Bacterial Genetics

Bacterial Genome Structure - DNA & Plasmids Galore

• Bacterial Chromosome (Nucleoid):
  • Primary genetic material; typically single, circular, double-stranded DNA (dsDNA).
  • Located in cytoplasm (nucleoid region); no nuclear membrane.
  • Haploid: one copy of each gene.
  • Highly supercoiled (by DNA gyrase/topoisomerases).
  • Associated with histone-like proteins (not true histones).
• Plasmids:
  • Extrachromosomal, small, circular, dsDNA molecules.
  • Replicate autonomously (own origin of replication - ori).
  • Carry non-essential genes:
    • Antibiotic resistance (R-plasmids).
    • Fertility factors (F-plasmids).
    • Toxins, virulence factors.
  • Variable size and copy number per cell.

⭐ Plasmids are key tools in recombinant DNA technology and major contributors to the spread of antibiotic resistance.

Bacterial Gene Transfer - Gene Swap Shop

📌 Mnemonic: Take (Transformation), Through (Transduction), Connect (Conjugation)

• Transformation: Uptake of naked DNA (plasmids, fragments) from environment by "competent" cells.
  • Examples: S. pneumoniae (Griffith's), H. influenzae, Neisseria.
  • Artificial: Electroporation, $CaCl_2$ heat shock.
• Transduction: Bacteriophage transfers bacterial DNA.
  • Generalized: Random bacterial DNA packaged into phage (lytic cycle). Any gene.
  • Specialized: Specific genes near prophage site transferred via faulty excision (lysogenic cycle).
• Conjugation: Direct DNA transfer (plasmids, chromosomal DNA) via sex pilus; cell-to-cell contact.
  • F-plasmid ($F$ factor): $F^+$ (donor) transfers plasmid to $F^-$ (recipient); recipient becomes $F^+$.
  • Hfr: Integrated F-plasmid allows transfer of chromosomal genes.

⭐ Conjugation, via R-plasmids, is a primary mechanism for spreading multidrug resistance (MDR) among bacteria.

Bacterial Mutation & Repair - Code Changes & Fixes

• Mutations: Heritable DNA sequence alterations.
  • Point Mutations: Single base changes.
    • Silent: No amino acid change.
    • Missense: Different amino acid.
    • Nonsense: STOP codon created.
  • Frameshift Mutations: Insertions/deletions (not multiples of 3 bp), alters reading frame.
• Mutagens: Agents increasing mutation rate.
  • Physical: UV light (forms pyrimidine dimers, e.g., $T=T$), Ionizing radiation (causes dsDNA breaks).
  • Chemical: Base analogs (e.g., 5-bromouracil), Alkylating agents, Intercalating agents (e.g., ethidium bromide).
• Repair Mechanisms:
  • Direct Repair: E.g., Photolyase (light-dependent, repairs $T=T$ dimers).
  • Excision Repair:
    • Base Excision Repair (BER): Removes specific damaged bases.
    • Nucleotide Excision Repair (NER): UvrABC endonuclease removes bulky lesions (e.g., $T=T$ dimers).
  • Mismatch Repair (MMR): MutS, MutL, MutH; corrects errors post-replication.
  • Recombinational Repair: RecA-mediated; repairs dsDNA breaks or gaps.
  • SOS Response: Inducible, error-prone repair system (RecA, LexA); activated by extensive DNA damage. 📌 Last resort defense.

⭐ The Ames test uses Salmonella typhimurium auxotrophs (histidine-dependent) to screen for chemical mutagenicity by observing reversion to prototrophy.

Bacterial Gene Regulation - Operon Operations

• Operon: Cluster of genes transcribed together from one promoter; allows coordinated gene expression.
  • Components: Promoter (P), Operator (O), Structural genes.
  • Regulator gene: Codes for repressor/activator protein; may be distant.
• Lac Operon (Inducible System): Catabolizes lactose.
  • Default: OFF (Repressor bound to Operator).
  • Inducer (Allolactose): Binds repressor → conformational change → repressor detaches → transcription ON.
  • Positive regulation: Catabolite Activating Protein (CAP) + cAMP enhance transcription when glucose is low.
• Trp Operon (Repressible System): Synthesizes tryptophan.
  • Default: ON (Repressor inactive).
  • Corepressor (Tryptophan): Binds repressor → activates it → repressor binds operator → transcription OFF.
  • Attenuation: Fine-tunes transcription based on Trp availability.

⭐ The Lac operon is an example of an inducible operon, meaning its genes are expressed only when an inducer (lactose/allolactose) is present. This prevents wasteful synthesis of enzymes when the substrate is unavailable. 📌 Inducible = Inactivated repressor by Inducer (Lac operon).

High‑Yield Points - ⚡ Biggest Takeaways

• Transformation: Uptake of naked DNA from environment; classic example S. pneumoniae.
• Transduction: Bacteriophage-mediated DNA transfer; generalized (any gene) or specialized (specific genes).
• Conjugation: Direct DNA transfer via sex pilus; requires cell contact (F-plasmid, Hfr strains).
• Plasmids: Extrachromosomal DNA carrying antibiotic resistance (R-factors) or virulence genes.
• Transposons: "Jumping genes" causing insertional mutagenesis and spreading drug resistance.
• Operons (Lac, Trp): Key for coordinated bacterial gene expression and regulation.