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Chapter 4

1. a. Deoxyribosylthymine e. 2-amino-6-oxy purine


b. 2-oxy-4-amino pyrimidine f. Orotic acid
c. 2,4-dioxy pyrimidine g. Cyclic adenosine 3′,5′-monophosphate
d. 2,6-dioxy purine h. Deoxythymidine triphosphate

2. Upon complete hydrolysis, a dATP yields one adenine, one sugar, and three phosphates. Similarly,
a dTMP yields one thymine, one sugar, and one phosphate.

3. a.

b. 5’-dACATCTAG-3’ or 5’-ACATCTAG-3’
4. a. and b.

c. The nontemplate DNA strand has the same base sequence as the RNA transcribed from that
DNA molecule (thymine instead of uracil).

5. If adenine is at 15%, then so is uracil. The total, 30%, is subtracted to give G/C content of
70%. If A = T and G = C, then G is 35% and so is C.

6. At pH 3.8, each phosphate contributes −1.0 to the charge on each molecule. To calculate the partial
positive charge on the amino group, consider the protonated nucleotide AH+ and the unprotonated
nucleotide A.

pH = pK a + log [A]/[HA+]

Nucleotide [A]/[HA] Amino group +charge Phosphate charge Net charge

AMP 1.0 +0.5 −1.0 −0.5


CMP 0.2 +0.83 −1.0 −0.17
GMP 25 +0.04 −1.0 −0.96
UMP — — −1.0 −1.0

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Chapter 4

7. a. Density

b. GC-rich DNA is denser than AT-rich DNA because guanine has a higher molecular mass than
adenine, while occupying the same volume. Therefore, high guanine content of one strand could give
that strand a sufficiently higher density to permit strand separation under denaturing conditions.

8. a. Semiconservative:
No of replications after Location of bands (low,
adding light N No of bands appeared middle, high )
Nil 1 Low
One 1 Middle
Two 2 Middle, high
Three 2 Middle, high

b. Conservative:
No of replications after Location of bands (low,
adding light N No of bands appeared middle, high )
Nil 1 Low
One 2 Low, high
Two 2 Low, high
Three 2 Low, high

9. The RNA would be completely hydrolyzed.

10. Steric factors would probably prevent a fully hydrogen-bonded structure in the center of the cross.

11. The DNA is mostly single-stranded because the hyperchromic effect is very small. The fact that
there is any hyperchromicity at all means that there may be a small amount of intramolecular base-
pairing.
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Chapter 4

12. Since each nucleotide in a strand of DNA is about 0.34 nanometers (0.34 × 10−9 meters) in length,
the length of the human genome is 3 × 109 base pairs × 0.34 × 10−9 meters = 1.02 meters.

13. L0 = 4200 bp × 1 turn/10.5 bp = 400 turns

σ = ∆L/L 0 = 12/400 = 0.03

14. a. Ethidium bromide induces positive superhelical writhe because T becomes less positive.
Therefore, the amount of supercoiling would decrease.

b. Supercoiling would disappear because the ends could rotate more freely.

c. EtBr would decrease negative supercoiling until W = 0 and electrophoretic mobility would
reach a minimum. Continued addition would cause positive supercoiling and increase electrophoretic
mobility.

15. The GGG at the 3' terminus can pair with the internal CCC, thereby providing a duplex segment
that can bind DNA polymerase, a 3' hydroxyl terminus (GGG-OH) and a template for nucleotide
addition (GATTTGGACACAGT-5').

16. The 3' GGG-OH sequence could serve as a primer, if properly aligned with the CCC internal
sequence, yielding a gel pattern that would yield bands corresponding to the 14 nucleotides at the 5'
end of the oligonucleotide.

17. One reason for fixing the orientation in one direction would be a desire to express a cloned gene
driven from a promoter located near one end of the link between vector and insert. The 5' end of the
sense strand would need to be located downstream from the promoter. Also, cloning in a fixed
direction prevents the vector from becoming ligated to itself and forming either a circle or an end-to-
end aggregate.

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