Microbiology: Transcription, Translation & Gene Regulation

Comprehensive vocabulary flashcards reviewing bacterial transcription, translation, and genetic regulatory mechanisms based on Exam 3 lecture review materials.

Catabolite repression

The preferential utilization of a favored carbon source, such as glucose, while the expression of pathways for alternative carbon sources is repressed.

Diauxic growth

A biphasic growth curve characterized by two distinct growth phases separated by an intervening lag phase as cells switch from one carbon substrate to another.

CRP (cAMP Receptor Protein)

A regulatory activator protein (also known as CAP) that binds cyclic AMP (cAMP) to form a complex that binds specific DNA sites and stimulates transcription of catabolic operons.

Beta-galactosidase

An enzyme encoded by lacZ that cleaves lactose into glucose and galactose, and also isomerizes lactose into allolactose.

Lactose permease

A membrane transport protein encoded by lacY that facilitates the uptake of lactose into the bacterial cell.

LacI

A regulatory repressor protein encoded by a distinct gene outside the lac operon that binds the lac operator in the absence of inducer to repress transcription.

Allolactose

An isomer of lactose that functions as the physiological inducer by binding to the LacI repressor, inducing a conformational change that lowers its operator affinity.

Homodimer

A macromolecular protein complex assembled from two identical polypeptide subunits, a common quaternary structure for DNA-binding regulatory proteins.

Inverted repeats

DNA nucleotide sequences that are reverse complements of each other on opposite strands, commonly serving as recognition target sites for dimeric regulatory proteins.

Helix-turn-helix motif

A structural DNA-binding motif consisting of two $\alpha$-helices joined by a short turn; one helix positions itself into the major groove of DNA as a recognition element.

Recognition helix

The specific $\alpha$-helix within a helix-turn-helix motif that directly interacts with nucleotide base sequences inside the major groove of the DNA double helix.

Operator

A specific regulatory DNA sequence to which a repressor protein binds to inhibit or block transcription initiation by RNA polymerase.

Effector molecule

A low-molecular-weight ligand that interacts with a regulatory protein, altering its conformation and modulating its DNA-binding capacity.

Allosteric protein

A protein whose tertiary or quaternary structure and functional activity are altered upon binding an effector molecule at a site distinct from the active or functional binding site.

Inducer

A small regulatory molecule that increases gene expression, typically by binding a repressor protein and causing it to dissociate from operator DNA.

Corepressor

A small molecule that binds to an inactive aporepressor, enabling the resulting complex to bind an operator sequence and block transcription initiation.

Enzyme repression

A downregulatory mechanism that decreases the synthesis of specific biosynthetic enzymes when the end product of their pathway is abundant.

Enzyme induction

An upregulatory mechanism that stimulates the synthesis of specific catabolic enzymes in response to the presence of a substrate or inducer molecule.

Negative control

A mode of transcriptional regulation mediated by a repressor protein whose binding decreases transcription output.

Positive control

A mode of transcriptional regulation mediated by an activator protein whose binding enhances or facilitates transcription initiation by RNA polymerase.

Two-component regulatory system

A bacterial signal transduction circuit composed of a membrane-bound sensor histidine kinase and an intracellular response regulator.

Kinase

An enzyme that catalyzes the transfer of a phosphate group from a high-energy donor molecule, typically ATP, onto a target substrate.

Phosphatase

An enzyme that removes a covalently bound phosphate group from a phosphorylated target protein or metabolite.

Chemotaxis

The directed movement of a bacterial cell toward chemical attractants or away from chemical repellents.

Methyl-accepting chemotaxis proteins (MCPs)

Transmembrane sensory receptor proteins that bind environmental attractants or repellents to transmit chemical signals across the plasma membrane.

CheY

A chemotaxis response regulator protein that, when phosphorylated into CheY-P, binds the flagellar motor to induce clockwise rotation and cause tumbling.

Quorum sensing

A cell-density-dependent communication mechanism through which bacteria coordinate gene expression using diffusible signaling molecules.

Autoinducer

A diffusible chemical signal synthesized and secreted by bacterial cells that accumulates in the local environment as population density rises.

LuxI

The autoinducer synthase enzyme in the classic quorum-sensing circuit responsible for synthesizing the acyl-homoserine lactone signaling molecule.

LuxR

A transcriptional activator protein that binds its cognate autoinducer at threshold concentrations to activate target gene transcription, including luciferase operons.

Stringent response

A global stress response triggered by nutrient or amino acid limitation that shifts resources away from stable RNA synthesis toward survival and amino acid biosynthesis.

RelA

A ribosome-associated synthetase that becomes activated by uncharged tRNA molecules in the ribosomal A site to produce the alarmone (p)ppGpp.

(p)ppGpp

Guanosine polyphosphate alarmones (ppGpp and pppGpp), historically called 'magic spots', that downregulate rRNA and tRNA transcription during the stringent response.

Sigma S ($\sigma^S$)

The master alternative sigma factor that directs RNA polymerase core enzyme to promoters required for stationary-phase adaptation and general stress responses.

Heat-shock sigma factor ($\sigma^{32}$ / $\sigma^H$)

An alternative sigma factor encoded by rpoH that redirects RNA polymerase to transcribe heat-shock genes encoding chaperones and proteases when unfolded proteins accumulate.

DnaK

A molecular chaperone that assists in protein folding and binds to $\sigma^{32}$ under uninduced conditions to facilitate its degradation or limit its regulatory activity.

Small regulatory RNA (sRNA)

Non-coding RNA molecules that modulate gene expression post-transcriptionally by base-pairing with complementary target mRNAs to alter their translation or stability.

Riboswitch

A structured domain within the untranslated region of an mRNA molecule that binds a specific metabolite directly to modulate transcription termination or translation initiation.

Attenuation

A regulatory mechanism in prokaryotes whereby transcription elongation is terminated prematurely in response to ribosome positioning during the coupled translation of a leader peptide.

Shine-Dalgarno sequence

A conserved purine-rich motif located upstream of bacterial start codons that base-pairs with 16S rRNA within the $30\text{S}$ ribosomal subunit to position translation initiation.

Aminoacyl-tRNA synthetase

An enzyme that uses ATP hydrolysis to covalently attach a specific amino acid to its cognate tRNA molecule, yielding a charged aminoacyl-tRNA.

Peptidyl transferase center

The ribozyme catalytic center located in the large ($50\text{S}$) ribosomal subunit, composed of 23S rRNA, that forms peptide bonds during translation elongation.

Translocation

The elongation step wherein the ribosome advances three nucleotides ($1$ codon) along mRNA, shifting deacylated tRNA from P to E site and peptidyl-tRNA from A to P site.

Polysome

A macromolecular complex consisting of multiple ribosomes simultaneously engaged in translating a single mRNA molecule in the $5'$ to $3'$ direction.

Degeneracy

A property of the universal genetic code wherein multiple distinct three-nucleotide codons can encode the exact same amino acid residue.

Sigma factor

A dissociable bacterial transcription initiation protein that associates with core RNA polymerase to confer promoter sequence recognition and melting capability.

Rho-dependent termination

A transcription termination mechanism requiring the hexameric protein factor Rho, which tracks along nascent RNA transcripts and unzips the RNA-DNA hybrid at paused polymerase complexes.

Intrinsic termination

A factor-independent transcription termination mechanism mediated by an RNA stem-loop (hairpin) followed immediately by a run of uracil residues that destabilizes the ternary complex.