Chapter 20: Bacteria and Archaea
Antigen- Substances that stimulate antibody production by the immune system
20.1 The Full Extent of the Diversity of Bacteria and Archaea is Unknown
Everything known about bacteria and archaea is based on tiny fraction of total number of speices
Only isolated and identified 6000 species, what is as low as 1% of total number
Know nothing of prokaryotes in oceans
In past, we identified and classified bacteria and archaea based on external features (cell wall structure)
and physiological differences which meant that we had to grow the organism in culture
Most prokaryotic organisms cannot be grown in culture because they require extreme physiochemical
conditions so not much have been learnt about these organisms.
Molecular techniques have been developed that isolate and clone DNA from an environment and analyze
Thus identifying and characterizing bacteria and archaea with having to culture them
Approach known as metagenomics now enables us to investigate the diversity of prokaryotic organisms
However, some environments are remote and are difficult/costly to sample organisms from there.
20.1a Prokaryotic Organisms Make up Two of the Three Domains of Life
Two of three domains of living organisms, archaea and bacteria consist of prokaryotic organisms
Bacteria is known to us as some are responsible for diseases and others are relied for production of
cheese yogurt and other foods.
Archaea are not well known, as they were only discovered 40 years ago
Archaea share some features with bacteria and some with eukaryotes and some are completely unique
Many archaea live under very extreme conditions that no other organism can survive.
20.2 Prokaryotic Structure and Function
Generally, prokaryotic organisms are the smallest in world
Few species are more than 1-2 um long
500-600 could fit on the dot in this “i”
Despite small size, the dominate life on Earth; billions of species and collective mass (biomass) exceeds
that of animals and may be greater than all of plant life
Colonize every survivable area off Earth, even deep in the curst
Also colonize other organisms by inhibiting the surfaces of health human bodies including the skin mouth,
naval passages and large intestine
Bacteria in and on your body outnumber other cells in body
Diversity if greater because they have been on planet for 3 billion years, before eukaryotes appeared
20.2a Prokaryotic Cells Appear simple in Structure Compared to Eukaryotic Cells
Three cell shapes are common among prokaryotes: spiral, spherical (coccoid =berry) and cylindrical (rods),
and but some archaea even have square cells. Prokaryotic cell seems simpler than eukaryotic cell; images tkane with standard electron microscopy
typical reveals little more than a cell wall and plasma membrane surrounding cytoplasm with DNA
concentrated in one region and ribosomes scattered throughout.
The chromosome is not contained in a membrane-bound nucleus but is packed into an area of the cell
called the nucleoid.
Prokaryotic cells have no cytoplasmic organelles equivalent to the endoplasmic reticulum or Golgi
complex of eukaryotic cells.
Usually, the reaction carried out by organelles in eukaryotes are distributed between the plasma
membrane and the cytoplasmic solution of prokaryotic cells
This means that macro molecules such as proteins are very concentrated in the cytoplasm of these cells,
making the cytoplasm quite viscous.
Because prokaryotic cells were seen as simple, people disregarded them as featureless and disorganized.
Apparent simplicity is misleading
Prokaryotic cells do have a cytoskeleton- not homologous to that of a eukaryote but serving the same
functions (thus more sophisticated organization)
Recent research has identified a prokaryotic organelle
Bacteria that obtain energy by oxidizing ammonia have an internal membrane-bound compartment
where ammonia oxidation occurs.
Hypothesized that as ammonia oxidation proceeds inside the compartment, a proton motive force could
be generated across the membrane, generating ATP.
Research found that the membrane around this compartment does contain ATP synthase, supporting the
Therefore, some prokaryotic cells have organelles with specialized funtions.
Genome of most prokaryotic cells consist of single, circular DNA molecules, although some have a
Many prokaryotic cells also contain small circles of DNA called plasmids, which generally contain
genes for nonessential but beneficial function such as antibiotic resistance
Plasmids replicate independently of the cell’s chromosome and can be transferred from one cell to
This means that the genes for antibiotic resistance are readily shared among prokaryotic cell, even
among cells of different species
Horizontal gene transfer allows antibiotic resistance and other traits to spread very quickly in
Horizontal gene transfer also occurs when bacteria cells take up DNA from their environment (form
other cells that have lysed) or when viruses transfer DNA from one bacterium to another
Prokaryotic cells contain ribosomes like eukaryotic cells
Bacterial ribosomes smaller than eukaryotic ribosome but carry out protein synthesis by essentially
the same mechanisms.
Archael ribosome resemble those of bacteria in size but differ in structure
Protein synthesis in Archae is combination of bacterial and eukaryotic processes with some unique
features Antibiotics that stop bacterial infections by targeting ribosome activity do not interfere with archael
Prokaryotic Cell Walls
Most prokaryotic cells have a cell wall that lies outside their plasma membrane and protects the cell
from lysing if subjected to hypnotic conditions or exposed to membrane-disputing compounds such
Peptidoglycan is the primary component of bacterial cell walls, which is a polymer of sugars and
amino acids that forms linear chains.
Peptide cross linkages between the chains give the cell wall great strength and rigidity
Antibiotic penicillin prevents the formation of these cross linkages resulting in a weak cell wall that is
easily ruptured, killing the cell.
Bacteria can be divided into two main groups: gram positive and gram negative cells, based on their
reaction to the gram stain procedure (first step in identifying an unknown bacterium)
Cells are first stained with crystal-violet and then treated with iodine which forms a complex with
Cells are then rinsed with ethanol and counterstained with safranin
Some cells retain the crystal violet iodine complex and thus appear purple when viewed under the
microscope; these are termed Gram-positive cells
In other bacteria, ethanol washes the crystal- violet iodine complex out of the cells which are
colourless until counterstained with safranin; these are gram-negative cells and appear pink.
Different response to staining related to differences in cell wall structure
Gram positive bacteria have cell walls composed almost entirely of a single relatively thick layer of
peptidoglycan, a complex polymer of sugars and amino acids.
The thick peptidoglycan layer retain the crystal violet-iodine complex inside the cell.
Gram-negative cells have only a think peptidoglycan layer in their walls, and the crystal-violet iodine
complex is washed out
In contrast, the cell wall of Gram-negative bacteria has two distinct layers; a thin peptidoglycan later
and an outer membrane external (outside plasma membrane) to the peptidoglycan layer.
Outer layer contains lipopolysaccharides and thus is very different from the plasma membrane.
Outer membrane protects gram-negative bacteria from potentially harmful substances in the
environment (ex; inhibits entry of penicillin)
Gram-negative cells are less sensitive to penicillin than Gram-positive cells.
Cell wall of some Archaea are made form a molecule related to peptidoglycan but with different
molecular components and bonding structure.
Others have walls made fomr proteins or polysaccharides instead of peptidoglycan.
Archaea have a variable response to the Gram stain, so this procedure is not useful in identifying
Cell wall of many prokaryotic cells is surrounded by a layer of polysaccharides known as a capsule.
Capsules are sticky and play important roles in protecting cells in different environments
Cells with capsules are protected from extreme temperatures, desiccation, viruses and harmful
molecules In many pathogenic bacteria, the presence or absence of the capsule makes a difference of an
infective from noninfective form.
Capsulated and virulent bacteria causes server harm in humans and animals where as non capsulated
bacteria can easily be eliminated by the body’s immune system.
Flagella and Pilli:
Many prokaryotic cells can move through liquids and even through films of liquid on a surface,
usually through the flagella which extends from the cell wall
Prokaryotic flagella is very different from eukaryotic flagella both in structure in movement
Prokaryotic flagella are made of rigid helical proteins, some which act like a motor which rotates
the flagellum much like a propeller of a boat
Archael flagella are similar to bacterial flagella and carry out the same function but the two
flagella contain different components, develop differently and are coded for by different genes.
Some prokaryotic cells have rigid shafts of protein called pili extending from their cell walls which
allows them to adhere to or move along a surface.
One type called sex pilus not only allows bacteria cells to adhere to each other, but acts as a
conduit for the transfer of plasmids from one cell to another.
Other pili enable bacteria to bind to animal cells
Pilli of some bacteria conduct electricity; nanowires transfer electrons out of the cell into mineral
such as iron oxides in their environment.
Such electricity generation bacteria hold promise for development of microbial fuel cells as
alternative energy source.
Prokaryotic cells are much simpler and less diverse structurally but are more diverse
20.2b Prokaryotic Organisms Have the Greatest Metabolic Diversity of All Organisms
Organisms grouped into four modes of nutrition based on sources of energy and carbon.
Focus on carbon, instead of other nutrients because carbon is backbone to all organic molecules
synthesized by an organism
Autotrophs are organisms like plants that synthesize organic carbon molecules using inorganic carbon
Heterotrophs obtain carbon from organic molecules either from living hosts or from organic molecules in
the products, waste or remains of dead organisms.
Organisms are also divided according to the source of energy they use to drive biological activities.
Chemotrophs obtain energy by oxidizing inorganic or organic substances, whereas phototrophs obtain
energy from light.
Combining carbon and energy sources groups organisms into 4 categories.
Prokaryotic organisms show the greatest diversity in their modes of securing carbon and energy; only
represent two of the categories (chemoautotrophs, and photoheterotrophs)
Photoheterotrophs use light as an energy source and obtain carbon from organic molecules rather than
Chemoautotrophs are known as lithotrophs Chemoautotrophs obtain energy by oxidizing inorganic substances such as hydrogen, iron, sulfur,
ammonia and nitrites and use Co2 as their carbon source.
Chemolithotrophs thrive in habitats such as deep sea vents where reduced inorganic compounds are
abundant; their ability to harness energy from these compounds make them the foundation which the
rest of the vent community depends on
Similar to how terrestrial organisms rely on plants to capture light energy
Some prokaryotic organisms use oxygen as a final electron acceptors; like humans these are aerobic
organisms also knowns as aerobes
Aerobes may be obligate, that is they cannot survive without oxygen
Some prokaryotic organisms breathe metals using metal as the final electron acceptor for electrons;
obtain energy via anaerobic respiration
Anaerobic respiration can involve other inorganic molecules (nitrate, sulfate) as final electron acceptors.
Only prokaryotic organisms are capable of this type of respiration
Obligate anaerobes are poisoned by oxygen and survive either by fementation, in which organic
molecules are the final electron acceptors, or by anaerobic respiration.
Facultative anaerobes use O2 when it is present, but under anaerobic condition, they live by fermentation
or anaerobic respiration.
20.2c Bacteria and Archaea Play Key Roles in Biogeochemical Cycles
Prokaryotes can metabolize a wide range of substances which makes them key players in the life
sustaining recycling of elements such as carbon, oxygen and nitrogen.
Biogeochemical cycle is the pathway by which a chemical element moves through an ecosystem.
As elements flow from through its cycle, it is transformed from one form to another, prokaryotic
organisms are crucial in many of these transformations.
Nitrogen cycle will used as an example of the key role prokaryotic organisms play in biogeochemical
Nitrogen is component of proteins and nucleotides and so is of vital importance for all organisms
Atmosphere contains 80% nitrogen
Most organisms can’t use this nitrogen because they cannot break the strong triple bond between
the two nitrogen atoms.
Some bacteria and archaea can, using the enzyme nitrogenase and convert N2 into forms that can be
used by other organisms.
In conversion process known as nitrogen fixation, N2 is reduced to ammonia (Nh3) and ammonia is
quickly ionized to ammonium (Nh4+)
Prokaryotic cells then use this to produce nitrogen containing molecules such as amino acids and
Nitrogen fixation is the only way of replenishing the nitrogen sources used by most organisms
(meaning that all organism rely on nitrogen fixed by bacteria, including cynabacteria)
Other prokaryotic organisms carry out nitrification, the oxidation of ammonium (Nh4+) to nitrate
The oxidation is carried out in two steps by two types of nitrifiers, ammonia oxidizers and nitrate
oxidizers, present in soil and water
Ammonia oxidizers convert ammonium intro nitrite (No2-) whereas nitire oxidizers convert nitrite to
nitrate. Nitrate is then taken up by plants and fungi and incorporated into their organic molecules
Animals obtain nitrogen in organic form by eating other organism.
Nitrification makes nitrogen available to many other organisms including plants, animals and bacteria
that cannot metabolize ammonia.
Metabolic versatility of bacteria and archaea is one factor that accounts for their abundance and
persistence on the planet; another factor is reproductive capacity
20.2d Asexual Reproduction Can Result in Rapid Population Growth
In prokaryotic organisms asexual reproduction is the normal mode of reproduction.
A parent cell divides my binary fission into two daughter cells that are exact genetic copies of the parents.
Reproducing by binary fission means that under favourable conditions, populations of prokaryotic
organisms can have very rapid exponential growth.
Some prokaryotic cells can produce double their population in 20 minutes and will even begin a second
round of cell division before the first is complete.
Thus one cell can produce millions in only a few hours.
Short generation times and small genomes means that prokaryotic organism have higher mutation rates
than eukaryotic organisms.
1000 times more mutations per gene, per unit time, per individual
The basis for their dibersity is the genetic variability and it dertives largely from mutation and to a lesser
degree from horizontal gene transfer.
Large population of prokaryotic organisms compared with eukaryotes contribute to the much greater
genetic variability in bacteria and archaea.
Prokaryotic organisms have an enormous capacity to adapt which is a reason for their evolutionary
Success of bacteria is beneficial to humans in many ways, but can also be determintal when detailing with
20.2e Pathogenic Bacteria Causes Diseases by Different Mechanisms
Some bacteria produce exotoxins, toxic proteins that leak from or are secreted from the bacterium.
For example, botulism food poisioning is caused by the exotoxin of the Gram-positive bacterium
Clostridium botulinum which grows in poorly preserved foods.
Just a few nanograms of botulin can cause sever illness because it produces muscle paralysis that can be
fatal if that muscles that are controlling breathing are affected.
Exotoxins produced by certain strain of Stretoccus pyogens have superantigen properties that cause
necrotizing fasciitis (flesh eating disease)
Other bacteria cause disease through endotoxins.