GENE 603 Exam 3 December 1, 2017 Name

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1 GENE 603 Exam 3 December 1, 2017 Name 1. When the arc gene of phage P22 is defective, the phage cannot enter lysogeny, so these strains are always lytic and cause clear plaques on lawns of S. typhimurium strain LT2. (Wildtype gives cloudy plaques since integration can occur which protects those cells from lysis). A number of reverting and non reverting arc- mutants were isolated and tested using pairwise inoculation of the host strain followed by collecting the progeny phage and testing for plaque phenotype on new lawns of LT2. Reverting strains: H1605, H1601, H102 Nonreverting strains: AP68, AP69, AP1425 No pairwise combination of mutants inoculated into the host resulted in survival of the host in a frequency beyond what was observed with the reverting strains. The results of plating the phage progeny of all possible pairs is shown in the matrix below, where H indicates a significantly higher frequency of cloudy plaques than are observed with self combinations, L means a very low level and N means no cloudy plaques were observed. AP68 AP69 AP1425 H102 H1601 H1605 AP68 N N N L L L AP69 N H H H L AP1425 N L L H H102 L H H H1601 L H H1605 L Regarding the information provided: a) Make a map consistent with the data presented. b) Why do the H strains always show at least Low levels in testing the cross progeny? c) How many functional units (cistrons) could be present in the arc gene? Could there be explanation other than complementation?

2 2. A trisomic plant with the genotype PPp is used to make reciprocal crosses with a Ppp plant. Assuming that disomic eggs are functional but disomic pollen is not and that a single P provides the dominant phenotype predict a) the frequency of recessive progeny in each of the reciprocal crosses and b) the relative frequency of trisomic progeny in each cross.

3 3. In Drosophila, gene R that codes for smooth eyes (rr gives rough eyes) is on chromosome 2, next to gene V, a dominant required for viability of larvae. The following 4 chromosome 2s have been verified through a series of studies: (0 is the centromere) #1 Normal Chr2 a b O c R V d #2 Deletion 2: a b 0 c (missing) d #3. Translocation 2/3 a b 0 c 6 7 #4. Translocation 3/ r V d #5. Normal Chr ) Note that the translocation disrupted the R gene. a) Show meiotic pairing in flies with chromosomes #1 and #2 and predict the adult eye phenotypic ratio in progeny of a mating of 2 such flies. b) Show meiotic pairing of flies heterozygous for the normal and translocation chromosomes? Also predict the progeny phenotypes. c) What factors would affect fertility and viability of the flies in parts a and b?

4 4. Calculate a) the inbreeding coefficient for individual X in the following pedigree: D B A R T V G F X b) How would this change if B is the product of a brother/sister mating? 5. A patch of self-pollinating annual flowers at an abandoned cabin is found to have 1 pink (R R) in 160 (0.625%) plants, while most are red but some are white. Assuming none of the originally planted seeds were from white flowers, how many years ago (as a maximum) was the flower bed established. What was the planting distribution at that time and what are the allele frequencies in the population?

5 6. Spinal muscular atrophy (SMA) is perhaps the most common human recessive lethal, showing a rate of occurrence of about 1 in 10,000 births. It is related to a defect in the SMN1 gene (survival of motor neurons) on chromosome 5q. a) Calculate the expected allele and genotype frequencies for the SMN1 gene. b) At this point, does it seem likely that Hardy Weinberg equilibrium is being maintained as a result of mutation? Explain c) Sequencing has shown that almost all cases come from lack of exon 7. It also reveals that there are two fairly large inverted repeats in the region of the gene around exon 7. How does this change your perspective on part b? d) What is the probability that at least one of an individuals 4 grandparents is heterozygous for SMA? If one of them is, will the risk that the individual is heterozygous increase? 7. A population has 8 times as many recessive alleles as homozygous recessives. What is the frequency of the recessive allele.

6 8. An allele s that has been neutral in a population results in susceptibility to a newly introduced pathogen that is essentially 100% fatal to ss individuals. Before the pathogen was introduced, the S and s alleles were present at a frequency of 0.6 and 0.4, respectively. What will the allele frequencies be in the first two generations after the arrival of the pathogen and eventually (as a formula) when equilibrium is re-established? 9. Short answer questions: a) A large mouse colony has an average weight of 30 g for adults. Mice that averaged 34 g were selected as parents for a new generation that average 30.5 g. What are the values for the selection differential, response to selection and heritability. b) A petite yeast of mating type a is crossed to a normal (grande) mating type α. What would you expect to see happen over time in colonies derived from the cross if the petite is: 1) a segregational petite 2) a neutral petite 3) a suppressive petite?

7 10. The amino acids found at positions 3, 4, & 5 of cytochrome c for 5 plant species are shown in the table below: plant aa # 3 aa # 4 aa # 5 castor bean val lys ala cotton ala lys ala sunflower pro thr thr buckwheat ile lys ser wheat pro asp ala Based just on these three sites, answer the following questions: 1) Which two plants are the most similar? What is the minimum number of SNP mutations that separates them? 2) What is the minimum number of SNPs between cotton and sunflower and between cotton and buckwheat? 3) How about buckwheat and wheat? 11. What critical feature(s) is/are the same and what is different between a) Ac and Ds elements in maize b) Ac element in maize and P elements in Drosophila? c) A bacterial IS sequences and a bacterial Transposon?

8 12. Just this month several news articles have talked about a study where 177 Amish individuals (a religious group that does not use any modern amenities) from a small kindred in Indiana were tested for alleles of a gene called PAI-1. It had previously been been shown that individuals homozygous for a defective allele have a problem with blood clotting after trauma. This report said that 12 homozygotes, all Amish, been identified in 10,000 individuals overall. This version of the article inferred that the 177 tested were heterozygous, a situation not seen in other populations. The heterozygous individuals are characterized as having characters associated with long life span, including longer telomeres an well above normal cardiovascular measurements and no diabetes. What factors related to population genetics are associated with this information Based on this report, is there any evidence for a selective advantage or disadvantage? What information do you think is missing from this report that would allow a better population genetics analysis to be made? A different report said that this group had been studied because a young girl from the kindred had nearly died from bleeding after surgery. In this article, it was stated that 44 of the 177 adults tested were heterozygous, a condition that could enhance life span and that all 12 known homozygous individuals came from the same kindred. How do population genetics calculations fit in this case?

9 13. Give an example of a mechanism involving genes that play a role in development that is conserved from: a) Yeast to Drosophila b) From insects to mouse and man