Lodish8e Ch10 TestBank

10 - 1
10 Post-transcriptional
Gene Control
PART A: Linking Concepts and Facts

10.1 Processing of Eukaryotic Pre-mRNA
1. pre-mRNPs that are capped, spliced, and cleaved must be _____ before they are called nuclear mRNPs.
a. elongated
b. phosphorylated
c. polyadenylated
d. transcribed
Ans: c
Question Type: Multiple choice
Chapter: 10
Blooms: Remembering, Understanding
Difficulty: Easy
2. The RNA recognition motif is the most common RNA-binding domain in hnRNP proteins. Another name for this
motif is:
a. RNA-binding domain.
b. RNA motif.
c. KH motif.
d. all of the above
Ans: a
Chapter: 10
Difficulty: Easy
3. In an experiment you have used recombinant DNA technology to create hnRNP C protein tagged with green
fluorescent protein and hnRNP A1 protein tagged with red fluorescent protein. What would you expect to see when
the proteins are expressed and visualized in Xenopus cells?
a. green fluorescence only in the cytoplasm
b. red fluorescence only in the nucleus
c. red fluorescence only in the cytoplasm
d. green and red fluorescence in the nucleus
Ans: d
Chapter: 10
Blooms: Applying, Analyzing
Difficulty: Difficult
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4. Mutations that affect the binding of an SR protein to an exonic splicing enhancer can cause exon skipping in some
genes, producing mRNAs that when translated yield nonfunctional proteins. In addition to an RNA-binding domain,
SR proteins also contain an RS domain that is involved in binding:
a. DNA.
b. RNA.
c. protein.
d. none of the above
Ans: c
Chapter: 10
Difficulty: Moderate
5. Sequencing of small RNAs isolated from metazoan cells revealed low levels of short, capped
RNAs transcribed from both the sense and antisense strands of DNA. What is the term used to describe the fact that
the majority of the metazoan genome is transcribed?
a. permissive transcription.
b. persuasive transcription.
c. pervasive transcription.
d. progressive transcription.
Ans: c
Chapter: 10
6. The consensus sequence for poly(A) addition is

a. the site of poly(A) tail addition.
b. AAUAAA.
c. downstream of the cleavage site.
Ans: b
Chapter 10
Difficulty: Easy
7. Histone mRNAs lack

a. poly(A) tails.
b. introns.
c. a 3´UTR.
d. all of the above
Ans: d
Chapter 10
Difficulty: Easy
8. Which process involves two transesterification reactions?

a. splicing
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b. RNA editing
c. capping
d. nuclear transport
Ans: a
Chapter 10
9. Splice sites in pre-mRNA are marked by two universally conserved sequences located
a. in the middle of introns.
b. at the ends of exons.
c. at the ends of introns.
Ans: c
Chapter 10
10. Splicing joins

a. two intron sequences.
b. two polypeptides.
c. two DNA molecules.
d. two exon sequences.
Ans: d
Chapter 10
Difficulty: Easy
11. The branch-point A residue involved in lariat formation is part of the

a. intron.
b. exon.
c. 5´'UTR.
d. 3´UTR.
Ans: a
Chapter 10
12. Indicate the order in which the following steps occur in the production of a mature mRNA.
a. initiation of transcription, splicing, addition of 5´ cap, addition of poly(A) tail, transport to cytoplasm
b. initiation of transcription, addition of 5´ cap, splicing, addition of poly(A) tail, transport to cytoplasm
c. initiation of transcription, addition of poly(A) tail, addition of 5´ cap, splicing, transport to cytoplasm
d. initiation of transcription, addition of 5´ cap, addition of poly(A) tail, splicing, transport to cytoplasm
Ans: d
Chapter 10
10 - 4
13. Components of the spliceosome include

a. a pre-mRNA
b. proteins that react immunologically with the sera of patients with systemic lupus erythematosus.
c. U1 snRNA, which interacts with the 5´ splice site in pre-mRNA.
d. all of the above
Ans: d
Chapter 10
14. This type of RNA functions in the removal of introns from pre-RNAs.
a. snRNA (small nuclear RNA)
b. snoRNA (small nucleolar RNA)
c. siRNA (small interfering RNA)
d. miRNA (micro RNA)
Ans: a
Chapter 10
10.2 Regulation of Pre-mRNA Processing

15. In birds, a gene encoding a Ca2+-activated K+ channel is expressed in auditory hair cells as multiple mRNAs,
which encode for proteins that open at different Ca2+ concentrations. The Ca2+ concentration at which the channel
opens allows these cells to respond to different sound frequencies. Which one of the following would explain the
appearance of the various isoforms of this particular channel?
a. the presence of chain-terminating mutations
b. exon skipping
c. the absence of compensating mutations
d. alternative splicing
Ans: d
Chapter 10
16. Sex-lethal protein in Drosophila can best be described as a(n)

a. splicing regulatory factor.
b. RNA editing factor.
c. transcription factor.
d. all of the above
Ans: a
Chapter 10
10 - 5
17. Which of the following does not require enzymes?

a. RNA editing
b. excision of group II introns
c. trans-splicing
d. excision of group III introns
Ans: b
Chapter 10
18. RNA editing is

a. post-transcriptional alteration of mRNA sequences.
b. pretranscriptional alteration of RNA sequences.
c. post-transcriptional joining of two RNA molecules.
Ans: a
Chapter 10
Difficulty: Easy
10.3 Transport of mRNA Across the Nuclear Envelope
19. The export of mRNAs outside the nucleus requires several proteins that are post-translationally modified by:
a. acetylation.
b. methylation.
c. phosphorylation.
d. ubiquitination.
Ans: c
Chapter 10
20. Some _____ have evolved a constitutive transport element within their genome, which allows for the export of
unspliced RNAs into the cytoplasm.
a. nematodes
b. mammals
c. retroviruses
d. trypanosomes
Ans: c
Chapter 10
Difficulty: Easy
21. Which of these events does not occur within the nucleus?
a. RNA editing in mammals
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b. RNA capping
c. polyadenylation
d. RNA editing in protozoans
Ans: d
Chapter 10
22. Which type of RNA participates in nuclear export of mRNA?

a. snRNA
b. hnRNA
c. tRNA
d. rRNA
Ans: b
Chapter 10
Difficulty: Easy
23. Transport of unspliced HIV mRNA from the nucleus to the cytoplasm of host cells is promoted by a virus-
encoded protein named
a. Tat.
b. Rev.
c. nucleoplasmin.
d. Ran.
Ans: b
Chapter 10
10.4 Cytoplasmic Mechanisms of Post-transcriptional Control

24. The RISC complex contains which one of the following proteins?
a. Argonaute
b. DGCR8
c. Dicer
d. Drosha
Ans: a
Chapter 10
25. Knocking out the dicer gene in mammals would lead to a loss of:
a. mRNAs.
b. miRNAs.
c. shRNAs.
d. snRNAs.
10 - 7
Ans: b
Chapter 10
26. You are using a variety of techniques to study how the RISC complex differs between siRNAs and miRNAs and
have found that what distinguishes an RISC complex containing an siRNA from one containing an miRNA is that:
a. the miRNA base-pairs perfectly with its target mRNA.
b. the siRNA base-pairs perfectly with its target mRNA.
c. the miRNA-RISC complex inhibits transcription.
d. the siRNA-RISC complex blocks translation.
Ans: b
Chapter 10
27. The mammalian target of rapamycin (mTOR) complex 1 plays an integral role in all but one of these processes.
Which one is mTOR not directly involved in?
a. Pol III transcription
b. protein degradation
c. ribosome biogenesis
d. promoting cell growth
Ans: b
Chapter 10
28. The cell contains numerous organelles, all with specific functions, but the one that plays a key role in the
digestion of ribosomes, mitochondria, and other organelles is the:
a. autophagosome.
b. endosome.
c. nucleosome.
d. proteasome.
Ans: a
Chapter 10
Difficulty: Easy
29. Which of the following regarding the P-body is FALSE?

a. it contains decapping enzymes
b. it is a deadenylase complex
c. it has exoribonuclease activity
d. it is the site where polysomes form
Ans: d
Chapter 10
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30. Cells use several ways to avoid the translation of improperly processed mRNA molecules. _____ is(are)
considered mRNA surveillance mechanisms.
a. Nonsense-mediated decay
b. Non-stop decay
c. No-go decay
d. all of the above
Ans: d
Chapter 10
31. microRNAs play a key role in which of the following?

a. translational repression
b. viral RNA degradation
c. RNA interference
d. all of the above
Ans: a
Chapter 10
Difficulty: Easy
33. Which of the following does not take part in the degradation process of eukaryotic mRNAs?
a. capping
b. endonucleolytic cleavage
c. exonucleolytic decay
d. poly(A) shortening
Ans: a
Chapter 10
10.5 Processing of rRNA and tRNA

34. Which of the following are NOT found within the nucleus?
a. Cajal bodies
b. histone locus bodies
c. nucleoli
d. P-bodies
Ans: d
Chapter 10
35. Synthesis of pre-rRNA occurs in the

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a. nucleolus.
b. endoplasmic reticulum.
c. extranucleolar area of the nucleus.
d. cytosol.
Ans: a
Chapter 10
Difficulty: Easy
36. The 45S pre-rRNA molecule

a. can organize a nucleolus when present in a single copy.
b. is encoded by tandemly arranged genes.
c. is methylated on specific bases.
d. all of the above
Ans: d
Chapter 10
37. A ribozyme is an RNA sequence

a. that uses Mg2+ ions as a cofactor.
b. with catalytic ability to cleave RNA.
c. that acts in the spliceosome.
d. all of the above
Ans: d
Chapter 10
PART B: Testing on the Concepts

10.1 Processing of Eukaryotic Pre-mRNA
38. How is the 5´ cap added to nascent RNAs?
Ans: A capping enzyme removes the -phosphate from the 5´ end of the nascent RNA emerging from the surface of
a RNA polymerase II complex. A separate subunit of the capping enzyme then transfers a GMP moiety from a GTP
donor to the 5´ diphosphate of the nascent transcript, creating a 5´-5´ triphosphate structure. Separate enzymes
transfer a methyl group from an S-adenosinemethionine donor to the N7 position of the guanine and the 2´ oxygen
of riboses at the 5´ end of the nascent RNA.
Question Type: Essay
Chapter 10
39. In animal cells, nearly all cytoplasmic mRNAs have a 3´ poly(A) tail, which is added to the pre-mRNA before
splicing. What proteins are involved in polyadenylation? Indicate their order of association with pre-mRNA and
their functions.
10 - 10
Ans: (1) Poly(A) signal, which often is an AAUAAA sequence and binds the cleavage and polyadenylation
specificity factor (CPSF); (2) poly(A) site, at which cleavage occurs and addition of A residues begins; and (3) G/U-
rich region, which binds cleavage stimulatory factor (CStF). Polyadenylation of pre-mRNA begins with binding of
CPSF, which is composed of several proteins, to the poly(A) signal. Then, at least three other proteins, including
CStF, bind to the CPSF-RNA complex; interaction of CStF with the downstream GU-rich sequence stabilizes the
entire complex. Binding of poly(A) polymerase to the complex then stimulates cleavage of the RNA at the poly(A)
site and subsequent addition of A residues. Polymerization of A residues initially occurs slowly, but its rate is
enhanced by binding of multiple copies of a protein called PABII. The mechanism by which the length of the
poly(A) tail is restricted to about 200 nucleotides is not known.
Chapter 10
40. What are hnRNP proteins? How were they identified?
Ans: hnRNP proteins are the major protein components of heterogeneous nuclear RNA particles, which consist of
unspliced nuclear mRNA and other nuclear RNAs. To identify hnRNP proteins, investigators exposed cells to UV
irradiation, which causes covalent cross-links to form between RNA and closely associated proteins.
Chromatography of nuclear extracts from irradiated cells on an oligo-dT cellulose column binds the poly(A) tails of
unspliced mRNAs and can be used to recover proteins that have become cross-linked to these RNAs.
Chapter 10
41. snRNP-dependent splicing of pre-mRNA is thought to have evolved from the self-splicing properties inherent
in the sequence of either group I or II introns. Alternative splicing of pre-mRNAs processed by spliceosomes has
been demonstrated, whereas this phenomenon does not occur in RNA transcripts that undergo self-splicing. Explain
this difference.
Ans: In the case where splicing is self-mediated in response to sequence features, splicing is an intrinsic property of
the molecule. This is the case with group I and II introns. In snRNP-mediated splicing, the splicing process,
although responsive to the pre-mRNA sequence, is not dictated by the sequence of the RNA being spliced. For this
reason, splicing of the molecule may be regulated and alternative RNA splicing may occur.
Chapter 10
42. The finding that the short consensus sequence at the 5´ end of introns is complementary to a sequence near the
5´ end of U1 snRNA suggested that this snRNA must interact with pre-mRNA for splicing to occur. Describe three
types of experimental evidence that indicate U1 snRNA is required for splicing.
Ans: Addition of antiserum specific for U1 snRNP prevents in vitro splicing. A synthetic oligonucleotide of the
same sequence as the 5´ end of U1 snRNA competes for the normal U1 snRNA and prevents splicing. Mutations in
either the 5´ splice site of pre-mRNA or U1 snRNA prevent splicing; however, if a compensatory mutation that
restores base pairing is present in the second component, then splicing occurs.
Chapter 10
Blooms: Applying, Analyzing
10 - 11
43. The spliceosomal splicing cycle involves ordered interactions among a pre-mRNA and several U snRNPs.
According to the current model of spliceosomal splicing, which intermediate(s) in the splicing of a pre-mRNA
containing one intron should be immunoprecipitated by anti-U2 snRNP? Which additional intermediate(s) should be
immunoprecipitated by anti-U2AF?
Ans: Four different potential intermediates should be immunoprecipitated by anti-U2 snRNP: (1) a structure
involved in the process of joining the two exons together but still containing the intron; (2) a structure that contains
the excised intron in lariat form; (3) the pre-mRNA with U2 snRNP bound to the 5´ end of the intron; and (4) a
structure consisting of the pre-mRNA, U1 snRNP, and U2 snRNP bound to the branch site. Because U2AF assists
U2 snRNP in binding the pre-mRNA, antibodies against this protein will immunoprecipitate the same complexes.
Chapter 10
44. In yeast, U2 snRNA base-pairs to a short sequence near branch-point A in introns. In higher eukaryotes, this
branch-point sequence is not highly conserved, and a protein called U2AF promotes binding of U2 snRNA to pre-
mRNA. You have produced mice with a knockout mutation in the U2AF gene. Would you expect mice
heterozygous for the U2AF knockout mutation to be viable? Would you expect mice homozygous for the U2AF
knockout mutation to be viable?
Ans: Association of the U2 snRNP with pre-mRNA is a necessary step in splicing. In higher eukaryotes, viability
depends on proper splicing of pre-mRNA. However, assuming that U2AF normally is produced in excess,
heterozygous knockout mice most likely would have sufficient U2AF to support splicing. Thus, little, if any, effect
on the viability of these mice would be observed. Because proper splicing of pre-mRNA is a necessity for the
viability of higher eukaryotes, a homozygous knockout mutation for UA2AF would be expected to be lethal in mice.
Nonlethality would indicate the existence of redundancy in the pre-mRNA splicing mechanism. Because biological
systems often exhibit redundancy to protect the organism, the homozygous knockout mice might survive.
Chapter 10
10.2 Regulation of Pre-mRNA Processing

45. Describe how the Sex-lethal (Sxl) protein is regulated during the development of Drosophila females.
Ans: Early in development, females utilize the Pe promoter to synthesize sxl mRNA containing exons 1 and 2,
which is spliced normally, resulting in the production of early Sxl protein. Later in development, the Pl promoter
located upstream is utilized, producing exons 1 through 4. The Sxl protein made earlier in development binds to this
sxl mRNA, preventing splicing of exons 2 and 3. The resulting mRNA, containing only exons 1, 2, and 4, is
translated into functional late Sxl protein, which also binds to the late sxl pre-mRNA, ensuring its continued
production.
Chapter 10
10.3 Transport of mRNA Across the Nuclear Envelope

46. How does HIV bypass the normal restriction that prevents unspliced mRNAs from being transported from the
nucleus to the cytoplasm?
Ans: The HIV genome codes for a viral protein called Rev. Rev binds to a sequence in the viral RNA called the Rev
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response element (RRE). Once the Rev protein builds up to a sufficient concentration in the host cell, it binds to the
RRE and allows viral RNA to be exported from the host cell nucleus.
Chapter 10
10.4 Cytoplasmic Mechanisms of Post-Transcriptional Control

47. The oocytes of multicellular animals contain stored mRNAs that encode numerous proteins required for early
embryonic development. These proteins, however, are not translated until after fertilization and, therefore, a
mechanism must be in place to ensure the stored mRNAs remain intact and untranslated before they are needed.
Discuss the mechanism that keeps these stored mRNAs from being translated in the oocyte.
Ans: Stored mRNAs in oocytes have short poly(A) tails, consisting of ~20–40 residues. These short tails can bind
only a few molecules of cytoplasmic poly(A)-binding protein (PABPI), which is not enough to interact with the
initiation factor eIF4G. Following fertilization, the poly(A) tail increases in length with the addition of ≈150 A
residues. This facilitates the binding of several PABPI molecules, allowing them to interact with eIF4G in a
multimeric complex with eIF4E, other initiation factors, and the cap at the 5´ end of the mRNA. The stable
conformation that forms is required for the initiation of translation. Thus, stored mRNAs are not translated
efficiently because their short poly(A) tails do not provide enough binding sites to allow PABPI to implement the
stability the complex requires for translation initiation.
Chapter 10
48. How do researchers visualize the cellular locations of specific RNA molecules?
Ans: In one method, researchers manipulate the RNA sequence to include high-affinity binding sites for RNA
binding proteins. They fuse the RNA binding proteins with other proteins that fluoresce as different colors (such as
the green fluorescent protein or the red fluorescent protein). Using these kinds of probes, the subcellular locations of
RNA molecules can be determined by fluorescence microscopy.
Chapter 10
10.5 Processing of rRNA and tRNA

49. The tissue-specific expression of antisense RNA is one experimental approach for selectively shutting down
production of a protein. For example, some researchers have proposed that this approach could be used to regulate
the production of pollen in tobacco, oilseed rape, and maize. The controlled production of sterile male plants, for
example, would eliminate the problem of self-fertilization in the production of hybrid maize seeds. In this approach,
expression of antisense RNA would be controlled by coupling it to a promoter that is specific to anthers, the part of
flowers where pollen is produced. Alternatively, the RNase activity inherent in self-splicing RNA might provide a
sequence-specific means to regulate pollen production. Discuss how a catalytic RNA (i.e., a ribozyme) might be
designed to prevent the expression of proteins needed for pollen production.
Ans: Some RNAs are capable of both sequence-specific base pairing and catalytic activity as an RNase. For
example, when the 400-nucleotide-long intron sequence from Tetrahymena rRNA, a group I self-splicing RNA, is
synthesized in a test tube, it folds and can bind two substrates, a guanine nucleotide and a substrate RNA chain. This
synthetic intron then catalyzes the covalent attachment of the G to the substrate RNA, thereby cleaving the substrate
RNA at a specific site. The release of the two RNA fragments frees the catalytic RNA for repeated rounds of
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catalysis. In principle, through the inclusion of the appropriate sequence for base pairing, a catalytic RNA can be
designed that will bind to any substrate RNA and sever it at a specific site. Engineering a DNA sequence encoding a
properly designed catalytic RNA under control of a tissue-specific set of promoter/enhancer elements and
incorporating it into the germ line of plants could result in the tissue-specific synthesis of a ribozyme capable of
selectively destroying a differentiation-specific mRNA required for pollen production.
Chapter 10
51. What are the main features of splicing pre-tRNAs that distinguish it from splicing pre-mRNAs?
Ans: Splicing of pre-tRNA does not involve spliceosomes. In the first step, an endonuclease-catalyzed reaction
excises the intron, which is released as a linear fragment, and a 2,3-cyclic monophosphate ester forms on the
cleaved end of the 5 exon. A multistep reaction that requires the energy derived from hydrolysis of one GTP and
one ATP then joins the two exons. In contrast, pre-mRNA splicing occurs in spliceosomes, involves two
transesterification reactions, releases the intron as a lariat structure, and does not require GTP. Although these
transesterification reactions do not require ATP hydrolysis, it probably is necessary for the rearrangements that
occur in the spliceosome.
Chapter 10

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10 - 1

PART A: Linking Concepts and Facts

6. The consensus sequence for poly(A) addition is

7. Histone mRNAs lack

8. Which process involves two transesterification reactions?

10. Splicing joins

11. The branch-point A residue involved in lariat formation is part of the

13. Components of the spliceosome include

10.2 Regulation of Pre-mRNA Processing

16. Sex-lethal protein in Drosophila can best be described as a(n)

17. Which of the following does not require enzymes?

18. RNA editing is

10.3 Transport of mRNA Across the Nuclear Envelope

22. Which type of RNA participates in nuclear export of mRNA?

10.4 Cytoplasmic Mechanisms of Post-transcriptional Control

29. Which of the following regarding the P-body is FALSE?

31. microRNAs play a key role in which of the following?

10.5 Processing of rRNA and tRNA

35. Synthesis of pre-rRNA occurs in the

36. The 45S pre-rRNA molecule

37. A ribozyme is an RNA sequence

PART B: Testing on the Concepts

38. How is the 5´ cap added to nascent RNAs?

40. What are hnRNP proteins? How were they identified?

10.2 Regulation of Pre-mRNA Processing

10.3 Transport of mRNA Across the Nuclear Envelope

10.4 Cytoplasmic Mechanisms of Post-Transcriptional Control

10.5 Processing of rRNA and tRNA

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