OLD EXAM 1

OLD EXAM 1 - Faculty of Science FINAL EXAMINATION BIOLOGY-3 00 MOLECULAR BIOLOGY OF THE GENE VERSION 1 Examiner Prof P Holland Thursday December

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Unformatted text preview: Faculty of Science FINAL EXAMINATION BIOLOGY-3 00 MOLECULAR BIOLOGY OF THE GENE VERSION 1 Examiner: Prof. P. Holland Thursday, December 16"“, 2004 Associate Examiner: Prof. R. Dunn 2 RM. -5 RM. Including the cover page, this exam comprises 12 pages. All questions are multiple choice: There are 50 multiple choice questions worth 2 points each. These questions are to be answered using the first 50 places on the SHORT (120 responsi or less) SCANTRON sheet provided. You should answer all 50 questions. Be sure to fill in the STUDENT NUMBER BOX 011 the left Side of the SCAN TRON sheet as well as the VERSION BOX to the immediate right of the student box. indicating which version number of the exam you used. WARNING: The Examination Security Monitor Program detects pairs of students with unusually similar answer patterns on multiple choice exams. Data generated by this program can be used as admissible evidence. either to initiate or corroborate an investigation or a charge ol‘ cheating under Section 16 of the Code of Student Conduct and Disciplinary Procedures. Each student is responsible for checking that his/her question set contains the correct number of pages and questions. Calculators are NOT required or permitted. No notes or texts are allowed You may keep the exam but be sure to turn in your completed SCANTRON sheet. BIOLOGY 300A VERSION I l. The y2 mutation in Drosophila, caused by the gypsy transposable element, is characterized by a loss of pigmentation in wing and body cuticle, but not in mouth, bristles or tarsal claws. What effect would a mutation which prevents synthesis of the mod (mdg4) protein have on pigmentation in a fly of the y2 phenotype? l) Pigmentation of wing and body cuticle would be restored. 2) There would be no detectable effect on pigmentation ol'wing, body cuticle, mouth parts, bristles or tarsal claws. 3) Pigmentation of mouth parts, bristles and tarsal claws would be lost, whereas pigmentation of wing and body cuticle would be restored. 4) Pi gmentation of mouth parts, bristles and tarsal claws would be lost. Wing anc body cuticle would remain unpigmented 5) Pigmentation would be lost in mouth parts only 2. In the ease of an Olympic skier with an elevated hematocrit, the excess production of red blood cells was due to which of these? 1) excess expression ol‘eryrthropoietin due to a mutant receptor 2) an overactive JAK kinase due to a mutation in the kinase enzyme 3) an overactive JAK kinase due to a mutation in the receptor that inhibited SHP‘ binding 4) an overactive JAK kinase due to a mutation in the receptor that inhibited SOC‘ protein binding 5) excess expression ol‘erythropoietin due to a mutation in the EPO gene 3. Which of the following statements regarding the beta-globin LCR is n_ot correct? 1) HSl—4 are erythroid cell specific. 2) H35 is found in many cell types. 3) Each 118 contains binding sites for a single transcription factor. 4) Both erythroid cell specific and more widely expressed activators bind to the beta—globin LCR. 5) The beta-globin LCR contains 5 DNase hypersensitive sites. 4. DRB (diehloro—ribol'uranosyl—benzimidazole) inhibits the activity of: l) P—TEFb 2) DSIF 3) NELF 4) T lr‘llS 5) None ofthe above 5. Son ol‘sevenless protein is involved in the regulation of gene expression during development of the Drosophila eye. What is the function of son of sevenless protein in this process? 1) binds to the Boss ligand 2) acts as a receptor tyrosine kinase enzyme 3) acts to exchange GTP for GDP on the Ras protein 4) binds to MAPK enzyme 5) adds phosphates to the MAPK enzyme 6. Which of these proteins is activated by the 'l‘orso receptor? 1) Ras protein 2) protein kinase C 3) protein kinase A 4) JAK2 kinase 5) STAT transcription factor 7. During the process of termination oi'transcription by RNA polymerase II, which ofthi following proteins binds directly to the GU—rich sequence found downstream of the highly conserved AAU AAA sequence in the transcript? 1) PAP 2) PABII 3) csnr 4') crsr 5) CFI 8. Which of the lbllowing statements is n_ot correct? 1) The Ada complex contains Spt proteins. 2) Both nuclear and cytoplasmic histone acetyltransferases exist. 3) GcnS is a coactivator of transcription. 4') Certain TAFlIs have acetyltranslerase activity. 5) The yeast HDAC A and IIDAC B complexes have different catalytic subunits. 9. Which of the following statements is M correct? 1) Reporter genes placed under the control of the HIV LTR are expressed at a higher level in cells previously infected by MW than in non—infected cells. 2) TAR only functions when placed 5' to the HIV promoter. 3') Mutations that destabilize base pairing in the stem ol‘the TAR stem—loop structure abolish the effect of TAT on transcription. 4) TAK contains a cyclin T1 subunit. 5) TAT is a transactivating transcription factor. 10. In the Ras—MAPK signal transduction pathway, which protein is phosphorylated on both threonine and tyrosine? 1) MAPK kinase 2) Raf kinase 3) MEK kinase 4) p90RSK kinase 5) TCP transcription factor I l . Biochemical studies with purified Swi/Snf complex and chromatin incubated in the test tube have shown that nucleosome sliding can occur with as little as: 1) One Swi/Snf complex per nucleosomc. 2) One Swi/Snl‘complex per 2 nucleosomes. 3) One Swi/Snf complex per 20 nucleosomes. 4) One Swi/Snfcomplex per 200 nucleosomes. 5) One Swi/Snl‘ complex per 2000 nucleosomes. 12. Consider the following properties of chromatin: (i) Highly condensed (ii) Ilypoacetylated (iii) Readily acecsible to transcription factors (iv) Resistant to DNase digestion Which of the above properties are found in euchromatin‘? 1) (i) 2) (ii) 3) (iii) 4) (iv) 5) (i), (ii). (iii) & (iv) BIOLOGY 300A VERSION '1 13. Cytokines are a family of small proteins containing approximately how many amino acids? U26 356 3)86 @106 $160 14. The structure of the eytokine can be best described by which of these: 1) a dimer of four anti-parallel beta strands 2) a monomer of four anti—parallel beta strands 3) a dimer of [our parallel alpha—helices 4) a monomer of four alpha-helices 5) a dimer of four alpha-helices 15. In transgenic mouse studies to demonstrate LCR l'unction a beta—globin mini gene was introduced into mice with and without a normal or a mutated beta—globin LCR as illustrated below. From top to bottom these transgenes have: 1) The beta—globin mini—gene linked to an LCR. 2) The beta—globin mini gene alone 3) The beta-globin gene linked to a LCR with deletion ol'HS3. “s assasai a Consider the following possible consequences of introducing the transgenes illustrated above: (i) High level, erythroid cell specific, copy number dependent, position inependent expression. (ii) Low level, variable expression in many cell types. Which of the following patterns of expression of these transgenes would be expected? 1) Transgene 1, expression pattem (i); Transgene 2, expression pattern (ii); Transgene 3. expression pattern (i). 2) Transgene 1, expression pattern (i); Transgene 2, expression pattern (ii); Transgene 3. expression pattern (ii). 3) Transgene 1. expression pattern (ii); Transgene 2, expression pattern (i); Transgene 3, expression pattern (i) 4) Transgene 1, expression pattern (ii); Transgene 2, expression pattern (ii); 'l'ransgene 3, expression pattern (i) 5) Transgene 1, expression pattern (i); Transgene 2, expression pattern (i); Transgene 3, expression pattern (i) BIOLOGY 300A VERSION 1 16. Consider the following proteins and protein complexes: (i) Gcn4 (ii) (icn5 (iii) Ada (iv) SAGA Which of the above have histone acctyltransferase activity? 1) (i) only. 2) (i), (iii) and (iv) only. 3) (i) and (ii) only. 4) (ii) and (iv) only. 5) (ii). (iii) and (iv) only. 17. Binding of erythropoictin to its receptor causes which of these events? 1) the R1 receptor adds a phosphate to the RH receptor 2) the RH receptor adds a phosphate to the RI receptor 3) two Epo receptor monomers come together to form a dimer 4) JAK—2 kinase associated with one receptor adds a phosphate to the JAK-Z kinase associated with the second receptor in the dimer 5) the Epo receptor kinase phosphorylates itself 18. Which unique feature of insect development allows the diffusion of transcription factors between nuclei in early development? 1) The presence 0 l‘ microtubu1es connecting nurse cells to the oocyte 2) The perivitelline space between the follicle cells and the oocyte membrane 3) The position of the oocyte nucleus in the dorsal quadrant 4) The formation of the syncitial blastoderm 5) The expression of pipe protein in the perivitelline space 19. in the erythropoictin signal transduction pathway, which of these events does not require the binding of an SH2 domain to a phospho—tyrosine residue ofa target protein? 1) binding of SOCS protein to the receptor 2) formation of the STAT dimer 3) binding of SHPl to the receptor 4) binding ofSTAT to the receptor 5) binding ol'EPO to the receptor 20. Consider the following statements: (i) The bulk of RNA turnover occurs in the nucleus. (ii) Transcripts lacking a poly (A) tail will be degraded by 3'—5' exonucleases in the nucleus. (iii) The nuclear exosome is a complex of eleven 5'-3' exonucleases involved in the transient retention ol‘processed transcripts at the transcription site. (iv) The rate of deadenylation varies inversely with the rate of translation initiation for 3] mRNA. Which of the above statements is/are correct 1') (i). (iii) and (iv) only. 2) (i) and (ii) only. 3) (i). (ii), (iii) and (iv). 4) (iii) and (iv) only. 5') (i), (ii) and (iv) only BIOLOGY 300A VERSION 1 2l . The receptor Toll binds to its ligand only on the ventral side of the embryo. What is responsible for inhibition of Toll activation on the dorsal side? 1) expression of hunchback protein only on the ventral side 2) inhibition of Pipe synthesis on the dorsal side 3) activation of Pipe synthesis on the dorsal side 4) expression ol‘bicoid protein in the anterior region 5) expression ol‘hunchback protein in the dorsal region 22. Which residue on the H3 N—terminal tail can be acetylated or methylated? 1)Arginine 2. 2) Lysine 4. 3) Lysine 9. 4) Scrine 10. 5) Lysine 14. 23. Consider the following protein domains: 1) Bromodomain 2) Chromodomain 3) SANT domain Consider also the Following binding sites: A) Acetylated lysine B) Methylated lysine C) Phosphorylated serine 0) DNA Which of the following alternatives indicates the best match ol‘eaeh of the listed protein domains to target binding site? 1) 1A, 213, 3C 2)1B,2C,3A 3)1C,2A,3B 4) 1A, 213, 3D 5) 1D.2A,3C 24. In the Ras signal transduction pathway. the two 8H3 domains ofGRB2 bind to whic ol‘these? l) MAPK kinase 2) Ras protein 3) SOS protein 4) JAK2 kinase 5) RTK receptor 25. Which of the following statements regarding the yeast Swi/Snf complex is not correct? 1) Inactivation oi'the complex results in activation of approximately 3% o l‘ the genes in the yeast genome. 2) Inactivation of the complex results in repression of approximately 3% of the genes in the yeast genome. 3) Its ATPase subunit has a chromodomain. 4) It can catalyze histone octarner transfer in vitro. 5) It is recruited to the H0 gene by the SW15 activator. BIOLOGY 300A VERSION 1 26. The ubiquitin directcd protein degradation pathway requires covalent attachment 0 ubiquitin to which amino acid in the target protein? 1) glycine 2) lysine 3) tyrosine 4) serine 5) thrconinc 27. The sequence elements involved in the termination of transcription by RNA polymerase I] are illustrated below: Which ol‘ the lollowing proteins binds directly to the sequence AAU AAA depicted above? 1) PAP 2) PABll 3) CStF 4) CPSF 5) CFI 28. Consider the following properties: (i) Activation of gene expression. (ii) Blocking unwanted enhancer promoter interactions. (iii) Preventing the spread of heterochromatin. (iv) Preventing the positional effect when present in transgenes introduced into mice. Which of the above properties isfare shared by enhancers, insulators and LCRs? l) (i) only 2) (ii) only 3) (i) and (iv) only 4) (i), (ii), (iii) and (iv) 5) None 01‘ (i) — (iv) BIOLOGY 300A VERSION 1 29. The protein torpedo binds to the ligand gurkcn. Which cells express torpedo? l) follicle cells 2) oocyte cells 3) nurse cells 4) all of the above 5) none of the above 30. The Ras signal transduction pathway results in activation of specific genes, for example the gene c-fos. Which of the following 5 proteins is found in the nucleus when the c—fos gene is being activated? I MAPK kinase II SRF factor 111 TCP factor IV MEK kinase v p90RSK kinase 1) l and II 2) III and IV 3) I, II, III, IV and V 4) I, III, IV and V 5) I, II, III and V 31 . The matemal gene Torso encodes a receptor protein that is expressed in the egg plasma membrane. Why is Torso activation restricted to the most extreme ends of the embryo? l) the ligand Spatzlc is expressed at the ends of the embryo 2) the bicoid protein binds Torso mRNA and holds it in the end regions 3) the protein dorsal inhibits activation of the Torso receptor 4) the Trunk protein is restricted to the perivitelline space at the ends 5) the Pipe protein is restricted to the perivitelline space at the ends 32. Which of the following has both histone deacctylase activity and ATP—dependent chromatin remodeling activity? '1) Gcn4 2) OcnS 3) de3 4) NuRD 5) Sin3 33. Which of these maternal transcription factors both activates and represses the GAP gene Kruppel? l) bicoid protein 2) hunchback protein 3) dorsal protein 4) nanos protein 5) decapentaplegic protein BIOLOGY 300A VERSION 1 34. The mouse Ing/Hl 9 locus is imprinted so that [g]? is not expressed from the matemi allele, although it can be expressed from the paternal allele. Expression of 1’ng at this locus is under the control of an imprinted control region (lCR). Consider the Following events: (i) An inactivating mutation of CTCF protein. (ii) Methylation of CTCF binding sites at the ICR, on the maternal allele. (iii) Demcthylation of CTCF binding sites at the ICR. on the maternal allele. (iv) Deletion of CTCF binding sites at the ICR, on the maternal allele. (v) Transgenic overexpression of CTCF. Which of these events would be expected to pennit lgl‘2 expression from the materanl allele? 1) (i) ()R (iii) OR (iv) 2) (i) 0R (ii) OR (iv) 3) (ii) OR (iv) OR (v) 4) (i) OR (iii) OR (iv) 5) (i) on (ii) OR (iv) ()R (v) 35. Which of the following stimulates the latent endonuclease activity of RNA polymerase Ii 1) him 2) DSIF 3) PTEFb 4) FACT 5) THIS 36. Activated Ras protein binds to the regulatory o I' region of'a protein kinase causing th reliel‘ol' 14—3—3 protein binding. Which ofthese is that protein kinase‘? 1) EGF receptor protein kinase 2) Raf kinase 3) MEK kinase 4) MAPK kinase 5) ERK kinase 37. Micro RNAs (miRs) l) Encode small transiently expressed proteins. 2) Have been found in animals but not in plants. 3) Regulate transcription initiation. 4) Regulate the activity of mRNAs by anti sense base pairing. 5) Are 8—1 2 nucleotides long 38. The binding ofHPl to chromatin is activated by: 1) Methylation of H3K4 (i.e. lysine at position 4 ot‘histone 3) 2) Methylation of H3K9 3) Acctylation ofH3Kl4 4) Phosphorylation of H3810 (i.c. scrine at position 10 of histone 3) 5) All ofthe above modifications BIOLOGY 300A VERSION 1 39. Which of the following statements regarding RNA—binding SR proteins is n_ot correct? 1) They are rich in serine and arginine residues. 2) They bind to intronic splicing enhancers. 3) They associate with other nuclear proteins to form exon-junetion complexes (FJ Cs). 4) They can play a role in nonsense-mediated decay omeNA. 5) Inactivating mutations of these proteins would be expected to adversely affect nuclear transport of m RNPS. 40. Which ofthe following statements is not correct? I) P—TEFb preferentially phosphorylates serine 5 of the RNA polymerase 11 C11) 2) FACT has no effect on the rate of transcription on naked DNA templates. 3) Spt6 can displace an entire histone octamer in a chromatin template. 4) FACT binds H2A/H2B dimers in vilm. 5) Elongator has HAT activity. 41. Which of the following is not found in the HIV LTR? 1) NF —kappaB binding sites. 2) Spl binding sites. 3) A TATA box. 4) Sequence encoding TAR. 5) Sequence encoding TAT. 42. Which of the following types of covalent modification has been observed at the greatest number of different positions on the histone N—terminal tails? 1) Acetylation of lysine. 2) Methylation of lysine. 3) Methylation of arginine. 4) Phosphorylation of serine. 5) Ubiquitinylation of lysine 43. The binding of Delta to Notch receptor causes specific proteolytic cleavage of the Notch receptor. Which of these is a protease involved in this process? 1) Proteosome 2) ’l‘rypsin protease 3) Ubiquitin 4) Presenilin 5) p65/p50 BIOLOGY 300A VERSION 1 44. The figure below illustrates a signaling process that can occur at the membrane after receptor tyrosine kinase has been activated. 0-! a E s: .2 ' “'9’: . o . .5: B (.3 e0 e0 as two 0 e o o \ t \ t gag—camera? gngmCHmCH? {£3 es s a _ o :3 in O .5 Which of these enzymes is responsible for the reaction (A goes to B + C)? 1) Mitogen activated protein kinase 2) Phosphatidylinositol—3-kinase 3) Ubiquitin ligasc 4) Protein kinase C 5) Phospholipase C 45. After the reaction shown in the figure above, product C is released into the cell. Whe does product C do? 1) Binds to protein kinasc A and stimulates its activity 2) Binds to protein kinase C and stimulates its activity 3') Binds to the Cart | channel in the endoplasmic reticulum and stimulates Ca++ release 4') Binds to Ras protein and stimulates its activity 5) Binds to protein kinase B and stimulates its activity 46. After the reaction shown in figure above. product B is found in the cell membrane. What dOes product B do? 1) Binds to protein kinase A and stimulates its activity 2) Binds to protein kinase C and stimulates its activity 3) Binds to the Cal | channel in the endoplasmic reticulum and stimulates Ca++ release 4) Binds to Ras protein and stimulates its activity 5) Binds to protein kinase B and stimulates its activity BIOLOGY 300A VERSION 1 47. This is a drawing of a normal and a mutant larva. Mutations in which of these genes causes the observed change in the mutant?. 1) maternal gene bicoid 2) maternal gcnc nanos 3) maternal genc torso 4) maternal gene dorsal 5) maternal gene orthodenticle 48. Which of these describes the problem for gene regulation that causes the defective in the mutant shown above? 1) excess transcription of the hunchback gene 2) insufficient transcription ol'the hunchhack gene 3) insufficient translation of the hunchback gene 4) excess translation of the hunchback gene 5) none of the above 49. the ligand Spatzle binds to its receptor on the ventral surface of the embryo, causing the proteolysis of which of these proteins? 1) easter protein 2) gurken protein 3) pelle/tube protein 4) cactus protein 5) dorsal protein 50. Proteolysis of the protein from the previous question causes the release of which of these into the embryonic nuclei? 1) caster protein 2) gurken protein 3) pelle/tube protein 4) cactus protein 5) dorsal protein ...
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OLD EXAM 1 - Faculty of Science FINAL EXAMINATION BIOLOGY-3 00 MOLECULAR BIOLOGY OF THE GENE VERSION 1 Examiner Prof P Holland Thursday December

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