Molecular Genetics: Mechanisms of Transcription and Post-Transcriptional Processing

Vocabulary practice flashcards covering prokaryotic and eukaryotic transcription mechanisms, RNA polymerase structures, promoter consensus sequences, termination pathways, and post-transcriptional processing.

RNA Polymerase (RNAP)

An enzyme that directs the synthesis of RNA using a DNA template and ribonucleoside triphosphates without requiring a primer.

RNA Polymerase Holoenzyme

The complete, active bacterial enzyme complex formed when the sigma factor ($\sigma$) joins the core RNA polymerase enzyme ($2\alpha$, $\beta$, $\beta'$, $\omega$) to recognize promoters and initiate transcription.

Sigma Factor ($\sigma$)

A bacterial trans-acting protein subunit of RNA polymerase responsible for binding specific promoter sequences to initiate transcription under various environmental conditions.

Transcription Start Site (TSS)

The specific position on the DNA template strand where transcription of RNA begins, designated as position $+1$.

Consensus Sequence

A DNA sequence consisting of the most commonly encountered nucleotides at each position across homologous genes in the same organism.

Cis-acting Elements

DNA sequences located near the region to be transcribed (such as promoter regions) that regulate the expression of adjacent genes on the same DNA molecule.

Trans-acting Factors

Proteins (such as the $\sigma$ factor and transcription factors) that regulate gene expression by moving to and binding with cis-acting DNA elements.

Pribnow Box

A conserved promoter consensus sequence with the nucleotide pattern $\text{TATAAT}$ located at position $-10$ upstream of the transcription initiation site in bacteria.

$-35$ Consensus Sequence

A bacterial promoter consensus sequence with the nucleotide sequence $\text{TTGACA}$, positioned approximately 35 base pairs upstream of the transcription start site.

Intrinsic Termination

A Rho-independent termination mechanism in bacteria where transcribed inverted repeats fold into a stable $\text{GC}$-rich hairpin loop followed by a poly-$\text{U}$ tract, causing RNA polymerase to stall and dissociate.

Rho-dependent Termination

A bacterial transcription termination mechanism requiring the Rho ($\rho$) factor protein, which binds the transcript and uses helicase activity to break the DNA-RNA hybrid.

Rho Utilization Site (rut)

An RNA sequence upstream of the termination site that serves as the binding region for the Rho ($\rho$) termination protein.

RNA Polymerase I

A eukaryotic RNA polymerase located in the nucleolus that transcribes ribosomal RNA (rRNA).

RNA Polymerase II (RNAP II)

A eukaryotic RNA polymerase located in the nucleoplasm responsible for synthesizing pre-mRNA and small nuclear RNAs (snRNAs).

RNA Polymerase III

A eukaryotic RNA polymerase located in the nucleoplasm that synthesizes transfer RNA (tRNA) and $5\text{S}$ rRNA.

TATA Box

A core-promoter consensus element in eukaryotes that binds the TATA-binding protein (TBP) subunit of TFIID to establish the transcription start site.

TATA-binding Protein (TBP)

A component of the general transcription factor TFIID that straddles the minor groove of DNA, bending the double helix to open 11–15 base pairs during initiation.

Enhancers

Cis-acting DNA regulatory elements located upstream, downstream, or within a gene that increase the rate or efficiency of transcription initiation.

Silencers

Cis-acting DNA sequences that decrease transcription levels when bound by repressor proteins.

Basal Transcription Apparatus

The minimal complex composed of RNA polymerase II, general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH), and the mediator complex required to initiate transcription.

Abortive Transcription

An initial phase in eukaryotic transcription where RNA polymerase II repeatedly synthesizes and releases short transcripts (fewer than 11 nucleotides) before clearing the promoter.

Rat1 Exonuclease

A $5' \rightarrow 3'$ exonuclease in yeast that attaches to the cleaved 5' end of trailing RNA and degrades it toward RNA polymerase II to force termination.

5' Cap (7-mG Cap)

A modified 7-methylguanosine nucleotide added to the 5' end of eukaryotic pre-mRNA to protect against nuclease degradation and assist in translation initiation.

Poly-A Tail

A chain of approximately 50–250 adenylic acid residues added to the 3' end of eukaryotic pre-mRNA by poly-A polymerase following the $\text{AAUAAA}$ polyadenylation signal sequence.

Introns

Intervening non-coding sequences of gene transcripts that are removed by pre-mRNA splicing before translation.

Exons

Expressed regions of pre-mRNA that remain in mature mRNA after splicing and encode amino acids in the final protein product.

Untranslated Regions (UTRs)

Non-coding RNA sequences at the 5' and 3' ends of mature mRNA that regulate transcript stability, localization, degradation, and ribosome binding.

Alternative RNA Splicing

A post-transcriptional process where different combinations of exons are joined together from a single pre-mRNA to generate distinct protein isoforms.

Ribozymes

RNA molecules with catalytic function capable of carrying out enzymatic reactions, such as self-splicing group I introns.

Spliceosome

A molecular complex containing snRNAs and snRNPs that carries out two transesterification reactions to cut 5' $\text{GU}$ and 3' $\text{AG}$ splice sites, forming an intron lariat.