Molgen practice questions - Exam 2

10. Which of the following is/are true? a. RNA polymerase III promoters usually contain positions that lie downstream of the startpoint b. RNA polymerase III can initiate at its promoters in the absence of any additional factors c. RNA Polymerase III functions primarily within the nucleolus d. all of the above e. only b. and c.

a

118. Which of the following statements about telomerase is incorrect? a. It is a DNA Polymerase that generates a double stranded DNA. b. It is a reverse transcriptase. c. It requires a primer. d. It does not require a template at the end of the chromosome because it carries its own template. e. None of the above.

a

124. Which of the following is/are true of snRNPs (snurps)? a. They are made up of both protein(s) and RNA. b. They bind to splice sites at each end of the exon. c. They are involved in splicing reactions of group II intron. d. All of the above. e. Only A. and C

a

128. A scientist studying a "new" organism isolated splicing intermediates, representing excised intron(s), and determined their structure. These molecules were linear and all had a G at the 5' end... From what you know about splicing, what is the most likely explanation of these results? a. Group I introns were involved b. Group II introns were involved c. This was RNA editing not splicing d. Alternative tail signals were used e. Trans splicing was taking place.

a

131. Statement A. An origin (e.g. oriC) is a cis-acting element that can support replication of any DNA sequence joined to it (in appropriate cell). Statement B. Some bacterial chromosomes (genomes) that are single replicons may contain multiple origins to increase the efficiency of DNA replication. a. Only A is true b. Only B is true c. Both A and B are true d. Both A and B are false

a

31. Concerning the promoters recognized by general sigma factor (σ70) in E. coli, mutations in the -35 region tend to affect the formation of the ______ complexes and the mutations in the -10 region affect the formation of the ______ complexes. a. closed/open b. closed/closed c. open/closed d. open/open e. close or open depending on the gene

a

52. The 3' end of most eukaryotic mRNAs contains a ______, while the 5' end has a ______. a. poly(A) tail, methylated guanosine cap b. poly(U) tail, methylated guanosine cap c. methylated guanosine cap, poly(A) tail d. poly(A) tail, sulfonated guanosine cap e. methylated guanosine cap, poly(U) tail

a

53. What is(are) the major difference(s) between intron removal in group I and group II introns? a. Group I introns are self-splicing but group II introns are not. b. Group I introns are not self-splicing but group II introns are. c. There are two transeterification reactions for group II introns but only one for group I introns. d. Group II introns are released as "lariats" but group I introns are released in linear form. e. both b. and d.

a

59. Which of the following is false? a. RNA polymerase I transcribes 5S rRNA b. RNA polymerase I requires TBP for initiation of transcription c. RNA polymerase I (generally) requires only two ancillary factors for efficient initiation of transcription d. RNA polymerase I promoters are bipartite consisting of core promoter and UCE e. None of the above

a

11. Which of the following statements best describes the termination of transcription in prokaryotes? a. RNA polymerase transcribes through a stop codon, causing the polymerase to stop advancing through the gene and release the mRNA. b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript. c. RNA polymerase transcribes through an intron, and the snRNPs cause the polymerase to let go of the transcript. d. Once transcription has initiated, RNA polymerase transcribes until it reaches the end of the chromosome. e. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase.

b

111. In order to create the replication forks (initiate DNA replication) in E.coli, oriC needs to be "activated". The first step in this process involves binding of _______ proteins to oriC and melting of short stretch of DNA before other proteins can join the complex. This protein is referred to as the __________. a. DnaA/originator b. DnaA/initiator c. DnaB/helicase loader d. DnaC/helicase e. DnaA/primase

b

114. If the position of a nucleotide (base) in (or near) a transcription unit is assigned the value of -1 this base is _____. a. the startpoint of transcription b. one base upstream from the startpoint of transcription c. the startpoint of translation. d. the last base of transcription unit e. none of the above because bases are never assigned a value of -1

b

119. Which of the following mechanisms can correct and remove/repair pyrimidine dimers in humans? a. photoreactivation b. NER c. Translesion synthesis d. All of the above e. B. and C. only

b

120. What happens when the core DNA polymerase III (in E.coli) on the lagging strand template completes the synthesis of an Okazaki fragment? a. It starts removal of the RNA primer and replaces it with DNA. b. It disengages from the beta clamp. c. It cycles to a clamp loader on the holoenzyme that has been assembled at an RNA primer-DNA template junction closer to the replication fork. d. It cycles to a primase/helicase complex at the replication fork. e. All of the above

b

123. Which of the following is (are) false about RNA? a. snoRNAs aid in processing pre-rRNA transcripts in the nucleolus. b. miRNAs are essential components of spliceosome. c. If it can form an appropriate 3D structure it may act as a catalyst. d. snRNAs as part of snurps are required for splicing of all nuclear pre-mRNAs e. None of the above.

b

138. Statement A. The activation of origins of replication is very similar in all organisms and requires sequence-specific binding of initiator proteins, melting of AT rich region by initiators that is followed by recruitment of replication machinery. Statement B. At all origins of replication helicases are loaded onto DNA by helicase loaders but only in bacteria they are loaded directly onto single stranded DNA that was melted by the initiators. a. only A. is true c. both A. and B. are true b. only B. is true d. both A. and B. are false

b

14. A mutation in which of the following parts of a protein coding gene is likely to be most damaging to a cell? a. Intron b. internal exon c. 5' UTR d. 3' UTR e. All would be equally damaging

b

2. The optimal promoter for the RNA polymerase holoenzyme with the general sigma factor in E. coli consists of the following features: a. A purine startpoint, -10 hexamer composed mostly of Gs and Cs and -35 hexamer separated from -10 region by at least 20 nucleotides b. A purine startpoint, -10 hexamer composed only of As and Ts and -35 hexamer separated from -10 region by 17-19 nucleotides c. A pyrimidine startpoint, -10 hexamer composed mostly of As and Cs and -35 hexamer separated from -10 region by 17-19 nucleotides d. A purine startpoint, -10 pentamer composed only of As and Ts and -35 pentamer separated from -10 region by at least 20 nucleotides e. Both b. and c. would work equally well

b

20. RNA polymerase moves along the template strand of DNA in the ____ direction, and adds nucleotides to the ____ end of the growing transcript. a. 3' to 5'; 5' b. 3' to 5'; 3' c. 5' to 3'; 5' d. 5' to 3'; 3' e. B. or D. depending on the gene

b

24. What is a ribozyme? a. An enzyme that uses RNA as a substrate b. An enzyme made up of RNA c. An enzyme that catalyzes the association between the large and small ribosomal subunits d. An enzyme that synthesizes RNA as part of the transcription process e. An enzyme that synthesizes RNA primers during DNA replication

b

28. Why is only one strand of DNA transcribed into mRNA? a. Because mRNA is only required in small quantities. b. Because transcribing both DNA strands would produce mRNA molecules coding for entirely different amino acid sequences. c. Because the other strand would produce mRNA coding the same amino acid sequence but in reverse order. d. Because all genes are located on the same DNA strand, while the other strand acts as protection. e. Because the other strand is translated directly into a polypeptide.

b

33. Which of the following is/are true about gene expression in eukaryotic cells a. Transcription, translation and even transcript degradation occur almost simultaneously b. All pre-mRNAs are modified, not just the ones that correspond to interrupted genes c. Modification of pre-mRNAs is "coordinated" by the CTD of the largest subunit of RNA Pol I d. only b. and c. are true e. none of the above

b

57. What is the CTD of the RNA Pol.II thought to do when it is phosphorylated? a. inhibit the enzyme b. recruit a wide variety of processing factors c. unwind the DNA d. unwind the RNA e. separate the DNA and RNA after transcription

b

63. In transcription-coupled repair (TCR), how is the presence of a lesion thought to be detected? a. There are special enzymes that scan the DNA for such lesions. b. The lesion is signaled by a stalled RNA polymerase. c. The lesion is signaled by a stalled DNA polymerase. d. The lesion is signaled by a stalled peptidyl transferase. e. The lesion is detected by single-strand binding proteins.

b

64. Statement A. In eukaryotes the pre-replicative complex (pre-RC) can be formed only during G2 but it remains inactive until the onset of S phase. Statement B. The ability to form pre-RCs or to activate them during different stages of the cell cycle is controlled by the level of activity of Cdk (cyclin dependent kinase) a. only A. is true c. both A. and B. are true b. only B. is true d. both A. and B. are false

b

67. Which of the following is analogous to telomeres? a. the pull tab on a soft drink can b. the two ends of a shoelace c. the central spindle that a CD fits around while in the case d. the mechanism of a zipper that allows the separated parts to be joined e. the correct letters used to replace errors in a document after they have been deleted in a word processor

b

7. One of the RNA polymerase I ancillary factors, SL1, consists of four proteins. One of its component proteins is also required for the initiation by RNA polymerase II and RNA polymerase III as a part of a "positioning" factor. This protein common to all three "positioning" factors is called _______. a. TFIID b. TBP c. TFIIIB d. UBF1 e. PABP

b

73. Which of the following is false about Ames test? a. Mutagens at high concentrations may be cytotoxic and result in fewer colonies than on the control plates (no test chemical present) b. Chemicals that are genotoxic, at concentrations that are not cytotoxic, result in fewer colonies than on the control plates. c. Auxothrophic bacterial strains are used to look for revertants. d. Chemicals that may be converted during the detoxification process to mutagens are treated 1st with liver extracts. e. None of the above

b

77. In order to create the replication forks (initiate DNA replication) in E.coli, oriC needs to be "activated". The first step in this process involves binding of _______ proteins to oriC and melting of short stretch of DNA before other proteins can join the complex. This protein is referred to as the __________. a. DnaX/replicator c. DnaB/helicase loader e. DnaD/primase b. DnaA/initiator d. DnaC/helicase

b

78. Every organism has several different DNA polymerases. There are several families of DNA polymerase that are involved in _______ which, involves addition of nucleotides across abasic sites or damaged/abnormal bases. These enzymes usually are not capable of proofreading which, depends on ____________ activity. a. translational synthesis / a helicase b. translesion synthesis / a 3'to 5' exonuclease c. transdimensional synthesis / a polymerase d. translesion synthesis / a ligase e. transliteral synthesis / a 5' to 3' exonuclease

b

81. Which DNA repair mechanism removes single nucleotides altered by reactive chemicals that may be present in the diet or be produced by metabolism? Such alterations are recognized by enzymes called glycosylases. a. nucleotide excision repair b. base excision repair c. mismatch repair d. double-strand breakage repair e. all of the above

b

83. The best term to describe the extension of the lagging strand template at vertebrate telomeres is a. replication. c. termination. e. transcription. b. reverse transcription. d. translation.

b

90. Assume that the following single strand of DNA was synthesized using standard dA TP , dGTP , dCTP , and dTTP precursors; however, the innermost phosphate (alpha phosphate) of all the dGTPs was labeled with 32P. 3'—CT AGT AGCTT A—5'. Assume also that the strand was degraded to completion by the enzyme spleen diesterase. Spleen diesterase cleaves DNA at the covalent bond that connects the 5' carbon of the sugar to the phosphate. Which of the resulting nucleotide(s) might now carry the 32P? a. A, C, and G b. C and T c. A only d. C, G, and T e. G only

b

93. What must the mismatch repair system be able to distinguish in order to tell which nucleotide of a mismatched pair to replace? a. It must be able to distinguish which chain possesses the right sequence. b. It must be able to distinguish the newly-made strand from the parental strand. c. It must be able to distinguish which chain is of the right polarity. d. It must be able to distinguish which chain contains more incorrect bases. e. all of the above

b

Which of the following is false when activation of oriC and ARS are compared? a. The initiator that binds to oriC is DnaA and the initiator that binds to ARS is a heterohexamer called ORC. b. The activation of both types of origins involves melting of short stretch of DNA by the intitiators c. In both cases the initiators bind to the cis-acting elements within the origins in a sequence specific manner. d. In both cases binding of the initiators to the origins is required for the recruitment of other proteins that are necessary for the formation of replication forks e. none of the above

b

1. Which of the following statements best describes the termination of transcription in eukaryotes by RNA Pol II? a. RNA polymerase transcribes through a stop codon, causing the polymerase to stop advancing through the gene and release the mRNA. b. RNA polymerase transcribes through the terminator sequence, causing the polymerase to fall off the DNA and release the transcript. c. RNA polymerase transcribes through the polyadenylation signal, causing proteins to associate with the transcript and cut it free from the polymerase, which continues to synthesize more "nonfunctional" RNA. d. Once transcription has initiated, RNA polymerase transcribes until it reaches the end of the chromosome. e. It may be a, b or c. depending on a gene.

c

100. Which of the following is not a type of cis-acting element? a. Promoter b. Origin of replication c. Repressor d. Operator e. All of the above are cis¬-acting elements

c

107. O6- methylG may be generated by ______ and this modified base has a tendency to pair with T. Therefore if it is not repaired prior to replication its presence in DNA would lead to _________. a. oxidation/transitions b. deamination/transversions c. alkylation/transitions d. oxidation/deletions or insertions e. alkylation/transversions

c

109. What is the advantage of transcription-coupled repair? a. It allows the cell to do two things at once. b. It ensures that the genes of least importance to the cell receive the highest priority on the repair list. c. It ensures that the genes of greatest importance to the cell receive the highest priority on the repair list. d. It repairs noncoding sequences preferentially. e. It is the most accurate method of repair.

c

12. Which of the following is not an activity of bacterial core RNA polymerase? a. unwinding and rewinding of DNA b. catalyzing addition of ribonucleotides c. recognition of promoters d. holding a newly synthesized portion of RNA product e. holding separated DNA strands

c

121. Which of the following statements about mammalian telomeres is incorrect? a. They all contain multiple copies of a short DNA sequence that is specific for each organism. b. They may protect chromosomes from degradation. c. They can be extended by an enzyme called telomerase that carries an DNA molecule that is complementary to the telomeric repeats. d. They may protect the cell from chromosomal fusions. e. None of the above.

c

122. Which of the following statements about telomerase is incorrect? a. It is a DNA polymerase that generates single stranded DNA. b. It is a reverse transcriptase. c. It does not require a primer. d. It does not require a template at the end of the chromosome because it carries its own template in the form of RNA. e. None of the above.

c

125. All mRNAs contain all of the following except: a. 3' - UTR b. Coding sequence c. Poly A tail d. 5' - UTR e. C. and D.

c

133. Which of the following is a type of cis-acting element primarily "acting" in RNA rather than DNA? a. Promoter b. "up" element c. Intrinsic transcription terminator d. Operator e. Both c. and d.

c

136. A eukaryotic cell having a high level of telomerase activity would a. have a very low probability of becoming cancerous. b. not be able to repair Okazaki fragments. c. be able to proliferate. d. all of the above e. a. and b. only

c

141. Statement A. In eukaryotes the pre-replicative complex (pre-RC) can be formed only during G1 but it remains inactive until the onset of S phase. Statement B. The ability to form pre-RCs or to activate them during different stages of the cell cycle is controlled by the level of activity of Cdk (cyclin dependent kinase) a. only A. is true c. both A. and B. are true b. only B. is true d. both A. and B. are false

c

143. Concerning the promoters recognized by general sigma factor in E. coli, mutations in the -10 region tend to affect the formation of the _______ complexes and the mutations in the -35 region affect the formation of the ______ complexes. a. closed/open d. open/open b. closed/closed e. closed or open depending on the gene c. open/closed

c

16. Why must RNA splicing be absolutely precise? a. A single base error at a splice junction will cause a large deletion. b. A single base error at a splice junction will cause a large addition. c. A single base error at a splice junction will change the reading frame and result in mRNA mistranslation. d. A single base error at a splice junction will lead to premature transcription termination e. All of the above

c

17. _____________ and all the general factors (TFII'X"s) comprise a basal transcription apparatus. a. Sigma factor b. RNA polymerase I c. RNA polymerase II d. A core promoter e. chromatin

c

18. DNA is composed of two strands, only one of which typically is used as a template for RNA synthesis. By what mechanism is the correct strand chosen? a. Both strands are tried and the one that works is remembered. b. Only one strand has the start codon. c. The promoter acts to aim (position) the RNA polymerase. d. A start factor signals the initiation complex. e. It is chosen randomly.

c

19. RNA polymerase and DNA polymerase differ in that a. RNA polymerase uses RNA as a template, and DNA polymerase uses a DNA template. b. RNA polymerase binds to single-stranded DNA, and DNA polymerase binds to double-stranded DNA. c. DNA polymerase is much more accurate than RNA polymerase. d. DNA polymerase can initiate RNA synthesis, but RNA polymerase requires a primer to initiate RNA synthesis. e. RNA polymerase does not need to separate the two strands of DNA in order to synthesize an RNA copy, whereas DNA polymerase must unwind the double helix before it can replicate the DNA.

c

21. What is the name of the enzyme that synthesizes the poly(A) tails of the eukaryotic mRNAs? a. poly(A) endonuclease b. poly(A) exonuclease c. poly(A) polymerase d. RNA polymerase II e. RNA polymerase III

c

22. Which of the following is a type of cis-acting element primarily "acting" in RNA rather than DNA a. promoter b. operator c. exonic splicing silencer d. "up" element e. None of the above

c

25. Alternative sigma factors are used as a means to regulate gene expression in bacteria. A replacement of one sigma factor for another on bacterial RNA polymerase will enable __________ a. a promoter to function as a terminator b. a terminator to function as promoter c. RNA polymerases to initiate transcription using a new (different) set of promoters d. RNA polymerase to read through transcription terminators e. RNA polymerase to terminate at a new set of terminators

c

47. Statement A. Prokaryotic intrinsic transcription terminators consist of two features that are both required for termination to occur: a hairpin that is followed by a run of Us Statement B. Eukaryotic RNA Pol. I and III terminate transcription right after specific terminator sequences similarly to prokaryotic RNA Pol. a. only A. is true c. both A. and B. are true b. only B. is true d. both A. and B. are false

c

48. A specific prokaryotic transcription unit that is 8,000 nucleotides long uses only 1,200 nucleotides to make a protein consisting of 400 amino acids. This is best explained by the fact that a. it may contain several introns that are spliced out. b. there is redundancy and ambiguity in the genetic code. c. many nucleotides may be present within 5' and 3'UTRs. d. nucleotides break off and are lost during the transcription process. e. a. or c.

c

51. What is a maximum number of mature mRNA products resulting from alternative splicing of 4 exons? Assume the most common mechanism. a. 2 b. 3 c. 4 d. 5 e. 6

c

56. Considering a typical prokaryotic or eukaryotic cell what is the most abundant type of RNA? a. mRNA b. tRNA c. rRNA d. miRNA e. snRNA

c

62. As replication proceeds, the lagging strand template of DNA is looped back on itself so that it has the same orientation as the leading strand template; the looped DNA repeatedly grows and shortens during lagging strand replication. This model is often referred to as the _________. a. telescope model c. trombone model e. piccolo model b. extension model d. French horn model

c

68. Which protein/enzyme is used to decatenate E. coli chromosomes after replication? a. DNA Pol. b. telomerase c. topoisomerase d. ligase e. helicase

c

70. One of the factors that may affect initiation of DNA replication in E.coli is _______. a. the acetylation state of histones at oriC b. the acetylation state of As at ori C c. the methylation state of As at oriC d. the methylation state of DnaA e. the methylation state of Ts and ARS

c

71. Nick translation where a part of one DNA strand is replaced by a new strand (e.g. incorporating labeled nucleotides to generate radioactive or fluorescent probes) requires the following enzymatic activities: a. DNA polymerase adding new nucleotides to the 5' end and 3' to 5' exonuclease activity for "old" strand degradation b. DNA polymerase adding new nucleotides to the 5' end followed by ligase activity c. DNA polymerase adding new nucleotides to the 3' end and 5' to 3' exonuclease activity for "old" strand degradation d. Primase activity followed by DNA polymerase adding new nucleotides to the 5' end e. DNA polymerase adding new nucleotides to the 3' end and 3' to 5' exonuclease activity for "old" strand degradation

c

79. All of the following may contribute to stabilizing the 2D and/or 3D structures of RNA except? a. hydrogen bonding via 2'OH group b. base stacking c. C-U base pairing d. G-U base pairing e. U-A-U base triples

c

87. Which of the following is false about the E. coli general sigma factor ( ∂70) a. it contacts promoter directly at -10 and -35 b. mutations in sigma may suppress mutations in promoters c. removal of C-terminus allows sigma (alone) to bind promoters d. It has several DNA binding domains e. none of the above

c

88. The function of eukaryotic telomerase is to a. synthesize DNA primers at the end of each chromosome. b. extend the lagging strand to the end of each chromosome. c. extend the lagging strand template at the end of each chromosome. d. finish the synthesis of the leading strand at the end of each chromosomes e. extend the leading strand template at the end of each chromosome.

c

89. Assume that the following single strand of DNA was synthesized using standard dA TP , dGTP , dCTP , and dTTP precursors; however, the innermost phosphate (alpha phosphate) of all the dTTPs was labeled with 32P. 3'—CTAGTAGCTTA—5'. Assume also that the strand was degraded to completion by the enzyme spleen diesterase. Spleen diesterase cleaves DNA at the covalent bond that connects the 5' carbon of the sugar to the phosphate. Which of the resulting nucleotide(s) might now carry the 32P? a. A, C, and G b. T only c. A and T d. C, G, and T e. A, C, G, and T

c

97. _________ is the correct designation of consensus sequence for the following sequences: AATGCA, GGTGTA, TAGGCG, CGTATA a. RRTGCA b. NATRYA c. NRTGYA d. NYGGYA e. YRTGYA

c

101. Eukaryotic cell lacking a telomerase activity would a. Have a high probability of becoming cancerous. b. Not be able to repair Okazaki fragments. c. Never be able to divide. d. Undergo a reduction in chromosome length during each cell cycle. e. All of the above

d

102. Which of the following is false when activation of oriC and ARS are compared? a. The initiator that binds to oriC is DnaA and the initiator that binds to ARS is a heterohexamer called ORC. b. In both cases the initiators bind to the cis-acting elements within the origins in a sequence specific manner. c. In both cases binding of the initiators to the origins is required for the recruitment of other proteins that are necessary for the formation of replication forks d. none of the above e. both b. and c. are false

d

103. Which of the following is false about A-form double helices? a. they are left handed with ~ 11 bp/turn b. they are a typical confirmation of all nucleic acids under physiological conditions c. they are never found in nature d. all of the above e. a. and b. only

d

104. RNA polymerase and DNA polymerase differ in that a. RNA polymerase uses RNA as a template, and DNA polymerase uses a DNA template. b. RNA polymerase binds to single-stranded DNA, and DNA polymerase binds to double-stranded DNA. c. RNA polymerase is much more accurate than DNA polymerase. d. RNA polymerase can initiate RNA synthesis, but DNA polymerase requires a primer to initiate DNA synthesis. e. RNA polymerase does not need to separate the two strands of DNA in order to synthesize an RNA copy, whereas DNA polymerase must unwind the double helix before it can replicate the DNA.

d

105. Which of the following is false about bacterial RNA polymerase catalyzed reactions (synthesis of RNA) a. NTPs act as substrates b. new nucleotides are always added at the 3' end c. they can occur in the absence of sigma d. they can occur in the alpha subunit e. none of the above

d

108. Transcription involves synthesis of an RNA chain representing one strand of a DNA duplex. The strand with the complementary sequence to RNA product is the ________ strand and the one that has the "same" sequence as the RNA product is the ________ strand. a. antisense/sense b. non coding/non template c. template/coding d. all of the above e. only B. and C. are correct

d

110. 8-OxoG may be generated by ______ and this modified base has a tendency to pair with A. Therefore if it is not repaired prior to replication its presence in DNA would lead to _________. a. oxidation/transitions b. deamination/transversions c. alkylation/transitions d. oxidation/transversions e. alkylation/transversions

d

113. In higher eukaryotes many of the Cs followed by Gs in the so called CpG islands are methylated resulting in 5- mC. These bases have a tendency to be _______ by water giving rise to Ts. If these Ts are not removed prior to replication by ______ they will cause ________. a. alkylation/BER/transversions d. deamination/BER/transitions b. deamination/NER/insertions c. alkylation/BER/transitions d. deamination/BER/transitions e. deaminator/NER/transitions

d

115. Which of the fallowing is false about heat shock or heat shock proteins in E. coli? a. Many of the heat shock proteins function in either protein folding or degradation. b. Many of the heat shock protein genes are transcribed by RNA Pol. holoenzyme with a specialized alternative sigma factor, like RpoH or RpoE. c. At high temperatures general sigma factor (sigma 70) gets inactivated requiring alternative sigma factors for any gene expression to take place. d. Core RNA polymerase is very stable and remains active even above 65 degrees C. e. None of the above

d

126. The 5' end of each Okazaki fragment begins with: a. The same RNA primer that began synthesis on the leading strand b. A DNA primer binding to the template DNA c. DNA polymerase binding to the template DNA d. A separate RNA primer e. A small DNA primer

d

13. Many of the RNA polymerase II promoters are TATA-less but they are still recognized by the same specific GTF in a sequence specific manner. These promoters must contain ______ plus DPE or DCE that are all recognized by a _______ subunit of ________. a. BRE element/TBP/TFIIB b. -35 hexamer/sigma/TFIID c. Lnr/TBP/SL1 d. Inr/T AF/TFIID e. CAAT box/TBP/TFII

d

134. How does active CRP (or CAP) induce expression of the genes of the lac operon? a. It terminates production of repressor molecules. b. It degrades the substrate lactose. c. It stimulates the splicing of the encoded genes. d. It stimulates the binding of RNA polymerase to the promoter. e. It binds steroid hormones and controls translation.

d

139. Which of the following could have an effect on initiation of DNA replication in E.coli? a. binding of seqA at oriC d. all of the above b. binding of DnaA-A TP to oriC e. b. and c. only c. the methylation state at oriC

d

142. Why do eukaryotic nuclear chromosomes have multiple initiation sites (origins of replication) in their DNA unlike bacteria that usually have only one? a. Nuclei of higher organisms can have up to 1000 times the amount of DNA as bacteria. b. Prokaryotic cells incorporate nucleotides at much faster rates. c. Eukaryotic Okazaki fragments are ~10X shorter. d. all of the above e. a. and b. only

d

145. Which of the following may contribute to stabilizing the 2D and/or 3D structures of RNA? a. hydrogen bonding via 2'OH group d. all of the above b. base stacking e. a. and b.only c. G-U base pairing

d

15. Before RNA polymerase II can leave the promoter its CTD needs to be phosphorylated by the ________ activity of ________. a. Phosphatase/TFIIJ b. Kinase/TFIID c. Phosphatase/TFIIH d. Kinase/TFIIH e. TPase/TFIIF

d

23. Which of the following could generate alternative protein products? a. alternative promoter selection b. trans splicing c. alternative splicing d. all of the above e. a. and c. only

d

29. Which of the following is characteristic of the lytic cycle? a. Many bacterial cells containing viral DNA are produced. b. Viral DNA is incorporated into the host genome. c. The viral genome replicates without destroying the host. d. New phages are produced and released while killing the host. e. The virus-host relationship usually lasts for generations.

d

3. How would one describe the bond that holds the inverted methylguanosine cap on the 5' end of a mature mRNA? a. 5'-3' triphosphate bridge b. 3'-5' triphosphate bridge c. 3'-3' triphosphate bridge d. 5'-5' triphosphate bridge e. 5'-3' phosphodiester linkage

d

36. Many of the RNA polymerase II promoters contain ______ , an element generally present at a "fixed" distance upstream from startpoint. When present, this element is bound by ________ via its subunit called _________. a. BRE element/TFIID/T AF b. -35 hexamer/RNAP/sigma c. DPE element/TFIID/T AF d. TATA box/TFIIDTBP e. C. or D.

d

37. Statement A. Some of the nuclear eukaryotic RNA polymerases do not require any accessory factors for recognition of their promoters and the initiation of transcription Statement B. Recognition and stable binding to promoters by prokaryotic RNA polymerases requires only core subunits. a. only A. is true c. both A. and B. are true b. only B. is true d. both A. and B. are false

d

4. Statement A. Eukaryotic RNA Pol. I transcribes both the rRNA and tRNA genes Statement B. Eukaryotic RNA Pol. III transcribes large rRNAs a. Only A. is true c. Both A. and B. are true b. Only B. is true d. Both A. and B. are false

d

41. Alternative splicing a. can allow the production of different mRNAs from a single gene. b. can allow the production of proteins of different sizes from a single gene. c. can allow the production of proteins with different amino acid sequences from a single gene. d. all of the above e. a. and b. only

d

42. Which of the following statements about telomerase is incorrect? a. It is a DNA Polymerase. b. It is a reverse transcriptase c. It carries its own template in the form of RNA. d. It does not require a primer. e. None, because they are all true.

d

43. A eukaryotic DNA sequence containing regulatory elements (binding sites for transcription factors) that can influence transcription activation from a distant location that may even be downstream from the regulated gene is called ______ . a. promoter b. operator c. upstream control element d. enhancer e. terminator

d

44. Which of the following is false about nuclear genes for (large) rRNAs in higher eukaryotes? a. they are transcribed in the nucleolus b. each gene is transcribed into a large precursor RNA that needs to be cut and trimmed to give rise to 3 mature rRNAs c. they are transcribed by RNA Pol I d. they are translated into r-proteins e. none of the above is false; all are true

d

46. Bacterial RNA polymerase passes through several steps prior to elongation. These steps include 1. release or change of association with sigma, 2. formation of an open binary complex. 3. formation of a closed binary complex. 4. abortive initiation. 5. promoter clearance. The correct sequence of events is: a. 3-1-5-2-4 c. 3-2-1-5-4 e. 2-5-1-3-4 b. 2-3-4-5-1 d. 3-2-4-1-5

d

5. If antitermination is utilized to regulate gene expression, this mechanism enables _____ a. promoter to function as a terminator b. a terminator to function as promoter c. RNA polymerases to initiate transcription using a new (different) set of promoters d. RNA polymerase to read through transcription terminators e. RNA polymerase to terminate at a new set of promoters

d

50. Which of the following are not transcribed from DNA? a. Introns b. exons c. rRNA d. poly A tails e. snoRNAs

d

58. A eukaryotic cell lacking telomerase would a. have a high probability of becoming cancerous. b. produce Okazaki fragments. c. be unable to repair thymine dimers. d. undergo a reduction in chromosome length. e. be highly sensitive to sunlight.

d

60. There are 11 GATC sequences within oriC which is 245 bp long. Assuming that all bases are present in the same amounts what would be the (theoretical) minimum length of a DNA fragment to find this sequence once if its occurrence was random? a. 16 b. 64 c. 120 d. 260 e. 400

d

66. Which one of the following is not directly involved in mismatch repair in E.coli? a. MutS b. DNA Pol. c. MutH endonuclease d. Methyltransferase e. exonuclease

d

69. The enzyme polynucleotide phosphorylase randomly assembles nucleotides into a polynucleotide polymer. You add polynucleotide phosphorylase to a solution of adenosine triphosphate and guanosine triphosphate. The resulting artificial mRNA molecule would have ____ possible different codons if the code involved three-base sequences and ____ possible different codons if the code involved four-base sequences. a. 16;32 b. 4;8 c. 4;16 d. 8;16 e. 16;64

d

72. Which of the following is most likely to produce a frameshift mutation? a. alkylaing agents b. nitrous acid c. UV radiation d. Intercalating agents e. Oxidation of a base

d

74. Water can be DNA's "enemy" by participating in all of the following reactions except: a. Hydrolysis generating AP sites (abasic). b. Deamination of Cs converting them to Us. c. Deamination of 5 methyl Cs converting them to Ts. d. Deamination of Ts converting them to Cs e. None of the above

d

76. RNA polymerase and DNA polymerase differ in that a. RNA polymerase uses RNA as a template, and DNA polymerase uses a DNA template. b. RNA polymerase binds to single-stranded DNA, and DNA polymerase binds to double-stranded DNA. c. RNA polymerase is much more accurate than DNA polymerase. d. RNA polymerase can initiate RNA synthesis, but DNA polymerase requires a primer to initiate DNA synthesis. e. RNA polymerase does not need to separate the two strands of DNA in order to synthesize an RNA copy, whereas DNA polymerase must unwind the double helix before it can replicate the DNA.

d

8. Which of the following is true for both prokaryotic and eukaryotic gene expression? a. After transcription, a 3' poly-A tail and a 5' cap are added to mRNA. b. Translation of mRNA can begin before transcription is complete. c. RNA polymerase assisted by a sigma factor binds to the promoter region to begin transcription. d. mRNA is synthesized in the 5' to 3' direction. e. The mRNA transcript is the exact complement of the gene from which it was copied.

d

80. Individuals with the disorder xeroderma pigmentosum are hypersensitive to sunlight because their cells have an impaired ability to a. replicate DNA by translesion polymerases. b. repair chromosomal breaks. c. correct mismatches generated during replication d. remove pyrimidine dimers by NER pathway e. repair pyrimidine dimers by photoreactivation pathway

d

82. Statement A. The activation of origins of replication is very similar in all organisms and requires sequence- specific binding of initiator proteins, melting of AT rich region by initiators that is followed by recruitment of replication machinery. Statement B. At all origins of replication helicases are loaded, by helicase loaders, directly onto single stranded DNA generated by the initiators. a. only A. is true c. both A. and B. are true b. only B. is true d. both A. and B. are false

d

85. What is the proper order of the steps involved in nucleotide excision repair? 1 - Release of the damaged DNA segment between the incisions by a helicase 2 - Sealing of strand by DNA ligase 3 - Lesion recognition 4 - Separation of the duplex's two strands in the region of the lesion by one of the "recognition" proteins in preparation for its removal. 5 - Filling of gap by DNA polymerase 6 - Cutting of the damaged strand on both sides of lesion by endonucleases a. 4-3-6-1-5-2 c. 3-6-4-1-5-2 e. 3-6-4-2-1-5 b. 3-4-6-1-2-5 d. 3-4-6-1-5-2

d

9. Which of the following strategies is not used by phages to organize the expression of their genes into regulatory cascade? a. successive alternative sigma factors b. phage specific RNA polymerase(s) c. antitermination proteins d. successive alternative ribosomes e. All of the above may be used by different phages

d

91. Place the steps in base excision repair (BER) in the correct order. 1 - Damaged base is removed by cleavage of glycosidic linkage attaching it to deoxyribose. 2 - Baseless deoxyribose phosphate in site is excised by a specialized AP endo/exonuclease. 3 - DNA glycosylase recognizes specific altered base. 4 - The strand is sealed by DNA ligase. 5 - Gap is filled by DNA polymerase; it inserts a nucleotide complementary to the undamaged strand. a. 1-3- 2-5-4 c. 1-3- 2-4-5 e. 3-2- 1-5-4 b. 3-1- 2-4-5 d. 3-1- 2-5-4

d

92. In eukaryotic cells, a complex of proteins binds to the broken ends (ds breaks) of the DNA duplex and catalyzes a series of reactions that rejoin the broken strands by a process that usually results in some DNA loss. This is an example of what kind of repair? a. nucleotide excision repair b. base excision repair c. homologous recombination d. nonhomologous end joining e. single-strand breakage repair

d

99. Every organism has several different DNA polymerases. There are several families of DNA polymerases that are involved in __________ which involves addition of nucleotides across abasic sites or damaged/abnormal bases. These enzymes usually are not capable of proofreading which, depends on ____________ activity. a. translational synthesis / a 5' to 3' exonuclease b. translesion synthesis / a 5' to 3' exonuclease c. translesion synthesis / a ligase d. translesion synthesis / a 3'to 5' exonuclease e. translational synthesis / a 5' to 3' exonuclease

d

Which of the following is false about nuclear genes for the 3 largest rRNAs in higher eukaryotes? a. They are transcribed in the nucleolus b. Each "gene" is transcribed into a large precursor RNA that needs to be cut and trimmed to give rise to 3 mature rRNAs c. They are transcribed by RNA Pol I d. They are translated into r-proteins in the cytoplasm e. None of the above

d

106. Which of the following is false about the E. coli general sigma factor ( ∂70) a. it contacts promoter directly at -10 and -35 b. mutations in sigma may suppress mutations in promoters c. removal of N-terminus allows sigma (alone) to bind promoters d. It has several DNA binding domains e. none of the above

e

112. Which type of DNA repair involves the preferential repair of strands of genes that are actively serving as templates for RNA synthesis. a. transcription-coupled repair (TCR) b. nonhomologous end joining (NHEJ) c. base excision repair (BER) d. nucleotide excision repair (NER) e. A. and D. only

e

116. Why do eukaryotic cells have multiple initiation sites in their DNA unlike bacteria that usually have only one? a. Cells of higher organisms can have up to 1000 times the amount of DNA as bacteria. b. Prokaryotic cells incorporate nucleotides at much slower rates. c. Eukaryotic Okazaki fragments are ~10X shorter. d. all of the above e. a. and c. only

e

117. Which one of the following is not directly involved in mismatch repair in E.coli? a. MutS b. DNA Pol c. MutH endonuclease d. Mut L e. They are all involved.

e

127. Which of the following statements about mammalian telomeres is incorrect? a. They all contain multiple copies of a short DNA sequence that is specific for each organism. b. They may protect chromosomes from degradation. c. They can be extended by an enzyme called telomerase that carries an RNA molecule that is complementary to the telomeric repeats. d. They may protect the cell from chromosomal fusions. e. None of the above.

e

129. Which of the following is false about bacterial RNA polymerase catalyzed reactions (synthesis of RNA)? a. dNTPs act as substrates b. New nucleotides are always added to the 3' end c. These reactions occur at the catalytic site located in the sigma subunit d. They can occur in the absence of sigma e. Both A. and C. are false

e

132. Which of the following is a type of cis-acting element primarily "acting" in RNA rather than DNA? a. Promoter b. "up" element c. Intrinsic transcription terminator d. Poly A tail signal e. Both C. and D.

e

137. Which of the following statements about telomerase is incorrect? a. It is a DNA Polymerase that generates a single stranded DNA. b. It is a reverse transcriptase. c. It requires a primer. d. It does not require a template at the end of the chromosome because it carries its own template. e. None of the above.

e

140. Which of the following is false when activation of oriC and ARS are compared? a. The initiator that binds to oriC is DnaB and the initiator that binds to ARS is a homohexamer called ORC. b. In both cases the initiators bind to the trans-acting elements within the origins in a sequence specific manner. c. In both cases binding of the initiators to the origins is required for the recruitment of other proteins that are necessary for the formation of replication forks d. none of the above e. both a. and b. are false

e

144. Which of the following is false about A-form double helices? a. they are left handed with ~ 11 bp/turn b. they are a typical confirmation of all nucleic acids under physiological conditions c. they are a typical confirmation of complementary RNA molecules under physiological conditions d. all of the above e. a. and b. only

e

26. During splicing of nuclear pre-mRNAs the splicing apparatus called _________ has to be assembled in a specific sequence in order to precisely remove all of the _________ and splice together the ____ a. spliceosome/exons/introns b. ribosome/introns/exons c. RNAP holoenzyme/exons/introns d. CTD tail/introns/exons e. spliceosome/introns/exons

e

27. If the position of a nucleotide (base) in (or near) a transcription unit is assigned the value of 0 (zero), this base is _________. a. the startpoint of replication b. the startpoint of transcription c. the startpoint of translation d. the end point of transcription e. none of the above because bases are never assigned a value of 0 (zero)

e

30. Which of the following may help to stabilize eukaryotic mRNAs? a. miRNAs c b. 5' cap c. Poly A tail d. all of the above e. both b. and c.

e

32. Which of the following statements is false about transcription termination in E.coli. a. The responsibility for termination lies (primarily) in the sequences already transcribed b. Intrinsic terminators do not require additional factors, core enzyme is sufficient for termination to occur (at least in vitro). c. E.coli transcription terminators are cis -acting factors d. Rho-dependent terminators require rho factor in addition to RNA polymerase e. None of the above

e

34. Which of the following is false about bacterial RNA pol. catalyzed reactions (RNA synthesis) a. dNTPs act as substrates b. new nucleotides are always added at the 3' end c. these reactions occur at the catalytic site located in the sigma subunit d. they can occur in the absence of sigma e. both a. and c. are false

e

35. In some cases a nonsense mutation in one gene of a bacterial polycistronic transcription unit prevents the expression of the downstream genes in the same unit, an effect referred to as polarity. The most likely explanation for this phenomenon is that... a. the downstream genes are transcribed but not translated because nonsense mutations result in translation termination b. the promoter is not recognized and the transcription is not initiated c. the downstream genes are not recognized by DNA polymerase and thus not replicated d. the downstream genes are not transcribed because of premature transcription termination caused by the exposure of cryptic intrinsic terminator e. the downstream genes are not transcribed because of premature transcription termination caused by the exposure of cryptic rho-dependent terminator

e

38. Transcribe the following sequence: 5' - TCTAGGC- 3'? a. 5' - AGAUCCG- 3' b. 5' - UCUAGGC- 3' c. 5'- GCTAGA- 3' d. 5' CGGAUCU- 3' e. 5' - GCCUAGA- 3

e

39. Using RNA as a template for protein synthesis instead of translating proteins directly from the DNA is advantageous for the cell because a. RNA is much more stable than DNA. b. RNA acts as an expendable copy of the genetic material, allowing the DNA to serve as a permanent, pristine repository of the genetic material. c. many RNA molecules can be transcribed from a single gene, increasing the potential rate of gene expression. d. all of the above e. b. and c. only

e

40. A scientist studying a "new" organism isolated splicing intermediates, representing excised intron(s), and determined their structure. These molecules looked linear, no loops present, but they were branched and resembled the letter "y". explanation of these results? From what you know about splicing what is the most likely a. Group I introns were involved b. Group II introns were involved c. This was RNA editing not splicing d. Alternative tail signals were used e. Trans splicing was taking place

e

45. Which of the following is true about the E. coli general sigma factor ( σ70) a. it contacts promoter directly at -10 and -35 b. mutations in sigma may suppress mutations in promoters c. removal of N-terminus allows sigma (alone) to bind promoters d. It has several DNA binding domains e. all of the above

e

49. Which of the following is (are) true about RNA? a. snoRNA aids in processing pre-rRNA transcripts in the nucleolus. b. miRNAs are essential components of spliceosome. c. It has functional groups that allow it to act as a catalyst. d. all of the above e. a. and c. only

e

54. Transcription involves synthesis of an RNA chain representing one strand of a DNA duplex. The strand that has the "same" sequence as the RNA product is the ________ strand and the one with the complementary sequence (to RNA) is the ________ strand. a. antisense/sense b. sense/antisense c. coding/template d. template/coding e. both b. and c. are correct

e

55. Which of the following is false about a transcription unit a. It is a region of DNA expressed via the production of a single RNA molecule b. The startpoint is assigned a value of +1 (on DNA) c. It always includes nucleotides (bases) assigned only positive values d. It may consist of several genes e. None of the above

e

6. Which of the following does not constitute a difference between intron removal in nuclear pre-mRNAs and group II introns? a. Nuclear pre-RNA introns cannot autosplice and group II introns can. b. Nuclear pre-RNA introns can autosplice but group II introns cannot. c. Nuclear pre-RNAs require spliceosome to carry out the splicing but group II introns do not. d. Nuclear splicing proceeds through a lariat formation but group II intron splicing does not. e. both b. and d. are not true

e

65. Which type of DNA repair involves the preferential repair of strands of genes that are actively serving as templates for RNA synthesis. a. transcription-coupled pathway b. global pathway c. base excision repair d. nucleotide excision repair e. A. and D. only

e

75. What happens when the core DNA polymerase on the lagging strand template completes the synthesis of an Okazaki fragment? a. It disengages from the beta clamp. b. It binds more tightly to the beta clamp. c. It cycles to a new beta clamp that has been assembled at an RNA primer-DNA template junction closer to the replication fork. d. It cycles to a new beta clamp that has been assembled at an RNA primer-DNA template junction farther from the replication fork. e. A. and C. only

e

84. Why do eukaryotic cells have multiple initiation sites in their DNA unlike bacteria that usually have only one? a. Cells of higher organisms can have up to 1000 times the amount of DNA as bacteria. b. Eukaryotic cells incorporate nucleotides at much slower rates. c. Eukaryotic DNA sequences are much more complicated. d. all of the above e. A. and B. only

e

86. Which of the following would have no effect on initiation of DNA replication in E.coli? a. binding of seqA at oriC b. binding of DnaA-A TP to oriC c. the methylation state at oriC d. deletion of oriC from the chromosome e. all of the above will affect initiation of DNA replication

e

94. If the position of a nucleotide (base) in (or near) a transcription unit is assigned the value of 0 (zero), this base is ___________. a. the startpoint of replication b. the startpoint of transcription c. the startpoint of translation d. the end point of transcription e. none of the above because bases are never assigned a value of 0 (zero)

e

95. Which of the following statements is false when comparing prokaryotes with eukaryotes? a. The prokaryotic chromosome is usually circular, whereas eukaryotic nuclear chromosomes are linear. b. Prokaryotic chromosomes usually have a single origin of replication, whereas eukaryotic chromosomes have many. c. The rate of elongation during DNA replication is higher in prokaryotes than in eukaryotes. d. Prokaryotes produce longer Okazaki fragments during DNA replication than eukaryotes. e. The ends of eukaryotic and prokaryotic chromosomes comprise telomeres.

e

96. Which of the following could have an effect on initiation of DNA replication in E.coli? a. binding of seqA at oriC b. binding of ORC to oriC c. the methylation state at oriC d. all of the above e. A. and C. only

e

98. Alternative sigma factors are used as a means to regulate gene expression in bacteria. A replacement of one sigma factor for another on bacterial core RNA polymerase will enable __________ . a. a promoter to function as a terminator b. a terminator to function as promoter c. RNA polymerase to terminate at a new set of terminators d. RNA polymerase to read through transcription terminators e. RNA polymerases to initiate transcription using a new set of promoters

e

Which of the following statements about transcription regulation is incorrect? a. In negative control the default state is "on" unless a repressor binds the operator (in prokaryotes) and turns the gene off. b. The binding of a repressor rotein blocks or reduces transcription. c. Some repressor proteins require the presence of a corepressor molecule in order to bind an operator. d. In positive control the default state is "off" and the transcription is activated to above the basal level only when the activator is bound to its binding element (site). e. In positive control an activator always binds the operator and allows RNA polymerase to initiate transcription.

e