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CHE 476 Biochemistry I Exam II: Molecular Biology Summer 2016 14.

Summer 2016 14. Which Roman numeral labels the site where H-bonding would never
occur?
O O a) i b) ii c) iii d) iv e) v
B)
NH2 A) N NH
i i i NH 15. Which Roman numeral labels the site where H-bonding in normal
iv double helices occurs?
N v iii
N O N O a) i b) ii c) iii d) iv e) v
N
N H H
NH2 16. Which of the following is an advantage of having double-stranded
O NH2
C) D) DNA (dsDNA) as opposed to double-stranded RNA (dsRNA)?
m o le c u le X N
N N a) It allows cells to use thymine instead of uracil.
b) It allows for more information to be stored than double-stranded
RNA would.
N N NH2 N O c) It allows for better protection for the bases than double-stranded
H H RNA would.
Please consider the molecules above for Questions 1 - 14. d) It allows for anti-parallel, complementary strands.
1. Molecule X is: e) MTOON.
a) a pyrimidine. b) a purine. c) cytosine.
d) a purine not normally found in nucleic acids. 17. Which of the following is true of dsDNA but not of dsRNA?
e) MTOON. a) They are antiparallel.
b) They are made 5' 3'.
2. Which of the following is NOT true? c) They must be separated to be used as a template.
a) Molecule X could be deaminated to form cytosine. d) They must contain thymine, not uracil, to form properly.
b) Molecule X could be deaminated to form uracil. e) You can't fool me! None of these are true of dsDNA but not of
c) Molecule X could undergo a true keto-enol shift. dsRNA.
d) Molecule X could H-bond well with Molecule B).
e) Molecule X could be deaminated and methylated to form 18. Which of the following is an advantage of using thymine, and not
thymine. uracil, in dsDNA?
a) It is cheaper to make.
3. In a DNA double helix, Molecule X would H-bond best with: b) It allows for strands to be separated more easily.
a) A) b) B) c) C) d) D) e) MTOON. c) It allows for double helices to be antiparallel more easily.
d) It H-bonds better with adenine .
4. In an RNA double helix, Molecule X would H-bond best with: e) You can't fool me! None of these are advantages to using thymine
a) A) b) B) c) C) d) D) in dsDNA.
e) You can't fool me! RNA cannot form double helices!
19. The use of U, and not T, in RNA occurs:
5. Molecule X could form three H-bonds with: a) because it is easier (and cheaper!) to make.
a) A) b) B) c) C) d) D) e) MTOON. b) to reduce mutations due to mismatches.
c) to reduce mutations due to deaminations.
6. Which of the following is NOT true? d) because it binds to adenine better (more specifically.)
a) Molecule A) could be aminated to form Molecule C). e) to keep RNA single-stranded.
b) Molecule A) could not H-bond with Molecule C).
c) Molecule A) could H-bond with Molecule D) in a double helix. 20. Which of the following is an advantage of having double-stranded, as
d) Molecule A) could H-bond with Molecule D) better than with opposed to single-stranded, DNA?
Molecule C). a) It allows cells to use thymine instead of uracil.
e) Molecule A) could H-bond with Molecule D) better than with b) It allows for more information to be stored than single-stranded
Molecule C) in a normal double helix. DNA would.
c) It allows for better protection for the bases than single-stranded
7. Which of the following is NOT true? DNA would.
a) Molecule A) could be aminated to form Molecule D). d) It allows for anti-parallel, complementary strands.
b) Molecule A) could be aminated to form Molecule C). e) MTOON.
c) Molecule B) be aminated to form Molecule D).
d) Molecule D) be deaminated to form Molecule B). 21. Which of the following is true of replication but not of transcription?
e) Molecule C) be deaminated to form Molecule A). a) It normally occurs on both strands simultaneously.
b) It ends when there are no more sequences to be copied.
8. Which of the statements in Question 7 is actually true of nitrogenous c) The lagging strand template is opening in the wrong direction.
base synthesis in you? d) It occurs by linking nucleotides forming phosphodiester bonds.
a) a) b) b) c) c) d) d) e) MTOON. e) MTOON.

9. Which of the five molecules in the figure would require the most amino 22. Which of the following is true of both replication and transcription?
acid parts to be made? a) It normally occurs on both strands simultaneously.
a) A) b) B) c) C) d) D) e) X b) It ends when there are no more sequences to be copied.
c) The lagging strand template is opening in the wrong direction.
10. On the molecule labelled A) there are five Roman numerals labelling d) It occurs by linking nucleotides forming phosphodiester bonds.
five atoms on the molecule. Which Roman numeral labels the site e) MTOON.
where a pentose would be attached in a ribonucleotide?
a) i b) ii c) iii d) iv e) v
23. Which of the following is true of neither replication nor transcription?
11. Which Roman numeral labels the site where a pentose would be a) The nucleotides that are polymerized must be triphosphates.
attached in a deoxyribonucleoside? b) The template strand is ssDNA.
a) i b) ii c) iii d) iv e) v c) The nucleotides that are polymerized are linked to each other by
H-bonds.
12. Which of these molecules could undergo a keto-enol shift to H-bond d) The nucleotides that are polymerized are chosen by their ability
well with Molecule X in a normal double helix? to fit with the template.
a) A) b) B) c) C) d) D) e) The template is read 3 5.

13. The double helix decribed in Question 12 above would have to be: 24. If dsRNA molecules were to be replicated using your RNA
a) DNA b) RNA c) DNA-RNA polymerase, which of the following absolutely not be required (not
d) You can't fool me! It could be any of these. be used)?
a) Okazaki fragments
b) thymidine as a ribonucleotide d) A uracil incorporated via complementarity with guanine in the enol
c) primers form.
d) an RNA template e) A uracil in the enol form incorporated via complementarity with
guanine.
25*. When RNA molecules from retroviruses are replicated as DNA
molecules an enzyme from the virus known as reverse Consider the figure to the right for
transcriptase. This enzyme does use dTTP, not dUTP. This is Questions 33-40. Y points to the 3 end of a
because: double-helical piece of nucleic acid in the midst
a) dTTP is the only complement to adenine that it recognizes. of replication.
b) thymidine is the only base that could be a complement to adenine
in double helices. 33. The lagging strand template is:
c) that is what the primers use. a) 1 Y. b) 2 3. c) 4 5. d) 67.
d) that is the only way to make Okazaki fragments.
e) that is the only triphosphate complement to adenine it finds. 34. Which of these would have the most RNA?
a) 1 Y. b) 2 3. c) 4 5. d) 67.
26*. When RNA molecules from retroviruses are replicated as DNA
molecules, the reverse transcriptase (RT) works only continuously. 35. This must be replication because in normal transcription, one of these
The following list describes several characteristics of this enzyme. pieces would not be present. Which one?
Which cause it to work continuously and not discontinuously? a) 1 Y. b) 2 3. c) 4 5. d) 67.
i. RT uses dTTP.
ii. RT only copies (replicates) one strand at a time. 36. Which of these would have the most ligase activity?
iii. RT does not need traditional primers. a) 1 Y. b) 2 3. c) 4 5. d) 67.
iv. RT only works 5 3.
v. RT only reads a template 3 5. 37. Which of these would actually be Okazaki fragments?
a) 1 Y. b) 2 3. c) 4 5. d) 67.
a) i, ii, iii. b) i, iii, v c) ii, iii, v d) ii, iv, v e) iii, iv, v.
38. Which of these would made discontinuously?
27*. More mistakes are made when RT is working. Which two of the a) 1 Y. b) 2 3. c) 4 5. d) MTOON
following RT characteristics are the are the probable causes of these
errors? 39. At which of the these points would you find a piece of RNA for
i. RT uses dTTP. certain?
ii. RT only copies (replicates) one strand at a time. a) 1. b) 2. c) 3. d) 4. e) 5.
iii. RT does not need traditional primers.
iv. RT only works 5 3. 40. Which of these would contain NO RNA?
v. RT only reads a template 3 5. a) 1 Y. b) 2 3. c) 4 5.

a) i, ii b) ii, iii c) iii, iv d) iv, v e) iii, v 41. Which of the following is NOT an example of post-transcriptional
modification of RNA?
28. Okazaki fragments occur because of each of the following EXCEPT: a) removal of intron regions in the middle of RNA pieces.
a) polymerases read in only one direction. b) attachment of nucelotides to the 5 end.
b) large regions of single-stranded DNA are more reactive. c) attachment of an amino acid to the 3 end.
c) double-helices open in opposite directions. d) attachment of a poly A tail (to the 3 end.)
d) the lagging strand template is opening in the wrong direction. e) MTOON.
e) proofreading requires a double-stranded region of about 5-10
base pairs (bp.) 42. Transcription begins by protein factors binding to:
a) promoter regions.
29. Replication is semi-discontinuous because: b) a start codon.
a) only one strand (semi) is copied at a time (discontinuously.) c) a start codon near the 5 end.
b) one strand (semi) is replicated continuously while the other (semi) d) RNA polymerase which then binds to a start codon.
is made in pieces that are linked (or discontinuously). e) RNA polymerase which then binds to promoters.
c) half (semi) of each daughter double helix is new strand
(discontinuously) while the other half is old (continuously.)
d) half of the template is opening 5 3while the other half is
opening N C (semi-discontinuously.)
e) You cant fool me! All of these are clown answers, Bro. 43. All promoter regions:
a) are exactly identical.
b) are start codons.
c) are immediately prior to the first transcribed region.
d) are part of the first transcribed regions.
30. RNA is made with uracil, thymine because: e) MTOON.
a) RNA polymerases only recognize uracil.
b) thymine as a ribonucleotide is not available in cells.
c) uracil is cheaper to make.
d) the advantages of using thymine dont work with single-stranded
nucleic acids.

31. Which of the following is the least probable mechanism for uracil
appearing in DNA?
a) demethylation of thymine
b) deamination of cytosine
c) incorporation via complementarity with adenine
d) incorporation via complementarity with guanine enol-shifted.
e) incorporation via complementarity with guanine when the uracil is
enol-shifted.

32. Which of the following is the only uracil that would recognized as a
mistake by the proofreading function of DNA polymerase?
a) A uracil formed by demethylation of thymine
b) A uracil formed by deamination of cytosine
c) A uracil incorporated via complementarity with adenine
a) tRNA. b) mRNA c) rRNA

55. In any given cell (and actually between different cells), which of these
types of RNA has the most different bases?
a) tRNA. b) mRNA c) rRNA

56. In all cells, which of these types of RNA is the most varied in terms of
size and sequence, but not general shape?
a) tRNA. b) mRNA c) rRNA

57. For which of these types of RNA is shape least important (as long as
it is not double-helical)?
a) tRNA. b) mRNA c) rRNA

58. The answer to Question 54 is what it is because these types of RNA


all need to get recognized by the same proteins:
a) for removal of intron regions.
b) attachment of a stop codon.
Please consider the figure above for questions 44-50. It depicts a c) attachment of an amino acid (to the 3 end.)
part of some process described in class. d) on the ribosomes (in the same sites.)
e) for alteration of their bases.
44. If R1 is just a few nucleotides and R4 is a hydroxyl group, this could
be depicting: On Omicron Persei 7, a mistrusted species, Kiwis gingerus, has
a) the initiation of replication. proteins that have 7 different amino acids. This goofy organism has two
b) transcription. different bases in its nucleic acid which is double-stranded RNA.
c) translation.
d) splicing (intron removal.) 59. Compared to you, this organism would need fewer codons because it:
e) MTOON. a) YOU CANT FOOL ME! IT WOULD NEED MORE CODONS!.
b) only uses RNA.
45. This could NOT be depicting: c) only uses double-stranded RNA.
a) the initiation of replication. d) uses two different bases.
b) transcription. e) has 7 different amino acids.
c) translation.
60. According to this information, this organism would need codons that
46. The template in this picture is: are at least __ bases long!
a) The part with R1 and R4. a) 7 b) 2 c) 3 d) 8 e) 14
b) The part with R2, R3 and R5.
c) Both of these parts. 61. If this organism had codons that were the minimum length, which of
d) Neither of these parts. the following would be true?
a) It could only have one stop codon.
47. The part labelled R5 must be: b) It would have to have multiple codons for at least one amino acid.
a) U. b) T. c) G. d) A. e) MTOON c) It would have to have at least one amino acid with multiple
tRNAs.
48. If R1 is many nucleotides and R4 is a hydroxyl group, this could be d) It would have to have at least one tRNA capable of carrying more
depicting: than one amino acid.
a) the initiation of replication. e) It would need at least two stop codons.
b) transcription.
c) translation. 62. Which of the answers to Question 61. could never be true of any
d) splicing (intron removal.) organism ever?
e) MTOON. a) a) b) b) c) c) d) d) e) e)
49. If this figure is depicting the end of this process, which of these would 63. The two bases would necessarily have to be:
have to be phosphates? a) a pyrimidine and a purine.
a) R1 - R5 b) two pyrimidines.
b) R1 & R5 c) two purines.
c) R2 & R3 d) complementary.
d) R1 - R3
e) R1 R4

50. If this figure is depicting the very first step of this process, which of 64. If this organism had pyrimidines and/or purines as its bases, then the
these would have to be phosphates? two bases could be:
a) R1 - R5 a) a pyrimidine and a purine.
b) R1 & R5 b) two pyrimidines.
c) R2 & R3 c) two purines.
d) R1 - R3 d) All of the above as long as they were complementary.
e) R1 R4
65. Compared to you, this organisms replication would be WAY cheaper
51. If this figure is depicting the middle or end of this process, which of because it:
these would have to be a ribose? a) has codons that are shorter.
a) R1 b) R2 c) R3 d) R4 e) R5 b) only uses RNA.
c) only uses double-stranded RNA.
52. If this figure is depicting the end of this process, the next nucleotide d) uses 14 different amino acids.
would be attached to:
a) R1 b) R2 c) R3 d) R4 e) R5 66. Transcription ends when:
a) a stop codon is encountered.
53. The nucleotide described in Question 52. Above would be b) RNA polymerase binds to a DNA double helical sequence
complementary to a base attached to: (promoter) to promote polymerization.
a) R1 b) R2 c) R3 d) R4 e) R5 c) the RNA piece being made falls off the template.
d) the lagging strand encounters a leading strand.
54. In any given cell (and actually between different cells), which of these e) MTOON.
types of RNA has the least varied shapes and sizes?
67. You observe the sequence UAGCA on the chromosome of some
new orrganism. You observe the complement to this sequence is:
UGCUG. From these two bits of information, you would know that
the mistake on the original sequence is:
a) the U b) the first A c) the G
d) the C e) It is impossible to tell.

68. If the sequence GAU Is a codon for glutamate (E), ____ is an


anticodon for E.
a) AUG b) UAG c) GAA d) GAC e) AUC

69. If the sequence GAC is a codon for glycine (G), which of the
following is also a codon for G for sure?
a) GAG b) GAA c) GAU d) GUU e) CUA

70. If the sequence GAC is a codon for glycine (G), which of the
following is an anticodon for G for sure?
a) GAG b) GAA c) GAU d) GUU e) CUA

71. If an amino acid has six different codons, you would expect that this
amino acid is:
a) very common in proteins.
b) very rare in proteins.
c) very basic.
d) very acidic.
e) very polar.

72. In a typical ribonucleotide. this


molecule would have a O
phosphate(s) at: IV .
a) I b) II c) III d) IV
OH OH
e) You cant fool me! This molecule
HO OH
wouldnt have a phosphate attached!
III. II. I.
73. In a typical useful nucleotide
containing thymine, this molecule would need __(1) at __(2) and to
be __(3) at __(4)___.
1 2 3 4
a) phosphate I reduced II
b) phosphate IV methylated III
c) phosphate I reduced III
d) sugar IV Aminated III
e) Sugar I methylated III
74. Which of the pieces in the figure could be used by a DNA polymerase
with a proofreading function?
a) A b) B c) C d) D e) MTOON

75. Which of the pieces in the figure could not be used by a primase?
a) A b) B c) C d) D e) MTOON

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