Bacteria have 3 types of symbiotic relationships:

1. parasitic
   the bacteria's fitness increases, the other's fitness decreases.
2. mutualistic
   both symbionts benefit. Example:  Nitrogen fixation
   in cyanobacteria:  N₂  NH₃ (ammonia)
   in other organisms:  NH₃  NO₂^-
                                 NO₃^-  N₂
3. commensualistic
   the bacteria's fitness increases without affecting the other's fitness.

Some bacteria are encapsulated in a slime layer and some are not.  Bacteria also come in many shapes:  rodlike (bacillus), spherical (coccus) and spiral (spirillum).  There are two types of aerobic bacteria:  obligate aerobe (must use cellular respiration) and facultative anaerobe (can use oxygen to respire or can ferment).  The table below represents characteristics of archae- and eubacteria.

Archaebacteria	Eubacteria	Evolution of Bacteria
earliest anaerobic adapted to harsh environments - lack peptidoglycan in cell wall do not have sex pili	- aerobic - more numerous have peptidoclycan in cell wall have sex pili	Chemo-hetero-trophs Chemo-auto-trophs Photo-auto-trophs
signature sequences:  unique sequences of rRNA which appear to indicate distinct ancestral relationships between archaebacteria, eubacteria, and eukaryotic organisms.

Eubacteria

Gram stain.

Eubacteria are separating along gram-positive (g+) and gram-negative (g-) mean.  The gram stain identifies bacteria based on components in their cell wall, primarily the location of peptidoglycan.  As its name indicates peptidoglycans are comprised of peptides and carbohydrates.  G+ bacteria are known to have peptidoglycan above their lipid bilayer in the ECM (extracellular matrix) because the dye targets the "peptido" part of the peptidoglycan molecule and thus the bacteria are "stained."  Peptidoglycan weaves itself into the ECM; penicillins inhibit this and thus prevent proper cell wall formation in gram-positive bacteria (penicillins cannot reach the peptidoglycan in g- bacteria and thus do nothing against them).  G- bacteria have a double lipid bilayer (the outer being primarily a lipopolysaccharide toxic to animals) and their peptidoglycan are located in the space between the inner and outer membrane thereby inhibiting the bonding of the dye to peptidoglycan.  It just so happens that there is a more significant percentage of pathogenic g- bacteria than g+ bacteria.

Motility of Prokaryotes.
50% can be motile.  The most common form of motility is the flagellum.  This flagellum has one-tenth the width of a eukaryotic flagellum.  The basic method of flagella power in g- bacteria is caused by a basal body connected to the "whip" at its base rotating thereby causing the "hook" (part outside the cell wall) to rotate like a propeller.  This basal body is powered by ATP which is powered a hydrogen ion pump similar to that in mitochondria where the ions are pumped into the intermembrane space and diffuse back into the bacterium.  The structure of g- flagella differs from eukaryotes in that globular proteins are wound into a filament that is connected to a curved hook-like protein which is inserted into a basal apparatus made up of 35 different proteins.  Other methods of motility are spirochetes and slime secreting prokaryotes that glide;  this may result from flagella without filaments.
Spirochetes. (sphere shaped) move in a spring-like manner with flagella on the ends of the cell.  Examples are syphilis and lyme disease. Cyanobacteria. These are believed to have created the first molecular oxygen in the atmosphere Chlamydia. These are obligate intracellular g- parasites that are the cause the most common disease.  Infection by chlamydia can lead to blindness.

Taxis, movement.

Chemotaxis:  positive (attracting) and negative (repulsing) chemical stimulants.

Phototaxis:  any movement corresponding to the presence of light.

Magnetotaxis:  tiny magnets inside of prokaryotes indicate up from down and help them migrate to nutrient rich sedimentary levels in shallow bodies of water.

Internal Membrane Organization.

There are respiratory membranes ,and photosynthetic (thylakoid) membranes in cyanobacteria.

Prokaryote Genomes.

DNA is concentrated in a tangled mass.  This mass is called the nucleoid region.  The genophore is the linear prokaryotic genome including 1 major and many minor plasmids unnecessary for most environments but can add metabolic, resistive and other special capabilities to the bacteria.

Question:  How do antibiotics like tetracycline and chloroamphenicol work?
Answer:  Both bind to ribosomes and block protein synthesis.

Growth, Reproduction and Gene Exchange.

Binary fission
     most divide every 1 to 3 hours, but some divide every 20 minutes in an optimal environment.
Endospores
     microbiologists use autoclaves (giant pressure cookers) to kill endospores. Endospores are hard protective "seeds" that bacteria form to protect themselves from destruction and can allow them to survive boiled water.

Bacterial Nutrition. top

	Energy Source	Carbon Source
Autotroph
photo-           chemo-	light inorganic chemicals	carbon dioxide carbon dioxide
Heterotroph
photo-           chemo-	light organic chemicals	organic chemicals organic chemicals

Chemoheterotrophs.

saprobe:  decomposes nutrients from dead organisms

parasite:  absorbs nutrients from the body fluids of the host.

Origins of Chemical Cycles.

Glycolysis:  the universal role of ATP today suggests it was used by early life.  Glycolysis is the oldest common metabolic process.

ETC and Chemiosmosis:

1. proton pumps driven by ATP regulate cell pH
2. ETCs take over the function by using glycolysis to power the proton pumps
3. ETC is so efficient it generates enough of a gradient to drive ATP synthesis as well.

Photosynthesis:
     1st crisis = the ATP supply dwindles.
     2nd crisis = fermenting prokaryotes use ATP faster than chemiosmosis can create it.
     Solution.

1. UV absorbing pigments develop:  Today, bacteriorhodopsin is in the plasmid membrane of modern halophiles.  It absorbs light and uses it to power the hydrogen gradient.  It is also structurally related to human retinal (eye) pigments.
2. This - called bacteriochlorophyll - combines itself with the ETC
3. Energy from sulfuric acid creates NADP⁺
4. However cyanobacteria are the ones to create the oxygen rich atmosphere because they were the first to use water instead of acid and other less plentiful.

Types of Archaebacteria.

methanogens	extreme halophiles	extreme thermophiles
use hydrogen gas to reduce carbon dioxide to methane are the strictest anaerobes use methane as their energy source	thrive in great salinity form a red-purple scum (because of the bacteriorhodopsin)	high temperatures such as geothermal vents

The 5 Major Subdivisions of Eubacteria.

1. Proteobacteria: the most diverse group
   1. obligate anaerobes ("purple"):  many flagellated, found in watery sediments, include all phototrophs.
   2. chemoautotrophs:  have key nitrogen cycle roles in legumes, can be free-living or symbiotic.
   3. chemoheterotrophs:  are enteric (inside you), most are rodshaped facultative anaerobes, examples include salmonella and E. coli.
2. Gram-positive bacteria:  
   • most are g+ some are g- though (this classification is due to similar molecular systematics).
   • most are chemoheterotrophs, some are photosynthetic.
   • Bacillus and Clostridium make endospores; Mycoplasmas do not and are the smallest of all known cells, lack cell walls, found in soil, and some are pathogenic.
   • Actinomycetes makes antibiotics and form branching colonies that look like fungi.
3. Cyanobacteria:
   • include photoautotrophs with plantlike photosynthesis.
   • have chlorophyll a and use the 2 photosystem method of splitting water.
   • have thick gelatinous cell walls.
   • motility:  gliding.
   • are single-celled, colonial cells, and multi-cellular organisms (called such because of a division of labor among the cells in a colony).
4. Spirochetes:
   • are helical and very long and thin
   • types include free-living and pathogenic (remember syphilis and lyme disease)
5. Chlamydia:
   • are gram-negative and have no peptidoglycan what-so-ever
   • cause blindness and gonorrhea

Robert Koch's Postulates.

1. find some pathogen in all diseased subjects.
2. isolate and grow in pure culture.
3. induce host to intake pathogen.
4. isolate the same pathogen as you began with.
5. Congratulations!  You've just substantiated a pathogen as a cause of a disease!

How do you get symptoms from a bacterial infection?

1. growth or tissue invasion (e.g. tuberculosis, leprosy).
2. exotoxins:  a secreted proteinaceous toxin that produces symptoms without the bacteria present
3. endotoxins: a proteinaceous toxin located in the cell membrane

Next:  "Endosymbiosis."