Bacteria/Archaea

Four main biological molecules present in all cells:
- Carbohydrates: Variants include sugars and polysaccharides.
- Proteins: Built from amino acids; perform cellular functions.
- Lipids: Includes phospholipids, triglycerides, and steroids.
- Nucleic Acids: Primarily DNA for genetic information storage and transfer.
All cells possess:
- Cytoplasm: The jelly-like matrix inside the cell.
- Ribosomes: Machinery for protein synthesis.
- Plasma Membrane: Separates interior of the cell from the external environment.

Prokaryotic Cells:
- Lack a nucleus (DNA is freely floating in the cytoplasm).
- Generally smaller and simpler, typically less than 2 micrometers.
- Are single-celled organisms.
Eukaryotic Cells:
- Contain a nucleus (DNA enclosed in a double membrane).
- Larger and more complex, with membrane-bound organelles.
- Can be single-celled or multicellular.

Cell Size:
- Prokaryotic cells are usually less than 2 micrometers.
- Eukaryotic cells generally around 10 micrometers.
DNA Structure:
- Bacterial DNA is circular and exists in a concentrated region called the nucleoid.
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Distinct from eukaryotic nucleus: No membrane separation, DNA appears as supercoiled structure.
- Peptidoglycan Cell Wall:
Composed of sugars and amino acids, key component of bacterial cell structure, providing protection.
Essential for maintaining cell shape and integrity.

Shape Types:
- Cocci: Spherical (singular: coccus).
- Bacilli: Rod-shaped (singular: bacillus).
- Vibrios: Curved shapes.
- Other shapes include Coccobacillus, Spirillum, and Spirochetes.
Arrangement Types:
- Single (Coccus).
- Diplococci: Pair of cocci.
- Tetrad: Group of four cocci.
- Streptococci: Chains of cocci.
- Staphylococci: Clusters resembling grapes.
- Bacilli can also be arranged in chains (Streptobacillus).

Nucleoid:
- Contains a single circular chromosome, distinct from the eukaryotic linear chromosomes.
- Possible presence of plasmids, extra DNA which can carry antibiotic resistance or virulence factors.
- Discussed as a crucial tool for horizontal gene transfer.
Ribosomes:
- Responsible for protein synthesis; function identical to eukaryotic ribosomes but size differs (70s ribosomes in prokaryotes vs 80s in eukaryotes).
- Two subunits labeled as 30s (small) and 50s (large).
Inclusions:
- Areas of concentrated materials, variable functions, not membrane-bound.
- Types include starch granules, chromatic granules, and magnetosomes.
Endospores:
- Structures for survival in unfavorable conditions (e.g., heat, desiccation).
- Surrounded by a resistant coat; can remain dormant for extended periods.
- C. Diff mentioned as an organism producing endospores, resistant to many cleaning agents.
Plasma Membrane:
- Composed of phospholipids and proteins forming a lipid bilayer; selectively permeable barrier.
- Facilitates passive and active transport mechanisms (simple diffusion, facilitated diffusion, osmosis, and active transport).

Passive Transport Types:
- Simple Diffusion: Movement from high to low concentration.
- Facilitated Diffusion: Requires a protein helper for movement across membranes.
- Osmosis: Diffusion of water via aquaporins.
Active Transport:
- Requires energy (ATP) to move molecules against concentration gradients.
- Examples include Sodium-Potassium pumps and group translocation seen in bacteria.

Peptidoglycan Structure:
- Composed of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).
Gram-Positive vs. Gram-Negative Cell Walls:
- Gram-Positive:
- Thick peptidoglycan layer with teichoic acids.
- Stains purple in Gram staining.
- Gram-Negative:
- Thin peptidoglycan layer with an outer membrane (contains LPS).
- Stains pink; periplasmic space exists between membranes.
Lipopolysaccharide (LPS):
- Functions as an endotoxin, causing inflammatory responses in humans.

Mycoplasma: Lack a cell wall altogether, instead have stabilizing compounds in plasma membrane.
Acid-Fast Bacteria: Contain mycolic acids (e.g., Mycobacterium tuberculosis), appearing purple when stained.

Glycocalyx: External carbohydrate layer, can be capsule (organized, protective) or slime layer (loose, less organized).
- Offers attachment and protects from host immune response.
Extracellular Appendages:
- Flagella: Used for movement; structure varies between Gram-positive and Gram-negative.
- Different arrangements: monotrichous, amphitrichous, lophotrichous, and peritrichous.
Fimbriae: Shorter than flagella, primarily for attachment (e.g., E. coli in urinary tract infections).
Pili: Longer than fimbriae; involved in attachment and genetic exchange, e.g., during conjugation.

Archaea share similarities with both bacteria and eukaryotes:
- Lack a nucleus and generally lack peptidoglycan in their cell walls.
- Often have cell walls made from pseudomurein.
- Reside in extreme environments but can also inhabit human bodies and are part of the microbiome.

Early classification methods were morphological and based on staining techniques (e.g., Gram staining).
Evolved to biochemical classification assessing metabolic capabilities.
Presently leverage genetic sequencing for more accurate classification, leading to the three-domain system: Bacteria, Archaea, and Eukarya.
Use of Bergey’s Manual of Systematic Bacteriology and Cultural Techniques to identify and differentiate species based on physical and biochemical properties.

Challenges due to lack of reproductive isolation in bacteria.
Bacterial species are defined as a collection of cells sharing common traits, often categorized into subspecies or strains based on specific characteristics (e.g., E. coli variants).