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1 Biology 105: Introduction to Genetics Name Student ID Before starting, write your name on the top of each page Make sure you have all pages You can use the back-side of the pages for scratch, but we will not grade answers written on the back-side of the page. Unsolved fractions are acceptable answers NO PARTIAL POINTS for INCOMPLETE ANSWERS! Part I Definitions 15 points Part II True/False 5 Points Part II Short Answer 10 points Part I Multiple Choice 30 points Part V Extended Calculation 40 points Total

2 Definitions (3 pt each) 1 Convergent genes 2 Mini satellite DNA 3 Auxotroph 4 RFLP 5 Microarray 2

3 True:False (1 pt each) 1 There are seven chromosomes in the garden pea and seven independently assorting RFLPs are identified in this organism. These results fit the hypothesis that each RFLP maps to a different chromosome. True/False 2 cdna libraries possess promoter sequences True/False 3 PCR is a method that allows you to amplify a specific DNA sequence True/False 4 Heterochromatin sequences would most likely be present in genomic libraries True/False 5 The probability of isolating a gene from a cdna library is not dependent on the cell type from which the library was originally constructed True / False 3

4 Short answers (2 pt each) 1 Consider two different antigen molecules produced on the blood cells of wild type mice according to the biosynthetic pathway below antigen1 /enzb enza / Precursor Intermediate \ \enzc \ antigen2 Two different true breeding strains of mice have been isolated that do not make either antigen1 or 2. When an individual from one strain is crossed with an individual from the other strain all of the F1 produce both antigens. What is the parental genotype (Use A, B, and C for wild type and a, b, and c to designate mutants). 2 In Drosophila, generation of wings is a multi-step pathway. Independently induced wingless mutations A, B and C are isolated. They are all autosomal. The pure breeding wingless mutant lines are intercrossed as described below: Mutant Crosses: F1 F2 (self crossed) MutA x mutb all winged 9/16 winged 7/16 wingless MutA x mutc all winged 1/2 winged 1/2 wingless Explain the A x B results (genotype of parent and F1 and the genetic pathway) Explain the A x C result (genotype of parent and F1 and the genetic pathway) 3 How will a cdna library made from male dog brain differ from a cdna library made from male dog liver? 4 The diagram shows a Southern Blot of an EcoRI digest of genomic DNA from 4

5 two parents (F and M) and their child (P). The child has trisomy-21. The probe used in the blot detects a RFLP located on chromosome 21. The shading of the bands -heavy vs. light, roughly indicates the relative amount of DNA in a band. What event during meiosis can best explain the child s karyotype and in which parent did this event occur. 5 Seven mutations are isolated in the haploid banana slug- all of which require compound X to grow. The precursors in the pathway that leads to the production of compound X are known. These include compounds E,T,N,I,G and X. Each compound is tested for its ability to support growth of each mutations. (+ indicates growth and indicates no growth). E T N I G X What is the order of compounds B, H, I, S, T and X in the biochemical pathway? At what point in the pathway is each of the mutations blocked? 5

6 Multiple Choice (2 pt each) 1 precursor > Intermediate > product enzymea enzymeb A= functional enzyme, a= nonfunctional enzyme B= functional enzyme, b= nonfunctional enzyme AAbb individuals are crossed to aabb individuals. The F1 cross with one another and the phenotypes of their progeny are scored as : 4 white mice : 9 yellow mice : 3 red mice. The results indicate that the coloring produced by the precursor, intermediate and product are A red, white, yellow respectively B white, red, yellow respectively C yellow, white, red respectively D yellow, red white respectively E none of the above 2 Histones interact with DNA to form A nucleosomes B chromosomes C centromeres D all of the above E none of the above 3 If you were looking for regions of the genome most likely to contain lots of genes you would look in A Heterochromatin B Euchromatin C centromeric chromatin D the cytoplasm E mitochondria 4 Which of the polypeptides below is most likely to represent the beginning of a protein sequence: A Met-Gly-Gly-Val-Pro B Gly-Gly-Val-Pro-Met C Val-Gly-Gly-Met-Pro D Pro-Val-Gly-Gly-Met E all of the above 5 Minisatellite polymorphisms in individuals are detected using A PCR B Southern blots C Northern blots D sequencing E none of the above 6

7 6 Eukaryotic RNA polymeraseiii transcribes A protein coding genes B trna genes C rrna genes D intron containing protein coding genes E exon containing protein coding genes 7 Reverse transcriptase makes A DNA from RNA B RNA from DNA C protein from RNA D RNA from protein E DNA from DNA 8 The following diagram shows a fragment of transcribed DNA, the upper strand is the template strand: 5 ATTGCC3 3 TAACGG5 The transcribed RNA can be represented by: A 5 AUUGCC3 B 5 TAACGG3 C 3 AUUGCC5 D 5 UAACGG3 E 5 GGCAAU3 9 Three unlinked genes code for enzymes involved in the synthesis of black pigment. White > white > white >black enzymea enzymeb enzymec Alleles that give abnormal function of these enzymes are designated a, b and c. A black A/A B/B C/C strain is crossed with a colorless a/a b/b c/c strain to give a black F1. The F1 is selfed. What proportion of the F2 individuals are colorless A 7/9 B 1/9 C 1/64 D 27/64 E 37/64 10 Nonsense mutations are the result of mutations in the a) anti-codon of the trna b) codon of the trna c) anti-codon of the mrna d) codon of the mrna e) codon of the rrna 7

8 11 Which of the following genetic elements are not transcribed a) exons b) introns c) ribosome binding site d) stop codon e) promoter 12 RFLP are detected in a) exons b) introns c) promoters d) all of the above e) none of the above 13 A chromosome is discovered in which all of the transcripts originate from the same DNA strand. This implies that in this chromosome a) promoters are all oriented in the same direction b) adjacent promoters are oriented in opposing directions c) promoters are randomly oriented d) none of the above e) all of the above 14 GeneP is a sequence that is transcribed but never translated. The gene is only active in liver cells. In which of the following will genep sequence be found a) kidney cdna library b) kidney genomic library c) liver cdna library d) A and B e) B and C 15 The most common mutation in cystic fibrosis results in a protein that is missing a single amino acid- phenylalanine at position 508 (DF508). At the DNA (base pair) level, what alteration would you expect to find in a DF508 mutation? A addition of 1 base pairs B loss of 1 base pair C loss of 2 base pairs D loss of 3 base pairs E loss of 508 base pairs 8

9 Extended Calculation (40 pts) A) Prof. Robo is studying skin color of Banana Slugs. He has isolated 8 recessive mutants that are white instead of yellow. He performs the following complementation analysis. (+) indicates yellow color(-) indicates white color. Based on complementation analysis, how many genes affect skin color? Place the various mutants in the different complementation groups B) He decides to map one of these mutants- white1 (w1-). He finds that the mutation maps to chromosome2. To map this mutation precisely he uses two RFLP loci located on chromosome2 and performs a three point cross. RFLP locusa gives either a 2kb (A2) or a 3kb band (A3) on a Southern blot with probea. RFLP Locus B gives either a 5kb (B5) or a 7kb (B7) band on a Southern with probeb. A heterozygous slug for all three loci (w1-/w1+, A2/A3, B5/B7) is test crossed to a w1/w1, A2/A2, B5/B5 homozygous recessive slug. The following progeny are obtained: (The RFLP marker is only scored for band size in the heterozygous slug) No. of progeny w1- A3 B7 410 W1+ A2 B5 390 W1+ A2 B7 39 w1- A3 B5 41 W1+ A3 B5 50 w1- A2 B7 50 w1- A2 B5 9 W1+ A3 B7 11 Total 1000 What is the correct order of these three loci? Also what are the map distances between the W1 gene and the two RFLPs 9

10 C) Chromosomal DNA containing the W1+ gene is cut with EcoR1 and cloned into a 9kb plasmid (pucsc) at its unique EcoR1 site. Prof Robo decides to determine the restriction map of the recombinant plasmid. The circular plasmid that he generated is digested with either EcoR1 or HinDIII. In addition, a reaction is performed in which EcoR1 and HinDIII are used together and the DNA fragments are resolved on an agarose gel shown below. Diagram a restriction map of this plasmid What is the size of the W1 DNA insert? How many HinDIII sites are present in the recombinant plasmid? How many HinDIII sites are present in the W1 gene? D) Next, Prof. Robo decides to generate a restriction map of the chromosomal DNA containing the W1 gene in wildtype and mutant slugs using a Southern blot. He isolates 10

11 chromosomal DNA from wildtype and w1- mutant slugs. He digests the DNA with either EcoRI or HindIII or the two together, resolves the DNA on an agarose gel, blots the gel and probes it with the EcoRI fragment containing the W1 gene that he cloned. The blot is shown. Draw restriction maps of the W1 gene locus in the wildtype and mutant slugs. Also identify the likely location of the w1- mutation. To study the effect of the mutation on gene expression, Prof. Robo performs a northern blot. He isolates mrna from the skin of wildtype and w1- mutant slugs. He resolves the RNA on a agarose gel, blots the gel and probes the RNA with the W1 gene probe. The blot is shown. What kind of mutations (silent, missense, nonsense, addition, deletion etc) best explains the northern blot pattern? 11