[HARD] Ch. 12 (Part 2)

Which process occurs simultaneously in prokaryotes but is separated in eukaryotes?
A. DNA replication and repair
B. Splicing and replication
C. RNA processing and translation
D. Transcription and translation

D

Explain why transcription and translation are coupled in prokaryotes but separated in eukaryotes, including the role of cellular compartments.

In prokaryotes, there is no nucleus, so transcription occurs in the cytoplasm. Ribosomes can bind mRNA immediately, allowing simultaneous transcription and translation. In eukaryotes, transcription occurs in the nucleus and translation in the cytoplasm. Additionally, RNA processing (capping, splicing, polyadenylation) must occur before export, preventing coupling.

In eukaryotic cells, transcription takes place in the:
A. Cytoplasm
B. Nucleus
C. Ribosome
D. Endoplasmic reticulum

B

Newly synthesized mRNA exits the nucleus through ______ before being translated.

nuclear pores

List and explain the three major RNA processing events required to produce mature mRNA.

RNA processing includes: (1) 5’ capping, where a methylated guanine is added via a 5’-5’ linkage to protect RNA and promote translation; (2) splicing, removing introns and joining exons; (3) polyadenylation, adding ~200 adenines to stabilize RNA and aid export.

Which structure is removed during RNA splicing?
A. Exons
B. Promoters
C. Introns
D. Enhancers

C

Which structure is removed during RNA splicing?
A. Exons
B. Introns
C. Promoters
D. Enhancers

B

Why does eukaryotic transcription require many more proteins than prokaryotic transcription?

Eukaryotic transcription is more complex due to chromatin structure, requirement for multiple transcription factors, mediator complex, and coupling with RNA processing.

The core promoter for RNA polymerase II is approximately:
A. 10 bp
B. 20 bp
C. 40 bp
D. 100 bp

C

The TATA box is recognized by the protein ______.

TFIID (TBP)

Which transcription factor directly binds the TATA box?
A. TFIID
B. TFIIB
C. TFIIH
D. TFIIF

A

Describe the role of TBP (TATA-binding protein) in transcription initiation.

TBP binds the TATA box and bends DNA, enabling recruitment of transcription machinery.

Which element is located downstream of the transcription start site?
A. Inr and DPE
B. TATA box
C. BRE
D. Enhancer

A

Explain the difference between core promoter elements and regulatory sequences.

Core promoter elements are required for initiation; regulatory sequences control expression levels.

Which of the following is NOT a regulatory sequence?
A. Enhancer
B. Silencer
C. Insulator
D. Ribosome

D

What is the role of enhancers in gene expression?

Increase transcription by recruiting activators.

General transcription factors (GTFs) in eukaryotes function similarly to:
A. Ribosomes
B. DNA ligase
C. Sigma factors
D. Helicase

C

Define the pre-initiation complex and list its components.

PIC includes GTFs and RNA Pol II assembled at promoter.

Which factor is responsible for promoter melting and requires ATP?
A. TFIIH
B. TFIIE
C. TFIIB
D. TFIID

A

Explain how TFIIH contributes to transcription initiation.

TFIIH unwinds DNA and phosphorylates CTD.

What triggers promoter escape in eukaryotes?
A. DNA replication
B. CTD phosphorylation
C. Ribosome binding
D. Polyadenylation

B

Describe the structure and function of the CTD (C-terminal domain) of RNA polymerase II.

CTD is a repeat sequence tail that coordinates transcription and processing.

Which amino acid residues in the CTD are phosphorylated during transcription?
A. Glycine
B. Lysine
C. Alanine
D. Serine

D

Explain how CTD phosphorylation changes the behavior of RNA polymerase II.

Phosphorylation enables elongation and recruits processing enzymes, releasing factors.

The mediator complex functions to:
A. Degrade RNA
B. Translate proteins
C. Replicate DNA
D. Link activators to RNA polymerase II

D

Describe the role of the mediator complex in transcription regulation.

Mediator connects activators with RNA Pol II.

Which proteins help access DNA wrapped around nucleosomes?
A. Chromatin remodelers
B. Ribosomes
C. Ligases
D. Polymerases

A

Why is chromatin remodeling necessary for transcription in vivo?

Chromatin remodeling allows access to DNA.

Which elongation factor reduces transcriptional pausing?
A. TFIIS
B. TBP
C. CPSF
D. PAP

A

Explain how TFIIS contributes to proofreading during elongation.

TFIIS stimulates RNA cleavage to correct errors.

P-TEFb kinase phosphorylates:
A. DNA
B. RNA
C. CTD of RNA polymerase II
D. Ribosomes

C

Describe how P-TEFb regulates transcription elongation.

P-TEFb phosphorylates CTD to promote elongation.

5’ capping occurs when RNA is approximately:
A. After transcription ends
B. 100 nucleotides long
C. 20–40 nucleotides long
D. 1–5 nucleotides long

C

Describe the unusual 5’-5’ linkage found in the mRNA cap and its significance.

5’ cap protects RNA and aids translation.

Which enzyme adds the methyl group during capping?
A. RNA polymerase
B. Helicase
C. Methyltransferase
D. Ligase

C

List the four major functions of the 5’ cap.

Cap functions: protection, export, translation, splicing.

Polyadenylation adds approximately how many adenines?
A. 10
B. 50
C. 200
D. 1000

C

Describe the roles of CPSF and CstF in polyadenylation.

CPSF and CstF mediate cleavage and polyadenylation.

Poly-A polymerase uses which molecule as a substrate?
A. ATP
B. GTP
C. UTP
D. CTP

A

Explain why the poly-A tail is important for mRNA stability and export.

Poly-A tail stabilizes RNA and aids export/translation.

Termination in eukaryotes involves:
A. Immediate stopping at gene end
B. DNA replication
C. Ribosome activity
D. Continued transcription followed by release

D

Describe how termination is linked to polyadenylation.

Termination follows cleavage and continued transcription.

RNA polymerase I primarily transcribes:
A. mRNA
B. tRNA
C. rRNA
D. snRNA

C

Compare the promoters used by RNA polymerase I and II.

Pol I uses UCE/core; Pol II uses TATA etc.

Pol III promoters are often located:
A. Upstream only
B. Downstream of start site
C. In introns
D. In ribosomes

B

Describe Box A and Box B elements in Pol III promoters.

Box A and B are internal Pol III promoter elements.

Which factor is universal across all RNA polymerases?
A. TBP
B. CPSF
C. Rho
D. DNA ligase

A

Explain how transcription, RNA processing, and elongation are coordinated.

CTD coordinates transcription and processing.

Predict what would happen if CTD phosphorylation did not occur.

No elongation; transcription stalls.

A mutation prevents 5’ capping. Predict the fate of the mRNA and explain.

Rapid degradation; no translation.