Microbiology Study Guide: Viruses, Antibiotics, Immune System, and Hypersensitivity

Viruses: Structure and Replication

Basic Viral Structure

Viruses are acellular infectious agents that require a host cell for replication. All viruses share certain structural features, while some possess additional components that enhance their infectivity.

• Genetic Material: Can be DNA or RNA, single or double stranded.

• Capsid: Protein shell that encases the genetic material.

• Optional Structures:

  • Envelope: Lipid membrane derived from the host cell, helps evade immune detection.

  • Spike Proteins: Glycoproteins that facilitate attachment and entry into host cells.

Example: Influenza virus has an envelope and spike proteins (hemagglutinin and neuraminidase).

Viral Replication Pathways

Viruses replicate by hijacking host cell machinery. The primary method is the lytic cycle, but some viruses utilize lysogenic (lysogenesis) pathways.

• Lytic Cycle:

  1. Attachment: Virus binds to host cell receptors.

  2. Uncoating: Capsid is shed, genetic material enters host cell.

  3. Assembly: Viral components are synthesized and assembled.

  4. Lysis: Host cell bursts, releasing new viral particles.

• Lysogenic Cycle: Viral genome integrates into host chromosome, replicates with cell, can reactivate to lytic cycle under stress.

Example: Herpes simplex virus can alternate between lytic and lysogenic cycles.

Viral Genome Types and Replication Enzymes

Viruses possess diverse genome types and utilize specific enzymes for replication.

• Genome Types:

  • Double stranded DNA (dsDNA)

  • Single stranded (+) DNA (ssDNA)

  • Single stranded (-) DNA (ssDNA)

  • Double stranded RNA (dsRNA)

  • Single stranded (+) RNA (ssRNA)

  • Single stranded (-) RNA (ssRNA)

• 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)

Example: Retroviruses (e.g., HIV) use RDDP to integrate into host genome.

Viral Replication Pathways by Genome Type

Each viral genome type follows a distinct replication pathway, utilizing host or viral enzymes.

• dsDNA Virus: Uses DDRP to make mRNA, DDDP to replicate DNA.

• ss(+)DNA Virus: DDDP makes (-) DNA, DDRP makes (+) RNA.

• ss(-)DNA Virus: DDRP makes mRNA, DDDP makes (+) DNA.

• ss(+)RNA Virus: Ribosome reads (+) RNA, RDRP makes (-) RNA.

• ss(-)RNA Virus: RDRP (brought by virus) makes (+) RNA.

• dsRNA Virus: RDRP copies RNA.

• ss(+)RNA Retrovirus: RDDP makes (-) DNA, DDDP makes (+) DNA, integrates into host genome.

Example: HIV is a ss(+)RNA retrovirus.

Antibiotics: Mechanisms and Side Effects

Common Antibiotic Targets

Antibiotics are designed to target structures unique to bacteria, minimizing harm to human cells.

• Cell Wall: Peptidoglycan synthesis (e.g., beta-lactams)

• Bacterial Ribosomes: 70S ribosomes (e.g., tetracycline, azithromycin, gentamycin)

• DNA Replication: DNA gyrase (e.g., ciprofloxacin)

• Metabolic Pathways: Folate synthesis (e.g., sulfa drugs)

Beta-Lactam Antibiotics

• Example: Penicillin

• Mechanism: Inhibits peptidoglycan synthesis, effective against Gram-positive bacteria.

• Side Effects: Allergic reactions, upset GI tract due to loss of beneficial gut bacteria.

Ribosomal Inhibitors

• Bacterial Ribosome Size: 70S (30S + 50S subunits)

• Eukaryotic Ribosome Size: 80S

• Examples:

  • Tetracycline: Targets 30S; side effect: brown teeth (binds calcium in developing teeth).

  • Azithromycin: Targets 50S; side effect: blocks Ca+ channels, risk of arrhythmia.

  • Gentamycin: Targets 30S; side effects: nephrotoxicity, hearing loss (targets mitochondria in ears).

Additional info: Mitochondria evolved from prokaryotic ancestors, so ribosomal inhibitors may affect mitochondrial function.

DNA Replication Inhibitors

• Example: Ciprofloxacin

• Mechanism: Inhibits DNA gyrase (bacterial enzyme); humans use topoisomerase.

• Side Effects: Tendon rupture, agitation, seizures (GABA receptor blockage).

Metabolic Inhibitors

• Example: Sulfa drugs (e.g., trimethoprim)

• Mechanism: Inhibits folate synthesis (not used by humans).

• Side Effects: Stevens-Johnson Syndrome (severe skin reaction), arrhythmia.

Antibiotic Risk Ranking

Antibiotic	Risk Level (Low to High)
Penicillin	Lowest
Tetracycline	Low
Azithromycin	Moderate
Gentamycin	High
Ciprofloxacin	Higher
Sulfa drugs	Highest

Microbial Quantification: Plate Count Assays

Plate Count Calculations

Plate count assays estimate the number of viable bacteria in a sample using serial dilutions and colony counts.

• Formula: $\text{CFU/ml} = \frac{\text{Number of colonies}}{\text{Volume plated (ml)} \times \text{Dilution factor}}$

• FDA Convention: Count plates with 30-300 colonies for accuracy.

Example: 1 ml of 1:103 dilution plated, 54 colonies observed: $\text{CFU/ml} = 54 \times 10^3 = 54,000$

Immune System: Structure and Function

Innate vs. Adaptive Immunity

The immune system protects against pathogens and environmental threats. It is divided into innate (rapid, nonspecific) and adaptive (specific, memory-based) components.

• Innate Immunity: First line of defense, rapid response (e.g., skin, macrophages, dendritic cells, mast cells, complements, cytokines).

• Adaptive Immunity: More effective, slower initial response, includes B-cells, T-killer cells, memory cells.

Immune System Organs and Cells

• Bone Marrow: Produces pluripotent stem cells.

• Lymph Nodes: Filter blood, house immune cells.

• Thymus: Site of T-cell maturation.

Innate Immune Cells

• Macrophages: Antigen-presenting cells (APCs), phagocytosis, inflammation.

• Dendritic Cells: APCs, activate naive T cells.

• Mast Cells: Release histamine, cause vasodilation.

• Complements: Form membrane attack complex (MAC), lyse bacteria.

• Cytokines: Promote inflammation and fever.

Adaptive Immune Cells

• B-cells: Produce antibodies.

• T-killer cells (CD8): Destroy infected cells.

• Helper T-cells (CD4): Link innate and adaptive immunity.

• Memory Cells: Provide rapid response upon re-exposure.

Immune Cell Development

Stem Cell	Progenitor	Cell Types	System
Pluripotent Stem Cell	Myeloid	Erythroblast, Megakaryoblast, Myeloblast, Immature Dendritic	Innate
Pluripotent Stem Cell	Lymphoid	Immature T-cell, Immature B-cell, Natural Killer cell	Adaptive

Major Histocompatibility Complex (MHC)

• MHC I: All nucleated cells (except RBCs).

• MHC II: Macrophages and dendritic cells.

Immune Response Steps

• APCs present antigens to Helper T-cells.

• B-cells and T-cells double-check antigen presence before launching response.

• Plasma cells and memory cells are produced.

Antibody Structure and Function

Antibody Types and Functions

Antibody	Structure	Function
IgM	Pentamer	Agglutination, complement activation
IgD	Monomer	Binds membranes, function unclear
IgE	Monomer	Histamine release, allergy response
IgA	Dimer	Agglutination, anti-viral
IgG	Monomer	Opsonization, agglutination, crosses placenta, neutralizes toxins

Antibody Regions

• Variable Region: Determines antigen specificity.

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

Hypersensitivity Reactions

Types of Hypersensitivity

Type	Mechanism	Antibody/Cell	Onset	Examples
I	IgE-mediated, mast cell degranulation	Antibody	Immediate	Allergies, anaphylaxis
II	IgG/IgM-mediated, complement activation	Antibody	Immediate	Hemolytic anemia, Rh incompatibility
III	Immune complex deposition	Antibody	Immediate	Serum sickness, nephritis
IV	Cell-mediated (T-cells, macrophages)	Cell	Delayed (24-72 hrs)	Contact dermatitis, TB test, poison ivy

Type I Hypersensitivity (Allergy)

• First exposure: APC presents antigen, B-cell produces IgE, IgE binds mast cells.

• Second exposure: Antigen binds mast cell, degranulation, histamine release, anaphylaxis.

• Symptoms: Bronchoconstriction, hypotension, hives.

Type II Hypersensitivity (Cytotoxic)

• Antibodies bind to cell membranes (RBCs, platelets), complement activation.

• Examples: Penicillin-induced anemia, Rh incompatibility, thrombocytopenia.

Type III Hypersensitivity (Immune Complex)

• Antigen-antibody complexes deposit in tissues, activate complement.

• Examples: Antivenoms, strep-induced nephritis, dust-induced lung inflammation.

Type IV Hypersensitivity (Delayed, Cell-Mediated)

• APC presents antigen to Helper T-cell, activates cytotoxic T-cells and macrophages.

• Examples: Poison ivy, TB skin test, latex allergy.

• Treatment: Steroids.

Key Terms and Concepts

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

• Opsonization: Antibody/complement binding to antigens, promotes phagocytosis.

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

• Pluripotent Stem Cell: Can differentiate into any blood cell type.

• MAC (Membrane Attack Complex): Complement proteins that lyse bacteria.

• Antibody Dependent Cell Mediated Cytotoxicity: Safer alternative to chemotherapy/radiation for targeting infected cells.