Chapter 29 RNA Synthesis and Processing

Matching Questions
Use the following to answer questions 1-10:

Choose the correct answer from the list below. Not all of the answers will be used.
a) cis-acting sequences
b) primer
c) alternative splicing
d) spliceosome
e) intercalation
f) amanatin
g) transcription
h) translation
i) RNA editing
j) transcription bubble
k) ribozyme
l) transacting elements

1. mRNA precursors may be spliced by ____________ complexes.

Ans d
:
Section: Introduction

2. RNA synthesis (tRNA, mRNA, and rRNA) is called ____________.

Ans g
:
Section: Introduction

3. Sequences found on the same molecule of DNA that contain information

such as promoter sites are called ____________.

Ans a
:
Section: Introduction
4. Activator and repressor proteins that participate in gene regulation are called
____________.

Ans l
:
Section: Introduction

5. Unlike DNA synthesis, RNA synthesis does not require a ____________.

Ans b
:
Section: 29.1

6. The region of RNA synthesis containing the DNA, RNA, and enzymes is called
the ____________.

Ans j
:
Section: 29.1

7. ____________ The term used to describe the mechanism by which drugs and
other molecules slip between the bases of the DNA helix.

Ans e
:
Section: 29.1

8. A change made to the base sequence of RNA following transcription is called

____________.

Ans i
:
Section: 29.3
 9. ____________ A mechanism of splicing that allows diversity in the proteins
generated from a particular gene.

Ans c
:
Section: 29.3

10. An RNA molecule that is catalytic is called a ____________.

Ans k
:
Section: 29.4

Fill in the Blank Questions

11. At least __________ % of all genetic diseases are caused by mutations that
affect RNA splicing.
Ans: 15 Section: Introduction

12. There are approximately _______________ promoter sites found in E. coli.

Ans: 2000 Section: Introduction

13. The _______________ sequence is determined by an alignment of DNA base

sequences used to deduce a recurring pattern or motif.
Ans: consensus Section: 29.1

14. The coding strand has the _______________ sequence as the RNA transcript
(except T instead of U).
Ans: same Section: 29.1

15. The _______________ subunit of RNA polymerase recognizes promoters

during heat-shock conditions.
Ans: σ32 Section: 29.1

16. The RNA polymerase can unwind approximately _______________ bases, or

about 1.6 turns of B-DNA.
Ans: 17 Section: 29.1
 17. The rate of RNA synthesis in E. coli is approximately _______________
nucleotides per minute.
Ans: 50 Section: 29.1

18. The Rho protein terminates transcription by acting as a ________________.

Ans: helicase Section: 29.1

19. The enzyme _________________ transcribes a single precursor that encodes

for the 18S rRNA, the 28S rRNA, and the 5.8S rRNA.
Ans: RNA polymerase I Section: 29.3

20. RNA self-splicing demonstrates the role of RNA as a __________________.

Ans: catalyst Section: 29.4

Multiple Choice Questions

21. Percentage of diseases caused by mutations that affect mRNA splicing.

A) 2 B) 15 C) 20 D) 30 E) None of the above.
Ans: B Section: Introduction

22. Functions of RNA polymerase include

A) searching for promoter sites. D) a and c.
B) unwinding short stretches of E) a, b, and c.
DNA.
C) detecting termination signals.
Ans: E Section: Introduction

23. DNA footprinting is a technique that allows one to determine

A) the homology between various DNA sequences.
B) how proteins interact with each other when bound to DNA.
C) where proteins bind to DNA.
D) all of the above.
E) none of the above.
Ans: C Section: 29.1
24. The structure of DNA must be in the ________________ for transcription to
occur.
A) closed promoter complex D) all of the above
B) biphasic promoter complex E) none of the above
C) open promoter complex
Ans: C Section: 29.1

25. RNA modification in prokaryotes includes the following:

A) cleavage and modification of nascent RNA.
B) addition of nucleotides.
C) spliceosome-mediated splicing of the nascent RNA.
D) a and b.
E) a, b, and c.
Ans: D Section: 29.1

26. Actinomycin interferes with transcription by

A) binding to the RNA polymerase.
B) disrupting the DNA-RNA duplex.
C) binding to the DNA helix and preventing its use as an RNA template.
D) all of the above.
E) none of the above.
Ans: C Section: 29.1

27. RNA polymerase I transcribes the genes for

A) mRNA precursors. D) all of the above.
B) 18S, 5.8 S, and 28S rRNA. E) none of the above.
C) most tRNA.
Ans: B Section: 29.2

28. Many eukaryotic promoters contain the following significant sites:

A) TATAAT box near –10. D) a and b.
B) a TATA site near –30 to –100. E) b and c.
C) a CAAT site near –40 to –150.
Ans: E Section: 29.2
29. The key event in eukaryotic transcriptional activation is
A) binding of the TATA-box-binding protein (TBP) to the TATA box.
B) binding of the SP-1 protein to the CAAT box.
C) binding of the RNA polymerase 500 base pairs upstream of the CAAT
and TATA boxes.
D) all of the above.
E) none of the above.
Ans: A Section: 29.2

30. Which of the following modifications are made to eukaryotic tRNA

transcripts?
A) modification of base and ribose moieties.
B) removal of 3’ trailer.
C) cleavage of 5’ leader by RNase P.
D) CCA is added.
E) All of the above.
Ans: E Section: 29.3

31. The chemical reaction(s) in RNA splicing include

A) two transesterifications.
B) one transesterification.
C) one transesterification and an oxidation.
D) all of the above.
E) none of the above.
Ans: A Section: 29.3

32. The carboxyl-terminal domain (CTD) of RNA polymerase II is involved in

A) binding to promoter regions of DNA.
B) formation of the transcription bubble.
C) coordinating post-transcriptional processing events.
D) recognition of the termination signal.
E) none of the above.
Ans: D Section: 29.3
 33. Diseases caused by mutations in pre-mRNA or in the splicing factors include
A) Birketts lymphoma. D) a and c.
B) Thalassemia. E) a, b, and c.
C) Retinitis pigmentosa.
Ans: C Section: 29.3

34. Proteins that possess alternative splicing products include

A) calcitonin. D) a and c.
B) hemoglobin β. E) b and c.
C) apolipprotein.
Ans: A Section: 29.3

35. The role of GTP in self-splicing is

A) to provide energy.
B) as a cofactor.
C) as a necessary base for RNA editing.
D) all of the above.
E) none of the above.
Ans: B Section: 29.4

Short-Answer Questions

36. Name the three stages of RNA synthesis.

Ans The three stages of RNA synthesis are initiation, elongation, and
: termination.
Section: Introduction

37. What is the definition of a promoter?

Ans A promoter is a sequence of DNA that directs the RNA polymerase to
: the proper site for transcription initiation.
Section: 29.1
38. What is the significance of the subunit?
Ans The subunit contributes to initiation in several ways. It allows RNA
: polymerase to recognize promoter sites, and decreases nonspecific DNA
to RNA polymerase interaction by decreasing the binding affinity of
nonspecific interactions.
Section: 29.1

39. How does RNA polymerase find the proper binding site?
Ans The RNA polymerase binds to the DNA and slides along it until the
: proper site is found.
Section: 29.1

40. What is the theory for how palindromic RNA polymerase transcription
termination signals function?
Ans In the palindromic region, the bases form a hairpin stem and loop
: structure that is followed by a series of U-A base pairs. It is theorized
that the RNA polymerase stalls at the palindromic sequence, and the
DNA template separates from the nascent RNA at this point.
Section: 29.1

41. What is a common feature of both protein-dependent and protein-

independent termination signals in transcription?
Ans The signals that mediate termination events appear to function in the
: newly synthesized RNA, and not in the template DNA.
Section: 29.1

42. How does the antibiotic rifamycin function mechanistically?

Ans Rifamycin functions by interfering with RNA synthesis initiation. The
: antibiotic binds in a channel required by the RNA-DNA complex,
interfering with formation of the initial phosphodiester bonds.
Section: 29.1
43. Describe a few of the significant differences between eukaryotic and
prokaryotic transcription and translation.
Ans In eukaryotes the two processes are separated: one takes place in the
: nucleus and the other in the cytoplasm. In prokaryotes, the two occur in
the same place, and can be coupled. In addition, eukaryotes have more
complicated RNA processing to form mRNA. Prokaryotes typically have
only one RNA polymerase, whereas eukaryotes contain three types.
Section: 29.2

44. How does binding of heat-shock proteins differ between E. coli and
Drosophila?
Ans Heat-shock transcription factor (HSTF) I Drosophila differs from σ32, E.
: coli, in binding directly to response elements in heat-shock promoters
rather than first becoming associated with RNA polymerase.
Section: 29.2

45. Where are enhancer sequences found in the gene?

Ans Enhancers can be found upstream, downstream, or in the middle of a
: transcribed gene. They are often located thousands of bases away from
the transcriptional start site.
Section: 29.2

46. Approximately, how many mRNA transcripts in higher eukaryotes undergo

processing?
Ans Nearly all mRNA precursors in higher eukaryotes are spliced.
:
Section: 29.3

47. What is unique about the type of RNA editing that occurs in the transcript for
Apolipoprotein B?
Ans The nucleotide sequence of mRNA is changed AFTER its synthesis. A
: specific cytidine residue of mRNA is deaminated to uridine, which
changes an amino acid from Gln to stop.
Section: 29.3
48. What is present in the spliceosome complex?
Ans The spliceosome complex contains the snRNPs, splicing factor proteins,
: and the mRNA molecule.
Section: 29.3

49. Draw the mechanism of lariat formation in a splicing pathway.

Ans Several comparisons are shown in Figure 29.40.
:
Section: 29.4 and Figure 29.40

50. What are the two types of splicing categories?

Ans The reactions are grouped in categories of Group I and Group II. Group I
: uses a guanosine cofactor, whereas Group II utilizes the 2' OH group of
an intron adenylate.
Section: 29.4