molecular chapter8_1

What is transcription?

The process of copying one DNA strand into RNA using RNA polymerase, using the template strand.

Which strand matches the RNA sequence in transcription?

The coding strand (same as the RNA except T is replaced by U).

In which direction is RNA synthesized?

5′ to 3′ direction.

What are the three stages of transcription?

Initiation, elongation, and termination.

What is the transcription start site (TSS)?

The first base transcribed, denoted +1.

What is promoter clearance?

When RNA polymerase synthesizes a short RNA (~12–15 nt) and then escapes the promoter.

What forms the transcription bubble?

RNA polymerase separating DNA strands (~14 bp) during initiation.

What happens during elongation?

RNA polymerase moves along DNA, elongating RNA, unwinding DNA ahead and re-pairing it behind.

What is a terminator in transcription?

A DNA sequence that signals the RNA polymerase to stop transcription.

Why is transcription tightly regulated?

To produce only necessary RNA at the right time.

What challenges does chromatin present in eukaryotic transcription?

Nucleosomes block access to DNA.

What are the three enzymes involved in overcoming chromatin during transcription?

Nucleosome remodeling enzymes, histone chaperones, histone modifying enzymes.

What does RNA polymerase I transcribe?

Large rRNAs

What does RNA polymerase II transcribe?

mRNA and small regulatory RNAs.

What does RNA polymerase III transcribe?

tRNA, 5S rRNA, and other small RNAs.

What is special about RNA polymerase II?

It couples transcription with RNA processing via its CTD.

What sequence repeats are found in RNA Pol II’s CTD?

Heptad repeats of Tyr-Ser-Pro-Thr-Ser-Pro-Ser.

What are sigma factors?

Bacterial proteins that direct RNA polymerase to specific promoters.

What is a bacterial holoenzyme?

RNA core enzyme + sigma factor.

How do sigma factors regulate gene expression?

By recognizing specific -10 and -35 promoter sequences and spacing.

What is the extended -10 region?

Additional two bases allowing promoter recognition without -35 element.

What are UP elements?

AT-rich sequences upstream that enhance transcription by binding RNA polymerase α-CTD.

What domains of sigma factor recognize promoter elements?

Domain 2 (-10), Domain 3 (extended -10), Domain 4 (-35).

What is Region 1.1 of sigma factor?

Prevents DNA binding in free sigma.

What is Region 3.2 of sigma factor?

Extends into RNA polymerase active site to help position incoming nucleotide.

How can sigma factor levels be regulated?

Transcriptionally, translationally, by mRNA/protein stability, pro-sigma cleavage, and anti-sigma factors.

What is FlgM?

An anti-sigma factor that binds σF during flagellum base synthesis to prevent premature transcription.

How is σF activated?

FlgM is exported from cell after flagellum base is made, freeing σF to promote late gene transcription.

What are general transcription factors?

Eukaryotic proteins that help RNA polymerases initiate transcription (e.g., TFIID, TFIIB, TFIIH).

What does TFIID do?

Binds TATA box via TBP, bends DNA, and helps initiate complex formation.

What is TFIIH’s function?

Unwinds DNA with helicase and phosphorylates CTD of RNA Pol II.

What is the Mediator complex?

A large protein complex that links transcription factors with RNA Pol II and regulates chromatin.

Which TBP complexes work with Pol I, II, and III?

SL1 (Pol I), TFIID (Pol II), TFIIIB (Pol III).

What promoter elements are recognized by RNA Pol I?

Core promoter and upstream control element (UCE).

Where are Pol III promoter elements located?

Both upstream and downstream of the transcription start site.

What is TFIIIA specific for?

5S rRNA gene transcription by Pol III.