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 (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 and increase virulence.

Viral Replication Pathways

• Primary method: Lytic cycle

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

1. Attachment: Virus binds to host cell surface.

2. Uncoating: Viral capsid is shed, 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.

• Lysogenic pathway (Lysogenesis): Viral genome integrates into host chromosome and replicates with the cell. This allows the virus to remain dormant and evade the immune system until triggered to re-enter the lytic cycle.

Viral Genomes and Replication Enzymes

• Viral genomes can be:

  • 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)

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

Summary Table: Viral Genome Types and Replication Enzymes

Genome Type	Key Enzyme(s)	Replication Pathway
dsDNA	DDDP, DDRP	DNA → mRNA → Protein; DNA copied for new virions
ss(+) DNA	DDDP, DDRP	(+) DNA → (-) DNA → mRNA → Protein
ss(-) DNA	DDRP, DDDP	(-) DNA → mRNA → Protein; DDDP for DNA synthesis
dsRNA	RDRP	RNA → Protein; RDRP copies RNA
ss(+) RNA	RDRP	(+) RNA → Protein; RDRP makes (-) RNA → (+) RNA
ss(-) RNA	RDRP (in capsid)	(-) RNA → (+) RNA → Protein; RDRP makes more (-) RNA
ss(+) RNA (retrovirus)	RDDP, DDDP	(+) RNA → (-) DNA → dsDNA → Integration → mRNA → Protein

• Note: RDRP is an ideal antiviral target because it is not present in human cells.

Antimicrobial Drugs: Mechanisms and Side 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)

• Metabolic pathways (e.g., sulfa drugs like trimethoprim)

Mechanisms of Action and Examples

• β-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: brown teeth in children (binds calcium in developing teeth).

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

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

• DNA replication inhibitors (e.g., ciprofloxacin): Inhibit DNA gyrase (bacterial topoisomerase); 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 Key Features

Class	Target	Example	Side Effects
β-lactams	Cell wall	Penicillin	Allergy, GI upset
Tetracyclines	30S ribosome	Tetracycline	Brown teeth in children
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

• Note: Bacterial ribosomes (70S) differ from eukaryotic ribosomes (80S), but mitochondrial ribosomes are similar to bacterial ones, leading to possible side effects.

Antibiotic Risk Ranking (Lowest to Highest)

1. Penicillin

2. Tetracycline

3. Azithromycin

4. Gentamycin

5. Ciprofloxacin

6. Sulfa drugs

Antibiotic Development Challenges

• Pharmaceutical companies are reluctant to develop new antibiotics due to limited profitability and short shelf life compared to chronic medications.

Microbial Growth: Plate Count Assays and Calculations

Plate Count Assay

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

• Involves serial dilution and plating a known volume on agar plates.

• Colony-forming units (CFU) are counted after incubation.

Key Calculation

• CFU/mL = (Number of colonies × Dilution factor) / Volume plated (in mL)

Examples

• 54 colonies from 1 mL of 1:1000 dilution: $54 \times 1000 = 54,000$ CFU/mL

• 83 colonies from 1 mL of 1:10,000 dilution: $83 \times 10,000 = 830,000$ CFU/mL

• 191 colonies from 0.1 mL of 1:100 dilution: $191 \times 100 \times 10 = 191,000$ CFU/mL

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

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; involves B cells (antibody production), T cells (cell-mediated immunity), and memory cells.

Key Immune Cells and Functions

• Macrophages: Phagocytose pathogens, present antigens to other immune cells.

• Dendritic cells: Antigen-presenting cells (APCs), activate naive T cells.

• Mast cells: Release histamine, cause inflammation and allergic responses.

• Complement system: Forms membrane attack complex (MAC) to lyse bacteria.

• Cytokines: Mediate inflammation and fever.

• B cells: Produce antibodies, present antigens to T cells.

• T-killer (cytotoxic) cells: Destroy infected or abnormal cells.

• Helper T cells (CD4): Coordinate immune response, link innate and adaptive immunity.

• Natural killer cells: Kill tumor and infected cells without prior activation.

Immune Cell Development

• Pluripotent stem cells in bone marrow differentiate into myeloid (innate) or lymphoid (adaptive) progenitors.

• Myeloid progenitors: Erythroblasts (→ RBCs), megakaryoblasts (→ platelets), myeloblasts (→ neutrophils, monocytes, eosinophils, basophils), immature dendritic cells.

• Lymphoid progenitors: Immature T cells (→ thymus), immature B cells (→ lymph nodes), natural killer cells.

Summary Table: Immune Cell Lineages

Progenitor	Cell Types	Main Function
Myeloid	RBCs, platelets, neutrophils, monocytes/macrophages, eosinophils, basophils, dendritic cells	Innate immunity, oxygen transport, clotting
Lymphoid	B cells, T cells, natural killer cells	Adaptive immunity, cytotoxicity

Major Histocompatibility Complex (MHC)

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

• MHC II: Present on APCs (macrophages, dendritic cells); presents exogenous antigens to helper T cells.

Antibody Structure and Function

• Antibodies (immunoglobulins, Ig) are proteins with two regions:

  • Variable region: Determines antigen specificity (down to the amino acid level).

  • Constant region: Determines antibody class (IgG, IgM, etc.).

Summary Table: Antibody Classes

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

• IgG is the only antibody that crosses the placenta.

Hypersensitivity Reactions

Types of Hypersensitivity

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

• Type II (Antibody-dependent, IgG/IgM): Cytotoxic; antibodies bind to cell surfaces (e.g., RBCs), activate complement, cause 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 involved (e.g., contact dermatitis, TB skin test, poison ivy).

Summary Table: Hypersensitivity Types

Type	Immune Mechanism	Examples
I	IgE, mast cells	Allergies, anaphylaxis
II	IgG/IgM, complement	Hemolytic anemia, Rh disease
III	Immune complexes	Serum sickness, nephritis
IV	T cells, macrophages	Contact dermatitis, TB test

Key Features and Examples

• Type I: Requires sensitization; second exposure triggers mast cell degranulation, histamine release, and anaphylaxis (bronchoconstriction, hypotension, hives).

• Type II: Antibodies bind to cells (e.g., RBCs, platelets), activate complement, cause cell lysis (e.g., penicillin-induced hemolysis, Rh incompatibility in pregnancy).

• Type III: Immune complexes deposit in tissues (e.g., kidneys, lungs), activate complement, cause inflammation (e.g., nephritis after strep throat, dust-induced alveolitis).

• Type IV: Delayed (24–72 hours); T cells and macrophages attack antigen-primed cells (e.g., poison ivy, latex allergy); can occur on first exposure.

Key Terms and Concepts

• Opsonization: Process by which antibodies or complement proteins enhance phagocytosis of pathogens.

• Agglutination: Clumping of pathogens by antibodies, facilitating phagocytosis.

• Antibody-dependent cell-mediated cytotoxicity (ADCC): Immune cells kill antibody-coated target cells; considered safer than chemotherapy or radiation for some therapies.

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

• PAMP (Pathogen-Associated Molecular Pattern): Molecules on pathogens recognized by immune cells (e.g., peptidoglycan, LPS).

Additional info: These notes integrate and expand upon the provided material, ensuring coverage of viral structure and replication, antimicrobial drugs, microbial growth assays, and immunology, including hypersensitivity reactions, as relevant to a college-level microbiology course.