Chapter 8 Nucleotides and Nucleic Acids
Multiple Choice Questions
1. Some basics
The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is:
A) a deoxyribonucleoside.
B) a purine nucleotide.
C) a pyrimidine nucleotide.
D) adenosine monophosphate.
E) adenosine.
2. Some basics
Purines have ____ ring(s), (each) containing _____ nitrogen(s), whereas pyrimidines have _____
ring(s), (each) containing _____ nitrogens.
A) 1; 1; 1; 1
B) 1; 2; 1; 2
C) 2; 1; 1; 2
D) 2; 2; 1; 1
E) 2; 2; 1; 2
3. Some basics
A major component of RNA but not of DNA is:
A) adenine.
B) cytosine.
C) guanine.
D) thymine.
E) uracil.
4. Some basics
The difference between thymine and uracil is:
A) one methylene group on the pyrimidine ring.
B) one methyl group on the pyrimidine ring.
C) one hydroxyl group on the ribose ring.
D) one amine group on the pyrimidine ring.
E) one methyl group on the purine ring.
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5. Some basics
The difference between a ribonucleotide and a deoxyribonucleotide is:
A) a deoxyribonucleotide has an —H instead of an —OH at C-2.
B) a deoxyribonucleotide has an —H instead of an —OH at C-3.
C) a ribonucleotide has an extra —OH at C-4.
D) a ribonucleotide has more structural flexibility than deoxyribonucleotide.
E) a ribonucleotide is a pyranose, deoxyribonucleotide is a furanose.
6. Some basics
Which one of the following is true of the pentoses found in nucleic acids?
A) C-5 and C-1 of the pentose are joined to phosphate groups.
B) The pentoses are in a planar configuration.
C) The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond.
D) The pentoses are always in the -furanose forms.
E) The straight-chain and ring forms undergo constant interconversion.
7. Some basics
The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA:
A) always link A with T and G with C.
B) are susceptible to alkaline hydrolysis.
C) are uncharged at neutral pH.
D) form between the planar rings of adjacent bases.
E) join the 3‘ hydroxyl of one nucleotide to the 5‘ hydroxyl of the next.
8. Some basics
The phosphodiester bond that joins adjacent nucleotides in DNA:
A) associates ionically with metal ions, polyamines, and proteins.
B) is positively charged.
C) is susceptible to alkaline hydrolysis.
D) Links C-2 of one base to C-3 of the next.
E) links C-3 of deoxyribose to N-1 of thymine or cytosine.
9. Some basics
The alkaline hydrolysis of RNA does not produce:
A) 2‘– AMP.
B) 2‘,3‘-cGMP.
C) 2‘-CMP.
D) 3‘,5‘-cAMP.
E) 3‘-UMP.
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10. Some basics
The DNA oligonucleotide abbreviated pATCGAC:
A) has seven phosphate groups.
B) has a hydroxyl at its 3‘ end.
C) has a phosphate on its 3‘ end.
D) has an A at its 3‘ end.
E) violates Chargaff’s rules.
11. Some basics
For the oligoribonucleotide pACGUAC:
A) the nucleotide at the 3‘ end has a phosphate at its 3‘ hydroxyl.
B) the nucleotide at the 3‘ end is a purine.
C) the nucleotide at the 5‘ end has a 5‘ hydroxyl.
D) the nucleotide at the 5‘ end has a phosphate on its 5‘ hydroxyl.
E) the nucleotide at the 5‘ end is a pyrimidine.
12. Some basics
The nucleic acid bases:
A) absorb ultraviolet light maximally at 280 nm.
B) are all about the same size.
C) are relatively hydrophilic.
D) are roughly planar.
E) can all stably base-pair with one another.
13. Some basics
Which of the following statements concerning the tautomeric forms of bases such as uracil is correct?
A) The double-lactim form contains a ketone group.
B) The lactam form contains an alcohol group.
C) The lactam form predominates at neutral pH.
D) Formation of the lactim from the lactam is irreversible.
E) The lactim and double-lactim forms are stabilized at high pH.
14. Some basics
In a double-stranded nucleic acid, cytosine typically base-pairs with:
A) adenosine.
B) guanine.
C) inosine.
D) thymine.
E) uracil.
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15. Nucleic acid structure
In the Watson-Crick model for the DNA double helix (B form) the A–T and G–C base pairs share
which one of the following properties?
A) The distance between the two glycosidic (base-sugar) bonds is the same in both base pairs,
within a few tenths of an angstrom.
B) The molecular weights of the two base pairs are identical.
C) The number of hydrogen bonds formed between the two bases of the base pair is the same.
D) The plane of neither base pair is perpendicular to the axis of the helix.
E) The proton-binding groups in both base pairs are in their charged or ionized form.
16. Nucleic acid structure
The experiment of Avery, MacLeod, and McCarty in which nonvirulent bacteria were made virulent
by transformation was significant because it showed that:
A) bacteria can undergo transformation.
B) genes are composed of DNA only.
C) mice are more susceptible to pneumonia than are humans.
D) pneumonia can be cured by transformation.
E) virulence is determine genetically.
17. Nucleic acid structure
Chargaff’s rules state that in typical DNA:
A) A = G.
B) A = C.
C) A = U.
D) A + T = G + C.
E) A + G = T + C.
18. Nucleic acid structure
Based on Chargaff’s rules, which of the following are possible base compositions for double-stranded
DNA?
%A %G %C %T %U
A) 5 45 45 5 0
B) 20 20 20 20 20
C) 35 15 35 15 0
D) All of the above
E) None of the above
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19. Nucleic acid structure
In the Watson-Crick structure of DNA, the:
A) absence of 2‘-hydroxyl groups allows bases to lie perpendicular to the helical axis.
B) adenine content of one strand must equal the thymine content of the same strand.
C) nucleotides are arranged in the A-form.
D) purine content (fraction of bases that are purines) must be the same in both strands.
E) two strands are parallel.
20. Nucleic acid structure
In the Watson-Crick model for the DNA double helix, which of the following is not true?
A) The two strands run anti-parallel to one another.
B) The base-pairing occurs on the inside of the double helix.
C) The double helix is right-handed.
D) There are two equally sized grooves that run up the sides of the helix.
F) The two strands have complementary sequences.
21. Nucleic acid structure
In the Watson-Crick model of DNA structure:
A) both strands run in the same direction, 3‘ → 5‘; they are parallel.
B) phosphate groups project toward the middle of the helix, where they are protected from
interaction with water.
C) T can form three hydrogen bonds with either G or C in the opposite strand.
D) the distance between the sugar backbone of the two strands is just large enough to accommodate
either two purines or two pyrimidines.
E) the distance between two adjacent bases in one strand is about 3.4 Å.
22. Nucleic acid structure
Which of the following is not true of all naturally occurring DNA?
A) Deoxyribose units are connected by 3‘,5‘-phosphodiester bonds.
B) The amount of A always equals the amount of T.
C) The ratio A+T/G+C is constant for all natural DNAs.
D) The two complementary strands are antiparallel.
E) Two hydrogen bonds form between A and T.
23. Nucleic acid structure
In the Watson-Crick model of DNA structure (now called B-form DNA):
A) a purine in one strand always hydrogen bonds with a purine in the other strand.
B) A–T pairs share three hydrogen bonds.
C) G–C pairs share two hydrogen bonds.
D) the 5‘ ends of both strands are at one end of the helix.
E) the bases occupy the interior of the helix.
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24. Nucleic acid structure
The double helix of DNA in the B-form is stabilized by:
A) covalent bonds between the 3‘ end of one strand and the 5‘ end of the other.
B) hydrogen bonding between the phosphate groups of two side–by-side strands.
C) hydrogen bonds between the riboses of each strand.
D) nonspecific base-stacking interaction between two adjacent bases in the same strand.
E) ribose interactions with the planar base pairs.
25. Nucleic acid structure
In nucleotides and nucleic acids, syn and anti conformations relate to:
A) base stereoisomers.
B) rotation around the phosphodiester bond.
C) rotation around the sugar-base bond.
D) sugar pucker.
E) sugar stereoisomers.
26. Nucleic acid structure
B-form DNA in vivo is a ________-handed helix, _____ Å in diameter, with a rise of ____ Å per
base pair.
A) left; 20; 3.9
B) right; 18; 3.4
C) right; 18; 3.6
D) right; 20; 3.4
E) right; 23; 2.6
27. Nucleic acid structure
For the helix in double-stranded B-form DNA, the majority of the stability can be attributed to:
A) base-pairing interactions via H-bonds.
B) interactions along the phosphate backbone.
C) base-stacking interactions via van-der-Waals interactions.
D) covalent bonds between adjacent bases in one strand.
E) ionic interactions with metal ions.
28. Nucleic acid structure
Which of the following is a palindromic sequence?
A) AGGTCC
TCCAGG
B) CCTTCC
GCAAGG
C) GAATCC
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CTTAGG
D) GGATCC
CCTAGG
E) GTATCC
CATAGG
29. Nucleic acid structure
Triple-helical DNA structures can result from Hoogsteen (non Watson-Crick) interactions. These
interactions are primarily:
A) covalent bonds involving deoxyribose.
B) covalent bonds involving the bases.
C) hydrogen bonds involving deoxyribose.
D) hydrogen bonds involving the bases.
E) hydrophobic interactions involving the bases.
30. Nucleic acid structure
Which of the following are possible base compositions for single-stranded RNA?
%A %G %C %T %U
A) 5 45 45 0 5
B) 25 25 25 0 25
C) 35 10 30 0 25
D) All of the above
E) None of the above
31. Nucleic acid structure
Double-stranded regions of RNA:
A) are less stable than double-stranded regions of DNA.
B) can be observed in the laboratory, but probably have no biological relevance.
C) can form between two self-complementary regions of the same single strand of RNA.
D) do not occur.
E) have the two strands arranged in parallel (unlike those of DNA, which are antiparallel).
32. Nucleic acid structure
Double stranded regions of RNA typically take on a(n):
A) A-form left-handed helix.
B) A-form right-handed helix.
C) B-form left-handed helix.
D) B-form right-handed helix.
E) Z-form left-handed helix.
33. Nucleic acid chemistry
When double-stranded DNA is heated at neutral pH, which change does not occur?
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A) The absorption of ultraviolet (260 nm) light increases.
B) The covalent N-glycosidic bond between the base and the pentose breaks.
C) The helical structure unwinds.
D) The hydrogen bonds between A and T break.
E) The viscosity of the solution decreases.
34. Nucleic acid chemistry
Which of the following deoxyoligonucleotides will hybridize with a DNA containing the sequence
(5‘)AGACTGGTC(3‘)?
A) (5‘)CTCATTGAG(3‘)
B) (5‘)GACCAGTCT(3‘)
C) (5‘)GAGTCAACT(3‘)
D) (5‘)TCTGACCAG(3‘)
E) (5‘)TCTGGATCT(3‘)
35. Nucleic acid chemistry
The ribonucleotide polymer (5‘)GTGATCAAGC(3‘) could only form a double-stranded structure with:
A) (5‘)CACTAGTTCG(3‘).
B) (5‘)CACUAGUUCG(3‘).
C) (5‘)CACUTTCGCCC(3‘).
D) (5‘)GCTTGATCAC(3‘).
E) (5‘)GCCTAGTTUG(3‘).
36. Nucleic acid chemistry
In comparison with DNA-DNA double helices, the stability of DNA-RNA and RNA-RNA helices is:
A) DNA-DNA > DNA-RNA > RNA-RNA.
B) DNA-DNA > RNA-RNA > DNA-RNA.
C) RNA-DNA > RNA-RNA > DNA-DNA.
D) RNA-RNA > DNA-DNA > DNA-RNA.
E) RNA-RNA > DNA-RNA > DNA-DNA.
37. Nucleic acid chemistry
In the laboratory, several factors are known to cause alteration of the chemical structure of DNA. The
factor(s) likely to be important in a living cell is (are):
A) heat.
B) low pH.
C) oxygen.
D) UV light.
E) both C and D.
38. Nucleic acid chemistry
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Compounds that generate nitrous acid (such as nitrites, nitrates, and nitrosamines) change DNA
molecules by:
A) breakage of phosphodiester bonds.
B) deamination of bases.
C) depurination.
D) formation of thymine dimers.
E) transformation of A → T.
39. Nucleic acid chemistry
In DNA sequencing by the Sanger (dideoxy) method:
A) radioactive dideoxy ATP is included in each of four reaction mixtures before enzymatic
synthesis of complementary strands.
B) specific enzymes are used to cut the newly synthesized DNA into small pieces, which are then
separated by electrophoresis.
C) the dideoxynucleotides must be present at high levels to obtain long stretches of DNA sequence.
D) the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of DNA where Gs
occur in the template strands.
E) the template DNA strand is radioactive.
40. Nucleic acid chemistry
In the chemical synthesis of DNA:
A) the dimethoxytrityl (DMT) group catalyzes formation of the phosphodiester bond.
B) the direction of synthesis is 5‘ to 3‘.
C) the maximum length of oligonucleotide that can be synthesized is 8–10 nucleotides.
D) the nucleotide initially attached to the silica gel support will become the 3‘ end of the finished
product.
E) the protecting cyanoethyl groups are removed after each step.
41. Other functions of nucleotides
In living cells, nucleotides and their derivatives can serve as:
A) carriers of metabolic energy.
B) enzyme cofactors.
C) intracellular signals.
D) precursors for nucleic acid synthesis.
E) all of the above.
42. Other functions of nucleotides
The “energy carrier” ATP is an example of a(n):
A) deoxyribonucleoside triphosphate
B) di-nucleotide
C) peptide
D) ribonucleotide
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E) ribonucleoside triphosphate
Short Answer Questions
43. Some basics
Pages: 281–282 Difficulty: 1
How are a nucleoside and a nucleotide similar and how are they different?
44. Some basics
Pages: 281–283 Difficulty: 1
Match the type of bond with the role below:
Bond_type Role
(a) phosphodiester ___ links base to pentose in nucleotide
(b) N-glycosidic ___ joins adjacent nucleotides in one strand
(c) phosphate ester ___ joins complementary nucleotides in two
strands
(d) hydrogen ___ difference between a nucleoside and a
nucleotide
45. Nucleic acid structure
Pages: 281–283 Difficulty: 2
Compounds that contain a nitrogenous base, a sugar, and a phosphate group are called (a)________.
Two purines found in DNA are (b)______________ and __________________.
A pyrimidine found in all DNA but in only some RNA is (c)_________________.
In DNA, the base pair (d)___ –___ is held together by three hydrogen bonds;
the base pair (e)___ –___ has only two such bonds.
46. Nucleic acid structure
Page: 287 Difficulty: 3
Draw the structure of both an adenine-thymine and a guanine-cytosine base pair as found in the
Watson-Crick double-helical structure of DNA. Include all hydrogen bonds.
47. Nucleic acid structure
Page: 288 Difficulty: 2
Briefly describe the experimental evidence of Avery, MacLeod, and McCarty that DNA is the genetic
material.
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48. Nucleic acid structure
Pages: 288–289 Difficulty: 3
The composition (mole fraction) of one of the strands of a double-helical DNA is [A] = 0.3, and [G] =
0.24. Calculate the following, if possible. If impossible, write “I.”
For the same strand:
[T] = (a) ____
[C] = (b) ____
[T] + [C] = (c) ____
For the other strand:
[A] = (d) ____
[T] = (e) ____
[A] + [T] = (f) ____
[G] = (g) ____
[C] = (h) ____
[G] + [C] = (i) ____
49. Nucleic acid structure
Page: 291 Difficulty: 2
What is the approximate length of a DNA molecule (in the B form) containing 10,000 base pairs?
50. Nucleic acid structure
Page: 289 Difficulty: 2
Describe briefly what is meant by saying that two DNA strands are complementary.
51. Nucleic acid structure
Pages: 290–291 Difficulty: 2
In one sentence, identify the most obvious structural difference between A-form (Watson-Crick)
DNA and Z-form DNA.
52. Nucleic acid structure
Pages: 291–292 Difficulty: 2
Write a double-stranded DNA sequence containing a six-nucleotide palindrome.
53. Nucleic acid chemistry
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Pages: 294–296 Difficulty: 3
Describe briefly how noncovalent interactions contribute to the three-dimensional shapes of RNA
molecules.
54. Nucleic acid chemistry
Pages: 297–298 Difficulty: 3
Why does lowering the ionic strength of a solution of double-stranded DNA permit the DNA to
denature more readily (for example, to denature at a lower temperature than at a higher ionic strength)?
55. Nucleic acid chemistry
Pages: 297–298 Difficulty: 2
Describe qualitatively how the tm for a double-stranded DNA depends on its nucleotide composition.
56. Nucleic acid chemistry
Pages: 297–298 Difficulty: 2
A solution of DNA is heated slowly until the tm is reached. What is the likely structure of the DNA
molecules at this temperature?
57. Nucleic acid chemistry
Pages: 298–299 Difficulty: 2
Mouse DNA hybridizes more extensively with human DNA than with yeast DNA. Explain by
describing the factor or factors that determine extent of hybridization.
58. Nucleic acid chemistry
Page: 299 Difficulty 3
Based on the spontaneous deamination of cytosine, explain why it is advantageous for DNA to
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contain thymine, not uracil.
59. Nucleic acid chemistry
Pages: 300–301 Difficulty: 2
What is the principal effect of ultraviolet radiation on DNA?
60. Nucleic acid chemistry
Pages: 302–304 Difficulty: 3
What happens in automated Sanger DNA sequencing reaction if you forget to add
a) all fluorescent ddNTPs?
b) fluorescent ddGTP?
c) all dNTPs?
d) dGTP?
61. Other functions of nucleotides
Pages: 306–308 Difficulty: 2
Explain how nucleoside triphosphates (such as ATP) act as carriers of chemical energy.