CH 3 - Problems

Problems http://edugen.wiley.com/edugen/courses/crs1900/rc/voet9301c03/dm9ld...
1. Kinases are enzymes that transfer a phosphoryl group from a nucleoside triphosphate. Which of the
following are valid kinase-catalyzed reactions?
(a) ATP + GDP → ADP + GTP

(b) ATP + GMP → AMP + GTP
(c) ADP + CMP → AMP + CDP
(d) AMP + ATP → 2 ADP
Answer:
(a) Yes;
(b) no;
(c) no;
(d) yes.
2. A diploid organism with a 45,000-kb haploid genome contains 21% G residues. Calculate the number of
A, C, G, and T residues in the DNA of each cell in this organism.
Answer:
Since the haploid genome contains 21% G, it must contain 21% C (because G = C) and 58% A + T (or
29% A and 29% T, because A = T). Each cell is diploid, containing 90,000 kb or 9 × 107 bases. Therefore,
3. A segment of DNA containing 20 base pairs includes 7 guanine residues. How many adenine residues are
in the segment? How many uracil residues are in the segment?
Answer:
The DNA contains 40 bases in all. Since G = C, there are 7 cytosine residues. The remainder (40 – 14 =
26) must be adenine and thymine. Since A = T, there are 13 adenine residues. There are no uracil residues
(U is a component of RNA but not DNA).
4. Draw the tautomeric forms of (a) adenine and (b) cytosine.
Answer:
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5. The adenine derivative hypoxanthine can base-pair with both cytosine and adenine. Show the structures
of these base pairs.
Answer:
6. Explain why the strands of a DNA molecule can be separated more easily at pH > 11.
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Answer:
The high pH eliminates hydrogen bonds between bases, making it easier to separate the strands of DNA.
7. How many different amino acids could theoretically be encoded by nucleic acids containing four different
nucleotides if (a) each nucleotide coded for one amino acid; (b) consecutive sequences of two nucleotides
coded for one amino acid; (c) consecutive sequences of three nucleotides coded for one amino acid; (d)
consecutive sequences of four nucleotides coded for one amino acid?
Answer:
The number of possible sequences of four different nucleotides is 4n where n is the number of nucleotides
in the sequence. Therefore, (a) 41 = 4, (b) 42 = 16, (c) 43 = 64, and (d) 44 = 256.
8. The recognition sequence for the restriction enzyme TaqI is T↓CGA. Indicate the products of the reaction
of TaqI with the DNA sequence shown.
5′-AC GT C GAA T C –3′

3′-T G C AGC T T A G–5′
Answer:
9. Using the data in Table 3-2, identify restriction enzymes that (a) produce blunt ends; (b) recognize and
cleave the same sequence (called isoschizomers); (c) produce identical sticky ends.
Answer:
(a) AluI, EcoRV, HaeIII, PvuII;

(b) HpaII and MspI;
(c) BamHI and BglII; HpaII and TaqI; SalI and XhoI.
10. Describe the outcome of a chain-terminator sequencing procedure in which (a) too little ddNTP is added;
(b) too much ddNTP is added; (c) too few primers are present; (d) too many primers are present.
Answer:
(a) Newly synthesized chains would be terminated less frequently, so the bands representing
truncated fragments on the sequencing gel would appear faint.
(b) Chain termination would occur more frequently, so longer fragments would be less abundant.
(c) The amount of DNA synthesis would decrease and the resulting gel bands would appear faint.
(d) No effect.
11. Calculate the number of clones required to obtain with a probability of 0.99 a specific 5-kb fragment
from C. elegans (Table 3-3).
Answer:
The C. elegans genome contains 97,000 kb, so
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Using Eq. 3-2,
N = log(1 – P)/log(1 – f)
N = log(1 – 0.99)/log(1 – 5.2 × 10–5)
N = –2/(–2.24 × 10–5) = 8.91 × 104
12. Describe how to select recombinant clones if a foreign DNA is inserted into the polylinker site of pUC18
and then introduced into E. coli cells.
Answer:
The desired clones are colorless when grown in the presence of ampicillin and X-gal. Nontransformed
bacteria cannot grow in the presence of ampicillin, because they lack the ampR gene carried by the
plasmid. Clones transformed with the plasmid only are blue, since they have an intact lacZ gene and
produce β-galactosidase, which cleaves the chromogenic substrate X-gal. Clones that contain the
plasmid with the foreign DNA insert are colorless because the insert interrupts the lacZ gene.
13. Describe the possible outcome of a PCR experiment in which (a) one of the primers is inadvertently
omitted from the reaction mixture; (b) one of the primers is complementary to several sites in the starting
DNA sample; (c) there is a single-stranded break in the target DNA sequence, which is present in only
one copy in the starting sample; (d) there is a double-stranded break in the target DNA sequence, which
is present in only one copy in the starting sample.
Answer:
(a) Only single DNA strands of variable length extending from the remaining primer would be
obtained. The number of these strands would increase linearly with the number of cycles rather
than geometrically.
(b) PCR would yield a mixture of DNA segments whose lengths correspond to the distance between
the position of the primer with a single binding site and the various sites where the multispecific
primer binds.
(c) The first cycle of PCR would yield only the new strand that is complementary to the intact DNA
strand, since DNA synthesis cannot proceed when the template is broken. However, since the
new strand has the same sequence as the broken strand, PCR can proceed normally from the
second cycle on.
(d) DNA synthesis would terminate at the breaks in the first cycle of PCR.
14. Write the sequences of the two 12-residue primers that could be used to amplify the following DNA
segment by PCR.
Answer:
ATAGGCATAGGC and CTGACCAGCGCC.

15.
(a) Why is a genomic library larger than a cDNA library for a given organism?
(b) Why do cDNA libraries derived from different cell types within the same organism differ from
each other?
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Answer:
(a) The genomic library contains DNA sequences corresponding to all the organism''s DNA, which
includes genes and nontranscribed sequences. A cDNA library represents only the DNA
sequences that are transcribed into mRNA.
(b) Different cell types express different sets of genes. Therefore, the populations of mRNA
molecules used to construct the cDNA libraries also differ.
16. A blood stain from a crime scene and blood samples from four suspects were analyzed by PCR using
fluorescent primers associated with three STR loci: D3S1358, vWA, and FGA. The resulting
electrophoretograms are shown below. The numbers beneath each peak identify the allele (upper box)
and the height of the peak in relative fluorescence units (lower box).
(a) Since everyone has two copies of each chromosome and therefore two alleles of each gene, what
accounts for the appearance of only one allele at some loci?
(b) Which suspect is a possible source of the blood?
(c) Could the suspect be identified using just one of the three STR loci?
(d) What can you conclude about the amount of DNA obtained from Suspect 1 compared to Suspect
4?
[From Thompson, W.C., Ford, S., Doom, T., Raymer, M., and Krane, D.E., Evaluating forensic DNA
evidence: Essential elements of a competent defense review, The Champion 27, 16–25 (2003)]
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Answer:
(a) If an individual is homozygous (has two copies of the same allele) at a locus, then only one peak
will appear in the electrophoretogram (for example, the D3S1358 locus from Suspect 2).
(b) Suspect 3, whose alleles exactly match those from the blood stain, is the most likely source of the
blood.
(c) Analysis of each of the three STR loci in this example shows a match between the sample and
Suspect 3, and no matches with the other suspects. In practice, however, multiple loci are
analyzed in order to minimize the probability of obtaining a match by chance.
(d) The peak heights are lower for Suspect 1 compared to Suspect 4, suggesting that less DNA was
available for PCR amplification from Suspect 1.
Copyright © 2009 John Wiley & Sons, Inc. All rights reserved.
6 of 6 4/17/2010 9:10 AM

CH 3 - Problems

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CH 3 - Problems

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Problems http://edugen.wiley.com/edugen/courses/crs1900/rc/voet9301c03/dm9ld...

(a) ATP + GDP → ADP + GTP

5′-AC GT C GAA T C –3′

(a) AluI, EcoRV, HaeIII, PvuII;

The C. elegans genome contains 97,000 kb, so

Using Eq. 3-2,

ATAGGCATAGGC and CTGACCAGCGCC.

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