Deck 27: Information Readout: Transcription and Post-Transcriptional Processing

Question 1

How does the concentration of ribonucleotide triphosphates play a role in the regulation of initiation?

A)a high concentration of ATP is required to form the open-promoter complex
B)high concentration of both ATP and GTP are required to form the open-promoter complex
C)the single nucleotide binding site of RNA polymerase undergoes a conformational change after the first nucleotide to allow subsequent nucleotides to bind more readily
D)binding of the first nucleotide requires a half-saturating concentration of ~100 $\mu$ M while the half-saturating concentration for subsequent nucleotides is only ~10 $\mu$ M
E)none of the above

Answer 1

binding of the first nucleotide requires a half-saturating concentration of ~100 $\mu$ M while the half-saturating concentration for subsequent nucleotides is only ~10 $\mu$ M

Question 2

What type of enzyme activity is associated with the termination factor $\rho$ ?

A)topoisomerase
B)endonuclease
C)exonuclease
D)helicase
E)ligase

Answer 2

helicase

Question 3

Rapid transcription of ribosomal RNA is thought to occur as a result of what unique feature in the DNA that encodes these genes?

A)high A-T content
B)highly repetitive sequence
C)multiple promoter sites that allow high affinity with RNA polymerase
D)presence of hairpin structures in the DNA
E)absence of nucleosomes

Answer 3

E

Question 4

The E. coli core polymerase is missing the ____ subunit and binds to DNA with _______ specificity than the holoenzyme.

A) $\sigma$ ; less
B) $\sigma$ ; greater
C) $\alpha$ ; less
D) $\alpha$ ; greater
E)none of the above

Question 5

What is required for conversion from the closed-promoter complex to open-promoter complex?

A)ATP binding
B)ATP hydrolysis
C)GTP binding
D)GTP hydrolysis
E)DNA bending

Question 6

In eukaryotic cells, RNA polymerase ____ transcribes most of the ribosomal RNA, RNA polymerase ____ transcribes the major structural genes and RNA polymerase ____ transcribes tRNAs.

A)I; II; III
B)I; III; II
C)II; I; III
D)II; III; I
E)III; II; I

Question 7

Rifampicin is known to inhibit RNA synthesis in E. coli. Once the first ten nucleotides have been incorporated, rifampicin does not inhibit RNA synthesis. Which of the following best explains how rifampicin functions?

A)rifampicin binds only to the core enzyme when bound to DNA but can bind to the holoenzyme when not bound to DNA
B)rifampicin can bind to RNA polymerase when the polymerase is not bound to DNA but cannot bind when the polymerase is bound to DNA
C)rifampicin only inhibits when the $\alpha$ subunit is bound to the core enzyme
D)rifampicin is able to bind to the nucleotide binding site at any time
E)none of the above

Question 8

E. coli cells achieve a great deal of gene regulatory expression through the $\sigma$ subunit of RNA polymerase. Which $\sigma$ subunit is present most often since it promotes the production of most of the proteins required under normal conditions within the cell?

A) $\sigma$ ^N
B) $\sigma$ ^S
C) $\sigma$ ^H
D) $\sigma$ ³⁰
E) $\sigma$ ⁷⁰

Question 9

What is the mechanism by which enhancers, despite the fact that they are often several kilobase pairs away from the promoter, activate transcription?

A)DNA unwinding
B)DNA looping
C)chromatin remodeling
D)DNA hairpin formation
E)none of the above

Question 10

The concept of the operon was proposed based on the ability of E. coli to metabolize the disaccharide ________ only when present in large excess over glucose.

A)sucrose
B)cellobiose
C)galactose
D)lactose
E)maltose

Question 11

Which of the following is the first event in the post-translational processing of an E. coli tRNA?

A)ribonuclease P cleavage to create the proper 5' end of the molecule
B)methylation of guanine residues
C)conversion of some uridine residues to pseudouridine
D)endonuclease cleavage of about 170 bases from the 3' end of the molecule
E)removal of 9 nucleotides from the 3' end by ribonuclease D

Question 12

Which subunit of E. coli RNA polymerase is responsible for DNA binding?

A) $\alpha$
B) $\beta$
C) $\beta$ '
D) $\sigma$
E) $\omega$

Question 13

The E. coli promoter region contains a -10 consensus sequence of _________ on the sense strand.

A)GAGAGA
B)CTCTCT
C)GAGGAG
D)GACGTC
E)TATAAT

Question 14

Phosphorylation of the Rpb1 subunit of pol II causes what to occur?

A)binding to histone proteins
B)hydrogen bonding with guanine residues near the start of transcription
C)dissociation from the promoter
D)transcription termination
E)none of the above

Question 15

During factor-independent termination, RNA polymerase pauses upon encountering a _____________ and is then displaced downstream upon encountering a ___________.

A)TATAAT sequence; G-C rich segment
B)G-C rich segment; TATAAT sequence
C)G-C rich segment; string of 4-8 A residues
D)string of 4-8 A residues; TATAAT sequence
E)string of 4-8 A residues; G-C rich segment

Question 16

As RNA polymerase moves along the DNA, it creates a single stranded region of about 18 base pairs that is called a ________________.

A)transcription bubble
B)transcription single-stranded region
C)transcription droplet
D)transcription vesicle
E)transcription bead

Question 17

In vivo, which of the following transcription initiation factors is required for binding to a TATA box?

A)TFIID
B)TFIIE
C)TFIIF
D)TFIIH
E)TAF

Question 18

Transcription of the 5S rRNA gene occurs by ________ covering the entire gene so that pol III can ____________.

A)TFIIB; transcribe the gene several times before dissociating
B)TFIIIC; transcribe the gene several times before dissociating
C)TFIIB; transcribe both strands of DNA before dissociating
D)TFIIIC; transcribe both strands of DNA before dissociating
E)none of the above

Question 19

Which of the following is the most common promoter element for pol II?

A)CAAT box (GGCCAATCT)
B)GC box (GGGCGG)
C)TRE (GAGGGACGTACCGCA)
D)TATA box (TATAAAA)
E)Octamer (ATTTGCAT)

Question 20

Which subunit of E. coli RNA polymerase is responsible for the RNA polymerization reaction?

A) $\alpha$
B) $\beta$
C) $\beta$ '
D) $\sigma$
E) $\omega$

Question 21

Give the mRNA sequence that would result from the following sense strand:
5'-A-T-C-T-C-G-A-T-C-G-T-A-C-G-A-T-G-T-C-A-3'

Question 22

What type of RNA is found in the spliceosome?

A)snRNA
B)tRNA
C)rRNA
D)triple-stranded RNA
E)all of the above

Question 23

Draw a transcription bubble, clearly labeling the proteins and nucleic acids involved in the process.

Question 24

The figure below shows a newly transcribed mRNA still associated with the template DNA. Draw the stem-loop structure that often forms during termination.
3'-GGTCGGGCGGATTACTCGCCCGAAAAAAAA-5'
5'-CCAGCCCGCCUAAUGAGCGGGCUUUUUUUU-3'

Question 25

Which of the following events commonly occur in the processing of eukaryotic mRNA?

A)addition of a 5' cap
B)RNA editing
C)splicing to remove introns
D)alternative splicing to combine different exons into mature mRNA
E)all of the above