Test 2 2010
1. The volume of a solution of 0.25 M NaOH that must be added to adjust the pH from 9.6 to 12.38 in 10 mL of a 100 mM solution of phosphoric acid is:
10 0.036 a) 1 mL 160 0.578 b) 2 mL## 8 0.029 c) 3 mL 95 0.343 d) 4 mL 3 0.011 e) 5 mL
2. Restriction fragments from which of the following enzymes could be ligated together. The cleavage site is indicated with an apostrophe (').
Enzyme A B C D E
Cleavage site G'ATATC G'TATAC GTATA'C T'ATATA TATAT'A 18 0.065 a) A and B
6 0.022 b) B and D 6 0.022 c) C and E 226 0.816 d) D and A## 19 0.069 e) none of the rest
3. Which of the following statements is correct regarding buffer strength at pH = 7.1 (MOPS: pK=7.15; Tris:pK=8.08)?
19 0.069 a) MOPS is more effective against acid and Tris is more effective against base 4 0.014 b) MOPS is more effective against base and Tris is more effective against acid 244 0.881 c) MOPS is more effective against both acid and base##
7 0.025 d) Tris is more effective against both acid and base 2 0.007 e) None of the rest
4. Which of the followings is correct when a foreign DNA is being inserted between the XmnI and ScaI sites of pUC18 (refer to Figure 1 for a map of pUC18) and introduced into E. coli cells? 42 0.152 a) Clones transformed with the recombinant plasmid are sensitive to ampicillin 7 0.025 b) Clones transformed with the recombinant plasmid are sensitive to tetracycline 9 0.032 c) Clones transformed with pUC18 are resistant to ampicillin
1 0.004 d) Clones transformed with pUC18 are sensitive to tetracycline 217 0.783 e) all of the rest are correct##
5. According Table 2.2 on thermodynamic changes for transferring hydrocarbons from water to nonpolar solvents at 25¡ãC. Which of the following statements is(are) correct. "-" refers to direct interaction; "//" refers to no direction interaction.
5 0.018 a) Methane molecules move spontaneously from water to benzene due to negative DH
51 0.184 b) Methane-water system has higher Gibbs free energy than Methane-benzene system
15 0.054 d) Methane molecules move spontaneously from benzene to water due to negative DG
15 0.054 e) None of the rest is correct
6. Figure 2 is a picture of
258 0.931 a) Holliday junction## 7 0.025 b) B-type DNA
2 0.007 c) A-type DNA 9 0.032 d) Z-type DNA 0 0.000 e) ribozyme
7. Which of the following structures was not deduced from fibre diffraction experiments 23 0.083 a) double helical structure of A-type DNA
20 0.072 b) double helical structure of B-type DNA 76 0.274 c) double helical structure of Z-type DNA##
136 0.491 d) all of the rest were deduced from fibre diffraction experiments 21 0.076 e) none of the rest was deduced from fibre diffraction experiments
8. Which of the following statements is incorrect?
1 0.004 a) Naturally occurring DNA is negatively supercoiled.
4 0.014 b) Topoisomerases relax supercoils by cleaving one or both strands of the DNA, passing the DNA through the break or allowing controlled rotation of the uncleaved strand, and resealing the broken strand(s).
163 0.588 c) Stacking interaction between bases is entropically driven##
1 0.004 d) The structures of nucleic acids are stabilized by divalent cations that shield adjacent phosphate groups
107 0.386 e) All listed statements are correct
9. What is false about the denaturation of DNA?
0 0.000 a) it involves the separation of DNA's double helix 2 0.007 b) viscosity of the DNA solution decreases
267 0.964 c) UV absorbance decreases## 3 0.011 d) It is a cooperative phenomenon 4 0.014 e) it is often reversible
10. The flexibility of nucleotides in nucleic acids is constrained by the followings except 7 0.025 a) the allowed rotation angles around the glycosidic bond
6 0.022 b) the puckering of the ribose ring
4 0.014 c) the torsion angles of the sugar-phosphate backbone 173 0.625 d) the 3'OH group on the ribose##
86 0.310 e) all listed factors constrain the flexibility of nucleotides in nucleic acids
11. Which of the following operations will increase the Tm of a duplex DNA 211 0.762 a) increase the ionic strength of the solution##
40 0.144 d) all listed operations will decrease the Tm of a duplex DNA 14 0.051 e) all listed operations will increase the Tm of a duplex DNA
12. A plasmid with 2400 bp of closed circular duplex DNA was isolated from E. coli. The plasmid was transferred to a high salt solution and then treated with an enzyme with type IB topoisomerase activity. After topoisomerase treatment the plasmid is transferred back to a low salt solution. This plasmid has a 300-bp segment of alternating C and G. This segment undergoes equilibrium transition from the B conformation to the Z conformation upon transfer to the high salt solution. Given that B-DNA contains one right-handed turn per 10 base pairs, Z-DNA contains one left-handed turn per 12 base pairs and linking number (L) equals twist (T) plus writhing number (W). Which of the followings is incorrect?
17 0.061 a) Its original twist is equal to 240 85 0.307 b) Its final writhing number is -55 63 0.227 c) Its final linking number is 185 100 0.361 d) Its final twisting number is 185## 10 0.036 e) All answers are correct
13. If 25% of the DNA in a relaxed circular-covalently-closed plasmid is induced to change from B-DNA to Z-DNA and then treated by an enzyme with type IA topoisomerase activity. What happens to the value of the writhing number?
196 0.708 a) increases## 35 0.126 b) decreases
44 0.159 c) remains the same
1 0.004 d) mutiplies by a factor of 3 0 0.000 e) none of the answers
14. Which component would act as a sliding clamp during replication? 83 0.300 a) DNA polymerase I
8 0.029 b) DNA ligase 117 0.422 c) PCNA ## 46 0.166 d) helicase 22 0.079 e) RecA
15. Which of the followings is incorrect about telomerase 1 0.004 a) it is for the addition of telomeric sequences 13 0.047 b) it is not found in somatic cells
10 0.036 c) its existence is related to the requirement for replication of the 5'end of the lagging strand
202 0.729 d) increased telomeric activities in all somatic cells can enable the organism to lead a longer healthy life##
50 0.181 e) all listed are correct
16. After Okazaki fragements are formed by DNA polymerase III and primase, which of the following enzyme(s) is(are) required to join them together after the RNA primers were removed? 2 0.007 a) DNA polymerase I
1 0.004 c) DNA polymerase II 0 0.000 d) DNA gyrase
154 0.556 e) DNA polymerase I and DNA ligase
17. Which of the following statements about Pol I is false? 4 0.014 a) Pol I has exonuclease activity.
12 0.043 b) Pol I is not the primary replicase in E. coli. 6 0.022 c) Pol I functions in DNA repair.
230 0.830 d) Mutation analysis demonstrates the Pol I activity is not necessary for cell survival.##
24 0.087 e) Pol I is used to radioactively label DNA in lab experiments.
18. Which of the following is not correct about the SOS response: 0 0.000 a) Induced by DNA damage
8 0.029 b) Decreased cell division
226 0.816 c) Decreased DNA repair capacity## 10 0.036 d) Decreased error checking capacity 32 0.116 e) All answers are correct
19. Which of the following statements is true about DNA: 4 0.014 a) G-C has a lower boiling point than A-T
8 0.029 b) G-C has a lower absolute stacking energy than A-T 24 0.087 c) Higher stacking energies indicate less stable structure
163 0.588 d) Hydrophobic effects contribute significantly to DNA's stability## 77 0.278 e) Hydrogen bonding is what primarily makes C-G more stable than A-T
20. Which of the following statements about sugar pucker in nucleic acids is correct: 4 0.014 a) it adds to the polarity of the molecule
154 0.556 b) it governs the relative orientations of the base substituents to each ribose residue##
10 0.036 c) it affects the charge of the phosphate groups in the sugar-phosphate backbone 31 0.112 d) none of rest is correct
77 0.278 e) all of the rest are correct
21. Which of the following is not a benefit of the DNA Pol III holoenzyme sliding clamp: 8 0.029 a) clamp increases the rate of nucleotide polymerization
190 0.686 b) the clamp protects the template from denaturation by UV light## 14 0.051 c) the clamp increases the processivity of Pol III
60 0.217 d) all of the rest are benefits of the DNA Pol III sliding clamp 4 0.014 e) none of the rest is benefit of the DNA Pol III sliding clamp
22. Which of the following statements is true
9 0.032 a) Liquid water at 0 degree C has greater enthalpy than ice at 0 degree C 0 0.000 b) Ice has more entropy at -50 degree C than at -5 degree C
7 0.025 c) Liquid water spontaneously form Ice at 0 degree C
260 0.939 e) At 0 degree C, free energies of ice and liquid are the same##
23. Common structural motifs in DNA-binding proteins include the followings except 6 0.022 a) the helix-turn-helix motif
3 0.011 b) zinc fingers 37 0.134 c) leucine zipper
5 0.018 d) basic helix-loop-helix motifs
225 0.812 e) all of the listed are common structural motifs found in DNA-binding proteins##
24. The high fidelity of DNA replication is achieved by the followings except 0 0.000 a) the regulation of dNTP levels
14 0.051 b) the requirement for RNA primers 1 0.004 c) 3' -> 5' proofreading
1 0.004 d) DNA repair mechanisms
260 0.939 e) all listed are important for achieving the high fidelity of DNA replication##
25. Loss of which of the following genes (proteins) in E. coli would not be lethal 2 0.007 a) dnaB (helicase DnaB)
12 0.043 b) polA (Pol I) 2 0.007 c) ssb (SSB) 78 0.282 d) topoisomerase
