Viruses: Structure, Replication, and Genomes

Basic Viral Structure

• All viruses possess two essential structures:

  • Genetic material (DNA or RNA)

  • Capsid (protein coat surrounding the genetic material)

• Optional structures include:

  • Envelope: A lipid membrane derived from the host cell, helps the virus evade the immune system by mimicking host membranes.

  • Spike proteins: Glycoproteins protruding from the envelope or capsid, function as attachment factors (fake cell receptors) to facilitate entry into host cells and increase virulence.

Viral Replication Pathways

• Primary method: Lytic phase

• Goals of viral replication:

  • Copy genetic material

  • Assemble new viral particles

• Lytic cycle steps:

  1. Attachment: Virus binds to host cell surface.

  2. Uncoating: Capsid is shed, viral genome enters host cell.

  3. Assembly: New viral genomes and proteins are synthesized and assembled into new virions.

  4. Lysis: Host cell bursts, releasing new viruses.

• Alternative pathway: Lysogenic cycle (Lysogenesis)

  • Viral genome integrates into host chromosome and replicates with the cell.

  • Allows virus to hide from immune system; can reactivate into lytic cycle under stress or immune suppression.

Viral Genomes and Replication Enzymes

• Possible viral genome types:

  • Double-stranded DNA (dsDNA)

  • Single-stranded (+) DNA

  • Single-stranded (−) DNA

  • Double-stranded RNA (dsRNA)

  • Single-stranded (+) RNA

  • Single-stranded (−) RNA

• Key enzymes:

  • DDDP: DNA-dependent DNA polymerase (makes DNA from DNA)

  • DDRP: DNA-dependent RNA polymerase (makes RNA from DNA)

  • RDRP: RNA-dependent RNA polymerase (makes RNA from RNA; not found in human cells, making it a good antiviral target)

  • RDDP: RNA-dependent DNA polymerase (reverse transcriptase; makes DNA from RNA, used by retroviruses)

Summary Table: Viral Genome Replication Pathways

Additional info: (+) RNA is equivalent to mRNA; only a few antibiotics are risk-free; RDRP is a unique viral target.

Antimicrobial Drugs: Mechanisms and Effects

Common Antibiotic Targets

• Cell wall synthesis (e.g., β-lactams like penicillin)

• Bacterial ribosomes (e.g., tetracycline, azithromycin, gentamycin)

• DNA replication (e.g., ciprofloxacin targets DNA gyrase)

• Metabolic pathways (e.g., sulfa drugs inhibit folate synthesis)

Mechanisms of Action and Side Effects

• Bacterial ribosomes: 70S; Eukaryotic ribosomes: 80S

• Mitochondria have prokaryotic-like ribosomes, so ribosomal inhibitors can affect mitochondria (e.g., hearing loss with gentamycin).

• DNA gyrase is unique to bacteria; humans use topoisomerase.

Antibiotic Risk Ranking (Lowest to Highest)

1. Penicillin

2. Tetracycline

3. Azithromycin

4. Gentamycin

5. Ciprofloxacin

6. Sulfa drugs

Plate Count Assays and Dilution Calculations

• Colony-forming units (cfu/ml) are calculated as:

$\text{cfu/ml} = \frac{\text{Number of colonies}}{\text{Volume plated (ml)} \times \text{Dilution factor}}$

• FDA convention: count plates with 30–300 colonies.

Examples:

• Milk sample: 54 colonies from 1 ml of 1:1000 dilution → 54,000 cfu/ml

• Well water: 83 colonies from 1 ml of 1:10,000 dilution → 830,000 cfu/ml

• Ocean water: 191 colonies from 0.1 ml of 1:100 dilution → 191,000 cfu/ml

Immunology: Innate and Adaptive Immunity

Overview of the Immune System

• Innate immunity: First line of defense, rapid but non-specific (e.g., skin, macrophages, dendritic cells, mast cells, complements, cytokines).

• Adaptive immunity: Slower but highly specific and effective (B-cells, T-cells, memory cells).

• Bone marrow: Produces pluripotent stem cells (can become any blood cell).

• Lymph nodes: Filter blood/dead cells, site of immune cell activation.

• Thymus: Site of T-cell maturation and selection.

Cells of the Immune System

Major Histocompatibility Complex (MHC)

• MHC I: Present on all nucleated cells (not RBCs); presents endogenous antigens to CD8+ (Killer T) cells.

• MHC II: Present on antigen-presenting cells (macrophages, dendritic cells); presents exogenous antigens to CD4+ (Helper T) cells.

Immune Response Steps

1. Pathogen entry (e.g., cut in skin)

2. Recognition by macrophages (via PAMPs/antigens such as peptidoglycan, LPS)

3. Phagocytosis and cytokine release

4. Activation of mast cells (histamine release, inflammation)

5. Complement activation (MAC formation, opsonization)

6. Recruitment of neutrophils, monocytes (diapedesis)

7. Activation of adaptive immunity (antigen presentation to T and B cells)

Antibodies (Immunoglobulins)

• Antibody regions: Variable (antigen specificity), Constant (antibody class)

Hypersensitivity Reactions

Types of Hypersensitivity

• Type I: Sensitization on first exposure, reaction on second (anaphylaxis: bronchoconstriction, hypotension, hives)

• Type II: Antibodies bind to cells (e.g., RBCs), complement activation, cell lysis (e.g., penicillin-induced anemia)

• Type III: Immune complexes deposit in capillaries, activate complement, cause inflammation (e.g., nephritis after strep)

• Type IV: T-cell mediated, delayed (24–72 hrs), no antibodies (e.g., poison ivy, latex allergy)

Key Terms and Concepts

• Opsonization: Antibody/complement coating enhances phagocytosis.

• Agglutination: Clumping of pathogens by antibodies, facilitates clearance.

• Antibody-Dependent Cell-Mediated Cytotoxicity (ADCC): Antibodies direct immune cells to kill target cells; safer than chemotherapy/radiation.

• Stevens-Johnson Syndrome: Severe allergic reaction affecting skin and mucous membranes.

• Diapedesis: Movement of white blood cells from blood vessels into tissues.

Example: Rh Incompatibility

• First pregnancy (Rh− mother, Rh+ baby): IgG antibodies form, but baby is usually unaffected.

• Second pregnancy: Maternal IgG attacks fetal RBCs, causing anemia and possible death.

Summary Table: Immune Cell Differentiation

Additional info: The immune system can be harmful if misdirected (autoimmunity, allergies). Memory cells provide rapid response upon re-exposure to pathogens. MHC presentation is crucial for self/non-self recognition and prevention of autoimmunity.