bacteria and archaea

Common Features of All Cells

• Shared Components: All cells (prokaryotic and eukaryotic) possess:

  • DNA and chromosomes (genetic material)

  • Cell membrane (plasma membrane)

  • Cytoplasm

  • Ribosomes (protein synthesis)

  • Cytoskeleton (structural support)

Overview of Bacteria (Prokaryotes)

• Key Characteristics:

  • Genome: Single, circular chromosome located in the nucleoid region; not membrane-bound.

  • DNA Packaging: Lacks histones (unlike eukaryotic cells).

  • Organelles: Lacks membrane-bound organelles; contains $70S$ ribosomes.

  • Cell Wall: Typically composed of peptidoglycan.

  • Reproduction: Primarily divides via binary fission.

  • Archaea: Most of these prokaryotic traits are also observed in archaea.

Size, Shape, and Cellular Arrangement

• Average Size: $0.2 - 1.0\,\mu m \times 2 - 8\,\mu m$

• Three Basic Shapes:

  • Bacillus (plural: Bacilli): Rod-shaped. Note that Bacillus is also a genus name.

  • Coccus (plural: Cocci): Spherical or round shape.

  • Spiral: Curved or helical cells:

  • Vibrio: Comma-shaped curves.

  • Spirillum: Rigid helical structure.

  • Spirochete: Flexible helical structure.

• Variations in Morphology:

  • Monomorphic: Maintains a single, constant shape (most bacteria).

  • Pleomorphic: Can alter shape and size depending on environmental conditions.

  • Arrangements: Distinct groupings (especially common in Cocci, e.g., chains or clusters).

External Structures

Located outside the bacterial cell wall to facilitate protection, attachment, or movement:

1. Glycocalyx

• Composition: Sticky layer composed of polysaccharides, polypeptides, or both, secreted on the cell surface.

• Types:

  • Capsule: Highly organized and firmly attached to the cell wall.

  • Slime Layer: Unorganized and loosely attached to the cell wall.

• Functions:

  • Biofilm Formation: Allows cells to adhere to biological and non-biological surfaces.

  • Virulence Factor: Prevents phagocytosis by immune cells (e.g., Bacillus anthracis, Streptococcus pneumoniae, Streptococcus mutans).

2. Flagella and Motility

• Structure: Long filamentous appendages anchored to the cell wall and plasma membrane. Composed of three distinct parts:

  • Filament: Outermost region containing flagellin protein.

  • Hook: Flexible attachment sheath connecting filament to the basal body.

  • Basal Body: Anchors the flagellum into the cell wall and membrane.

• Flagellar Arrangements:

  • Atrichous: Lacks flagella.

  • Monotrichous: Single flagellum at one pole.

  • Lophotrichous: Tuft of multiple flagella at one pole.

  • Amphitrichous: Flagella located at both opposite poles.

  • Peritrichous: Flagella distributed across the entire cell surface.

• Motility Mechanism:

  • Movement: Driven by rotation of flagella in a "run and tumble" pattern.

  • Taxis: Directional movement toward (positive) or away from (negative) stimuli:

  • Chemotaxis: Response to chemical signals.

  • Phototaxis: Response to light.

  • Magnetotaxis: Response to magnetic fields.

3. Axial Filaments (Endoflagella)

• Occurs in: Spirochetes.

• Structure: Bundles of fibrils anchored at one end of the cell beneath an outer sheath.

• Function: Rotation causes a corkscrew motion that propels the bacterium.

4. Fimbriae, Pili, and Nanotubes

• Fimbriae: Short, hair-like structures enabling attachment to surfaces and epithelial tissues, allowing host tissue colonization and infection.

• Pili: Longer appendages used for motility and DNA transfer between cells (conjugation).

• Nanotubes (Nanowires): Intercellular channels used to transfer amino acids or harvest energy by shuttling electrons to iron-rich extracellular substances.

Cell Wall

• Primary Functions: Provides rigid structural shape, protection, and prevents osmotic lysis (cell bursting due to fluid influx).

• Composition (Peptidoglycan / Murein):

  • Polymer of repeating disaccharide units:

  • N-acetylglucosamine (NAG)

  • N-acetylmuramic acid (NAM)

  • Cross-linked by polypeptides (forming peptide cross-bridges) attached to tetrapeptide side chains on NAM.

  • Permeability: Fully permeable to small ions, amino acids, and sugars.

Gram-Positive vs. Gram-Negative Cell Walls

• Gram-Positive Cell Wall:

  • Peptidoglycan: Thick, dense multi-layered peptidoglycan.

  • Teichoic Acids: Negatively charged polymers of alcohol and phosphate group on the surface.

  • Help regulate cation movement.

  • Provide antigenic variation.

• Gram-Negative Cell Wall:

  • Peptidoglycan: Thin single layer of peptidoglycan.

  • Outer Membrane: Surrounds peptidoglycan; contains Lipopolysaccharide (LPS), lipoproteins, and phospholipids.

  • LPS Function: Acts as a signaling molecule and endotoxin.

  • Periplasmic Space: Fluid-filled region between plasma membrane and outer membrane.

  • Sensitivity: Less sensitive to medications and antibiotics because the outer membrane acts as an additional permeability barrier.

Gram Stain Mechanism

• Crystal Violet-Iodine (CV-I): Large complexes form inside the cell.

• Gram-Positive Response:

  • Alcohol dehydrates peptidoglycan.

  • CV-I crystals remain trapped inside (cells retain purple color).

• Gram-Negative Response:

  • Alcohol dissolves lipid outer membrane and leaves holes in thin peptidoglycan.

  • CV-I washes out completely (cells counterstained pink/red with safranin).

Atypical Cell Walls

• Mycoplasmas: Naturally lack a cell wall; sterols in the plasma membrane stabilize against osmotic lysis. Cannot be detected by standard light microscopy (e.g., Mycoplasma pneumoniae, causing "walking pneumonia").

• L-Forms: Bacterial strains that naturally possess a cell wall but lose it during part of their lifecycle; resistant to cell wall-targeting antibiotics.

• Acid-Fast Cell Walls: Found in Mycobacterium and Nocardia. Thin peptidoglycan layer enveloped by mycolic acid (waxy lipid). Stain poorly with Gram stain; require acid-fast staining.

• Archaea Cell Walls: Chemically distinct non-peptidoglycan walls made of pure proteins or polysaccharides (e.g., pseudomurein); some lack a wall entirely.

• Cell Wall Damage:

  • Lysozyme: Enzymatically hydrolyzes disaccharide bonds in peptidoglycan.

  • Penicillin: Antibiotic that inhibits peptide cross-bridge synthesis in peptidoglycan.

Internal Structures

Plasma Membrane

• Structure: Phospholipid bilayer with embedded proteins (Fluid Mosaic Model).

• Function: Selectively permeable membrane regulating transport (diffusion, osmosis, transport systems).

• Prokaryotic Metabolic Role: Serves as the site for energy transformation (electron transport chain for ATP production), substituting for missing mitochondria.

• Membrane Damage: Disruption by alcohols, quaternary ammonium detergents, and polymyxin antibiotics causes leakage of cellular contents.

Cytoplasm and Internal Components

• Cytoplasm: Watery solvent site for most biochemical activity.

• Nucleoid: Nuclear rawegion containing a single, circular chromosome (up to $3500$ genes).

• Plasmids: Small, non-essential extrafefchromosomal circular DNA ($5 - 100$ genes) replicating independently; often carry resistance or virulence factors.

• Ribosomes: Protein synthesis machinery ($70S$ in prokaryotes, composed of a $50S$ large subunit and a $30S$ small subunit; $80S$ in eukaryotic cytoplasm).

• Inclusion Bodies: Storage granules containing accumulated nutrients, monomers, or iron compounds (magnetosomes).

Endospores

• Overview: Extremely tough, dormant, non-reproductive structures that form inside cells during starvation or environmental stress.

• Spore-Forming Genera: Clostridium and Bacillus.

• Resistance: Highly resistant to UV radiation, desiccation, lysozyme, high temperature, starvation, and chemical disinfectants.

• Processes:

  • Sporulation: Process of endospore formation.

  • Germination: Return of an endospore back to an active vegetative state.

• Steps of Sporulation:

  1. Spore septum isolates replicated DNA and a small portion of cytoplasm.

  2. Plasma membrane surrounds the isolated DNA, cytoplasm, and inner membrane.

  3. Spore septum completely encloses the isolated portion, forming a forespore.

  4. Peptidoglycan layer forms between internal and external membranes.

  5. Tough protein spore coat forms around peptidoglycan.

  6. Mature endospore is freed from the dying parent cell.

Classification Systems for Bacteria and Archaea

Bergey's Manuals

• Bergey's Manual of Systematic Bacteriology:

  • Organizes prokaryotes based on genetic relatedness and rRNA gene sequencing.

• Bergey's Manual of Determinative Bacteriology:

  • Organizes bacteria based entirely on phenotypic characteristics (e.g., cell morphology, staining properties, metabolic requirements) used for laboratory identification.

Taxonomic Divisions

Categorizes bacteria and archaea into four major divisions based on cell wall type:

• Gracilicutes: Gram-negative bacteria with thin peptidoglycan walls.

• Firmicutes: Gram-positive bacteria with thick peptidoglycan walls.

• Tenericutes: Bacteria lacking cell walls (soft body).

• Mendosicutes: Archaea with atypical, non-peptidoglycan cell walls.

Species and Subspecies Concepts

• Bacterial Species: Collection of bacterial cells sharing overall similar traits and at least $95\%$ genetic similarity.

• Subspecies, Strain, or Type: Bacteria of the same species exhibiting distinct biochemical, structural, or pathogenic variations.