Eubacteria & Archaebacteria Notes

Discovery of Bacteria:
- Identified in 1677 by Antonie van Leeuwenhoek.
- Originally called "animalcules".

Original 5 Kingdom Classification:
- Bacteria classified under Kingdom Monera (Prokaryotes).
- Kingdom Monera evolved into Kingdom Protista (single-celled Eukaryotes).
- Kingdom Protista separated into Kingdoms Animalia, Fungi, and Plantae.
Modern Classification:
- Kingdom Monera divided into Domain Archaea and Domain Bacteria (Eubacteria).
- Kingdom Protista divided into multiple protistan kingdoms.

Endosymbiosis:
- Took place 2 billion years ago, forming Eukaryotic Life.
Process:
- Photosynthetic bacterium (prokaryote) enters a cell and becomes a chloroplast.
- Aerobic bacterium (prokaryote) enters a larger anaerobic prokaryote cell and becomes a mitochondrion.
- Invaginations of cell membrane develop into nuclear membrane and endoplasmic reticulum.
Result:
- Creation of the first Eukaryote Cell, the beginning of Domain Eukarya.
- Eukaryotic cell contains chloroplast and mitochondrion.
- Mitochondria have their own DNA and can reproduce in cells by themselves.
Prokaryotic Cells (bacteria):
- Lack organelles beyond a cell membrane, cytoplasm, DNA, and ribosomes.
Domain Archaea:
- Undergo glycolysis to produce some energy & lactic acid.

Cellular Respiration (aerobic - mitochondrion):
- $C6H{12}O7 + O2 \rightarrow CO2 + H2O + ATP$
Glycolysis (anaerobic - general):
- glucose -> lactic acid + ATP (lesser amount)
Photosynthesis (plants - chloroplasts):
- $CO2 + H2O + Sunlight \rightarrow O2 + C6H{12}O6$

Eukaryotic Cell (Domain Eukarya):
- Led to protists, animals, fungi, and plants.
- Linear chromosomes in the nucleus.
- Chloroplasts (in plants and photosynthetic protists).
- Mitochondrion (in plants, animals, fungi, protists).
Prokaryotes (Domain Bacteria, Domain Archaea):
- Circular DNA.
- Ribosomes.
- Cytoplasm.
- Cell membrane.
- Undergo glycolysis: glucose -> lactic acid + Energy.
- Cellular Respiration: glucose + oxygen -> $CO2$ + $H2O$ + Much Energy.

Rod-shaped:
- Termed: Bacilli.
- Some bacilli form endospores during unfavorable conditions.
  - Consist of a central core of DNA surrounded by an impenetrable layer.
  - Resistant to severe physical and chemical stresses.
  - Can remain viable for millions of years.
    - e.g., Anthrax (Bacillus anthracis) & Tetanus (Clostridium tetani)
Spherical-shaped:
- Can be found as single cocci, chains, or clumps.
- Diploids – pairs of spherical shaped bacteria.
  - e.g., Neisseria (can cause gonorrhea, bacterial meningitis & septicemia)
- Chains of spherical shaped bacteria.
  - e.g., Streptococcus (cause a variety of human diseases including Strept Throat, meningitis, flesh-eating disease, and bacterial pneumonia)
- Clusters of spherical shaped bacteria.
  - e.g., Staphylococcus aureus (can cause a variety of human infections including skin infections, Toxic Shock Syndrome, meningitis….)
Spiral-shaped
- Actually a form of rod-shaped bacteria
  - Leptospirillum
  - Sizes range from: 0.5 – 10 micrometers long, 0.2 – 0.3 micrometers wide (1micrometer = 0.001 mm)

Internal:
- Cell membrane: Acts as a barrier.
  - Allows for transport of energy and materials across it via a concentration gradient.
- Ribosomes: For protein synthesis.
- Single ring of genetic material (chromosome).
External:
- Cell wall:
  - Gram negative: thin cell wall made of lipids (fats) and carbohydrates
    - Stains with safranin.
  - Gram positive: have a similar inner cell wall and a second outer cell wall made of peptidoglycans (proteins and carbohydrates)
    - Stains purple with a chemical called crystal violet.
- Flagella: Used for motility and are driven by energy.
- Pili (sing. Pilus): Used for transferring genetic material between cells.
- Fimbriae: Fine filaments of protein that aid in the attachment to other cells.

Flagella: Rotates and is driven by energy at the base.
Bacterial gliding: Exact mechanism is currently unknown.
Twitching motility: Special pili are used as a hook that is extended repeatedly and used to pull the bacterium along.
Changes of buoyancy: Ex. Cyanobacteria can produce internal gas vesicles to regulate buoyancy in water to find food and light.

Obligate aerobes: Must have oxygen to survive.
- e.g., Mycobacteria tuberculosis (cause of T.B. or Tuberculosis).
Obligate anaerobes: Can only grow in the absence of oxygen. Oxygen is a poison for them.
- e.g., Clostridium botulinum causes botulism.
Facultative anaerobes: Can live in environments without or with oxygen.
- e.g., E. coli is found in oceans, lakes, and the guts of vertebrates.

Autotrophs (make their own food):
- Photosynthetic: Use of light for energy. e.g., cyanobacteria or blue-green algae.
- Chemosynthetic: Use of chemical substances for energy.
 - e.g., $H2S + CO2 \rightarrow S2 + C6H{12}O6$ (H2S being an energy compound found in Hot Vents).
Heterotrophs (obtain food from other sources):
- Saprophytic: Obtain raw materials from dead and decomposing matter (decomposers).
- Symbiotic Bacteria:
  - Mutualistic (eg. Bacteria in the human colon)
  - Parasites (disease-causing: pathenogenic bacteria)
  - Commensalism (host not harmed).
Chemotrophs (eg. perform fermentation)
- e.g. use in the production of cheese, yogurt or soy

In the late 1800s, Louis Pasteur, Joseph Lister, and Robert Koch were the first to link pathogenic microbes to disease.
Koch identified bacteria to anthrax and tuberculosis
To establish that a specific pathogen is the cause, a researcher must:
- Find the same pathogen in each diseased organism
- Isolate the pathogen from a diseased organism and grow the microorganism in a pure culture
- Induce the disease in experimental animals from the pure culture
- Isolate the same pathogen from the experimental animals