Lodish 8e Ch 10 Test Bank PDF

10 - 4 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 ar...

10 - 4 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 Question Type: Multiple choice Chapter: 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter: 10 Blooms: Applying, Analyzing Difficulty: Difficult 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 Question Type: Multiple choice Chapter: 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter: 10 Blooms: Remembering, Understanding Difficulty: Moderate 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. d. none of the above Ans: b Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Easy 7. Histone mRNAs lack a. poly(A) tails. b. introns. c. a 3´UTR. d. all of the above Ans: d Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Easy 8. Which process involves two transesterification reactions? a. splicing b. RNA editing c. capping d. nuclear transport Ans: a Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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. d. none of the above Ans: c Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 10. Splicing joins a. two intron sequences. b. two polypeptides. c. two DNA molecules. d. two exon sequences. Ans: d Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 10.2 Regulation of Pre-mRNA Processing 2+ + 15. In birds, a gene encoding a Ca -activated K channel is expressed in auditory hair cells as multiple mRNAs, 2+ 2+ which encode for proteins that open at different Ca concentrations. The Ca 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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. d. none of the above Ans: a Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Easy 21. Which of these events does not occur within the nucleus? a. RNA editing in mammals b. RNA capping c. polyadenylation d. RNA editing in protozoans Ans: d Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 22. Which type of RNA participates in nuclear export of mRNA? a. snRNA b. hnRNA c. tRNA d. rRNA Ans: b Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 25. Knocking out the dicer gene in mammals would lead to a loss of: a. mRNAs. b. miRNAs. c. shRNAs. d. snRNAs. Ans: b Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 35. Synthesis of pre-rRNA occurs in the a. nucleolus. b. endoplasmic reticulum. c. extranucleolar area of the nucleus. d. cytosol. Ans: a Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding 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 Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 37. A ribozyme is an RNA sequence 2+ a. that uses Mg ions as a cofactor. b. with catalytic ability to cleave RNA. c. that acts in the spliceosome. d. all of the above Ans: d Question Type: Multiple choice Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 Blooms: Remembering, Understanding Difficulty: Moderate 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. 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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. Question Type: Essay Chapter 10 Blooms: Applying, Analyzing Difficulty: Moderate 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Moderate 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 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult 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. Question Type: Essay Chapter 10 Blooms: Remembering, Understanding Difficulty: Difficult