Bacterial Gene Regulation, Replication Initiation, and Translation

Comprehensive practice flashcards covering prokaryotic gene regulation, operons, DNA replication initiation, translation control, bacterial growth phases, and global stress responses.

Positive Control

A regulatory mechanism in which a regulatory protein (an activator) binds to DNA to promote or increase the rate of transcription.

Negative Control

A regulatory mechanism in which a regulatory protein (a repressor) binds to DNA to decrease or prevent transcription.

Autoregulation

A regulatory mechanism in which the product of a gene directly regulates its own expression, such as a protein binding its own promoter to repress transcription.

Co-regulation

The simultaneous regulation of two or more distinct genes in response to a common condition, such as genes activated together under nitrogen starvation.

Cis-acting Element

A local DNA sequence on the same DNA molecule that regulates the expression of an adjacent gene by acting as a binding site for regulatory factors.

Trans-acting Factor

A diffusible molecule (typically a protein transcription factor) encoded elsewhere that binds to target DNA sites to modulate gene expression.

Operon

A transcriptional unit common in bacteria and archaea where multiple functionally related structural genes are transcribed together from a single shared promoter into a polycistronic mRNA.

Regulon

A collection of multiple independent operons distributed across the chromosome that are controlled simultaneously by a common regulator protein.

Modulon

A group of operons or regulons that are co-regulated in response to general metabolic or environmental factors.

Stimulon

A set of genes and operons co-regulated simultaneously in response to a specific environmental stimulus.

Structural Genes

Genes within an operon that encode enzymes or structural proteins involved in a metabolic pathway rather than regulatory proteins.

Regulatory Genes

Genes that encode proteins (such as repressors or activators) responsible for controlling the transcription of other genes.

Constitutive Operon

An operon whose genes are continuously transcribed, typically encoding housekeeping functions essential for basic cellular survival such as DNA repair.

Repressible Operon

An operon that is normally active (default on) but is turned off when a specific metabolite binds to and activates a repressor protein.

Inducible Operon

An operon that is normally inactive (default off) due to a bound repressor, but becomes activated when an inducer molecule binds and releases the repressor.

Diauxic Growth

A two-step bacterial growth curve observed when two carbon sources are present; glucose is utilized first, followed by a lag period before lactose metabolism begins.

Catabolite Activator Protein (CAP)

A transcriptional activator (also known as CRP) that, when bound by cAMP, binds upstream of the promoter to recruit, stabilize, and activate RNA polymerase.

Enzyme IIA (EIIA)

A glucose transport protein that becomes phosphorylated when glucose drops, subsequently activating adenylyl cyclase to synthesize cAMP.

Cyclic AMP (cAMP)

A second messenger molecule whose concentration increases as glucose levels drop, binding to CAP to activate transcription of alternative catabolic operons.

DnaA

The bacterial replication initiation protein that binds to specific recognition sites at $oriC$; active ATP-DnaA promotes DNA unwinding to begin replication.

SeqA

A negative regulator of replication initiation that binds newly replicated, hemi-methylated GATC sequences at $oriC$ and the $dnaA$ promoter, preventing premature re-initiation.

Regulatory Inactivation of DnaA (RIDA)

A replication-coupled negative feedback mechanism that promotes the hydrolysis of active DnaA-ATP to inactive DnaA-ADP via the Hda-clamp-DNA complex.

datA Locus

A chromosomal DNA site in E. coli that titrates and binds $200\text{--}300$ DnaA molecules, preventing untimely initiation by lowering free DnaA at $oriC$.

DARS (DnaA Reactivating Sequences)

Chromosomal loci (DARS1 and DARS2) that facilitate nucleotide exchange by regenerating active DnaA-ATP from inactive DnaA-ADP.

Shine–Dalgarno Sequence

A purine-rich ribosome binding site (RBS) located $6\text{--}8$ nucleotides upstream of the start codon on bacterial mRNA that base-pairs with 16S rRNA.

Anti-Shine-Dalgarno (ASD) Site

A complementary pyrimidine-rich sequence at the $3'$ end of the 16S rRNA in the small ($30\text{S}$) ribosomal subunit that binds the mRNA Shine-Dalgarno sequence.

Codon Usage Bias

The unequal frequency of synonymous codon occurrence in an organism's genome, matching cellular tRNA abundances and influencing translation elongation speed.

Elongation Factor P (EF-P)

A specialized bacterial translation elongation factor that alleviates ribosomal stalling caused by consecutive proline residues in the nascent peptide chain.

Ribosome Stalling

The temporary halt of a translating ribosome caused by factors such as rare codons, uncharged tRNAs, mRNA secondary structure, or proline stretches.

Balanced Growth

A steady-state growth condition during the exponential phase where all cellular components (DNA, RNA, proteins) double at the exact same constant rate.

Unbalanced Growth

A non-steady-state growth condition occurring during environmental shifts (shift-up or shift-down) where synthesis rates of cellular components change disproportionately.

Lag Phase

The initial period in bacterial culture growth during which cells adapt to new conditions and synthesize necessary components without a net increase in cell count.

Log Phase

The period of exponential growth in a bacterial culture characterized by a constant maximal growth rate and balanced cellular synthesis.

Stationary Phase

The growth phase plateau where net population increase ceases because the rate of cell division equals the rate of cell death, or cells enter metabolic dormancy.

Decline (Death) Phase

The terminal phase of a bacterial batch culture marked by an exponential decrease in the number of living cells due to nutrient depletion and toxin buildup.

Functional Ribosome Composition

The complete catalytic translation machine consisting of $3\text{--}4$ rRNA molecules (which form the catalytic peptidyl transferase center) and approximately $50$ ribosomal proteins.

rRNA Promoters (P1 and P2)

Tandem promoters driving rRNA operons in E. coli; $P_1$ mediates rapid transcription with high polymerase affinity during fast growth, whereas $P_2$ provides lower basal activity.

Unstable Open Complex

A transient DNA-promoter open complex at bacterial rRNA promoters that allows rapid initiation and immediate sensitivity to fluctuating cellular NTP levels.

Head-on Collision (Replication-Transcription)

A conflict occurring when the replication fork and RNA polymerase move in opposing directions, resulting in replication arrest and transcription abortion.

Co-oriented Collision (Replication-Transcription)

A collision where the replication machinery and RNA polymerase travel in the same direction, causing a replication slowdown while allowing transcription to complete.

Attenuation

A transcriptional regulatory mechanism in bacteria that couples translation of a leader peptide to the formation of alternative mRNA secondary structures that control transcription termination.

trpL Leader Sequence

A transcribed regulatory region located between the operator and structural genes of the trp operon containing four segments capable of forming mutually exclusive stem loops.

Antiterminator Stem-Loop

A secondary structure formed by pairing of regions 2 and 3 in the trpL leader mRNA during low tryptophan levels, allowing RNA polymerase to continue transcription.

Terminator Stem-Loop

A secondary hairpin structure formed by pairing of regions 3 and 4 in the trpL leader mRNA when tryptophan is abundant, causing RNA polymerase to terminate transcription.

Riboswitch

A noncoding RNA element in the $5'$ end of some mRNAs that directly binds small metabolites to regulate transcription termination, translation initiation, or mRNA stability.

Thiamine Pyrophosphate (TPP) Riboswitch

A specific bacterial riboswitch that binds thiamine pyrophosphate to sequester the ribosome binding site, thereby inhibiting the translation of thiamine biosynthetic genes.

Stringent Response

A global bacterial response to amino acid starvation mediated by the alarmone (p)ppGpp that downregulates rRNA and tRNA synthesis while upregulating amino acid biosynthesis genes.

(p)ppGpp

A small nucleotide alarmone (guanosine pentaphosphate/tetraphosphate) produced during starvation that inhibits stable RNA transcription and translation while activating stress genes.

RelA

A ribosome-associated (p)ppGpp synthase that detects uncharged tRNAs in the ribosomal A-site during amino acid starvation and catalyzes $\text{ATP} + \text{GTP} \rightarrow \text{AMP} + \text{pppGpp}$.

SpoT

A bifunctional bacterial enzyme that degrades (p)ppGpp into GTP or GDP and pyrophosphate ($\text{PP}_i$) when amino acid levels are restored.

RNA Polymerase Holoenzyme

The complete bacterial transcription complex composed of core RNA polymerase ($\alpha_2\beta\beta'\omega$) and a sigma ($\sigma$) factor that provides promoter specificity.

Alternative Sigma Factors

Specialized sigma subunits that replace the primary housekeeping sigma factor in RNA polymerase holoenzyme to redirect transcription to specific stress-responsive regulons.

$\sigma^{70}$ (RpoD)

The primary housekeeping sigma factor in E. coli responsible for directing RNA polymerase to promoters of genes required during normal exponential growth.

$\sigma^{32}$ (RpoH)

The heat shock alternative sigma factor in E. coli that directs the transcription of genes encoding molecular chaperones and proteases in response to elevated temperatures.

$\sigma^{38}$ (RpoS)

The stationary phase and starvation sigma factor in E. coli that coordinates the global transcriptional program for general stress resistance and survival.

$\sigma^{54}$ (RpoN)

An alternative bacterial sigma factor that recognizes $-24/-12$ promoter elements to activate transcription of genes involved in nitrogen assimilation and limitation.

Nucleoid-Associated Proteins (NAPs)

Small, histone-like bacterial proteins (such as H-NS, IHF, Fis, and HU) that structure and compact the chromosome while modulating global transcription.

H-NS (Heat-Stable Nucleoid-Structuring Protein)

A nucleoid-associated protein that binds curved, AT-rich DNA to repress transcription, including silencing rRNA promoters during the stationary phase.

Integration Host Factor (IHF)

A bacterial nucleoid-associated protein that binds specific DNA sequences and induces sharp bends, participating in DNA replication initiation and recombination.

Fis (Factor for Inversion Stimulation)

A nucleoid-associated protein abundant during early exponential growth that regulates DNA supercoiling and can both activate and repress transcription.