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)

  • 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 cycle

• Goals of viral replication:

  • Copy genetic material

  • Assemble new viral particles

• Lytic cycle steps:

  1. Attachment: Virus binds to host cell surface.

  2. Uncoating: Viral capsid is removed, and genetic material enters the 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 the virus to remain dormant and evade the immune system.

  • Can switch to the lytic cycle if environmental conditions change or the immune system weakens.

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

Genome Type	Key Enzymes	Replication Pathway
dsDNA	DDDP, DDRP	DNA → mRNA (via DDRP) → Protein; DNA copied by DDDP
ss(+) DNA	DDDP, DDRP	(+) DNA → (−) DNA (by DDDP) → mRNA (by DDRP) → Protein
ss(−) DNA	DDRP, DDDP	(−) DNA → mRNA (by DDRP) → Protein; DDDP makes (+) DNA
dsRNA	RDRP	(+) RNA → Protein; RDRP copies RNA
ss(+) RNA	RDRP	(+) RNA → Protein; RDRP makes (−) RNA → (+) RNA
ss(−) RNA	RDRP (brought by virus)	(−) RNA → (+) RNA (by RDRP) → Protein; (+) RNA → (−) RNA
ss(+) RNA (retrovirus)	RDDP, DDDP	(+) RNA → (−) DNA (by RDDP) → (+) DNA (by DDDP) → Integration into host genome

Additional info: RDRP is a prime antiviral drug target because it is not present in human cells.

Antimicrobial Drugs: Mechanisms and Effects

Antibiotic Targets and Examples

• Common bacterial targets:

  • Cell wall (e.g., peptidoglycan synthesis)

  • Bacterial ribosomes (protein synthesis)

  • DNA replication enzymes

  • Metabolic pathways (e.g., folate synthesis)

• Examples:

  • β-lactams (e.g., penicillin): Block peptidoglycan synthesis; effective mainly against Gram-positive bacteria; side effects include allergic reactions and GI upset.

  • Tetracycline: Inhibits 30S ribosomal subunit; can cause brown teeth in children due to calcium binding.

  • Azithromycin: Inhibits 50S ribosomal subunit; may cause heart arrhythmias by blocking Ca2+ channels.

  • Gentamycin: Inhibits 30S subunit; side effects include nephrotoxicity and hearing loss (due to mitochondrial targeting).

  • Ciprofloxacin: Inhibits DNA gyrase (bacterial topoisomerase); side effects include tendon rupture and seizures.

  • Sulfa drugs (e.g., trimethoprim): Inhibit folate synthesis; side effects include Stevens-Johnson Syndrome and arrhythmia.

Ribosome Differences and Clinical Implications

• Bacterial ribosomes: 70S

• Eukaryotic ribosomes: 80S

• Mitochondria have ribosomes similar to prokaryotes, so ribosomal inhibitors can affect mitochondrial function (e.g., ATP synthesis disruption).

Antibiotic Risk Ranking (Lowest to Highest)

Drug	Relative Risk
Penicillin	Lowest
Tetracycline	Low
Azithromycin	Moderate
Gentamycin	High
Ciprofloxacin	Higher
Sulfa drugs	Highest

Antibiotic Selection and Resistance

• Drug choice depends on infection severity and risk-benefit analysis.

• Antibiotic development is limited due to short-term use and resistance concerns.

Microbial Growth: Plate Count Assays and Calculations

Plate Count Assay Calculations

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

• Procedure involves serial dilution, plating, and colony counting.

• Calculation formula:

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

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

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, mast cells, complements, cytokines).

• Adaptive immunity: Slower initial response, highly specific, and has memory (e.g., B cells, T cells, memory cells).

• Bone marrow: Produces pluripotent stem cells for all blood and immune cells.

• Lymph nodes: Filter blood and dead cells; sites for immune cell activation.

• Thymus: Site of T cell maturation and selection.

Cells of the Immune System

Cell Type	Origin	Function
Macrophage	Myeloid	Phagocytosis, antigen presentation
Dendritic cell	Myeloid/Lymphoid	Antigen presentation, activate naive T cells
Mast cell	Myeloid	Histamine release, inflammation
Neutrophil	Myeloid	Phagocytosis, first responder
Eosinophil	Myeloid	Attack parasites
Basophil	Myeloid	Inflammation, allergic response
B cell	Lymphoid	Antibody production
T cell (Helper/Killer)	Lymphoid	Coordinate/adaptive response, cytotoxicity
Natural Killer cell	Lymphoid	Kill infected/tumor cells

Major Histocompatibility Complex (MHC)

• MHC I: Present on all nucleated cells (except RBCs); presents endogenous antigens to cytotoxic T cells (CD8+).

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

Immune Cell Development

• Pluripotent stem cells (in bone marrow) differentiate into:

  • Myeloid progenitors: Give rise to erythrocytes, platelets, granulocytes, monocytes, dendritic cells.

  • Lymphoid progenitors: Give rise to B cells, T cells, and natural killer cells.

• T cell selection in thymus: 95% of immature T cells undergo apoptosis if they cannot distinguish self from non-self.

Phagocytosis and Inflammation

• Phagocytes (macrophages, neutrophils, dendritic cells) recognize PAMPs (Pathogen-Associated Molecular Patterns) such as peptidoglycan, lipoteichoic acid, and LPS.

• Phagocytosis triggers cytokine release, activating mast cells and complement system (MAC formation).

• Inflammation symptoms: Edema, redness, heat, pain (due to increased blood flow and vascular permeability).

• Diapedesis: White blood cells migrate from blood vessels to tissues.

Antibodies (Immunoglobulins)

Structure and Types

• All antibodies have a variable region (antigen specificity) and a constant region (determines antibody class).

• Types:

  • IgM: Pentamer; main agglutinator, activates complement.

  • IgD: Monomer; function not fully understood, binds to membranes.

  • IgE: Monomer; triggers histamine release, involved in allergies.

  • IgA: Dimer; agglutination, antiviral properties, found in mucosal areas.

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

Antibody Functions

• Agglutination: Clumping of pathogens for easier phagocytosis (mainly IgM, IgA, IgG).

• Opsonization: Enhances phagocytosis by marking antigens for immune cells.

• Neutralization: Blocks toxins and pathogens from interacting with host cells.

• ADCC (Antibody-Dependent Cell-Mediated Cytotoxicity): Antibodies recruit immune cells to kill target cells.

Hypersensitivity Reactions

Types of Hypersensitivity

Type	Mechanism	Antibody/Cell Involved	Examples
I (Immediate)	IgE-mediated mast cell degranulation	IgE	Allergies, anaphylaxis
II (Cytotoxic)	Antibody binds to cell surface antigen, complement activation	IgG, IgM	Hemolytic anemia, thrombocytopenia, Rh incompatibility
III (Immune Complex)	Antigen-antibody complexes deposit in tissues	IgG, IgM	Serum sickness, nephritis
IV (Delayed)	T cell-mediated cytotoxicity	T cells	Contact dermatitis, TB test, poison ivy

Key Features

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

• Type I: Requires sensitization (first exposure), reaction on second exposure (e.g., anaphylaxis).

• Type II: Antibodies target cells (e.g., RBCs, platelets), leading to cell lysis.

• Type III: Immune complexes deposit in tissues, causing inflammation (e.g., nephritis, lung inflammation).

• Type IV: Delayed response (24–72 hours), T cell-mediated destruction of host cells (e.g., poison ivy, latex allergy).

Clinical Examples

• Type I: Allergic reactions, anaphylaxis (bronchoconstriction, hypotension, hives).

• Type II: Hemolytic anemia (penicillin-induced), thrombocytopenia (quinine-induced), endocarditis (strep-induced), Rh incompatibility in pregnancy.

• Type III: Serum sickness, nephritis after strep, hypersensitivity pneumonitis (dust exposure).

• Type IV: Contact dermatitis, TB skin test, poison ivy reaction.

Immune System Disorders and Treatments

• Autoimmune diseases can result from failure of thymic deletion (e.g., diabetes, multiple sclerosis).

• Type IV hypersensitivity is treated with steroids.

Summary

• Viruses have diverse structures and replication strategies, with unique enzymes as drug targets.

• Antibiotics target bacterial structures and processes, but have varying risks and side effects.

• The immune system is complex, with innate and adaptive arms, and can malfunction to cause hypersensitivity or autoimmune disease.

• Understanding these mechanisms is crucial for microbiology, immunology, and clinical practice.