CM156-Final-Winter 2023-Mar

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Moorpark College *

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CM156

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Biology

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Feb 20, 2024

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1 Name (Last) (First) Student ID KEY CM156/256 Final Exam (March 21, 2023) BEFORE YOU BEGIN THE EXAM, circle your discussion teaching assistant: GABRIELLA LINDSEY 1. (54pts) 9. (5pts) 17. (15pts) 2. (4pts) 10. (5pts) 18. (10pts) 3. (4pts) 11. (4pts) 19. (6pts) 4. (6pts) 12. (10pts) 20. (5pts) 5. (15pts) 13. (5pts) 21. (6pts) 6. (5pts) 14. (10pts) 22. (5pts) 7. (10pts) 15. (5pts) 23. (5pts extra credit) 8. (5pts) 16. (6pts) Final Exam Total /200 pts Midterm Exam I /100 pts Midterm Exam II /100 pts Pop Quizzes /60 pts Discussion Section /140 pts Total /600 pts

2 (54 pts, 1. Indicate the best answer for each of the following multiple-choice questions 3pts each) A. What is the most likely phenotype of a female mouse heterozygous for a null mutation of XIST? i) Random inactivation of the two X chromosomes ii) The X chromosomes carrying the null XIST allele would remain active iii) The X chromosomes carrying the null XIST all allele would be inactivated iv) Lethal, as X chromosomes carry genes active on both copies in females v) None of the above B. Some differences that distinguish common diseases and Mendelian diseases include the following EXCEPT: i) Rare variants contribute to Mendelian disorders but not to common disease ii) The genetic contributions of individual chromosomal loci in common disease are small compared to Mendelian disease iii) Most of the causal variants in common diseases are in noncoding regions whereas in Mendelian diseases they are mainly in coding regions iv) The heritabilities of Mendelian diseases tend to be higher than those of common diseases v) Environmental factors tend to be more important for common disease than Mendelian diseases C. Genes associated with Prader-Willi syndrome are maternally imprinted. Which of the following scenarios at the locus will most likely lead to Angelman syndrome? i) Maternal deletion or maternal UPD ii) Paternal deletion or maternal UPD iii) Maternal deletion or paternal UPD iv) Paternal deletion or maternal UPD v) None of these combinations D. I want to detect whether a patient has a deletion in a unique 2000 bp region of a chromosome that I suspect is causing their phenotype. Which of the following would NOT be a technique that I could use to determine whether they have this deletion? i) FISH using probe for the region ii) G-banding karyotypes of cells in metaphase iii) Sequencing of the region iv) Comparative genomic hybridization of the region v) Loss of heterozygosity E. The table below shows lod scores calculated for 4 families exhibiting the disease. Lod score θ = 0 θ = 0.05 θ = 0.1 θ = 0.2 θ = 0.3 θ = 0.4 1 2.3 1.7 1.1 0.8 0.4 0.03 2 - ∞ 2.4 1.9 1.7 1.2 0.4 3 - ∞ -1.7 -1.0 -0.5 -0.1 0.1 4 - ∞ 3.1 2.4 1.8 1.2 0.4 The most likely distance between the marker and the disease gene is: i) 0 centimorgans ii) About 5 centimorgans iii) About 10 centimorgans iv) About 20 centimorgans v) The disease is not linked to the marker Note: This question was discarded for the exam

3 F. Cancers often improperly turn on telomerase expression. This would result in the following property: i) Self-sufficiency in growth signals ii) Insensitivity to anti-growth signals iii) Apoptosis avoidance iv) Limitless replicative potential v) Tissue invasion G. Genetic counseling for breast cancer is complicated by the following EXCEPT : i) Mutations of BRCA1 and BRCA2 are heterogeneous ii) A small fraction of breast cancer is Mendelian iii) BRCA2 mutations exhibit incomplete penetrance iv) BRCA1 mutations exhibit incomplete penetrance v) Breast cancer primarily affects women H. The BCR-ABL translocation has which of the following properties? i) DNA repair deficiency ii) Loss of heterozygosity iii) Telomerase activation iv) Gain of function v) Chromosome instability I. You conduct a case-control association study between Type 1 diabetes and a certain haplotype at the MHC locus. The tallied frequencies are as follows: Patients Controls MHC A1 Locus 100 20 Without A1 Locus 60 120 What is the odds ratio of association between the autoimmune disease and the MHC haplotype? i) 4 ii) 6 iii) 8 iv) 10 v) 12 J. Massively parallel exome sequencing usually identifies 10–30 genes with deleterious mutations shared among sibs affected with a rare disease. Which of the following would NOT be helpful to identify the relevant gene? i) Eliminate common mutants by reference to the SNP database ii) Classify mutant changes as nonsense, frame-shift, deletion, conservative missense, synonymous, etc. iii) Study identical twins with the disorder iv) Perform linkage analyses on families v) Examine evolutionary conservation of the gene K. The following points concerning the Major Histocompatibility Complex (MHC) are correct EXCEPT : i) The class I and class II HLA molecules present antigens to B cells ii) GWAS analysis of the MHC would likely exhibit poor resolution due to large linkage disequilibrium blocks iii) The T cell receptor recognizes antigens in the context of HLA molecules iv) The HLA molecules show a relatively low level of variation due to selection against autoimmune disease v) The MHC is involved in the rejection of transplanted tissues

4 L. Which of the following is NOT a likely explanation for why penetrance, severity, or age of onset of a Mendelian disease may vary in the population? i) Locus heterogeneity ii) Gene-by-environment interactions iii) Allelic heterogeneity iv) Linkage disequilibrium v) Triplet repeat expansion M. Germline missense mutations of p53 are often more deleterious than deletion mutations. The explanation is: i) p53 deletion mutation promotes apoptosis ii) p53 deletion mutations are removed during early development iii) Dominant-negative activity of mutant p53 iv) Gain-of-function in mutant p53 v) p53 deletion mutation promotes cell cycle arrest N. Shown below is a pathway for codeine metabolism. Two enzymes (CYP2D6 and CYP1A3) are involved, and each varies in the population in the level of activity. What is the genotype of an individual that requires the highest dose of codeine for relief of pain? i) Low CYP2D6, High CYP1A3 ii) Low CYP2D6, Low CYP1A3 iii) High CYP2D6, High CYP1A3 iv) High CYP2D6, Low CYP1A3 v) Insufficient data to determine Explanation: Low CYPD6 will reduce the amount of codeine converted to the active form (morphine), and high CYP1A3 activity will increase the rate of excretion, also reducing the amount of active drug. O. Which one of the following statements relating to pharmacogenetics is FALSE ? i) Drug dosage depends on the rates of absorption, metabolism, and excretion of the drug ii) Individuals in a population can respond differently to drugs depending upon genetic background iii) Some important considerations in drug development include efficacy, toxicity, and genetic interactions iv) Generally, drug development is done by screens that require an understanding of the protein targets v) Pharmacogenetic approaches can be applied to mendelian but not complex diseases Explanation: The only false statement is e, since pharmacogenetic approaches can be applied to treat any disease. An example of a complex disease treatment that has benefitted from pharmacogenetics is to define variants that influence statin adverse effects. P, Breast cancers expressing estrogen receptor are often treated with Tamoxifen, a competitive inhibitor of the estrogen receptor. A patient with high estrogen receptor levels in breast tumors showed no beneficial effect after Tamoxifen treatment. Which of the following do you suspect as contributing factor(s)? i) The patient has high CYP3A4 activity ii) The patient has low CYP2D6 activity iii) The patient has high HER2 levels on the surface of cancer cells Codeine CYP2D6 Excretion CYP1A3 Morphine

5 iv) The patient has both low CYP2D6 activity and high CYP3A4 activity v) The patient has both low CYP2D6 activity and high HER2 levels on the surface of cancer cells Explanation: When CYP2D6 activity is low, processing of Tamoxifen to the therapeutic molecule is reduced, explaining the lack of response to the therapy. The presence or absence of HER2 on the cancer cells does not influence response to Tamoxifen. Q. Suppose you are setting up a diagnostics laboratory. Which of the following genetic disorders would NOT be a good candidate for targeted mutation testing? i) Sickle cell anemia ii) Huntington disease iii) Fragile X syndrome iv) Cystic fibrosis v) Spinocerebellar ataxia R. Haplotypes for two SNPs (A and B) on chromosome 1 are in linkage equilibrium. The frequency of allele A1 is 0.4 and the frequency of allele B2 is 0.3. The frequency of haplotype A1,B2 is: i) 0.24 ii) 0.14 iii) 0.12 iv) 0.11 v) Cannot be determined from above (4pts) 2. Lupus is a common disorder that has a much higher incidence in women than in men due to a higher threshold for disease in men. Would sons of affected men or of affected women be more likely to develop lupus? Explain. Affected man probably have more risk genes than affected woman. Therefore, sons of affected men are at higher risk 45pts) 3. Sequencing of mitochondria from Native Americans has revealed a number of unrelated haplotypes. What does this suggest about the populating of the Americas? Multiple migrations (6pts) 4. List two reasons that mitochondrial DNA is particularly useful for examining the relationships of extinct hominids to present day human populations. • Mitochondria are haploid and the DNA does not recombine • There are multiple copies per cell and so sequencing is easier • Mitochondrial DNA replication is more error prone and, therefore, more variable than nuclear DNA in sequence

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