Microbial Genetics, Gene Regulation, Variation, and Genomics

Comprehensive vocabulary flashcards covering microbial transcription, translation, operon regulation, DNA mutations, repair pathways, horizontal gene transfer, PCR, and modern genomics.

Head-on collision (replication-transcription)

An encounter occurring when the replisome moves opposite to RNA polymerase along DNA, causing stalled replication, replisome dissociation, replication errors (mutations), and increased supercoiling.

Rear-end collision (replication-transcription)

An encounter where the replisome moves in the same direction behind RNA polymerase; the replisome is temporarily interrupted but can bypass RNAP, potentially utilizing the transcript as a primer while evicting RNAP.

Polyribosomal complex

A bacterial macromolecular complex formed during coupled transcription and translation in which multiple ribosomes translate a single nascent mRNA molecule simultaneously as it is being synthesized by RNA polymerase.

Housekeeping genes

Constitutively expressed genes encoding enzymes continually required for basic cellular functions and maintenance, such as central metabolic pathways and peptidoglycan synthesis.

Two-component chemotaxis system

A bacterial signal transduction cascade where an MCP sensor detects an environmental stimulus, CheA acts as an amplifier to translate sensory information, and CheY functions as an effector acting on flagellar rotation.

Inducer

A small regulatory molecule that stimulates the transcription of an inducible gene or operon by binding and inactivating a repressor protein.

Corepressor

A small effector molecule (such as tryptophan) that binds to an inactive aporepressor protein to form an active complex capable of binding the operator and blocking transcription.

lac operon

An inducible catabolic operon containing $lacZ$, $lacY$, and $lacA$ required for lactose transport and catabolism; its expression requires CAP activation via $\text{cAMP}$ and deactivation of the LacI repressor by allolactose.

Allolactose

An isomer of lactose formed as a side product by $\beta$-galactosidase that serves as the physiological inducer of the $lac$ operon by binding and inactivating the LacI repressor.

Catabolite activator protein (CAP)

A transcriptional activator protein that binds DNA upstream of target promoters when complexed with $\text{cAMP}$, which accumulates under low-glucose conditions to stimulate positive control of the $lac$ operon.

trp operon

A repressible anabolic operon containing five structural genes ($trpE$, $trpD$, $trpC$, $trpB$, $trpA$) for tryptophan biosynthesis, controlled by TrpR repression and attenuation.

Attenuation (trp operon)

A regulatory mechanism where ribosome stalling at tryptophan codons in the leader peptide determines whether an anti-terminator stem-loop ($2:3$) or a transcription terminator hairpin ($3:4$) forms in the nascent mRNA.

AraC

A regulatory protein of the $araBAD$ operon that mediates both negative and positive transcriptional control by binding $araO_1$, $araO_2$, and $araI$, bending DNA into an inhibitory loop in the absence of arabinose.

Silent mutation

A point mutation that changes the nucleotide sequence of a codon without altering the encoded amino acid, preserving the wild-type polypeptide sequence.

Missense mutation

A base substitution that alters a codon to specify a different amino acid, altering the resulting polypeptide sequence.

Nonsense mutation

A base substitution that converts a sense codon into a premature stop codon, leading to premature termination of polypeptide synthesis.

Frameshift mutation

A mutation resulting from the insertion or deletion of base pairs in numbers not divisible by three, shifting the translational reading frame and altering all subsequent downstream codons.

Strand-slippage

A spontaneous replication error occurring within repeated base tracts; looping out of the nascent strand results in an insertion, whereas looping out of the template strand causes a deletion.

Intercalating agent

A planar chemical mutagen (such as ethidium bromide, polycyclic aromatic hydrocarbons, or actinomycin D) that inserts between stacked DNA base pairs, distorting the double helix to cause insertions and deletions.

Photoreactivation

A direct light-dependent DNA repair mechanism where the enzyme photolyase uses visible light energy to cleave cyclobutane pyrimidine (thymine) dimers produced by nonionizing UV radiation.

Mismatch repair (MMR)

A single-strand repair mechanism that distinguishes the parent template strand by its adenine methylation at GATC sequences, enabling Mut enzymes and UvrD to excise the mismatched error on the transiently unmethylated daughter strand.

Nucleotide-excision repair (NER)

A single-strand DNA repair pathway where UvrA scans for damage, UvrB recruits UvrC to nick the DNA backbone on both sides of a lesion, UvrD helicase excises the damaged oligomer, and DNA polymerase I and ligase fill the gap.

SOS response

An extensive error-prone DNA damage response activated when RecA forms nucleofilaments that stimulate the autoproteolytic cleavage of the LexA repressor, derepressing more than $40$ genes including low-fidelity error-prone DNA polymerases.

Ames test

A bioassay developed by Bruce Ames in the 1970s that utilizes a histidine-auxotrophic ($\text{his}^-$) Salmonella strain to evaluate chemical mutagenicity by measuring the rate of reversion mutations to wild-type prototrophy ($\text{his}^+$).

Bacterial transformation

A horizontal gene transfer mechanism in which competent cells bind free extracellular DNA via an uptake pilus, degrade one strand, translocate the remaining single strand across the membrane via ComEC, and incorporate it through RecA.

Bacterial conjugation

A horizontal gene transfer mechanism requiring direct cell-to-cell contact through a sex pilus, during which a single strand of plasmid DNA (such as the F plasmid) transfers from an $\text{F}^+$ donor cell to an $\text{F}^-$ recipient.

Transduction

A mode of horizontal gene transfer where host bacterial chromosomal DNA is accidentally packaged into a bacteriophage capsid and transferred into a new recipient bacterium.

Transposon

A mobile genetic element flanked by terminal palindromic/inverted repeat sequences that can move ("jump") or replicate to other genomic sites or plasmids.

Polymerase Chain Reaction (PCR)

An automated in vitro technique that exponentially amplifies a targeted DNA region through iterative thermal cycles of denaturation, annealing, and extension using a thermostable DNA polymerase.

Denaturation (PCR step 1)

The initial step of a PCR cycle where double-stranded template DNA is briefly heated (typically to $95^\circ\text{C}$) to break hydrogen bonds and separate the complementary strands.

Annealing (PCR step 2)

The second step of a PCR cycle where reaction temperature is lowered (typically to $55^\circ\text{C}$) to permit excess synthetic oligonucleotide primers to hydrogen bond specifically to the ends of the target sequence.

Extension (PCR step 3)

The third step of a PCR cycle where a thermostable enzyme (such as Taq polymerase) synthesizes new DNA complementary strands by adding dNTPs to the $3'$ end of each annealed primer at approximately $72^\circ\text{C}$.

Dideoxynucleoside triphosphate (ddNTP)

A chain-terminating nucleotide analog lacking a $3'\text{-OH}$ group on its deoxyribose sugar ring, which prevents further phosphodiester bond formation when incorporated into a growing DNA strand.

Sanger sequencing

The classical chain-termination DNA sequencing method that employs DNA polymerase, dNTPs, and four distinct dideoxynucleotides (ddNTPs) to produce nested sets of DNA fragments terminating at specific bases.

Bridge PCR

A solid-phase amplification method utilized in Illumina sequencing where single-stranded, adapter-ligated DNA fragments arch over to hybridize with complementary primers on a flow cell surface, generating dense monoclonal clusters.

Contig

A continuous consensus segment of reconstructed DNA sequence generated in silico by aligning overlapping short sequencing reads without gaps.

Scaffold

A higher-order bioinformatic assembly constructed by ordering and orienting multiple contigs separated by known sequencing gaps.

Metagenomics

The culture-independent genomic analysis of total microbial DNA extracted directly from environmental or clinical samples, providing access to uncultivated organisms.

Core genome

The conserved set of genes shared across all individuals or strains belonging to a specific bacterial species.

Genomic island

A discrete region of foreign, mobile genetic material integrated into a bacterial chromosome via horizontal gene transfer, often carrying accessory metabolic, antibiotic resistance, or virulence traits.