large intestine where water is
absorbed and the drier waste material is compacted into feces; it is stored until it is excreted through the rectum.

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 Figure [Link] : (a) Humans and herbivores, such as the (b) rabbit, have a monogastric digestive system. However, in the rabbit the
small intestine and cecum are enlarged to allow more time to digest plant material. The enlarged organ provides more surface area
for absorption of nutrients. Rabbits digest their food twice: the first time food passes through the digestive system, it collects in the
cecum, and then it passes as soft feces called cecotrophes. The rabbit re-ingests these cecotrophes to further digest them.

Avian
Birds face special challenges when it comes to obtaining nutrition from food. They do not have teeth and so their digestive system,
shown in Figure [Link], must be able to process un-masticated food. Birds have evolved a variety of beak types that reflect the
vast variety in their diet, ranging from seeds and insects to fruits and nuts. Because most birds fly, their metabolic rates are high in
order to efficiently process food and keep their body weight low. The stomach of birds has two chambers: the proventriculus, where
gastric juices are produced to digest the food before it enters the stomach, and the gizzard, where the food is stored, soaked, and
mechanically ground. The undigested material forms food pellets that are sometimes regurgitated. Most of the chemical digestion
and absorption happens in the intestine and the waste is excreted through the cloaca.

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 Figure [Link] : The avian esophagus has a pouch, called a crop, which stores food. Food passes from the crop to the first of two
stomachs, called the proventriculus, which contains digestive juices that break down food. From the proventriculus, the food enters
the second stomach, called the gizzard, which grinds food. Some birds swallow stones or grit, which are stored in the gizzard, to
aid the grinding process. Birds do not have separate openings to excrete urine and feces. Instead, uric acid from the kidneys is
secreted into the large intestine and combined with waste from the digestive process. This waste is excreted through an opening
called the cloaca.

Evolution Connection: Avian Adaptations

Birds have a highly efficient, simplified digestive system. Recent fossil evidence has shown that the evolutionary divergence of
birds from other land animals was characterized by streamlining and simplifying the digestive system. Unlike many other
animals, birds do not have teeth to chew their food. In place of lips, they have sharp pointy beaks. The horny beak, lack of
jaws, and the smaller tongue of the birds can be traced back to their dinosaur ancestors. The emergence of these changes seems
to coincide with the inclusion of seeds in the bird diet. Seed-eating birds have beaks that are shaped for grabbing seeds and the
two-compartment stomach allows for delegation of tasks. Since birds need to remain light in order to fly, their metabolic rates
are very high, which means they digest their food very quickly and need to eat often. Contrast this with the ruminants, where
the digestion of plant matter takes a very long time.

Ruminants
Ruminants are mainly herbivores like cows, sheep, and goats, whose entire diet consists of eating large amounts of roughage or
fiber. They have evolved digestive systems that help them digest vast amounts of cellulose. An interesting feature of the ruminants’

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mouth is that they do not have upper incisor teeth. They use their lower teeth, tongue and lips to tear and chew their food. From the
mouth, the food travels to the esophagus and on to the stomach.
To help digest the large amount of plant material, the stomach of the ruminants is a multi-chambered organ, as illustrated in Figure
[Link]. The four compartments of the stomach are called the rumen, reticulum, omasum, and abomasum. These chambers contain

many microbes that break down cellulose and ferment ingested food. The abomasum is the “true” stomach and is the equivalent of
the monogastric stomach chamber where gastric juices are secreted. The four-compartment gastric chamber provides larger space
and the microbial support necessary to digest plant material in ruminants. The fermentation process produces large amounts of gas
in the stomach chamber, which must be eliminated. As in other animals, the small intestine plays an important role in nutrient
absorption, and the large intestine helps in the elimination of waste.

Figure [Link] : Ruminant animals, such as goats and cows, have four stomachs. The first two stomachs, the rumen and the
reticulum, contain prokaryotes and protists that are able to digest cellulose fiber. The ruminant regurgitates cud from the reticulum,
chews it, and swallows it into a third stomach, the omasum, which removes water. The cud then passes onto the fourth stomach, the
abomasum, where it is digested by enzymes produced by the ruminant.

Pseudo-ruminants
Some animals, such as camels and alpacas, are pseudo-ruminants. They eat a lot of plant material and roughage. Digesting plant
material is not easy because plant cell walls contain the polymeric sugar molecule cellulose. The digestive enzymes of these
animals cannot break down cellulose, but microorganisms present in the digestive system can. Therefore, the digestive system must
be able to handle large amounts of roughage and break down the cellulose. Pseudo-ruminants have a three-chamber stomach in the
digestive system. However, their cecum—a pouched organ at the beginning of the large intestine containing many microorganisms
that are necessary for the digestion of plant materials—is large and is the site where the roughage is fermented and digested. These
animals do not have a rumen but have an omasum, abomasum, and reticulum.

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Parts of the Digestive System
The vertebrate digestive system is designed to facilitate the transformation of food matter into the nutrient components that sustain
organisms.

Oral Cavity
The oral cavity, or mouth, is the point of entry of food into the digestive system, illustrated in Figure [Link]. The food consumed
is broken into smaller particles by mastication, the chewing action of the teeth. All mammals have teeth and can chew their food.
The extensive chemical process of digestion begins in the mouth. As food is being chewed, saliva, produced by the salivary glands,
mixes with the food. Saliva is a watery substance produced in the mouths of many animals. There are three major glands that
secrete saliva—the parotid, the submandibular, and the sublingual. Saliva contains mucus that moistens food and buffers the pH of
the food. Saliva also contains immunoglobulins and lysozymes, which have antibacterial action to reduce tooth decay by inhibiting
growth of some bacteria. Saliva also contains an enzyme called salivary amylase that begins the process of converting starches in
the food into a disaccharide called maltose. Another enzyme called lipase is produced by the cells in the tongue. Lipases are a class
of enzymes that can break down triglycerides. The lingual lipase begins the breakdown of fat components in the food. The chewing
and wetting action provided by the teeth and saliva prepare the food into a mass called the bolus for swallowing. The tongue helps
in swallowing—moving the bolus from the mouth into the pharynx. The pharynx opens to two passageways: the trachea, which
leads to the lungs, and the esophagus, which leads to the stomach. The trachea has an opening called the glottis, which is covered
by a cartilaginous flap called the epiglottis. When swallowing, the epiglottis closes the glottis and food passes into the esophagus
and not the trachea. This arrangement allows food to be kept out of the trachea.

Figure [Link] : Digestion of food begins in the (a) oral cavity. Food is masticated by teeth and moistened by saliva secreted from
the (b) salivary glands. Enzymes in the saliva begin to digest starches and fats. With the help of the tongue, the resulting bolus is
moved into the esophagus by swallowing. (credit: modification of work by the National Cancer Institute)

Esophagus
The esophagus is a tubular organ that connects the mouth to the stomach. The chewed and softened food passes through the
esophagus after being swallowed. The smooth muscles of the esophagus undergo a series of wave like movements called peristalsis
that push the food toward the stomach, as illustrated in Figure [Link]. The peristalsis wave is unidirectional—it moves food from
the mouth to the stomach, and reverse movement is not possible. The peristaltic movement of the esophagus is an involuntary
reflex; it takes place in response to the act of swallowing.

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 Figure [Link] : The esophagus transfers food from the mouth to the stomach through peristaltic movements.
A ring-like muscle called a sphincter forms valves in the digestive system. The gastro-esophageal sphincter is located at the
stomach end of the esophagus. In response to swallowing and the pressure exerted by the bolus of food, this sphincter opens, and
the bolus enters the stomach. When there is no swallowing action, this sphincter is shut and prevents the contents of the stomach
from traveling up the esophagus. Many animals have a true sphincter; however, in humans, there is no true sphincter, but the
esophagus remains closed when there is no swallowing action. Acid reflux or “heartburn” occurs when the acidic digestive juices
escape into the esophagus.

Stomach
A large part of digestion occurs in the stomach, shown in Figure [Link]. The stomach is a saclike organ that secretes gastric
digestive juices. The pH in the stomach is between 1.5 and 2.5. This highly acidic environment is required for the chemical
breakdown of food and the extraction of nutrients. When empty, the stomach is a rather small organ; however, it can expand to up
to 20 times its resting size when filled with food. This characteristic is particularly useful for animals that need to eat when food is
available.

Art Connection

Figure [Link] : The human stomach has an extremely acidic environment where most of the protein gets digested. (credit:
modification of work by Mariana Ruiz Villareal)
Which of the following statements about the digestive system is false?

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 A. Chyme is a mixture of food and digestive juices that is produced in the stomach.
B. Food enters the large intestine before the small intestine.
C. In the small intestine, chyme mixes with bile, which emulsifies fats.
D. The stomach is separated from the small intestine by the pyloric sphincter.

The stomach is also the major site for protein digestion in animals other than ruminants. Protein digestion is mediated by an
enzyme called pepsin in the stomach chamber. Pepsin is secreted by the chief cells in the stomach in an inactive form called
pepsinogen. Pepsin breaks peptide bonds and cleaves proteins into smaller polypeptides; it also helps activate more pepsinogen,
starting a positive feedback mechanism that generates more pepsin. Another cell type—parietal cells—secrete hydrogen and
chloride ions, which combine in the lumen to form hydrochloric acid, the primary acidic component of the stomach juices.
Hydrochloric acid helps to convert the inactive pepsinogen to pepsin. The highly acidic environment also kills many
microorganisms in the food and, combined with the action of the enzyme pepsin, results in the hydrolysis of protein in the food.
Chemical digestion is facilitated by the churning action of the stomach. Contraction and relaxation of smooth muscles mixes the
stomach contents about every 20 minutes. The partially digested food and gastric juice mixture is called chyme. Chyme passes
from the stomach to the small intestine. Further protein digestion takes place in the small intestine. Gastric emptying occurs within
two to six hours after a meal. Only a small amount of chyme is released into the small intestine at a time. The movement of chyme
from the stomach into the small intestine is regulated by the pyloric sphincter.
When digesting protein and some fats, the stomach lining must be protected from getting digested by pepsin. There are two points
to consider when describing how the stomach lining is protected. First, as previously mentioned, the enzyme pepsin is synthesized
in the inactive form. This protects the chief cells, because pepsinogen does not have the same enzyme functionality of pepsin.
Second, the stomach has a thick mucus lining that protects the underlying tissue from the action of the digestive juices. When this
mucus lining is ruptured, ulcers can form in the stomach. Ulcers are open wounds in or on an organ caused by bacteria
(Helicobacter pylori) when the mucus lining is ruptured and fails to reform.

Small Intestine
Chyme moves from the stomach to the small intestine. The small intestine is the organ where the digestion of protein, fats, and
carbohydrates is completed. The small intestine is a long tube-like organ with a highly folded surface containing finger-like
projections called the villi. The apical surface of each villus has many microscopic projections called microvilli. These structures,
illustrated in Figure [Link], are lined with epithelial cells on the luminal side and allow for the nutrients to be absorbed from the
digested food and absorbed into the blood stream on the other side. The villi and microvilli, with their many folds, increase the
surface area of the intestine and increase absorption efficiency of the nutrients. Absorbed nutrients in the blood are carried into the
hepatic portal vein, which leads to the liver. There, the liver regulates the distribution of nutrients to the rest of the body and
removes toxic substances, including drugs, alcohol, and some pathogens.

Art Connection

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 Figure [Link] : Villi are folds on the small intestine lining that increase the surface area to facilitate the absorption of
nutrients.
Which of the following statements about the small intestine is false?
A. Absorptive cells that line the small intestine have microvilli, small projections that increase surface area and aid in the
absorption of food.
B. The inside of the small intestine has many folds, called villi.
C. Microvilli are lined with blood vessels as well as lymphatic vessels.
D. The inside of the small intestine is called the lumen.

The human small intestine is over 6m long and is divided into three parts: the duodenum, the jejunum, and the ileum. The “C-
shaped,” fixed part of the small intestine is called the duodenum and is shown in Figure [Link]. The duodenum is separated
from the stomach by the pyloric sphincter which opens to allow chyme to move from the stomach to the duodenum. In the
duodenum, chyme is mixed with pancreatic juices in an alkaline solution rich in bicarbonate that neutralizes the acidity of chyme
and acts as a buffer. Pancreatic juices also contain several digestive enzymes. Digestive juices from the pancreas, liver, and
gallbladder, as well as from gland cells of the intestinal wall itself, enter the duodenum. Bile is produced in the liver and stored and
concentrated in the gallbladder. Bile contains bile salts which emulsify lipids while the pancreas produces enzymes that catabolize
starches, disaccharides, proteins, and fats. These digestive juices break down the food particles in the chyme into glucose,
triglycerides, and amino acids. Some chemical digestion of food takes place in the duodenum. Absorption of fatty acids also takes
place in the duodenum.
The second part of the small intestine is called the jejunum, shown in Figure [Link]. Here, hydrolysis of nutrients is continued
while most of the carbohydrates and amino acids are absorbed through the intestinal lining. The bulk of chemical digestion and
nutrient absorption occurs in the jejunum.
The ileum, also illustrated in Figure 17.1.2.11is the last part of the small intestine and here the bile salts and vitamins are absorbed
into blood stream. The undigested food is sent to the colon from the ileum via peristaltic movements of the muscle. The ileum ends
and the large intestine begins at the ileocecal valve. The vermiform, “worm-like,” appendix is located at the ileocecal valve. The
appendix of humans secretes no enzymes and has an insignificant role in immunity.

Large Intestine
The large intestine, illustrated in Figure [Link], reabsorbs the water from the undigested food material and processes the waste
material. The human large intestine is much smaller in length compared to the small intestine but larger in diameter. It has three
parts: the cecum, the colon, and the rectum. The cecum joins the ileum to the colon and is the receiving pouch for the waste matter.
The colon is home to many bacteria or “intestinal flora” that aid in the digestive processes. The colon can be divided into four
regions, the ascending colon, the transverse colon, the descending colon and the sigmoid colon. The main functions of the colon are

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to extract the water and mineral salts from undigested food, and to store waste material. Carnivorous mammals have a shorter large
intestine compared to herbivorous mammals due to their diet.

Figure [Link] : The large intestine reabsorbs water from undigested food and stores waste material until it is eliminated.

Rectum and Anus

The rectum is the terminal end of the large intestine, as shown in Figure [Link]. The primary role of the rectum is to store the
feces until defecation. The feces are propelled using peristaltic movements during elimination. The anus is an opening at the far-
end of the digestive tract and is the exit point for the waste material. Two sphincters between the rectum and anus control
elimination: the inner sphincter is involuntary and the outer sphincter is voluntary.

Accessory Organs
The organs discussed above are the organs of the digestive tract through which food passes. Accessory organs are organs that add
secretions (enzymes) that catabolize food into nutrients. Accessory organs include salivary glands, the liver, the pancreas, and the
gallbladder. The liver, pancreas, and gallbladder are regulated by hormones in response to the food consumed.
The liver is the largest internal organ in humans and it plays a very important role in digestion of fats and detoxifying blood. The
liver produces bile, a digestive juice that is required for the breakdown of fatty components of the food in the duodenum. The liver
also processes the vitamins and fats and synthesizes many plasma proteins.
The pancreas is another important gland that secretes digestive juices. The chyme produced from the stomach is highly acidic in
nature; the pancreatic juices contain high levels of bicarbonate, an alkali that neutralizes the acidic chyme. Additionally, the
pancreatic juices contain a large variety of enzymes that are required for the digestion of protein and carbohydrates.
The gallbladder is a small organ that aids the liver by storing bile and concentrating bile salts. When chyme containing fatty acids
enters the duodenum, the bile is secreted from the gallbladder into the duodenum.

Summary
Different animals have evolved different types of digestive systems specialized to meet their dietary needs. Humans and many
other animals have monogastric digestive systems with a single-chambered stomach. Birds have evolved a digestive system that
includes a gizzard where the food is crushed into smaller pieces. This compensates for their inability to masticate. Ruminants that
consume large amounts of plant material have a multi-chambered stomach that digests roughage. Pseudo-ruminants have similar
digestive processes as ruminants but do not have the four-compartment stomach. Processing food involves ingestion (eating),
digestion (mechanical and enzymatic breakdown of large molecules), absorption (cellular uptake of nutrients), and elimination
(removal of undigested waste as feces).
Many organs work together to digest food and absorb nutrients. The mouth is the point of ingestion and the location where both
mechanical and chemical breakdown of food begins. Saliva contains an enzyme called amylase that breaks down carbohydrates.
The food bolus travels through the esophagus by peristaltic movements to the stomach. The stomach has an extremely acidic
environment. An enzyme called pepsin digests protein in the stomach. Further digestion and absorption take place in the small
intestine. The large intestine reabsorbs water from the undigested food and stores waste until elimination.

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Art Connections
Figure [Link]: Which of the following statements about the digestive system is false?
A. Chyme is a mixture of food and digestive juices that is produced in the stomach.
B. Food enters the large intestine before the small intestine.
C. In the small intestine, chyme mixes with bile, which emulsifies fats.
D. The stomach is separated from the small intestine by the pyloric sphincter.

Answer
B

Figure [Link]: Which of the following statements about the small intestine is false?
A. Absorptive cells that line the small intestine have microvilli, small projections that increase surface area and aid in the
absorption of food.
B. The inside of the small intestine has many folds, called villi.
C. Microvilli are lined with blood vessels as well as lymphatic vessels.
D. The inside of the small intestine is called the lumen.

Answer
C

Glossary
alimentary canal
tubular digestive system with a mouth and anus

anus
exit point for waste material

bile
digestive juice produced by the liver; important for digestion of lipids

bolus
mass of food resulting from chewing action and wetting by saliva

carnivore
animal that consumes animal flesh

chyme
mixture of partially digested food and stomach juices

duodenum
first part of the small intestine where a large part of digestion of carbohydrates and fats occurs

esophagus
tubular organ that connects the mouth to the stomach

gallbladder
organ that stores and concentrates bile

gastrovascular cavity
digestive system consisting of a single opening

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gizzard
muscular organ that grinds food

herbivore
animal that consumes strictly plant diet

ileum
last part of the small intestine; connects the small intestine to the large intestine; important for absorption of B-12

jejunum
second part of the small intestine

large intestine
digestive system organ that reabsorbs water from undigested material and processes waste matter

lipase
enzyme that chemically breaks down lipids

liver
organ that produces bile for digestion and processes vitamins and lipids

monogastric
digestive system that consists of a single-chambered stomach

omnivore
animal that consumes both plants and animals

pancreas
gland that secretes digestive juices

pepsin
enzyme found in the stomach whose main role is protein digestion

pepsinogen
inactive form of pepsin

peristalsis
wave-like movements of muscle tissue

proventriculus
glandular part of a bird’s stomach

rectum
area of the body where feces is stored until elimination

roughage
component of food that is low in energy and high in fiber

ruminant
animal with a stomach divided into four compartments

salivary amylase
enzyme found in saliva, which converts carbohydrates to maltose

small intestine

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 organ where digestion of protein, fats, and carbohydrates is completed

sphincter
band of muscle that controls movement of materials throughout the digestive tract

stomach
saclike organ containing acidic digestive juices

villi
folds on the inner surface of the small intestine whose role is to increase absorption area

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17.1.3: Nutrition and Energy Production
Skills to Develop
Explain why an animal’s diet should be balanced and meet the needs of the body
Define the primary components of food
Describe the essential nutrients required for cellular function that cannot be synthesized by the animal body
Explain how energy is produced through diet and digestion
Describe how excess carbohydrates and energy are stored in the body

Given the diversity of animal life on our planet, it is not surprising that the animal diet would also vary substantially. The animal
diet is the source of materials needed for building DNA and other complex molecules needed for growth, maintenance, and
reproduction; collectively these processes are called biosynthesis. The diet is also the source of materials for ATP production in the
cells. The diet must be balanced to provide the minerals and vitamins that are required for cellular function.

Food Requirements
What are the fundamental requirements of the animal diet? The animal diet should be well balanced and provide nutrients required
for bodily function and the minerals and vitamins required for maintaining structure and regulation necessary for good health and
reproductive capability. These requirements for a human are illustrated graphically in Figure [Link].

Figure [Link] : For humans, a balanced diet includes fruits, vegetables, grains, and protein. (credit: USDA)

Everyday Connection: Let’s Move! Campaign

Obesity is a growing epidemic and the rate of obesity among children is rapidly rising in the United States. To combat
childhood obesity and ensure that children get a healthy start in life, first lady Michelle Obama has launched the Let’s Move!
campaign. The goal of this campaign is to educate parents and caregivers on providing healthy nutrition and encouraging
active lifestyles to future generations. This program aims to involve the entire community, including parents, teachers, and

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 healthcare providers to ensure that children have access to healthy foods—more fruits, vegetables, and whole grains—and
consume fewer calories from processed foods. Another goal is to ensure that children get physical activity. With the increase in
television viewing and stationary pursuits such as video games, sedentary lifestyles have become the norm. Learn more at
[Link].

Organic Precursors
The organic molecules required for building cellular material and tissues must come from food. Carbohydrates or sugars are the
primary source of organic carbons in the animal body. During digestion, digestible carbohydrates are ultimately broken down into
glucose and used to provide energy through metabolic pathways. Complex carbohydrates, including polysaccharides, can be broken
down into glucose through biochemical modification; however, humans do not produce the enzyme cellulase and lack the ability to
derive glucose from the polysaccharide cellulose. In humans, these molecules provide the fiber required for moving waste through
the large intestine and a healthy colon. The intestinal flora in the human gut are able to extract some nutrition from these plant
fibers. The excess sugars in the body are converted into glycogen and stored in the liver and muscles for later use. Glycogen stores
are used to fuel prolonged exertions, such as long-distance running, and to provide energy during food shortage. Excess glycogen
can be converted to fats, which are stored in the lower layer of the skin of mammals for insulation and energy storage. Excess
digestible carbohydrates are stored by mammals in order to survive famine and aid in mobility.
Another important requirement is that of nitrogen. Protein catabolism provides a source of organic nitrogen. Amino acids are the
building blocks of proteins and protein breakdown provides amino acids that are used for cellular function. The carbon and
nitrogen derived from these become the building block for nucleotides, nucleic acids, proteins, cells, and tissues. Excess nitrogen
must be excreted as it is toxic. Fats add flavor to food and promote a sense of satiety or fullness. Fatty foods are also significant
sources of energy because one gram of fat contains nine calories. Fats are required in the diet to aid the absorption of fat-soluble
vitamins and the production of fat-soluble hormones.

Essential Nutrients
While the animal body can synthesize many of the molecules required for function from the organic precursors, there are some
nutrients that need to be consumed from food. These nutrients are termed essential nutrients, meaning they must be eaten, and the
body cannot produce them.
The omega-3 alpha-linolenic acid and the omega-6 linoleic acid are essential fatty acids needed to make some membrane
phospholipids. Vitamins are another class of essential organic molecules that are required in small quantities for many enzymes to
function and, for this reason, are considered to be co-enzymes. Absence or low levels of vitamins can have a dramatic effect on
health, as outlined in the tables below. Both fat-soluble and water-soluble vitamins must be obtained from food. Minerals, listed in
the table below, are inorganic essential nutrients that must be obtained from food. Among their many functions, minerals help in
structure and regulation and are considered co-factors. Certain amino acids also must be procured from food and cannot be
synthesized by the body. These amino acids are the “essential” amino acids. The human body can synthesize only 11 of the 20
required amino acids; the rest must be obtained from food. The essential amino acids are listed in the table below.
Table [Link]: Water-soluble Essential Vitamins
Vitamin Function Deficiencies Can Lead To Sources

Needed by the body to process

Muscle weakness, Beriberi:
lipids, proteins, and carbohydrates Milk, meat, dried beans, whole
Vitamin B1 (Thiamine) reduced heart function, CNS
Coenzyme removes CO2 from grains
problems
organic compounds

Cracks or sores on the outer

Takes an active role in surface of the lips (cheliosis);
metabolism, aiding in the inflammation and redness of the Meat, eggs, enriched grains,
Vitamin B2 (Riboflavin)
conversion of food to energy tongue; moist, scaly skin vegetables
(FAD and FMN) inflammation (seborrheic
dermatitis)

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 Vitamin Function Deficiencies Can Lead To Sources

Used by the body to release

energy from carbohydrates and to
Pellagra, which can result in
process alcohol; required for the
Vitamin B3 (Niacin) dermatitis, diarrhea, dementia, and Meat, eggs, grains, nuts, potatoes
synthesis of sex hormones;
death
component of coenzyme NAD+
and NADP+

Assists in producing energy from Fatigue, poor coordination,

Meat, whole grains, milk, fruits,
Vitamin B5 (Pantothenic acid) foods (lipids, in particular); retarded growth, numbness,
vegetables
component of coenzyme A tingling of hands and feet

The principal vitamin for

Irritability, depression, confusion,
processing amino acids and lipids; Meat, dairy products, whole
Vitamin B6 (Pyridoxine) mouth sores or ulcers, anemia,
also helps convert nutrients into grains, orange juice
muscular twitching
energy

Used in energy and amino acid Hair loss, dermatitis, depression,

metabolism, fat synthesis, and fat numbness and tingling in the Meat, eggs, legumes and other
Vitamin B7 (Biotin)
breakdown; helps the body use extremities; neuromuscular vegetables
blood sugar disorders

Assists the normal development of

Deficiency during pregnancy is
cells, especially during fetal Leafy green vegetables, whole
Vitamin B9 (Folic acid) associated with birth defects, such
development; helps metabolize wheat, fruits, nuts, legumes
as neural tube defects and anemia
nucleic and amino acids

Maintains healthy nervous system

and assists with blood cell Anemia, neurological disorders,
Vitamin B12 (Cobalamin) Meat, eggs, animal products
formation; coenzyme in nucleic numbness, loss of balance
acid metabolism

Helps maintain connective tissue: Scurvy, which results in bleeding,

Citrus fruits, broccoli, tomatoes,
Vitamin C (Ascorbic acid) bone, cartilage, and dentin; boosts hair and tooth loss; joint pain and
red sweet bell peppers
the immune system swelling; delayed wound healing

Table [Link]: Fat-soluble Essential Vitamins

Vitamin Function Deficiencies Can Lead To Sources

Critical to the development of

bones, teeth, and skin; helps Dark green leafy vegetables,
Night-blindness, skin disorders,
Vitamin A (Retinol) maintain eyesight, enhances the yellow-orange vegetables fruits,
impaired immunity
immune system, fetal milk, butter
development, gene expression

Critical for calcium absorption for

bone development and strength;
Vitamin D maintains a stable nervous system; Rickets, osteomalacia, immunity Cod liver oil, milk, egg yolk
maintains a normal and strong
heartbeat; helps in blood clotting

Lessens oxidative damage of

cells,and prevents lung damage Deficiency is rare; anemia, Wheat germ oil, unrefined
Vitamin E (Tocopherol)
from pollutants; vital to the nervous system degeneration vegetable oils, nuts, seeds, grains
immune system

Vitamin K (Phylloquinone) Essential to blood clotting Bleeding and easy bruising Leafy green vegetables, tea

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 Figure [Link] : A healthy diet should include a variety of foods to ensure that needs for essential nutrients are met. (credit: Keith
Weller, USDA ARS)
Table [Link]: Minerals and Their Function in the Human Body
Mineral Function Deficiencies Can Lead To Sources

Needed for muscle and neuron

function; heart health; builds bone
Osteoporosis, rickets, muscle Milk, yogurt, fish, green leafy
*Calcium and supports synthesis and
spasms, impaired growth vegetables, legumes
function of blood cells; nerve
function

Needed for production of

hydrochloric acid (HCl) in the Muscle cramps, mood
*Chlorine Table salt
stomach and nerve function; disturbances, reduced appetite
osmotic balance

Required component of many

redox enzymes, including Liver, oysters, cocoa, chocolate,
Copper (trace amounts) Copper deficiency is rare
cytochrome c oxidase; cofactor sesame, nuts
for hemoglobin synthesis

Required for the synthesis of Seafood, iodized salt, dairy

Iodine Goiter
thyroid hormones products

Required for many proteins and Anemia, which causes poor Red meat, leafy green vegetables,
Iron enzymes, notably hemoglobin, to concentration, fatigue, and poor fish (tuna, salmon), eggs, dried
prevent anemia immune function fruits, beans, whole grains

Required co-factor for ATP

formation; bone formation; Mood disturbances, muscle Whole grains, leafy green
*Magnesium
normal membrane functions; spasms vegetables
muscle function

A cofactor in enzyme functions;

Manganese (trace amounts) Manganese deficiency is rare Common in most foods
trace amounts are required

Acts as a cofactor for three

essential enzymes in humans:
Molybdenum (trace amounts) Molybdenum deficiency is rare
sulfite oxidase, xanthine oxidase,
and aldehyde oxidase

A component of bones and teeth;

Weakness, bone abnormalities, Milk, hard cheese, whole grains,
*Phosphorus helps regulate acid-base balance;
calcium loss meats
nucleotide synthesis

Vital for muscles, heart, and nerve Cardiac rhythm disturbance, Legumes, potato skin, tomatoes,
*Potassium
function muscle weakness bananas

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 Mineral Function Deficiencies Can Lead To Sources

A cofactor essential to activity of

antioxidant enzymes like
Selenium (trace amounts) Selenium deficiency is rare Common in most foods
glutathione peroxidase; trace
amounts are required

Systemic electrolyte required for

many functions; acid-base Muscle cramps, fatigue, reduced
*Sodium Table salt
balance; water balance; nerve appetite
function

Required for several enzymes

such as carboxypeptidase, liver Anemia, poor wound healing, can
Zinc (trace amounts) Common in most foods
alcohol dehydrogenase, and lead to short stature
carbonic anhydrase

*Greater than 200mg/day required

Table [Link]: Essential Amino Acids

Amino acids that must be consumed Amino acids anabolized by the body

isoleucine alanine

leucine selenocysteine

lysine aspartate

methionine cysteine

phenylalanine glutamate

tryptophan glycine

valine proline

histidine* serine

threonine tyrosine

arginine* asparagine

*The human body can synthesize histidine and arginine, but not in the quantities required, especially for growing children.

Food Energy and ATP

Animals need food to obtain energy and maintain homeostasis. Homeostasis is the ability of a system to maintain a stable internal
environment even in the face of external changes to the environment. For example, the normal body temperature of humans is 37°C
(98.6°F). Humans maintain this temperature even when the external temperature is hot or cold. It takes energy to maintain this
body temperature, and animals obtain this energy from food.
The primary source of energy for animals is carbohydrates, mainly glucose. Glucose is called the body’s fuel. The digestible
carbohydrates in an animal’s diet are converted to glucose molecules through a series of catabolic chemical reactions.
Adenosine triphosphate, or ATP, is the primary energy currency in cells; ATP stores energy in phosphate ester bonds. ATP releases
energy when the phosphodiester bonds are broken and ATP is converted to ADP and a phosphate group. ATP is produced by the
oxidative reactions in the cytoplasm and mitochondrion of the cell, where carbohydrates, proteins, and fats undergo a series of
metabolic reactions collectively called cellular respiration. For example, glycolysis is a series of reactions in which glucose is
converted to pyruvic acid and some of its chemical potential energy is transferred to NADH and ATP.
ATP is required for all cellular functions. It is used to build the organic molecules that are required for cells and tissues; it provides
energy for muscle contraction and for the transmission of electrical signals in the nervous system. When the amount of ATP is
available in excess of the body’s requirements, the liver uses the excess ATP and excess glucose to produce molecules called
glycogen. Glycogen is a polymeric form of glucose and is stored in the liver and skeletal muscle cells. When blood sugar drops, the
liver releases glucose from stores of glycogen. Skeletal muscle converts glycogen to glucose during intense exercise. The process

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of converting glucose and excess ATP to glycogen and the storage of excess energy is an evolutionarily important step in helping
animals deal with mobility, food shortages, and famine.

Everyday Connection: Obesity

Obesity is a major health concern in the United States, and there is a growing focus on reducing obesity and the diseases it may
lead to, such as type-2 diabetes, cancers of the colon and breast, and cardiovascular disease. How does the food consumed
contribute to obesity?
Fatty foods are calorie-dense, meaning that they have more calories per unit mass than carbohydrates or proteins. One gram of
carbohydrates has four calories, one gram of protein has four calories, and one gram of fat has nine calories. Animals tend to
seek lipid-rich food for their higher energy content.
The signals of hunger (“time to eat”) and satiety (“time to stop eating”) are controlled in the hypothalamus region of the brain.
Foods that are rich in fatty acids tend to promote satiety more than foods that are rich only in carbohydrates.
Excess carbohydrate and ATP are used by the liver to synthesize glycogen. The pyruvate produced during glycolysis is used to
synthesize fatty acids. When there is more glucose in the body than required, the resulting excess pyruvate is converted into
molecules that eventually result in the synthesis of fatty acids within the body. These fatty acids are stored in adipose cells—
the fat cells in the mammalian body whose primary role is to store fat for later use.
It is important to note that some animals benefit from obesity. Polar bears and seals need body fat for insulation and to keep
them from losing body heat during Arctic winters. When food is scarce, stored body fat provides energy for maintaining
homeostasis. Fats prevent famine in mammals, allowing them to access energy when food is not available on a daily basis; fats
are stored when a large kill is made or lots of food is available.

Summary
Animal diet should be balanced and meet the needs of the body. Carbohydrates, proteins, and fats are the primary components of
food. Some essential nutrients are required for cellular function but cannot be produced by the animal body. These include
vitamins, minerals, some fatty acids, and some amino acids. Food intake in more than necessary amounts is stored as glycogen in
the liver and muscle cells, and in fat cells. Excess adipose storage can lead to obesity and serious health problems. ATP is the
energy currency of the cell and is obtained from the metabolic pathways. Excess carbohydrates and energy are stored as glycogen
in the body.

Glossary
essential nutrient
nutrient that cannot be synthesized by the body; it must be obtained from food

mineral
inorganic, elemental molecule that carries out important roles in the body

vitamin
organic substance necessary in small amounts to sustain life

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OpenStax.
34.2: Nutrition and Energy Production by OpenStax is licensed CC BY 4.0.

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17.1.4: Digestive System Processes
Skills to Develop
Describe the process of digestion
Detail the steps involved in digestion and absorption
Define elimination
Explain the role of both the small and large intestines in absorption

Obtaining nutrition and energy from food is a multi-step process. For true animals, the first step is ingestion, the act of taking in
food. This is followed by digestion, absorption, and elimination. In the following sections, each of these steps will be discussed in
detail.

Ingestion
The large molecules found in intact food cannot pass through the cell membranes. Food needs to be broken into smaller particles so
that animals can harness the nutrients and organic molecules. The first step in this process is ingestion. Ingestion is the process of
taking in food through the mouth. In vertebrates, the teeth, saliva, and tongue play important roles in mastication (preparing the
food into bolus). While the food is being mechanically broken down, the enzymes in saliva begin to chemically process the food as
well. The combined action of these processes modifies the food from large particles to a soft mass that can be swallowed and can
travel the length of the esophagus.

Digestion and Absorption

Digestion is the mechanical and chemical break down of food into small organic fragments. It is important to break down
macromolecules into smaller fragments that are of suitable size for absorption across the digestive epithelium. Large, complex
molecules of proteins, polysaccharides, and lipids must be reduced to simpler particles such as simple sugar before they can be
absorbed by the digestive epithelial cells. Different organs play specific roles in the digestive process. The animal diet needs
carbohydrates, protein, and fat, as well as vitamins and inorganic components for nutritional balance. How each of these
components is digested is discussed in the following sections.

Carbohydrates
The digestion of carbohydrates begins in the mouth. The salivary enzyme amylase begins the breakdown of food starches into
maltose, a disaccharide. As the bolus of food travels through the esophagus to the stomach, no significant digestion of
carbohydrates takes place. The esophagus produces no digestive enzymes but does produce mucous for lubrication. The acidic
environment in the stomach stops the action of the amylase enzyme.
The next step of carbohydrate digestion takes place in the duodenum. Recall that the chyme from the stomach enters the duodenum
and mixes with the digestive secretion from the pancreas, liver, and gallbladder. Pancreatic juices also contain amylase, which
continues the breakdown of starch and glycogen into maltose, a disaccharide. The disaccharides are broken down into
monosaccharides by enzymes called maltases, sucrases, and lactases, which are also present in the brush border of the small
intestinal wall. Maltase breaks down maltose into glucose. Other disaccharides, such as sucrose and lactose are broken down by
sucrase and lactase, respectively. Sucrase breaks down sucrose (or “table sugar”) into glucose and fructose, and lactase breaks
down lactose (or “milk sugar”) into glucose and galactose. The monosaccharides (glucose) thus produced are absorbed and then
can be used in metabolic pathways to harness energy. The monosaccharides are transported across the intestinal epithelium into the
bloodstream to be transported to the different cells in the body. The steps in carbohydrate digestion are summarized in Figure
[Link].

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 Figure [Link] : Digestion of carbohydrates is performed by several enzymes. Starch and glycogen are broken down into glucose
by amylase and maltase. Sucrose (table sugar) and lactose (milk sugar) are broken down by sucrase and lactase, respectively.
Table [Link]: Digestion of Carbohydrates
Enzyme Produced By Site of Action Substrate Acting On End Products

Disaccharides (maltose),
Salivary amylase Salivary glands Mouth Polysaccharides (Starch)
oligosaccharides
Disaccharides (maltose),
Pancreatic amylase Pancreas Small intestine Polysaccharides (starch)
monosaccharides
Monosaccharides (e.g.,
Lining of the intestine;
Oligosaccharidases Small intestine Disaccharides glucose, fructose,
brush border membrane
galactose)

Protein
A large part of protein digestion takes place in the stomach. The enzyme pepsin plays an important role in the digestion of proteins
by breaking down the intact protein to peptides, which are short chains of four to nine amino acids. In the duodenum, other
enzymes—trypsin, elastase, and chymotrypsin—act on the peptides reducing them to smaller peptides. Trypsin elastase,
carboxypeptidase, and chymotrypsin are produced by the pancreas and released into the duodenum where they act on the chyme.
Further breakdown of peptides to single amino acids is aided by enzymes called peptidases (those that break down peptides).
Specifically, carboxypeptidase, dipeptidase, and aminopeptidase play important roles in reducing the peptides to free amino acids.
The amino acids are absorbed into the bloodstream through the small intestines. The steps in protein digestion are summarized in
Figure [Link].

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 Figure [Link] : Protein digestion is a multistep process that begins in the stomach and continues through the intestines.
Table [Link]: Digestion of Protein
Enzyme Produced By Site of Action Substrate Acting On End Products

Pepsin Stomach chief cells Stomach Proteins Peptides

Trypsin
Pancreas Small intestine Proteins Peptides
Elastase Chymotrypsin

Carboxypeptidase Pancreas Small intestine Peptides Amino acids and peptides

Aminopeptidase
Lining of intestine Small intestine Peptides Amino acids
Dipeptidase

Lipids
Lipid digestion begins in the stomach with the aid of lingual lipase and gastric lipase. However, the bulk of lipid digestion occurs in
the small intestine due to pancreatic lipase. When chyme enters the duodenum, the hormonal responses trigger the release of bile,
which is produced in the liver and stored in the gallbladder. Bile aids in the digestion of lipids, primarily triglycerides by
emulsification. Emulsification is a process in which large lipid globules are broken down into several small lipid globules. These

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small globules are more widely distributed in the chyme rather than forming large aggregates. Lipids are hydrophobic substances:
in the presence of water, they will aggregate to form globules to minimize exposure to water. Bile contains bile salts, which are
amphipathic, meaning they contain hydrophobic and hydrophilic parts. Thus, the bile salts hydrophilic side can interface with water
on one side and the hydrophobic side interfaces with lipids on the other. By doing so, bile salts emulsify large lipid globules into
small lipid globules.
Why is emulsification important for digestion of lipids? Pancreatic juices contain enzymes called lipases (enzymes that break down
lipids). If the lipid in the chyme aggregates into large globules, very little surface area of the lipids is available for the lipases to act
on, leaving lipid digestion incomplete. By forming an emulsion, bile salts increase the available surface area of the lipids many
fold. The pancreatic lipases can then act on the lipids more efficiently and digest them, as detailed in Figure [Link]. Lipases
break down the lipids into fatty acids and glycerides. These molecules can pass through the plasma membrane of the cell and enter
the epithelial cells of the intestinal lining. The bile salts surround long-chain fatty acids and monoglycerides forming tiny spheres
called micelles. The micelles move into the brush border of the small intestine absorptive cells where the long-chain fatty acids and
monoglycerides diffuse out of the micelles into the absorptive cells leaving the micelles behind in the chyme. The long-chain fatty
acids and monoglycerides recombine in the absorptive cells to form triglycerides, which aggregate into globules and become coated
with proteins. These large spheres are called chylomicrons. Chylomicrons contain triglycerides, cholesterol, and other lipids and
have proteins on their surface. The surface is also composed of the hydrophilic phosphate "heads" of phospholipids. Together, they
enable the chylomicron to move in an aqueous environment without exposing the lipids to water. Chylomicrons leave the
absorptive cells via exocytosis. Chylomicrons enter the lymphatic vessels, and then enter the blood in the subclavian vein.

Figure [Link] : Lipids are digested and absorbed in the small intestine.

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Vitamins
Vitamins can be either water-soluble or lipid-soluble. Fat soluble vitamins are absorbed in the same manner as lipids. It is important
to consume some amount of dietary lipid to aid the absorption of lipid-soluble vitamins. Water-soluble vitamins can be directly
absorbed into the bloodstream from the intestine.

Art Connection

Figure [Link] : Mechanical and chemical digestion of food takes place in many steps, beginning in the mouth and ending in
the rectum.
Which of the following statements about digestive processes is true?
A. Amylase, maltase, and lactase in the mouth digest carbohydrates.
B. Trypsin and lipase in the stomach digest protein.
C. Bile emulsifies lipids in the small intestine.
D. No food is absorbed until the small intestine.

Elimination
The final step in digestion is the elimination of undigested food content and waste products. The undigested food material enters
the colon, where most of the water is reabsorbed. Recall that the colon is also home to the microflora called “intestinal flora” that
aid in the digestion process. The semi-solid waste is moved through the colon by peristaltic movements of the muscle and is stored

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in the rectum. As the rectum expands in response to storage of fecal matter, it triggers the neural signals required to set up the urge
to eliminate. The solid waste is eliminated through the anus using peristaltic movements of the rectum.

Common Problems with Elimination

Diarrhea and constipation are some of the most common health concerns that affect digestion. Constipation is a condition where the
feces are hardened because of excess water removal in the colon. In contrast, if enough water is not removed from the feces, it
results in diarrhea. Many bacteria, including the ones that cause cholera, affect the proteins involved in water reabsorption in the
colon and result in excessive diarrhea.

Emesis
Emesis, or vomiting, is elimination of food by forceful expulsion through the mouth. It is often in response to an irritant that affects
the digestive tract, including but not limited to viruses, bacteria, emotions, sights, and food poisoning. This forceful expulsion of
the food is due to the strong contractions produced by the stomach muscles. The process of emesis is regulated by the medulla.

Summary
Digestion begins with ingestion, where the food is taken in the mouth. Digestion and absorption take place in a series of steps with
special enzymes playing important roles in digesting carbohydrates, proteins, and lipids. Elimination describes removal of
undigested food contents and waste products from the body. While most absorption occurs in the small intestines, the large intestine
is responsible for the final removal of water that remains after the absorptive process of the small intestines. The cells that line the
large intestine absorb some vitamins as well as any leftover salts and water. The large intestine (colon) is also where feces is
formed.

Art Connections
Figure [Link]: Which of the following statements about digestive processes is true?
A. Amylase, maltase and lactase in the mouth digest carbohydrates.
B. Trypsin and lipase in the stomach digest protein.
C. Bile emulsifies lipids in the small intestine.
D. No food is absorbed until the small intestine.

Answer
C

Glossary
aminopeptidase
protease that breaks down peptides to single amino acids; secreted by the brush border of small intestine

carboxypeptidase
protease that breaks down peptides to single amino acids; secreted by the brush border of the small intestine

chylomicron
small lipid globule

chymotrypsin
pancreatic protease

digestion
mechanical and chemical break down of food into small organic fragments

dipeptidase
protease that breaks down peptides to single amino acids; secreted by the brush border of small intestine

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elastase
pancreatic protease

ingestion
act of taking in food

lactase
enzyme that breaks down lactose into glucose and galactose

maltase
enzyme that breaks down maltose into glucose

sucrase
enzyme that breaks down sucrose into glucose and fructose

trypsin
pancreatic protease that breaks down protein

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34.3: Digestive System Processes by OpenStax is licensed CC BY 4.0.

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17.1.5: Digestive System Regulation
Skills to Develop
Discuss the role of neural regulation in digestive processes
Explain how hormones regulate digestion

The brain is the control center for the sensation of hunger and satiety. The functions of the digestive system are regulated through
neural and hormonal responses.

Neural Responses to Food

In reaction to the smell, sight, or thought of food, like that shown in Figure [Link], the first hormonal response is that of
salivation. The salivary glands secrete more saliva in response to the stimulus presented by food in preparation for digestion.
Simultaneously, the stomach begins to produce hydrochloric acid to digest the food. Recall that the peristaltic movements of the
esophagus and other organs of the digestive tract are under the control of the brain. The brain prepares these muscles for movement
as well. When the stomach is full, the part of the brain that detects satiety signals fullness. There are three overlapping phases of
gastric control—the cephalic phase, the gastric phase, and the intestinal phase—each requires many enzymes and is under neural
control as well.

Figure [Link] : Seeing a plate of food triggers the secretion of saliva in the mouth and the production of HCL in the stomach.
(credit: Kelly Bailey)

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Digestive Phases
The response to food begins even before food enters the mouth. The first phase of ingestion, called the cephalic phase, is controlled
by the neural response to the stimulus provided by food. All aspects—such as sight, sense, and smell—trigger the neural responses
resulting in salivation and secretion of gastric juices. The gastric and salivary secretion in the cephalic phase can also take place
due to the thought of food. Right now, if you think about a piece of chocolate or a crispy potato chip, the increase in salivation is a
cephalic phase response to the thought. The central nervous system prepares the stomach to receive food.
The gastric phase begins once the food arrives in the stomach. It builds on the stimulation provided during the cephalic phase.
Gastric acids and enzymes process the ingested materials. The gastric phase is stimulated by (1) distension of the stomach, (2) a
decrease in the pH of the gastric contents, and (3) the presence of undigested material. This phase consists of local, hormonal, and
neural responses. These responses stimulate secretions and powerful contractions.
The intestinal phase begins when chyme enters the small intestine triggering digestive secretions. This phase controls the rate of
gastric emptying. In addition to gastrin emptying, when chyme enters the small intestine, it triggers other hormonal and neural
events that coordinate the activities of the intestinal tract, pancreas, liver, and gallbladder.

Hormonal Responses to Food

The endocrine system controls the response of the various glands in the body and the release of hormones at the appropriate times.
One of the important factors under hormonal control is the stomach acid environment. During the gastric phase, the hormone
gastrin is secreted by G cells in the stomach in response to the presence of proteins. Gastrin stimulates the release of stomach acid,
or hydrochloric acid (HCl) which aids in the digestion of the proteins. However, when the stomach is emptied, the acidic
environment need not be maintained and a hormone called somatostatin stops the release of hydrochloric acid. This is controlled by
a negative feedback mechanism.
In the duodenum, digestive secretions from the liver, pancreas, and gallbladder play an important role in digesting chyme during
the intestinal phase. In order to neutralize the acidic chyme, a hormone called secretin stimulates the pancreas to produce alkaline
bicarbonate solution and deliver it to the duodenum. Secretin acts in tandem with another hormone called cholecystokinin (CCK).
Not only does CCK stimulate the pancreas to produce the requisite pancreatic juices, it also stimulates the gallbladder to release
bile into the duodenum.
Another level of hormonal control occurs in response to the composition of food. Foods high in lipids take a long time to digest. A
hormone called gastric inhibitory peptide is secreted by the small intestine to slow down the peristaltic movements of the intestine
to allow fatty foods more time to be digested and absorbed.
Understanding the hormonal control of the digestive system is an important area of ongoing research. Scientists are exploring the
role of each hormone in the digestive process and developing ways to target these hormones. Advances could lead to knowledge
that may help to battle the obesity epidemic.

Summary
The brain and the endocrine system control digestive processes. The brain controls the responses of hunger and satiety. The
endocrine system controls the release of hormones and enzymes required for digestion of food in the digestive tract.

Glossary
cephalic phase
first phase of digestion, controlled by the neural response to the stimulus provided by food

cholecystokinin
hormone that stimulates the contraction of the gallbladder to release bile

endocrine system
system that controls the response of the various glands in the body and the release of hormones at the appropriate times

gastric inhibitory peptide

Access for free at OpenStax [Link] [Link]

 hormone secreted by the small intestine in the presence of fatty acids and sugars; it also inhibits acid production and peristalsis
in order to slow down the rate at which food enters the small intestine

gastric phase
digestive phase beginning once food enters the stomach; gastric acids and enzymes process the ingested materials

gastrin
hormone which stimulates hydrochloric acid secretion in the stomach

intestinal phase
third digestive phase; begins when chyme enters the small intestine triggering digestive secretions and controlling the rate of
gastric emptying

secretin
hormone which stimulates sodium bicarbonate secretion in the small intestine

somatostatin
hormone released to stop acid secretion when the stomach is empty

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34.4: Digestive System Regulation by OpenStax is licensed CC BY 4.0.

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17.1.E: Animal Nutrition and the Digestive System (Exercises)
34.1: Digestive Systems
Animals obtain their nutrition from the consumption of other organisms. Depending on their diet, animals can be classified into the
following categories: plant eaters (herbivores), meat eaters (carnivores), and those that eat both plants and animals (omnivores).
The nutrients and macromolecules present in food are not immediately accessible to the cells. There are processes that modify food
within the animal body to make the nutrients and organic molecules needed for cellular function.

Review Questions
Which of the following is a pseudo-ruminant?
A. cow
B. pig
C. crow
D. horse

Answer
D

Which of the following statements is untrue?

A. Roughage takes a long time to digest.
B. Birds eat large quantities at one time so that they can fly long distances.
C. Cows do not have upper teeth.
D. In pseudo-ruminants, roughage is digested in the cecum.

Answer
B

The acidic nature of chyme is neutralized by ________.

A. potassium hydroxide
B. sodium hydroxide
C. bicarbonates
D. vinegar

Answer
C

The digestive juices from the liver are delivered to the ________.
A. stomach
B. liver
C. duodenum
D. colon

Answer
C

Free Response
How does the polygastric digestive system aid in digesting roughage?

17.1.E.1 [Link]
 Answer
Animals with a polygastric digestive system have a multi-chambered stomach. The four compartments of the stomach are
called the rumen, reticulum, omasum, and abomasum. These chambers contain many microbes that break down the
cellulose and ferment the ingested food. The abomasum is the “true” stomach and is the equivalent of a monogastric
stomach chamber where gastric juices are secreted. The four-compartment gastric chamber provides larger space and the
microbial support necessary for ruminants to digest plant material.

How do birds digest their food in the absence of teeth?

Answer
Birds have a stomach chamber called a gizzard. Here, the food is stored, soaked, and ground into finer particles, often using
pebbles. Once this process is complete, the digestive juices take over in the proventriculus and continue the digestive
process.

What is the role of the accessory organs in digestion?

Answer
Accessory organs play an important role in producing and delivering digestive juices to the intestine during digestion and
absorption. Specifically, the salivary glands, liver, pancreas, and gallbladder play important roles. Malfunction of any of
these organs can lead to disease states.

Explain how the villi and microvilli aid in absorption.

Answer
The villi and microvilli are folds on the surface of the small intestine. These folds increase the surface area of the intestine
and provide more area for the absorption of nutrients.

34.2: Nutrition and Energy Production

Given the diversity of animal life on our planet, it is not surprising that the animal diet would also vary substantially. The animal
diet is the source of materials needed for building DNA and other complex molecules needed for growth, maintenance, and
reproduction; collectively these processes are called biosynthesis. The diet is also the source of materials for ATP production in the
cells. The diet must be balanced to provide the minerals and vitamins that are required for cellular function.

Review Questions
Which of the following statements is not true?
A. Essential nutrients can be synthesized by the body.
B. Vitamins are required in small quantities for bodily function.
C. Some amino acids can be synthesized by the body, while others need to be obtained from diet.
D. Vitamins come in two categories: fat-soluble and water-soluble.

Answer
A

Which of the following is a water-soluble vitamin?

A. vitamin A
B. vitamin E
C. vitamin K
D. vitamin C

17.1.E.2 [Link]
 Answer
D

What is the primary fuel for the body?

A. carbohydrates
B. lipids
C. protein
D. glycogen

Answer
A

Excess glucose is stored as ________.

A. fat
B. glucagon
C. glycogen
D. it is not stored in the body

Answer
C

Free Response
What are essential nutrients?

Answer
Essential nutrients are those nutrients that must be obtained from the diet because they cannot be produced by the body.
Vitamins and minerals are examples of essential nutrients.

What is the role of minerals in maintaining good health?

Answer
Minerals—such as potassium, sodium, and calcium—are required for the functioning of many cellular processes, including
muscle contraction and nerve conduction. While minerals are required in trace amounts, not having minerals in the diet can
be potentially harmful.

Discuss why obesity is a growing epidemic.

Answer
In the United States, obesity, particularly childhood obesity, is a growing concern. Some of the contributors to this situation
include sedentary lifestyles and consuming more processed foods and less fruits and vegetables. As a result, even young
children who are obese can face health concerns.

There are several nations where malnourishment is a common occurrence. What may be some of the health challenges posed
by malnutrition?

Answer
Malnutrition, often in the form of not getting enough calories or not enough of the essential nutrients, can have severe
consequences. Many malnourished children have vision and dental problems, and over the years may develop many serious

17.1.E.3 [Link]
 health problems.

34.3: Digestive System Processes

Obtaining nutrition and energy from food is a multi-step process. For true animals, the first step is ingestion, the act of taking in
food. This is followed by digestion, absorption, and elimination. In the following sections, each of these steps will be discussed in
detail.

Review Questions
Where does the majority of protein digestion take place?
A. stomach
B. duodenum
C. mouth
D. jejunum

Answer
A

Lipases are enzymes that break down ________.

A. disaccharides
B. lipids
C. proteins
D. cellulose

Answer
B

Free Response
Explain why some dietary lipid is a necessary part of a balanced diet.

Answer
Lipids add flavor to food and promote a sense of satiety or fullness. Fatty foods are sources of high energy; one gram of
lipid contains nine calories. Lipids are also required in the diet to aid the absorption of lipid-soluble vitamins and for the
production of lipid-soluble hormones.

34.4: Digestive System Regulation

The brain is the control center for the sensation of hunger and satiety. The functions of the digestive system are regulated through
neural and hormonal responses.

Review Questions
Which hormone controls the release of bile from the gallbladder
A. pepsin
B. amylase
C. CCK
D. gastrin

Answer
C

17.1.E.4 [Link]
 Which hormone stops acid secretion in the stomach?
A. gastrin
B. somatostatin
C. gastric inhibitory peptide
D. CCK

Answer
B

Free Response
Describe how hormones regulate digestion.

Answer
Hormones control the different digestive enzymes that are secreted in the stomach and the intestine during the process of
digestion and absorption. For example, the hormone gastrin stimulates stomach acid secretion in response to food intake.
The hormone somatostatin stops the release of stomach acid.

Describe one or more scenarios where loss of hormonal regulation of digestion can lead to diseases.

Answer
There are many cases where loss of hormonal regulation can lead to illnesses. For example, the bilirubin produced by the
breakdown of red blood cells is converted to bile by the liver. When there is malfunction of this process, there is excess
bilirubin in the blood and bile levels are low. As a result, the body struggles with dealing with fatty food. This is why a
patient suffering from jaundice is asked to eat a diet with almost zero fat.

17.1.E: Animal Nutrition and the Digestive System (Exercises) is shared under a CC BY license and was authored, remixed, and/or curated by
LibreTexts.
34.E: Animal Nutrition and the Digestive System (Exercises) is licensed CC BY 4.0.

17.1.E.5 [Link]
17.2: Nervous System
As you read this, your nervous system is performing several functions simultaneously. The visual system is processing what is seen
on the page; the motor system controls your eye movements and the turn of the pages (or click of the mouse); the prefrontal cortex
maintains attention. Even fundamental functions, like breathing and regulation of body temperature, are controlled by the nervous
system. The nervous system is one of two systems that exert control over all the organ systems of the body; the other is the
endocrine system. The nervous system’s control is much more specific and rapid than the hormonal system. It communicates
signals through cells and the tiny gaps between them rather than through the circulatory system as in the endocrine system. It uses a
combination of chemical and electrochemical signals, rather than purely chemical signals used by the endocrine system to cover
long distances quickly. The nervous system acquires information from sensory organs, processes it and then may initiate a response
either through motor function, leading to movement, or in a change in the organism’s physiological state.
Nervous systems throughout the animal kingdom vary in structure and complexity. Some organisms, like sea sponges, lack a true
nervous system. Others, like jellyfish, lack a true brain and instead have a system of separate but connected nerve cells (neurons)
called a “nerve net.” Flatworms have both a central nervous system (CNS), made up of a ganglion (clusters of connected neurons)
and two nerve cords, and a peripheral nervous system (PNS) containing a system of nerves that extend throughout the body. The
insect nervous system is more complex but also fairly decentralized. It contains a brain, ventral nerve cord, and ganglia. These
ganglia can control movements and behaviors without input from the brain.
Compared to invertebrates, vertebrate nervous systems are more complex, centralized, and specialized. While there is great
diversity among different vertebrate nervous systems, they all share a basic structure: a CNS that contains a brain and spinal cord
and a PNS made up of peripheral sensory and motor nerves. One interesting difference between the nervous systems of
invertebrates and vertebrates is that the nerve cords of many invertebrates are located ventrally (toward the stomach) whereas the
vertebrate spinal cords are located dorsally (toward the back). There is debate among evolutionary biologists as to whether these
different nervous system plans evolved separately or whether the invertebrate body plan arrangement somehow “flipped” during
the evolution of vertebrates.
The nervous system is made up of neurons, specialized cells that can receive and transmit chemical or electrical signals, and glia,
cells that provide support functions for the neurons. There is great diversity in the types of neurons and glia that are present in
different parts of the nervous system.

Neurons and Glial Cells

The nervous system of the common laboratory fly, Drosophila melanogaster, contains around 100,000 neurons, the same number
as a lobster. This number compares to 75 million in the mouse and 300 million in the octopus. A human brain contains around 86
billion neurons. Despite these very different numbers, the nervous systems of these animals control many of the same behaviors—
from basic reflexes to more complicated behaviors like finding food and courting mates. The ability of neurons to communicate
with each other as well as with other types of cells underlies all of these behaviors.
Most neurons share the same cellular components. But neurons are also highly specialized—different types of neurons have
different sizes and shapes that relate to their functional roles.
Like other cells, each neuron has a cell body (or soma) that contains a nucleus, smooth and rough endoplasmic reticulum, Golgi
apparatus, mitochondria, and other cellular components. Neurons also contain unique structures for receiving and sending the
electrical signals that make communication between neurons possible (Figure 17.2.1). Dendrites are tree-like structures that extend
away from the cell body to receive messages from other neurons at specialized junctions called synapses. Although some neurons
do not have any dendrites, most have one or many dendrites.
The bilayer lipid membrane that surrounds a neuron is impermeable to ions. To enter or exit the neuron, ions must pass through ion
channels that span the membrane. Some ion channels need to be activated to open and allow ions to pass into or out of the cell.
These ion channels are sensitive to the environment and can change their shape accordingly. Ion channels that change their
structure in response to voltage changes are called voltage-gated ion channels. The difference in total charge between the inside and
outside of the cell is called the membrane potential.
A neuron at rest is negatively charged: the inside of a cell is approximately 70 millivolts more negative than the outside (–70 mV).
This voltage is called the resting membrane potential; it is caused by differences in the concentrations of ions inside and outside the
cell and the selective permeability created by ion channels. Sodium-potassium pumps in the membrane produce the different ion

Access for free at OpenStax 17.2.1 [Link]

concentrations inside and outside of the cell by bringing in two K+ions and removing three Na+ ions. The actions of this pump are
costly: one molecule of ATP is used up for each turn. Up to 50 percent of a neuron’s ATP is used in maintaining its membrane
resting potential. Potassium ions (K+), which are higher inside the cell, move fairly freely out of the neuron through potassium
channels; this loss of positive charge produces a net negative charge inside the cell. Sodium ions (Na+), which are low inside, have
a driving force to enter but move less freely. Their channels are voltage dependent and will open when a slight change in the
membrane potential triggers them.
A neuron can receive input from other neurons and, if this input is strong enough, send the signal to downstream neurons.
Transmission of a signal between neurons is generally carried by a chemical, called a neurotransmitter, which diffuses from the
axon of one neuron to the dendrite of a second neuron. When neurotransmitter molecules bind to receptors located on a neuron’s
dendrites, the neurotransmitter opens ion channels in the dendrite’s plasma membrane. This opening allows sodium ions to enter
the neuron and results in depolarizationof the membrane—a decrease in the voltage across the neuron membrane. Once a signal is
received by the dendrite, it then travels passively to the cell body. A large enough signal from neurotransmitters will reach the
axon. If it is strong enough (that is, if the threshold of excitation, a depolarization to around –60mV is reached), then depolarization
creates a positive feedback loop: as more Na+ ions enter the cell, the axon becomes further depolarized, opening even more sodium
channels at further distances from the cell body. This will cause voltage dependent Na+ channels further down the axon to open and
more positive ions to enter the cell. In the axon, this “signal” will become a self-propagating brief reversal of the resting membrane
potential called an action potential.
An action potential is an all-or-nothing event; it either happens or it does not. The threshold of excitation must be reached for the
neuron to “fire” an action potential. As sodium ions rush into the cell, depolarization actually reverses the charge across the
membrane form -70mv to +30mV. This change in the membrane potential causes voltage-gated K+ channels to open, and K+ begins
to leave the cell, repolarizing it. At the same time, Na+ channels inactivate so no more Na+ enters the cell. K+ ions continue to leave
the cell and the membrane potential returns to the resting potential. At the resting potential, the K+ channels close and Na+channels
reset. The depolarization of the membrane proceeds in a wave down the length of the axon. It travels in only one direction because
the sodium channels have been inactivated and unavailable until the membrane potential is near the resting potential again; at this
point they are reset to closed and can be opened again.
An axon is a tube-like structure that propagates the signal from the cell body to specialized endings called axon terminals. These
terminals in turn then synapse with other neurons, muscle, or target organs. When the action potential reaches the axon terminal,
this causes the release of neurotransmitter onto the dendrite of another neuron. Neurotransmitters released at axon terminals allow
signals to be communicated to these other cells, and the process begins again. Neurons usually have one or two axons, but some
neurons do not contain any axons.
Some axons are covered with a special structure called a myelin sheath, which acts as an insulator to keep the electrical signal from
dissipating as it travels down the axon. This insulation is important, as the axon from a human motor neuron can be as long as a
meter (3.2 ft)—from the base of the spine to the toes. The myelin sheath is produced by glial cells. Along the axon there are
periodic gaps in the myelin sheath. These gaps are called nodes of Ranvier and are sites where the signal is “recharged” as it travels
along the axon.
It is important to note that a single neuron does not act alone—neuronal communication depends on the connections that neurons
make with one another (as well as with other cells, like muscle cells). Dendrites from a single neuron may receive synaptic contact
from many other neurons. For example, dendrites from a Purkinje cell in the cerebellum are thought to receive contact from as
many as 200,000 other neurons.

Access for free at OpenStax 17.2.2 [Link]

 Figure 17.2.1: Neurons contain organelles common to other cells, such as a nucleus and mitochondria. They also have more
specialized structures, including dendrites and axons.

BIOLOGY IN ACTION: Neurogenesis

At one time, scientists believed that people were born with all the neurons they would ever have. Research performed during
the last few decades indicates that neurogenesis, the birth of new neurons, continues into adulthood. Neurogenesis was first
discovered in songbirds that produce new neurons while learning songs. For mammals, new neurons also play an important
role in learning: about 1,000 new neurons develop in the hippocampus (a brain structure involved in learning and memory)
each day. While most of the new neurons will die, researchers found that an increase in the number of surviving new neurons
in the hippocampus correlated with how well rats learned a new task. Interestingly, both exercise and some antidepressant
medications also promote neurogenesis in the hippocampus. Stress has the opposite effect. While neurogenesis is quite limited
compared to regeneration in other tissues, research in this area may lead to new treatments for disorders such as Alzheimer’s,
stroke, and epilepsy.
How do scientists identify new neurons? A researcher can inject a compound called bromodeoxyuridine (BrdU) into the brain
of an animal. While all cells will be exposed to BrdU, BrdU will only be incorporated into the DNA of newly generated cells
that are in S phase. A technique called immunohistochemistry can be used to attach a fluorescent label to the incorporated
BrdU, and a researcher can use fluorescent microscopy to visualize the presence of BrdU, and thus new neurons, in brain tissue
(Figure 17.2.2).

Access for free at OpenStax 17.2.3 [Link]

 Figure 17.2.2: This image shows new neurons in a rat hippocampus. New neurons tagged with BrdU glow red in this
micrograph. (credit: modification of work by Dr. Maryam Faiz, University of Barcelona)

CONCEPT IN ACTION

Visit this link interactive lab to see more information about neurogenesis, including an interactive laboratory simulation and a
video that explains how BrdU labels new cells.

While glial cells are often thought of as the supporting cast of the nervous system, the number of glial cells in the brain actually
outnumbers the number of neurons by a factor of 10. Neurons would be unable to function without the vital roles that are fulfilled
by these glial cells. Glia guide developing neurons to their destinations, buffer ions and chemicals that would otherwise harm
neurons, and provide myelin sheaths around axons. When glia do not function properly, the result can be disastrous—most brain
tumors are caused by mutations in glia.

How Neurons Communicate

All functions performed by the nervous system—from a simple motor reflex to more advanced functions like making a memory or
a decision—require neurons to communicate with one another. Neurons communicate between the axon of one neuron and the
dendrites, and sometimes the cell body, of another neuron across the gap between them, known as the synaptic cleft. When an
action potential reaches the end of an axon it stimulates the release of neurotransmitter molecules into the synaptic cleft between
the synaptic knob of the axon and the post-synaptic membrane of the dendrite or soma of the next cell. The neurotransmitter is
released through exocytosis of vesicles containing the neurotransmitter molecules. The neurotransmitter diffuses across the
synaptic cleft and binds to receptors in the post-synaptic membrane. These receptor molecules are chemically regulated ion
channels and will open, allowing sodium to enter the cell. If sufficient neurotransmitter has been released an action potential may
be initiated in the next cell, but this is not guaranteed. If insufficient neurotransmitter is released the nerve signal will die at this
point. There are a number of different neurotransmitters that are specific to neuron types that have specific functions.

The Central Nervous System

The central nervous system (CNS) is made up of the brain and spinal cord and is covered with three layers of protective coverings
called meninges (“meninges” is derived from the Greek and means “membranes”) (Figure 17.2.3). The outermost layer is the dura
mater, the middle layer is the web-like arachnoid mater, and the inner layer is the pia mater, which directly contacts and covers the
brain and spinal cord. The space between the arachnoid and pia maters is filled with cerebrospinal fluid (CSF). The brain floats in
CSF, which acts as a cushion and shock absorber.

Access for free at OpenStax 17.2.4 [Link]

 Figure 17.2.3: The cerebral cortex is covered by three layers of meninges: the dura, arachnoid, and pia maters. (credit:
modification of work by Gray's Anatomy)

The Brain
The brain is the part of the central nervous system that is contained in the cranial cavity of the skull. It includes the cerebral cortex,
limbic system, basal ganglia, thalamus, hypothalamus, cerebellum, brainstem, and retinas. The outermost part of the brain is a thick
piece of nervous system tissue called the cerebral cortex. The cerebral cortex, limbic system, and basal ganglia make up the two
cerebral hemispheres. A thick fiber bundle called the corpus callosum (corpus = “body”; callosum = “tough”) connects the two
hemispheres. Although there are some brain functions that are localized more to one hemisphere than the other, the functions of the
two hemispheres are largely redundant. In fact, sometimes (very rarely) an entire hemisphere is removed to treat severe epilepsy.
While patients do suffer some deficits following the surgery, they can have surprisingly few problems, especially when the surgery
is performed on children who have very immature nervous systems.
In other surgeries to treat severe epilepsy, the corpus callosum is cut instead of removing an entire hemisphere. This causes a
condition called split-brain, which gives insights into unique functions of the two hemispheres. For example, when an object is
presented to patients’ left visual field, they may be unable to verbally name the object (and may claim to not have seen an object at
all). This is because the visual input from the left visual field crosses and enters the right hemisphere and cannot then signal to the
speech center, which generally is found in the left side of the brain. Remarkably, if a split-brain patient is asked to pick up a
specific object out of a group of objects with the left hand, the patient will be able to do so but will still be unable to verbally
identify it.

CONCEPT IN ACTION

Visit the following website to learn more about split-brain patients and to play a game where you can model split-brain
experiments yourself.

Each hemisphere contains regions called lobes that are involved in different functions. Each hemisphere of the mammalian cerebral
cortex can be broken down into four functionally and spatially defined lobes: frontal, parietal, temporal, and occipital (Figure
17.2.4).

Access for free at OpenStax 17.2.5 [Link]

 Figure 17.2.4: The human cerebral cortex includes the frontal, parietal, temporal, and occipital lobes.
The frontal lobe is located at the front of the brain, over the eyes. This lobe contains the olfactory bulb, which processes smells.
The frontal lobe also contains the motor cortex, which is important for planning and implementing movement. Areas within the
motor cortex map to different muscle groups. Neurons in the frontal lobe also control cognitive functions like maintaining
attention, speech, and decision-making. Studies of humans who have damaged their frontal lobes show that parts of this area are
involved in personality, socialization, and assessing risk. The parietal lobe is located at the top of the brain. Neurons in the parietal
lobe are involved in speech and also reading. Two of the parietal lobe’s main functions are processing somatosensation—touch
sensations like pressure, pain, heat, cold—and processing proprioception—the sense of how parts of the body are oriented in space.
The parietal lobe contains a somatosensory map of the body similar to the motor cortex. The occipital lobe is located at the back of
the brain. It is primarily involved in vision—seeing, recognizing, and identifying the visual world. The temporal lobe is located at
the base of the brain and is primarily involved in processing and interpreting sounds. It also contains the hippocampus (named from
the Greek for “seahorse,” which it resembles in shape) a structure that processes memory formation. The role of the hippocampus
in memory was partially determined by studying one famous epileptic patient, HM, who had both sides of his hippocampus
removed in an attempt to cure his epilepsy. His seizures went away, but he could no longer form new memories (although he could
remember some facts from before his surgery and could learn new motor tasks).
Interconnected brain areas called the basal ganglia play important roles in movement control and posture. The basal ganglia also
regulate motivation.
The thalamus acts as a gateway to and from the cortex. It receives sensory and motor inputs from the body and also receives
feedback from the cortex. This feedback mechanism can modulate conscious awareness of sensory and motor inputs depending on
the attention and arousal state of the animal. The thalamus helps regulate consciousness, arousal, and sleep states.
Below the thalamus is the hypothalamus. The hypothalamus controls the endocrine system by sending signals to the pituitary
gland. Among other functions, the hypothalamus is the body’s thermostat—it makes sure the body temperature is kept at
appropriate levels. Neurons within the hypothalamus also regulate circadian rhythms, sometimes called sleep cycles.
The limbic system is a connected set of structures that regulates emotion, as well as behaviors related to fear and motivation. It
plays a role in memory formation and includes parts of the thalamus and hypothalamus as well as the hippocampus. One important
structure within the limbic system is a temporal lobe structure called the amygdala. The two amygdala (one on each side) are
important both for the sensation of fear and for recognizing fearful faces.
The cerebellum (cerebellum = “little brain”) sits at the base of the brain on top of the brainstem. The cerebellum controls balance
and aids in coordinating movement and learning new motor tasks. The cerebellum of birds is large compared to other vertebrates
because of the coordination required by flight.
The brainstem connects the rest of the brain with the spinal cord and regulates some of the most important and basic functions of
the nervous system including breathing, swallowing, digestion, sleeping, walking, and sensory and motor information integration.

Spinal cord
Connecting to the brainstem and extending down the body through the spinal column is the spinal cord. The spinal cord is a thick
bundle of nerve tissue that carries information about the body to the brain and from the brain to the body. The spinal cord is
contained within the meninges and the bones of the vertebral column but is able to communicate signals to and from the body

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through its connections with spinal nerves (part of the peripheral nervous system). A cross-section of the spinal cord looks like a
white oval containing a gray butterfly-shape (Figure 17.2.5). Axons make up the “white matter” and neuron and glia cell bodies
(and interneurons) make up the “gray matter.” Axons and cell bodies in the dorsa spinal cord convey mostly sensory information
from the body to the brain. Axons and cell bodies in the spinal cord primarily transmit signals controlling movement from the brain
to the body.
The spinal cord also controls motor reflexes. These reflexes are quick, unconscious movements—like automatically removing a
hand from a hot object. Reflexes are so fast because they involve local synaptic connections. For example, the knee reflex that a
doctor tests during a routine physical is controlled by a single synapse between a sensory neuron and a motor neuron. While a
reflex may only require the involvement of one or two synapses, synapses with interneurons in the spinal column transmit
information to the brain to convey what happened (the knee jerked, or the hand was hot).

Figure 17.2.5: A cross-section of the spinal cord shows gray matter (containing cell bodies and interneurons) and white matter
(containing myelinated axons).

The Peripheral Nervous System

The peripheral nervous system (PNS) is the connection between the central nervous system and the rest of the body. The PNS can
be broken down into the autonomic nervous system, which controls bodily functions without conscious control, and the sensory-
somatic nervous system, which transmits sensory information from the skin, muscles, and sensory organs to the CNS and sends
motor commands from the CNS to the muscles.

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Figure 17.2.6: In the autonomic nervous system, a preganglionic neuron (originating in the CNS) synapses to a neuron in a
ganglion that, in turn, synapses on a target organ. Activation of the sympathetic nervous system causes release of norepinephrine on
the target organ. Activation of the parasympathetic nervous system causes release of acetylcholine on the target organ.

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The autonomic nervous system serves as the relay between the CNS and the internal organs. It controls the lungs, the heart, smooth
muscle, and exocrine and endocrine glands. The autonomic nervous system controls these organs largely without conscious control;
it can continuously monitor the conditions of these different systems and implement changes as needed. Signaling to the target
tissue usually involves two synapses: a preganglionic neuron (originating in the CNS) synapses to a neuron in a ganglion that, in
turn, synapses on the target organ (Figure 17.2.6). There are two divisions of the autonomic nervous system that often have
opposing effects: the sympathetic nervous system and the parasympathetic nervous system.
The sympathetic nervous system is responsible for the immediate responses an animal makes when it encounters a dangerous
situation. One way to remember this is to think of the “fight-or-flight” response a person feels when encountering a snake (“snake”
and “sympathetic” both begin with “s”). Examples of functions controlled by the sympathetic nervous system include an
accelerated heart rate and inhibited digestion. These functions help prepare an organism’s body for the physical strain required to
escape a potentially dangerous situation or to fend off a predator.

Figure 17.2.7: The sympathetic and parasympathetic nervous systems often have opposing effects on target organs.

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While the sympathetic nervous system is activated in stressful situations, the parasympathetic nervous system allows an animal to
“rest and digest.” One way to remember this is to think that during a restful situation like a picnic, the parasympathetic nervous
system is in control (“picnic” and “parasympathetic” both start with “p”). Parasympathetic preganglionic neurons have cell bodies
located in the brainstem and in the sacral (toward the bottom) spinal cord (Figure 17.2.7). The parasympathetic nervous system
resets organ function after the sympathetic nervous system is activated including slowing of heart rate, lowered blood pressure, and
stimulation of digestion.
The sensory-somatic nervous system is made up of cranial and spinal nerves and contains both sensory and motor neurons. Sensory
neurons transmit sensory information from the skin, skeletal muscle, and sensory organs to the CNS. Motor neurons transmit
messages about desired movement from the CNS to the muscles to make them contract. Without its sensory-somatic nervous
system, an animal would be unable to process any information about its environment (what it sees, feels, hears, and so on) and
could not control motor movements. Unlike the autonomic nervous system, which usually has two synapses between the CNS and
the target organ, sensory and motor neurons usually have only one synapse—one ending of the neuron is at the organ and the other
directly contacts a CNS neuron.

Section Summary
The nervous system is made up of neurons and glia. Neurons are specialized cells that are capable of sending electrical as well as
chemical signals. Most neurons contain dendrites, which receive these signals, and axons that send signals to other neurons or
tissues. Glia are non-neuronal cells in the nervous system that support neuronal development and signaling. There are several types
of glia that serve different functions.
Neurons have a resting potential across their membranes and when they are stimulated by a strong enough signal from another
neuron an action potential may carry an electrochemical signal along the neuron to a synapse with another neuron.
Neurotransmitters carry signals across synapses to initiate a response in another neuron.
The vertebrate central nervous system contains the brain and the spinal cord, which are covered and protected by three meninges.
The brain contains structurally and functionally defined regions. In mammals, these include the cortex (which can be broken down
into four primary functional lobes: frontal, temporal, occipital, and parietal), basal ganglia, thalamus, hypothalamus, limbic system,
cerebellum, and brainstem—although structures in some of these designations overlap. While functions may be primarily localized
to one structure in the brain, most complex functions, like language and sleep, involve neurons in multiple brain regions. The spinal
cord is the information superhighway that connects the brain with the rest of the body through its connections with peripheral
nerves. It transmits sensory and motor input and also controls motor reflexes.
The peripheral nervous system contains both the autonomic and sensory-somatic nervous systems. The autonomic nervous system
provides unconscious control over visceral functions and has two divisions: the sympathetic and parasympathetic nervous systems.
The sympathetic nervous system is activated in stressful situations to prepare the animal for a “fight-or-flight” response. The
parasympathetic nervous system is active during restful periods. The sensory-somatic nervous system is made of cranial and spinal
nerves that transmit sensory information from skin and muscle to the CNS and motor commands from the CNS to the muscles.

Glossary

action potential
a momentary change in the electrical potential of a neuron (or muscle) membrane

amygdala
a structure within the limbic system that processes fear

autonomic nervous system

the part of the peripheral nervous system that controls bodily functions

axon
a tube-like structure that propagates a signal from a neuron’s cell body to axon terminals

basal ganglia
an interconnected collections of cells in the brain that are involved in movement and motivation

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brainstem
a portion of brain that connects with the spinal cord; controls basic nervous system functions like breathing and swallowing

central nervous system (CNS)

the nervous system made up of the brain and spinal cord; covered with three layers of protective meninges

cerebellum
the brain structure involved in posture, motor coordination, and learning new motor actions

cerebral cortex
the outermost sheet of brain tissue; involved in many higher-order functions

cerebrospinal fluid (CSF)

a clear liquid that surrounds the brain and fills its ventricles and acts as a shock absorber

corpus callosum
a thick nerve bundle that connects the cerebral hemispheres

dendrite
a structure that extends away from the cell body to receive messages from other neurons

depolarization
a change in the membrane potential to a less negative value

frontal lobe
the part of the cerebral cortex that contains the motor cortex and areas involved in planning, attention, and language

glia
(also, glial cells) the cells that provide support functions for neurons

hippocampus
the brain structure in the temporal lobe involved in processing memories

hypothalamus
the brain structure that controls hormone release and body homeostasis

limbic system
a connected brain area that processes emotion and motivation

membrane potential
a difference in electrical potential between the inside and outside of a cell

meninges
(singular: meninx) the membranes that cover and protect the central nervous system

myelin sheath
a cellular extension containing a fatty substance produced by glia that surrounds and insulates axons

neuron
a specialized cell that can receive and transmit electrical and chemical signals

occipital lobe
the part of the cerebral cortex that contains visual cortex and processes visual stimuli

parasympathetic nervous system

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 the division of autonomic nervous system that regulates visceral functions during relaxation

parietal lobe
the part of the cerebral cortex involved in processing touch and the sense of the body in space

peripheral nervous system (PNS)

the nervous system that serves as the connection between the central nervous system and the rest of the body; consists of the
autonomic nervous system and the sensory-somatic nervous system

sensory-somatic nervous system

the system of sensory and motor nerves

spinal cord
a thick fiber bundle that connects the brain with peripheral nerves; transmits sensory and motor information; contains neurons
that control motor reflexes

sympathetic nervous system

the division of autonomic nervous system activated during stressful "fight-or-flight” situations

synapse
a junction between two neurons where neuronal signals are communicated

synaptic cleft
a space between the presynaptic and postsynaptic membranes

temporal lobe
the part of the cerebral cortex that processes auditory input; parts of the temporal lobe are involved in speech, memory, and
emotion processing

thalamus
the brain area that relays sensory information to the cortex

threshold of excitation
the level of depolarization needed for an action potential to fire

Contributors and Attributions

Samantha Fowler (Clayton State University), Rebecca Roush (Sandhills Community College), James Wise (Hampton
University). Original content by OpenStax (CC BY 4.0; Access for free at [Link]
e119a8aafbdd).

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16.6: Nervous System by OpenStax is licensed CC BY 4.0.

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 SECTION OVERVIEW

17.3: Sensory Systems

In more advanced animals, the senses are constantly at work, making the animal aware of stimuli—such as light, or sound, or the
presence of a chemical substance in the external environment—and monitoring information about the organism’s internal
environment. All bilaterally symmetric animals have a sensory system, and the development of any species’ sensory system has
been driven by natural selection; thus, sensory systems differ among species according to the demands of their environments.

17.3.1: Introduction

17.3.2: Sensory Processes

17.3.3: Somatosensation

17.3.4: Taste and Smell

17.3.5: Hearing and Vestibular Sensation

17.3.6: Vision

17.3.E: Sensory Systems (Exercises)

Contributors and Attributions

Connie Rye (East Mississippi Community College), Robert Wise (University of Wisconsin, Oshkosh), Vladimir Jurukovski
(Suffolk County Community College), Jean DeSaix (University of North Carolina at Chapel Hill), Jung Choi (Georgia Institute
of Technology), Yael Avissar (Rhode Island College) among other contributing authors. Original content by OpenStax (CC BY
4.0; Download for free at [Link]

This page titled 17.3: Sensory Systems is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.

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17.3.1: Introduction
In more advanced animals, the senses are constantly at work, making the animal aware of stimuli—such as light, or sound, or the
presence of a chemical substance in the external environment—and monitoring information about the organism’s internal
environment. All bilaterally symmetric animals have a sensory system, and the development of any species’ sensory system has
been driven by natural selection; thus, sensory systems differ among species according to the demands of their environments. The
shark, unlike most fish predators, is electrosensitive—that is, sensitive to electrical fields produced by other animals in its
environment. While it is helpful to this underwater predator, electrosensitivity is a sense not found in most land animals.

Figure [Link] : This shark uses its senses of sight, vibration (lateral-line system), and smell to hunt, but it also relies on its ability
to sense the electric fields of prey, a sense not present in most land animals. (credit: modification of work by Hermanus
Backpackers Hostel, South Africa)

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36.0: Introduction by OpenStax is licensed CC BY 4.0.

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17.3.2: Sensory Processes
Skills to Develop
Identify the general and special senses in humans
Describe three important steps in sensory perception
Explain the concept of just-noticeable difference in sensory perception

Senses provide information about the body and its environment. Humans have five special senses: olfaction (smell), gustation
(taste), equilibrium (balance and body position), vision, and hearing. Additionally, we possess general senses, also called
somatosensation, which respond to stimuli like temperature, pain, pressure, and vibration. Vestibular sensation, which is an
organism’s sense of spatial orientation and balance, proprioception (position of bones, joints, and muscles), and the sense of limb
position that is used to track kinesthesia (limb movement) are part of somatosensation. Although the sensory systems associated
with these senses are very different, all share a common function: to convert a stimulus (such as light, or sound, or the position of
the body) into an electrical signal in the nervous system. This process is called sensory transduction.
There are two broad types of cellular systems that perform sensory transduction. In one, a neuron works with a sensory receptor, a
cell, or cell process that is specialized to engage with and detect a specific stimulus. Stimulation of the sensory receptor activates
the associated afferent neuron, which carries information about the stimulus to the central nervous system. In the second type of
sensory transduction, a sensory nerve ending responds to a stimulus in the internal or external environment: this neuron constitutes
the sensory receptor. Free nerve endings can be stimulated by several different stimuli, thus showing little receptor specificity. For
example, pain receptors in your gums and teeth may be stimulated by temperature changes, chemical stimulation, or pressure.

Reception
The first step in sensation is reception, which is the activation of sensory receptors by stimuli such as mechanical stimuli (being
bent or squished, for example), chemicals, or temperature. The receptor can then respond to the stimuli. The region in space in
which a given sensory receptor can respond to a stimulus, be it far away or in contact with the body, is that receptor’s receptive
field. Think for a moment about the differences in receptive fields for the different senses. For the sense of touch, a stimulus must
come into contact with body. For the sense of hearing, a stimulus can be a moderate distance away (some baleen whale sounds can
propagate for many kilometers). For vision, a stimulus can be very far away; for example, the visual system perceives light from
stars at enormous distances.

Transduction
The most fundamental function of a sensory system is the translation of a sensory signal to an electrical signal in the nervous
system. This takes place at the sensory receptor, and the change in electrical potential that is produced is called the receptor
potential. How is sensory input, such as pressure on the skin, changed to a receptor potential? In this example, a type of receptor
called a mechanoreceptor (as shown in Figure [Link]) possesses specialized membranes that respond to pressure. Disturbance of
these dendrites by compressing them or bending them opens gated ion channels in the plasma membrane of the sensory neuron,
changing its electrical potential. Recall that in the nervous system, a positive change of a neuron’s electrical potential (also called
the membrane potential), depolarizes the neuron. Receptor potentials are graded potentials: the magnitude of these graded
(receptor) potentials varies with the strength of the stimulus. If the magnitude of depolarization is sufficient (that is, if membrane
potential reaches a threshold), the neuron will fire an action potential. In most cases, the correct stimulus impinging on a sensory
receptor will drive membrane potential in a positive direction, although for some receptors, such as those in the visual system, this
is not always the case.

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 Figure [Link] : (a) Mechanosensitive ion channels are gated ion channels that respond to mechanical deformation of the plasma
membrane. A mechanosensitive channel is connected to the plasma membrane and the cytoskeleton by hair-like tethers. When
pressure causes the extracellular matrix to move, the channel opens, allowing ions to enter or exit the cell. (b) Stereocilia in the
human ear are connected to mechanosensitive ion channels. When a sound causes the stereocilia to move, mechanosensitive ion
channels transduce the signal to the cochlear nerve.
Sensory receptors for different senses are very different from each other, and they are specialized according to the type of stimulus
they sense: they have receptor specificity. For example, touch receptors, light receptors, and sound receptors are each activated by
different stimuli. Touch receptors are not sensitive to light or sound; they are sensitive only to touch or pressure. However, stimuli
may be combined at higher levels in the brain, as happens with olfaction, contributing to our sense of taste.

Encoding and Transmission of Sensory Information

Four aspects of sensory information are encoded by sensory systems: the type of stimulus, the location of the stimulus in the
receptive field, the duration of the stimulus, and the relative intensity of the stimulus. Thus, action potentials transmitted over a
sensory receptor’s afferent axons encode one type of stimulus, and this segregation of the senses is preserved in other sensory
circuits. For example, auditory receptors transmit signals over their own dedicated system, and electrical activity in the axons of the
auditory receptors will be interpreted by the brain as an auditory stimulus—a sound.
The intensity of a stimulus is often encoded in the rate of action potentials produced by the sensory receptor. Thus, an intense
stimulus will produce a more rapid train of action potentials, and reducing the stimulus will likewise slow the rate of production of
action potentials. A second way in which intensity is encoded is by the number of receptors activated. An intense stimulus might

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initiate action potentials in a large number of adjacent receptors, while a less intense stimulus might stimulate fewer receptors.
Integration of sensory information begins as soon as the information is received in the CNS, and the brain will further process
incoming signals.

Perception
Perception is an individual’s interpretation of a sensation. Although perception relies on the activation of sensory receptors,
perception happens not at the level of the sensory receptor, but at higher levels in the nervous system, in the brain. The brain
distinguishes sensory stimuli through a sensory pathway: action potentials from sensory receptors travel along neurons that are
dedicated to a particular stimulus. These neurons are dedicated to that particular stimulus and synapse with particular neurons in the
brain or spinal cord.
All sensory signals, except those from the olfactory system, are transmitted though the central nervous system and are routed to the
thalamus and to the appropriate region of the cortex. Recall that the thalamus is a structure in the forebrain that serves as a
clearinghouse and relay station for sensory (as well as motor) signals. When the sensory signal exits the thalamus, it is conducted to
the specific area of the cortex (Figure [Link]) dedicated to processing that particular sense.
How are neural signals interpreted? Interpretation of sensory signals between individuals of the same species is largely similar,
owing to the inherited similarity of their nervous systems; however, there are some individual differences. A good example of this
is individual tolerances to a painful stimulus, such as dental pain, which certainly differ.

Figure [Link] : In humans, with the exception of olfaction, all sensory signals are routed from the (a) thalamus to (b) final
processing regions in the cortex of the brain. (credit b: modification of work by Polina Tishina)

Scientific Method Connection: Just-Noticeable Difference

It is easy to differentiate between a one-pound bag of rice and a two-pound bag of rice. There is a one-pound difference, and
one bag is twice as heavy as the other. However, would it be as easy to differentiate between a 20- and a 21-pound bag?
Question: What is the smallest detectible weight difference between a one-pound bag of rice and a larger bag? What is the
smallest detectible difference between a 20-pound bag and a larger bag? In both cases, at what weights are the differences
detected? This smallest detectible difference in stimuli is known as the just-noticeable difference (JND).
Background: Research background literature on JND and on Weber’s Law, a description of a proposed mathematical
relationship between the overall magnitude of the stimulus and the JND. You will be testing JND of different weights of rice in
bags. Choose a convenient increment that is to be stepped through while testing. For example, you could choose 10 percent
increments between one and two pounds (1.1, 1.2, 1.3, 1.4, and so on) or 20 percent increments (1.2, 1.4, 1.6, and 1.8).
Hypothesis: Develop a hypothesis about JND in terms of percentage of the whole weight being tested (such as “the JND
between the two small bags and between the two large bags is proportionally the same,” or “. . . is not proportionally the
same.”) So, for the first hypothesis, if the JND between the one-pound bag and a larger bag is 0.2 pounds (that is, 20 percent;
1.0 pound feels the same as 1.1 pounds, but 1.0 pound feels less than 1.2 pounds), then the JND between the 20-pound bag and

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 a larger bag will also be 20 percent. (So, 20 pounds feels the same as 22 pounds or 23 pounds, but 20 pounds feels less than 24
pounds.)
Test the hypothesis: Enlist 24 participants, and split them into two groups of 12. To set up the demonstration, assuming a 10
percent increment was selected, have the first group be the one-pound group. As a counter-balancing measure against a
systematic error, however, six of the first group will compare one pound to two pounds, and step down in weight (1.0 to 2.0,
1.0 to 1.9, and so on.), while the other six will step up (1.0 to 1.1, 1.0 to 1.2, and so on). Apply the same principle to the 20-
pound group (20 to 40, 20 to 38, and so on, and 20 to 22, 20 to 24, and so on). Given the large difference between 20 and 40
pounds, you may wish to use 30 pounds as your larger weight. In any case, use two weights that are easily detectable as
different.
Record the observations: Record the data in a table similar to the table below. For the one-pound and 20-pound groups (base
weights) record a plus sign (+) for each participant that detects a difference between the base weight and the step weight.
Record a minus sign (-) for each participant that finds no difference. If one-tenth steps were not used, then replace the steps in
the “Step Weight” columns with the step you are using.
Table [Link]: Results of JND Testing (+ = difference; – = no difference)
Step Weight One pound 20 pounds Step Weight

1.1 22

1.2 24

1.3 26

1.4 28

1.5 30

1.6 32

1.7 34

1.8 36

1.9 38

2.0 40

Analyze the data/report the results: What step weight did all participants find to be equal with one-pound base weight? What
about the 20-pound group?
Draw a conclusion: Did the data support the hypothesis? Are the final weights proportionally the same? If not, why not? Do
the findings adhere to Weber’s Law? Weber’s Law states that the concept that a just-noticeable difference in a stimulus is
proportional to the magnitude of the original stimulus.

Summary
A sensory activation occurs when a physical or chemical stimulus is processed into a neural signal (sensory transduction) by a
sensory receptor. Perception is an individual interpretation of a sensation and is a brain function. Humans have special senses:
olfaction, gustation, equilibrium, and hearing, plus the general senses of somatosensation.
Sensory receptors are either specialized cells associated with sensory neurons or the specialized ends of sensory neurons that are a
part of the peripheral nervous system, and they are used to receive information about the environment (internal or external). Each
sensory receptor is modified for the type of stimulus it detects. For example, neither gustatory receptors nor auditory receptors are
sensitive to light. Each sensory receptor is responsive to stimuli within a specific region in space, which is known as that receptor’s
receptive field. The most fundamental function of a sensory system is the translation of a sensory signal to an electrical signal in
the nervous system.
All sensory signals, except those from the olfactory system, enter the central nervous system and are routed to the thalamus. When
the sensory signal exits the thalamus, it is conducted to the specific area of the cortex dedicated to processing that particular sense.

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Glossary
kinesthesia
sense of body movement

mechanoreceptor
sensory receptor modified to respond to mechanical disturbance such as being bent, touch, pressure, motion, and sound

perception
individual interpretation of a sensation; a brain function

proprioception
sense of limb position; used to track kinesthesia

reception
receipt of a signal (such as light or sound) by sensory receptors

receptive field
region in space in which a stimulus can activate a given sensory receptor

receptor potential
membrane potential in a sensory receptor in response to detection of a stimulus

sensory receptor
specialized neuron or other cells associated with a neuron that is modified to receive specific sensory input

sensory transduction
conversion of a sensory stimulus into electrical energy in the nervous system by a change in the membrane potential

vestibular sense
sense of spatial orientation and balance

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17.3.3: Somatosensation
Skills to Develop
Describe four important mechanoreceptors in human skin
Describe the topographical distribution of somatosensory receptors between glabrous and hairy skin
Explain why the perception of pain is subjective

Somatosensation is a mixed sensory category and includes all sensation received from the skin and mucous membranes, as well
from as the limbs and joints. Somatosensation is also known as tactile sense, or more familiarly, as the sense of touch.
Somatosensation occurs all over the exterior of the body and at some interior locations as well. A variety of receptor types—
embedded in the skin, mucous membranes, muscles, joints, internal organs, and cardiovascular system—play a role.
Recall that the epidermis is the outermost layer of skin in mammals. It is relatively thin, is composed of keratin-filled cells, and has
no blood supply. The epidermis serves as a barrier to water and to invasion by pathogens. Below this, the much thicker dermis
contains blood vessels, sweat glands, hair follicles, lymph vessels, and lipid-secreting sebaceous glands (Figure [Link]). Below
the epidermis and dermis is the subcutaneous tissue, or hypodermis, the fatty layer that contains blood vessels, connective tissue,
and the axons of sensory neurons. The hypodermis, which holds about 50 percent of the body’s fat, attaches the dermis to the bone
and muscle, and supplies nerves and blood vessels to the dermis.

Figure [Link] : Mammalian skin has three layers: an epidermis, a dermis, and a hypodermis. (credit: modification of work by Don
Bliss, National Cancer Institute)

Somatosensory Receptors
Sensory receptors are classified into five categories: mechanoreceptors, thermoreceptors, proprioceptors, pain receptors, and
chemoreceptors. These categories are based on the nature of stimuli each receptor class transduces. What is commonly referred to
as “touch” involves more than one kind of stimulus and more than one kind of receptor. Mechanoreceptors in the skin are described
as encapsulated (that is, surrounded by a capsule) or unencapsulated (a group that includes free nerve endings). A free nerve
ending, as its name implies, is an unencapsulated dendrite of a sensory neuron. Free nerve endings are the most common nerve
endings in skin, and they extend into the middle of the epidermis. Free nerve endings are sensitive to painful stimuli, to hot and
cold, and to light touch. They are slow to adjust to a stimulus and so are less sensitive to abrupt changes in stimulation.
There are three classes of mechanoreceptors: tactile, proprioceptors, and baroreceptors. Mechanoreceptors sense stimuli due to
physical deformation of their plasma membranes. They contain mechanically gated ion channels whose gates open or close in
response to pressure, touch, stretching, and sound.” There are four primary tactile mechanoreceptors in human skin: Merkel’s disks,
Meissner’s corpuscles, Ruffini endings, and Pacinian corpuscle; two are located toward the surface of the skin and two are located
deeper. A fifth type of mechanoreceptor, Krause end bulbs, are found only in specialized regions. Merkel’s disks (shown in Figure

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[Link] ) are found in the upper layers of skin near the base of the epidermis, both in skin that has hair and on glabrous skin, that
is, the hairless skin found on the palms and fingers, the soles of the feet, and the lips of humans and other primates. Merkel’s disks
are densely distributed in the fingertips and lips. They are slow-adapting, unencapsulated nerve endings, and they respond to light
touch. Light touch, also known as discriminative touch, is a light pressure that allows the location of a stimulus to be pinpointed.
The receptive fields of Merkel’s disks are small with well-defined borders. That makes them finely sensitive to edges and they
come into use in tasks such as typing on a keyboard.

Figure [Link] : Four of the primary mechanoreceptors in human skin are shown. Merkel’s disks, which are unencapsulated,
respond to light touch. Meissner’s corpuscles, Ruffini endings, Pacinian corpuscles, and Krause end bulbs are all encapsulated.
Meissner’s corpuscles respond to touch and low-frequency vibration. Ruffini endings detect stretch, deformation within joints, and
warmth. Pacinian corpuscles detect transient pressure and high-frequency vibration. Krause end bulbs detect cold.

Exercise
Which of the following statements about mechanoreceptors is false?
A. Pacini corpuscles are found in both glabrous and hairy skin.
B. Merkel’s disks are abundant on the fingertips and lips.
C. Ruffini endings are encapsulated mechanoreceptors.
D. Meissner’s corpuscles extend into the lower dermis.

Answer
D

Meissner’s corpuscles, (shown in Figure [Link]) also known as tactile corpuscles, are found in the upper dermis, but they project
into the epidermis. They, too, are found primarily in the glabrous skin on the fingertips and eyelids. They respond to fine touch and
pressure, but they also respond to low-frequency vibration or flutter. They are rapidly adapting, fluid-filled, encapsulated neurons
with small, well-defined borders and are responsive to fine details. Like Merkel’s disks, Meissner’s corpuscles are not as plentiful
in the palms as they are in the fingertips.

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 Figure [Link] : Meissner corpuscles in the fingertips, such as the one viewed here using bright field light microscopy, allow for
touch discrimination of fine detail. (credit: modification of work by "Wbensmith"/Wikimedia Commons; scale-bar data from Matt
Russell)
Deeper in the epidermis, near the base, are Ruffini endings, which are also known as bulbous corpuscles. They are found in both
glabrous and hairy skin. These are slow-adapting, encapsulated mechanoreceptors that detect skin stretch and deformations within
joints, so they provide valuable feedback for gripping objects and controlling finger position and movement. Thus, they also
contribute to proprioception and kinesthesia. Ruffini endings also detect warmth. Note that these warmth detectors are situated
deeper in the skin than are the cold detectors. It is not surprising, then, that humans detect cold stimuli before they detect warm
stimuli.
Pacinian corpuscles (seen in Figure [Link]) are located deep in the dermis of both glabrous and hairy skin and are structurally
similar to Meissner’s corpuscles; they are found in the bone periosteum, joint capsules, pancreas and other viscera, breast, and
genitals. They are rapidly adapting mechanoreceptors that sense deep transient (but not prolonged) pressure and high-frequency
vibration. Pacinian receptors detect pressure and vibration by being compressed, stimulating their internal dendrites. There are
fewer Pacinian corpuscles and Ruffini endings in skin than there are Merkel’s disks and Meissner’s corpuscles.

Figure [Link] : Pacinian corpuscles, such as these visualized using bright field light microscopy, detect pressure (touch) and high-
frequency vibration. (credit: modification of work by Ed Uthman; scale-bar data from Matt Russell)
In proprioception, proprioceptive and kinesthetic signals travel through myelinated afferent neurons running from the spinal cord to
the medulla. Neurons are not physically connected, but communicate via neurotransmitters secreted into synapses or “gaps”
between communicating neurons. Once in the medulla, the neurons continue carrying the signals to the thalamus.

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Muscle spindles are stretch receptors that detect the amount of stretch, or lengthening of muscles. Related to these are Golgi tendon
organs, which are tension receptors that detect the force of muscle contraction. Proprioceptive and kinesthetic signals come from
limbs. Unconscious proprioceptive signals run from the spinal cord to the cerebellum, the brain region that coordinates muscle
contraction, rather than to the thalamus, like most other sensory information.
Barorecptors detect pressure changes in an organ. They are found in the walls of the carotid artery and the aorta where they monitor
blood pressure, and in the lungs where they detect the degree of lung expansion. Stretch receptors are found at various sites in the
digestive and urinary systems.
In addition to these two types of deeper receptors, there are also rapidly adapting hair receptors, which are found on nerve endings
that wrap around the base of hair follicles. There are a few types of hair receptors that detect slow and rapid hair movement, and
they differ in their sensitivity to movement. Some hair receptors also detect skin deflection, and certain rapidly adapting hair
receptors allow detection of stimuli that have not yet touched the skin.

Integration of Signals from Mechanoreceptors

The configuration of the different types of receptors working in concert in human skin results in a very refined sense of touch. The
nociceptive receptors—those that detect pain—are located near the surface. Small, finely calibrated mechanoreceptors—Merkel’s
disks and Meissner’s corpuscles—are located in the upper layers and can precisely localize even gentle touch. The large
mechanoreceptors—Pacinian corpuscles and Ruffini endings—are located in the lower layers and respond to deeper touch.
(Consider that the deep pressure that reaches those deeper receptors would not need to be finely localized.) Both the upper and
lower layers of the skin hold rapidly and slowly adapting receptors. Both primary somatosensory cortex and secondary cortical
areas are responsible for processing the complex picture of stimuli transmitted from the interplay of mechanoreceptors.

Density of Mechanoreceptors
The distribution of touch receptors in human skin is not consistent over the body. In humans, touch receptors are less dense in skin
covered with any type of hair, such as the arms, legs, torso, and face. Touch receptors are denser in glabrous skin (the type found on
human fingertips and lips, for example), which is typically more sensitive and is thicker than hairy skin (4 to 5 mm versus 2 to 3
mm).
How is receptor density estimated in a human subject? The relative density of pressure receptors in different locations on the body
can be demonstrated experimentally using a two-point discrimination test. In this demonstration, two sharp points, such as two
thumbtacks, are brought into contact with the subject’s skin (though not hard enough to cause pain or break the skin). The subject
reports if he or she feels one point or two points. If the two points are felt as one point, it can be inferred that the two points are
both in the receptive field of a single sensory receptor. If two points are felt as two separate points, each is in the receptive field of
two separate sensory receptors. The points could then be moved closer and re-tested until the subject reports feeling only one point,
and the size of the receptive field of a single receptor could be estimated from that distance.

Thermoreception
In addition to Krause end bulbs that detect cold and Ruffini endings that detect warmth, there are different types of cold receptors
on some free nerve endings: thermoreceptors, located in the dermis, skeletal muscles, liver, and hypothalamus, that are activated by
different temperatures. Their pathways into the brain run from the spinal cord through the thalamus to the primary somatosensory
cortex. Warmth and cold information from the face travels through one of the cranial nerves to the brain. You know from
experience that a tolerably cold or hot stimulus can quickly progress to a much more intense stimulus that is no longer tolerable.
Any stimulus that is too intense can be perceived as pain because temperature sensations are conducted along the same pathways
that carry pain sensations

Pain
Pain is the name given to nociception, which is the neural processing of injurious stimuli in response to tissue damage. Pain is
caused by true sources of injury, such as contact with a heat source that causes a thermal burn or contact with a corrosive chemical.
But pain also can be caused by harmless stimuli that mimic the action of damaging stimuli, such as contact with capsaicins, the
compounds that cause peppers to taste hot and which are used in self-defense pepper sprays and certain topical medications.
Peppers taste “hot” because the protein receptors that bind capsaicin open the same calcium channels that are activated by warm
receptors.

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Nociception starts at the sensory receptors, but pain, inasmuch as it is the perception of nociception, does not start until it is
communicated to the brain. There are several nociceptive pathways to and through the brain. Most axons carrying nociceptive
information into the brain from the spinal cord project to the thalamus (as do other sensory neurons) and the neural signal
undergoes final processing in the primary somatosensory cortex. Interestingly, one nociceptive pathway projects not to the
thalamus but directly to the hypothalamus in the forebrain, which modulates the cardiovascular and neuroendocrine functions of the
autonomic nervous system. Recall that threatening—or painful—stimuli stimulate the sympathetic branch of the visceral sensory
system, readying a fight-or-flight response.

Link to Learning

Video 1 Phases of Nociceptive Pain

View this video that animates the five phases of nociceptive pain.

Summary
Somatosensation includes all sensation received from the skin and mucous membranes, as well as from the limbs and joints.
Somatosensation occurs all over the exterior of the body and at some interior locations as well, and a variety of receptor types,
embedded in the skin and mucous membranes, play a role.
There are several types of specialized sensory receptors. Rapidly adapting free nerve endings detect nociception, hot and cold, and
light touch. Slowly adapting, encapsulated Merkel’s disks are found in fingertips and lips, and respond to light touch. Meissner’s
corpuscles, found in glabrous skin, are rapidly adapting, encapsulated receptors that detect touch, low-frequency vibration, and
flutter. Ruffini endings are slowly adapting, encapsulated receptors that detect skin stretch, joint activity, and warmth. Hair
receptors are rapidly adapting nerve endings wrapped around the base of hair follicles that detect hair movement and skin
deflection. Finally, Pacinian corpuscles are encapsulated, rapidly adapting receptors that detect transient pressure and high-
frequency vibration.

Glossary
free nerve ending
ending of an afferent neuron that lacks a specialized structure for detection of sensory stimuli; some respond to touch, pain, or
temperature

glabrous
describes the non-hairy skin found on palms and fingers, soles of feet, and lips of humans and other primates

Golgi tendon organ

muscular proprioceptive tension receptor that provides the sensory component of the Golgi tendon reflex

Meissner’s corpuscle
(also, tactile corpuscle) encapsulated, rapidly-adapting mechanoreceptor in the skin that responds to light touch

Merkel's disc

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 unencapsulated, slowly-adapting mechanoreceptor in the skin that responds to touch

muscle spindle
proprioceptive stretch receptor that lies within a muscle and that shortens the muscle to an optimal length for efficient
contraction

nociception
neural processing of noxious (such as damaging) stimuli

Pacinian corpuscle
encapsulated mechanoreceptor in the skin that responds to deep pressure and vibration

Ruffini ending
(also, bulbous corpuscle) slowly-adapting mechanoreceptor in the skin that responds to skin stretch and joint position

This page titled 17.3.3: Somatosensation is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
36.2: Somatosensation by OpenStax is licensed CC BY 4.0.

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17.3.4: Taste and Smell
Skills to Develop
Explain in what way smell and taste stimuli differ from other sensory stimuli
Identify the five primary tastes that can be distinguished by humans
Explain in anatomical terms why a dog’s sense of smell is more acute than a human’s

Taste, also called gustation, and smell, also called olfaction, are the most interconnected senses in that both involve molecules of
the stimulus entering the body and bonding to receptors. Smell lets an animal sense the presence of food or other animals—whether
potential mates, predators, or prey—or other chemicals in the environment that can impact their survival. Similarly, the sense of
taste allows animals to discriminate between types of foods. While the value of a sense of smell is obvious, what is the value of a
sense of taste? Different tasting foods have different attributes, both helpful and harmful. For example, sweet-tasting substances
tend to be highly caloric, which could be necessary for survival in lean times. Bitterness is associated with toxicity, and sourness is
associated with spoiled food. Salty foods are valuable in maintaining homeostasis by helping the body retain water and by
providing ions necessary for cells to function.

Tastes and Odors

Both taste and odor stimuli are molecules taken in from the environment. The primary tastes detected by humans are sweet, sour,
bitter, salty and umami. The first four tastes need little explanation. The identification of umami as a fundamental taste occurred
fairly recently—it was identified in 1908 by Japanese scientist Kikunae Ikeda while he worked with seaweed broth, but it was not
widely accepted as a taste that could be physiologically distinguished until many years later. The taste of umami, also known as
savoriness, is attributable to the taste of the amino acid L-glutamate. In fact, monosodium glutamate, or MSG, is often used in
cooking to enhance the savory taste of certain foods. What is the adaptive value of being able to distinguish umami? Savory
substances tend to be high in protein.
All odors that we perceive are molecules in the air we breathe. If a substance does not release molecules into the air from its
surface, it has no smell. And if a human or other animal does not have a receptor that recognizes a specific molecule, then that
molecule has no smell. Humans have about 350 olfactory receptor subtypes that work in various combinations to allow us to sense
about 10,000 different odors. Compare that to mice, for example, which have about 1,300 olfactory receptor types, and therefore
probably sense more odors. Both odors and tastes involve molecules that stimulate specific chemoreceptors. Although humans
commonly distinguish taste as one sense and smell as another, they work together to create the perception of flavor. A person’s
perception of flavor is reduced if he or she has congested nasal passages.

Reception and Transduction

Odorants (odor molecules) enter the nose and dissolve in the olfactory epithelium, the mucosa at the back of the nasal cavity (as
illustrated in Figure [Link]). The olfactory epithelium is a collection of specialized olfactory receptors in the back of the nasal
cavity that spans an area about 5 cm2 in humans. Recall that sensory cells are neurons. An olfactory receptor, which is a dendrite of
a specialized neuron, responds when it binds certain molecules inhaled from the environment by sending impulses directly to the
olfactory bulb of the brain. Humans have about 12 million olfactory receptors, distributed among hundreds of different receptor
types that respond to different odors. Twelve million seems like a large number of receptors, but compare that to other animals:
rabbits have about 100 million, most dogs have about 1 billion, and bloodhounds—dogs selectively bred for their sense of smell—
have about 4 billion. The overall size of the olfactory epithelium also differs between species, with that of bloodhounds, for
example, being many times larger than that of humans.
Olfactory neurons are bipolar neurons (neurons with two processes from the cell body). Each neuron has a single dendrite buried in
the olfactory epithelium, and extending from this dendrite are 5 to 20 receptor-laden, hair-like cilia that trap odorant molecules. The
sensory receptors on the cilia are proteins, and it is the variations in their amino acid chains that make the receptors sensitive to
different odorants. Each olfactory sensory neuron has only one type of receptor on its cilia, and the receptors are specialized to
detect specific odorants, so the bipolar neurons themselves are specialized. When an odorant binds with a receptor that recognizes
it, the sensory neuron associated with the receptor is stimulated. Olfactory stimulation is the only sensory information that directly
reaches the cerebral cortex, whereas other sensations are relayed through the thalamus.

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 Figure [Link] : In the human olfactory system, (a) bipolar olfactory neurons extend from (b) the olfactory epithelium, where
olfactory receptors are located, to the olfactory bulb. (credit: modification of work by Patrick J. Lynch, medical illustrator; C. Carl
Jaffe, MD, cardiologist)

Evolution Connection: Pheromones

A pheromone is a chemical released by an animal that affects the behavior or physiology of animals of the same species.
Pheromonal signals can have profound effects on animals that inhale them, but pheromones apparently are not consciously
perceived in the same way as other odors. There are several different types of pheromones, which are released in urine or as
glandular secretions. Certain pheromones are attractants to potential mates, others are repellants to potential competitors of the
same sex, and still others play roles in mother-infant attachment. Some pheromones can also influence the timing of puberty,
modify reproductive cycles, and even prevent embryonic implantation. While the roles of pheromones in many nonhuman
species are important, pheromones have become less important in human behavior over evolutionary time compared to their
importance to organisms with more limited behavioral repertoires.
The vomeronasal organ (VNO, or Jacobson’s organ) is a tubular, fluid-filled, olfactory organ present in many vertebrate
animals that sits adjacent to the nasal cavity. It is very sensitive to pheromones and is connected to the nasal cavity by a duct.
When molecules dissolve in the mucosa of the nasal cavity, they then enter the VNO where the pheromone molecules among
them bind with specialized pheromone receptors. Upon exposure to pheromones from their own species or others, many
animals, including cats, may display the flehmen response (Figure [Link]), a curling of the upper lip that helps pheromone
molecules enter the VNO.

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 Figure [Link] : The flehmen response in this tiger results in the curling of the upper lip and helps airborne pheromone
molecules enter the vomeronasal organ. (credit: modification of work by "chadh"/Flickr)
Pheromonal signals are sent, not to the main olfactory bulb, but to a different neural structure that projects directly to the
amygdala (recall that the amygdala is a brain center important in emotional reactions, such as fear). The pheromonal signal
then continues to areas of the hypothalamus that are key to reproductive physiology and behavior. While some scientists assert
that the VNO is apparently functionally vestigial in humans, even though there is a similar structure located near human nasal
cavities, others are researching it as a possible functional system that may, for example, contribute to synchronization of
menstrual cycles in women living in close proximity.

Taste
Detecting a taste (gustation) is fairly similar to detecting an odor (olfaction), given that both taste and smell rely on chemical
receptors being stimulated by certain molecules. The primary organ of taste is the taste bud. A taste bud is a cluster of gustatory
receptors (taste cells) that are located within the bumps on the tongue called papillae (singular: papilla) (illustrated in Figure
[Link]). There are several structurally distinct papillae. Filiform papillae, which are located across the tongue, are tactile,

providing friction that helps the tongue move substances, and contain no taste cells. In contrast, fungiform papillae, which are
located mainly on the anterior two-thirds of the tongue, each contain one to eight taste buds and also have receptors for pressure
and temperature. The large circumvallate papillae contain up to 100 taste buds and form a V near the posterior margin of the
tongue.

Figure [Link] : (a) Foliate, circumvallate, and fungiform papillae are located on different regions of the tongue. (b) Foliate
papillae are prominent protrusions on this light micrograph. (credit a: modification of work by NCI; scale-bar data from Matt
Russell)
In addition to those two types of chemically and mechanically sensitive papillae are foliate papillae—leaf-like papillae located in
parallel folds along the edges and toward the back of the tongue, as seen in the micrograph. Foliate papillae contain about 1,300

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taste buds within their folds. Finally, there are circumvallate papillae, which are wall-like papillae in the shape of an inverted “V” at
the back of the tongue. Each of these papillae is surrounded by a groove and contains about 250 taste buds.
Each taste bud’s taste cells are replaced every 10 to 14 days. These are elongated cells with hair-like processes called microvilli at
the tips that extend into the taste bud pore (illustrated in Figure [Link]). Food molecules (tastants) are dissolved in saliva, and
they bind with and stimulate the receptors on the microvilli. The receptors for tastants are located across the outer portion and front
of the tongue, outside of the middle area where the filiform papillae are most prominent.

Figure [Link] : Pores in the tongue allow tastants to enter taste pores in the tongue. (credit: modification of work by Vincenzo
Rizzo)
In humans, there are five primary tastes, and each taste has only one corresponding type of receptor. Thus, like olfaction, each
receptor is specific to its stimulus (tastant). Transduction of the five tastes happens through different mechanisms that reflect the
molecular composition of the tastant. A salty tastant (containing NaCl) provides the sodium ions (Na+) that enter the taste neurons
and excite them directly. Sour tastants are acids and belong to the thermoreceptor protein family. Binding of an acid or other sour-
tasting molecule triggers a change in the ion channel and these increase hydrogen ion (H+) concentrations in the taste neurons, thus
depolarizing them. Sweet, bitter, and umami tastants require a G-protein coupled receptor. These tastants bind to their respective
receptors, thereby exciting the specialized neurons associated with them.
Both tasting abilities and sense of smell change with age. In humans, the senses decline dramatically by age 50 and continue to
decline. A child may find a food to be too spicy, whereas an elderly person may find the same food to be bland and unappetizing.

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 Link to Learning

Taste & Smell: Crash Course Anatomy…

Anatomy…

View this animation that shows how the sense of taste works.

Smell and Taste in the Brain

Olfactory neurons project from the olfactory epithelium to the olfactory bulb as thin, unmyelinated axons. The olfactory bulb is
composed of neural clusters called glomeruli, and each glomerulus receives signals from one type of olfactory receptor, so each
glomerulus is specific to one odorant. From glomeruli, olfactory signals travel directly to the olfactory cortex and then to the frontal
cortex and the thalamus. Recall that this is a different path from most other sensory information, which is sent directly to the
thalamus before ending up in the cortex. Olfactory signals also travel directly to the amygdala, thereafter reaching the
hypothalamus, thalamus, and frontal cortex. The last structure that olfactory signals directly travel to is a cortical center in the
temporal lobe structure important in spatial, autobiographical, declarative, and episodic memories. Olfaction is finally processed by
areas of the brain that deal with memory, emotions, reproduction, and thought.
Taste neurons project from taste cells in the tongue, esophagus, and palate to the medulla, in the brainstem. From the medulla, taste
signals travel to the thalamus and then to the primary gustatory cortex. Information from different regions of the tongue is
segregated in the medulla, thalamus, and cortex.

Summary
There are five primary tastes in humans: sweet, sour, bitter, salty, and umami. Each taste has its own receptor type that responds
only to that taste. Tastants enter the body and are dissolved in saliva. Taste cells are located within taste buds, which are found on
three of the four types of papillae in the mouth.
Regarding olfaction, there are many thousands of odorants, but humans detect only about 10,000. Like taste receptors, olfactory
receptors are each responsive to only one odorant. Odorants dissolve in nasal mucosa, where they excite their corresponding
olfactory sensory cells. When these cells detect an odorant, they send their signals to the main olfactory bulb and then to other
locations in the brain, including the olfactory cortex.

Glossary
bipolar neuron
neuron with two processes from the cell body, typically in opposite directions

glomerulus
in the olfactory bulb, one of the two neural clusters that receives signals from one type of olfactory receptor

gustation
sense of taste

odorant
airborne molecule that stimulates an olfactory receptor

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olfaction
sense of smell

olfactory bulb
neural structure in the vertebrate brain that receives signals from olfactory receptors

olfactory epithelium
specialized tissue in the nasal cavity where olfactory receptors are located

olfactory receptor
dendrite of a specialized neuron

papilla
one of the small bump-like projections from the tongue

pheromone
substance released by an animal that can affect the physiology or behavior of other animals

tastant
food molecule that stimulates gustatory receptors

taste bud
clusters of taste cells

umami
one of the five basic tastes, which is described as “savory” and which may be largely the taste of L-glutamate

This page titled 17.3.4: Taste and Smell is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
36.3: Taste and Smell by OpenStax is licensed CC BY 4.0.

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17.3.5: Hearing and Vestibular Sensation
Skills to Develop
Describe the relationship of amplitude and frequency of a sound wave to attributes of sound
Trace the path of sound through the auditory system to the site of transduction of sound
Identify the structures of the vestibular system that respond to gravity

Audition, or hearing, is important to humans and to other animals for many different interactions. It enables an organism to detect
and receive information about danger, such as an approaching predator, and to participate in communal exchanges like those
concerning territories or mating. On the other hand, although it is physically linked to the auditory system, the vestibular system is
not involved in hearing. Instead, an animal’s vestibular system detects its own movement, both linear and angular acceleration and
deceleration, and balance.

Sound
Auditory stimuli are sound waves, which are mechanical, pressure waves that move through a medium, such as air or water. There
are no sound waves in a vacuum since there are no air molecules to move in waves. The speed of sound waves differs, based on
altitude, temperature, and medium, but at sea level and a temperature of 20º C (68º F), sound waves travel in the air at about 343
meters per second.
As is true for all waves, there are four main characteristics of a sound wave: frequency, wavelength, period, and amplitude.
Frequency is the number of waves per unit of time, and in sound is heard as pitch. High-frequency (≥15.000Hz) sounds are higher-
pitched (short wavelength) than low-frequency (long wavelengths; ≤100Hz) sounds. Frequency is measured in cycles per second,
and for sound, the most commonly used unit is hertz (Hz), or cycles per second. Most humans can perceive sounds with
frequencies between 30 and 20,000 Hz. Women are typically better at hearing high frequencies, but everyone’s ability to hear high
frequencies decreases with age. Dogs detect up to about 40,000 Hz; cats, 60,000 Hz; bats, 100,000 Hz; and dolphins 150,000 Hz,
and American shad (Alosa sapidissima), a fish, can hear 180,000 Hz. Those frequencies above the human range are called
ultrasound.
Amplitude, or the dimension of a wave from peak to trough, in sound is heard as volume and is illustrated in Figure [Link]. The
sound waves of louder sounds have greater amplitude than those of softer sounds. For sound, volume is measured in decibels (dB).
The softest sound that a human can hear is the zero point. Humans speak normally at 60 decibels.

Figure [Link] : For sound waves, wavelength corresponds to pitch. Amplitude of the wave corresponds to volume. The sound
wave shown with a dashed line is softer in volume than the sound wave shown with a solid line. (credit: NIH)

Reception of Sound
In mammals, sound waves are collected by the external, cartilaginous part of the ear called the pinna, then travel through the
auditory canal and cause vibration of the thin diaphragm called the tympanum or ear drum, the innermost part of the outer ear
(illustrated in Figure [Link]). Interior to the tympanum is the middle ear. The middle ear holds three small bones called the
ossicles, which transfer energy from the moving tympanum to the inner ear. The three ossicles are the malleus (also known as the

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hammer), the incus (the anvil), and stapes (the stirrup). The aptly named stapes looks very much like a stirrup. The three ossicles
are unique to mammals, and each plays a role in hearing. The malleus attaches at three points to the interior surface of the tympanic
membrane. The incus attaches the malleus to the stapes. In humans, the stapes is not long enough to reach the tympanum. If we did
not have the malleus and the incus, then the vibrations of the tympanum would never reach the inner ear. These bones also function
to collect force and amplify sounds. The ear ossicles are homologous to bones in a fish mouth: the bones that support gills in fish
are thought to be adapted for use in the vertebrate ear over evolutionary time. Many animals (frogs, reptiles, and birds, for
example) use the stapes of the middle ear to transmit vibrations to the middle ear.

Figure [Link] : Sound travels through the outer ear to the middle ear, which is bounded on its exterior by the tympanic membrane.
The middle ear contains three bones called ossicles that transfer the sound wave to the oval window, the exterior boundary of the
inner ear. The organ of Corti, which is the organ of sound transduction, lies inside the cochlea. (credit: modification of work by
Lars Chittka, Axel Brockmann)

Transduction of Sound
Vibrating objects, such as vocal cords, create sound waves or pressure waves in the air. When these pressure waves reach the ear,
the ear transduces this mechanical stimulus (pressure wave) into a nerve impulse (electrical signal) that the brain perceives as
sound. The pressure waves strike the tympanum, causing it to vibrate. The mechanical energy from the moving tympanum
transmits the vibrations to the three bones of the middle ear. The stapes transmits the vibrations to a thin diaphragm called the oval
window, which is the outermost structure of the inner ear. The structures of the inner ear are found in the labyrinth, a bony, hollow
structure that is the most interior portion of the ear. Here, the energy from the sound wave is transferred from the stapes through the
flexible oval window and to the fluid of the cochlea. The vibrations of the oval window create pressure waves in the fluid
(perilymph) inside the cochlea. The cochlea is a whorled structure, like the shell of a snail, and it contains receptors for
transduction of the mechanical wave into an electrical signal (as illustrated in Figure [Link]). Inside the cochlea, the basilar
membrane is a mechanical analyzer that runs the length of the cochlea, curling toward the cochlea’s center.
The mechanical properties of the basilar membrane change along its length, such that it is thicker, tauter, and narrower at the
outside of the whorl (where the cochlea is largest), and thinner, floppier, and broader toward the apex, or center, of the whorl
(where the cochlea is smallest). Different regions of the basilar membrane vibrate according to the frequency of the sound wave
conducted through the fluid in the cochlea. For these reasons, the fluid-filled cochlea detects different wave frequencies (pitches) at
different regions of the membrane. When the sound waves in the cochlear fluid contact the basilar membrane, it flexes back and
forth in a wave-like fashion. Above the basilar membrane is the tectorial membrane.

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 Figure [Link] : In the human ear, sound waves cause the stapes to press against the oval window. Vibrations travel up the fluid-
filled interior of the cochlea. The basilar membrane that lines the cochlea gets continuously thinner toward the apex of the cochlea.
Different thicknesses of membrane vibrate in response to different frequencies of sound. Sound waves then exit through the round
window. In the cross section of the cochlea (top right figure), note that in addition to the upper canal and lower canal, the cochlea
also has a middle canal. The organ of Corti (bottom image) is the site of sound transduction. Movement of stereocilia on hair cells
results in an action potential that travels along the auditory nerve.

Exercise
Cochlear implants can restore hearing in people who have a nonfunctional cochlear. The implant consists of a microphone that
picks up sound. A speech processor selects sounds in the range of human speech, and a transmitter converts these sounds to
electrical impulses, which are then sent to the auditory nerve. Which of the following types of hearing loss would not be
restored by a cochlear implant?
A. Hearing loss resulting from absence or loss of hair cells in the organ of Corti.
B. Hearing loss resulting from an abnormal auditory nerve.
C. Hearing loss resulting from fracture of the cochlea.
D. Hearing loss resulting from damage to bones of the middle ear.

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 Answer
B

The site of transduction is in the organ of Corti (spiral organ). It is composed of hair cells held in place above the basilar membrane
like flowers projecting up from soil, with their exposed short, hair-like stereocilia contacting or embedded in the tectorial
membrane above them. The inner hair cells are the primary auditory receptors and exist in a single row, numbering approximately
3,500. The stereocilia from inner hair cells extend into small dimples on the tectorial membrane’s lower surface. The outer hair
cells are arranged in three or four rows. They number approximately 12,000, and they function to fine tune incoming sound waves.
The longer stereocilia that project from the outer hair cells actually attach to the tectorial membrane. All of the stereocilia are
mechanoreceptors, and when bent by vibrations they respond by opening a gated ion channel. As a result, the hair cell membrane is
depolarized, and a signal is transmitted to the chochlear nerve. Intensity (volume) of sound is determined by how many hair cells at
a particular location are stimulated.
The hair cells are arranged on the basilar membrane in an orderly way. The basilar membrane vibrates in different regions,
according to the frequency of the sound waves impinging on it. Likewise, the hair cells that lay above it are most sensitive to a
specific frequency of sound waves. Hair cells can respond to a small range of similar frequencies, but they require stimulation of
greater intensity to fire at frequencies outside of their optimal range. The difference in response frequency between adjacent inner
hair cells is about 0.2 percent. Compare that to adjacent piano strings, which are about six percent different. Place theory, which is
the model for how biologists think pitch detection works in the human ear, states that high frequency sounds selectively vibrate the
basilar membrane of the inner ear near the entrance port (the oval window). Lower frequencies travel farther along the membrane
before causing appreciable excitation of the membrane. The basic pitch-determining mechanism is based on the location along the
membrane where the hair cells are stimulated. The place theory is the first step toward an understanding of pitch perception.
Considering the extreme pitch sensitivity of the human ear, it is thought that there must be some auditory “sharpening” mechanism
to enhance the pitch resolution.
When sound waves produce fluid waves inside the cochlea, the basilar membrane flexes, bending the stereocilia that attach to the
tectorial membrane. Their bending results in action potentials in the hair cells, and auditory information travels along the neural
endings of the bipolar neurons of the hair cells (collectively, the auditory nerve) to the brain. When the hairs bend, they release an
excitatory neurotransmitter at a synapse with a sensory neuron, which then conducts action potentials to the central nervous system.
The cochlear branch of the vestibulocochlear cranial nerve sends information on hearing. The auditory system is very refined, and
there is some modulation or “sharpening” built in. The brain can send signals back to the cochlea, resulting in a change of length in
the outer hair cells, sharpening or dampening the hair cells’ response to certain frequencies.

Higher Processing
The inner hair cells are most important for conveying auditory information to the brain. About 90 percent of the afferent neurons
carry information from inner hair cells, with each hair cell synapsing with 10 or so neurons. Outer hair cells connect to only 10
percent of the afferent neurons, and each afferent neuron innervates many hair cells. The afferent, bipolar neurons that convey
auditory information travel from the cochlea to the medulla, through the pons and midbrain in the brainstem, finally reaching the
primary auditory cortex in the temporal lobe.

Vestibular Information
The stimuli associated with the vestibular system are linear acceleration (gravity) and angular acceleration and deceleration.
Gravity, acceleration, and deceleration are detected by evaluating the inertia on receptive cells in the vestibular system. Gravity is
detected through head position. Angular acceleration and deceleration are expressed through turning or tilting of the head.
The vestibular system has some similarities with the auditory system. It utilizes hair cells just like the auditory system, but it
excites them in different ways. There are five vestibular receptor organs in the inner ear: the utricle, the saccule, and three
semicircular canals. Together, they make up what’s known as the vestibular labyrinth that is shown in Figure [Link]. The utricle
and saccule respond to acceleration in a straight line, such as gravity. The roughly 30,000 hair cells in the utricle and 16,000 hair
cells in the saccule lie below a gelatinous layer, with their stereocilia projecting into the gelatin. Embedded in this gelatin are
calcium carbonate crystals—like tiny rocks. When the head is tilted, the crystals continue to be pulled straight down by gravity, but
the new angle of the head causes the gelatin to shift, thereby bending the stereocilia. The bending of the stereocilia stimulates the

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neurons, and they signal to the brain that the head is tilted, allowing the maintenance of balance. It is the vestibular branch of the
vestibulocochlear cranial nerve that deals with balance.

Figure [Link] : The structure of the vestibular labyrinth is shown. (credit: modification of work by NIH)
The fluid-filled semicircular canals are tubular loops set at oblique angles. They are arranged in three spatial planes. The base of
each canal has a swelling that contains a cluster of hair cells. The hairs project into a gelatinous cap called the cupula and monitor
angular acceleration and deceleration from rotation. They would be stimulated by driving your car around a corner, turning your
head, or falling forward. One canal lies horizontally, while the other two lie at about 45 degree angles to the horizontal axis. When
the brain processes input from all three canals together, it can detect angular acceleration or deceleration in three dimensions. When
the head turns, the fluid in the canals shifts, thereby bending stereocilia and sending signals to the brain. Upon cessation
accelerating or decelerating—or just moving—the movement of the fluid within the canals slows or stops. For example, imagine
holding a glass of water. When moving forward, water may splash backwards onto the hand, and when motion has stopped, water
may splash forward onto the fingers. While in motion, the water settles in the glass and does not splash. Note that the canals are not
sensitive to velocity itself, but to changes in velocity, so moving forward at 60mph with your eyes closed would not give the
sensation of movement, but suddenly accelerating or braking would stimulate the receptors.

Higher Processing
Hair cells from the utricle, saccule, and semicircular canals also communicate through bipolar neurons to the cochlear nucleus in
the medulla. Cochlear neurons send descending projections to the spinal cord and ascending projections to the pons, thalamus, and
cerebellum. Connections to the cerebellum are important for coordinated movements. There are also projections to the temporal
cortex, which account for feelings of dizziness; projections to autonomic nervous system areas in the brainstem, which account for
motion sickness; and projections to the primary somatosensory cortex, which monitors subjective measurements of the external
world and self-movement. People with lesions in the vestibular area of the somatosensory cortex see vertical objects in the world as
being tilted. Finally, the vestibular signals project to certain optic muscles to coordinate eye and head movements.

Link to Learning

Click through this interactive tutorial to review the parts of the ear and how they function to process sound.

Access for free at OpenStax [Link] [Link]

Summary
Audition is important for territory defense, predation, predator defense, and communal exchanges. The vestibular system, which is
not auditory, detects linear acceleration and angular acceleration and deceleration. Both the auditory system and vestibular system
use hair cells as their receptors.
Auditory stimuli are sound waves. The sound wave energy reaches the outer ear (pinna, canal, tympanum), and vibrations of the
tympanum send the energy to the middle ear. The middle ear bones shift and the stapes transfers mechanical energy to the oval
window of the fluid-filled inner ear cochlea. Once in the cochlea, the energy causes the basilar membrane to flex, thereby bending
the stereocilia on receptor hair cells. This activates the receptors, which send their auditory neural signals to the brain.
The vestibular system has five parts that work together to provide the sense of direction, thus helping to maintain balance. The
utricle and saccule measure head orientation: their calcium carbonate crystals shift when the head is tilted, thereby activating hair
cells. The semicircular canals work similarly, such that when the head is turned, the fluid in the canals bends stereocilia on hair
cells. The vestibular hair cells also send signals to the thalamus and to somatosensory cortex, but also to the cerebellum, the
structure above the brainstem that plays a large role in timing and coordination of movement.

Glossary
audition
sense of hearing

basilar membrane
stiff structure in the cochlea that indirectly anchors auditory receptors

cochlea
whorled structure that contains receptors for transduction of the mechanical wave into an electrical signal

incus
(also, anvil) second of the three bones of the middle ear

inner ear
innermost part of the ear; consists of the cochlea and the vestibular system

labyrinth
bony, hollow structure that is the most internal part of the ear; contains the sites of transduction of auditory and vestibular
information

malleus
(also, hammer) first of the three bones of the middle ear

middle ear
part of the hearing apparatus that functions to transfer energy from the tympanum to the oval window of the inner ear

organ of Corti
in the basilar membrane, the site of the transduction of sound, a mechanical wave, to a neural signal

ossicle
one of the three bones of the middle ear

outer ear
part of the ear that consists of the pinna, ear canal, and tympanum and which conducts sound waves into the middle ear

oval window
thin diaphragm between the middle and inner ears that receives sound waves from contact with the stapes bone of the middle
ear

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pinna
cartilaginous outer ear

semicircular canal
one of three half-circular, fluid-filled tubes in the vestibular labyrinth that monitors angular acceleration and deceleration

stapes
(also, stirrup) third of the three bones of the middle ear

stereocilia
in the auditory system, hair-like projections from hair cells that help detect sound waves

tectorial membrane
cochlear structure that lies above the hair cells and participates in the transduction of sound at the hair cells

tympanum
(also, tympanic membrane or ear drum) thin diaphragm between the outer and middle ears

ultrasound
sound frequencies above the human detectable ceiling of approximately 20,000 Hz

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17.3.6: Vision
Skills to Develop
Explain how electromagnetic waves differs from sound waves
Trace the path of light through the eye to the point of the optic nerve
Explain tonic activity as it is manifested in photoreceptors in the retina

Vision is the ability to detect light patterns from the outside environment and interpret them into images. Animals are bombarded
with sensory information, and the sheer volume of visual information can be problematic. Fortunately, the visual systems of species
have evolved to attend to the most-important stimuli. The importance of vision to humans is further substantiated by the fact that
about one-third of the human cerebral cortex is dedicated to analyzing and perceiving visual information.

Light
As with auditory stimuli, light travels in waves. The compression waves that compose sound must travel in a medium—a gas, a
liquid, or a solid. In contrast, light is composed of electromagnetic waves and needs no medium; light can travel in a vacuum
(Figure [Link]). The behavior of light can be discussed in terms of the behavior of waves and also in terms of the behavior of the
fundamental unit of light—a packet of electromagnetic radiation called a photon. A glance at the electromagnetic spectrum shows
that visible light for humans is just a small slice of the entire spectrum, which includes radiation that we cannot see as light because
it is below the frequency of visible red light and above the frequency of visible violet light.
Certain variables are important when discussing perception of light. Wavelength (which varies inversely with frequency) manifests
itself as hue. Light at the red end of the visible spectrum has longer wavelengths (and is lower frequency), while light at the violet
end has shorter wavelengths (and is higher frequency). The wavelength of light is expressed in nanometers (nm); one nanometer is
one billionth of a meter. Humans perceive light that ranges between approximately 380 nm and 740 nm. Some other animals,
though, can detect wavelengths outside of the human range. For example, bees see near-ultraviolet light in order to locate nectar
guides on flowers, and some non-avian reptiles sense infrared light (heat that prey gives off).

Figure [Link] : In the electromagnetic spectrum, visible light lies between 380 nm and 740 nm. (credit: modification of work by
NASA)
Wave amplitude is perceived as luminous intensity, or brightness. The standard unit of intensity of light is the candela, which is
approximately the luminous intensity of a one common candle.
Light waves travel 299,792 km per second in a vacuum, (and somewhat slower in various media such as air and water), and those
waves arrive at the eye as long (red), medium (green), and short (blue) waves. What is termed “white light” is light that is
perceived as white by the human eye. This effect is produced by light that stimulates equally the color receptors in the human eye.
The apparent color of an object is the color (or colors) that the object reflects. Thus a red object reflects the red wavelengths in
mixed (white) light and absorbs all other wavelengths of light.

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Anatomy of the Eye
The photoreceptive cells of the eye, where transduction of light to nervous impulses occurs, are located in the retina (shown in
Figure [Link]) on the inner surface of the back of the eye. But light does not impinge on the retina unaltered. It passes through
other layers that process it so that it can be interpreted by the retina (Figure 17.3.6.2b). The cornea, the front transparent layer of
the eye, and the crystalline lens, a transparent convex structure behind the cornea, both refract (bend) light to focus the image on
the retina. The iris, which is conspicuous as the colored part of the eye, is a circular muscular ring lying between the lens and
cornea that regulates the amount of light entering the eye. In conditions of high ambient light, the iris contracts, reducing the size of
the pupil at its center. In conditions of low light, the iris relaxes and the pupil enlarges.

Figure [Link] : (a) The human eye is shown in cross section. (b) A blowup shows the layers of the retina.

Exercise
Which of the following statements about the human eye is false?
A. Rods detect color, while cones detect only shades of gray.
B. When light enters the retina, it passes the ganglion cells and bipolar cells before reaching photoreceptors at the rear of the
eye.
C. The iris adjusts the amount of light coming into the eye.
D. The cornea is a protective layer on the front of the eye.

Answer
A

The main function of the lens is to focus light on the retina and fovea centralis. The lens is dynamic, focusing and re-focusing light
as the eye rests on near and far objects in the visual field. The lens is operated by muscles that stretch it flat or allow it to thicken,
changing the focal length of light coming through it to focus it sharply on the retina. With age comes the loss of the flexibility of
the lens, and a form of farsightedness called presbyopia results. Presbyopia occurs because the image focuses behind the retina.
Presbyopia is a deficit similar to a different type of farsightedness called hyperopia caused by an eyeball that is too short. For both
defects, images in the distance are clear but images nearby are blurry. Myopia (nearsightedness) occurs when an eyeball is
elongated and the image focus falls in front of the retina. In this case, images in the distance are blurry but images nearby are clear.
There are two types of photoreceptors in the retina: rods and cones, named for their general appearance as illustrated in Figure
[Link]. Rods are strongly photosensitive and are located in the outer edges of the retina. They detect dim light and are used

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primarily for peripheral and nighttime vision. Cones are weakly photosensitive and are located near the center of the retina. They
respond to bright light, and their primary role is in daytime, color vision.

Figure [Link] : Rods and cones are photoreceptors in the retina. Rods respond in low light and can detect only shades of gray.
Cones respond in intense light and are responsible for color vision. (credit: modification of work by Piotr Sliwa)
The fovea is the region in the center back of the eye that is responsible for acute vision. The fovea has a high density of cones.
When you bring your gaze to an object to examine it intently in bright light, the eyes orient so that the object’s image falls on the
fovea. However, when looking at a star in the night sky or other object in dim light, the object can be better viewed by the
peripheral vision because it is the rods at the edges of the retina, rather than the cones at the center, that operate better in low light.
In humans, cones far outnumber rods in the fovea.

Link to Learning

Review the anatomical structure of the eye, clicking on each part to practice identification.

Transduction of Light
The rods and cones are the site of transduction of light to a neural signal. Both rods and cones contain photopigments. In
vertebrates, the main photopigment, rhodopsin, has two main parts Figure [Link]): an opsin, which is a membrane protein (in the
form of a cluster of α-helices that span the membrane), and retinal—a molecule that absorbs light.

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 Figure [Link] : (a) Rhodopsin, the photoreceptor in vertebrates, has two parts: the trans-membrane protein opsin, and retinal.
When light strikes retinal, it changes shape from (b) a cis to a trans form. The signal is passed to a G-protein called transducin,
triggering a series of downstream events.
When light hits a photoreceptor, it causes a shape change in the retinal, altering its structure from a bent (cis) form of the molecule
to its linear (trans) isomer. This isomerization of retinal activates the rhodopsin, starting a cascade of events that ends with the
closing of Na+ channels in the membrane of the photoreceptor. Thus, unlike most other sensory neurons (which become
depolarized by exposure to a stimulus) visual receptors become hyperpolarized and thus driven away from threshold (Figure
[Link]).

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 Figure [Link] : When light strikes rhodopsin, the G-protein transducin is activated, which in turn activates phosphodiesterase.
Phosphodiesterase converts cGMP to GMP, thereby closing sodium channels. As a result, the membrane becomes hyperpolarized.
The hyperpolarized membrane does not release glutamate to the bipolar cell.

Trichromatic Coding
There are three types of cones (with different photopsins), and they differ in the wavelength to which they are most responsive, as
shown in Figure [Link]. Some cones are maximally responsive to short light waves of 420 nm, so they are called S cones (“S” for
“short”); others respond maximally to waves of 530 nm (M cones, for “medium”); a third group responds maximally to light of
longer wavelengths, at 560 nm (L, or “long” cones). With only one type of cone, color vision would not be possible, and a two-
cone (dichromatic) system has limitations. Primates use a three-cone (trichromatic) system, resulting in full color vision.
The color we perceive is a result of the ratio of activity of our three types of cones. The colors of the visual spectrum, running from
long-wavelength light to short, are red (700 nm), orange (600 nm), yellow (565 nm), green (497 nm), blue (470 nm), indigo (450

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nm), and violet (425 nm). Humans have very sensitive perception of color and can distinguish about 500 levels of brightness, 200
different hues, and 20 steps of saturation, or about 2 million distinct colors.

Figure [Link] : Human rod cells and the different types of cone cells each have an optimal wavelength. However, there is
considerable overlap in the wavelengths of light detected.

Retinal Processing
Visual signals leave the cones and rods, travel to the bipolar cells, and then to ganglion cells. A large degree of processing of visual
information occurs in the retina itself, before visual information is sent to the brain.
Photoreceptors in the retina continuously undergo tonic activity. That is, they are always slightly active even when not stimulated
by light. In neurons that exhibit tonic activity, the absence of stimuli maintains a firing rate at a baseline; while some stimuli
increase firing rate from the baseline, and other stimuli decrease firing rate. In the absence of light, the bipolar neurons that connect
rods and cones to ganglion cells are continuously and actively inhibited by the rods and cones. Exposure of the retina to light
hyperpolarizes the rods and cones and removes their inhibition of bipolar cells. The now active bipolar cells in turn stimulate the
ganglion cells, which send action potentials along their axons (which leave the eye as the optic nerve). Thus, the visual system
relies on change in retinal activity, rather than the absence or presence of activity, to encode visual signals for the brain. Sometimes
horizontal cells carry signals from one rod or cone to other photoreceptors and to several bipolar cells. When a rod or cone
stimulates a horizontal cell, the horizontal cell inhibits more distant photoreceptors and bipolar cells, creating lateral inhibition.
This inhibition sharpens edges and enhances contrast in the images by making regions receiving light appear lighter and dark
surroundings appear darker. Amacrine cells can distribute information from one bipolar cell to many ganglion cells.
You can demonstrate this using an easy demonstration to “trick” your retina and brain about the colors you are observing in your
visual field. Look fixedly at Figure [Link] for about 45 seconds. Then quickly shift your gaze to a sheet of blank white paper or a
white wall. You should see an afterimage of the Norwegian flag in its correct colors. At this point, close your eyes for a moment,
then reopen them, looking again at the white paper or wall; the afterimage of the flag should continue to appear as red, white, and
blue. What causes this? According to an explanation called opponent process theory, as you gazed fixedly at the green, black, and
yellow flag, your retinal ganglion cells that respond positively to green, black, and yellow increased their firing dramatically. When
you shifted your gaze to the neutral white ground, these ganglion cells abruptly decreased their activity and the brain interpreted
this abrupt downshift as if the ganglion cells were responding now to their “opponent” colors: red, white, and blue, respectively, in
the visual field. Once the ganglion cells return to their baseline activity state, the false perception of color will disappear.

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 Figure [Link] : View this flag to understand how retinal processing works. Stare at the center of the flag (indicated by the white
dot) for 45 seconds, and then quickly look at a white background, noticing how colors appear.

Higher Processing
The myelinated axons of ganglion cells make up the optic nerves. Within the nerves, different axons carry different qualities of the
visual signal. Some axons constitute the magnocellular (big cell) pathway, which carries information about form, movement, depth,
and differences in brightness. Other axons constitute the parvocellular (small cell) pathway, which carries information on color and
fine detail. Some visual information projects directly back into the brain, while other information crosses to the opposite side of the
brain. This crossing of optical pathways produces the distinctive optic chiasma (Greek, for “crossing”) found at the base of the
brain and allows us to coordinate information from both eyes.
Once in the brain, visual information is processed in several places, and its routes reflect the complexity and importance of visual
information to humans and other animals. One route takes the signals to the thalamus, which serves as the routing station for all
incoming sensory impulses except olfaction. In the thalamus, the magnocellular and parvocellular distinctions remain intact, and
there are different layers of the thalamus dedicated to each. When visual signals leave the thalamus, they travel to the primary
visual cortex at the rear of the brain. From the visual cortex, the visual signals travel in two directions. One stream that projects to
the parietal lobe, in the side of the brain, carries magnocellular (“where”) information. A second stream projects to the temporal
lobe and carries both magnocellular (“where”) and parvocellular (“what”) information.
Another important visual route is a pathway from the retina to the superior colliculus in the midbrain, where eye movements are
coordinated and integrated with auditory information. Finally, there is the pathway from the retina to the suprachiasmatic nucleus
(SCN) of the hypothalamus. The SCN is a cluster of cells that is considered to be the body’s internal clock, which controls our
circadian (day-long) cycle. The SCN sends information to the pineal gland, which is important in sleep/wake patterns and annual
cycles.

Link to Learning

The Sense of Sight

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 View this interactive presentation to review what you have learned about how vision functions.

Summary
Vision is the only photo responsive sense. Visible light travels in waves and is a very small slice of the electromagnetic radiation
spectrum. Light waves differ based on their frequency (wavelength = hue) and amplitude (intensity = brightness).
In the vertebrate retina, there are two types of light receptors (photoreceptors): cones and rods. Cones, which are the source of color
vision, exist in three forms—L, M, and S—and they are differentially sensitive to different wavelengths. Cones are located in the
retina, along with the dim-light, achromatic receptors (rods). Cones are found in the fovea, the central region of the retina, whereas
rods are found in the peripheral regions of the retina.
Visual signals travel from the eye over the axons of retinal ganglion cells, which make up the optic nerves. Ganglion cells come in
several versions. Some ganglion cell axons carry information on form, movement, depth, and brightness, while other axons carry
information on color and fine detail. Visual information is sent to the superior colliculi in the midbrain, where coordination of eye
movements and integration of auditory information takes place. Visual information is also sent to the suprachiasmatic nucleus
(SCN) of the hypothalamus, which plays a role in the circadian cycle.

Glossary
candela
(cd) unit of measurement of luminous intensity (brightness)

circadian
describes a time cycle about one day in length

cone
weakly photosensitive, chromatic, cone-shaped neuron in the fovea of the retina that detects bright light and is used in daytime
color vision

cornea
transparent layer over the front of the eye that helps focus light waves

fovea
region in the center of the retina with a high density of photoreceptors and which is responsible for acute vision

hyperopia
(also, farsightedness) visual defect in which the image focus falls behind the retina, thereby making images in the distance clear,
but close-up images blurry

iris
pigmented, circular muscle at the front of the eye that regulates the amount of light entering the eye

lens
transparent, convex structure behind the cornea that helps focus light waves on the retina

myopia
(also, nearsightedness) visual defect in which the image focus falls in front of the retina, thereby making images in the distance
blurry, but close-up images clear

presbyopia
visual defect in which the image focus falls behind the retina, thereby making images in the distance clear, but close-up images
blurry; caused by age-based changes in the lens

pupil
small opening though which light enters

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retina
layer of photoreceptive and supporting cells on the inner surface of the back of the eye

rhodopsin
main photopigment in vertebrates

rod
strongly photosensitive, achromatic, cylindrical neuron in the outer edges of the retina that detects dim light and is used in
peripheral and nighttime vision

superior colliculus
paired structure in the top of the midbrain, which manages eye movements and auditory integration

suprachiasmatic nucleus
cluster of cells in the hypothalamus that plays a role in the circadian cycle

tonic activity
in a neuron, slight continuous activity while at rest

vision
sense of sight

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36.5: Vision by OpenStax is licensed CC BY 4.0.

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17.3.E: Sensory Systems (Exercises)
36.1: Sensory Processes
Senses provide information about the body and its environment. Humans have five special senses: olfaction (smell), gustation
(taste), equilibrium (balance and body position), vision, and hearing. Additionally, we possess general senses, also called
somatosensation, which respond to stimuli like temperature, pain, pressure, and vibration.

Review Questions
Where does perception occur?
A. spinal cord
B. cerebral cortex
C. receptors
D. thalamus

Answer
B

If a person’s cold receptors no longer convert cold stimuli into sensory signals, that person has a problem with the process of
________.
A. reception
B. transmission
C. perception
D. transduction

Answer
D

After somatosensory transduction, the sensory signal travels through the brain as a(n) _____ signal.
A. electrical
B. pressure
C. optical
D. thermal

Answer
A

Free Response
If a person sustains damage to axons leading from sensory receptors to the central nervous system, which step or steps of
sensory perception will be affected?

Answer
Transmission of sensory information from the receptor to the central nervous system will be impaired, and thus, perception
of stimuli, which occurs in the brain, will be halted.

In what way does the overall magnitude of a stimulus affect the just-noticeable difference in the perception of that stimulus?

Answer

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 The just-noticeable difference is a fraction of the overall magnitude of the stimulus and seems to be a relatively fixed
proportion (such as 10 percent) whether the stimulus is large (such as a very heavy object) or small (such as a very light
object).

36.2: Somatosensation
Somatosensation is a mixed sensory category and includes all sensation received from the skin and mucous membranes, as well
from as the limbs and joints. Somatosensation is also known as tactile sense, or more familiarly, as the sense of touch.
Somatosensation occurs all over the exterior of the body and at some interior locations as well. A variety of receptor types—
embedded in the skin, mucous membranes, muscles, joints, internal organs, and cardiovascular system—play a role.

Review Questions
_____ are found only in _____ skin, and detect skin deflection.
A. Meissner’s corpuscles: hairy
B. Merkel’s disks: glabrous
C. hair receptors: hairy
D. Krause end bulbs: hairy

Answer
B

If you were to burn your epidermis, what receptor type would you most likely burn?
A. free nerve endings
B. Ruffini endings
C. Pacinian corpuscle
D. hair receptors

Answer
A

Free Response
What can be inferred about the relative sizes of the areas of cortex that process signals from skin not densely innervated with
sensory receptors and skin that is densely innervated with sensory receptors?

Answer
The cortical areas serving skin that is densely innervated likely are larger than those serving skin that is less densely
innervated.

36.3: Taste and Smell

Taste, also called gustation, and smell, also called olfaction, are the most interconnected senses in that both involve molecules of
the stimulus entering the body and bonding to receptors. Smell lets an animal sense the presence of food or other animals—whether
potential mates, predators, or prey—or other chemicals in the environment that can impact their survival. Similarly, the sense of
taste allows animals to discriminate between types of foods.

Review Questions
Which of the following has the fewest taste receptors?
A. fungiform papillae
B. circumvallate papillae
C. foliate papillae

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 D. filiform papillae

Answer
D

How many different taste molecules do taste cells each detect?

A. one
B. five
C. ten
D. It depends on the spot on the tongue

Answer
A

Salty foods activate the taste cells by _____.

A. exciting the taste cell directly
B. causing hydrogen ions to enter the cell
C. causing sodium channels to close
D. binding directly to the receptors

Answer
A

All sensory signals except _____ travel to the _____ in the brain before the cerebral cortex.
A. vision; thalamus
B. olfaction; thalamus
C. vision; cranial nerves
D. olfaction; cranial nerves

Answer
B

Free Response
From the perspective of the recipient of the signal, in what ways do pheromones differ from other odorants?

Answer
Pheromones may not be consciously perceived, and pheromones can have direct physiological and behavioral effects on
their recipients.

What might be the effect on an animal of not being able to perceive taste?

Answer
The animal might not be able to recognize the differences in food sources and thus might not be able to discriminate
between spoiled food and safe food or between foods that contain necessary nutrients, such as proteins, and foods that do
not.

Access for free at OpenStax 17.3.E.3 [Link]

36.4: Hearing and Vestibular Sensation
Audition, or hearing, is important to humans and to other animals for many different interactions. It enables an organism to detect
and receive information about danger, such as an approaching predator, and to participate in communal exchanges like those
concerning territories or mating. On the other hand, although it is physically linked to the auditory system, the vestibular system is
not involved in hearing. Instead, an animal’s vestibular system detects its own movement.

Review Questions
In sound, pitch is measured in _____, and volume is measured in _____.
A. nanometers (nm); decibels (dB)
B. decibels (dB); nanometers (nm)
C. decibels (dB); hertz (Hz)
D. hertz (Hz); decibels (dB)

Answer
D

Auditory hair cells are indirectly anchored to the _____.

A. basilar membrane
B. oval window
C. tectorial membrane
D. ossicles

Answer
A

Which of the following are found both in the auditory system and the vestibular system?
A. basilar membrane
B. hair cells
C. semicircular canals
D. ossicles

Answer
B

Free Response
How would a rise in altitude likely affect the speed of a sound transmitted through air? Why?

Answer
The sound would slow down, because it is transmitted through the particles (gas) and there are fewer particles (lower
density) at higher altitudes.

How might being in a place with less gravity than Earth has (such as Earth’s moon) affect vestibular sensation, and why?

Answer
Because vestibular sensation relies on gravity’s effects on tiny crystals in the inner ear, a situation of reduced gravity would
likely impair vestibular sensation.

Access for free at OpenStax 17.3.E.4 [Link]

36.5: Vision
Vision is the ability to detect light patterns from the outside environment and interpret them into images. Animals are bombarded
with sensory information, and the sheer volume of visual information can be problematic. Fortunately, the visual systems of species
have evolved to attend to the most-important stimuli. The importance of vision to humans is further substantiated by the fact that
about one-third of the human cerebral cortex is dedicated to analyzing and perceiving visual information.

Review Questions
Why do people over 55 often need reading glasses?
A. Their cornea no longer focuses correctly.
B. Their lens no longer focuses correctly.
C. Their eyeball has elongated with age, causing images to focus in front of their retina.
D. Their retina has thinned with age, making vision more difficult.

Answer
B

Why is it easier to see images at night using peripheral, rather than the central, vision?
A. Cones are denser in the periphery of the retina.
B. Bipolar cells are denser in the periphery of the retina.
C. Rods are denser in the periphery of the retina.
D. The optic nerve exits at the periphery of the retina.

Answer
C

A person catching a ball must coordinate her head and eyes. What part of the brain is helping to do this?
A. hypothalamus
B. pineal gland
C. thalamus
D. superior colliculus

Answer
D

Free Response
How could the pineal gland, the brain structure that plays a role in annual cycles, use visual information from the
suprachiasmatic nucleus of the hypothalamus?

Answer
The pineal gland could use length-of-day information to determine the time of year, for example. Day length is shorter in
the winter than it is in the summer. For many animals and plants, photoperiod cues them to reproduce at a certain time of
year.

How is the relationship between photoreceptors and bipolar cells different from other sensory receptors and adjacent cells?

Answer
The photoreceptors tonically inhibit the bipolar cells, and stimulation of the receptors turns this inhibition off, activating the
bipolar cells.

Access for free at OpenStax 17.3.E.5 [Link]

This page titled 17.3.E: Sensory Systems (Exercises) is shared under a CC BY license and was authored, remixed, and/or curated by OpenStax.
36.E: Sensory Systems (Exercises) by OpenStax is licensed CC BY 4.0.

Access for free at OpenStax 17.3.E.6 [Link]

Index
A areolar biotechnology
absorption spectrum 15.1.3: Animal Primary Tissues 5.2.1: Cloning and Genetic Engineering
11.1.2: The Light-Dependent Reactions of arteriole bipolar neuron
Photosynthesis 16.4: Mammalian Heart and Blood Vessels 17.3.4: Taste and Smell
abstract artery blood pressure
1.1.2: The Science of Biology 16.4: Mammalian Heart and Blood Vessels 16.5: Blood Flow and Blood Pressure Regulation
acclimatization articulation BMR
15.1.4: Homeostasis 15.2: Types of Skeletal Systems 15.1.2: Animal Form and Function
acetyl CoA asymmetrical bolus
12.1.2: Citric Acid Cycle and Oxidative 15.1.2: Animal Form and Function 17.1.2: Digestive Systems
Phosphorylation Atherosclerosis bone
acid 16.4: Mammalian Heart and Blood Vessels 15.3: Bone
2.2: Water atom bone remodeling
activation energy 1.1.3: Themes and Concepts of Biology 15.3: Bone
10.1: Free and Activation Energy atomic number Botany
active site 2.1: The Building Blocks of Molecules 1.1.3: Themes and Concepts of Biology
10.2: Enzymes ATP buffer
active transport 10.3: ATP in Living Systems 2.2: Water
3.1.6: Active Transport 12.1.1: Glycolysis
adhesion ATP synthase C
2.2: Water 12.1.2: Citric Acid Cycle and Oxidative
Phosphorylation
calcification
alimentary canal 15.3: Bone
17.1.2: Digestive Systems atrioventricular
16.4: Mammalian Heart and Blood Vessels
Calvin cycle
allele 11.1.3: The Calvin Cycle
6.1.2: Laws of Inheritance atrioventricular valve
16.4: Mammalian Heart and Blood Vessels
canaliculus
allosteric inhibition 15.1.3: Animal Primary Tissues
10.2: Enzymes atrium
16.2: Overview of the Circulatory System
candela
alteration 17.3.6: Vision
15.1.4: Homeostasis audition
17.3.5: Hearing and Vestibular Sensation
capillary
alternation of generations 16.4: Mammalian Heart and Blood Vessels
4.2.1: Sexual Reproduction auditory ossicle
15.2: Types of Skeletal Systems
capillary bed
alternative RNA splicing 16.4: Mammalian Heart and Blood Vessels
5.1.5: How Genes Are Regulated autosome
4.2.3: Errors in Meiosis
carbohydrate
Amino acid 2.3: Biological Molecules
2.3: Biological Molecules autotroph
11.1.1: Overview of Photosynthesis
carbon fixation
aminopeptidase 11.1.3: The Calvin Cycle
17.1.4: Digestive System Processes axial skeleton
15.2: Types of Skeletal Systems
carboxypeptidase
anaerobic cellular respiration 17.1.4: Digestive System Processes
12.1.3: Fermentation cardiac cycle
anaphase B
16.4: Mammalian Heart and Blood Vessels
4.1.2: The Cell Cycle basal metabolic rate cardiac output
aneuploid 15.1.2: Animal Form and Function
16.5: Blood Flow and Blood Pressure Regulation
4.2.3: Errors in Meiosis base cardiomyocyte
angina 2.2: Water
16.4: Mammalian Heart and Blood Vessels
16.4: Mammalian Heart and Blood Vessels basic science carnivore
anion 1.1.2: The Science of Biology
17.1.2: Digestive Systems
2.1: The Building Blocks of Molecules basilar membrane carpus
anneal 17.3.5: Hearing and Vestibular Sensation
15.2: Types of Skeletal Systems
5.2.1: Cloning and Genetic Engineering bicuspid valve cartilage
anus 16.4: Mammalian Heart and Blood Vessels
15.1.3: Animal Primary Tissues
17.1.2: Digestive Systems binary fission cation
aorta 4.1.4: Prokaryotic Cell Division
2.1: The Building Blocks of Molecules
16.4: Mammalian Heart and Blood Vessels biochemistry cell
apodeme 1.1.3: Themes and Concepts of Biology
1.1.3: Themes and Concepts of Biology
15.1.2: Animal Form and Function biodiversity cell cycle
appendicular skeleton 9.3: Conservation and Biodiversity
4.1.2: The Cell Cycle
15.2: Types of Skeletal Systems biology cell cycle checkpoints
applied science 1.1.2: The Science of Biology
4.1.2: The Cell Cycle
1.1.2: The Science of Biology biosphere cell plate
appositional growth 1.1.3: Themes and Concepts of Biology
4.1.2: The Cell Cycle
15.3: Bone

1 [Link]
cell wall codominance deoxyribonucleic acid (DNA)
3.1.3: Eukaryotic Cells 6.1.3: Extensions of the Laws of Inheritance 2.3: Biological Molecules
cellulose codon deoxyribose
2.3: Biological Molecules 5.1.4: Translation 5.1.1: The Structure of DNA
Central Dogma cohesion descriptive science
5.1.3: Transcription 2.2: Water 1.1.2: The Science of Biology
central vacuole columnar epithelia desmosome
3.1.3: Eukaryotic Cells 15.1.3: Animal Primary Tissues 3.1.3: Eukaryotic Cells
centriole community diaphysis
4.1.2: The Cell Cycle 1.1.3: Themes and Concepts of Biology 15.3: Bone
cephalic phase compact bone diastole
17.1.5: Digestive System Regulation 15.3: Bone 16.4: Mammalian Heart and Blood Vessels
Chargaff's rules competitive inhibition diffusion
5.1.1: The Structure of DNA 10.2: Enzymes 3.1.5: Passive Transport
chemical bond concentration gradient Digestion
2.1: The Building Blocks of Molecules 3.1.5: Passive Transport 17.1.4: Digestive System Processes
chemiosmosis conclusion dihybrid
12.1.2: Citric Acid Cycle and Oxidative 1.1.2: The Science of Biology 6.1.2: Laws of Inheritance
Phosphorylation cone dipeptidase
chiasmata 17.3.6: Vision 17.1.4: Digestive System Processes
4.2.2: Meiosis conifer diploid
chitin 19.3: Seed Plants - Gymnosperms 3.3: The Genome
2.3: Biological Molecules connective tissue 4.1.1: The Genome
chlorophyll 15.1.3: Animal Primary Tissues Disaccharide
11.1.1: Overview of Photosynthesis conservation biology 2.3: Biological Molecules
chlorophyll a 9.3: Conservation and Biodiversity discontinuous variation
11.1.2: The Light-Dependent Reactions of continuous variation 6.1.1: Mendel’s Experiments
Photosynthesis discussion
6.1.1: Mendel’s Experiments
chlorophyll b control 1.1.2: The Science of Biology
11.1.2: The Light-Dependent Reactions of DNA ligase
1.1.2: The Science of Biology
Photosynthesis
cornea 5.1.2: DNA Replication
chloroplast DNA polymerase
17.3.6: Vision
3.1.3: Eukaryotic Cells
coronal plane 5.1.2: DNA Replication
11.1.1: Overview of Photosynthesis
cholecystokinin 15.1.2: Animal Form and Function dominant
coronary artery 6.1.1: Mendel’s Experiments
17.1.5: Digestive System Regulation
chondrocyte 16.4: Mammalian Heart and Blood Vessels dorsal cavity
coronary vein 15.1.2: Animal Form and Function
15.1.3: Animal Primary Tissues
chromosome inversion 16.4: Mammalian Heart and Blood Vessels double circulation
covalent bond 16.2: Overview of the Circulatory System
4.2.3: Errors in Meiosis
chylomicron 2.1: The Building Blocks of Molecules double helix
coxal bone 5.1.1: The Structure of DNA
17.1.4: Digestive System Processes
chyme 15.2: Types of Skeletal Systems duodenum
cranial bone 17.1.2: Digestive Systems
17.1.2: Digestive Systems
Chymotrypsin 15.2: Types of Skeletal Systems
17.1.4: Digestive System Processes crossing over E
cilium 4.2.2: Meiosis ECG
3.1.3: Eukaryotic Cells cuboidal epithelia 16.4: Mammalian Heart and Blood Vessels
circadian 15.1.3: Animal Primary Tissues ecosystem
17.3.6: Vision cytokinesis 1.1.3: Themes and Concepts of Biology
circulatory system 4.1.2: The Cell Cycle ectotherm
16: Circulatory System cytoplasm 15.1.2: Animal Form and Function
citric acid cycle 3.1.3: Eukaryotic Cells elastase
12.1.2: Citric Acid Cycle and Oxidative cytoskeleton 17.1.4: Digestive System Processes
Phosphorylation 3.1.3: Eukaryotic Cells electrocardiogram
clavicle cytosol 16.4: Mammalian Heart and Blood Vessels
15.2: Types of Skeletal Systems 3.1.3: Eukaryotic Cells electrochemical gradient
cleavage furrow 3.1.6: Active Transport
4.1.2: The Cell Cycle D electromagnetic spectrum
Cloning deductive reasoning 11.1.2: The Light-Dependent Reactions of
5.2.1: Cloning and Genetic Engineering Photosynthesis
1.1.2: The Science of Biology
closed circulatory system Denaturation electron
16.2: Overview of the Circulatory System 2.1: The Building Blocks of Molecules
2.3: Biological Molecules
cochlea denature electron transfer
17.3.5: Hearing and Vestibular Sensation 2.1: The Building Blocks of Molecules
10.2: Enzymes

2 [Link]
Electron transport chain exoskeleton gametophyte
12.1.2: Citric Acid Cycle and Oxidative 15.2: Types of Skeletal Systems 4.2.1: Sexual Reproduction
Phosphorylation Extracellular Matrix gap junction
element 3.1.3: Eukaryotic Cells 3.1.3: Eukaryotic Cells
2.1: The Building Blocks of Molecules gastric inhibitory peptide
endergonic F 17.1.5: Digestive System Regulation
10.1: Free and Activation Energy gastric phase
F1
endocardium 6.1.1: Mendel’s Experiments 17.1.5: Digestive System Regulation
16.4: Mammalian Heart and Blood Vessels gastrin
F2
endochondral ossification 6.1.1: Mendel’s Experiments 17.1.5: Digestive System Regulation
15.3: Bone gastrovascular cavity
facial bone
endocrine system 15.2: Types of Skeletal Systems 17.1.2: Digestive Systems
17.1.5: Digestive System Regulation gel electrophoresis
facilitated transport
Endocytosis 3.1.5: Passive Transport 5.2.1: Cloning and Genetic Engineering
3.1.6: Active Transport gene
falsifiable
endomembrane system 1.1.2: The Science of Biology 3.3: The Genome
3.1.3: Eukaryotic Cells 4.1.1: The Genome
fat
endoplasmic reticulum 2.3: Biological Molecules
gene expression
3.1.3: Eukaryotic Cells 5.1.5: How Genes Are Regulated
femur
endoskeleton 15.2: Types of Skeletal Systems
genetic code
15.2: Types of Skeletal Systems 5.1.4: Translation
fermentation
endosymbiosis 12.1.3: Fermentation
genetic drift
3.2: Eukaryotic Origins 7.2: Mechanisms of Evolution
13.1.2: Eukaryotic Origins
fertilization
4.2.2: Meiosis
genetic engineering
18.2: Eukaryotic Origins
5.2.1: Cloning and Genetic Engineering
endotherm fibrous connective tissue
15.1.3: Animal Primary Tissues
genetically modified organism (GMO)
15.1.2: Animal Form and Function
5.2.1: Cloning and Genetic Engineering
enzyme fibula
15.2: Types of Skeletal Systems
genome
2.3: Biological Molecules
3.3: The Genome
10.2: Enzymes flagellum 4.1.1: The Genome
epicardium 3.1.3: Eukaryotic Cells
genotype
16.4: Mammalian Heart and Blood Vessels flat bone 6.1.2: Laws of Inheritance
epigenetic 15.3: Bone
germ cell
5.1.5: How Genes Are Regulated Fluid Mosaic Model 4.2.1: Sexual Reproduction
epiphyseal plate 3.1.4: The Cell Membrane
gill circulation
15.3: Bone forearm 16.2: Overview of the Circulatory System
epiphysis 15.2: Types of Skeletal Systems
gizzard
15.3: Bone fossil 17.1.2: Digestive Systems
Epistasis 7.3: Evidence of Evolution
glabrous
6.1.3: Extensions of the Laws of Inheritance fovea 17.3.3: Somatosensation
epithelial tissue 17.3.6: Vision
Glomerulus
15.1.3: Animal Primary Tissues Free Energy 17.3.4: Taste and Smell
esophagus 10.1: Free and Activation Energy
Glycogen
17.1.2: Digestive Systems free nerve ending 2.3: Biological Molecules
essential nutrient 17.3.3: Somatosensation
glycolysis
17.1.3: Nutrition and Energy Production frontal plane 12.1.1: Glycolysis
estivation 15.1.2: Animal Form and Function
Golgi apparatus
15.1.2: Animal Form and Function FtsZ 3.1.3: Eukaryotic Cells
eukaryote 4.1.4: Prokaryotic Cell Division
Golgi tendon organ
1.1.3: Themes and Concepts of Biology fusiform 17.3.3: Somatosensation
eukaryotic cell 15.1.2: Animal Form and Function
granum
3.1.2: Comparing Prokaryotic and Eukaryotic Cells
11.1.1: Overview of Photosynthesis
euploid G gustation
4.2.3: Errors in Meiosis G0 phase 17.3.4: Taste and Smell
evaporation 4.1.2: The Cell Cycle gymnosperm
2.2: Water G1 phase 19.3: Seed Plants - Gymnosperms
Evolution 4.1.2: The Cell Cycle
1.1.3: Themes and Concepts of Biology G2 phase H
exergonic 4.1.2: The Cell Cycle
haploid
10.1: Free and Activation Energy gallbladder 3.3: The Genome
Exocytosis 17.1.2: Digestive Systems 4.1.1: The Genome
3.1.6: Active Transport gamete Haversian canal
exon 3.3: The Genome 15.3: Bone
5.1.3: Transcription 4.1.1: The Genome

3 [Link]
helicase ingestion law of segregation
5.1.2: DNA Replication 17.1.4: Digestive System Processes 6.1.2: Laws of Inheritance
hemizygous inner ear leading strand
6.1.3: Extensions of the Laws of Inheritance 17.3.5: Hearing and Vestibular Sensation 5.1.2: DNA Replication
hemocoel interkinesis lens
16.2: Overview of the Circulatory System 4.2.2: Meiosis 17.3.6: Vision
hemolymph interphase life cycle
16.2: Overview of the Circulatory System 4.1.2: The Cell Cycle 4.2.1: Sexual Reproduction
herbivore interstitial fluid life science
17.1.2: Digestive Systems 16.2: Overview of the Circulatory System 1.1.2: The Science of Biology
heterotroph intervertebral disc linkage
11.1.1: Overview of Photosynthesis 15.2: Types of Skeletal Systems 6.1.3: Extensions of the Laws of Inheritance
heterozygous intestinal phase lipase
6.1.2: Laws of Inheritance 17.1.5: Digestive System Regulation 17.1.2: Digestive Systems
hibernation intramembranous ossification lipids
15.1.2: Animal Form and Function 15.3: Bone 2.3: Biological Molecules
Homeostasis introduction litmus paper
1.1.3: Themes and Concepts of Biology 1.1.2: The Science of Biology 2.2: Water
15.1.4: Homeostasis intron liver
homologous chromosomes 5.1.3: Transcription 17.1.2: Digestive Systems
3.3: The Genome ion locus
4.1.1: The Genome
2.1: The Building Blocks of Molecules 3.3: The Genome
homozygous ionic bond 4.1.1: The Genome
6.1.2: Laws of Inheritance loose connective tissue
2.1: The Building Blocks of Molecules
horizontal plane iris 15.1.3: Animal Primary Tissues
15.1.2: Animal Form and Function lower limb
17.3.6: Vision
hormone isotonic 15.2: Types of Skeletal Systems
2.3: Biological Molecules lymph node
3.1.5: Passive Transport
humerus isotope 16.5: Blood Flow and Blood Pressure Regulation
15.2: Types of Skeletal Systems lysosome
2.1: The Building Blocks of Molecules
hybridization 3.1.3: Eukaryotic Cells
6.1.1: Mendel’s Experiments
J
hydrogen bond M
2.1: The Building Blocks of Molecules
jejunum
17.1.2: Digestive Systems macromolecule
hydrophilic 1.1.3: Themes and Concepts of Biology
2.2: Water 2.3: Biological Molecules
hydrophobic K
malleus
2.2: Water karyogram 17.3.5: Hearing and Vestibular Sensation
hydrostatic skeleton 4.2.3: Errors in Meiosis
maltase
15.2: Types of Skeletal Systems karyotype 17.1.4: Digestive System Processes
hyoid bone 4.2.3: Errors in Meiosis
mass number
15.2: Types of Skeletal Systems kinesthesia 2.1: The Building Blocks of Molecules
hyperopia 17.3.2: Sensory Processes
materials and methods
17.3.6: Vision kinetochore 1.1.2: The Science of Biology
hypertonic 4.1.2: The Cell Cycle
matrix
3.1.5: Passive Transport 15.1.3: Animal Primary Tissues
hypothesis L matter
1.1.2: The Science of Biology labyrinth 2.1: The Building Blocks of Molecules
hypotonic 17.3.5: Hearing and Vestibular Sensation mechanoreceptor
3.1.5: Passive Transport lactase 17.3.2: Sensory Processes
17.1.4: Digestive System Processes meiosis
I lacuna 4.2.1: Sexual Reproduction
ileum 15.1.3: Animal Primary Tissues meiosis I
17.1.2: Digestive Systems lagging strand 4.2.2: Meiosis
incomplete dominance 5.1.2: DNA Replication meiosis II
6.1.3: Extensions of the Laws of Inheritance lamella 4.2.2: Meiosis
incus 15.3: Bone Meissner’s corpuscle
17.3.5: Hearing and Vestibular Sensation large intestine 17.3.3: Somatosensation
induced fit 17.1.2: Digestive Systems Merkel's disc
10.2: Enzymes law of dominance 17.3.3: Somatosensation
inductive reasoning 6.1.2: Laws of Inheritance mesophyll
1.1.2: The Science of Biology law of independent assortment 11.1.1: Overview of Photosynthesis
inferior vena cava 6.1.2: Laws of Inheritance metacarpus
16.4: Mammalian Heart and Blood Vessels 15.2: Types of Skeletal Systems

4 [Link]
metaphase nitrogenous base osmosis
4.1.2: The Cell Cycle 5.1.1: The Structure of DNA 3.1.5: Passive Transport
metaphase plate nociception osseous tissue
4.1.2: The Cell Cycle 17.3.3: Somatosensation 15.3: Bone
metatarsal Noncompetitive Inhibition ossicle
15.2: Types of Skeletal Systems 10.2: Enzymes 17.3.5: Hearing and Vestibular Sensation
microbiology nondisjunction ossification
1.1.3: Themes and Concepts of Biology 4.2.3: Errors in Meiosis 15.3: Bone
microscope nonpolar covalent bond osteoblast
3.1.1: How Cells Are Studied 2.1: The Building Blocks of Molecules 15.3: Bone
middle ear nontemplate strand osteoclast
17.3.5: Hearing and Vestibular Sensation 5.1.3: Transcription 15.3: Bone
midsagittal plane nuclear envelope osteocyte
15.1.2: Animal Form and Function 3.1.3: Eukaryotic Cells 15.3: Bone
mineral nucleic acid osteon
17.1.3: Nutrition and Energy Production 2.3: Biological Molecules 15.1.3: Animal Primary Tissues
mismatch repair nucleolus ostium
5.1.2: DNA Replication 3.1.3: Eukaryotic Cells 16.2: Overview of the Circulatory System
mitochondria nucleotide outer ear
3.1.3: Eukaryotic Cells 2.3: Biological Molecules 17.3.5: Hearing and Vestibular Sensation
Mitosis nucleotide excision repair oval window
4.1.2: The Cell Cycle 5.1.2: DNA Replication 17.3.5: Hearing and Vestibular Sensation
mitotic phase nucleus oxidative phosphorylation
4.1.2: The Cell Cycle 2.1: The Building Blocks of Molecules 12.1.2: Citric Acid Cycle and Oxidative
mitotic spindle 3.1.3: Eukaryotic Cells Phosphorylation
4.1.2: The Cell Cycle
model system O P
6.1.1: Mendel’s Experiments octet rule P
molecular biology 2.1: The Building Blocks of Molecules 6.1.1: Mendel’s Experiments
1.1.3: Themes and Concepts of Biology odorant Pacinian corpuscle
molecule 17.3.4: Taste and Smell 17.3.3: Somatosensation
1.1.3: Themes and Concepts of Biology oil paleontology
monogastric 2.3: Biological Molecules 1.1.3: Themes and Concepts of Biology
17.1.2: Digestive Systems Okazaki fragments pancreas
monohybrid 5.1.2: DNA Replication 17.1.2: Digestive Systems
6.1.2: Laws of Inheritance olfaction papilla
Monosaccharide 17.3.4: Taste and Smell 17.3.4: Taste and Smell
2.3: Biological Molecules olfactory bulb passive transport
monosomy 17.3.4: Taste and Smell 3.1.5: Passive Transport
4.2.3: Errors in Meiosis olfactory epithelium patella
mRNA 17.3.4: Taste and Smell 15.2: Types of Skeletal Systems
5.1.3: Transcription olfactory receptor pectoral girdle
muscle spindle 17.3.4: Taste and Smell 15.2: Types of Skeletal Systems
17.3.3: Somatosensation omnivore Pedigree
mutation 17.1.2: Digestive Systems 6.2: Pedigrees review
5.1.2: DNA Replication oncogene pelvic girdle
myocardial infarction 4.1.3: Cancer and the Cell Cycle 15.2: Types of Skeletal Systems
16.4: Mammalian Heart and Blood Vessels open circulatory system pepsin
myocardium 16.2: Overview of the Circulatory System 17.1.2: Digestive Systems
16.4: Mammalian Heart and Blood Vessels organ pepsinogen
myopia 1.1.3: Themes and Concepts of Biology 17.1.2: Digestive Systems
17.3.6: Vision organ of Corti perception
17.3.5: Hearing and Vestibular Sensation 17.3.2: Sensory Processes
N organ system pericardium
natural science 1.1.3: Themes and Concepts of Biology 16.4: Mammalian Heart and Blood Vessels
1.1.2: The Science of Biology organelle periodic table of elements
natural selection 1.1.3: Themes and Concepts of Biology 2.1: The Building Blocks of Molecules
3.1.2: Comparing Prokaryotic and Eukaryotic Cells peripheral resistance
7.2: Mechanisms of Evolution
negative feedback loop organism 16.5: Blood Flow and Blood Pressure Regulation
1.1.3: Themes and Concepts of Biology peristalsis
15.1.4: Homeostasis
neurobiology origin 17.1.2: Digestive Systems
4.1.4: Prokaryotic Cell Division peroxisome
1.1.3: Themes and Concepts of Biology
neutron osmolarity 3.1.3: Eukaryotic Cells
3.1.5: Passive Transport
2.1: The Building Blocks of Molecules

5 [Link]
pH scale primer red queen hypothesis
2.2: Water 5.1.2: DNA Replication 4.2.1: Sexual Reproduction
phagocytosis prokaryote reduction division
3.1.6: Active Transport 1.1.3: Themes and Concepts of Biology 4.2.2: Meiosis
phalange prokaryotic cell replication fork
15.2: Types of Skeletal Systems 3.1.2: Comparing Prokaryotic and Eukaryotic Cells 5.1.2: DNA Replication
phenotype prometaphase reproductive cloning
6.1.2: Laws of Inheritance 4.1.2: The Cell Cycle 5.2.1: Cloning and Genetic Engineering
pheromone promoter resorption
17.3.4: Taste and Smell 5.1.3: Transcription 15.3: Bone
phosphate group prophase restriction enzyme
5.1.1: The Structure of DNA 4.1.2: The Cell Cycle 5.2.1: Cloning and Genetic Engineering
phospholipid proprioception results
2.3: Biological Molecules 17.3.2: Sensory Processes 1.1.2: The Science of Biology
photoautotroph protein retina
11.1.1: Overview of Photosynthesis 2.3: Biological Molecules 17.3.6: Vision
photon proton reverse genetics
11.1.2: The Light-Dependent Reactions of 2.1: The Building Blocks of Molecules 5.2.1: Cloning and Genetic Engineering
Photosynthesis proventriculus review article
photosynthesis 17.1.2: Digestive Systems 1.1.2: The Science of Biology
11.1: Photosynthesis pseudostratified rhodopsin
photosystem 15.1.3: Animal Primary Tissues 17.3.6: Vision
11.1.2: The Light-Dependent Reactions of pulmocutaneous circulation rib
Photosynthesis
16.2: Overview of the Circulatory System 15.2: Types of Skeletal Systems
phylogenetic tree pulmonary circulation ribonucleic acid (RNA)
1.1.3: Themes and Concepts of Biology
16.2: Overview of the Circulatory System 2.3: Biological Molecules
physical science Punnett square ribosome
1.1.2: The Science of Biology
6.1.2: Laws of Inheritance 3.1.3: Eukaryotic Cells
pigment pupil RNA polymerase
11.1.1: Overview of Photosynthesis
17.3.6: Vision 5.1.3: Transcription
pinna rod
17.3.5: Hearing and Vestibular Sensation
Q 17.3.6: Vision
pinocytosis rough endoplasmic reticulum
3.1.6: Active Transport
quiescent
4.1.2: The Cell Cycle 3.1.3: Eukaryotic Cells
plagiarism roughage
1.1.2: The Science of Biology
plasma R 17.1.2: Digestive Systems
radioactive isotope rRNA
16.3: Components of the Blood
2.1: The Building Blocks of Molecules 5.1.4: Translation
plasma membrane Rubisco
3.1.3: Eukaryotic Cells radius
15.2: Types of Skeletal Systems 11.1.3: The Calvin Cycle
plasmid Ruffini ending
5.2.1: Cloning and Genetic Engineering reception
17.3.2: Sensory Processes 17.3.3: Somatosensation
plasmodesma ruminant
3.1.3: Eukaryotic Cells receptive field
17.3.2: Sensory Processes 17.1.2: Digestive Systems
platelet
16.3: Components of the Blood receptor potential
17.3.2: Sensory Processes S
polar covalent bond
2.1: The Building Blocks of Molecules recessive S phase
6.1.1: Mendel’s Experiments 4.1.2: The Cell Cycle
polymerase chain reaction (PCR)
5.2.1: Cloning and Genetic Engineering reciprocal cross Sagittal Plane
6.1.1: Mendel’s Experiments 15.1.2: Animal Form and Function
Polypeptide
2.3: Biological Molecules recombinant salivary amylase
4.2.2: Meiosis 17.1.2: Digestive Systems
polyploid
4.2.3: Errors in Meiosis recombinant DNA Saturated fatty acid
5.2.1: Cloning and Genetic Engineering 2.3: Biological Molecules
Polysaccharide
2.3: Biological Molecules recombinant protein scapula
5.2.1: Cloning and Genetic Engineering 15.2: Types of Skeletal Systems
population
1.1.3: Themes and Concepts of Biology recombination science
6.1.3: Extensions of the Laws of Inheritance 1.1.2: The Science of Biology
positive feedback loop
15.1.4: Homeostasis rectum scientific method
17.1.2: Digestive Systems 1.1.2: The Science of Biology
precapillary sphincter
16.5: Blood Flow and Blood Pressure Regulation red blood cell secretin
16.3: Components of the Blood 17.1.5: Digestive System Regulation
presbyopia
17.3.6: Vision
selectively permeable
3.1.5: Passive Transport

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semicircular canal sternum thoracic cage
17.3.5: Hearing and Vestibular Sensation 15.2: Types of Skeletal Systems 15.2: Types of Skeletal Systems
semiconservative replication steroid thylakoid
5.1.2: DNA Replication 2.3: Biological Molecules 11.1.1: Overview of Photosynthesis
semilunar valve stoma tibia
16.4: Mammalian Heart and Blood Vessels 11.1.1: Overview of Photosynthesis 15.2: Types of Skeletal Systems
sensory receptor stomach tight junction
17.3.2: Sensory Processes 17.1.2: Digestive Systems 3.1.3: Eukaryotic Cells
sensory transduction stop codon tonic activity
17.3.2: Sensory Processes 5.1.4: Translation 17.3.6: Vision
septum stratified epithelia tonicity
4.1.4: Prokaryotic Cell Division 15.1.3: Animal Primary Tissues 3.1.5: Passive Transport
serendipity stroke volume torpor
1.1.2: The Science of Biology 16.5: Blood Flow and Blood Pressure Regulation 15.1.2: Animal Form and Function
serum stroma trabecula
16.3: Components of the Blood 11.1.1: Overview of Photosynthesis 15.1.3: Animal Primary Tissues
sesamoid bone substrate trabeculae
15.3: Bone 10.2: Enzymes 15.3: Bone
Set Point sucrase trait
15.1.4: Homeostasis 17.1.4: Digestive System Processes 6.1.1: Mendel’s Experiments
short bone superior colliculus transcription bubble
15.3: Bone 17.3.6: Vision 5.1.3: Transcription
simple epithelia superior vena cava transgenic
15.1.3: Animal Primary Tissues 16.4: Mammalian Heart and Blood Vessels 5.2.1: Cloning and Genetic Engineering
sinoatrial node suprachiasmatic nucleus transitional epithelia
16.4: Mammalian Heart and Blood Vessels 17.3.6: Vision 15.1.3: Animal Primary Tissues
skull surface tension translocation
15.2: Types of Skeletal Systems 2.2: Water 4.2.3: Errors in Meiosis
small intestine suture bone Transverse Plane
17.1.2: Digestive Systems 15.3: Bone 15.1.2: Animal Form and Function
smooth endoplasmic reticulum synapsis tricuspid valve
3.1.3: Eukaryotic Cells 4.2.2: Meiosis 16.4: Mammalian Heart and Blood Vessels
SMR systemic circulation Triglyceride
15.1.2: Animal Form and Function 16.2: Overview of the Circulatory System 2.3: Biological Molecules
solute systole trisomy
3.1.5: Passive Transport 16.4: Mammalian Heart and Blood Vessels 4.2.3: Errors in Meiosis
solvent tRNA
2.2: Water T 5.1.4: Translation
somatic cell tarsal trypsin
4.2.2: Meiosis 15.2: Types of Skeletal Systems 17.1.4: Digestive System Processes
somatostatin tastant tumor suppressor gene
17.1.5: Digestive System Regulation 17.3.4: Taste and Smell 4.1.3: Cancer and the Cell Cycle
speciation taste bud tympanum
7.4: Speciation 17.3.4: Taste and Smell 17.3.5: Hearing and Vestibular Sensation
sphincter tectorial membrane
17.1.2: Digestive Systems 17.3.5: Hearing and Vestibular Sensation U
splicing telomerase ulna
5.1.3: Transcription 5.1.2: DNA Replication 15.2: Types of Skeletal Systems
spongy bone tissue telomere ultrasound
15.3: Bone 5.1.2: DNA Replication 17.3.5: Hearing and Vestibular Sensation
sporophyte telophase umami
4.2.1: Sexual Reproduction 4.1.2: The Cell Cycle 17.3.4: Taste and Smell
squamous epithelia temperature unidirectional circulation
15.1.3: Animal Primary Tissues 2.2: Water 16.2: Overview of the Circulatory System
standard metabolic rate template strand unified cell theory
15.1.2: Animal Form and Function 5.1.3: Transcription 3.1.1: How Cells Are Studied
stapes test cross unsaturated fatty acid
17.3.5: Hearing and Vestibular Sensation 6.1.2: Laws of Inheritance 2.3: Biological Molecules
Starch tetrad
2.3: Biological Molecules 4.2.2: Meiosis V
start codon theory vacuole
5.1.4: Translation 1.1.2: The Science of Biology 3.1.3: Eukaryotic Cells
stereocilia thermoregulation
17.3.5: Hearing and Vestibular Sensation 15.1.4: Homeostasis

7 [Link]
van der Waals interaction vertebral column W
2.1: The Building Blocks of Molecules 15.2: Types of Skeletal Systems wavelength
variable Vesicle 11.1.2: The Light-Dependent Reactions of
1.1.2: The Science of Biology 3.1.3: Eukaryotic Cells Photosynthesis
vasoconstriction vestibular sense white blood cell
16.4: Mammalian Heart and Blood Vessels 17.3.2: Sensory Processes 16.3: Components of the Blood
vasodilation villi wild type
16.4: Mammalian Heart and Blood Vessels 17.1.2: Digestive Systems 6.1.3: Extensions of the Laws of Inheritance
vein Viruses
16.4: Mammalian Heart and Blood Vessels 13.2.1: Viruses X
vena cava vision X inactivation
16.4: Mammalian Heart and Blood Vessels 17.3.6: Vision 4.2.3: Errors in Meiosis
ventral cavity vitamin
15.1.2: Animal Form and Function 17.1.3: Nutrition and Energy Production Z
ventricle vomeronasal organ (VNO) zoology
16.2: Overview of the Circulatory System 17.3.4: Taste and Smell
1.1.3: Themes and Concepts of Biology
venule
16.4: Mammalian Heart and Blood Vessels

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Glossary
Sample Word 1 | Sample Definition 1

1 [Link]
SECTION OVERVIEW

BIOL 307 Modules

Topic hierarchy

1 [Link]
SECTION OVERVIEW

Reference Material
Topic hierarchy

1 [Link]
Detailed Licensing
Overview
Title: BIOL 310: General Biology (Wada)
Webpages: 189
Applicable Restrictions: Noncommercial
All licenses found:
CC BY 4.0: 68.3% (129 pages)
Undeclared: 30.7% (58 pages)
CC BY-NC-SA 4.0: 1.1% (2 pages)

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BIOL 310: General Biology (Wada) - Undeclared 4.1: Reproduction at the Cellular Level - Undeclared
Front Matter - Undeclared 4.1.1: The Genome - Undeclared
TitlePage - Undeclared 4.1.2: The Cell Cycle - Undeclared
InfoPage - Undeclared 4.1.3: Cancer and the Cell Cycle - Undeclared
Table of Contents - Undeclared 4.1.4: Prokaryotic Cell Division - Undeclared
Licensing - Undeclared 4.1.E: Reproduction at the Cellular Level
(Exercises) - Undeclared
1: Scientific Method and Designing Experiments -
Undeclared 4.2: The Cellular Basis of Inheritance - Undeclared
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1.1.E: The Study of Life (Exercises) - CC BY 4.0 5: DNA; DNA Technology - Undeclared
1.2: The Scientific Process - CC BY 4.0 5.1: Molecular Biology - Undeclared
1.3: Presenting Data - Graphs and Tables - CC BY 4.0 5.1.1: The Structure of DNA - Undeclared
2: Biological Macromolecules - Undeclared 5.1.2: DNA Replication - Undeclared
2.1: The Building Blocks of Molecules - Undeclared 5.1.3: Transcription - Undeclared
2.2: Water - Undeclared 5.1.4: Translation - Undeclared
2.3: Biological Molecules - Undeclared 5.1.5: How Genes Are Regulated - Undeclared
2.E: Chemistry of Life (Exercises) - Undeclared 5.1.E: Molecular Biology (Exercises) -
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5.2.2: Biotechnology in Medicine and Agriculture
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5.2.3: Genomics and Proteomics - CC BY 4.0
3.1.4: The Cell Membrane - Undeclared
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3.1.5: Passive Transport - Undeclared
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4: Cell Division - Undeclared BY 4.0

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 6.1.E: Patterns of Inheritance (Exercises) - CC BY 11.1.2: The Light-Dependent Reactions of
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6.2: Pedigrees review - CC BY-NC-SA 4.0 11.1.3: The Calvin Cycle - CC BY 4.0
7: Evolution - CC BY 4.0 11.1.E: Photosynthesis (Exercises) - CC BY 4.0
12: Respiration - Undeclared
7.1: Discovering How Populations Change - CC BY
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7.2: Mechanisms of Evolution - CC BY 4.0 12.1.1: Glycolysis - CC BY 4.0
7.3: Evidence of Evolution - CC BY 4.0 12.1.2: Citric Acid Cycle and Oxidative
7.4: Speciation - CC BY 4.0 Phosphorylation - CC BY 4.0
7.5: Common Misconceptions about Evolution - CC 12.1.3: Fermentation - CC BY 4.0
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4.0 12.1.E: How Cells Obtain Energy (Exercises) -
8: Diversity of Life - CC BY 4.0 CC BY 4.0
8.1: Organizing Life on Earth - CC BY 4.0 12.2: Cellular Respiration Overview - CC BY-NC-SA
8.2: Determining Evolutionary Relationships - CC BY 4.0
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9.1: Population and Community Ecology - CC BY 4.0 13.1.1: Prokaryotic Diversity - CC BY 4.0
9.1.1: Population Demographics and Dynamics - 13.1.2: Eukaryotic Origins - CC BY 4.0
CC BY 4.0 13.1.3: Protists - CC BY 4.0
9.1.2: Population Growth and Regulation - CC BY 13.1.4: Fungi - CC BY 4.0
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9.1.3: The Human Population - CC BY 4.0 (Exercises) - CC BY 4.0
9.1.4: Community Ecology - CC BY 4.0 13.2: The Immune System and Disease - CC BY 4.0
9.1.E: Population and Community Ecology 13.2.1: Viruses - CC BY 4.0
(Exercises) - CC BY 4.0 13.2.2: Innate Immunity - CC BY 4.0
9.2: Ecosystems and the Biosphere - CC BY 4.0 13.2.3: Adaptive Immunity - CC BY 4.0
9.2.1: Energy Flow through Ecosystems - CC BY 13.2.4: Disruptions in the Immune System - CC
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9.2.2: Biogeochemical Cycles - CC BY 4.0 13.2.E: The Immune System and Desease
9.2.3: Terrestrial Biomes - CC BY 4.0 (Exercises) - CC BY 4.0
9.2.4: Aquatic and Marine Biomes - CC BY 4.0 14: Reproductive System - CC BY 4.0
9.2.E: Ecosystems and the Biosphere (Exercises) - 14.1: How Animals Reproduce - CC BY 4.0
CC BY 4.0 14.2: Development and Organogenesis - CC BY 4.0
9.3: Conservation and Biodiversity - CC BY 4.0 14.3: Human Reproduction - CC BY 4.0
9.3.1: Importance of Biodiversity - CC BY 4.0 14.E: Animal Reproduction and Development
9.3.2: Threats to Biodiversity - CC BY 4.0 (Exercises) - CC BY 4.0
9.3.3: Preserving Biodiversity - CC BY 4.0 15: Skeletal System - Undeclared
9.3.E: Conservation and Biodiversity (Exercises) - 15.1: The Animal Body - Basic Form and Function -
CC BY 4.0 CC BY 4.0
10: Energy and Enzymes - Undeclared 15.1.1: Prelude to The Animal Body - CC BY 4.0
10.1: Free and Activation Energy - CC BY 4.0 15.1.2: Animal Form and Function - CC BY 4.0
10.2: Enzymes - CC BY 4.0 15.1.3: Animal Primary Tissues - CC BY 4.0
10.3: ATP in Living Systems - Undeclared 15.1.4: Homeostasis - CC BY 4.0
11: Photosynthesis - Undeclared 15.1.E: The Animal Body - Basic Form and
11.1: Photosynthesis - CC BY 4.0 Function (Exercises) - CC BY 4.0

11.1.1: Overview of Photosynthesis - CC BY 4.0 15.2: Types of Skeletal Systems - CC BY 4.0

15.3: Bone - CC BY 4.0

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16: Circulatory System - CC BY 4.0 Glossary - Undeclared
16.1: Prelude to the Circulatory System - CC BY 4.0 BIOL 307 Modules - Undeclared
16.2: Overview of the Circulatory System - CC BY 18: Fungi and Protists - CC BY 4.0
4.0 18.1: Prokaryotic Diversity - CC BY 4.0
16.3: Components of the Blood - CC BY 4.0 18.2: Eukaryotic Origins - CC BY 4.0
16.4: Mammalian Heart and Blood Vessels - CC BY 18.3: Protists - CC BY 4.0
4.0 18.4: Fungi - CC BY 4.0
16.5: Blood Flow and Blood Pressure Regulation - 18.E: Diversity of Microbes, Fungi, and
CC BY 4.0 Protists (Exercises) - CC BY 4.0
16.E: The Circulatory System (Exercises) - CC BY
19: Plants - CC BY 4.0
4.0
19.1: The Plant Kingdom - CC BY 4.0
17: Nutrition and Digestion - Undeclared
19.2: Seedless Plants - CC BY 4.0
17.1: Animal Nutrition and the Digestive System - 19.3: Seed Plants - Gymnosperms - CC BY 4.0
CC BY 4.0 19.4: Seed Plants- Angiosperms - CC BY 4.0
17.1.1: Prelude to Animal Nutrition and the 19.E: Diversity of Plants (Exercises) - CC BY
Digestive System - CC BY 4.0 4.0
17.1.2: Digestive Systems - CC BY 4.0 20: Animal Diversity - CC BY 4.0
17.1.3: Nutrition and Energy Production - CC BY 20.1: Features of the Animal Kingdom - CC
4.0 BY 4.0
17.1.4: Digestive System Processes - CC BY 4.0 20.2: Sponges and Cnidarians - CC BY 4.0
17.1.5: Digestive System Regulation - CC BY 4.0 20.3: Flatworms, Nematodes, and Arthropods -
17.1.E: Animal Nutrition and the Digestive CC BY 4.0
System (Exercises) - CC BY 4.0 20.4: Mollusks and Annelids - CC BY 4.0
17.2: Nervous System - CC BY 4.0 20.5: Echinoderms and Chordates - CC BY 4.0
17.3: Sensory Systems - CC BY 4.0 20.6: Vertebrates - CC BY 4.0
17.3.1: Introduction - CC BY 4.0 20.E: Diversity of Animals (Exercises) - CC
17.3.2: Sensory Processes - CC BY 4.0 BY 4.0
17.3.3: Somatosensation - CC BY 4.0 Reference Material - Undeclared
17.3.4: Taste and Smell - CC BY 4.0
A: The Periodic Table of Elements - CC BY 4.0
17.3.5: Hearing and Vestibular Sensation - CC BY
B: Geological Time - CC BY 4.0
4.0
C: Measurements and the Metric System - CC BY
17.3.6: Vision - CC BY 4.0
4.0
17.3.E: Sensory Systems (Exercises) - CC BY 4.0
Detailed Licensing - Undeclared
Back Matter - Undeclared
Index - Undeclared

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