Exam 2 Spring 2011

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MOLECULAR BIOLOGY (BIO 3913) 2011

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D. transcription-activation domain and kinase domain E. DNA-binding domain 5) Which of the following is present in the core RNA polymerase of bacteria? A. γ B. สน′β C. σ D.ε E. δ. 6) An experiment was designed to obtain nonspecific transcription from both strands of a DNA molecule in bacteria. Which of the following strategies would be most effective in achieving this? A. Include the RNA holoenzyme in the reaction. B. Use intact DNA. C. Enrich the preparation with sigma subunit. D. Use the core enzyme of RNA polymerase. E. Include the RNA holoenzyme in the reaction, and use the core enzyme of RNA polymerase. 7) Which of the following statements is true about a lac operon with this genotype? I-d O+ Z+ Y- AA. The operon is nonrepressible. B. The operon is repressible. C. The mutation is only cis-dominant. D. The operon is uninducible. E. None of the choices is correct. 8) You are planning an experiment to look at the specific binding of the TATA-box binding proteins (TBP) to the promoter. Which of the following would be a suitable negative control for this experiment? A. DNA strand containing the TATA box linked to multiple adenine B. a DNA strand containing the TATA box linked to multiple guanines C. a DNA sequence made with multiple cytosines D. a DNA sequence made with multiple cytosines and a DNA strand with the TATA box linked to multiple adenine E. All above likely 9) Which of the following is true about the holoenzyme of bacterial RNA polymerase in an open complex of bacteria? A. It is true that the DNA is bound mainly by the sigma-subunit, and there is no interaction between the sigma factor and the -10 region. B. There no interaction between the sigma factor and the -10 region. C. There are two Na+ ions in the core enzyme. D. The DNA is bound mainly to the sigma-subunit. E. Region 2.4 of the sigma-factor binds to the -35 region.

Exam # 2 Transcription 6-13
INSTRUCTION AND EXAMPLE: Circle ONLY ONE. Microorganisms include a. Humans b. Animals c. Plants d. Bacteria Circle d = 2 point; No circle, multiple circles or circle a-c = 0

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Place the following in the order that they occur during transcription initiation in bacteria: 1 - formation of open complex; 2 - formation of closed complex; 3 promoter clearance; 4 - synthesis of about 10 nucleotides A. 3, 1, 2, 4 B. 1, 2, 3, 4 C. 2, 1, 2, 4 D. 2, 1, 4, 3 E. 3, 2, 1, 4

2) An antibody was produced and used in an immunohistochemical assay to detect the location of eukaryotic RNA polymerase I in a thin section of a liver biopsy. The section was probed with the antibodies labeled with a fluorescent tag, and then viewed under a fluorescent microscope. State where you would expect to find positive staining if the enzyme is present. A. rough endoplasmic reticulum B. nucleoplasm C. endoplasmic reticulum D. nucleolus E. ribosomes 3) The Histone Code states that the a primary sequence of the histone proteins never changes over time. b combination of histone modification on a given nucleosome near a gene's control region affects the efficiency of transcription of all the nearby genes. c combination of histone modification on a given nucleosome near a gene's control region affects the efficiency of transcription of that gene. d lysines are the only amino acids found in histones that can be acetylated and deacetylated. e histones are found in all living cells. 4) Which of the following are typical features of transcription activators in eukaryotes? They carry A. transcription-activation domain B. transcription-activation domain and DNA-binding domain C. kinase domain

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10) Which of the following is the correct order of chromatin folding? A. radial loop structure, 30 nM fiber formation, nucleosome formation B. nucleosome formation, radial loop formation, nucleosome formation C. 30 nM fiber formation, nucleosome formation, radial loop formation D. nucleosome formation, 30 nM fiber formation, radial loop structure E. 30 nM fiber formation, radial loop formation, nucleosome formation 11) Which of the following would most likely occur in bacteria if an in vitro transcription assay is preformed using a cell extract containing an αsubunit without the C-terminal domain? A. RNA polymerase would become tightly associated with the promoter. B. RNA polymerase would become more susceptible to proteolysis. C. RNA polymerase complex would be loosely associated with the promoter. D. Transcription will be accelerated. E. Recognition of the UP element would be faster. 12) Determine which of the following would most likely lead to a dramatic reduction in eukaryotic transcription. A. absence of the TATA box B. removal of some TAFs (TBP-associated factors) C. removal of TAFII250 D. absence of the TATA box and removal of some TAFs E. none of the choices are correct. 13) Which of the following is the correct order of addition of general transcription factors to the initiation complex in eukaryotes? A. TFIIA+TFIID, TFIIIIB, TFIIF + pol II, TFIIE, TFIIH B. TFIIA+TFIID, TFIIB, TFIIH, TFIIF + pol II, TFIIE C. TFIIA+TFIID, TFIIB, TFIIE, TFIIF + pol II, TFIIH D. TFIIA+TFIID, TFIIH, TFIIIIB, TFIIF + pol II, TFIIE E. TFIIA+TFIID, TFIIE, TFIIIIB, TFIIF + pol II, TFIIH 14) Which of the following plasmids could be used to restore inducible regulation of β-galatosidase in this mutant: I+ Oc Z- Y+ A+? A. I+ Oc Z- Y+ A+ B. I+ Oc Z- Y- AC. I- O+ Z+ Y+ A+ D. I-Oc Z+ Y+ A+ E. Both I+ Oc Z- Y+ A+ and I+ Oc Z- Y- A- are correct.

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15) A new mutant cell line was developed and was found to be defective in polymerase III activity of eukaryotes. Which of the following is likely to be observed in this cell line? a A. There will be an overabundance of secreted proteins. b Splicing function is impaired. c There will be an overproduction of 7 SL RNA. d There will be an overabundance of secreted proteins, and splicing function will be impaired. e All above likely 16) Which of the following techniques would you use to study the role of the BRE in a eukaryotic promoter region? A. S1 nuclease protection analysis B. X-ray crystallography C. linker scanning mutations D. S1 nuclease protection analysis and linker scanning mutations E. linker scanning mutations and X-ray crystallography 17) Predict a possible effect of deleting the enhancers region of the polymerase I gene in eukaryotes. A. reduced transcription of ribosomes B. reduction in the production of most hnRNAs C. reduction in the production of Rpb1 D. reduction in the amount of rRNA made E. reduction in the production of Rpb2 18) Studying Xenopus transcription of somatic and oocyte 5S rRNA genes, Donald Brown and colleagues demonstrated that the difference in the expression patterns in the two types of cells could be seen as a race between A. transcription factors and RNA Pol III. B. histones and transcription factors. C. RNA Pol III and repressors. D. histones and enhancer elements. E. histones and DNA gyrase. 19) Which of the following sigma specificity factors is involved in middle gene transcription during SPO1 phage infection of bacteria? A. gp34 B. gp33 C. gp28 D. gp43 E. host sigma 20) Which of the following is true about the early phase of T7 infection of bacteria? A. Class II genes are the first to be transcribed. B. The host polymerase transcribes class II genes. C. The phage-encoded polymerase transcribes the class I phage genes. D. Class I genes are the first to be transcribed. E. All of the choices are correct.

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21) Which of the following operators is a target of cI gene production of the λ phage? A. OR1 B. OR2 C. OL1 D. OL2 E. all of the choices are correct. 22) Which of the following is true about the interaction with the λ repressor and RNA polymerase at PRM? A. Interaction involves region 4 of σ-factor. B. Interaction between repressor and polymerase is essential for activation of transcription, and interaction involves region 4 of σ-factor. C. Interaction can be disrupted by the binding of CIII. D. Interaction between repressor and polymerase is essential for activation of transcription. E. Interaction between repressor and polymerase is essential for activation of transcription, and interaction can be disrupted by the binding of CIII. 23) One effect of mutating or deleting the activation domain of a transcription activator in eukaryotes would be A. binding of the activator to DNA, without activating transcription. B. reduction in the binding of TFIIA. C. reduction in the binding TFIID. D. reduction in the binding of TFIIA and reduction in the binding TFIID. E. reduction in the binding TFIID and binding of the activator to DNA, without activating transcription. 24) Which of the following statements is true about the cro gene of the λ phage? A. It is adjacent to the cIII gene. B. Its product promotes repressor activity. C. It must be stimulated during lysogeny. D. cro repression is important to lysogeny. E. It must be stimulated during lysogeny and its product promotes repressor activity are correct. 25) An electrophoretic mobility shift assay (EMSA) was conducted to check for the binding of TFIIB to a segment of a DNA promoter region. Which of the following approaches could be used to confirm that TFIIB is indeed binding? A. Complete TFIIB binding with TFIID. B. Use an antibody to TFIIB and check for a supershift by EMSA. C. Conduct a nuclear run-off assay. D. Use an antibody to TFIIB and check for a supershift by EMSA and complete TFIIB binding with TFIID are correct. E. Complete TFIIB binding with TFIID and conduct a nuclear run-off assay are correct.

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26) Predict the outcome of the removal of the N from the DNA sequence of the λ phage: A. lysogenic cycle will be induced. B. entry into the bacterial host will be blocked. C. antitermination will be affected. D. transcription from the left promoter will be interrupted. E. antitermination will be affected, and transcription from the left promoter will be interrupted. 27) HMG I (Y) plays a role in IFN-β transcription by a suppressing IFN-β expression during a viral infection. b suppressing IFN-β expression during a viral infection and binding to the HMG domain of LEF. c binding to the HMG domain of LEF. d bending the DNA, causing more activators to bind and interact with each other to enhance transcription and suppressing IFN-β expression during a viral infection. e bending the DNA, causing more activators to bind and to interact with each other to enhance transcription. 28) During an experiment to study the rate of infection of bacteria with T4, the bacterial cultures were accidentally exposed to a UV light source. Which of the following would be expected for this exposure? A. recA gene is turned off. B. Coprotease activity in RecA protein is activated, and SOS response is induced. C. Coprotease activity in RecA protein is activated. D. SOS response is induced. E. recA gene is turned off, and coprotease activity in RecA protein is activated. 29) Which of the following statements is true about a lac operon with the following genotype? I- Oc Z+ YI- O+ Z- YA. β-galactosidase will be constitutively produced. B. A repressor protein will be constitutively produced. C. A trans-dominant mutation is present. D. Permease will be constitutively produced. E. A repressor protein will be constitutively produced, and a cis-dominant mutation is present. 30) Which of the following can be found in DNA-binding domains of transcription activators in eukaryotes? A. zinc fingers B. glutamine-rich regions C. bZIP motifs D. bHLH motif E. all of the choices are correct. 31) Which of the following techniques is most useful in determining if RNA polymerase has initiated transcription from the lac DNA template? A. Southern analysis B. DNA fingerprinting C. RACE

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D. run-off transcription assay E. DNA sequencing 32) In an in vitro transcription assay to detect the level of transcription from a lac operon, one of the RNA precursors was tagged with a fluorescent label on the γphosphate. Which of the following is a likely outcome if transcription occurred? A. The level of fluorescence would increase along the new RNA strand. B. The level of fluorescence would be very high in the assay buffer. C. Each RNA would have a fluorescent tag on every other nucleotide. D. No fluorescence would be detected in the buffer at the end of the assay. E. All of the choices are possible. 33) Which of the following is mostly likely to occur if the level of glucose is low in a bacterial cell? A. CRP activity will be inhibited. B. Cyclic-AMP levels will be depressed. C. CAP will assist in stimulating transcription of the lac operon if lactose is added. D. Both Cyclic-AMP levels will be depressed and CRP activity will be inhibited are correct. E. None of the choices is correct. 34) Which of the following would be effective in vitro in blocking the transcription from the lac operon in the presence of permease? A. antibody to RNA polymerase B. antibody to the repressor protein C. mutation in the operator D. an antibody to β-galactosidase E. All above likely 35) Which of the following is true about the regulation of the trp operon? A. An aporepressor is involved. B. A corepressor is involved. C. Attenuation is one of the control mechanisms. D. Negative control is involved. E. All of the choices are true. 36) Which of the following is absent in an operon? A. both operator and promoter B. promoter C. operator D. Exon E. both promoter and gene 37) Which of the following techniques would be most useful in testing the ability of the core RNA polymerase of bacteria to bind to the promoter? A. gel filtration B. S1 mapping C. Northern blotting

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D. immunoblotting E. DNase footprinting 38) Which of the following is a possible mechanism for the action of NusA in transcription termination of the λ phage? A. It binds to the RNA polymerase causing it to stall. B. It binds to NusB to promote detachment of the RNA polymerase for the DNA template. C. It stimulates termination at intrinsic terminator by facilitating hairpin loop formation. D. It interacts with S10 to promote dissociation of the RNA polymerase. E. It binds to the RNA polymerase causing it to stall and it stimulates termination at intrinsic terminator by facilitating hairpin loop formation. 39) Which of the following statement is false regarding the sigma-factor of bacterial RNA polymerase? A. Interaction with the core enzyme unmasks the DNA-binding region. B. It does not have a DNA-binding domain. C. Subregions 2.4 and 4.2 are involved in promoter recognition. D. It can also bind to the nontemplate strand. E. It can bind to the -10 box. 40) Which of the following are products of RNA polymerase II activity in eukaryotes? A. tRNA B. snRNA C. hnRNA D. snRNA and hnRNA E. tRNA and snRNA 41) Which of the following techniques is suitable for the study of DNA:RNA hybrid formation during transcription? A. DNA:protein crosslinking B. DNA:RNA crosslinking C. DNAase I footprinting D. two-dimensional PAGE E. FRET analysis 42) Which of the following is true about the action of CAP at the lac promoter? A. CAP monomer binds directly to the promoter stimulating polymerase to bind. B. CAP-AMP blocks recruitment of polymerase to the promoter. C. CAP blocks the αCTD of RNA polymerase. D. CAP monomer binds directly to the promoter stimulating polymerase to bind, and CAP blocks the αCTD of RNA polymerase. E. Binding of the CAP-cAMP to the lac activatorbinding site recruits RNA polymerase.

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43) Which of the following is incorrect regarding rhodependent terminators in bacterial transcription? A. They consist of inverted repeats. B. Rho has no helicase activity C. They contain several T's in the non-template strand. D. Rho binds to the growing transcripts. E. They form hairpin loops. 44) Which of the following does not have a DNA-binding domain? A. UP region B. sigma-factor C. alpha-factor D. beta E. beta prime 45) Which of the following conditions does not lead to a change in gene expression patterns in bacterial cells? A. sporulation B. heat shock C. nutrient availability D. nitrogen deprivation E. none of the choices are correct. 46) You were asked to choose a method to separate a mixture of eukaryotic polymerases. Which of the following methods would you choose? A. chromatography B. western blotting C. S1 nuclease assay D. DNase 1 footprinting E. chromatography and UMP incorporation assay 47) Which of the following is involved in maintaining lysogeny in λ phage? A. PRE B. PRO C. PRM D. PRL E. all of the choices are correct. 48) Which of the following would you choose to specifically collect polymerase subunits in cell extracts? A. epitope tagging B. immunoprecipitation C. in vitro transcription D. western blotting E. DNAase footprinting 49) Which of the following is a reasonable way to explain the ability of enhancers to act at a distance? A. The activator binds to an enhancer, changing the supercoiling state of the DNA and opening up the promoter to general transcription factors.

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B. The activator binds to an enhancer, slides along the DNA until it encounters the promoter, and activates transcription. C. An activator binds to an enhancer, creating loops in the DNA, which leads to the interaction of proteins at the promoter and activation of transcription. D. An activator binds to an enhancer and a downstream segment to form a loop, which causes the protein to track toward the promoter and activate transcription. E. All of the choices explanations are possible. 50) One method used by researchers to demonstrate the existence of nucleosome free DNA regions is A. Nuclear Run on experiments. B. DNase hypersensitivity experiments. C. Reporter gene experiments. D. RNA Polymerase Run-off experiments. E. Anion Exchange chromatography.

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