Physical and Chemical Principles

Selected Solutions for Students

Prepared by James Fraser and Samuel Leachman
Chapter 1
From Genes to RNA
and Proteins

Problems and Solutions

True/False and Multiple Choice

2. Ionic interactions are stronger in water than in in energy when the atoms are moved away from
vacuum because water forms strong hydrogen each other). We can classify bonds into the following
bonds with polar molecules. categories, based on their dissociation energies:
True/False Strong: > 200 kJ•mol−1
Medium: 20–200 kJ•mol−1
4. A by-product of forming a peptide bond from two
amino acids is water. Weak: 5–20 kJ•mol−1
True/False Very weak: 0–5 kJ•mol−1

6. Proteins fold with their hydrophobic amino acids on Consider the bonds highlighted in purple in the
the surface and their hydrophilic amino acids in the diagram below.
core. a. First consider the bonds in molecules isolated
True/False from all other molecules (in a vacuum). Classify each
of them into the four categories given above, based
8. The central dogma of molecular biology states that on your estimation of the bond strength.
RNA is translated from proteins. b. Which of these bonds could be broken readily by
True/False thermal fluctuations?
10. DNA primase synthesizes DNA molecules. c. Next, consider what happens when these
molecules are immersed in water (fully solvated).
For each bond, indicate whether it becomes weaker,
stronger, or stays the same in water.
Fill in the Blank
d. Which of these bonds could be broken readily by
12. The van der Waals attraction arises due to _______ Question 1.18
thermal fluctuations in water?
induced dipoles in atoms.
(i) (ii)
Answer: mutually P O

14. ________ is an operational nucleic acid, whereas
_________ is strictly an informational nucleic acid.
Answer: RNA, DNA
(iii) (iv) O
16. The ______ consists of two subunits that assemble
O –
around messenger RNA. C C
Answer: ribosome O C
Quantitative/Essay HH
18. The stabilization energy of a bond or interatomic Answer:
interaction is the change in energy upon breakage a. i. Strong.
of a bond between two atoms (that is, the change ii. Very weak.

The Molecules of Life by John Kuriyan, Boyana Konforti, and David Wemmer © Garland Science
2 Chapter 1: From Genes to RNA and Proteins

iii. Weak. longer true after the discovery of retroviruses.
iv. Weak. Retroviruses use reverse transcription to create a
b. Only iv could be broken readily by thermal DNA copy and then generate many RNA copies.
26. How do size considerations forbid G-A base pairs in a
c. i. Same. double helix?
ii. Slightly stronger; the Van der Waals
interactions do not change, but the net Answer:
interaction becomes stronger because of the Both G and A are purines and have two rings. The
hydrophobic effect. double helix only has enough space for a single
iii. Weaker. purine (two rings) and pyrimidine (one ring), but not
iv. Weaker. enough for four rings total.
d. ii, iii, and iv.
28. Chemists are able to synthesize modified
20. With 64 possible codons and 21 options to code (20 oligonucleotides (that is, polymers of nucleotides) in
amino acids + stop), (a) what is the average number Question
the phosphate linkage is replaced by a neutral
of codons per amino acid/stop codon? (b) Which amide linkage, as shown in the diagram below.
amino acids occur more often than expected in the
actual codon table? phosphodiester DNA amide DNA
a. Average = 64 codons/21 amino acids = O base O base
3.05 codons per amino acid.
b. Leucine (6 codons), valine (4 codons), serine
(6 codons), proline (4 codons), threonine H H
(4 codons), alanine (4 codons), arginine O– O
(6 codons), glycine (4 codons). P
22. The human immunodeficiency virus (HIV) is a O base H O base
retrovirus with an RNA genome.
a. Assume that each HIV contains two RNA
genomes and 50 molecules of the reverse
transcriptase enzyme.
b. Assume that each reverse transcriptase
molecule acts on each RNA genome 10 times to (Adapted from M. Nina et al., and S. Wendeborn,
produce DNA. J. Am. Chem. Soc. 127: 6027–6038, 2005. With
c. Assume that an integrase enzyme successfully permission from the American Chemical Society.)
integrates 1% of the available reverse transcribed a. Such modified oligonucleotides are able to form
HIV genomes into the genome of a human host cell. double-helical structures similar to those seen for
d. Assume that each integrated copy of the viral DNA and RNA. Often these double helices are more
genome is transcribed 500 times/day. stable than the natural DNA and RNA double helices
with the same sequence of bases. Explain why such
How many HIV RNA genomes are created per day helices can form, and why they can be more stable.
from one infected cell?
b. Given the increased stability of such modified
Answer: nucleotides, why has nature not used them to build
50 reverse transcriptases × 10 replications × the genetic material? Provide two different reasons
2 genomes = 1000 DNA genomes created. that could explain why these molecules are not used.
1000 genomes created × 0.01 successfully integrated Answer:
by integrase = 10 integrated genomes.
a. The amide DNA helices lack the unfavorable
10 copies of the genome integrated × 500 negative charge concentration present in
transcriptions per day = 5000 HIV genomes created phosphodiester DNA.
from one infection per day.
b. If the amide DNA double helices were too
24. What changes to the central dogma were necessary stable, it wouldn’t be possible to unwind them
after the discovery of retroviruses? for replication and transcription. Also, without a
high-energy phosphate linkage, the amide DNA
Answer: monomers can’t internally store the energy needed
The unidirectional flow from DNA to RNA was no for synthesis.

The Molecules of Life by John Kuriyan, Boyana Konforti, and David Wemmer © Garland Science

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