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BioMG2800 © Department of Molecular Biology and Genetics Cornell University 1 PBIOMG 2800 Lectures in Genetics and Genomics Third Preliminary Exam November 14, 2023 There are 14 pages to this exam, including this page. Be sure you have a complete set before you begin. Pages 13 and 14 are blank pages at the end. You may remove these and use them for scratch paper (you do not need to turn them in). Put all answers in the boxes or on the lines provided. Only answers in the boxes or lines will be graded. Please turn off all cell phones and other electronic devices. You may use a non-internet capable calculator. __ANSWER KEY_________________ _______________ Name: LAST, FIRST Net ID 1. ________/11 2. ________/15 3. ________/14 4. ________/16 5. ________/12 6. ________/16 7. ________/16 Total ________/100

BioMG2800 © Department of Molecular Biology and Genetics Cornell University 2 1. (11 pts total) Short Answer questions a. (8 pts) For the following statements, indicate whether they are true or false. i. The heritability of the height of a field of sunflowers in a season with lots of variable hot and cold days would be higher compared to those in a season with consistently warm days. F ii. The Linkage Disequilibrium score between the genetic marker SNP007 and the SSR variant 003 is close to 0 in a population. We would expect to see random segregation of the alleles for SNP007 and SSR003 in this population. T iii. To package the long DNA molecules in the small space of the nucleus, eukaryotic cells rely on histone proteins, which are the major protein constituent of the chromatin and can effectively compact the DNA with little help from other factors. F iv. Deleterious alleles that have a severe consequence would be strongly selected against and rapidly disappear from a population over a few generations, regardless of whether they are dominant or recessive in nature. F b. (3 pts) Having a proper set of chromosomes undergo meiosis is critical for the development of normal gametes. Watermelon and bananas are exploited in agriculture to produce seedless fruits. Indicate all possible ploidies for those seedless fruits' somatic cells by placing an X in the box(es) to the left of your answer choice(s). Diploid (2x) X Triploid (3x) Tetraploid (4x) X Pentaploid (5x) +1.5 pts per correct answer. -1.5 pts per missing/incorrect answer.

BioMG2800 © Department of Molecular Biology and Genetics Cornell University 3 2. (15 pts total) A bacterial species is discovered that can tolerate high levels of toxic petroleum hydrocarbons such as benzene. Realizing the commercial importance of these bacteria in cleaning up chemical spills, you decide to characterize the pathway that allows them to break down benzene into non-toxic molecules. Two enzymes D and E are expressed at high levels when the bacterial cells encounter benzene. You discover that the genes encoding these enzymes are organized into an operon. A diagram of the operon and its regulatory gene are shown below. The regulatory gene is an activator that, when bound to benzene, binds to the J region to activate the expression of the D and E genes. State the enzyme activities, + or - , of the enzymes encoded by genes D and E in the below genotypes in the presence of benzene. • The mutants reg-, D-, and E- are null alleles. • The J- mutant is a deletion of the entire J sequence. • The Reg 141 allele produces an activator that cannot bind benzene. • The Reg 537 allele produces an activator that cannot bind to the J region. Genotype D E Reg+ ; P+ J+ D+ E+ / reg- ; P+ J+ D+ E+ + + Reg+ ; P+ J- D+ E+ / reg- ; P+ J+ D- E+ - + reg- ; P+ J- D+ E+ / reg 537 ; P+ J+ D- E+ - - reg 141 ; P+ J- D+ E+ / reg- ; P+ J+ D- E+ - - reg 537 ; P+ J+ D+ E- / Reg+ ; P+ J- D+ E+ + - +1.5 pts per box.

BioMG2800 © Department of Molecular Biology and Genetics Cornell University 4 3. (14 pts total) You identified a SNP that correlates with dark brown vs blond hair in a population. You hypothesize that the SNP affects an enhancer that regulates the expression of the gene KITLG , which encodes a melanin receptor. KITLG is expressed at higher levels in individuals with brown hair compared to those with blond hair. a. (8 pts) You developed a series of reporters to test the function of this SNP. In column 1 of the table on the next page, indicate in the table on the next page, the expected GFP expression levels (“high” or “low”) for each of the reporter constructs. b. (6 pts) This enhancer is regulated by the MITF transcription factor that binds to and acts on the enhancer sequence (containing either SNP) you have discovered. In columns 2 and 3 of the table on the next page, indicate the expected GFP expression levels upon RNAi knockdown of MITF (“Higher than no RNAi”, “Lower than no RNAi”, or “Same as no RNAi”). For column 2 assume MITF is a transcriptional activator. For column 3 assume MITF is a transcriptional repressor. promoter GFP C A CTAAAG promoter GFP C G CTAAAG 5kb 1kb promoter GFP C G CTAAAG 10kb promoter GFP GAAATC A C 4.5kb 1 2 3 4

BioMG2800 © Department of Molecular Biology and Genetics Cornell University 5 Table for question 3 Reporter construct GFP Levels (high or low) If MITF is an activator, expected GFP expression upon RNAi. (“Higher than no RNAi”, “Lower than no RNAi”, or “Same as no RNAi”) If MITF is a repressor, expected GFP expression upon RNAi. (“Higher than no RNAi”, “Lower than no RNAi”, or “Same as no RNAi”) 1 high Lower than no RNAi Higher than no RNAi 2 low Lower than no RNAi Higher than no RNAi 3 low Lower than no RNAi Higher than no RNAi 4 Low Same as no RNAi Same as no RNAi +2 pts per box for “GFP levels” +0.75 pts per box for “expected GFP expression upon RNAi”

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