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Unformatted text preview: Name_______________________________ ID #________________________________ FINAL EXAM March 22, 2003 Question 1 2 3 4 5 6 7 8 9 10 11 12 13 Total A. B. C. D. Points 15 12 16 15 27 12 8 4 16 24 15 22 15 200 Score MCB164 Winter 2003 Page 1 of 10 This examination is closed book. There are 6 pages to the exam. Please count them before you start to make sure all are present. Please write your name on each page of the exam. Answer each question in the space provided. If additional space is required use the back of the page and indicate clearly that you continued your answer on the back. Do not attach additional pages. A. GOOD LUCK! Student authorization: I authorize the instructor to return the graded exam to me in the main office or to distribute it in the bin for me to pick up. Signature _____________________________ Name_______________________________ MCB164 Winter 2003 Page 2 of 10 Date_____________________ 1. (15 points) Mark the following statements as being either TRUE or FALSE ___T_____ Recombination between repeated elements is suppressed during meiosis ___F_____ Plants have much larger genomes than mammals because they have about 10 times as many genes. ___T_____ Barr-bodies (the inactive X chromosome) and centromeric heterochromatin are examples of facultative and constitutive heterochromatin, respectively. ____F____ Condensins must be released from chromosomes prior to anaphase in order to segregate sister chromatids. ____F____ The genomes of mouse and human are thought to be syntenic because both have large numbers of transposable elements. 2. (12 points) Barbara McClintock established that recombination involves the physical exchange of genetic material using maize. For her analysis she followed cytologically detectable regions of heterochromatin called "knobs" during meiosis using a strain that was heterozygous for such knobs. The drawing below shows a representation of the bivalent she might have seen during metaphase I. The bivalent as shown has one chiasma. A. Draw the structure of the two chromosomes immediately following the first meiotic division. B. Name the two sources of tension that stabilize the bivalent on the metaphase I plate when the centromeres of the two homologs are pulled by the spindle? 1. Chiasma (cross over) 2. sister chromatid cohesion distal to the site of crossing over Name_______________________________ MCB164 Winter 2003 Page 3 of 10 3. (16 points) Consider the following ordered linear asci showing meiotic segregation patterns of wild type and mutant alleles of arg2. Indicate in the table below (i) the type of segregation pattern of arg+: arg- (e.g. 2:6), (ii) whether or not crossing over occurred (or if you can tell) and (iii) if gene conversion has occurred. 1 + + arg arg arg arg arg arg i. 2:6 2 + + + + arg arg arg arg 4:4 no no 3 + + + arg arg arg arg arg 3:5 can't tell yes 4 + + arg arg arg arg + + 4:4 yes no (or can't tell) ii. can't tell iii. yes 4. (15 points) Dosage compensation equalizes expression of genes from the X chromosome in two sexes of the same species. Mark the following statements related to dosage compensation as TRUE or FALSE __F_____ Female identical twins share more phenotypic characteristics than male identical twins __T_____ A mother shares more expressed genes in common with her sons compared with her daughters. __F______ X inactivation in the inner cell mass favors the paternal X chromosome ___T_____ Calico cats are typically female, except for rare XXY cats ___F_____ One mechanism for dosage compensation is to decrease X chromosome expression in the heterogametic sex Name_______________________________ MCB164 Winter 2003 Page 4 of 10 5. (27 points) Banana slugs found in the mountains near Santa Cruz are normally bright yellow. Since starting graduate school at UC Santa Cruz you have become an avid hiker, somewhat to the dismay of your Ph.D. advisor. Along your hikes you have found 6 pink colored banana slugs which you believe to be independent isolates. You take them back to the lab to initiate a project to define the genes that define skin pigmentation in this organism. Fortunately, half of your mutants are male and the other half are female. A. You first cross each of your mutants to true-breeding, yellow "wild type" banana slugs of the opposite sex and score the F1 progeny for skin color. What information might this test tell you? Circle one answer from the statements below: I. II. III. IV. the mutation segregates as a single gene the mutant phenotype is dominant or recessive there is a dominant suppressor mutation in the mutant strain two mutations fail to complement one another B. Second, you cross female F1 progeny from the first cross to their brothers and analyze their progeny. You find that crosses involving mutants #1, #2, #3, #4 and #5 give 1/4 pink progeny. In contrast, when you cross the F1 progeny of mutant #6 only 1/16 of the F2 progeny are pink. Circle the most likely answer that accounts for these data: I. II. III. IV. There is one mutation resulting in a pink skin color in mutants #1 through #5 and two mutations in mutant #6. Mutant #6 carries a dominant suppressor of the pink phenotype Mutants #1 through #5 are loss-of-function mutations while mutant #6 is likely a gain-of-function mutation. Mutant #6 is epistatic to mutants #1 through #5. C. You mate male homozygous mutants 1-5 to female homozygous mutants 1-5 and score the F1 progeny for the skin color phenotype. What kind of test is this? I. II. III. IV. V. Epistasis test (regulatory heirarchy) Epistasis test (biosynthetic pathway) Complementation test Segregation analysis Suppression analysis Name_______________________________ 5 (cont.) MCB164 Winter 2003 Page 5 of 10 D. For question 3C what specific caveats must be considered in interpreting the results of such a cross? Must give two out of three of the following answers for full credit. 1. Intragenic complementation 2. Second site noncomplementation 3. Mutants are recessive E. From the above crosses you have found that your mutants define three genes pink1, pink2 and pink3. During your analysis you have isolated a spontaneous suppressor of the recessive pink21 mutant so you call it Su(pink2). Further characterization reveals it to be an unlinked dominant suppressor that segregates as a single gene. You want to know if the Su(pink2) mutation is an allele-specific suppressor so you set up the following cross with strain homozygous for another allele of pink2 called pink2-2. Fortunately there is a balancer chromosome (Bal) containing both a recessive lethal mutation and a dominant marker for bent antennas that allows you to follow the suppressor in the cross. male Su(pink2)/Bal pink2+/pink2+ x female Su(pink2)+/Bal pink2-2/pink2-2 F1 Su(pink2)/Bal pink2-2/pink2+ x Su(pink2)/Bal pink2-2/pink2+ F2 I. What is the phenotype of the F1 Su(pink2)/Bal pink2-2/pink2+ animal with respect to color and antenna shape? yellow, bent antenna If Su(pink2) is not a supressor of pink2-2 then what fraction of viable F2 progeny will be pink? 1/4 If Su(pink2) is a supressor of pink2-2 then what fraction of viable F2 progeny will be pink? none II. III. Name_______________________________ MCB164 Winter 2003 Page 6 of 10 6. (12 points) You analyze a single tetrad from the cross MATa trp1 x MATa ura3 and collect the following phenotypic data for the resulting spore clones: Mat a a a a Trp + + Ura + + - 1a 1b 1c 1d Answer the following questions TRUE or FALSE. Assume that all markers are unlinked to one another and that TRP1 is tightly linked to its own centromere: ___T____ The pattern observed for tetrad #1 indicates a crossover occurred between the MATa locus and its adjacent centromere. ___F____Tetrad #1 is a Nonparental-ditype with respect to the Ura and Trp markers. ___T____ The occurrence of a tetratype can indicate either a single crossover or a three-strand double crossover. ___F____Nonparental-ditypes arise only from four-strand double crossovers between two linked genes. 7. (8 points) Prior to 1983 the prevailing model for recombination was the Meselson-Radding model, where recombination is initiated by a single-strand nick in one of the sister chromatids. What key experiment carried out by Terry Orr-Weaver suggested that the initiating event might be a double-strand break? What organism did she use? She used budding yeast to show that transformation of a marked plasmid was increased if she introduced a double-strand break compared to introducing a nick or no nick. She also showed that the information removed by creating a gap in the plasmid could be replaced by the intact chromosoma; locus (gene conversion). Name_______________________________ MCB164 Winter 2003 Page 7 of 10 8. (4 points) Match the colony sectoring patterns shown below with the expected patterns for the following two systems (assume that the shaded areas are pink): A. Chromosome loss assay: A yeast artifical chromosome containing the ochre-suppressor SUP11 is present in an ade2-100 strain background. ade2-100 is an allele with an ochre nonsense mutation. ade2-100 strains are pink while ade2-100 SUP11 strains are white. Pink color in the colony in indicates loss of the artificial chromosome. B. Position effect variegation: A reporter gene inserted near a yeast telomere will be silenced due to spreading of the SIR3, SIR4 complex. Silenced chromatin can be maintained for many generations but may also be lost. A B 9. (16 points) Match the chromatin component most likely associated with the following processes or events. __E___ Often found in association with active gene expression __B___ Characteristic of imprinted loci in mammals __D___ Likely involved in assembly of the kinetochore __A___ Consequence of double-stranded RNA expressed from cenH region in S. pombe. A. B. C. D. E. Histone methylation Cytosine methylation Histone phosphorylation Histone variant Histone acetylation Name_______________________________ MCB164 Winter 2003 Page 8 of 10 10. (24 points) Match the type of epigenetic inhertiance with the descriptions below ___E____Imprinting ___A____RIP/MIP ___F____Position effect variegation ___B____Paramutation ___D____RNAi ___C____Prion A. A phenomenon occurring in filamentous fungi at the dikaryon stage where all repeated DNA sequences in the genome over 1 kb are inactivated by methylation or point mutation preceded by methylation. B. A phenomenon occurring in plants where an allele is invariably altered after interaction with another specific allele. C. The agent that causes mad cow disease. D. Has been demonstrated to lead to the formation of silent heterochromatin in fisson yeast S. pombe. E. A phenomenon occurring in mammals where transcription is silenced on one parental allele. F. A phenomenon described in several species whereby the position of a reporter gene in the genome affects its expression. 11. (15 points) For each set circle the chromatin type that would exhibit the highest packing ratio (i.e. most condensed): A. 30 nm fiber B. Euchromatin C. Metaphase chromosome D. nucleosome wrapped DNA E. X chromosomes in XX C. elegans 10 nm fiber heterochromatin interphase chromosome DNA loops attached to a scaffold X chromosomes in XO C. elegans Name_______________________________ MCB164 Winter 2003 Page 9 of 10 12. (22 points) You have isolated several X-chromosome to autosome translocations in feline embryonic stem cells with the aim of mapping the X chromosome inactivating center (XIC). For each cell line you can tell if the autosomal region is inactivated by immunostaining with antibodies specific to MacroH2A. You are able to determine the portion of X chromosome fused by its characteristic Geimsa staining pattern in spread, metaphase preparations. You tabulate the following data where the solid lines represent aligned region of the translocated X chromosome and the dotted lines represent the autosome to which the X-chromosome region is fused (not aligned): Macro H2A staining + + + A B C D E F X-chromosome A. To which region of the X chromosome does the XIC presumably map? C B. What gene would you expect to find expressed at the XIC on the inactive X chromosome? Xist C. You are able to create a deletion of the XIC on one chromosome and create a XxicD/XXIC+ heterozygote. What pattern of X inactivation do you expect? Circle the answer below: I. II. III. random XxicD is always inactive while XXIC+ is always active XxicD is always active while XXIC+ is always inactive D. Name three properties of chromatin associated with the inactive X chromosome. Bound by Xist; bound by MacroH2A; condensed; hypoacetylated; late replicating; located at nuclear periphery, high levels of DNA methylation not correct: repeated DNA sequences; low gene density; low meiotic recombination Name_______________________________ MCB164 Winter 2003 Page 10 of 10 13. (15 points) Work from Dr. Gottschling's laboratory has shown that a reporter gene inserted near a telomere in yeast is silenced. Four genes in yeast are required for silencing: RAP1, SIR2, SIR3, and SIR4. Rap1 protein binds to a specific DNA sequence found only at telomeres. Binding of Rap1 recruits Sir3 and Sir4, which can also bind to unacetylated histone H3. SIR2 encodes a histone deacetylase. Spreading is thought to occur by the action of Sir2 clearing a binding site for Sir3 and Sir4 proteins. A. The limiting component of spreading is Sir3 protein. What would you expect the effect of overexpressing SIR3 would be with respect to silencing of the reporter gene? there will be increased silencing of the reporter B. Would you expect rap1D to be epistatic SIR3 overexpression (SIR3OE)with respect to silencing of the reporter? Yes. This is like a biosynthetic or developmental pathway where one event is required for the next event to occur. Rap1 protein is required for Sir3 binding and thus acts before Sir3 in the assembly of the silencing complex. C. Describe the expected rap1D SIR3OE phenotype based on the information given above. If no Rap1 is present, Sir3 will not be able to initiate spreading. There will be no telomeric silencing. ...
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