Module 5 - BIOENERGETICS

Site: New Era University Printed by: Raymundo, Mharc Jhefferson P.

Course: Earth and Life Science Date: Tuesday, 16 January 2024, 12:25 AM
Book: Module 5 - BIOENERGETICS
 Description

In this module you will understand the basic unit of life and how it works to provide life to living organisms. This module will also make you appreciate life.
 Table of contents

Introduction

Learning Outcomes

Contents

Lesson 1: The cell

Lesson 2: Cellular Respiration

Forum

Quiz

Assignment
 Introduction

Bioenergetics is the part of biochemistry concerned with the energy involved in making and breaking of chemical bonds in the molecules found in
biological organisms. It can also be defined as the study of energy relationships and energy transformations and transductions in living organisms. The ability to
harness energy from a variety of metabolic pathways is a property of all living organisms that contains earth
science. Growth, development, anabolism and catabolism are some of the central processes in the study of biological organisms, because the role of energy is
fundamental to such biological processes. Life is dependent on energy transformations; living organisms survive because of exchange of energy between living
tissues/ cells and the outside environment. Some organisms, such as autotrophs, can acquire energy from sunlight (through photosynthesis) without needing to
consume nutrients and break them down. Other organisms, like heterotrophs, must intake nutrients from food to be able to sustain energy by breaking down
chemical bonds in nutrients during metabolic processes such as glycolysis and the citric acid cycle. Importantly, as a direct consequence of the first law of
thermodynamics, autotrophs and heterotrophs participate in a universal metabolic network—by eating autotrophs (plants), heterotrophs harness energy that was
initially transformed by the plants during photosynthesis.
 Learning Outcomes

At the end of this module, you should be able to:

1. explain how cells carry out functions required for life.

2. explain how photosynthetic organisms use light energy to combine carbon dioxide and water to form energy-rich compounds.

3. trace the energy flow from the environment to the cells.

4. describe how organisms obtain and utilize energy.

5. recognize that organisms require energy to carry out functions required for life.
 Contents

Lesson 1: The Cell

Lesson 2: Photosynthesis
Lesson 3: Cellular Respiration
 Lesson 1: The cell

Nature of Life

• We define life by describing the set of properties that is unique to living things

• Life is a property that emerges from cellular components, but a collection of those components in the right amounts and proportions is not necessarily
alive

• Life continues only as long as a continuous flow of energy sustains its organization

Properties of living things:

• Make and use the organic molecules of life

• Consist of one or more cells

• Engage in self-sustaining biological processes such as metabolism and homeostasis

• Change over their lifetime, for example by growing, maturing, and aging

• Use DNA as their hereditary material

• Have the collective capacity to adapt to the environment over successive generations

What is a cell?

A cell is the basic unit of life. It was first observed under a microscope by Antoine Van Leuwenhoek, eventually called “cell” by Robert Hooke.

According to the cell theory by Matthias Jakob Schleiden and Theodor Schwann: 1. every organism consists of one or more cells; 2. The cell is the structural and
functional unit of all organisms. A cell is the smallest unit of life, individually alive even as part of a multicelled organism; 3. All living cells arise by division of
preexisting cells; 4. Cells contains hereditary material, which they pass to their offspring when they divide.

Components of all cells

All cells have three common features

– Plasma membrane

• Separates cell contents from the external environment

• Controls exchanges between cell and environment

– Cytoplasm

• Jellylike mixture of water, sugars, ions, and proteins with all cellular components inside cell

– DNA

• The hereditary material of cells

General organization of a cell

How do we see cells?

• Most cells are 10-20 micrometers in diameter, much too small to see with the unaided human eye

• One micrometer (μm) is one-thousandth of a millimeter, which is one-thousandth of a meter

Microscopes

• Used to visualize cells

– Light microscopes use visible light to illuminate samples

– Electron microscopes use electrons to image samples

• Scanning electron microscopes image surface of sample by bouncing electrons off sample

• Transmission electron microscopes image internal details by passing electrons through sample

Cell sizes

Prokaryotes

• Prokaryotic cells

– No nucleus

– Bacteria and archaea

– Single-celled organisms

– Smallest and most metabolically diverse life forms we know

– Share basic structures

Generalized Prokaryotes
• Cell wall

– Surrounds the plasma membrane

– Made of peptidoglycan (in bacteria) or proteins (in archaea)

– Coated with a sticky capsule

• Flagellum

– For motion

• Pili

– Help cells move across surfaces

– “Sex” pilus aids in sexual reproduction

• Ribosomes

– Organelles upon which polypeptides are assembled

• Nucleoid

– Irregularly shaped region of cytoplasm containing single large circular DNA molecule

• Plasmids

– Small circles of DNA carrying only a few genes

Eukaryotic cells

– DNA contained inside nucleus

– Contain many other membrane-enclosed organelles

• Membranes allow organelles to:

– Regulate substances entering and exiting

– Specialized environment allows organelle to have particular function

Plant cell

Animal cell
The Nucleus

• Eukaryotic nucleus contains the cell’s DNA, separating it from potential damage in the cytoplasm

The Endomembrane System

• Series of interacting organelles between nucleus and plasma membrane

• Makes, modifies, and transports proteins and lipids for secretion or insertion into cell membranes
• Destroys toxins, recycles wastes, and has other specialized functions

The Endoplasmic Reticulum

• Endoplasmic reticulum (ER)

– An extension of the nuclear envelope that forms a continuous, folded compartment

• Two kinds of endoplasmic reticulum

– Rough ER (with ribosomes) folds polypeptides into their tertiary form

– Smooth ER (no ribosomes) makes lipids, breaks down carbohydrates and lipids, and detoxifies poisons

Vesicles

• Small, membrane-enclosed saclike organelles that store or transport substances

• Peroxisomes

– Vesicles containing enzymes that break down hydrogen peroxide, alcohol, and other toxins

• Lysosomes

– Vesicles containing enzymes that fuse with vacuoles and digest waste materials

Vacuoles

• Vesicles with various functions depending on cell type

– Many isolate or dispose of waste, debris, and toxins

• Central vacuole

– Occupies 50 to 90 percent of a cell’s interior

– Stores amino acids, sugars, ions, wastes, toxins

– Fluid pressure keeps plant cells firm

Golgi Bodies

• A folded membrane containing enzymes that finish polypeptides and lipids delivered by the ER

– Packages finished products in vesicles that carry them to the plasma membrane or to lysosomes

Interaction in the endomembrane system

Mitochondria

• Eukaryotic organelle that makes the energy molecule ATP through aerobic respiration

• Contains two membranes, forming inner and outer compartments

– Buildup of hydrogen ions in the outer compartment drives ATP synthesis

• Has its own DNA and ribosomes

• Resembles bacteria

– May have evolved from aerobic bacteria

Chloroplast and other plastids

• Plastids

– Organelles that function in photosynthesis or storage in plants and algae

– Includes chromoplasts, amyloplasts, and chloroplasts

• Chloroplasts

– Plastids specialized for photosynthesis

– Resemble photosynthetic bacteria

Cytoskeleton

• An interconnected system of many protein filaments – some permanent, some temporary

– Parts of the cytoskeleton reinforce, organize, and move cell structures, or even a whole cell

Cytoskeletal Elements

• Microtubules

– Long, hollow cylinders made of tubulin

– Form dynamic scaffolding for cell processes

• Microfilaments

– Consist mainly of the globular protein actin

– Make up the cell cortex

• Intermediate filaments

– Maintain cell and tissue structures

Motor Proteins

• Accessory proteins that move molecules through cells on tracks of microtubules and microfilaments

– Energized by ATP
– Example: kinesins

Cilia and Flagella

– Cilia are usually short, hairlike structures that move in waves

– Flagella are long whiplike structures

False Feet

• Pseudopods or “false feet”

– Temporary, irregular lobes formed by amoebas and some other eukaryotic cells

– Bulge outward to move the cell or engulf prey

– Elongating microfilaments force the lobe to advance in a steady direction

– Motor proteins attached to microfilaments drag the plasma membrane along with them

Cell surface Specialization

• Many cells secrete materials that form a covering or matrix outside their plasma membrane

• Extracellular matrix (ECM)

– A nonliving, complex mixture of fibrous proteins and polysaccharides secreted by and surrounding cells

– Structure and function varies with the type of tissue

– Examples: cell walls and cuticles

Eukaryotic Cell Walls

• Animal cells do not have walls, but plant cells and many protist and fungal cells do

• Primary cell wall

– A thin, pliable wall formed by secretion of cellulose into the coating around young plant cells

• Secondary cell wall

– A strong wall composed of lignin, formed in some plant stems and roots after maturity

Cuticle

• A type of ECM secreted by cells at a body surface

• Plant cuticles consist of waxes and proteins, and help plants retain water and fend off insects

• Cuticles of crabs, spiders, and other arthropods is mainly chitin, a polysaccharide

Cell Junctions

• Cell junctions allow cells to interact with each other and the environment

• In plants, plasmodesmata extend through cell walls to connect the cytoplasm of two cells

• Animals have three types of cell junctions: tight junctions, adhering junctions, gap junctions

Animal Cell Junctions

• Tight junctions
– Fasten together plasma membranes of adjacent cells

• Adhering junctions

– Fasten cells to one another and to basement membrane

• Gap junctions

– Closable channels that connect the cytoplasm of adjoining animal cells

 Lesson 2: Cellular Respiration

Cellular respiration

The aerobic process by which living cells break down glucose molecules, release energy, and form molecules of ATP. Overall, this three-stage process involves
glucose and oxygen reacting to form carbon dioxide and water.

The stages of cellular respiration include glycolysis, pyruvate oxidation, the citric acid or Krebs cycle, and oxidative phosphorylation.

C 6 H 12 O 6 + 6 O 2 --> 6 CO 2 + 6 H 2 O + ATP

is the complete balanced chemical formula for cellular respiration.

Glycolysis
The first stage of cellular respiration is glycolysis. It takes place in the cytosol of the cytoplasm.

Splitting Glucose
The word glycolysis means “glucose splitting,” which is exactly what happens in this stage. Enzymes split a molecule of glucose into two molecules of pyruvate
(also known as pyruvic acid). This occurs in several steps, as shown in the following diagram.

Results of Glycolysis
Energy is needed at the start of glycolysis to split the glucose molecule into two pyruvate molecules. These two molecules go on to stage II of cellular
respiration. The energy to split glucose is provided by two molecules of ATP. As glycolysis proceeds, energy is released, and the energy is used to make four
molecules of ATP. As a result, there is a net gain of two ATP molecules during glycolysis. During this stage, high-energy electrons are also transferred to
molecules of NAD+ to produce two molecules of NADH, another energy-carrying molecule. NADH is used in stage III of cellular respiration to make more ATP.
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.
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.

The Krebs Cycle

Recall that glycolysis produces two molecules of pyruvate (pyruvic acid). These molecules enter the matrix of a mitochondrion, where they start the Krebs cycle.
The reactions that occur next are shown in the following figure.
In the citric acid cycle, the acetyl group from acetyl CoA is attached to a four-carbon oxaloacetate molecule to form a six-carbon citrate molecule. Through a
series of steps, citrate is oxidized, releasing two carbon dioxide molecules for each acetyl group fed into the cycle. In the process, three NAD+ molecules are
reduced to NADH, one FAD molecule is reduced to FADH2, and one ATP or GTP (depending on the cell type) is produced (by substrate-level phosphorylation).
Because the final product of the citric acid cycle is also the first reactant, the cycle runs continuously in the presence of sufficient reactants.
Before the Krebs cycle begins, pyruvic acid, which has three carbon atoms, is split apart and combined with an enzyme known as CoA, which stands for
coenzyme A. The product of this reaction is a two-carbon molecule called acetyl-CoA. The third carbon from pyruvic acid combines with oxygen to form carbon
dioxide, which is released as a waste product. High-energy electrons are also released and captured in NADH.

Steps of the Krebs Cycle

The Krebs cycle itself actually begins when acetyl-CoA combines with a four-carbon molecule called OAA (oxaloacetate). This produces citric acid, which has six
carbon atoms. This is why the Krebs cycle is also called the citric acid cycle. After citric acid forms, it goes through a series of reactions that release energy. The
energy is captured in molecules of NADH, ATP, and FADH2 (another energy-carrying compound.) Carbon dioxide is also released as a waste product of these
reactions. The final step of the Krebs cycle regenerates OAA, the molecule that began the Krebs cycle. This molecule is needed for the next turn through the
cycle. Two turns are needed because glycolysis produces two pyruvic acid molecules when it splits glucose.

Results of the Krebs Cycle

After the second turn through the Krebs cycle, the original glucose molecule has been broken down completely. All six of its carbon atoms have combined with
oxygen to form carbon dioxide. The energy from its chemical bonds has been stored in a total of 16 energy-carrier molecules. These molecules are:
 4 ATP (including 2 from glycolysis)
10 NADH (including 2 from glycolysis)
2 FADH22

Oxidative phosphorylation
Oxidative phosphorylation is the final stage of aerobic cellular respiration. There are two substages of oxidative phosphorylation, Electron transport chain and
Chemiosmosis. In these stages, energy from NADH and FADH2, which result from the previous stages of cellular respiration, is transferred to ATP.

Outer membrane

ATP
Synthase
NADH

ATP Citric
acid
Matrix cycle

Succinate
Fumarate

Inner membrane

Intermembrane space

Electron Transport Chain

During this stage, high-energy electrons are released from NADH and FADH2, and they move along electron-transport chains on the inner membrane of the
mitochondrion. An electron-transport chain is a series of molecules that transfer electrons from molecule to molecule by chemical reactions. Some of the energy
from the electrons is used to pump hydrogen ions (H+) across the inner membrane, from the matrix into the intermembrane space. This ion transfer creates an
electrochemical gradient that drives the synthesis of ATP.

Chemiosmosis
The pumping of hydrogen ions across the inner membrane creates a greater concentration of the ions in the intermembrane space than in the matrix. This
gradient causes the ions to flow back across the membrane into the matrix, where their concentration is lower. the ATP synthase acts as a channel protein,
helping the hydrogen ions across the membrane. It also acts as an enzyme, forming ATP from ADP and inorganic phosphate in a process called oxidative
phosphorylation. The flow of hydrogen ions through ATP synthase gives energy for ATP synthesis. After passing through the electron-transport chain, the
“spent” electrons combine with oxygen to form water.

How Much ATP?

You have seen how the three stages of aerobic respiration use the energy in glucose to make ATP. How much ATP is produced in all three stages combined?
Glycolysis produces 2 ATP molecules, and the Krebs cycle produces 2 more. Electron transport begins with several molecules of NADH and FADH2 from the
Krebs cycle and transfers their energy into as many as 32 more ATP molecules. A total of up to 36 molecules of ATP from just one molecule of glucose in the
process of cellular respiration.

Summary
Cellular respiration is the aerobic process by which living cells break down glucose molecules, release energy, and form molecules of ATP. Overall, this
three-stage process involves glucose and oxygen reacting to form carbon dioxide and water.
The first stage of cellular respiration, called glycolysis, takes place in the cytoplasm. In this step, enzymes split a molecule of glucose into two molecules
of pyruvate, which releases energy that is transferred to ATP.
The organelle called a mitochondrion is the site of the other two stages of cellular respiration. The mitochondrion has an inner and outer membrane
separated by an intermembrane space, and the inner membrane encloses a space called the matrix.
The second stage of cellular respiration, called the Krebs cycle, takes place in the matrix of a mitochondrion. During this stage, two turns through the cycle
result in all of the carbon atoms from the two pyruvate molecules forming carbon dioxide and the energy from their chemical bonds being stored in a total
of 16 energy-carrying molecules (including 4 from glycolysis).
The third and final stage of cellular respiration, called oxidative phosphorylation, takes place on the inner membrane of the mitochondrion. Electrons are
transported from molecule to molecule down an electron-transport chain. Some of the energy from the electrons is used to pump hydrogen ions across
the membrane, creating an electrochemical gradient that drives the synthesis of many more molecules of ATP.
In all three stages of cellular respiration combined, as many as 36 molecules of ATP are produced from just one molecule of glucose.
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