CHE 450 Biochemistry Final Exam Study Guide, Fall 2013

CHE 450 biochemistry final exam study guide, Wednesday, Dec 11, 2013, 2pm ALL of the questions on your final exam are found on this study guide! Note: next term in CHE 451, I will also provide a study guide but it will probably have only SOME of the questions for that final exam. Final exam format: (250 pts total) 40 pts translation, microRNA and viruses. (answer all questions given) 54 pts, comprehensive short questions (6 pts each, answer 9 of 11 given) 112 pts, comprehensive longer questions (14 pts each, answer 8 of 10 given) 44 pts, key term fill in the blanks (4 pts each, answer 11 of 12 given) Translation, microRNA and viruses. study guide 1. What is the function of aminoacyl tRNA synthetases? Why does the cell need (20) different kinds of t-RNA synthetases? What does the Wobble hypothesis allow for? What determines the reading frame for translation? 2. What is transpeptidation? How many t-RNAs are present during transpeptidation? What happens during the translocation step of translation? 3. What is special about AUG, UAA, UAG and UGA codons? Draw the general structure of an AUG tRNA, showing the bases of the anticodon loop (5-3) and labeling the acceptor stem. Why must all tRNAs be structurally similar?\ 4. How are microRNAs produced/processed? In what two ways can microRNAs attenuate gene expression? 5. How could microRNAs affect cancer? 6. Describe the typical life-cycle of the herpesvirus, which is a double-stranded DNA virus. 7. Describe the typical life-cycle of HIV, which is a single-stranded RNA virus. 8. In HIV, what do HIV protease, reverse transcriptase and integrase do? Where is CD4 receptor found, and why is it important in the HIV life-cycle? 9. In poliovirus, what is +-strand RNA? In poliovirus, what does RNA-directed RNA polymerase do?

10. What is the difference between a viral envelope and a viral capsid? Quiz / HW #1 11. Draw a schematic diagram of a phospholipid bilayer. Why is the hydrophobic effect so important to its formation? 12. For each of the following statements, identify a specific, medically relevant example. You need not name the proteins, but for full credit, you should be as specific as possible. proteins catalyze chemical reactions proteins carry messages across membranes proteins recognize and bind to other molecules

CHE 450 Biochemistry Final Exam Study Guide, Fall 2013

13. Vitamin A (shown at right) is relatively soluble in phospholipid membranes, but quite insoluble in water. Explain the entropic and enthalpic contributions that make this so. Water molecules form an ordered shell around a potassium ion, yet (unlike vitamin A) it is energetically favorable to dissolve KCl in water. Why is this so? 14. What are fatty acid salts? Why do they form micelles in water? 15. Draw an example of a hydrogen bond between two molecules, which is NOT a dipole-dipole interaction. Label the parts of the hydrogen bond. 16. Glucose is readily soluble in water. Describe the enthalpic and entropic considerations that make this so. 17. Compare and contrast London dispersion forces with the hydrophobic effect. 18. What are the problems with the following statement? RNA is not very important, because DNA contains all the info needed to make proteins, and proteins perform all of the active roles in cells. 19. Describe the hydrophobic effect, and how it is related to entropy. 20. Compare and contrast ion-dipole interactions with hydrogen bonds. 21. Retroviruses such as HIV contain RNA as their genetic material, which is copied by reverse transcriptase into DNA once the virus enters a cell. In what way is this an exception to the central dogma? There are a few RNA molecules that have been found to catalyze chemical reactions, including the splicing of ends of RNA molecules together. In what way is this an exception to the central dogma? Quiz / HW #2 22. Label the major and minor grooves on the base-pairs shown here. Explain how a protein that binds to the DNA double-helix without separating the DNA strands would be able to distinguish between the two base-pairs shown here. Be specific. Label each of the bases as a pyrimidine (py) or purine (pu).
ribose N O N H O N H N H N N ribose N N ribose N N H H O N O N H N N ribose H H N

OH

H3C

23. Explain the shortcomings of the following statement: Because a G:C base-pair is stabilized by three hydrogen bonds, whereas an A:T base-pair is stabilized by only two hydrogen bonds, GC-rich DNA is harder to melt than AT-rich DNA 24. What is cooperativity? How does cooperativity apply to DNA?

CHE 450 Biochemistry Final Exam Study Guide, Fall 2013

25. A CG base-pair has additional H-bond donors/acceptors in the major groove, matching the pattern donor-acceptor-acceptor. What does this mean? How does this affect DNAs interactions with water? How does this affect DNAs possible interactions with a sequence-specific DNA-binding protein? 26. Compare and contrast human type I and type II topoisomerase. 27. List the chemical and biological differences between DNA and RNA. 28. Explain the molecular events of denaturation and renaturation of DNA. Describe how these terms apply to PCR. 29. What provides the main driving force favoring double-helix formation? How are hydrogen bonds involved in double-helix formation? Why is it unlikely to see two purines base-pair with each other in a double-helix? 30. List two similarities and four differences between positive supercoiling and negative supercoiling. 31. Label four features of this double helix.

Is this an A-helix or a B-helix? How do you know? Which form (A, B or Z) of DNA is most commonly found in vivo? Why do RNA double-helices not adopt this same form? The DNA double-helix is intrinsically straight, but flexible. What are two causes of DNA bending? 32. Why does DNA usually prefer to form a B-helix? Why does mRNA not form a B-helix? What does mRNA do instead? RNA-DNA hybrids are possible, where one strand of the double helix is RNA and the other is DNA. What form would you expect such a helix to take? Explain. 33. Ciprofloxacin inhibits DNA gyrase. Why is Cipro a relatively safe antibiotic? Compare and contrast DNA gyrase and topoisomerase I. 34. Compare and contrast positive and negative supercoiling. Which type of supercoiling is most commonly found in vivo? Which type of supercoiling can be caused by separating strands and opening a bubble in the double helix? What are two reasons why supercoiling is useful in vivo? 35. What does topoisomerase I do? How does it do it? What is the difference between topo I and an enzyme that simply produces single-stranded nicks in DNA (a nickase)?

CHE 450 Biochemistry Final Exam Study Guide, Fall 2013

HW / Quiz #3 36. Explain how the results of the Meselson-Stahl experiment strongly support semi-conservative replication. 37. What does negative supercoiling have to do with DNA replication? What does positive supercoiling have to do with DNA replication? What do topoisomerases have to do with DNA replication? 38. Where are helicase, single-strand binding protein (SSB) and topoisomerase found in the replication machinery? How do they work together? 39. Based on your knowledge of replication proteins, compare DNA polymerase and singlestrand binding protein (SSB) with respect to (a) affinity for DNA and (b) cellular concentration. 40. In DNA replication, compare and contrast 3-5 exonuclease with 5-3 exonuclease. 41. Describe what happens during initiation of replication. 42. List two important features of histones, the two main components of histones, and the two main components of nucleosomes. What related term is sometimes used to refer collectively to many nucleosomes together? 43. In the diagram below, DNA pol III has just finished an Okazaki fragment, and DNA pol I taken over. Label 5- and 3-ends in two places (each) on the diagram. Draw, step-by-step, what needs to happen in order for maturation to be completed. At each step, state what enzyme activity (or activities) is needed.
DNA pol I
dG dC dC dG C dG U dA dT dC dA dT dT dA

44. How does proofreading of newly synthesized DNA occur? Refer to specific enzyme activities in your answer. 45. What happens at an Origin site? How is it different in prokaryotes vs eukaryotes? Would you expect an Origin site to be rich in GC base-pairs? Why or why not? 46. What is processivity? How do cells ensure a high degree of processivity during replication? Why is high processivity not always desirable? 47. What does RNA polymerase do in replication? Why is it needed? How often is it needed? What does ligase do in replication? Why is it needed? Quiz / HW #4 48. Describe briefly two possible fates for pre-cancerous cells that ignore the senescence threshold

CHE 450 Biochemistry Final Exam Study Guide, Fall 2013

49. What normal adult human cells express telomerase? Which strand of the DNA is extended by telomerase? How can telomerase be involved in cancer? 50. Describe the molecular steps that telomerase uses to lengthen telomeres, using the Tetrahymena telomere repeat sequence (TTGGGG) as an example. Include a diagram to show those steps. 51. What is a G-quartet? What is the function of G-quartets? The human telomere repeat (TTAGGG) only has three Gs per repeat. How does it form Gquartets? 52. Briefly describe two possible medical uses for a telomerase inhibitor. Briefly describe a possible medical use for an anti-telomerase vaccine, and the advantage it may have over a telomerase inhibitor. Briefly describe a possible medical use for a telomerase activator. 53. As related to telomeres, what are ALT mechanisms (and what do they have to do with recombination)? What do they have to do with cancer? 54. For the following primer: 5-tggg and template: 3-aaccctaagatcgctgaa show what the sequencing gel results would look like. Label the ends/lanes of the gel appropriately. (note: the actual sequence and/or primer on the exam might be different from these) 55. Why might an Ames test of a highly mutagenic chemical cause a thick ring of revertant bacterial colonies at some distance from the filter disk (that contains the chemical), but no bacterial growth right next to the filter disk? 56. What is intercalation? What kind of mutation does it tend to cause? What type of mutation might chemical chlorination of a guanine base lead to? 57. Compare and contrast fluorescent dideoxy sequencing with 32P sequencing. 58. Compare and contrast PCR with dideoxy sequencing. HW / Quiz #5 59. What does DNA photolyase do? What is a Holliday junction? What kind of DNA repair might a Holliday junction be involved with? 60. What advantage does excision repair have over recombination repair? What advantage does recombination repair have over excision repair? 61. Explain how p53 links the cell cycle and DNA repair. 62. What basic function do TBP and a sigma factor both perform? List three differences between TBP and sigma factors. How does TBP recognize a TATA box? 63. List the main process differences between the elongation phase of replication and the elongation phase of transcription.

CHE 450 Biochemistry Final Exam Study Guide, Fall 2013

64. Draw a diagram illustrating rho-independent termination. Label the 5-ends of all DNA and RNA strands, and label the antisense strand of the DNA 65. Describe the steps that occur in initiation of transcription in E. coli. 66. Draw an elongating transcription complex. Label the 5-ends of all DNA and RNA strands, and label the sense strand of the DNA 67. What is a promoter sequence? What is the difference between a promoter sequence and a consensus sequence? 68. What is the difference between a promoter with a very low level of constitutive expression and a promoter that is repressed? HW / Quiz #6 69. At the lac promoter under the following four sets of conditions, describe what molecules bind to each other, and what the effect on transcription is. (what happens to CAP, cAMP, lacI and the lac operon?) A: high lactose, high glucose concentration B: no lactose, low glucose concentration C: high lactose, low glucose concentration D: no lactose, high glucose concentration (an exam question would likely focus on just one of these four conditions) 70. In what two ways is DNA bending important at the lac promoter? 71. What is an operon? What kind of organism are they (mainly) found in? Why are they useful/efficient? Name two examples of operons. 72. In eukaryotes, what do enhancers do? How are they related to activators? Why is the spacing between enhancers and promoters variable? 73. Why is the spacing between silencer DNA and promoters variable? 74. Arabinose is another sugar that is only utilized by E.coli when glucose is scarce, but unlike LacI, the AraC protein binds to the arabinose operons promoter (pAra) only when arabinose is present. Explain how AraC and CAP must work to regulate transcription in this instance. Relative to the lac promoter (pLac), should pAra be weaker, or stronger? Explain. 75. How does alternative splicing increase the variety of tropomyosin molecules available to different cell types? What implications does alternative splicing have for the human genome and for research on the human genome? 76. In two or three sentences of your own words, describe alternative splicing. [What happens? What benefit does it seem to provide? Why is it more common in complex organisms such as humans?] 77. In the biotechnology industry, plasmids are commonly engineered to express genes/proteins that come from other organisms. [The gene of interest is PCR-amplified, then spliced into the plasmid using sticky ends, restriction enzymes and DNA ligase, then stuffed into E. coli to grow.] Just upstream of the gene, a good plasmid might contain a sigma-70 promoter copied from T7 bacteriophage and a lacI binding site.

CHE 450 Biochemistry Final Exam Study Guide, Fall 2013

Explain how these features would work together to produce large amounts of the protein, only when triggered. In the engineered plasmid, there is no CAP binding site. Why is a CAP binding site not included? Why would this scheme probably not work with most genes copied from eukaryotic chromosomal DNA? 78. Explain why the action of histone acetylase is likely to increase transcription of genes in an area of a chromosome. Why is histone deacetylase a potential problem for gene therapy treatment? 79. How does chromatin structure affect gene expression in eukaryotes? What kind of enzyme is responsible for modulating this effect to decrease transcription? How does this lead to a potential problem for gene therapy treatment? 80. (8 pts) What are CpG islands? In mammals, how are they related to histones and to transcription? 81. How does cooperative binding help eukaryotic transcription respond to multiple signals? 82. (6 pts) How is DNA methylation different in prokaryotes vs mammals? How is it similar? 83. There is a mutation that abolishes the sensitivity of the lac operon to the absence of glucose while other metabolic operons continue to be sensitive to glucose levels. Where must this mutation occur? 84. In gene therapy, when a foreign gene is delivered into a human cell (often via a virus), the newly added gene often becomes hypermethylated. More specifically, where in the DNA would hypermethylation occur? What would be the probable consequences of this hypermethylation? [consider both an immediate, process-related consequence and a further biochemical consequence of that.]

CHE 450 Biochemistry Final Study Guide, Fall 2011 Key Terms central dogma PCR agarose gel electrophoresis nucleic acids proteins lipids sugars hydrogen bond London dispersion forces hydrophobic effect free energy enthalpy entropy bilayer micelle phospholipid fatty acid purine pyrimidine ribose phosphate ester activation energy cooperativity A-DNA B-DNA Z-DNA major groove minor groove positive supercoiling negative supercoiling topoisomerase nucleosome histone (core & linker) chromatin semi-conservative replication helicase SSB Origin site leading strand lagging strand Okazaki fragment maturation proofreading ring clamp processivity theta replication 3-5 exonuclease 5-3 exonuclease discontinuous synthesis RNA primer replication fork hairpin telomere G-quartet telomerase substitution mutation insertion mutation deletion mutation chemical modification intercalation thymine dimer Ames test revertant direct reversal of damage excision repair recombination repair DNA photolyase strand exchange dideoxy DNA sequencing initiation elongation termination promoter upstream/downstream sigma factor TATA binding protein sense/antisense strands transcription bubble RNA-DNA hybrid rho-independent termination rho-dependent termination promoter repressor activator operator silencer enhancer attenuator operon constitutive inducible lacI CAP cAMP

histone acetylase histone deacetylase CpG island hemi-methylated Methyltransferase de novo methylation intron exon RNA splicing alternative splicing ribozyme tRNA A site P site aminoacyl tRNA synthetase anticodon loop translocation transpeptidation lysogenic or latent lytic integrase reverse transcriptase polyprotein viral envelope capsid dicer microRNA