Prokaryotes include bacteria and archaea. Bacteria were first observed in 1674 and include diverse species found in many habitats. Prokaryotes are single-celled without internal membranes and reproduce through binary fission. Major groups include eubacteria like E. coli and archaea found in extreme environments like hot springs or salt lakes. Bacteria play important roles in ecosystems through processes like nitrogen fixation and photosynthesis.

1. Prokaryotes
• Bacteria were first
discovered in 1674 by
Antony van
Leeuwenhoek, using the
microscope he invented.
• The first recorded
observation were of the
bacteria found in the
dental plaque of two old
men who never cleaned
their teeth.

2. Prokaryote Introduction
• Prokaryotes are much more
diverse in both habitat and
metabolism than the eukaryotes.
• However, prokaryotes are not very
diverse in body shape or size.
Much of their classification into
different species is done by
examining their internal
biochemistry and their DNA.
• Nearly all prokaryotes are single-
celled. Differentiation into different
cell types almost never occurs in
prokaryotes.
• Two major groups: the Eubacteria
(sometimes just called Bacteria)
and the Archaea (or
Archaebacteria). Very different
genetically.

3. Prokaryote Structure
• Prokaryotes are simple cells. The
DNA is loose in the cytoplasm—
there is no separate nucleus. The
ribosomes are also in the
cytoplasm. In prokaryotes,
transcription (synthesis of RNA)
and translation (synthesis of
proteins) occurs simultaneously.
• The cell is surrounded by a
membrane, but there are no
internal membranes.
• Outside the membrane is a cell
wall, and sometimes an outer
capsule which can have structures
projecting form it.
• Bacteria move using flagella:
whip-like hairs similar to the
flagellum of a sperm cell.

4. Bacterial Reproduction
• Bacteria reproduce by the
process of binary fission.
The circular chromosome
replicates its DNA. Then,
the cell splits into 2
halves, each containing a
single chromosome
• No spindle apparatus (as
exists in eukaryotic
mitosis and meiosis).

5. Growth of Bacteria
• Under ideal conditions,
bacteria grow very rapidly:
some double in number every
20 minutes.
• Doubling in number: 1-2-4-8-
16-… is exponential growth. It
starts off slowly, but once
going the number of bacteria
increase very rapidly
• Usually some nutrient runs
short, or waste material builds
up, and growth ceases.
Eventually a die-off occurs,
reducing the number of live
bacteria.

6. Genetic Exchange in Bacteria
• Bacteria don’t have sexes or a
regular genetic exchange every
generation the way most
eukaryotes do.
• However, there are several means
of sharing DNA between
individuals, even if they are not of
the same species.
• Conjugation is one such
mechanism: the donor bacteria
grows tubes that project from its
surface to the surface of a
recipient. A copy of the
chromosomal DNA travels through
this tube into the recipient, where
it become incorporated into the
recipient’s genome.

7. Bacterial Morphology
• Bacteria only take a few basic shapes, which are found in many
different groups. Bacterial cells don’t have internal cytoskeletons, so
their shapes can’t be very elaborate.
• Shape: coccus (spheres) and bacillus (rods). Spirillum (spiral) is less
common.
• Aggregation of cells: single cells, pairs (diplo), chains (strepto),
clusters (staphylo).
• Thus we have types such as diplococcus (pair of spheres) and
streptobacillus (chain of rods).

8. Gram Stain
• A major distinction between
groups of bacteria is based on
the Gram stain. In this
method, bacteria are treated
with the dye “crystal violet”,
then washed. Often a second
stain, “safranin” is applies to
make the unstained bacteria
visible.
• Gram stain causes bacteria
with a lot of peptidoglycan and
very little lipid in their cells
walls to stain purple. The
presence or absence of
peptidoglycan is a fundamental
biochemical difference
between groups of bacteria

9. • The Gram stain, which divides most clinically significant
bacteria into two main groups, is the first step in bacterial
identification.
• Bacteria stained purple are Gram + - their cell walls have
thick petidoglycan and teichoic acid.
• Bacteria stained pink are Gram – their cell walls have
have thin peptidoglycan and lipopolysaccharides with no
teichoic acid.

10. In Gram-positive bacteria, the purple crystal violet stain is
trapped by the layer of peptidoglycan which forms the outer
layer of the cell. In Gram-negative bacteria, the outer
membrane of lipopolysaccharides prevents the stain from
reaching the peptidoglycan layer. The outer membrane is
then permeabilized by acetone treatment, and the pink safranin
counterstain is trapped by the peptidoglycan layer.

11. Metabolic Diversity
• Bacteria show far more metabolic diversity than eukaryotes
• General classification, based on carbon (food) source and energy
source.
• autotroph vs. heterotroph.
• phototroph vs. chemotroph
• Photoautotrophs
• Photoheterotrophs ( a rare category)
• Chemoautotrophs
• Chemoheterotrophs get both energy and organic compounds from
other organisms. We are chemoheterotrophs.

12. Relationship to Oxygen
• For more than half of Earth’s history, oxygen wasn’t
present in the atmosphere. Many bacteria evolved
under anaerobic conditions.
• Classification:
• strict aerobes (need oxygen to survive)
• strict anaerobes (killed by oxygen)
• aerotolerant (don’t use oxygen, but survive it).
• facultative anaerobes (use oxygen when it is present,
but live anaerobically when oxygen is absent).

13. Spores
• Some bacteria can form very tough spores,
which are metabolically inactive and can
survive a long time under very harsh
conditions.
• Allegedly, some bacterial spores that were
embedded in amber for 25 million years have
been revived. Others, trapped in salt deposits
for up to 250 million years, have also been
revived. These experiments are viewed
skeptically by many scientists.
• “Extraordinary claims demand extraordinary
proof”
• Spores can also survive very high or low
temperatures and high UV radiation for
extended periods.
• Panspermia: the idea that life got started on
Earth due to bacterial spores that drifted in
from another solar system. (However, it still
had to start somewhere!).

14. Archaea
• Sometimes called “Archaebacteria”
• Genetically as different from Eubacteria as we are.
• One distinguishing characteristic: cell membranes don’t contain fatty
acids, but instead use branched molecules called isoprenes.
• Three main type: methanogens, extreme halophiles, extreme
thermophiles.

15. Methanogens
• Methanogens: convert hydrogen
and carbon dioxide into
methane to generate energy
anaerobically. Methanogens are
obligate anaerobes: they are
killed by oxygen.
• Methanogens digest cellulose in
cow and termite guts.
 Each cow belches 50 liters of
methane a day. A major
greenhouse gas.

16. Halophiles
• Extreme halophiles. Grow in
very salty conditions.
Colorful bacteria
• Mostly aerobic metabolism.
• Some have a form of
photosynthesis that uses
bacteriorhodopsin, a pigment
very similar to the rhodopsin
pigment in our eyes. It is also
called “purple membrane
protein”

17. Thermophiles
• Extreme thermophiles. Live at very
high temperatures: ocean
hydrothermal vents (up to 113o C,
which would be boiling except for the
high pressure under the ocean), hot
springs in Yellowstone National Park.
• Use sulfur to generate energy just like
we use oxygen: donate electrons to
sulfur to create hydrogen sulfide.
Some generate sulfuric acid instead—
they live at very low pHs.

18. Eubacteria
• The most common types of bacteria
• Many categories: we will just look at a few of
them.
• Enteric bacteria live in the digestive tracts of
animals. Enterics are facultative anaerobes.
Best known example: Escherichia coli (E. coli),
found in the human gut and also used as a
common experimental organism in the lab.
Most E. coli strains are harmless, but a few
pathogenic (disease-causing) strains exist,
causing food poisoning. A common source is
ground meat, but it gets on unwashed
vegetables as well.
• Related enteric bacteria: Salmonella, Shigella.
Cause food poisoning. Chickens carry
Salmonella in their guts instead of E. coli.

19. Endospore-forming Bacteria
• Most of these are in the genus
Bacillus (named after their
normal shape).
• Their spores are very resistant
to environmental conditions,
and may survive millions of
years before they revive.
• Anthrax is caused by a
Bacillus species. Also is this
family are the bacteria that
cause botulism (a very bad
form of food poisoning) and
tetanus (lockjaw--the muscles
go rigid).

20. Nitrifying and Nitrogen-fixing
Bacteria
• The atmosphere is 80% nitrogen. However,
we can’t directly use atmospheric nitrogen,
because it is in the wrong form: N2. We need
it in the ammonia form: NH3.
• Nitrogen fixing bacteria are able to do this
conversion. Most of them live in root
nodules of certain plants, the legumes, such
as alfalfa and soybeans.
• Plants also need nitrogen in the form of
nitrate, NO3. Nitrifying bacteria convert
ammonia into nitrate.

21. Cyanobacteria
• A major group of photosynthetic bacteria
• The oceans contain large amounts of
cyanobacteria (called plankton), that
produce much of Earth’s oxygen.
• Cyanobacteria are the source of
chloroplasts in plant cells. They also
have a symbiotic relationship in lichens:
a fungus and a cyanobacteria provide
each other with shelter and food from
photosynthesis.
• Cyanobacteria form cell walls to
fossilize—among the oldest forms of life
known.
• Some have cell differentiation: they form
filaments in which some cells become
“heterocysts”, heavily walled cells that
perform nitrogen fixation for the other
cells in the filament.