Viral Replication and Cell Structure Quiz

Microbial World - Week 1

• Domains of Life: Bacteria, Archaea, and Eukarya share a common ancestor but differ in their evolutionary history. Bacteria and Archaea are prokaryotic (lack a nucleus and membrane-bound organelles), while Eukarya are eukaryotic. Archaea share similarities with Eukarya in some genetic processes but differ from bacteria in membrane structure and lack of peptidoglycan.

• Prokaryotic Cell Properties: These cells lack a nucleus and membrane-bound organelles; their DNA is circular and in the nucleoid. They contain cytoplasm, DNA, ribosomes, and a cytoplasmic membrane, and carry out growth, reproduction, and energy conversion. Some prokaryotes can differentiate, communicate, move, or exchange genetic material.

• Ecosystem Roles: Microbial activity is crucial for nutrient cycling, primary production (photosynthesis), and decomposition; their metabolism, growth, and reproduction define life in ecosystems.

• Prokaryotic vs. Eukaryotic Structure: Prokaryotic cells are simpler, lacking organelles, with circular DNA. Eukaryotic cells are more complex, have membrane-bound organelles, and linear DNA.

• Genome Definition: The genome is the complete set of genetic material (DNA or RNA) containing instructions for life in a cell or virus.

• RNA's Role in Early Cell Evolution: RNA, in the absence of DNA, likely served as both a catalyst (ribozymes) and genetic material, enabling replication and protein synthesis in early life.

• Microbial Impact on Human Health:

• Positive: Nutrient recycling, biotechnology, food production, and microbiota maintain health.

• Negative: Pathogenic microbes cause disease and food spoilage.

• Microbial Staining:

• Simple Staining: Uses a single dye to visualize cells (e.g., methylene blue).

• Differential Staining: Uses multiple dyes to differentiate structures, like the Gram stain or acid-fast stain.

• Microscopy Principles: Understand light microscopy (brightfield, phase contrast) and the principles of resolution and magnification.

Gram Stain Procedure and Interpretation

• Procedure:
  1. Crystal violet stains all cells purple.
  2. Iodine forms a crystal violet-iodine complex.
  3. Alcohol decolorizes Gram-negative cells.
  4. Safranin counterstains Gram-negative cells pink.
• Interpretation: Gram-positive cells remain purple; Gram-negative cells appear pink.
• Errors: Over-decolorization (false-negative) or under-decolorization (false-positive).

Acid-Fast and Spore Staining

• Acid-Fast Stain: Identifies bacteria containing mycolic acid (e.g., Mycobacterium).
• Spore Stain: Visualizes endospores in bacteria (e.g., Bacillus, Clostridium).

Microbial Cell Structure - Week 2

Morphology & Morphology Factors

• Basic Shapes: Cocci (spherical), bacilli (rod-shaped), spirilla (spiral).
• Influencing Morphology: Surface area-to-volume ratio, motility, and environment affect cell shape and growth.

Cytoplasmic Membrane

• Components: Phospholipid bilayer with embedded proteins.
• Functions: Transport, energy production, and cell integrity.

Archaeal vs. Bacterial Membranes

• Linkages: Bacteria: ester linkages; Archaea: ether linkages (more stable in extremes).
• Fatty Acid Chains: Bacteria: unbranched; Archaea: branched isoprenoids.
• Membrane Architecture: A conserved structure of hydrophobic tails and hydrophilic heads.

Archaeal Membrane

• Composition: Isoprene units (branched 5 carbons) with ether linkages; some have monolayers.
• Components: Phospholipids, sulfolipids, glycolipids.
• Other Features: Possess ribosomes, lack membrane-bound organelles, have a nucleoid region with a single circular chromosome, and include inclusion bodies (e.g., gas vacuoles).

Bacterial Cell Wall Structure

• Peptidoglycan: A mesh-like polymer of NAG and NAM linked by β-1,4-glycosidic bonds and cross-linked by peptides.

• Gram-Positive: Thick peptidoglycan layer, lack an outer membrane. Retains crystal violet stain.

• Gram-Negative: Thin peptidoglycan layer, have an outer membrane with lipopolysaccharides (LPS). Decolorized during Gram stain. (Includes periplasmic space, porins).

• Peptidoglycan Attackers: Lysozyme breaks bonds and antibiotics (e.g., penicillin) target it.

Lipopolysaccharide (LPS) Characteristics

• Location: Gram-negative bacteria outer membrane.
• Components: Lipid A, core polysaccharide, O-antigen.
• Consequences: Lipid A is toxic.

Archaeal Cell Walls

• Composition: No peptidoglycan, but use pseudopeptidoglycan, proteins, or polysaccharides.

Capsules and Slime Layers

• Capsule: Thick, well-organized layer protecting against immune system and desiccation. Important virulence factor, preventing phagocytosis.
• Slime Layer: Loose, unorganized layer; helps with attachment and biofilm formation; less protective against phagocytosis.

External Structures (Fimbriae, Pili, Flagella)

• Fimbriae: Short, thin hair-like appendages for motility, DNA uptake, and attachment.
• Pili: Longer, thicker; sex pili enable conjugation (DNA transfer).
• Flagella: Long, helical structures for motility and swarming; monotrichous, lophotrichous, amphitrichous, peritrichous.

Flagellar Arrangement

• Flagella rotate like propellers, counterclockwise rotation for movement forward. Arrangement types: monotrichous, lophotrichous, amphitrichous, peritrichous.

Archaeal Cell Surface Structures

• S Layer Proteins: Provide rigidity.
• Cannulae: Tube-like structures for cell networks.
• Hami: Hook-like appendages for adhesion.
• Pili: Involved in Archaeal adhesion mechanisms.

Cell Inclusions and Gas Vesicles

• Inclusions: Storage bodies for nutrients.
• Gas Vesicles: Buoyancy in aquatic photosynthetic bacteria and archaea.

Endospores

• Formation: Dormant structures formed by bacteria; resistant to heat, radiation, and chemicals due to calcium, small acid-soluble proteins, dehydrated core, and a thick spore coat.
• Features: Marked differences in structure and resistance compared to vegetative cells.

Motility

• Gliding Motility: Smooth movements along surfaces.
• Chemotaxis: Movement towards or away from chemicals.
• Other Taxes: Phototaxis (light), magnetotaxis (magnetic fields).

Flagellar Structure

• Filament: Composed of flagellin.
• Hook: Connects filament to motor.
• Basal body: Anchors flagellum and provides rotation.
• Bacterial flagella grow at the tip, not the base.

Archaeal Flagella

• Differences: Thinner; more than one flagellin protein type; not hollow filament; hook and basal body less distinct; grow at the base, not the tip; more related to type IV pili.

Property Comparison (Bacteria vs. Archaea)

Viruses - Week 4

Basic Viral Components

• Components: Infectious agents, acellular, composed of nucleic acid (DNA or RNA), a protein coat (capsid), and sometimes an envelope (from host cell membrane).
• Nucleic Acid: For replication.
• Capsid: Made of protein subunits (capsomers) protecting genetic material.
• Envelope: Contains viral glycoproteins for host cell attachment.

Viral Classification

• Genome: DNA or RNA (single-stranded or double-stranded).
• Capsid Shape: Helical, icosahedral, or complex.
• Envelope Presence: Enveloped or naked.
• Replication Strategy: Lytic or lysogenic (bacteriophages).

Viral Replication Mechanism (Enveloped and Non-Enveloped)

1. Attachment: Virion ligand attaches to host receptor.
2. Entry: Genome enters cytoplasm (fusion, endocytosis, release).
3. Uncoating: Genome released from capsid.
4. Synthesis: DNA viruses typically use host machinery; RNA viruses use viral enzymes.
5. Assembly: New viral particles are assembled.
6. Release:

• Non-enveloped: Host cell lysis.
• Enveloped: Budding from host membrane.

Bacteriophages

• Definition: Viruses that infect bacteria.
• Infection: Attach to bacterial cell wall, inject material inside.
• Life Cycle: Lytic (destroy host cell), lysogenic (integrate into host DNA).

Lysogeny

• Definition: Temperate phages integrate their genome into the host's DNA without killing it.
• Prophage: Viral DNA in host DNA, replicated with host. Trigger can reactivate the viral cycle.
• Temperate Phage: Can choose between lytic and lysogenic cycles.

Bacteriophage Structure

• Head (capsid): Contains viral DNA/RNA.
• Tail Fibers: Attach to bacterial cells.
• Base Plate & Tail Sheath: Inject viral genome.

Viral Replication (Primary and Secondary)

• Primary Replication: Initial site of infection, entry to replication and virus production.
• Systemic Spread: Virus spreads through the body; e.g., bloodstream, lymphatic system.
• Secondary Replication: Spread to secondary tissues.

Viral Infections (Acute and Chronic)

• Acute: Rapid onset, short duration (flu, norovirus) lytic cycle.
• Chronic: Persistent with continuous replication (HIV) lysogenic cycle.

Eukarya

• Examples: Protists, fungi.
• Cell Walls: Diverse; cellulose, pectin (algae); cellulose, chitin, glucan (fungi).
• Mitochondrial Structure: Outer membrane (porins), inner membrane (cristae, ETC enzymes), matrix (ribosomes, mitochondrial DNA, TCA cycle enzymes).