Cell Structure and Function in Prokaryotes and Archaea

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Prokaryotes are organisms that lack a nucleus and membrane-bound organelles. Their DNA is not enclosed within a membrane, allowing simultaneous transcription and translation.
Prokaryotes are typically small (about 1.0 μm or less in diameter) and include Bacteria and Archaea.
Eukaryotes possess a true nucleus and various internal membrane-bound organelles. They are generally larger (10–100 μm in diameter) and structurally more complex. Examples include algae, protozoa, fungi, animals, and plants.

Glycocalyces are gelatinous, sticky substances surrounding the outside of the cell, composed of polysaccharides, polypeptides, or both.
There are two main types:
- Capsule: Organized, firmly attached to the cell surface, and may help bacteria evade host immune recognition.
- Slime Layer: Loosely attached, water-soluble, and facilitates attachment to surfaces.

Flagella are long, whip-like structures responsible for bacterial movement.
They consist of three parts: filament, hook, and basal body (which anchors the flagellum to the cell wall).
Flagellar rotation propels the bacterium and can be clockwise or counterclockwise, resulting in runs (straight movement) or tumbles (random changes in direction).
Not all bacteria possess flagella.

Fimbriae are short, sticky, bristle-like projections that help bacteria adhere to each other and to surfaces. They are important in biofilm formation.
Pili (singular: pilus) are longer than fimbriae but shorter than flagella. They are usually present as one or two per cell and are involved in conjugation—the transfer of DNA between cells.

Cell walls provide structural support, shape, and protection from osmotic pressure.
They assist in cell attachment and resistance to antimicrobial agents.
Most bacterial cell walls are composed of peptidoglycan, a complex polymer of sugars and amino acids.

Feature	Gram-Positive	Gram-Negative
Peptidoglycan Layer	Thick	Thin
Teichoic Acids	Present	Absent
Outer Membrane	Absent	Present (contains LPS)
Gram Stain Color	Purple	Pink
Mycolic Acid (in some)	Up to 60% (acid-fast bacteria)	Absent
Lipid A (endotoxin)	Absent	Present (can cause fever, shock, etc.)

Gram-positive bacteria have thick peptidoglycan layers and teichoic acids; some (acid-fast) contain mycolic acid for desiccation resistance.
Gram-negative bacteria have a thin peptidoglycan layer and an outer membrane with lipopolysaccharides (LPS), including lipid A, which can trigger strong immune responses.

Some bacteria lack cell walls and are often mistaken for viruses but retain other prokaryotic features such as ribosomes.

The cell membrane is a phospholipid bilayer with embedded integral and peripheral proteins.
The fluid mosaic model describes the dynamic arrangement of lipids and proteins in the membrane.

Controls the passage of substances into and out of the cell (selectively permeable).
Harvests light energy in photosynthetic bacteria.
Maintains concentration and electrical gradients.
Proteins facilitate transport of substances across the membrane.
Active processes include:
- Active transport: Movement of substances against their concentration gradient using energy.
- Group translocation: Substances are chemically modified during transport into the cell.

Cytosol: The liquid portion, mostly water, containing dissolved substances and the nucleoid (region with DNA).
Inclusions: Reserve deposits of chemicals (e.g., nutrients, gas, or magnetic particles).
Genetic Components:
- Nucleoid: Contains essential genetic information for survival.
- Plasmids: Small, circular DNA molecules that provide survival advantages (e.g., antibiotic resistance).
Endospores: Highly resistant, dormant structures formed by some bacteria as a defense against unfavorable conditions. They can withstand extreme heat, radiation, and chemicals.

Ribosomes are the sites of protein synthesis, composed of polypeptides and ribosomal RNA.
Prokaryotic ribosomes are 70S (Svedberg units), while eukaryotic ribosomes are 80S.
Cytoskeleton: Nonmembranous organelles composed of protein fibers, involved in cell division, shape maintenance, DNA segregation, and movement.

Glycocalyces: Aid in biofilm formation and adherence to surfaces and other cells.
Flagella: Structurally similar to bacterial flagella (basal body, hook, filament) but with notable differences in composition and assembly.
Fimbriae and Hami: Many archaea have fimbriae; some possess hami, which are hook-like structures for attachment to surfaces.

Most archaea have cell walls, but these lack peptidoglycan and instead contain specialized polysaccharides and proteins.
All archaea possess cytoplasmic membranes that maintain electrical and chemical gradients and regulate substance import/export.

Similarities to bacteria: 70S ribosomes, fibrous cytoskeleton, circular DNA.
Differences from bacteria:
- Distinct ribosomal proteins.
- Unique metabolic enzymes for RNA synthesis.
- Genetic code more closely resembles that of eukaryotes.