Freeman Biological science
Life the science of biology, SADAVA
1950s : biologists had a staggering conclusion: At least one-half of the “ living protoplasm” on Earth is invisible to
the naked eye.
Prokaryotic—meaning that they lack a membrane-bound nucleus.
Eukaryotic organisms have cells with membrane-bound nuclei.
Although both bacteria and archaea have a relatively simple morphology,
they are strikingly different at the molecular level.
Antibiotics that poison bacterial ribosomes do not affect the
ribosomes of archaea or eukaryotes.
WHY DO BIOLOGIST STUDY THEM?
First: Intrinsically fascinating. Finding prokaryotic cells living a kilometer underground or in 95°C hot springs.
Second: understanding life on Earth and improving human health and welfare.
The oldest fossils of any type found to date are 3.5-billion-year-old carbon-rich deposits derived from bacteria.
Because eukaryotes do not appear in the fossil record until 1.75 billion years ago.
Abundance: Teaspoon of good-quality soil contains billions of microbial cells.
10,000 individuals per milliliter in most of the world’s oceans.
thrive inside rocks and sediments as much as 1600 meters in oceans.
Habitat Diversity: Prokaryotes are found almost everywhere.
They live in environments as unusual as oxygen-free mud, hot springs, and salt flats
Extremophiles
Pressure and microbial growth:
pH and microbial growth:
Water, Solute and microbial growth:
Oxygen and microbial growth
Temperature and microbial growth
The Germ Theory of Disease:
• Koch’s experimental results were the first test of the germ theory of disease.
• The germ theory of disease states that infectious diseases are caused by specific microbes in the body—such as
bacteria, archaea, and viruses.
Infectious diseases are spread in three main ways:
(1) Some are passed from person to person;
(2) Some are transmitted by bites from insects or animals;
(3) Some are acquired by ingesting contaminated food or water
What Makes Some Bacterial Cells Pathogenic?
Virulence, or the ability to cause disease, is a heritable trait that varies among individuals in a population.
E. coli strain O157:H7-
After entering a host cell, this toxin binds to ribosomes and inhibits protein synthesis, killing the host cells.
Key differences between the ribosomes of bacteria and eukaryotic cells.
Some Pathogenic Bacteria Produce Resistant Endospores
Endospores are resistant to high temperatures,
UV radiation, and even antibiotics.
The Past, Present, and Future of Antibiotics
• French medical student Ernest Duchesne: Discovered Penicillin (1896), the first true natural antibiotic.
• Alexander Fleming accidentally rediscovered penicillin in 1928.
• In 1939, Howard Florey and Ernst Chain, professors at Oxford University, obtained the Penicillium culture
from Fleming and purified the antibiotic.
Fleming, Florey, and Chain received the Nobel Prize in
1945 for the discovery and production of penicillin
• Selman Waksman, at Rutgers University, announced in 1944 that he and his associates had found a new
antibiotic, streptomycin (by Streptomyces griseus).
• Waksman received the Nobel Prize in 1952, and his success led to a worldwide search for other antibiotic-
producing soil microorganisms.
Antibiotic-Resistance Mechanisms.
Bacteria can resist the action of antibiotics by
(1) preventing access to (or altering) the target of the antibiotic,
(2) degrading the antibiotic,
(3) altering the antibiotic, or
(4) rapidly extruding the antibiotic.
Biofilms
• Attached microbes are members of complex, slime-
encased communities called biofilms.
• Biofilms are ubiquitous in nature (slime on rocks or
other objects in water or at water-air interfaces).
• Biofilms is formed after conditioning by
proteins and other molecules present in the
environment.
• Extracellular polymeric substances (EPS:
polysaccharides, proteins, glycoproteins,
glycolipids, and DNA).
• In mature biofilm, complex, dynamic community of microorganisms interact in a variety of ways (waste products
of one microbe may be the energy source for another microbe, DNA can be taken up by members of the biofilm
community).
• Considerable heterogeneity due to differences in the
metabolic activity of microbes at various locations
within the biofilm; some are persister cells
• Protected from harmful agents e.g. UV light and
antibiotics (treatment with antibiotics often fails, which
can lead to serious systemic infections).
Fact: Biofilm formation is ancient ability as per fossil record from about 3.4 billion years ago.
Bioremediation
• Oil fate is dependent on many
natural processes as the oil begins to
reach the surface.
• Oil can also sediment to the sea
floor or fall as marine snow.
• Emulsification and dispersion take place below the surface, which can assist with microbial degradation of the oil.
• Bacteria that are able to render harmless certain chlorinated compounds, such as polychlorobiphenyls (PCBs).
Instead of being poisoned by the pollutants, these bacteria use the chlorinated compounds as electron acceptors
during cellular respiration.
How Do Biologists study microbes?
Pure Culture
• A population of cells arising from a single cell.
• Characterize an individual species.
• Developed by Robert Koch.
• Human disease pathogens have been isolated.
• Few ways are: Spread, Streak and Pour plate.
A colony is a large number of bacterial cells
on solid medium, which is visible to the
naked eye as a discrete entity. We assume
that one colony comes from one cell.
Enrichment cultures are based on establishing a specified set of growing
conditions— temperature, lighting, substrate, types of available food, and so
on. Cells that thrive under the specified conditions increase in numbers
enough to be isolated and studied in detail.
A microbiome is the community of microbes that naturally
inhabit the body or parts of the body, such as the mouth, gut, and
other tissues.
In one microbiome study that focused on bacteria, biologists
extracted DNA from 125 human fecal samples and identified
over 500 billion base pairs of bacterial DNA sequence, over 150
times more than the entire human genome.
Biologists use data from enrichment culture and metagenomic studies to
build more accurate phylogenetic trees.
In the late 1960s Carl Woese and colleagues began a massive effort to
determine and compare the base sequences of 16S and 18S rRNA molecules
from a wide array of species.
Genetic variation through Gene Transfer
Genetic variation through Gene Transfer
Morphological Diversity
Cell wall composition
Metabolic Diversity
Metabolic Diversity
During cellular respiration (prokaryotes and eukaryotes), enzymes strip electrons from organic molecules that have
high potential energy and then transfer these high-energy electrons to the electron carriers NADH and FADH2. These
compounds feed electrons to an electron transport chain (ETC), where electrons are stepped down from a high-energy
state to a low-energy state.
Chemiosmosis
Producing ATP through Cellular Respiration: Variation in Electron Donors and Acceptors
Producing ATP via Fermentation: Variation in Substrates
Prokaryotes that produce ATP via fermentation use a wide variety of substrates:
• Species of Clostridium ferment complex carbohydrates (including cellulose or starch), proteins, purines, or
amino acids. Species that ferment amino acids produce by-products with names such as cadaverine and
putrescine. These molecules are responsible for the odor of rotting flesh.
• Other bacteria can ferment lactose, a prominent component of milk. In some species this fermentation has two
end products: propionic acid and CO2. Propionic acid is responsible for the taste of Swiss cheese, and the CO2
produced during fermentation creates the holes in Swiss cheese.
Producing ATP via Photophosphorylation: Variation in Electron Sources and Pigments
Among bacteria and archaea, photophosphorylation can happen in three different ways:
• Light activates a pigment called bacteriorhodopsin or archaerhodopsin, which uses the absorbed energy to
transport protons across the plasma membrane and out of the cell. The resulting flow of protons back into the cell
drives the synthesis of ATP via chemiosmosis.
• A recently discovered bacterium that lives near hydrothermal vents on the ocean floor performs
photophosphorylation not by absorbing sunlight, but by absorbing faint light from geothermal radiation.
• Pigments that absorb light raise electrons to high-energy states. As these electrons are stepped down to lower
energy states by electron transport chains, the energy released is used to generate ATP. Researchers have isolated
nine different chlorophyll pigments from different lineages of bacterial phototrophs. Each lineage has one or more
of these distinctive chlorophylls.
Cellular Respiration Can Produce More Energy:
When Oxygen Is the Final Electron Acceptor. More
potential energy in glucose can be released when oxygen
is the final acceptor compared to other molecules or ions.
Nitrogen Fixation and the Nitrogen Cycle
• The key enzyme that catalyzes the reaction- nitrogenase- is
found only in a few phyla of bacteria and archaea.
• Some species of cyanobacteria live in association with a
water fern that grows in rice paddies and help fertilize the
rice plants.
• In terrestrial environments, nitrogen-fixing bacteria live in
close association with certain plants (e.g., legumes)—often
taking up residence in special root structures called nodules.