Microbial Genetics — Mutations, Repair, and Recombination

Vocabulary flashcards covering microbial genetics, types of mutations, physical and chemical mutagens, cellular DNA repair systems, horizontal gene transfer mechanisms, and plasmid-mediated multi-drug resistance based on the lecture notes.

Genotype

The specific nitrogenous base sequence of an organism's DNA.

Phenotype

The observable physical, physiological, or biochemical traits expressed by an organism as a result of its genotype.

Mutation

A permanent change in phenotype caused by an alteration in genotype, which is a change in the nitrogen base sequence of DNA.

Wild Type (Wild Strain)

An organism exhibiting natural, non-mutated characteristics typically isolated from a natural environment.

Mutant Strain

An organism bearing a genetic mutation that exhibits phenotypic variance in morphological structure, nutritional requirements, genetic regulatory mechanisms, or chemical and antibiotic resistance.

Spontaneous Mutations

Mutations that occur naturally during DNA replication without exposure to external mutagens, caused by replication errors, tautomeric shifts, or spontaneous chemical degradation.

Tautomeric Shifts

Temporary structural isomeric shifts of nitrogenous bases that alter their hydrogen bonding properties during DNA replication.

Spontaneous Mutation Rate

The baseline rate of uncorrected replication errors, typically maintained between $10^{-6}$ and $10^{-10}$ per gene replication cycle due to proofreading and mismatch repair systems.

Induced Mutations

Mutations resulting from exposure to physical, chemical, or biological agents (mutagens) that disrupt DNA structure and elevate mutation rates above baseline levels.

Nucleoside (Base) Analogs

Chemical mutagens structurally similar to standard nitrogenous bases (GCAT) that DNA polymerase incorporates into new strands, resulting in altered base pairing during subsequent replication rounds.

Intercalating / Frameshift Agents

Hydrophobic planar molecules that slide between adjacent DNA base pairs, distorting the double helix and causing DNA polymerase to insert or delete extra nucleotides.

Base-Modifying Agents

Chemical compounds that directly react with and alter functional groups on existing nitrogenous bases, such as nitrous acid deaminating cytosine into uracil.

Non-Ionizing Radiation

Radiation such as ultraviolet (UV) light whose photons excite electrons in DNA, inducing the formation of covalent thymine-thymine dimers on the same strand that stall replication and transcription enzymes.

Ionizing Radiation

High-energy radiation (such as X-rays and gamma rays) that causes radiolysis of water, generating reactive free radicals that lead to double-strand breaks, chromosome fragments, and base damage.

Biological Mutagens

Oncoviruses and infectious pathogens (such as HPV, Hepatitis B virus, and Helicobacter pylori) that insert viral DNA into host genomes or disrupt host genetic stability.

Point Mutations

Localized genetic alterations involving a change in a single nucleotide base pair within a DNA sequence, divided into base substitutions and frameshift mutations.

Silent Mutation

A base substitution, typically occurring at the third 'wobble' position of a codon, that does not alter the translated amino acid due to the degeneracy and redundancy of the genetic code.

Missense Mutation

A base substitution that alters a codon to code for a different amino acid, altering the polypeptide chain and potentially affecting protein folding, enzymatic activity, or stability.

Nonsense Mutation

A base substitution that converts an amino acid-coding codon into a stop codon ($\text{UAA}$, $\text{UAG}$, or $\text{UGA}$), causing premature termination of translation and producing a truncated, non-functional protein.

Frameshift Mutations

Insertions or deletions of one or more base pairs where the number of changed bases is not divisible by $3$, shifting the downstream reading frame of mRNA triplets and altering all subsequent amino acids.

DNA Polymerase III Proofreading

An immediate repair mechanism occurring during DNA synthesis wherein DNA Polymerase III identifies mismatched bases and excises them using $3' \rightarrow 5'$ exonuclease activity.

Mismatch Repair

A post-replication enzymatic repair system carried out by DNA Polymerase I and associated enzymes to detect and correct un-proofread mismatched bases on newly synthesized strands.

Excision Repair

A multi-enzyme pathway repairing structural lesions like pyrimidine dimers, utilizing nuclease to cut around the damage, DNA polymerase to fill the resulting gap, and DNA ligase to seal the backbone nick.

Photoactivation (Light Repair)

A bacterial repair mechanism in which photolyase enzymes utilize visible light energy to cleave covalent bonds between adjacent thymine dimers without cleaving the phosphodiester backbone.

Xeroderma Pigmentosum

A rare human autosomal recessive genetic disorder caused by a congenital defect in the excision repair pathway, leaving individuals unable to repair UV-induced thymine dimers and highly vulnerable to skin malignancies.

Genetic Recombination

A process in which an organism acquires and expresses genes that originate from another organism.

Conjugation

A direct mode of horizontal gene transfer in bacteria involving the passage of a plasmid or chromosomal fragment from a live donor to a live recipient through a sex pilus bridge.

F Factor (Fertility Plasmid)

A specialized plasmid in $F^+$ donor cells that directs the synthesis of a conjugative sex pilus to mediate plasmid transfer to an $F^-$ recipient cell.

High-Frequency Recombination (Hfr)

A bacterial strain in which the F factor plasmid has integrated into the circular bacterial chromosome, initiating transfer of donor chromosomal genes across the conjugation bridge.

Transformation

An indirect horizontal gene transfer pathway in which a live, competent recipient imports free, naked fragments of extracellular DNA released by a dead or lysed donor cell.

Griffith's Experiment

A landmark study demonstrating transformation in Streptococcus pneumoniae, proving that non-encapsulated (R strain) cells acquired virulence and capsule genes ($\text{cap}^+$) from heat-killed smooth (S strain) cells.

Transduction

An indirect horizontal gene transfer mechanism mediated by a defective bacteriophage virus that transfers bacterial DNA from a lysed donor cell to a recipient cell.

Generalized Transduction

A form of transduction occurring during the lytic cycle where random fragments of degraded host DNA are mistakenly packaged inside assembling bacteriophage capsids and delivered to new host cells.

Specialized Transduction

A form of transduction occurring during the lysogenic cycle where an excised prophage carries specific adjacent host chromosomal genes and transfers them to recipient bacteria.

Plasmids

Extrachromosomal, self-replicating circular DNA molecules that carry non-essential but advantageous genes related to specialized metabolic enzymes, pathogenicity factors, or resistance.

Resistance Plasmids (R Factors)

Plasmids that contain Resistance Transfer Factor (RTF) regions carrying genes conferring resistance against antibiotics and toxic heavy metals.