Exam 1 - Fall 2023

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Indiana University, Bloomington *

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319

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Biology

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Apr 3, 2024

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1 L319: Genetics Lab Name:____________________________ Exam 1 Lab Section:_______________________ Fall 2023 1. You are given a liquid culture of yeast strain TD28 of the α -mating type with a concentration of 3 X 10 6 cells/ml. The culture has been subjected to EMS mutagenesis and then enrichment for mutants that are auxotrophic for leucine (Leu-). You perform a contiguous serial dilution series and plate out on three fresh plates getting 500, 100, and 25 colonies on the three plates. With this information answer the following and show all work: (20 points) a. Draw the contiguous, dilution series that you followed, including the volume plated to each of the three plates (You cannot make more than a 10 fold dilution at a time, and you cannot plate out less than 50 ul nor more than 200 ul). (10 points) Note: you should write this as ONE continuous series pulling the volumes out of different tubes. You also need to include the volumes for the dilutions. The dilutions for each plate are below: b. What is the effective volume that you plated on each of the three plates (give three values and show all work). (5 points) c. What is the dilution factor for each plate? (3 points) d. What types of solid media would you need to use and in what order would you use them to identify your Leu- mutants? (2 points)
2 2. The culture in Question 1 , above, had been EMS mutagenized and subjected to enrichment. Prior to enrichment (but after mutagenesis) the cell concentration was determined to be 2.3 x 10 8 cells/ml. An enrichment procedure was used to increase the frequency of leucine biosynthetic mutants (Leu- cells) in the culture. You identify a total of 18 leucine mutants on the three plates described above in Question 1 (625 total cells). Based on this information and the cell concentration given in Question 1 (3 X 10 6 cells/ml), answer the following: (20 points) a. What percentage (%) of cells was killed during the enrichment step? ( Show all work ) (4 points) b. What was the frequency (%) of Leu- mutants after enrichment? (Show all work) (4 points) c. What was the frequency (%) of Leu- mutants before enrichment? (Show all work) (4 points) d. What fold increase in the frequency (%) of Leu- mutants was achieved by enrichment? (Show all work) (4 points) e. Explain briefly how the TD28 strain was enriched for Leu- mutants. (4 points)
3 3. You now want to organize your mutants into complementation groups. By inducing sporulation, you are able to generate the same 18 Leu-mutants with the a-mating type. Below are the results of a portion of the complementation assay you performed to begin to characterize these mutants. Answer the following questions: (16 points) a. Place these 8 Leu- mutants into complementation groups. (8 points) b. How many different Leucine genes were isolated? (1 point) c. Does one of these groups demonstrate intragenic complementation? Why or why not? (1 point) d. If Mutant 1 had been a defective mater, what would row two look like? (1 point) e. If Mutant 8 had actually been Leu+, what would row four look like? (1 point) f. You now determine the DNA sequence of the mutated leu genes in each of your mutants. What is the most likely type of mutation you would expect to find for Mutant 4 ? (circle 1 answer) (2 pts) a) deletion b) insertion c) frameshift mutation c) missense mutation d) nonsense mutation g. Assume that there are actually a total of five different Leu genes. Which of the following matings would complement each other and grow on Leu- media? (circle all correct) (4 points) a) TD28 ( MAT α Leu1 ) and TD28 ( MATa Leu3 ) b) TD28 ( MAT α Leu2 ) and TD28 ( MATa Leu2 ) c) TD28 ( MATa Leu3 ) and TD28 ( MAT α Leu5 ) d) TD28 ( MAT α Leu5 ) and TD28 ( MATa Leu2 ) e) TD28 ( MATa Leu4 ) and TD28 ( MAT α Leu1 ) f) TD28 ( MATa Leu3 ) and TD28 ( MATa Leu5 ) g) TD28 ( MAT α Leu4 ) and TD28 ( MAT α Leu5 ) h) TD28 ( MATa Leu4 ) and TD28 ( MAT α Leu4 )
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4 4. Subsequent analysis of your mutants reveals that there are at least five genes involved in Leu biosynthesis. Your new data is shown below. (13 points) Leu1 Leu2 Leu3 Leu4 Leu5 Total Number of mutants 9 17 2 12 15 55 % of total mutants 16% 31% 4% 22% 27% 100% a. Did mutagenesis equally affect all 5 Leucine biosynthetic genes? Use Chi square analysis to support your answer. In this case look at all 5 classes and compare expected vs. observed for each. Calculate the Chi Square critical value and use the table below to determine the p value. Specifically state the null hypothesis, the degrees of freedom, the p value, and whether or not you reject or accept the null. Show your work! (11 points) b. Give two possible biological explanations for why we did not recover many Leu3 mutants in this experiment. (2 points)
5 5. In Experiment 2, you used CRISPR/Cas9 to attempt to knockout the His1 gene in yeast. We tested two different strategies for doing this (transformations #1 and #2). Explain these two strategies, the logic we used (including how the cell would repair DNA damage), and the expected outcome for each. (6 points) 6. At right is a picture of an agarose gel of the PCR products generated from Exp eriment 2. We’ve loaded 100 bp DNA ladder on each end (L) of our samples. The samples are labeled according to which transformation we used. For each lane, explain the result that we got and whether or not it is what we expected. If the result is not what we expected, make a suggestion for what happened. (8 points) 7. What technique and what media did we use to identify putative his1 mutants from our transformants in Experiment 2? (2 points)
6 8. You perform reciprocal crosses between Drosophila melanogaster strains 1 and 2. These two strains (1 and 2) breed true for their respective mutant traits. (15 points) Strain 1 has the mutant traits: red wing veins, bent antennae, pink body Strain 2 has the mutant traits: long bristles, small eyes You score 500 flies from each cross . Below are the mutant phenotypes of the F1 progeny as a result of each of the reciprocal crosses: Po: Strain 1 male X Strain 2 female F1 Males F1 Females Long bristles, small eyes, red wing veins 241 2 Small eyes, red wing veins 0 257 Po: Strain 2 male X Strain 1 female F1 Males F1 Females Red wing veins, small eyes 0 253 Red wing veins 247 0 Based on this information, state whether each of the mutant phenotypes behave as an autosomal or sex- linked, dominant or recessive trait. Also provide a brief rationale for your conclusion. 1. Red wing veins: Rationale: 2. Bent antennae is: Rationale: 3. Long bristles is: Rationale: 4. Small eyes is: Rationale: 5. Pink body is: Rationale:
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7 Extra Credit: 9. A couple of students received extra credit for finding rare (but accurately scored) flies in the progeny of the Strain 1 male X Strain 2 female (see Question 8). The rare flies were females that had red wing veins, small eyes, and long bristles. a. Explain how these flies were generated, stating specifically in which parent the rare event originated. You must draw a Punnett square to explain your answer. (3 points) 10. Using the proper format, state a possible hypothesis for Experiment 2 relating to the guide RNA used. Take into account what our actual data showed us. (2 points)