Molecular Genetics 01:447:482
Final Exam
December 21, 2000
Name___________________________________
Answer the following with the fewest possible words and in PRINT. Brevity Will Earn You Points!
What mutation will produce a  strain that’s able to lyse a lysogen? Explain why it is able to do so? 
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Explain how restricted transduction revealed how lambda can be used as a cloning vector.
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Referring to the phage P1 genome, what does terminally redundant and circularly permutated mean? 
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List all the components that make up a nucleosome? 
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Describe one function of introns. 
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Why do eukaryotic chromosomes need telomere’s? 
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1
Indicate whether the following types of DNA are more likely to be found in the DNA component with
Cot1/2 value of: (A) <0.001 (low value)
(B) >100 (high value)
(C) either
(D) neither
1. Genes encoding enzymes
2. Introns
3. Promoters
4. PolyA stretch at the 3’ end of genes
5. Satellite DNA
6. Telomere
7. Euchromatin
8. Constitutive heterochromatin
9. Centromere
10. Nucleosomes
Mini-Matching (match enzyme used as tool in molecular genetic studies with its property)
11. DNAse I
A. A nuclease that cleaves one strand of double stranded DNA
12. DNA ligase
B. A exonuclease that degrades RNA
13. Micrococcal nuclease
C. A nuclease that cleaves double stranded DNA at a specific sequence
14. Restriction endonuclease D. A nuclease that is active only in the presence of calcium
E. A Enzyme that forms phosphodiester bonds
Mini-Matching (match the protein its nucleosome-related function)
15. N1
A. Associated with the 30 nm fiber
16. H3
B. An acidic protein
17. H1
C. Part of the nucleosome core particle
18. RNA polymerase
D. Methylates lysine residues of histones
E. Can affect the phasing of nucleosomes
Mini-Matching (match the lambda phage gene with its function)
19. P
A. Required for lysogen formation
20. cro
B. Regulates the late genes
21. Q
C. Controls phage genome replication
22. int
D. A regulator of transcription initiation
E. The reason by lysogens are immune to superinfection
Mini-Matching (match the lambda phage gene or site with the description of its null mutant phenotype)
23. J (a tail-fiber mutant)
A. The lysogen cannot be induced with ultraviolet light
24. cro
B. Produces very turbid plaques because of lysogen growth
25. b2
C. Is unable to form lysogens, but cannot lyse a lysogen
26. OR and OL
D. Is unable to form lysogens, but can lyse a lysogen
E. Lysogen can’t be superinfected, but when lysogen is induced it produces
un-infective phage
Mini-Matching
27. codon
28. messenger RNA
29. transfer RNA
30. ribosomal RNA
A. structural component of ribosome
B. minimum unit of genetic sense
C. substrate of translational initiation
D. the substrate for aminoacyl-tRNA synthetase
E. minimum functional genetic unit
2
Mini-Matching
31. EFTu
32. IF-3
33. IF-2
34. EF-G
Mini-Matching
35. Diphtheria toxin
36. Puromycin
37. Kirromycin
38. Fusidic acid
A. peptidyl-tRNA acceptor
B. required for the ribosome translocation reaction
C. brings fMet-tRNA to 30s/mRNA complex
D. inhibits association of ribsomal subunits
E. forms a ternary complex with GTP and aminoacyl-tRNA
A. Blocks every step in the ribosome elongation cycle
B. An aminoacyl-tRNA mimic
C. Inactivates eEF2, thereby blocking translocation
D. Blocks release of EFG-GDP from ribosome
E. Blocks release of EFTu-GDP from ribosome
Mini-Matching (match the protein with the description of its function)
39. RelA
A. Transcriptional repressor requiring a co-repressor
40. LacI
B. Transcriptional repressor requiring an inducer
41. TrpR
C. Transcriptional activator requiring an inducer
42. CAP
D. RNA polymerase subunit that is the target of transactivation
E. Ribosome-associated protein that regulates transcription
Mini-Matching (match the mutation with a description of its phenotype)
43. lacI-S
A. Uninducible Lac genes, dominant over wild-type lacI
44. lacI-q
B. Uninducible Lac genes, recessive to wild-type lacI
-d
45. lacI
C. Constitutively expressed Lac genes, dominant over wild-type lacI
46. lacI+
D. Constitutively expressed Lac genes, recessive to wild-type lacI
E. Lac gene expression is wild-type
Mini-Matching (match the mutation with a description of its phenotype)
47. sigma32 gene (rpoH-)
A. Unable to grow on tryptophan as a carbon source
ts
48. rpoB
B. constitutively produces porins in the outer membrane
49. ompRC. cells die at high temperature
D. all gene expression is inhibited at a non-permissive temperature
E. cannot grow at very high or very low osmotic pressure
Choose the best answer
50. Kinetic genome complexity refers to...
A. The rate of transcription
C. The mutation rate
B. The rate of DNA reassociation
D. The rate of molecular evolution
51. What physical property of DNA is being measured when reassociation kinetics is studied?
A. DNA supercoiling B. DNA charge
C. Double strandedness
D. DNA density
52. What is being measured when reassociation kinetics is studied?
A. absorbance of ultraviolet 260 nm light
B. absorbance of visible light
C. viscosity of a solution of DNA
D. the rate of sedimentation in CsCl
53. How do DNA and histones interact?
A. Electrical charge
C. Hydrophobic interaction
B. Hydrogen bonding
D. Histones have a helix-turn-helix domain
3
54. What segment of the yeast centromere is essential for activity?
A. CDE-1
B. CDE-II
C. CDE-III
D. CDE-IV
55. What is the function of a centromere?
A. Attachment of chromosome to the meiotic and mitotic spindle apparatus
B. Chromosome replication
C. Sealing of chromosome ends
D. Transcriptional regulation
56. When are eukaryotic chromosomes most highly packaged?
A. During DNA replication
B. During transcription
C. During cell division
D. When they are by methylated
57. What do ribosomes and telomerase have in common?
A. Both are enzymes
B. Both are involved in nucleosome assembly
C. Both contain RNA and protein
D. Both are found in the cytoplasm
58. What does DNAse hypersensitivity refer to?
A. Mitotic chromosomes
B. DNA that is bound to histones
C. Facultative heterochromatin
D. DNA that can be accessed by DNAse I
59. In the term “C-value paradox”, what does C-value refer to?
A. Amount of DNA encoding expressed genes
B. Amount of DNA in a haploid cell
C. The amount of the genome contained in telomeres
D. Level of complexity of an organism
60. What is the approximate diameter of a nucleosome particle?
A. 1 nm
B. 10 nm
C. 30 nm
D. 100 nm
61. Why does micrococcal nuclease digestion of chromatin generate a ladder of DNA fragments, the
smallest fragment being ~200 bp and each successive fragment being larger by 200 bp
A. MN has cleaved the linker DNA between every nucleosome pair
B. MN has cleaved the linker DNA between some, but not all nucleosome pairs
C. MN can only cleave DNA that has been predigested with DNAse I
D. MN has cleaved the DNA at every DNAs I hypersensitive site in the chromatin
62. Which of the following is a "generalized transducing" phage"?
A. T-Even phage
B. P1
C. lambda
D. K12
63. What method of DNA replication is used for packaging of lambda DNA.
A. Bidirectional
B. Rolling circle
C. Discontinuous
D. All of the above
64. Which of the following is necessary for "DNA footprinting?
A. DNA polymerase B. DNAse I
C. DNA gyrase
D. RNA polymerase
65. How does osmotic shock destroy the infectivity of lambda phage?
A. It has a weak membrane
B. Phage DNA is separated from the capsid
C. The host cell is killed by osmotic shock D. Salt denatures the phage protein
4
66. What is the "Stringent Response"?
A. Repression of gene expression when bacteria are starved for a nutrient
B. Induction of gene expression when bacteria are starved for a nutrient
C. Bacterial response to infection by a phage
E. Initiation of homologous recombination
67. What is a plaque assay?
A. A method for quantitating the number of phage particles in a solution
B. A method for measuring the DNA binding ability of a transcription factor
C. A method of isolating bacterial mutants
D. A method for measuring -galactosidase
68. What is a helix-turn-helix motif?
A. Domain responsible for association of subunits in some transcription factors
B. DNA operator site where a transcription factor binds
C. DNA binding domain found in some DNA binding proteins
D. DNA region surrounding the transcription initiation site
69. At what position would an attenuator function most effectively?
A. 5' of the transcriptional start site
B. 3' of the last gene in the operon
C. Between the transcriptional start site and the translational initiation site
D. Between the -10 and -35 sequences
70. What is antisense RNA?
A. RNA that makes up the structural component of ribosomes
B. RNA transcript that is complementary to an mRNA
C. RNA transcript base paired with DNA during transcription elongation
D. mRNA transcribed from a mutated gene
71. Why are DNA operator sites palindromic?
A. These operators interact with a protein that is a symmetrical dimer
B. They serve as the recognition site for a restriction endonuclease
C. RNA polymerase initiates transcription at these sites
D. Palindromes make excellent protein binding sites
72. How does Rho function?
A. By preventing intramolecular base pairing within RNA
B. By binding DNA
C. By phosphorylating its target protein
D. By slowing the rate of RNA polymerase elongation reaction
True (choose A) or False (Choose B).
73. RNA polymerase core enzyme can initiate transcription at a promoter.
74. EnvZ is a transcription regulator that binds to DNA.
75. Puromycin causes the translational elongation complex to dissociate.
76. All transcriptional termination sites cause RNA polymerase to pause.
5
77. DNA footprinting is used to identify where a protein binds to DNA.
78. Polar mutants are associated only with operons.
79. 5-hydroxymethylcytosine is a modified nucleotide found in lambda phage.
80. Heat shock genes are transcribed by sigma70 RNA polymerase.
81. The phage Q protein is a transcriptional antitermination factor.
83. Termination tRNAs are required for translational termination.
84. Histone H1 is associated with the 30 nm chromatin fiber.
85. Histone H1 can be removed from chromatin with 0.5 M NaCl.
86. All eukaryotic genes contain introns.
87. Most of the histones are basic proteins, except for H2A which is acidic.
88. Introns form the coding regions of all eukaryotic genes.
True or False
89. In natural transformation the DNA enters the cell as a single stranded molecule
90. Plasmid replication always involves Okazaki fragments
91 Deletion of the gene for Rom protein from ColE1 causes the copy number of the plasmid to go up
92. The plasmid R6K pir protein (protein for initiation of recombination) is involved in mobilization of
other plasmids during conjugation
93. An HFR (high frequency replication) is a plasmid that replicates quite often
94. The OriR (origin of recombination) site of plasmid F is the place at which it integrates into the
chromosome of E. coli
95. Eclipse complex formation in natural DNA transformation involves complete degradation of both
DNA strands
96. Transposition always involves replication
97. Surface exclusion in conjugation is involved in keeping the DNA inside the cell, away from the
surface of the cell
Multiple Choice:
98. During conjugation how does DNA enter the new strain?
A. Double stranded linear
B. Double stranded circular
C. Single stranded 5' end first
D. Single stranded 3' end first
99. What determines the two ends of an insertion sequence? In other words, when an insertion sequence
moves to a new location what DNA is on the two ends of the region that moves?
A. The inverted repeats
B. The direct repeats
C. The beginning and end of the transposase gene
D. The hairpin loops
100. What enzyme resolves the cointegrate formed during transposition of a complex transposon?
A. Cointegrase
B. Integrase (reverse reaction)
C. Transposase
D. Resolvase
E. Recombinase
6
101. During natural transformation the DNA enters the cell
A. In double strand covalently closed circular (CCC) form
B. In double strand open circular (OC) form
C. In double strand linear form
D. In single strand form
E. Two of the above (gram negative and gram positive organisms are different)
102. What is oriT?
A. The origin of transfer for conjugation
B. The origin of transposition for an insertion sequence
C. The origin of transformation used to recognize DNA during natural transformation
D. The original transposon on plasmid F
103. What ions are used to make cells chemically competent for transformation?
A. Magnesium ions (Mg 2+)
B. Calcium ions (Ca 2+)
C. Sodium ions (Na 1+)
D. Either A or B
E. All of the above
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Answer Key
1. A
2. B
3. B
4. D
5. A
6. A
7. B
8. A
9. B
10. C
11. A
12. E
13. D
14. C
15. B
16. C
17. A
18. E
19. C
20. D
21. B
22. A
23. E
24. B
25. C
26. D
27. B
28. C
29. D
30. A
31. E
32. D
33. C
34. B
35. C
36. B
37. E
38. D
39. E
40. B
41. A
42. C
43. A
44. D
45. C
46. E
47. C
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48. D
49. E
50. B
51. C
52. A
53. A
54. C
55. A
56. C
57. C
58. D
59. B
60. B
61. B
62. B
63. B
64. B
65. B
66. A
67. A
68. C
69. C
70. B
71. A
72. D
73. B
74. B
75. A
76. A
77. A
78. A
79. B
80. B
81. A
82. A
83. B
84. A
85. A
86. B
87. B
88. B
89. A
90. B
91. A
92. B
93. B
94. B
95. B
96. A
97. B
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98. C
99. A
100.
101.
102.
103.
D
D
A
D
10