Microbial 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.

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); translation in cytoplasm.

Example: Decoding DNA to Protein

• 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, reducing lac operon transcription even if lactose is present.

• 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- transfers F plasmid; Hfr strains transfer chromosomal DNA.

• 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 acellular infectious agents with unique structural and genetic properties.

• Viruses vs. Cellular Organisms: Viruses lack plasma membranes, cytoplasm, and ribosomes; genome is DNA or RNA (never both).

• Host Range & Tropism: Determined by specific host cell receptors; highly species- and tissue-specific.

• 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 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)

Viral Pathology Types & Antivirals

• Latent Infections: Virus remains dormant (e.g., HSV-1, Varicella-zoster).

• Persistent (Chronic) Infections: Gradual pathology; continuous low-level viral production.

• Oncogenic Viruses: Induce host cell transformation and malignancy by integrating oncogenes or disrupting tumor suppressors.

• Antiviral Therapeutics: Target viral-specific enzymes (reverse transcriptase, proteases, polymerases); 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 for nutrients and attachment sites, produce bacteriocins, and modify local environment (e.g., pH).

• Disruption: Broad-spectrum antibiotics or harsh chemicals can eliminate normal flora, allowing opportunistic pathogens to proliferate.

Disease Classification & Terminology

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

• Focal Infection: Originates locally, spreads to secondary sites via blood/lymph.

• Sepsis & Septicemia: Systemic inflammatory response due to pathogens in blood.

• Predisposition: Factors increasing susceptibility (e.g., anatomical differences, immune status).

Transmission Modes

• Direct Contact: Physical interaction (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: Key Concepts

• Gene: Sequence of DNA coding for a functional product (not just any DNA segment or amino acid sequence).

• DNA Polymerase: Synthesizes DNA from DNA template; RNA polymerase uses DNA, not RNA, as template.

• DNA Structure: Two antiparallel nucleotide strands, not parallel or protein-based.

• Inducible Enzyme: Produced in response to substrate presence (e.g., lac operon enzymes).

• Operon Model: Inducible enzyme synthesis requires substrate binding to repressor, inactivating it.

• Conjugation: Horizontal DNA transfer between cells, not reproduction or cell division.

• Catabolite Repression: Glucose inhibits lac operon via cAMP/CAP system.

• Viruses vs. Bacteria: Viruses are acellular, not composed of cells.

• Lysogeny: Phage DNA integrates into host genome as prophage.

• Persistent Infection: Disease develops gradually over time with continuous viral production.

• Latent Infection: Virus remains dormant (e.g., cold sores from HSV-1).

• Budding: Mechanism for enveloped virus release from host cell.

• Shingles: Reactivation of latent Varicella-zoster virus.

• (+) ssRNA Viruses: Genome acts as mRNA in host cell.

• Viral Nomenclature: Not binomial; uses family/genus/common names.

• Botulism: Not spread by droplets; acquired via ingestion.

• Focal Infection: Begins as local, then spreads to secondary sites.

• Herd Immunity: Achieved primarily through vaccination.

• Fomite: Inanimate object transmitting pathogens (e.g., needle).

• Epidemiology: Study of disease occurrence and transmission.

Additional info: This guide integrates foundational concepts from microbial genetics, virology, and epidemiology, with emphasis on mechanisms, definitions, and exam-relevant distinctions. For equations, the central dogma can be represented as: