Exam 3: Transcription (RNA Synthesis) COMPLETE

Question 1

31. Which of the following strand of DNA is used as a template to direct primary transcript synthesis?

A) Leading strand
B) Lagging strand
C) Coding strand
D) Non-coding strand

Answer 1

D) Non-coding strand

Question 2

32. Promoters are specific DNA sequences that direct RNA polymerase to the proper initiation site. There are -10 (TATAAT) and -35 (TTGACA) consensus sequences that can be recognized by σ70 factor in prokaryotes. These sequences are located on which strand?

A) Coding strand
B) Non-coding strand
C) Template strand
D) Any of the above

Answer 2

A) Coding strand

Non-Template = Coding

Template = Non-Coding

Question 3

33. Catalytic RNA are also called ribozymes that catalyze a chemical reaction. The ribozymes catalyzes specific reactions in a similar way to that of protein enzymes. Which of the following are ribozymes’ activities observed in living organisms?

A) RNase P cleavage of 5’ end of pre-tRNA
B) Hammerhead ribozymes perform self-cleavage
C) Transesterification in spliceosomes
D) All of the above

Answer 3

D) All of the above

Question 4

35. Which statement is correct in terms the differences between DNA polymerase vs RNA polymerase?

A) DNA polymerase uses ATP, GTP, CTP, and UTP as required substrates

B) RNA polymerase requires a primer (either small piece of DNA or RNA)

C) RNA polymerase has proofreading activity (5’ to 3’ exonuclease)

D) RNA polymerase uses ATP, GTP, CTP, and UTP as required substrates

Answer 4

D) RNA polymerase uses ATP, GTP, CTP, and UTP as required substrates

Question 5

36. Molecular recognition of the promoter region (DNA) and E. coli σ70 plays essential roles during RNA transcription initiation complex formation (the figure shown to the right is based on x-ray crystallography). Interactions of σ70 domain 2 (green) with “flipped out” bases (purple) of strand of -10 regions are shown in the figure. The DNA strand in purple (flipped out) stands for which of the following?

A) Non-template strand
B) Okazaki fragment
C) Template strand
D) Anticodon

Answer 5

A) Non-template strand

Question 6

37. RNA synthesis occurs in a complex called ____________, where approximately _______ bases of the DNA are unwound.

A) replication fork; 34
B) transcription bubble; 17
C) ribosome; 30S
D) histone octamer; 8

Answer 6

B) transcription bubble; 17

Question 7

38. In rho-dependent RNA synthesis termination, the rho protein helps terminate the transcription. The rho protein is an ATP-dependent helicase that binds the nascent RNA and pulls it away from RNA polymerase and the DNA template. What is the oligomerization state of the functional rho-protein bound to the nascent RNA?

A) Monomer
B) Dimer
C) Trimer
D) Hexamer

Answer 7

D) Hexamer

Rho-dependant: Hexameric rho protein used to terminate transcription

Rho-independant: elongation complex is dissociated (RNA- Hairpin)

Question 8

39. Since prokaryotic RNA polymerase is distinct from eukaryotic RNA polymerase, it can be the target for antibiotics. Which statement(s) is (are) correct?

A) Rifampicin specifically inhibits bacterial transcription initiation, because it binds to double stranded DNA, preventing it to be used as a template.

B) Actinomycin binds to a pocket in the RNA polymerase channel that is normally occupied by the newly formed RNA-DNA hybrid. Thus, the antibiotic blocks elongation after only two or three nucleotides have been added.

C) Chloramphenicol binds to both prokaryotic and eukaryotic RNA polymerases

D) Rifampicin specifically binds to a channel that nascent RNA strand exits and subsequently blocks the RNA synthesis

Answer 8

D) Rifampicin specifically binds to a channel that nascent RNA strand exits and subsequently blocks the RNA synthesis

The antibotic blocks elongation after only two or three nucleotides have been added.

Question 9

Which of the following best describes Rifampicin?:

A) inhibits initiation by blocking the channel into which the RNA–DNA hybrid generated by the enzyme must pass- Specifically inhibits bacterial transcription elongation

B) binds to double stranded DNA, preventing it to be used as a template - Inhibits both prokaryotic and eukaryotic transcription

Answer 9

A) inhibits initiation by blocking the channel into which the RNA–DNA hybrid generated by the enzyme must pass- Specifically inhibits bacterial transcription elongation

Question 10

Which of the following best describes Actinomycin?:

A) inhibits initiation by blocking the channel into which the RNA–DNA hybrid generated by the enzyme must pass- Specifically inhibits bacterial transcription elongation

B) binds to double stranded DNA, preventing it to be used as a template - Inhibits both prokaryotic and eukaryotic transcription

Answer 10

B) binds to double stranded DNA, preventing it to be used as a template - Inhibits both prokaryotic and eukaryotic transcription

Question 11

40. There are three types of RNA polymerases in eukaryotic cells. RNA polymerase____ is located in a specialized structure called nucleolus, where it transcribes the tandem array of genes for 18S, 5.8S and 28S rRNA. The other rRNA (5S rRNA) and all the tRNA molecules are synthesized by RNA polymerase____, which is in the nucleoplasm. RNA polymerase ____ synthesize the precursor of mRNA as well as several RNA molecules.

A) I, II, III
B) III, II, I
C) I, III, II
D) III, I, II

Answer 11

C) I, III, II

(rRNA)
I: nucleolus (transcribes 18, 5.8, 28)

(mRNA)
II: Precursor for mRNA and snRNA

(tRNA)
III: Synthesizes tRNA and rRNA

Question 12

41. In higher eukaryotes, RNA polymerase II (RNAPII) has evolved a C-terminal domain (CTD) with a tandem array (as high as of 52 copies) of Y1S2P3T4S5P6S7, so-called consensus heptad-repeat sequence. The phosphorylation level of CTD can be read by many protein factors/enzymes, such as 5’ capping enzyme, gaunylyltransferases, which modify the _____end of the pre-mRNA where a _____ is added to the precursor in a _______ linkage.

A) 5’, GTP, 3’-5’
B) 3’, CTP, 3’-5’
C) 5’, GTP, 5’-5’
D) 3’, CTP, 5’-5’

Answer 12

C) 5’, GTP, 5’-5’

-Cap at 5’ end
-pre-mRNA is modified by the addition of the 5’ cap in whihc GTP is added to the precursor in an unusual 5’-5’ linkage

Question 13

42. There are three stages of removing an intron during RNA processing: spliceosome assembly & activation, splicing catalysis, and snRNP recycling. Splicing catalysis occurs via ______ transesterification reactions by ____ and _____. Once spliced out the introns are degraded and the snRNPs are recycled.

A) 2, U3, U6
B) 3, U2, U3
C) 2, U2, U6
D) 3, U6, U3

Answer 13

C) 2, U2, U6

U2: Binds the branch site and forms part of the catalytic center

U6: Catalyzes Splicing

U5: Binds the 5’ splice site and forms part of the catalytic center

Question 14

43. Which of the following posttranscriptional processes can lead to the production of multiple protein isoforms from a single gene?

A) Alternative splicing
B) Capping
C) Phosphorylation
D) Methylation

Answer 14

A) Alternative splicing

In alternative splicing, a pre-mRNA can be spliced in different patterns, generating proteins with different functions

Question 15

CLICKER:
The individual nucleotide units in the linear polymer of single-stranded RNA are linked to one another by:

a. amide bonds
b. glycosidic bonds
c. disulfide bonds
d. hydrogen bonds
e. phosphodiester bonds

Answer 15

e. phosphodiester bonds

Question 16

CLICKER:
Which of the following most accurately describes the relative abundance (by total mass) of RNA species inside cells?

a. mRNA < rRNA < tRNA
b. mRNA < tRNA < rRNA
c. rRNA < tRNA < mRNA
d. tRNA < mRNA < rRNA
e. tRNA < rRNA < mRNA

Answer 16

b. mRNA < tRNA < rRNA

Question 17

CLICKER:
Which of the following strands of DNA always has the same sequence (except T - U) as its corresponding primary transcript?

a. leading strand
b. Watson strand
c. Crick strand
d. template strand
e. coding strand

Answer 17

e. coding strand

Question 18

CLICKER:
The insertion of one nucleotide in the coding sequence of a gene
is most likely to lead to which of the following mutations?

a. frameshift mutation
b. missense mutation
c. nonsense mutation
d. silent mutation
e. transversion mutation

Answer 18

a. frameshift mutation

Frameshift mutations involve the insertion or deletion of nucleotides in the coding sequence of a gene. This insertion or deletion disrupts the normal reading frame of the codons.

Missense mutations (b) involve a change in a single nucleotide that results in the substitution of one amino acid for another. It’s possible that a single nucleotide insertion could shift the reading frame just enough to cause a missense mutation in the next codon, but it would also cause a frameshift mutation for all subsequent codons.

Nonsense mutations (c) involve a change in a single nucleotide that creates a premature stop codon. This results in a truncated protein that is often non-functional. It’s possible for a single nucleotide insertion to shift the reading frame in a way that creates a nonsense mutation downstream.

Silent mutations (d) involve a change in a single nucleotide that does not change the amino acid sequence of the protein. This occurs because the genetic code is degenerate, meaning that some amino acids are encoded by more than one codon. It is very unlikely that a single nucleotide insertion would result in a silent mutation, as it would change the reading frame for all subsequent codons.

Transversion mutations (e) are a type of point mutation in which a purine base (adenine or guanine) is replaced by a pyrimidine base (cytosine or thymine), or vice versa. [This information is not from the provided sources and may need to be independently verified.] Transversion mutations may result from the chemical conversion of one base to another. The insertion of a nucleotide would not result in a transversion mutation.

Question 19

CLICKER:
True or False: Rho-dependent termination of transcription makes use of a hexameric protein, which has RNA-DNA helicase activity.

A) True!
B) False!
C) I have no idea – help!

Answer 19

A) True!

In rho-dependent termination, the hexameric rho protein helps terminate the transcription. The rho protein is an ATP-dependent helicase that binds the nascent RNA strand and pulls it away from RNA polymerase and the DNA template

Question 20

CLICKER:
True or False: In bacteria, mRNA, tRNA and rRNA are all transcribed by the
same RNA polymerase.

A) True!
B) False!
C) I have no idea –
help!

Answer 20

A) True!

RNA polymerase (single) synthesizes all cellular RNA in prokaryotes

• Transcription and translation are linked in prokaryotes, as both processes occur in the cytoplasm of the unicellular organisms.
• Although mRNA undergoes little or no modification after synthesis in
  bacteria, the same is not true for rRNA or tRNA.

Question 21

CLICKER:
Which of the following best describes the TATA box in DNA?

a. It is a sequence in chromosomes that marks replication origins.

b. It is a sequence in the promoter
region of genes that marks transcription start sites.

c. It is a sequence in terminator region
of genes that marks cleavage and
polyadenylation sites.

d. It is a sequence in primary transcripts that marks splice sites to remove introns.

e. It is a sequence in mRNAs that
marks translation start sites.

Answer 21

b. It is a sequence in the promoter
region of genes that marks transcription start sites.

Question 22

CLICKER:
What is a 5’ Cap, structurally?

A. 7-methylguanosine on the 5’ end
of RNA

B. A sequence of adenosine residues
added to the 5’ end of the RNA

C. 3-methyluracil added to the 5’ end
of the RNA

D. 5-methylguanosine on the 3’ end
of the RNA

E. Methylation of the 5’ base of RNA,
preventing further addition of bases
What is a 5’ Cap, structurally?

Answer 22

A. 7-methylguanosine on the 5’ end
of RNA

Question 23

Spliceosomes are primarily composed of which of the following types of RNA?

a. miRNA
b. snoRNA
c. snRNA
d. rRNA
e. tRNA

Answer 23

c. snRNA

The spliceosome is a complex of small
nuclear ribonucleoprotein particles
(snRNPs), which are composed of small nuclear RNAs (snRNAs) and some associated proteins.

The catalytic moieties in the snRNPs are the snRNAs, granting the distinction that the spliceosome is an example of a ribozyme.

Question 24

CLICKER:
Which of the following posttranscriptional processes can lead to the production of multiple protein isoforms from a single gene?

a. alternative splicing
b. capping
c. nuclear export
d. polyadenylation
e. phosphorylation of the CTD

Answer 24

a. alternative splicing

Alternative splicing is a powerful mechanism for expanding protein diversity. In alternative splicing, a pre-mRNA can be spliced in different patterns, generating proteins with different functions

Question 25

(Question from discussion)
If a DNA template strand lacks a rut site, the polymerization of the RNA strand will occur when? (this refers to the DNA strand)

A. A string of adenine residues
B. GC rich sequence
C. A string of uracil residues
D. When the Rho protein reaches RNA polymerase

Answer 25

A. A string of adenine residues

The primary role of a rut site is to act as a signal for Rho protein to bind to the RNA transcript, which then enables Rho to unwind the RNA-DNA hybrid, effectively stopping transcription.

This site (region) consists of a primarily single-stranded, C-rich segment of 40 or more RNA nucleotides that allow stable binding of RNA to the extensive, primary RNA binding site of Rho.

A “rut site” in a DNA template refers to a specific sequence within the DNA that, when transcribed into RNA, becomes a binding site for the Rho protein, which is crucial for terminating transcription in bacteria; it stands for “Rho utilization site” and is characterized by a high concentration of cytosine nucleotides, allowing Rho to recognize and bind to the nascent RNA molecule to initiate termination at a specific point in the gene sequence.

Rut sites are typically rich in cytosine nucleotides and have a relatively low guanine content, forming a single-stranded region on the RNA that is easily recognized by Rho.

Question 26

(Question from discussion)
The -10 (TATAAT) and -35 (TTGACA) consensus sequences are located on which strand?

A. Template strand
B. Non-coding strand
C. Coding strand
D. Any of the above

Answer 26

C. Coding strand