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Name: (-1 if not included) Answer the questions below, and submit your answers only directly on Webcourses

(not Turnitin) by the deadline listed. Please use 12 point font, single-spaced answers, with a space between each response. Assignments will be given a 0 for the following reasons: The assignment is late or not submitted to Webcourses correctly Questions are copied or restated only submit your answers Answers are cut/paste from the book, notes, or other sources put answers in your own words Answers are copied from a friend (Turnitin is enabled for this assignment) The wrong file format is used only doc, docx, wpd, and pdf are accepted Also, do not leave a comment when submitting, this sends an email to the instructors Chapter 9: 1. Explain DNA mutation with regards to its impact, both positive and negative, on humans. Discuss mutations in intergenic DNA vs. exons, and the potential impact of each. 2. Which is more common, transitions or transversions, and why? 3. How might a chromosomal translocation cause a disease? 4. Why do RNA viruses have a higher mutation rate than humans? How might this benefit them? 5. a. b. c. d. e. How many mutations are there per billion base pairs replicated in the a human cell? How many new mutations arise every time a cell in your body divides? Approximately how many base pair differences are there between you and your parents? Approximately how many base pair differences are there between you and a random person? How many disease-causing mutations does each of us carry?

6. Why can mitochondrial DNA and the Y chromosome be used to track lineages and mutation rates? Does any paternal mitochondria get passed on to children? 7. What impact can SNPs have on an organism? 8. Give an example of a SNP causing the following: a. Disease: b. Survival advantage: c. Speciation: 9. Why are the majority of SNPs C to T transitions? 10. How many DNA modification events occur per day in each cell of your body? 11. Why are mutation hot spots more susceptible to mutations? 12. How long does the cell have to repair a mis-incorporation of a base by DNA polymerase (i.e. at what point does the mutation become permanent)?

13. How can DNA polymerase detect mispaired bases (i.e. A/A, G/T)? How does it detect tautomers? 14. Why are CpG transitions a frequent way for mutations to occur? 15. Why does DNA use thymine instead of uracil? 16. Define the following and give one example of each: a. Hydrolytic DNA damage: b. Alkylation: c. Oxidation: d. Radiation damage: e. Base analogs: f. Intercalating agents: 17. 5-bromouracil is incorporated across from an adenine. What type of mutation will be introduced the DNA, and what is the mechanism? Is this a transition or transversion? 18. What is the Ames Test? 19. Why is MutT so important? What occurs in cells lacking this enzyme? 20. How does DNA polymerase proofreading specifically recognize mispairs? 21. Define the roles of each in mismatch repair: a. MutS: b. MutL: c. MutH: 22. Does the mismatch repair system interact with the major or minor groove of DNA? Why? 23. How does E. coli distinguish between the old and new strand for mismatch repair? 24. How do human cells distinguish between the old and new strand for mismatch repair? 25. Give an example of the direct reversal of DNA damage. 26. What are the steps of base excision repair? 27. What is meant by the term failsafe enzyme? 28. Why does the OxoG failsafe system lead to more ATCG transversions than CGAT transversions? 29. What are the steps of nucleotide excision repair in bacteria?

30. Which repair system is tightly coupled to transcription? 31. What are the steps of homologous recombination repair? Specifically mention search proteins by name and their role in this process. 32. At which stages of the cell cycle can homologous recombination repair be used? Why? 33. Describe gene conversion. Which chromosome is this especially important to, and why? 34. What are the steps of nonhomologous end joining? 35. At what point is NHEJ used as a mechanism for DNA repair? What is its disadvantage? 36. What is translesion DNA synthesis and when is it used? 37. Name a type of cancer that results from failure of a DNA repair system (and name that system). 38. Why does repetitive DNA tend to expand over time, as one ages? 39. What do most cancers result from? 40. What steps lead to a cell becoming cancerous? 41. How do mutations and chromosomal abnormalities affect proteins and lead to disease? 42. What was observed in the study on prostate cancer? 43. What role do cell cycle checkpoints have in cancer? 44. What organelle is directly involved in apoptosis? What is MMP? 45. In the Cellular Apoptosis Pathway, describe the pathway from an external ligand through MMP to the caspases, to p53 activation. 46. Define a tumor suppressor and oncogene and give an example of each. 47. If oncogenes are so dangerous why do we have any at all? 48. Define the role of ATM in the cell and cancer. 49. Define the role of p53 in the cell and cancer. 50. Define the role of Myc in the cell and cancer.

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