Prokaryotes

1
Prokaryotes

• Bacteria were first discovered in the late 1600s
  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 cytoplasmthere 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 dont 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 recipients genome.

7
Bacterial Morphology

• Bacteria only take a few basic shapes, which are
  found in many different groups. Bacterial cells
  dont have internal cytoskeletons, so their
  shapes cant 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
Metabolic Diversity

• Bacteria show far more metabolic diversity than
  eukaryotes
• General classification, based on carbon (food)
  source and energy source.
• autotroph vs. heterotroph. Autotrophs make
  their own food from non-organic sources (usually
  carbon dioxide). Heterotrophs use organic
  compounds from other organisms.
• phototroph vs. chemotroph. Phototrophs get
  their energy from sunlight. Chemotrophs get
  their energy from chemical compounds.
• Photoautotrophs get energy from sunlight and
  synthesize their own food from scratch, like
  green plants.
• Photoheterotrophs ( a rare category) get energy
  from sunlight but need organic compounds made by
  other organisms.
• Chemoautotrophs get energy from chemicals such as
  hydrogen gas, hydrogen sulfide or ammonia, and
  they use carbon dioxide as the raw material for
  their organic compounds.
• Chemoheterotrophs get both energy and organic
  compounds from other organisms. We are
  chemoheterotrophs.

10
Relationship to Oxygen

• For more than half of Earths history, oxygen
  wasnt present in the atmosphere. Many bacteria
  evolved under anaerobic conditions.
• Classification
• strict aerobes (need oxygen to survive)
• strict anaerobes (killed by oxygen)
• aerotolerant (dont use oxygen, but survive
  it).
• facultative anaerobes (use oxygen when it is
  present, but live anaerobically when oxygen is
  absent).

11
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!).

12
Archaea

• Sometimes called Archaebacteria
• Genetically as different from Eubacteria as we
  are.
• One distinguishing characteristic cell membranes
  dont contain fatty acids, but instead use
  branched molecules called isoprenes.
• Three main type methanogens, extreme halophiles,
  extreme thermophiles.

13
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.
• Methanogens are also in swamps, wetlands, and
  garbage dumps.

14
Halophiles

• Extreme halophiles. Grow in very salty
  conditions. Colorful bacteria in seawater
  evaporation beds, Great Salt Lake.
• 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

15
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
  insteadthey live at very low pHs.

16
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.

17
Pyogenic Cocci

• Pyogenic cocci. Pyogenic means pus-forming.
  These bacteria produce many of the worse
  infections.
• Staphylococcus aureus and Neisseria gonorrheae
  are 2 examples Staphylococcus produces
  pneumonia, toxic shock syndrome, strep throat,
  meninginitis, and various skin diseases, such as
  impetigo. Neisseria produces gonorrhea, a common
  sexually transmitted disease
• Staphylococcus bacteria normally live on the skin
  and body cavities. Only occasionally cause
  disease.
• Some strains of Staphylococcus are resistant to
  all known antibiotics.

18
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).

19
Rickettsia and Chlamydia

• These bacteria are intracellular parasites of
  eukaryotic cells. They cant survive outside a
  cell. Sometimes they have very reduced genomes
  they rely on host genes for critical functions.
• Rickettsia live in the gut linings of insects,
  and they infect mammals through mosquito and tick
  bites. They cause diseases like Rocky Mountain
  spotted fever, typhus, and Q fever.
• Chlamydia infections are the most common sexually
  transmitted disease in the US.

20
Nitrifying and Nitrogen-fixing Bacteria

• All proteins contain much nitrogen. The
  atmosphere is 80 nitrogen. However, we cant
  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. Farmers plant these crops to enrich
  their soil by naturally adding ammonia to it.
• The nitrogen-fixing bacteria live in the soil and
  invade the nodules of young plants.
• The nitrogen-fixing enzymes are poisoned by
  oxygen. The root nodules function to keep oxygen
  away from the bacteria.
• 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 Earths
  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 fossilizeamong
  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.