Chapter 26 RNA Metabolism. Multiple Choice Questions. 1. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Ans: B RNA polymerase:

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1 Chapter 26 RNA Metabolism Multiple Choice Questions 1. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Ans: B RNA polymerase: A) binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed. B) can synthesize RNA chains de novo (without a primer). C) has a subunit called lambda, which acts as a proofreading ribonuclease. D) separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them. E) synthesizes RNA chains in the 3' 5' direction. 2. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Ans: B The sigma factor of E. coli RNA polymerase: A) associates with the promoter before binding core enzyme. B) combines with the core enzyme to confer specific binding to a promoter. C) is inseparable from the core enzyme. D) is required for termination of an RNA chain. E) will catalyze synthesis of RNA from both DNA template strands in the absence of the core enzyme. 3. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Ans: B After binding by E. coli RNA polymerase, the correct order of events for transcription initiation is: A) closed complex formation, open complex formation, promoter clearance, start of RNA synthesis. B) closed complex formation, open complex formation, start of RNA synthesis, promoter C) open complex formation, closed complex formation, start of RNA synthesis, promoter D) start of RNA synthesis, closed complex formation, open complex formation, promoter E) start of RNA synthesis, open complex formation, closed complex formation, promoter

2 4. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Ans: B Which one of the following statements about E. coli RNA polymerase (core enzyme) is false? A) It can start new chains de novo or elongate old ones. B) It has no catalytic activity unless the sigma factor is bound. C) It uses nucleoside 5'-triphosphates as substrates. D) Its activity is blocked by rifampicin. E) Its RNA product will hybridize with the DNA template. 5. RNA processing Pages: Difficulty: 1 Ans: B Processing of a primary mrna transcript in a eukaryotic cell does not normally involve: A) attachment of a long poly(a) sequence at the 3' end. B) conversion of normal bases to modified bases, such as inosine and pseudouridine. C) excision of intervening sequences (introns). D) joining of exons. 6. RNA processing Page: 1036 Difficulty: 2 Ans: B The excision (splicing) of many group I introns requires, in addition to the primary transcript RNA: A) a cytosine nucleoside or nucleotide and a protein enzyme. B) a guanine nucleoside or nucleotide (only). C) a protein enzyme only. D) a small nuclear RNA and a protein enzyme. E) ATP, NAD, and a protein enzyme. 7. RNA processing Page: 1036 Difficulty: 2 Ans: E Splicing of introns in nuclear mrna primary transcripts requires: A) a guanine nucleoside or nucleotide. B) endoribonucleases. C) polynucleotide phosphorylase. D) RNA polymerase II. E) small nuclear ribonucleoproteins (snurps). 8. RNA processing Page: 1040 Difficulty: 2 Ans: B Which one of the following is not true of the mrna for ovalbumin?

3 A) Exons are used for polypeptide synthesis. B) Introns are complementary to their adjacent exons and will form hybrids with them. C) The mature mrna is substantially shorter than the corresponding region on the DNA. D) The mrna is originally synthesized in the nucleus, but ends up in the cytoplasm. E) The splicing that yields a mature mrna occurs at very specific sites in the RNA primary transcript. 9. RNA processing Pages: Difficulty: 2 Ans: C Which of the following is not usually essential for the catalytic activity of ribozymes? A) Correct base pairing B) Correct base sequence C) Correct interaction with protein D) Correct secondary structure E) Correct three-dimensional structure 10. RNA-dependent synthesis of RNA and DNA Page: 1050 Difficulty: 2 Ans: A The reverse transcriptase of an animal RNA virus catalyzes: A) degradation of the RNA strand in a DNA-RNA hybrid. B) insertion of the viral genome into a chromosome of the host (animal) cell. C) RNA formation in the 3' 5' direction. D) RNA synthesis, but not DNA synthesis. E) synthesis of an antisense RNA transcript. 11. RNA-dependent synthesis of RNA and DNA Page: 1051 Difficulty: 2 Ans: D Reverse transcriptase: A) can utilize only RNA templates. B) has a 3' 5' proofreading exonuclease but not a 5' 3' exonuclease. C) is activated by AZT. D) is encoded by retroviruses. E) synthesizes DNA with the same fidelity as a typical DNA polymerase. 12. RNA-dependent synthesis of RNA and DNA Page: 1051 Difficulty: 2 Ans: C Compared with DNA polymerase, reverse transcriptase: A) introduces no errors into genetic material because it synthesizes RNA, not DNA. B) makes fewer errors in synthesizing a complementary polynucleotide. C) makes more errors because it lacks the 3' 5' proofreading exonuclease activity. D) synthesizes complementary strands in the opposite direction from 3' 5'.

4 13. RNA-dependent synthesis of RNA and DNA Page: 1056 Difficulty: 3 Ans: D Which one of the following statements about the reverse transcriptases of retroviruses and the RNA replicases of other single-stranded RNA viruses, such as R17 and influenza virus, is correct? A) Both enzymes can synthesize either RNA or DNA from an RNA template strand. B) Both enzymes can utilize DNA in addition to RNA as a template strand. C) Both enzymes carry the specificity for the RNA of their own virus. D) Both enzymes have error rates similar to those of cellular RNA polymerases. E) Both enzymes require host-encoded subunits for their replication function.short Answer Questions 14. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Write the sequence of the messenger RNA molecule synthesized from a DNA template strand (non-coding) having the sequence: (5')ATCGTACCGTTA(3') Ans: (3')UAGCAUGGCAAU(5'). Also acceptable is (5')UAACGGUACGAU(3'). Short Answers 15. DNA-dependent synthesis of RNA Pages: Difficulty: 2 List one basic property that distinguishes RNA polymerases from DNA polymerases, and list one basic property they share. Ans: Among the distinguishing characteristics: RNA polymerase does not require a primer, but DNA polymerase does; RNA polymerase lacks the 3' 5' proofreading exonuclease activity present in DNA polymerase. Among the shared properties: both enzymes use nucleoside triphosphates as substrates, require Mg 2+, produce an antiparallel complement to the template, and synthesize nucleic acids in the direction 5' 3'.

5 16. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Below, an RNA molecule is being transcribed from a strand of DNA. Indicate the 5' and 3' ends of the RNA molecule and of the strand of DNA that is complementary to the RNA molecule. In which direction is synthesis occurring? Ans: 17. DNA-dependent synthesis of RNA Page: 1025 Difficulty: 2 The specific sequences that E. coli RNA polymerase usually binds to in E. coli DNA before initiating transcription generally contain more A+T base pairs than G+C base pairs. In no more than a few sentences, speculate on why this might be the case. Ans: Because A=T base pairs are stabilized by only two hydrogen bonds (compared with three for G+C pairs), double-stranded regions rich in A+T pairs are easier for RNA polymerase to bind and unwind in preparation for the transcription of one of the DNA strands. 18. DNA-dependent synthesis of RNA Pages: Difficulty: 2 Describe the sequence of events in the initiation of transcription by E. coli RNA polymerase. Ans: The core enzyme plus sigma subunit, called holoenzyme, binds to the promoter region forming a closed complex (i.e., in which the DNA double helix is not unwound). This is converted to an open complex by the unwinding of a short region of the promoter. Synthesis of the RNA chain begins within the complex. The complex then moves along the DNA away

6 from the promoter region and the sigma subunit dissociates. 19. RNA processing Pages: 1035, Difficulty: 2 Describe in words (not using structures) the important features of the structures present on the 5' and 3' ends of mature (processed) eukaryotic mrnas. Ans: At the 5' end there is a cap consisting of a guanosine joined to the 5'-terminal nucleotide through a 5' to 5' triphosphate group. This guanine nucleotide is methylated on N- 7. The next two nucleotides in the chain are also sometimes methylated on their 2'-OH groups. At the 3' end is the poly(a) tail consisting of a run of adenylate residues. 20. RNA processing Pages: Difficulty: 2 Describe the mechanistic difference that distinguishes the splicing of group I introns from that of group II introns. Ans: In the group I introns, the initial break in the RNA chain is induced by a free guanine nucleoside. In group II introns, the attacking species is a nucleotide that is part of the intron itself. 21. RNA processing Pages: Difficulty: 2 Define ribozymes. Ans: Ribozymes are enzymes that consist in part or entirely of RNA. 22. RNA-dependent synthesis of RNA and DNA Pages: 1022, Difficulty: 2 Compare transcription and reverse transcription in terms of the following characteristics: (a) direction of polynucleotide synthesis (b) nature of template (c) nature of primer (d) incorporated nucleotides Ans: Reverse Transcription Transcription (a) direction of polynucleotide synthesis 5' 3' 5' 3' (b) nature of template RNA or DNA DNA (c) nature of primer RNA none (d) incorporated nucleotides dntps NTPs 23. RNA-dependent synthesis of RNA and DNA Page: 1051 Difficulty: 2

7 Describe all of the known catalytic activities of reverse transcriptase. Ans: Reverse transcriptase can (1) synthesize DNA complementary to an RNA template; (2) degrade the RNA strand of the resulting RNA-DNA hybrid; and (3) synthesize DNA complementary to the resulting single-stranded DNA.