Comprehensive Study Notes: Viruses, Antimicrobial Drugs, and Immunology

Viruses: Structure, Replication, and Genomes

Basic Viral Structure

• All viruses possess two essential structures: genetic material (DNA or RNA) and a capsid (protein coat).

• Optional structures include an envelope (a lipid membrane derived from the host cell) and spike proteins (glycoproteins protruding from the envelope).

• Viral envelope: Mimics the host cell membrane, helping the virus evade the immune system.

• Spike proteins: Function as attachment factors, acting as fake cell receptors to facilitate viral entry into host cells. Both envelope and spikes increase viral virulence.

Viral Replication Pathways

• Primary method: Lytic phase—virus rapidly replicates and destroys the host cell.

• Goals of a virus: (1) Copy genetic material, (2) Assemble new viral particles.

1. Attachment: Virus binds to host cell surface.

2. Uncoating: Viral capsid is shed; genetic material enters host cell.

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

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

• Secondary pathway: Lysogenesis—viral genome integrates into host chromosome and replicates with the cell, allowing immune evasion and survival during unfavorable conditions. Virus can later reactivate and enter the lytic cycle.

Viral Genomes and Replication Enzymes

• Possible viral genome types: dsDNA, ss(+)DNA, ss(-)DNA, dsRNA, ss(+)RNA, ss(-)RNA.

• Key enzymes:

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

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

  • RDRP (RNA-dependent RNA polymerase): RNA from RNA (not found in human cells; ideal antiviral target)

  • RDDP (RNA-dependent DNA polymerase): DNA from RNA (reverse transcriptase)

Summary Table: Viral Genome Replication Pathways

Genome Type	Key Steps	Enzymes Used
dsDNA	Transcription to mRNA, translation, genome replication	DDRP, DDDP
ss(+)DNA	Converted to dsDNA, then as above	DDDP, DDRP
ss(-)DNA	Converted to dsDNA, then as above	DDDP, DDRP
dsRNA	Transcription to mRNA, translation, genome replication	RDRP
ss(+)RNA	Acts as mRNA, translated, replicated via (-)RNA intermediate	RDRP
ss(-)RNA	Converted to (+)RNA (mRNA), then translated	RDRP (brought by virus)
ss(+)RNA (retrovirus)	Reverse transcription to DNA, integration, transcription	RDDP, DDDP

• (+) RNA is equivalent to mRNA.

• Human cells do not convert RNA to RNA; viruses must bring or encode RDRP.

Antimicrobial Drugs: Mechanisms and Effects

Antibiotic Targets and Examples

• Common bacterial targets: Cell wall, ribosomes, DNA replication machinery, metabolic pathways.

• B-lactams (e.g., penicillin): Inhibit peptidoglycan synthesis; effective mainly against Gram-positive bacteria. Side effects: allergic reactions, GI upset due to loss of normal flora.

• Ribosomal inhibitors:

  • Tetracycline: Targets 30S subunit; side effect—teeth discoloration (especially in children).

  • Azithromycin: Targets 50S subunit; side effect—blocks Ca2+ channels, may cause arrhythmia.

  • Gentamycin: Targets 30S subunit; side effects—nephrotoxicity, hearing loss (due to mitochondrial effects).

• DNA replication inhibitors: (e.g., Ciprofloxacin) Target DNA gyrase (bacterial enzyme); side effects—tendon rupture, agitation, seizures.

• Metabolic inhibitors: (e.g., Sulfa drugs, trimethoprim) Inhibit folate synthesis (not used by humans); side effects—Stevens-Johnson Syndrome, arrhythmia.

Summary Table: Antibiotic Classes and Effects

Class	Target	Example	Side Effects
B-lactams	Cell wall	Penicillin	Allergy, GI upset
Tetracyclines	30S ribosome	Tetracycline	Teeth discoloration
Macrolides	50S ribosome	Azithromycin	Arrhythmia
Aminoglycosides	30S ribosome	Gentamycin	Nephrotoxicity, hearing loss
Fluoroquinolones	DNA gyrase	Ciprofloxacin	Tendon rupture, seizures
Sulfa drugs	Folate synthesis	Trimethoprim	Stevens-Johnson Syndrome

• Antibiotic risk ranking (lowest to highest): Penicillin, Tetracycline, Azithromycin, Gentamycin, Ciprofloxacin, Sulfa drugs.

• Doctors choose antibiotics based on infection severity and risk-benefit analysis.

Antibiotic Resistance and Development

• Antibiotic development is limited due to short-term use and lower profitability compared to chronic medications.

• All antibiotics carry some risk of side effects.

Microbial Growth and Quantification

Plate Count Assays

• Used to estimate the number of viable bacteria in a sample.

• Procedure: Serial dilution, plating, colony counting.

• Calculation: CFU/ml = (Number of colonies) × (1/dilution factor) × (1/volume plated in ml)

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

Example Calculations

• 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, complement, cytokines).

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

• Bone marrow: Produces pluripotent stem cells for all blood cell types.

• Lymph nodes: Filter blood and house immune cells; swell during infection due to immune activity.

• Thymus: Site of T-cell maturation.

Cells of the Immune System

• Innate immune cells: Macrophages (APCs), dendritic cells (APCs), mast cells (histamine release), neutrophils (phagocytosis), eosinophils (attack parasites), basophils (inflammation/allergy), complements (form MAC).

• Adaptive immune cells: B-cells (antibody production), T-killer cells (cytotoxic), helper T-cells (coordinate response), memory cells (immunological memory), natural killer cells (kill infected/tumor cells).

Summary Table: Immune Cell Lineages

Progenitor	Cell Types	Function
Myeloid	Erythrocytes, megakaryocytes (platelets), myeloblasts (neutrophils, monocytes, eosinophils, basophils), immature dendritic cells	Innate immunity, oxygen transport, clotting
Lymphoid	B-cells, T-cells, natural killer cells	Adaptive immunity

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

Major Histocompatibility Complex (MHC)

• MHC I: Present on all nucleated cells; presents endogenous antigens.

• MHC II: Present on macrophages and dendritic cells; presents exogenous antigens to helper T-cells.

• Thymic selection: T-cells that cannot distinguish self from non-self undergo apoptosis (thymic deletion).

Antibody Structure and Function

• Regions: Variable (antigen specificity), constant (antibody class).

• Classes:

  • IgM: Pentamer; agglutination, complement activation.

  • IgD: Membrane-bound; function unclear.

  • IgE: Monomer; binds mast cells, triggers histamine release (allergy).

  • IgA: Dimer; agglutination, antiviral properties.

  • IgG: Monomer; most abundant, crosses placenta, opsonization, neutralizes toxins.

Summary Table: Antibody Classes

Class	Structure	Main Functions
IgM	Pentamer	Agglutination, complement activation
IgD	Monomer	Membrane-bound, unclear function
IgE	Monomer	Histamine release, allergy
IgA	Dimer	Agglutination, antiviral
IgG	Monomer	Opsonization, neutralization, crosses placenta

Hypersensitivity Reactions

• Type I (Immediate, IgE-mediated): Allergy, anaphylaxis; mast cell degranulation, histamine and leukotriene release.

• Type II (Antibody-dependent): IgG/IgM bind to cell surfaces (e.g., RBCs, platelets); complement activation, cell lysis (e.g., hemolytic anemia, thrombocytopenia, Rh incompatibility).

• Type III (Immune complex-mediated): Antigen-antibody complexes deposit in tissues, activate complement, cause inflammation (e.g., serum sickness, nephritis).

• Type IV (Delayed, cell-mediated): T-cell mediated, no antibodies; contact dermatitis, TB skin test, poison ivy. Occurs 24–72 hours after exposure.

Summary Table: Hypersensitivity Types

Type	Mechanism	Antibody Involved	Examples
I	IgE, mast cell degranulation	IgE	Allergy, anaphylaxis
II	IgG/IgM bind cells, complement	IgG, IgM	Hemolytic anemia, Rh disease
III	Immune complex deposition	IgG, IgM	Serum sickness, nephritis
IV	T-cell mediated	None	Contact dermatitis, TB test

• Type I, II, III: Antibody-mediated; Type IV: Cell-mediated (no antibodies).

• Type I, II, III: Require sensitization (first exposure); Type IV: Can occur on first exposure.

Key Immunological Processes

• Opsonization: Antibodies or complement coat pathogens, enhancing phagocytosis.

• Antibody-dependent cell-mediated cytotoxicity (ADCC): Antibodies flag cells for destruction by immune cells (safer than chemotherapy/radiation).

• Agglutination: Antibodies cause pathogens to clump, facilitating phagocytosis.

Additional info:

• Many immune disorders (e.g., autoimmune diseases) result from failures in self/non-self recognition during thymic selection.

• Memory cells provide rapid and robust responses upon re-exposure to pathogens, forming the basis for vaccination.