RNAP

Question 1

What is the role of promoter regions in transcription initiation?

Answer 1

Promoter regions are essential sequences upstream of the transcription start site (TSS) that serve as binding sites for general transcription factors (GTFs) and RNA Polymerase II (RNAP II). Key promoter elements include the TATA box, initiator element (Inr), and downstream promoter element (DPE).

Question 2

How does the TATA box interact with transcription factors?

Answer 2

The TATA box is recognized by the TATA-binding protein (TBP), a subunit of the transcription factor TFIID. This interaction induces a structural distortion in the DNA, bending it to facilitate the recruitment of additional transcription factors.

Question 3

What is the sequence of events in the assembly of the transcription pre-initiation complex?

Answer 3

1. TFIID binds the TATA box, inducing DNA bending. 2. TFIIB binds adjacent to TFIID, stabilizing its interaction with the promoter. 3. RNAP II, along with TFIIF, TFIIE, and TFIIH, forms the complete pre-initiation complex (PIC).

Question 4

What role does TFIIH play in transcription initiation?

Answer 4

TFIIH unwinds the DNA at the TSS, powered by ATP hydrolysis, exposing the template strand for transcription. It also phosphorylates serine residues in the C-terminal domain (CTD) of RNAP II, enabling the transition from transcription initiation to elongation.

Question 5

What are the structural motifs involved in transcription initiation?

Answer 5

1. TBP and DNA Binding: The β-sheet of TBP interacts with the minor groove of DNA. 2. TFIIH Helicase and Kinase Activity: TFIIH unwinds DNA and phosphorylates the CTD of RNAP II.

Question 6

How do activators and repressors regulate transcription initiation?

Answer 6

Activators bind to enhancer elements and facilitate the recruitment of GTFs and RNAP II by looping DNA, while repressors inhibit transcription through competitive binding or recruiting chromatin-modifying enzymes.

Question 7

What are the three types of eukaryotic RNA polymerases and their functions?

Answer 7

1. RNAP I: Synthesizes large ribosomal RNAs (rRNAs). 2. RNAP II: Transcribes mRNAs, microRNAs, and some small nuclear RNAs (snRNAs). 3. RNAP III: Transcribes tRNAs, 5S rRNA, and other small RNAs.

Question 8

What is the mechanism of transcription by RNA Polymerase I?

Answer 8

1. UBF binds to the promoter and induces a DNA loop. 2. SL1 binds, stabilizing the complex and recruiting RNAP I.

Question 9

What is the mechanism of transcription by RNA Polymerase II?

Answer 9

1. TFIID binds the TATA box, inducing DNA bending. 2. TFIIB, TFIIE, and TFIIH assemble with RNAP II to form the pre-initiation complex (PIC). 3. TFIIH unwinds DNA and phosphorylates the CTD, allowing transcription initiation.

Question 10

What is the mechanism of transcription by RNA Polymerase III?

Answer 10

1. TFIIIC binds internal promoter sequences for tRNAs or upstream elements for 5S rRNA. 2. TFIIIB, including TBP, recruits RNAP III to the promoter.