Molecular Biology: Transcription, RNA Processing, and Translation

Vocabulary practice flashcards covering key proteins, factors, models, and mechanisms across bacterial and eukaryotic transcription, RNA processing, and translation.

Core enzyme (bacterial)

The bacterial RNA polymerase complex composed of subunits $\alpha$, $\beta$, $\beta'$, and $\omega$ that synthesizes RNA but cannot recognize promoters on its own.

$\sigma$ factor (sigma factor)

The extra regulatory subunit of bacterial RNA polymerase that specifically recognizes promoter elements ($-35$ and $-10$) to form the functional holoenzyme.

Abortive initiation

A step during transcription initiation in which RNA polymerase synthesizes and releases short transcripts of $2\text{--}9\text{ nt}$ before clearing the promoter, requiring a loop of the initiation factor near the active site to move.

Intrinsic termination

A bacterial transcription termination mechanism mediated by an RNA hairpin structure followed immediately by a run of uracil (U) residues, prompting the polymerase to release the transcript.

Rho-dependent termination

A bacterial transcription termination mechanism where the hexameric protein Rho binds an exposed rut site on nascent RNA not covered by ribosomes and actively pulls the RNA off the polymerase.

RNA Polymerase I (Pol I)

The eukaryotic RNA polymerase dedicated exclusively to transcribing the genes that encode large ribosomal RNAs (rRNAs).

RNA Polymerase II (Pol II)

The eukaryotic RNA polymerase responsible for transcribing protein-coding messenger RNAs (mRNAs) as well as small regulatory RNAs.

RNA Polymerase III (Pol III)

The eukaryotic RNA polymerase that synthesizes transfer RNAs (tRNAs), $5\text{S rRNA}$, and small nuclear RNAs (snRNAs).

Pol II CTD (C-terminal domain)

A structure on the largest subunit of eukaryotic Pol II made of tandem repeats of a 7-amino-acid sequence whose changing phosphorylation state controls the recruitment of factors for transcription, chromatin modification, and RNA processing.

TATA-binding protein (TBP)

A general transcription factor component that binds the TATA box in the DNA minor groove, introduces a sharp bend in the DNA, and is universally required by all three eukaryotic RNA polymerases regardless of whether a TATA element is present.

TFIID

A general transcription factor complex consisting of TBP and several TAFs (TBP-associated factors) that recognizes core promoter elements and binds first during pre-initiation complex (PIC) assembly.

TFIIH

A eukaryotic general transcription factor possessing helicase activity that unwinds DNA to form the open complex and kinase activity that phosphorylates the Pol II CTD to allow promoter clearance.

Mediator

A large multi-protein coactivator complex of $20+$ subunits required to transmit regulatory signals to Pol II and activate transcription in eukaryotic cells.

Torpedo model

A model of eukaryotic Pol II transcription termination wherein, after endonucleolytic cleavage at the polyadenylation site, a $5'\rightarrow3'$ exonuclease degrades the downstream uncapped RNA until it catches the polymerase and displaces it from DNA.

LacI

The repressor protein of the bacterial lac operon that binds the operator to shut down transcription in the absence of lactose and is released upon binding allolactose.

CAP (Catabolite Activator Protein)

The activator protein of the lac operon that, when bound to cAMP in low-glucose conditions, binds promoter-proximal DNA and directly recruits RNA polymerase to stimulate high transcription levels.

cI (phage $\lambda$)

The lambda repressor protein that maintains lysogeny by binding $O_R$ and $O_L$ to silence early promoters $P_R$ and $P_L$, while activating its own promoter $P_{RM}$.

cII (phage $\lambda$)

An unstable early viral activator protein that triggers the lysogenic pathway by turning on $P_{RE}$ to produce cI; it is degraded by host proteases in well-fed, healthy cells.

Cro (phage $\lambda$)

A viral regulatory protein that promotes the lytic pathway by binding the same operator sites as cI but with opposite affinity, thereby shutting off $P_{RM}$ and preventing lysogeny establishment.

$P_{RE}$ and $P_{RM}$

Promoters that drive expression of phage $\lambda$ cI; $P_{RE}$ (repressor establishment) requires activation by cII, whereas $P_{RM}$ (repressor maintenance) requires cI for basal or activated expression.

Gal4

A modular yeast transcriptional activator that binds upstream activating sequences (UAS) and recruits coactivators, including SAGA and Mediator, to stimulate transcription of galactose-metabolizing genes.

Gal80

A negative regulator in the yeast GAL pathway that directly binds the activation domain of Gal4 to inhibit its activity when galactose is absent.

Gal3

The sensor protein of the yeast GAL circuit that binds galactose and ATP to relieve Gal80-mediated inhibition, freeing Gal4 to activate transcription.

Spliceosome

A dynamic ribonucleoprotein complex consisting of small nuclear ribonucleoproteins (snRNPs U1, U2, U4, U5, and U6) that base-pairs with pre-mRNA to catalyze the excision of introns via two transesterification steps.

Aminoacyl-tRNA synthetase

An enzyme responsible for coupling a specific amino acid to its cognate tRNA in a two-step ATP-dependent reaction, maintaining translation fidelity via structural identity elements and active-site or editing-site proofreading.

Wobble pairing

Non-Watson-Crick base pairing allowed exclusively at the third codon position (such as G–U or involving inosine in the anticodon), permitting a single tRNA species to read multiple synonymous codons.

Poly(A)-binding protein (PABP)

A protein that binds the eukaryotic $3'$ polyadenylated tail and interacts with initiation factors eIF4G and eIF4E to circularize mRNA into a closed loop, ensuring only intact, full-length transcripts undergo translation.

EF-Tu

A bacterial elongation GTPase that binds and delivers aminoacyl-tRNAs to the ribosomal A site, protecting the ester bond from premature hydrolysis until cognate base pairing triggers GTP hydrolysis.

EF-G

A bacterial elongation factor and GTPase that drives ribosomal translocation of tRNAs and mRNA from the A and P sites to the P and E sites by structurally mimicking the EF-Tu–tRNA binary complex.

tmRNA / SmpB

A bacterial ribosome-rescue system that enters stalled ribosomes on truncated mRNAs lacking a stop codon, adding a peptide degradation tag (degron) to direct the incomplete polypeptide to cellular proteases.

Gcn2

A eukaryotic protein kinase that senses starvation by binding uncharged tRNAs and phosphorylates eIF2$\alpha$, preventing GDP–GTP exchange by eIF2B and downregulating global translation initiation.

Internal ribosome entry site (IRES)

A structured secondary RNA element within an mRNA $5'$ UTR that enables cap-independent direct recruitment of ribosomes, commonly utilized by viruses to bypass host translational shutoff.

Riboswitch

A metabolite-binding structural domain located within the $5'$ untranslated region of an mRNA that directly binds small ligands (such as thiamine pyrophosphate) without accessory proteins to alter transcription termination or translation initiation.

Iron response element (IRE)

A conserved stem-loop sequence in the $5'$ UTR of ferritin mRNA bound by iron regulatory proteins (IRPs) under low-iron conditions to block translation, which dissociates when iron concentrations rise.