BIO 1570 Microbiology Exam 2 Study Guide: Microbial Genetics, Virology, and Epidemiology

1Microbial Genetics & Molecular Biology

Fundamentals of DNA Structure & Replication

Understanding DNA structure and replication is foundational to microbial genetics. DNA encodes genetic information and is replicated prior to cell division.

• Gene: A specific sequence of nucleotides in DNA that codes for a functional product (polypeptide/protein or functional RNA).

• DNA Double Helix: Two antiparallel strands (one 5' to 3', one 3' to 5').

• Base Pairing: Adenine (A) pairs with Thymine (T) via 2 hydrogen bonds; Guanine (G) pairs with Cytosine (C) via 3 hydrogen bonds.

• Sugar-Phosphate Backbone: Nitrogenous bases attach to deoxyribose at the 1' carbon; phosphates link the 3' and 5' carbons.

Enzyme	Biological Function	Key Features / Notes
DNA Polymerase	Synthesizes new DNA strands 5' to 3'	Requires template and free 3'-OH primer
RNA Polymerase	Synthesizes RNA from DNA template	Functions during transcription; does not use RNA as template
DNA Ligase	Joins DNA fragments	Creates covalent phosphodiester bonds
DNA Gyrase	Relaxes supercoiling ahead of fork	Type II topoisomerase; target of quinolone antibiotics
Transposase	Cuts and reseals DNA at insertion sequences	Enables transposon movement; leaves sticky ends
Helicase	Unwinds double-stranded DNA	Breaks hydrogen bonds at replication fork

Transcription, Translation, and the Genetic Code

Gene expression involves transcription (DNA to RNA) and translation (RNA to protein), governed by the genetic code.

• Transcription: RNA Polymerase reads the template (antisense) DNA strand 3' to 5', synthesizing mRNA 5' to 3'.

• Codon: Triplet of mRNA nucleotides coding for a specific amino acid.

• Anticodon: Triplet of tRNA nucleotides complementary to an mRNA codon.

• Prokaryotic vs. Eukaryotic Protein Synthesis:

  • Prokaryotes: Transcription and translation are coupled in the cytoplasm; initiator amino acid is Formylmethionine (fMet).

  • Eukaryotes: Transcription in nucleus; pre-mRNA processed (introns removed, exons spliced, 5' cap, 3' poly-A tail); initiator is Methionine (Met).

Example Problem:

• DNA Template: 3'-ATT ACG CTT TGC-5'

• mRNA Transcript: 5'-UAA UGC GAA ACG-3'

• Translation: 5'-UAA is a stop codon; translation halts immediately.

Gene Regulation, Metabolic Pathways, & Operons

Bacteria regulate gene expression using operons, allowing efficient adaptation to environmental changes.

• Inducible Operons (e.g., lac operon): Default OFF; turned ON when inducer inactivates repressor.

• Repressible Operons (e.g., trp operon): Default ON; turned OFF when corepressor (end-product) activates repressor.

• Catabolite Repression (Glucose Effect): High glucose lowers cAMP, inactivating CAP and reducing lac operon transcription.

• Allosteric Regulation & Feedback Inhibition: End-product binds allosteric site of early enzyme, inhibiting pathway without altering gene expression.

Mechanisms of Horizontal Gene Transfer (HGT) & Recombination

HGT allows bacteria to acquire new genetic traits, contributing to diversity and adaptation.

• Conjugation: DNA transfer via direct cell contact (sex pilus).

  • F+ x F-: F+ donor transfers F plasmid; both become F+.

  • Hfr: F factor integrated into chromosome; chromosomal genes transferred, recipient usually remains F-.

• Transformation: Uptake of free extracellular DNA by competent cells.

• Transduction: Bacteriophage-mediated DNA transfer between bacteria.

• Replica Plating: Technique to isolate mutants (e.g., auxotrophs, antibiotic resistance) by transferring colonies to selective media.

Virology

General Characteristics & Classification

Viruses are unique infectious agents, distinct from cellular life forms.

• Acellular: Lack plasma membranes, cytoplasm, and ribosomes; obligate intracellular parasites.

• Genome: Contains either DNA or RNA (never both), surrounded by a protein coat.

• Host Range & Tropism: Determined by specific host cell receptors.

• Nomenclature: Uses family (-viridae), genus (-virus), and common names; binomial nomenclature is not used.

Viral Structure & Morphology

• Capsid: Protein shell made of capsomeres; determines symmetry (helical, polyhedral, complex).

• Envelope: Lipid membrane acquired from host during budding; contains viral glycoprotein spikes.

• Complex Viruses: Additional structures (e.g., bacteriophage tails, base plates, fibers).

Multiplication Cycles & Replication Strategies

• Lytic Cycle (Phages): Attachment → Penetration → Biosynthesis → Maturation → Lysis (host cell dies).

• Lysogenic Cycle (Phages): Viral DNA integrates into host genome as a prophage; can later enter lytic cycle.

• Animal Virus Multiplication:

  1. Attachment

  2. Penetration (endocytosis or fusion)

  3. Uncoating

  4. Biosynthesis

  5. Maturation

  6. Release (budding for enveloped, lysis for non-enveloped)

Genome Type	Replication/Transcription Strategy	Key Viral Enzymes
(+) ssRNA	Acts as mRNA; translated immediately	RNA replicase (coded by virus)
(-) ssRNA	Must synthesize (+) strand before translation	RNA-dependent RNA polymerase (packaged in virion)
Retroviridae	ssRNA → dsDNA (integration as provirus)	Reverse transcriptase, integrase, protease
Hepadnaviridae	DNA genome via RNA intermediate	Reverse transcriptase

Viral Pathology Types & Antivirals

• Latent Infections: Virus remains dormant (e.g., Herpes simplex, Varicella-zoster).

• Persistent (Chronic) Infections: Gradual pathology with continuous viral production.

• Oncogenic Viruses: Induce host cell transformation and tumor formation.

• Antiviral Therapeutics: Target viral-specific enzymes (e.g., reverse transcriptase); selective toxicity is challenging due to reliance on host machinery.

Epidemiology, Normal Microbiota, & Disease Transmission

Normal Microbiota & Microbial Antagonism

Normal microbiota play a crucial role in host defense and health.

• Normal Microbiota: Permanent residents of specific body sites; usually non-pathogenic.

• Transient Microbiota: Temporary residents; do not establish permanent colonization.

• Microbial Antagonism: Normal flora outcompete pathogens, produce bacteriocins, and modify local environments (e.g., vaginal lactobacilli suppress Candida albicans).

• Disruption: Broad-spectrum antibiotics can eliminate normal flora, allowing opportunistic infections.

Disease Classification & Terminology

• Local Infection: Confined to a single region (e.g., abscess).

• Focal Infection: Starts local, spreads to secondary sites via blood/lymph.

• Sepsis & Septicemia: Systemic infection with pathogens multiplying in blood.

• Predisposition: Factors increasing susceptibility (e.g., female anatomy for UTIs).

Transmission Modes

• Direct Contact: Physical contact (e.g., handshake, sexual contact).

• Droplet Transmission: Short-range respiratory droplets (<1 meter; e.g., influenza).

• Vehicle Transmission: Through contaminated water, food, or air (>1 meter).

• Fomites: Inanimate objects transmitting pathogens (e.g., needles, door handles).

• Vectors: Arthropods/animals transmitting pathogens (mechanically or biologically).

Epidemiological Metrics & Studies

• Endemic: Constant, low-level presence of disease in a population.

• Epidemic: Sudden increase in disease incidence above baseline.

• Herd Immunity: Population resistance due to high immunity rates (mainly via vaccination).

• Study Designs:

  • Experimental: Controlled clinical trials.

  • Analytical: Observational cohort or case-control studies.

• Healthcare-Associated Infections (HAIs): Acquired in medical settings; influenced by host status, transmission chains, and resistant microbes.

Practice Exam Questions & Rationales

Selected high-yield questions with rationales to reinforce key concepts:

1. Gene Definition: A gene is a sequence of nucleotides in DNA that codes for a functional product (Answer: C).

2. RNA Polymerase: Synthesizes RNA from a DNA template, not RNA (Answer: B is mismatched).

3. DNA Structure: Two antiparallel nucleotide strands (Answer: C).

4. Inducible Enzyme: Produced in response to substrate presence (Answer: A).

5. Operon Model: Substrate binds repressor to allow inducible enzyme synthesis (Answer: C).

6. Conjugation: Horizontal DNA transfer without cell replication (Answer: C).

7. Catabolite Repression: Glucose inhibits lac operon via catabolite repression (Answer: A).

8. Viruses vs. Bacteria: Viruses are not composed of cells (Answer: D).

9. Lysogeny: Phage DNA incorporated into host DNA (Answer: A).

10. Persistent Infection: Disease develops gradually over time (Answer: C).

11. Latent Infection Example: Cold sores (Answer: B).

12. Enveloped Virus Release: Budding (Answer: B).

13. Shingles: Reactivation of latent virus (Answer: A).

14. (+) Sense RNA: Treated like mRNA in host cell (Answer: True).

15. Viral Nomenclature: Binomial nomenclature not used (Answer: False).

16. Droplet Transmission: Botulism is not spread by droplets (Answer: A).

17. Focal Infections: Begin as local infections (Answer: C).

18. Herd Immunity: Achieved via vaccination (Answer: C).

19. Fomite Example: Hypodermic needle (Answer: E).

20. Epidemiology: Study of disease occurrence and transmission (Answer: B).