Molecular Genetics - Gene Regulation in Prokaryotes

Comprehensive vocabulary flashcards covering the concepts, operon structures, regulatory modes, and mutation classes detailed in Lecture 16 on Prokaryotic Gene Regulation.

Housekeeping genes

Genes required in most cells and expressed continuously at steady levels to maintain basic life functions such as DNA repair, basic metabolism, transcription, and translation (comprising approximately 10–20% of coding genes, such as ~300 of 4,400 in E. coli).

Cis-acting regulatory elements

Non-coding DNA sequences (such as promoters, operators, enhancers, and silencer sites) located on the same DNA molecule that provide binding sites for regulatory proteins to control transcription.

Trans-acting regulatory factors

Diffusible molecules, typically transcription factor proteins, that bind directly or indirectly to cis-regulatory DNA sequences to modulate the transcriptional output of target genes.

Operon (1960 historical definition)

A genetic unit defined in 1960 as multiple protein-coding regions that can be negatively regulated in unison by a repressor acting at a single operator element.

Operon (modern definition)

A functional cluster of multiple protein-coding genes organized under a shared promoter and cis-regulatory elements, which are regulated in unison and typically transcribed into one or more polycistronic mRNAs.

Negative gene control

A regulatory mechanism in which transcription is inhibited or diminished by the binding of a trans-acting repressor protein to the DNA.

Positive gene control

A regulatory mechanism in which transcription is stimulated or enhanced by the binding of a trans-acting activator protein to the DNA.

Induction (operon regulation)

A regulatory response where an effector molecule (inducer) causes an increase in transcription, either by inactivating a repressor or by activating an activator.

Repression (operon regulation)

A regulatory response where an effector molecule (corepressor) causes a decrease or shut-off of transcription, either by activating a repressor or by inactivating an activator.

Inducer

A small signaling molecule or cofactor that turns on transcription by binding to a repressor (triggering its release from DNA) or by binding to an inactive activator (enabling it to bind DNA).

Corepressor

A small effector metabolite that binds to an aporepressor to enable DNA binding, or binds to an active activator to displace it from DNA, thereby turning off transcription.

Leaky expression

A low, basal level of transcription that occurs even when an operon is nominally repressed or silenced, ensuring that baseline levels of regulatory sensors and transport proteins remain available.

lacZ

A structural gene of the lac operon that encodes $\beta$-galactosidase, which cleaves lactose into glucose and galactose and isomerizes lactose into the inducer allolactose.

$\beta$-galactosidase

The enzyme encoded by lacZ that rearranges lactose into allolactose and hydrolyzes the glycosidic/ester bond of lactose to produce free D-galactose and D-glucose.

lacY

A structural gene of the lac operon that encodes $\beta$-galactoside permease.

$\beta$-galactoside permease

A transmembrane symporter encoded by lacY that brings lactose into the bacterial cell along with $H^+$ ions, expending energy by consuming part of the proton gradient.

lacA

A structural gene of the lac operon that encodes $\beta$-galactoside transacetylase, an enzyme that transfers acetyl groups to galactosides to detoxify metabolic byproducts, but is not strictly required for lactose catabolism.

Allolactose

An isomer of lactose generated by $\beta$-galactosidase that serves as the physiological inducer of the lac operon by binding the LacI repressor and decreasing its affinity for operator DNA.

LacI

The lac operon repressor protein encoded by the upstream lacI gene; synthesized as monomers that assemble into a homotetramer capable of binding simultaneously to operator sequences to block RNA polymerase.

Catabolite Activator Protein (CAP)

A positive transcription factor that, when complexed with cyclic AMP (cAMP), binds to the CAP site upstream of the lac promoter to recruit RNA polymerase and stimulate transcription under low-glucose conditions.

Cyclic AMP (cAMP)

A hunger-signal effector molecule whose synthesis is inversely proportional to glucose import; it binds to CAP to enable positive transcriptional activation of catabolic operons.

Operator 1 ($O_1$)

The primary operator sequence of the lac operon situated immediately downstream of the promoter; essential for strong repression, achieving maximal 1,300-fold repression only when cooperating with auxiliary operator $O_2$ or $O_3$ via DNA looping.

Operator constitutive mutation ($O^c$)

A cis-acting mutation within the operator DNA sequence that prevents the LacI repressor from binding, causing constitutive (unrepressed) transcription of downstream structural genes on that DNA molecule.

$lacI^-$ mutation

A recessive loss-of-function mutation affecting the dimer/tetramerization domain of the LacI repressor, preventing subunits from assembling into an active tetramer and resulting in constitutive operon expression.

$lacI^{-d}$ mutation

A dominant-negative mutation located in the N-terminal DNA-binding domain of LacI; mutant monomers co-assemble with wild-type subunits to poison the entire tetramer and disable DNA binding.

$lacI^s$ (super-repressor) mutation

A dominant mutation located in the core inducer-binding domain of LacI that prevents the repressor from binding allolactose, keeping the operon permanently shut off even in the presence of lactose.

Merodiploid (merozygote)

A partially diploid bacterial strain generated by introducing an $F'$ plasmid carrying a second set of genes, utilized genetically to test whether regulatory mutations are dominant, recessive, cis-acting, or trans-acting.

trp operon

A repressible biosynthetic operon containing five structural genes (trpE, trpD, trpC, trpB, trpA) that encode enzymes responsible for synthesizing the amino acid tryptophan.

TrpR

The aporepressor protein of the trp operon that requires free tryptophan as a corepressor to form an active repressor complex that binds the trp operator and blocks transcription initiation.

Attenuation (trp operon)

A regulatory mechanism relying on coupled transcription and translation in prokaryotes, wherein the rate of translation through the leader transcript determines whether an intrinsic termination hairpin forms in the mRNA.

Leader peptide (trpL)

A 5' regulatory region of the trp operon mRNA containing two tandem Trp codons within region 1 that acts as an intracellular sensor for charged $tRNA^{Trp}$.

Terminator hairpin (3:4 stem-loop)

An RNA secondary structure formed between leader regions 3 and 4 followed by a poly-U sequence that causes RNA polymerase to dissociate and arrest transcription before reaching the trp structural genes under high tryptophan conditions.

Antiterminator hairpin (2:3 stem-loop)

An alternate RNA hairpin formed between leader regions 2 and 3 when ribosome stalling at tandem Trp codons prevents region 2 from being covered, preventing formation of the 3:4 terminator and allowing transcription of the structural genes under low tryptophan conditions.

ara operon

An inducible operon encoding three structural genes (araB, araA, araD) responsible for L-arabinose catabolism, transcribed using $\sigma^{70}$ and regulated by AraC and CAP-cAMP.

AraC

A dual-function regulatory protein that represses the ara operon in the absence of arabinose by looping DNA between $araO_2$ and $araI_1$, and activates transcription in the presence of arabinose by binding adjacent $araI_1$ and $araI_2$ sites.

rrn operons

A set of seven operons in E. coli transcribed by RNA polymerase with $\sigma^{70}$ during rapid growth to synthesize ribosomal RNAs (rRNAs).

Stringent response

A global bacterial stress-response triggered by nutrient starvation that results in elevated levels of ppGpp, leading to transcriptional reprogramming that downregulates stable rRNA synthesis and shifts resources toward amino acid biosynthesis.

Guanosine tetraphosphate (ppGpp)

A nucleotide alarmone produced during nutritional stress that binds directly to two sites on RNA polymerase (with DksA) to alter promoter specificity and drive the stringent response.

minCDE operon

An operon encoding MinC, MinD, and MinE proteins, which oscillate from pole to pole in E. coli to prevent aberrant division at the cell poles and ensure that the FtsZ division septum forms precisely at midcell.