2810P2answerscorr - If you have any questions about an exam...

Info iconThis preview shows pages 1–14. Sign up to view the full content.

View Full Document Right Arrow Icon
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 2
Background image of page 3

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 4
Background image of page 5

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 6
Background image of page 7

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 8
Background image of page 9

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 10
Background image of page 11

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 12
Background image of page 13

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
Background image of page 14
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: If you have any questions about an exam problem please see the TA that graded that problem. If you want your exam regraded you must submit it to Debbie Nero. I reserve the right to regrade the entire exam. Please include a note with the submitted exam telling me which problem you are questioning. Regrades for Prelim 2 may be submitted to my office (204 Biotech Bldg) through noon, Friday, November 19. The mean for Prelim #2 is 60. Question 1: Pei Xin, Amy, Michael Question 2: Donghao, Tawny Question 3: Crystal, Aziana Question 4: Gongshi, Dr Nero September 28, 2010 BIOLOGICAL SCIENCES 2810 Prelim #2 Please write your name on the line in the middle of this page. There are 14 numbered pages with writing in this examination booklet; please check to see that all pages are present. You can tear out pages 12-14; page 12 contains a genetic code and wobble tables, and pages 13 and 14 are blanks for your own use. This is a closed book examination. There are 4 problems, with a total value of 100 points, plus 6 points of difficult Extra Credit. The correct answers can be communicated with a very few pictures, numbers, or sentences: you are only punishing yourself by being long-winded. Only answers in the spaces provided will be graded. ANSWER KEY Your Name TA Name or Lecture Only (Office Use Only) 1) (25 points) 2) (20 points) 3) (30 points) 4) (25 points) Total (100 points) Extra Credit (6 points) Question #1 (25 points total + 1 point Extra Credit) The human gene for I32 lens crystallin has the components listed below. The numbers represent nucleotide pairs. Assume for simplicity that no alternative splicing is involved. 5' UTR l 74 1st exon 1 19 1St intron 532 2nd exon 337 2nd intron 1431 3rd exon 208 3rd intron 380 4th exon 444 4th intron 99 5th exon 546 3' UTR 7 l 5 (a) (10 points; 1 point each) Answer the following questions about the 82 lens crystallin gene, primary transcript, and gene product. Questions asking "where" should be answered with one of the 11 components from the list or with "None". Assume poly(A) tails contain 150 A‘s. How large is the [32 lens crystallin gene in bp (base pairs)? How large is the primary transcript for 132 lens crystallin in bases? How large is the mature mRNA for [52 lens crystallin in bases? Where would you find the base pairs encoding the initiation codon? Where would you find the base pairs encoding the stop codon? Where would you find the base pairs encoding the 5' cap? Where would you find the base pairs comprising the promoter? Which intron interrupts the 3' UTR? (If none, write "None") Where would you find the sequences encoding the C terminus? 4096 4246 (4247 if cap counted) 1804 211 exon 4t exon None None 4th intron th 4 exon Where would you find the sequence encoding the poly(A)? Continued next page None (b) (10 points, 2 points each) Complete the following using the same instructions as in part (a). 765 (762 OK if3' UTR does not include stop; 768 OK if coding region includes the stop) 255 (254 if 3'UTR does not include stop) How large is the coding region of the gene in bp (base pairs)? How many amino acids are in the [32 lens crystallin protein? ) Which intron interrupts a codon? (If none, write "None" Which intron is located between codons? (If none, write "None") Where would you be likely to find the site specifying poly(A) addition? Note: the last entry in part (b) is meant to be different than the last entry in part (a). 5th exon / 3'UTR (c) (1 point Extra Credit) In the most widely accepted current definition, a gene is the genetic information that provides a unit of function. In the first line of part (a), your calculation of the size of the [32 lens crystallin gene had to ignore DNA sequences that are necessary for gene function but Whose length was not given. What are these sequences? Promoter — A gene needs a promoter to function, and the size of the promoter for The [32 lens crystallin gene was not provided. In fact, it is often difficult to locate the entire promoter, particularly in eukaryotes. This is because sequences called enhancers work with the so-called "basal" promoter at the gene's 5' end to allow transcripti at the proper place and time and in the proper amount. These enhancers can sometimes be far from the basal promoter, well upstream of the gene, dowstream of the gene, or even in the introns. (c) (5 points) Now consider a rRNA gene instead of that for [32 lens crystallin. From the list below, circle those structures that you could never find in any one of the following: the rRNA gene, its primary transcript, or its final gene product. Promoter Methylated cap (could be circled or not) Exons Introns 5' UTR Initiation codon Open reading frame Stop codon 3' UTR Poly(A) Start with +5 but then subtract -1 for every wrong answer; 5 or more wrong answers = 0. Question #2 (20 points total) (a) (2 points) At amino acid 25, a mutant protein has the amino acid Met, while the wild type allele encodes Arg at the same position. Using the 5' to 3' orientation in the box below, what is the most likely sequence of the template strand encoding the wildtype amino acid? CCT , 5' 3' (b) (1 point) Just under the box for the answer in part (a), draw an arrow indicating the direction RNA polymerase would move as it transcribes this gene. For the following parts of this problem, assume that tRNAs with inosine (I) in the anticodons are encoded by tRNA genes different from those with any other nucleotide in the same position. (c) (2 points) The minimum number of phenylalanine (Phe)-specific tRNAs an organism must have to respond to all possible Phe codons is 1. What is the anticodon of this tRNA? Use the 5’ to 3' orientation shown in the box. GAA 5' 3' (d) (2 points) In the box below, using the 5' to 3' orientation given, write the sequence of nucleotides in the RNA-like strand of the tRNA gene that could be transcribed into the anticodon of the tRNA described in part (c). (e) (1 point) Just under the box for the answer in part (d), draw an arrow indicating the direction RNA polymerase would move as it transcribes this tRNA gene. (1) (2 points) What is the minimum number of tRNAAla genes an organism must have to respond to all possible alanine codons? 2 tRNA genes (g) (2 points) What is the minimum number of tRNALeu genes an organism must have to respond to all possible leucine codons? 3 tRNA genes (h) (2 points) If you knew that you could obtain a mutant that had a nonsense-suppressing tRNA carrying Leu, what is the minimum number of genes the wildtype organism must have that can be transcribed into tRNALeu? 4 tRNA genes (i) (2 points) What is the maximum number of different anticodons an organism could have that would respond to tyrosine (Tyr)? 2 different anticodons (j) (4 points) In the box below, write the anticodon of a nonsense-suppressing tRNA that could carry tryptophan (Trp), but that would not illegitimately insert tryptophan in response to codons for some other amino acid. Use the 5' to 3' orientation provided. Question #3 (30 points total) Francois Jacob identified 8 closely linked raf point mutations (called raf-I through raf-8) that disrupted the ability of E. coli cells to grow with the sugar raffinose as the sole carbon source. (a) (5 points) Jacob must have started his experiments with a raf+strain of bacteria that can grow with raffinose as the sole carbon source. From the list below, circle a_ll of those procedures that Jacob would have used to obtain raf mutants in the most efficient manner possible. Note: Not surprisingly, bacterial cells need some source of carbon to grow, and they must be able to utilize at least one carbon source in their environment. Rich medium contains several potential sources of carbon atoms that can be utilized by wild type E. coli cells; minimal medium (for the purposes of this problem) contains m carbon sources at all; glucose is a different sugar that wildtype E. coli cells can use as their sole source of carbon. Direct selection on minimal medium Direct selection on minimal medium + glucose Direct selection on mimimal medium + raffinose Screening (master = rich; replica = rich + raffinose) Screening (master = minimal; replica = rich + raffinose) Screening (master = rich; replica = minimal) Screening (master = minimal + glucose; replica = minimal + raffinose) Screening (master = minimal + raffinose; replica = minimal + glucose) Screening (master = minimal + raffinose; replica = minimal) Treatment with a mutagen Penicillin enrichment Color selection with X-gal Observation of colony morphology Start with +5 but then subtract -1 for every wrong answer; 5 or more wrong answers = 0. (b) (1 point) Are the raf mutations Jacob obtained loss-of-function or gain-of-function? (Circle the correct answer.) loss-of-function gain-of-function The following part of the problem is independent of previous parts. By sexduction, Jacob then made merodiploids in which the bacterial chromosome carried one of the eight raf‘ mutations described above, and the F' episome also carried all relevant genes for raffinose utilization, one of which was affected by one of the raf' mutations. The results are presented in the table below. + means the bacteria can grow in medium in which raffinose is the sole carbon source, - means no growth in this condition. Mutation on Mutation on F' episome chromosome 1 2 3 4 5 6 7 8 1 _ 2 + - 3 - + — 4 + + + _ 5 + + + - - 6 — + - + + — 7 + + + - - + - 8 + - + + + + + - (c) (1 point) Is the above experiment a recombination experiment or a complementation experiment? (Circle the correct answer.) recombination complementation (d) (5 points) In the space below, indicate the mutations associated with each of the genes revealed by this data using brackets [ ]. [136] [28] [457] Continued next page The following part of the problem is independent of previous parts. Jacob then wanted to map the raf] mutation relative to two other genes, one associated with lysine utilization and the other with serine utilization. He set up a cross of the following form: Hfr amps raf+ lys+ ser+ X F‘ ampR raf-I lys' ser‘ He allowed the mating to proceed long enough for all 3 genes to be transferred, selected Ser+ exconjugants, and then used replica plating to test colonies for the transfer of the other two genes. The data he obtained for 1455 exconjugants is as follows: Exconjugant phenotype Number Raf+ Lys+ Ser+ 777 Raf+ Lys- Ser+ 426 Raf“ Lys' Ser+ 2 19 Raf' Lys+ Ser+ 33 (d) (3 points) What kind of plates did Jacob first use to select the Ser+ exconjugants? Remember that he wanted to select against the Hfr cells, against the unmated F' cells, and allow the desired exconjugants to grow regardless of their Raf and Lys phenotypes. Be as specific as possible. Minimal + ampicillin +lysine + glucose (e) (7 points) On the figure below, indicate the relative positions of the raf-I, lys, and ser genes and any relative distances that can be calculated. 459 252 or 459/1455 a 0.315 or 25211455 = 0.173 or 1-82 or 1 Note: you can only calculate two distances, and these are relative, not absolute. These relative distances can be expressed in three different ways. (f) (2 points) On your answer to part (e), show the position of the origin-of-transfer in the Hfr strain (assuming that Jacob performed the experiment correctly); the arrowhead indicates the first sequences transferred into the recipient. 10 The following part of the problem is independent of previous parts. Jacob finally attempted to order the raf mutations with respect to the outside markers pro (proline) and ade (adenine) by performing a pair of reciprocal crosses for each pair of raf mutants: (x and y refer to the raf mutant identification numbers; that is, 1-8). Cross A: Hfr pro' raf-x' ade+ X F' pro+ raf-y' ade' Cross B3 Hfr pro‘ raf-y' ade+ X F' pro+ raf-x' ade' The table below shows the number of colonies in the two crosses for each pair of mutants that could grow on minimal medium + raffinose as the only carbon source. Ac 1 Cross A Cross B l 2 173 2 1 3 156 4 1 4 6 218 1 5 7 197 1 6 168 3 1 7 1 215 1 8 226 5 2 3 3 187 2 8 153 8 3 6 2 175 4 5 205 1 5 7 199 9 (g) (6 points) Complete the map below to show the relative order of the 8 raf'mutations: 571532 tam4 8acre 11 Question #4 (25 points total + 5 points Extra Credit) (3) (8 points; -1 per wrong answer) A fruit fly has the genotype * a bJr / * a7L b. The * means the centromere and a and b are mutant alleles of two different genes affecting the cuticle (the outside surface of the fly) whose order on the chromosome is as shown in standard Drosophila nomenclature. From the list below, circle g of the types of "spots" that could be generated by a single mitotic crossing over event. Remember that these "spots" must be phenotypically different from the rest of the cuticle so that they can be observed. Single spots of phenotype a Single spots of phenotype b Single spots of phenotype a 13 Single spots of wildtype phenotype Twin spots of phenotype a and phenotype b Twin spots of phenotype a and wild type Twin spots of phenotype b and wild type Twin spots of phenotype a b and wild type Mitotic recombination is a very useful tool for answering interesting questions about the genetic control of the development of multicellular organisms. In Drosophila, mutations in a gene called zwilch are recessive lethals; homozygotes die as larvae well before the adult stage. You want to know whether the zwilch gene is important for the production of eggs by adult females: do ovarian cells homozygous for a null zwilch mutation produce normal eggs or eggs that have a specific defect? (Ovarian cells heterozygous for this zwilch mutation make normal eggs.) In addition to a null zwilch mutation, you will make use of Dofest, a dominant female-sterile mutation. Ovarian cells whose genomes contain the Dofest mutation cannot make eggs at all (egg development does not even start), while ovarian cells homozygous for the wildtype allele of this gene can make eggs. (b) (3 points) Why do you need to use mitotic recombination to determine if zwilch plays a specific role in egg production in adult females? ‘ Zwilch homozygous mutant females would die before they make eggs (they die as larvae), so you couldn't determine if the gene plays a specific role in egg production. Continued next page 12 (c) (7 points) To study zwilch's role in egg development, you want to construct female flies all of whose eggs are produced from ovarian cells homozygous for zwilch. On the figure below, show the alleles of zwilch and Dofest and their relative positions along the indicated homologous autosomes that you would need to make this adult female fly. Use a + superscript to indicate wildtype alleles. Show the chromosomes of normal cells in this female prior to mitotic recombination. integrase Notes: red is part (c), which is 7 points, blue is part (e) extra credit which is 4 points. For part (c), 2 must be further from the centromere than D, and the two genes must be in repulsion (that is, D- on one chromosome and z- on the homolog). Using the - superscript is optional, but the + superscript is mandatory. For part (e), each chromosome must have an att site between D and the centromere, and these att sites must be in the same position. Integrase must be on the other side of the centromere. You only need one copy of the integrase; -1 pt. for showing two copies. The integrase could be on either chromosome. -1 pt. for saying att- or integrase—, because these are wildtype genes or structures (a + superscript is optional). ((1) (7 points) Now show the genotype of the ovarian cells generated by mitotic recombination that can produce eggs whose phenotype will inform you about zwilch's role in egg development. Note: D+ required on both chromsomes; - superscript is optional but cannot be +. Order of genes is critical. 13 (e) (5 points Extra Credit) One difficulty with this approach is that mitotic recombination is very rare, so those females that could produce eggs would make very, very few of them. To increase the frequency of mitotic recombination, you can use two transgenes (cloned pieces of DNA from one organism introduced into the genome of another). One of these contains the att site from bacteriophage lambda that is important for prophage integration, the second transgene contains the gene for the integrase protein of bacteriophage lambda that catalyzes recombination between an‘ sites. You want to construct female flies like those in parts (b-d) whose only eggs will be from ovarian cells homozygous for zwilch, but these females will produce eggs at much higher rates because mitotic recombination between art sites is catalyzed by integrase protein made in my cell of the female. On your answer to part go; above, show the location of all needed art and integrase transgenes in the genome of these females prior to the mitotic recombination. ...
View Full Document

This note was uploaded on 11/01/2011 for the course BIOGD 2800 at Cornell University (Engineering School).

Page1 / 14

2810P2answerscorr - If you have any questions about an exam...

This preview shows document pages 1 - 14. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online