BS209 Molecular Biology 2010 Spring
Chapter 4: DNA, RNA, and the Flow of Genetic Information
1. Draw the structure of two nucleotides in DNA showing the linkage between the sugars
linked.
2. What advantage do phosphodiesters have compared with other esters?
3. Describe the DNA helix model proposed by Watson and Crick.
4. Draw the hydrogen bonded A:T base pair, and show why A does not hydrogen-bond with
C.
5. Briefly describe the Meselson and Stahl experiment that indicated that DNA replication is
semiconservative.
6. What is DNA hybridization?
7. What are the minimal requirements for DNA replication?
8. How is a dNTP added to a DNA strand at the 3' end?
9. How does RNA polymerase differ from DNA polymerase?
10. What is a consensus sequence?
11. What are the two primary components of a gene?
12. What are two features of eukaryotic mRNA that are unique as compared with
prokaryotic mRNA.
13. Why are deletion and insertion mutations usually lethal?
14. What is an advantage of codon degeneracy?
15. The genetic code is not universal. Where are exceptions found?
Chapter 5: Exploring Genes and Genomes
16. A number of tools are critical to gene exploration. Name at least four.
17. Design a potential DNA-restriction enzyme site. Show both strands.
18. How can DNA fragments of various sizes be separated?
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BS209 Molecular Biology 2010 Spring
19. What is a DNA probe?
20. What is the basis of the Sanger method?
21. Explain the basis of the polymerase chain reaction.
22. Describe two ways PCR can be used in medical diagnosis.
23. Briefly outline the steps necessary to create a recombinant DNA molecule.
24. How is a single gene of interest identified on a plate containing many different library
clones?
25. When a gene is inserted into an antibiotic (e.g. ampicilin) marker gene in a plasmid, will
the resulting clone be sensitive or resistant to the antibiotic?
26. Briefly outline how a cDNA library is made.
27. Why are foreign genes often inserted with a non-cognate promoter, such as the
metallothionein gene promoter?
28. How is gene disruption used to determine the function of a gene?
29. How is a gene gun used?
30. What advantage can be gained by splicing together portions of two different genes?
Chapter 6: Exploring Evolution and Bioinformatics
31. Why are protein comparisons of three-dimensional shape more revealing than primary
sequences?
32. How does one determine whether two homolog proteins are paralogs or orthologs?
33. Why is it more effective to compare protein sequences, rather than DNA sequences, in
evolutionary studies?
34. How are sequence alignments made?
35. What is a substitution matrix?
36. What is the difference between a simple scoring system for alignment and the Blosum62 matrix?
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BS209 Molecular Biology 2010 Spring
37. How are three-dimensional structures useful in evolutionary comparisons?
38. If a protein contains a repetitive region, what might be assumed, and what should be
done next in order to test the hypothesis?
39. In addition to examining the base sequence, what other features of RNA are useful in
determining evolutionary patterns?
40. What evidence exists for a duplication event that led to the  and  hemoglobin?
41. What are the inherent difficulties of using DNA from ancient samples?
42. What are the processes by which evolution occurs?
43. Although evolutionary relationships are determined better using protein structures than
using DNA sequences, why DNA sequences are used in most analyses?
44. Briefly explain why it is possible that two proteins with little sequence homology could
be related.
45. What types of mutations could lead to significant sequence changes, yet allow function
and shape to be retained?
Chapter 25: Nucleotide Biosynthesis
46. Why is nucleotide synthesis an important pathway for medical intervention? What types
of disease could be treated using this information?
47. Given the function of nucleotides, would you expect their synthesis to be simple or
complex and diverse?
48. What is an ATP-grasp fold?
49. Describe the reaction by which carbamoyl phosphate synthetase acquires ammonia to
make carbamoyl phosphate.
50. What is the advantage of channeling intermediates by carbamoyl phosphate synthetase?
51. What reaction actually forms the six-member ring found in pyrimidines?
52. What is the approximate rate change when the enzyme orotidylate-decarboxylase
decarboxylates orotidylate to form UMP?
53. Why do the purine-salvage pathways save the cell energy?
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BS209 Molecular Biology 2010 Spring
54. What is a general theme in purine ring synthesis, in terms of reaction logic and
mechanism?
55. How is the reciprocal use of nucleotides useful in purine synthesis?
56. What reasoning supports for the theory that proteins had existed before DNA became
the mechanism of genetic heredity?
57. What is the disadvantage of methotrexate as a therapeutic agent?
58. How is ATCase, a key enzyme in pyrimidine biosynthesis, inhibited?
59. What vitamin supplement is taken during the first trimester of pregnancy in order to
prevent the birth defect known as spina bifida?
60. What are advantages of high urate levels?
Chapter 28: DNA Replication, Repair and Recombination
61. Describe, in simple terms, the hallmarks of DNA structure.
62. Compare A- and B-DNA.
63. What did x-ray analysis of crystallized DNA indicate?
64. Describe Z-DNA.
65. Describe the three-step process of topoisomerase I type.
66. How are breaks sealed in discontinuous DNA formed during replication?
67. What is known about helicases by comparison of amino acid sequences?
68. What is a processive polymerase enzyme versus a distributive polymerase enzyme?
69. How is the processivity of DNA polymerase III accomplished?
70. How are single-stranded regions of DNA maintained?
71. Describe the consequences of incorrect DNA replication or DNA damage.
72. Name the types of DNA repair, categorized in groups.
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BS209 Molecular Biology 2010 Spring
73. Why is thymine used in DNA instead of uracil?
74. What does the phrase “recombination of genetic material” refer to?
75. What role does the protein RecA play in recombination?
Chapter 29: RNA Synthesis and Processing
76. Name the three stages of RNA synthesis.
77. What is the definition of a promoter?
78. What is the significance of the  subunit?
79. How does RNA polymerase find the proper binding site?
80. What is the theory for how palindromic RNA polymerase transcription termination
signals function?
81. What is a common feature of both protein-dependent and protein-independent
termination signals in transcription?
82. How does the antibiotic rifamycin function mechanistically?
83. Describe a few of the significant differences between eukaryotic and prokaryotic
transcription and translation.
84. How does binding of heat-shock proteins differ between E. coli and Drosophila?
85. Where are enhancer sequences found in the gene?
86. Approximately, how many mRNA transcripts in higher eukaryotes undergo processing?
87. What is unique about the type of RNA editing that occurs in the transcript for
apolipoprotein B?
88. What is present in the spliceosome complex?
89. Draw the mechanism of lariat formation in a splicing pathway.
90. What are the two types of splicing categories?
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