Module 3: Introduction to Prokaryotic Cell Anatomy and Morphology

Nucleus and Genetic Material Storage:
- Prokaryotic cells specifically lack a membrane-bound nucleus in the center of the cell.
- Instead of a nucleus, prokaryotes possess a centralized region referred to as the nucleoid, which contains the cell's genetic material.
- The genetic material, or chromosome, consists of a single loop of double-stranded DNA.
- Prokaryotic cells are classified as $1n$ or haploid, meaning they contain only one copy of their genome.
- Biological implications of haploidy: If a mutation occurs in the DNA, it is inevitably passed on to the offspring because there is no second, correct copy of the gene to mask or compensate for the mutation.
Internal Organelles:
- Prokaryotic cells lack all membrane-bound organelles.
- A notable example is the absence of mitochondria; these structures will never be found within a prokaryotic cell.
Cellular Size and Scale:
- Prokaryotic cells are significantly smaller than eukaryotic cells, typically measuring approximately $1/10$ the size of a eukaryotic cell.
- To provide a perspective on scale, a prokaryotic cell is roughly the same size as a single mitochondrion.

General Morphology:
- The term morphology is used interchangeably with "cell shape."
Bacillus (Rod-shaped):
- Bacillus refers to a rod-like shape.
- They can appear in diverse dimensions, such as long and thin or shorter and fatter.
- The defining characteristic is that they are always longer than they are wide.
Coccus (Spherical):
- These cells are spherical or round in shape.
Coccobacillus:
- This is a very short rod.
- Under a stain preparation, it is often difficult to distinguish a coccobacillus from a coccus because they are barely longer than they are wide.
Vibrio:
- A vibrio is specialized morphology characterized as a curved bacillus.
Square Morphology:
- An unusual, flat, tile-like square shape found in Archaea located in the salt lakes of Egypt.
- Square shapes are rare in nature because they are not considered the most efficient cellular structure.
Spiral Shapes:
- Spirillum: Rigid spiral shapes often described as having a corkscrew appearance.
- Spirochaetes: Flexible, worm-like shapes that move via a twitching motion.
Pleomorphic:
- This term refers to species that vary in shape rather than adhering to one single, distinctive morphology.

Individual Cells:
- Occurs when cells completely separate after division, remaining as singular cocci or bacilli.
Diplo (Pairs):
- Cells that remain together in pairs after division.
- A specific example is Streptococcus pneumoniae, which is a diplococcus.
Strepto (Chains):
- Arrangement where cells remain attached in long chains.
- Can occur as streptococcus (chains of spheres) or streptobacillus (chains of rods).
Tetrad:
- "Tetra" means four; this arrangement consists of four cocci that stay grouped together after division.
Sarcina (Cube):
- A cube-shaped arrangement formed when eight cocci divide along three-dimensional axes.
- In laboratory stainings, it may be difficult to distinguish sarcina from a tetrad, though sarcina typically looks "blurry" due to the three-dimensional stacking.
Staphylo (Clusters):
- Grape-like clusters of cells that remain attached as they divide and stick together.
- This arrangement is the hallmark of the Staphylococcus genus.
Palisade:
- An arrangement of bacilli that stay connected lengthwise during division, resembling a raft.
- Some species in this arrangement may stay connected at only one end, forming a "V" shape.

Composition and Purpose of Pili:
- Pili are short appendages on the outside of the cell wall composed of the protein pilin.
- They facilitate attachment, allowing cells to stick to surfaces or each other via adhesion proteins located at the tips.
Types of Pili:
1. Fimbriae: These are short pili used primarily for attachment to surfaces and other cells. They are critical for the formation of biofilms (the slime layer that forms on surfaces).
2. Sex Pilus: A longer appendage used for bacterial conjugation, which is the bacterial form of mating.
  - This structure allows for the exchange of plasmids, small circles of extra-chromosomal DNA often containing genes for antibiotic resistance.
  - The donor cell is designated as $F^{+}$ (capable of forming the sex pilus), and the recipient cell is designated as $F^{0}$ .

Flagellum (plural: Flagella):
- Long blue appendages (in diagrams) used for motility, allowing cells to swim.
Classifications by Flagellar Distribution:
- Monotrichous: A single flagellum located at one pole (mono = singular; trichous = hair).
- Amphitrichous: A flagellum located at each pole (amphi = both ways).
- Lophotrichous: A cluster or "lop" of flagella situated at one pole (end) of the cell.
- Peritrichous: Flagella distributed all over the cell surface ("peri" can be remembered as "hairy").
Structure:
- The flagellum is comprised of three basic parts (though the specific internal anatomy of the flagellum was omitted in this section of the transcript).

Cell Envelope Components:
1. Cell Wall: A rigid structure that maintains cell shape and prevents lysis (breaking apart) due to internal water pressure.
2. Cell Membrane: A phospholipid bilayer located inside the cell wall.
Gram-Positive Cell Wall Structure:
- Primarily composed of a thick layer of peptidoglycan, a macromolecule made of peptides (amino acids) and sugars (glycan).
- Sugar Subunits:
  1. NAG: N-acetylglucosamine.
  2. NAM: N-acetylmuramic acid.
- The NAG and NAM subunits alternate and are staggered in their layout to provide maximum three-dimensional strength.
- NAM subunits are interconnected by transpeptide chains (amino acid chains) that link above, below, in front, and behind.
Additional Components of Gram-Positive Walls:
- Teichoic Acid: A polysaccharide covalently bound to NAM subunits ("Tekos" means wall). Represented as blue squiggles within the peptidoglycan.
- Lipoteichoic Acid: Teichoic acid that extends further down to anchor into the underlying phospholipid bilayer (cell membrane).
- Functions: These acids help bind and regulate cations (positively charged ions) moving in and out of the cell and assist in cell growth by depositing new cell wall material.

Structural Difference:
- Gram-negative cell walls contain a very thin layer of peptidoglycan compared to Gram-positive walls.
- The Gram-negative cell envelope consists of: Cell Membrane → Thin Peptidoglycan → Periplasmic Space → Outer Membrane.
- The periplasmic space contains a fluid called periplasm.
The Outer Membrane and Lipopolysaccharide (LPS):
- The outer membrane is a phospholipid bilayer, but the outer leaf contains unique molecules.
- The outer leaf contains lipopolysaccharide (LPS).
- A critical component of the LPS is Lipid A, which is embedded in the membrane and functions as an endotoxin.