Comprehensive Study Guide on Prokaryotic Microbiology: Eubacteria and Archaebacteria

Taxonomic Groups: Prokaryotes comprise two primary kingdoms: Eubacteria and Archaebacteria.
General Context: Bacteria are prokaryotic organisms that may exist as single cells or within organized colonies.
Definition of Prokaryote: An organism characterized by the absence of a nucleus and the lack of any internal membrane-bound organelles.
Etymology of Prokaryote: * Pro-: Meaning "before." * Karyote: Meaning "nucleus."

Prokaryotic Cell Dimensions: Typically measure between $1-10\,\mu m$ . * Observation: In a light microscope, they can be viewed effectively only at a magnification of $1000\times$ or greater, requiring the use of OIL IMMERSION.
Eukaryotic Cell Dimensions: Typically measure between $10-1000\,\mu m$ . * Observation: In a light microscope, these cells are visible at lower magnifications ranging from $40\times$ to $400\times$ using standard lighting.
Specific Sub-cellular Structures Recognized in Eukaryotes for Size Contrast: * Nucleus. * Nucleolus. * Chromatin.
Prokaryotic Specific Feature: The Nucleoid (lacks a surrounding membrane).

Plasma (or Cell) Membrane: This structure regulates the passage of substances, controlling what enters or leaves the cell.
Cytoplasm: The internal fluid medium and matrix of the cell.
Ribosomes: These structures are responsible for building proteins based on genetic instructions from DNA. * Comparison to Eukaryotes: They are functionally identical to eukaryotic ribosomes (like those in humans) but are significantly smaller in size.
Cell Wall: An outer barrier that serves as the limit to cell expansion. * Primary Purpose: To prevent the cell from exploding (osmotic lysis) if it absorbs excessive amounts of water. * Survival Necessity: The cell wall is considered essential for bacterial survival. * Clinical Relevance of Penicillin: This antibiotic functions by weakening the bacterial cell wall, which subsequently allows the plasma membrane to rupture, killing the cell.
Capsule: An additional protective layer found on the outer surface of some bacteria.

Gram Stain Technique: Used by microbiologists to distinguish between different species of bacteria based on cell wall composition.
Gram Positive (Gram +): * Characterized by thick cell walls. * The bacteria change to a dark purple color during staining.
Gram Negative (Gram -): * Characterized by thin cell walls. * The bacteria remain light coloured after the staining process.

Nucleoid (Circular DNA): * This is the large "master" DNA of the bacterium. * It carries all essential information necessary for the organism's life.
Plasmids (Small Circular DNA): * Short independent strands of DNA. * Function: They frequently code for specific advantageous traits, such as antibiotic resistance. * Volume: Plasmids constitute approximately $5\%$ or less of the total DNA within a bacterium. * Metaphor: They are described as the "super-power-trading cards" of the bacterial world.

Bacterial Flagellum: A whip-like tail that functions as a propeller, allowing the bacteria to move through liquid environments (swimming).
Pili (singular: Pilus): * Sexual Reproduction Structure: Pili are used to form a physical bridge to another bacterial cell. * DNA Transfer: This bridge facilitates the transfer of plasmids during the process of conjugation. * Locomotion: In certain species, pili can also be utilized for movement.

1. Binary Fission (Asexual Reproduction): * Unique to Prokaryotes. * Produces IDENTICAL clones. * Step 1: The bacterium creates a copy of its circular DNA. * Step 2: Each ring of DNA is attached to the plasma membrane. * Step 3: New membrane material is added between the two DNA rings, pushing them apart and elongating the cell. * Step 4: Once the DNA rings are sufficiently separated, the cell splits into two.
2. Conjugation (Sexual Reproduction): * Involves the recombination of DNA between two members of the same species. * Creates NEW variations within the species. * Step 1: The donor bacterium (F+ cell) makes multiple copies of its plasmids. * Step 2: A Conjugation pilus forms a bridge between two adjacent bacteria of the same species. * Step 3: Plasmid DNA transfers from the donor cell to the recipient cell (F- cell). * Step 4: The recipient synthesizes a complementary strand to become an F+ cell; the donor restores its complete plasmid. Upon separation, both cells possess a copy of the plasmid.

Etymology: Archae- means "ancient."
Biological Classification: Although they are prokaryotes, their genetics are so distinct from Eubacteria that they are classified in a separate kingdom.
Evolutionary Background: Archae are believed to be the earliest form of life on Earth. They thrived in Earth's early seas before the presence of oxygen or photosynthetic organisms.
Environmental Adaptation: They are capable of surviving in EXTREME environmental conditions.

Thermophiles: * Etymology: Thermo- = temperature (related to thermometers); -phile = love (as in philanthropist/lover of society). * Habitat: Found in extremely hot environments, such as molten lava or hot springs near fissures in the Earth's crust. * Scientific Contribution: Thermus aquaticus is a famous thermophile that provided the enzymes (Taq polymerase) enabling rapid DNA replication in laboratory settings.
Halophiles: * Etymology: Hals (Greek) = "salt"; -phile = love. * Habitat: Can survive in saltwater concentrations $5 \times$ more concentrated than standard oceans. * Geographic Examples: Found in the Dead Sea (Israel) and the Great Salt Lake (USA).
Methanogens: * Etymology: -gen = genesis or formation; "methane producing." * Function: They operate in the absence of oxygen and perform a crucial ecological role by removing excess hydrogen. * Habitat and Effects: Commonly found in swampy conditions where water flow is minimal. * Bioproducts: They produce "swamp gas" in marshes and are the bacteria responsible for generating gas (flatulence) in humans and livestock (cows).