molecular chapter8_2

What is the closed complex in transcription?

The complex of RNA polymerase bound to promoter DNA before the DNA is unwound.

What forms the open complex during transcription initiation?

RNA polymerase unwinds ~14 bp of DNA to form a transcription bubble.

What opens the transcription bubble in Pol II?

Helicase subunits XPB and XPD of TFIIH using ATP.

What is abortive initiation?

RNA polymerase produces and releases short RNAs (2–9 nt) before successfully escaping the promoter.

What triggers transition to elongating complex?

When RNA reaches ~12–15 nt, polymerase changes conformation and loosens grip on sigma factor.

What are the 'lid', 'zipper', and 'rudder' in RNA polymerase?

Structures that hold DNA strands apart during transcription.

How are ribonucleotides added during transcription?

By nucleophilic attack of the 3′ OH on the incoming NTP, releasing pyrophosphate.

What is the role of two Mg2+ ions in RNA polymerase?

One activates the 3′ OH, and one stabilizes the leaving oxygen during nucleotide addition.

What blocks elongation during abortive initiation?

Loop 3.2 in sigma factor and beta-finger in TFIIB obstruct transcript elongation.

What is promoter clearance?

The step where polymerase escapes the promoter after synthesizing 9–11 nt, undergoing conformational change.

What phosphorylation marks promoter clearance in Pol II?

Serine 5 of the CTD by TFIIH.

How fast does RNA polymerase elongate?

About 20–50 nucleotides per second.

What causes transcriptional pausing?

Hairpins in RNA or weak AU-rich DNA-RNA hybrids.

What are elongation factors?

Proteins that modulate pausing or restart transcription after arrest.

What is promoter proximal pausing?

RNA Pol II stalling 30–60 nt downstream of TSS, a regulatory checkpoint.

What is pre-mRNA?

The unprocessed RNA produced by RNA Pol II before splicing and modification.

What causes pause in elongation for capping?

NELF and DSIF slow Pol II to allow time for 5′ capping.

What enzymes add the RNA cap?

Capping enzymes recruited by Ser5-phosphorylated CTD.

What triggers elongation resumption?

Phosphorylation of CTD Ser2 by p-TEFb.

What does S2 phosphorylation recruit?

Additional RNA processing enzymes.

What do transcript cleavage factors do?

Assist RNA Pol in resuming synthesis by cleaving backtracked RNA.

What cleavage factors are used in prokaryotes and eukaryotes?

GreA/GreB in E. coli; TFIIS in eukaryotes.

What structure do cleavage factors act through?

Funnel region of RNA polymerase.

What do histone chaperones do during elongation?

Remove nucleosomes ahead of RNA Pol and reassemble them behind.

Which histone chaperones are involved in transcription?

FACT, Asf1, and Spt6.

How is supercoiling managed during transcription?

DNA gyrase removes positive supercoils; topoisomerase I removes negative ones.

What are the two types of bacterial terminators?

Intrinsic terminators and Rho-dependent terminators.

What defines an intrinsic terminator?

A stem-loop in RNA followed by a string of U's causes RNA polymerase to dissociate.

How do Rho-dependent terminators work?

Rho binds rut sites, translocates with ATP, and pulls RNA from RNA polymerase.

What is the function of Rat1 in eukaryotic termination?

Rat1 degrades RNA downstream of poly(A) site to displace RNA Pol II (torpedo model).

What does the allosteric model of termination propose?

Conformational change in RNA Pol II after mRNA cleavage leads to transcription termination.