Microbiology: Microbial Genomes, Gene Expression, Mutations, and Virology

Vocabulary flashcards covering DNA replication, gene expression, transcriptional regulation, bacterial genetics, mutation, horizontal gene transfer, and virology.

Genome

The complete set of genetic information of an organism, comprising the chromosome(s) and any present plasmids.

Plasmid

Small, extrachromosomal circular double-stranded DNA molecules that replicate independently of the chromosome and carry nonessential or expendable genes.

Conjugative plasmid

A type of plasmid carrying tra genes that enable the cell-to-cell transfer of plasmid DNA from one bacterium to another via conjugation.

Antiparallel arrangement

The opposite directional orientation of the two strands in a DNA double helix, where one strand runs $5' \rightarrow 3'$ and the complement runs $3' \rightarrow 5'$.

Semiconservative replication

The mechanism of DNA replication where each newly synthesized double-stranded DNA molecule retains one original parent strand and one newly synthesized complementary strand.

DNA gyrase

A topoisomerase enzyme in Bacteria and Archaea that coils and uncoils DNA to release mechanical stress during unwinding; targeted by quinolone antibiotics.

Quinolones

Synthetic antibiotics that cross through bacterial porins and interfere with DNA gyrase and topoisomerase IV to inhibit DNA replication.

Central Dogma

The core principle of molecular biology stating that genetic information flows from DNA to RNA via transcription, and from RNA to protein via translation.

Sigma ($\sigma$) factor

A subunit of bacterial RNA polymerase that recognizes specific promoter sequences on DNA to initiate transcription.

Pribnow box

An A-T-rich consensus sequence located at the $-10$ region upstream of the transcription start site where DNA unwinding begins in prokaryotic promoters.

Hairpin loop (Stem-loop) termination

An intrinsic transcription termination mechanism where a G-C-rich region in the synthesized RNA forms a hairpin structure followed by a single-stranded U-run, causing RNA polymerase to release.

Rho factor

A protein that binds to the rut (rho utilization) site on naked RNA and translocates along the transcript to unwind the DNA-RNA hybrid and terminate transcription.

Polycistronic mRNA

A single messenger RNA transcript that encodes multiple distinct polypeptides, characteristic of bacterial operons.

Quorum sensing

A cell-to-cell communication mechanism in bacteria that detects cell density through signaling molecules to coordinate group gene expression.

Two-component regulatory system

A signal transduction mechanism comprising a membrane-spanning sensor protein that autophosphorylates upon environmental changes and transfers the phosphate to an internal response regulator protein.

Operon

A set of regulated structural genes transcribed as a single polycistronic mRNA, alongside shared regulatory elements including a promoter and operator.

Constitutive enzymes

Enzymes that are synthesized continuously by the cell due to their indispensable roles in central metabolic processes.

Inducible enzymes

Enzymes that are not routinely synthesized, but whose transcription can be switched on when their specific substrate is present in the environment.

Repressible enzymes

Enzymes that are produced routinely by default, but whose synthesis can be turned off when their end product accumulates in sufficient quantity.

Catabolite repression

A global control system that enables bacteria to preferentially utilize a primary carbon source (such as glucose) over alternative sources, leading to diauxic growth.

Mutation

A heritable change in the nucleotide sequence of an organism's genomic nucleic acid.

Auxotroph

A mutant organism that requires a specific organic growth factor not required by the parent wild-type strain due to a mutation in a metabolic pathway.

Prototroph

A wild-type organism that does not require organic growth factors beyond a basic minimal nutrient source.

Point mutation types

Base substitution mutations classified as silent (no effect on amino acid sequence), missense (results in an amino acid substitution), or nonsense (introduces a stop codon).

Frameshift mutation

A genetic mutation caused by the insertion or deletion of nucleotides in numbers not divisible by three, shifting the triplet reading frame during translation.

SOS Repair

An inducible, error-prone DNA repair process activated by extensive DNA damage that utilizes specialized polymerases lacking proofreading ability, causing SOS mutagenesis.

Ames test

A biological assay that evaluates the mutagenic potential of a chemical by measuring its effect on the reversion rate of histidine-requiring ($\text{his}^-$) Salmonella strains.

Transformation

A mechanism of horizontal gene transfer in which a competent bacterial cell takes up naked DNA fragments from its surrounding environment.

Competent cell

A bacterial cell that possesses specific membrane proteins allowing it to take up extracellular naked DNA and undergo genetic transformation.

Hfr cell

A High Frequency Recombination bacterial strain containing an F plasmid integrated directly into its main chromosome, facilitating high-frequency chromosomal gene transfer during conjugation.

Transduction

The process of horizontal gene transfer in bacteria where host bacterial DNA is transferred from a donor to a recipient cell inside a bacteriophage vector.

Generalized transduction

A form of transduction during the lytic cycle where random pieces of degraded host bacterial DNA are packaged into phage capsids by error.

Specialized transduction

A form of transduction during the lysogenic cycle where an improperly excised prophage transfers specific bacterial genes located adjacent to its integration site.

Lysogenic conversion

A change in the phenotype of a host bacterium resulting from the expression of prophage genes integrated into its chromosome, such as toxin production.

CRISPR system

An adaptive bacterial immune system consisting of clustered regularly interspaced short palindromic repeats and Cas nucleases that capture and degrade invading foreign viral or plasmid nucleic acids.

Virion

A complete, infectious viral particle consisting of a nucleic acid core enclosed by a protective protein capsid.

Capsid

The outer protein shell of a virus particle, constructed from individual protein subunits called capsomeres.

Nucleocapsid

The complex structure composed of the viral nucleic acid genome enclosed within its protein capsid.

Enveloped virus

A virus surrounded by an outer lipid bilayer membrane derived from host cell membranes, containing viral protein spikes.

Productive infection

A viral infection cycle resulting in the active production and release of new viral progeny, which may or may not lyse the host cell.

Latent viral state

A persistent viral state where the viral genome remains non-infectious and silent inside the host—either integrated into the host chromosome or as a plasmid—and replicates alongside cell division.

Reverse transcriptase

An RNA-dependent DNA polymerase enzyme encoded by retroviruses that transcribes a single-stranded RNA genome into complementary double-stranded DNA.

Plaque assay

A plaque counting procedure used to measure the concentration of infectious bacteriophages by observing clear zones of cell lysis on a bacterial lawn.

Viroid

An infectious plant pathogen consisting solely of a short, single-stranded naked RNA molecule without a protein coat.

Prion

An infectious misfolded protein ($\text{PrP}^{\text{Sc}}$) lacking nucleic acids that induces normal cellular proteins ($\text{PrP}^{\text{C}}$) to convert into the diseased conformation, causing transmissible spongiform encephalopathies.