Solutions To Even Numbered Problems

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SOLUTIONS
Chapter 1 Solutions Amido group

2. The functional groups are identified below. O O
⫹H N CH C NH CH C O⫺
3
Ether Carbonyl
OH CH2 CH2
O
HO CH O O Carboxyl
C C O SH
C CH C OH
H2
C C NH2
N
Hydroxyl HO OH Nicotinic acid (niacin)
Vitamin C
14. (a) Fructose has the same formula, C6H12O6, as glucose.
O Carbonyl (b) Fructose is a ketone, whereas glucose is an aldehyde.
O CH3
H3C 16. Nucleotides consist of a five-carbon sugar, a nitrogenous
Ether H
H3C C CH2 H ring, and one or more phosphate groups linked covalently together.
O C C n
H2 18. Glucose has several hydroxyl groups and is a polar mole-
Carbonyl O CH3
cule. As such, it will have difficulty crossing the nonpolar mem-
Coenzyme Q
brane. The 2,4-dinitrophenol molecule consists of a substituted
benzene ring and has greater nonpolar character. Of the two
molecules, the 2,4-dinitrophenol will traverse the membrane
4. (a) N-acetylglucosamine is a monosaccharide.
more easily.
(b) CMP is a nucleotide.
(c) Homocysteine is an amino acid. 20. Polysaccharides serve as fuel-storage molecules and can also
(d) Cholesteryl ester is a lipid. serve as structural support for the cell.
6. It is a lipid (it is actually lecithin). It is mostly C and H, with 22. The polymeric molecule is more ordered and thus has less
relatively little O and only one N and one P. It has too little O entropy. A mixture of constituent monomers has a large number
to be a carbohydrate, too little N to be a protein, and too little of different arrangements (like the balls scattered on a pool table)
P to be a nucleic acid. and thus has greater entropy.
8. A diet high in protein results in a high urea concentration, 24. The dissolution of calcium chloride in water is a highly exother-
since urea is the body’s method of ridding itself of extra nitrogen. mic process, as indicated by the negative value of DH. This means
Nitrogen is found in proteins but is not found in significant that when calcium chloride dissolves in water, the system loses heat
amounts in lipids or carbohydrates. A low-protein diet pro- to the surroundings and the surroundings become warm. The plas-
vides the patient with just enough protein for tissue repair and tic bag holding the calcium chloride solution becomes warm and
growth. In the absence of excess protein consumption, urea can be used as a hot pack by the hiker at cold temperatures.
production decreases, and this puts less strain on the patient’s 26. First, calculate DH and DS, as described in Sample
weakened kidneys. Calculation 1-1:
10. The carbon marked with an asterisk is chiral. This means that DH 5 HB – HA
alanine has two possible enantiomers, or mirror-image isomers. DH 5 60 kJ ? mol–1 – 54 kJ ? mol–1
DH 5 6 kJ ? mol–1
DS 5 SB – SA
H O DH 5 43 J ? K–1 ? mol–1 – 22 J ? K–1 ? mol–1
⫹H
3N C* C O⫺ DH 5 21 J ? K–1 ? mol–1
(a) DG 5 (6000 J ? mol–1) – (4 1 273 K)(21 J ? K–1 ? mol–1)
CH3 DG 5 180 J ? mol–1
The reaction is not favorable at 48C.
12. Two hydrogen atoms and one oxygen atom are lost when (b) DG 5 (6000 J ? mol–1) – (37 1 273 K)(21 J ? K21 ? mol–1)
Asn and Cys form a dipeptide. This is an example of a condensa- DG 5 –510 J ? mol–1
tion reaction. The carboxylate functional group on the Asn is The reaction is favorable at 378C.
lost and the amino functional group on the Cys is lost. An amido 28. (a) decrease
group is formed. (b) increase
CHAPTER 1 Solutions | 1
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30. (a) The reaction is exothermic because the value of DH because ammonia has a hydrogen bond donor and diethyl ether
is negative. has a hydrogen bond acceptor.
(b) DG 5 DH 2 TDS
DG 5 28190 J ? mol21 2 (310 K)(2.20 J ? K21 ? mol21) (B) N
DG 5 28870 J ? mol21 5 28.87 kJ ? mol–1 N
The negative value of DG indicates that the reaction is
H
spontaneous.
(c) The DH term makes a greater contribution to the DG N
value. This indicates that the reaction is spontaneous largely
N
because the reaction is exothermic. The reaction proceeds
without much change in entropy. H
32. (a) reduction (C) H3C CH2 O H
(b) oxidation
34. (a) oxidizing agent H3C CH2 O H
(b) oxidizing agent
(c) oxidizing agent (E) H N H
(d) reducing agent H O CH2 CH3
36. The complete oxidation of stearate to CO2 yields more H2C
energy because 17 of the 18 carbons of stearate are fully reduced. H3C
The conversion of these carbons to CO2 provides more free en-
ergy than some of the carbons of a-linolenate, which participate 8. (a) H , C , N , O , F
in double bonds and are therefore already partially oxidized. (b) The greater an atom’s electronegativity, the more polar
38. The first biological molecules would have had to polymer- its bond with H and the greater its ability to act as a hydro-
ize, and they would have had to find some way to make copies gen bond acceptor. Thus, N, O, and F, which have relatively
of themselves. high electronegativity, can form hydrogen bonds, whereas C,
whose electronegativity is only slightly greater than hydro-
40. It is difficult to envision how a single engulfment event
gen’s, cannot.
could have given rise to a stable and heritable association of
the eukaryotic host and the bacterial dependent within a single 10. Aquatic organisms that live in the pond are able to survive
generation. It is much more likely that natural selection gradu- the winter. Since the water at the bottom of the pond remains
ally promoted the interdependence of the cells. Over many gen- in the liquid form instead of freezing, the organisms are able to
erations, genetic information supporting the association would move around. The ice on top of the pond also serves as an insu-
have become widespread. lating layer from the cold winter air.
12. The positively charged ammonium ion is surrounded by
Chapter 2 Solutions a shell of water molecules that are oriented so that their par-
tially negatively charged oxygen atoms interact with the positive
2. Because the partial negative charges are arranged symmetri- charge on the ammonium ion. Similarly, the negatively charged
cally (and the shape of the molecule is linear), the molecule as a sulfate ion is hydrated with water molecules oriented so that the
whole is not polar. partially positively charged hydrogen atoms interact with the
negative charge on the sulfate anion. (Not shown in the diagram

O C O is the fact that the ammonium ions outnumber the sulfate ions
by a 2:1 ratio. Also note that the exact number of water mol-
ecules shown is unimportant.)
4. Water has the highest melting point because each water mol-
ecule forms hydrogen bonds with four neighboring water mole- H H
cules, and hydrogen bonds are among the strongest intermolecu- O O
lar forces. Ammonia is also capable of forming hydrogen bonds, H H
but they are not as strong (due to the electronegativity difference O H H
H H
between hydrogen and nitrogen). Methane cannot form hydro-
gen bonds; the molecules are attracted to their neighbors only O NH
4 O
O SO42 O
H H H H
via weak London dispersion forces. H H
O H H
6. Compound A does not form hydrogen bonds (the molecule H H
has a hydrogen bond acceptor but no hydrogen bond donor). O O
Compounds B and C form hydrogen bonds as shown because H H
each molecule contains at least one hydrogen bond donor and
a hydrogen bond acceptor. The molecules in D do not form 14. Structure A depicts a polar compound, while structure B
hydrogen bonds with each other, whereas the molecules in E do depicts an ionic compound similar to a salt like sodium chloride.
2 | CHAPTER 2 Solutions
This is more consistent with glycine’s physical properties as a shape with the lowest possible ratio of surface to volume). Water
white crystalline solid with a high melting point. While struc- does not bead on glass, because the glass presents a hydrophilic
ture A could be water soluble because of its ability to form hy- surface with which the water molecules can interact. This allows
drogen bonds, the high solubility of glycine in water is more the water to spread out.
consistent with an ionic compound whose positively and nega- 24. (a) CO2 is nonpolar and would be able to cross a bilayer.
tively charged groups are hydrated in aqueous solution by water (b) Glucose is polar and would not be able to pass through a
molecules. bilayer because the presence of the hydroxyl groups means glu-
16. (a) A 30X dilution is equivalent to multiplying one-tenth cose is highly hydrated and would not be able to pass through
(1021) by itself 30 times: (1021)30 5 10230. The concentra- the nonpolar tails of the molecules forming the bilayer.
tion would be 10230 M. (c) DNP is nonpolar and would be able to cross a bilayer.
(b) Use Avogadro’s number and multiply the concentration (d) Calcium ions are charged and are, like glucose, highly
by the volume to show that there is much less than one hydrated and would not be able to cross a lipid bilayer.
molecule present in 1 mL: 26. The amount of Na1 (atomic weight 23 g ? mol21) lost in
10.001 L2 110230 moles/L2 16.02 3 1023 molecules/mole2 15 minutes, assuming a fluid loss rate of 2 L per hour and a
5 6.02 3 10210 molecules sweat Na1 concentration of 50 mM, is
2L 0.05 mol 23 g 1000 mg Na 1
(c) The ability of water molecules to form a hydrogen- 0.25 h 3 3 3 3
bonded coating, or cage, around a solute molecule, particu- h L mol g Na 1
larly a hydrophobic one, might support the idea of water’s 1 oz chips
3 5 2.9 oz chips
memory. However, water molecules are constantly in motion, 200 mg Na 1
so a group of water molecules that have been in contact with a
solute do not retain an imprint of it. It would take 2.9 ounces of potato chips (about a handful) to
replace the lost sodium ions.
18. (a) In the nonpolar solvent, AOT’s polar head group faces the
interior of the micelle, and its nonpolar tails face the solvent. 28. (a) In a high-solute medium, the cytoplasm loses water;
therefore its volume decreases. In a low-solute medium, the
CH2CH3 O cytoplasm gains water and therefore its volume increases.
Nonpolar H3 C (CH2)3 CH CH2 O C CH2 O Polar (b) E. coli accumulates water when grown in a low-osmolarity
tails H3 C (CH2)3 CH CH2 O C CH S O head medium. However, regulation of water content only would
cause a large increase in cytoplasmic volume. To avoid this
CH2CH3 O O
large increase in volume, E. coli also exports K1 ions. The
AOT
opposite occurs when E. coli is grown in a high-osmolar-
(b) The protein, which contains numerous polar groups, in- ity medium—the cytoplasmic water content is decreased,
teracts with the polar AOT groups in the micelle interior. but cytoplasmic osmolarity increases as E. coli imports K1
ions. [From Record, M.T., et al., Trends Biochem. Sci. 23,
143–148 (1998).]
Isooctane
30. The HCl is a strong acid and dissociates completely. This
Water
means that the concentration of hydrogen ions contributed by
the HCl is 1.0 3 1029 M. But the concentration of the hydrogen
ions contributed by the dissociation of water is 100-fold greater
Protein than this: 1.0 3 1027 M. The concentration of the hydrogen
20. (a) It is doubtful that the contents of the ball could influ- ions contributed by the HCl is negligible in comparison. There-
ence the behavior of external water molecules separated by fore, the pH of the solution is equal to 7.0.
layers of rubber and plastic. 32. −
(b) Even if water clusters were disrupted (which they are not),
the removal of dirt requires more than one individual water
molecule. In order for a dirt molecule to be washed away, it
must be surrounded (solubilized) by many water molecules.
(c) Hot water, because of the higher energy of its water mole-
cules, has intrinsically better dirt-solubilizing power than cold
water, regardless of the presence or absence of detergent. In 34.
the absence of detergent, hot water has significant cleaning Acid, base, or neutral? pH [H1] (M) [OH2] (M)
power on its own, which could be attributed to the presence
of a laundry ball. A acid 5.60 2.5 3 1026 4.0 3 1029
22. The waxed car is a hydrophobic surface. To minimize its in- B base 7.65 2.2 3 1028 4.5 3 1027
teraction with the hydrophobic molecules (wax), each water drop C neutral 7.00 1.0 3 1027 1.0 3 1027
minimizes its surface area by becoming a sphere (the geometrical D acid 2.68 2.1 3 1023 4.8 3 10212
36. (a) The final concentration of HCl is 44. The pK of the fluorinated compound would be lower (it is
9.0); that is, the compound becomes less basic and more acidic.
10.0015 L2 13.0 M2
5 0.0045 M This occurs because the F atom, which is highly electronega-
1.0015 L tive, pulls on the nitrogen’s electrons, loosening its hold on the
Since HCl is a strong acid and dissociates completely, the proton.
added [H1] is equal to [HCl]. (The existing hydrogen ion 46. (a) 10 mM glycinamide buffer, because its pK is closer to
concentration in the water itself, 1.0 3 1027 M, can be the desired pH.
ignored because it is much smaller than the hydrogen ion (b) 20 mM Tris buffer, because the higher the concentra-
concentration contributed by the hydrochloric acid.) tion of the buffering species, the more acid or base it can
pH 5 2log [H 1 ] neutralize.
(c) Neither; each solution will contain an equilibrium mix-
pH 5 2log10.00452 ture of the boric acid and its conjugate base (borate).
pH 5 2.3 48.
(b) The final concentration of NaOH is H 1 1aq2 1 HCO32 1aq2 z y H2CO3 1aq2 z y H2O1l 2 1 CO2 1aq2
10.0015 L2 13.0 M2 Loss of CO2 through the shell would shift the above equations
5 0.0045 M to the right. Carbonic acid in the egg would produce more water
1.0015 L
and CO2 to make up for the loss of CO2. This in turn would
Since NaOH dissociates completely, the added [OH2] is cause additional hydrogen ions and bicarbonate ions to form
equal to the [NaOH]. (The existing hydroxide ion concen- more carbonic acid. The loss of hydrogen ions would result in an
tration in the water itself, 1.0 3 1027 M, can be ignored increased pH of the contents of the egg.
because it is much smaller than the hydroxide ion concen-
50. The aspirin is more likely to be absorbed in the stomach
tration contributed by the NaOH.)
at pH 2. At this pH, the carboxylate group is mostly proton-
Kw 5 1.0 3 10214 5 [H 1 ] [OH 2 ] ated and uncharged. This allows the aspirin to pass more easily
1.0 3 10214 through the nonpolar lipid bilayer. At the pH of the small in-
[H 1 ] 5
[OH 2 ] testine, the carboxylate group is mostly in the ionized form and
1.0 3 10214 will be negatively charged. Charged species are more polar than
[H 1 ] 5 uncharged species (and are likely to be hydrated) and will have
10.0045 M2
difficulty traversing a lipid bilayer.
[H 1 ] 5 2.2 3 10212 M
pH 5 2log [H 1 ] 52. Use the pK value in Table 2-4 and the Henderson–
Hasselbalch equation to calculate the ratio of imidazole (A2) and
pH 5 2log12.2 3 10212 2
the imidazolium ion (HA):
pH 5 11.6
[A2 ]
38. The carbonate ions accept protons from water and form pH 5 pK 1 log
[HA]
hydroxide ions (as shown in the equation below), resulting in [A 2 ]
basic urine. log 5 pH 2 pK
[HA]
3 1aq2 1 H2O1l 2 S HCO3 1aq2 1 OH 1aq2
CO22 2 2
[A 2 ]
5 101pH2pK 2
[HA]
40. (a) H2C2O4
[A2 ]
(b) H2SO3 5 1017.427.02 5 2.5
(c) H3PO4 [HA]
(d) H2CO3 54. At the final pH,
(e) H2AsO24
[ A2 ]
(f ) H2PO24 5 101pH2pK 2 5 1015.024.762 5 100.24 5 1.74
(g) H2O2 [HA]
42. (a) CH3 Adding NaOH to the acetic acid will convert some of the acetic
acid (HA) to acetate (A2):
C O NaOH 1 CH3COOH z y Na1 1 CH3COO2 1 H2O
COO For every mole of NaOH added, one mole of CH3COOH will be
consumed, and one mole of CH3COO2 will be generated.
Pyruvate If x is the number of moles of NaOH added, then x will also be
the number of moles of A2 generated.
(b) The structure of pyruvate will predominate in the cell at
Calculate the initial amount of acetic acid:
pH 7.4. The pK values for carboxylic acid groups are typi-
cally in the 2–3 range; therefore, the carboxylate group will 0.20 mol
10.50 L2 3 5 0.10 mol acetic acid
be unprotonated at physiological pH. L
The initial amount of acetic acid is 0.10 mol, so the final amount The final amount of A2 is 44 mmol 1 4.5 mmol 5
of acetic acid will be 0.10 mol 2 x. 48.5 mmol.
[ A2 ] x The final amount of HA is 56 mmol 2 4.5 mmol 5
5 1.74 5
[HA] 0.10 mol 2 x 51.5 mmol.
x 5 1.7410.10 mol 2 x2 5 0.174 mol 2 1.74x Use the Henderson–Hasselbalch equation to calculate the
new pH:
2.74x 5 0.174 mol
x 5 0.174 mol/2.74 5 0.0635 mol [ A2 ] 48.5
pH 5 pK 1 log 5 8.3 1 log
Calculate the mass of NaOH to add: [HA] 51.5
0.0635 mol 5 8.3 1 120.0262 5 8.27
5 1.58 g
40 g ? mol21 The buffer has been effective: The pH has increased only
56. (a) 0.07 unit (from pH 5 8.2 to pH 5 8.27) with the ad-
CH2OH CH2OH dition of the strong base. In comparison, the addition of
HOH2C C NH
3 HOH2C C NH2 the same amount of base to water, which is not buffered,
resulted in a pH change from approximately 7.0 to 11.6
CH2OH CH2OH (see Problem 36b).
Weak acid Conjugate base 58. The ratio of bicarbonate to carbonic acid in the patient’s
blood can be determined using the Henderson–Hasselbalch
(b) The pK of Tris is 8.30; therefore, its effective buffering equation:
range is 7.30–9.30.
[A2 ]
(c) Rearranging the Henderson–Hasselbalch equation gives pH 5 pK 1 log
[HA]
[A 2 ]
5 101pH2pK 2 5 1018.228.32 5 1020.1 5 0.79 [HCO32 ]
[HA] 7.55 5 6.35 1 log
[H2CO3 ]
Since [A2] 1 [HA] 5 0.1 M, [A2] 5 0.1 M 2 [HA], and
[HCO32 ]
10.1 M 2 [HA] 2 101.2 5
5 0.79, [H2CO3 ]
[HA]
[HCO32 ] 15.8
0.79 [ HA] 5 0.1 M 2 [ HA] 5
1.79 [ HA] 5 0.10 M [H2CO3 ] 1
[HA] 5 10.10 M2/1.79 5 0.056 M 5 56 mM pH 5 8.3 1 121.32 5 7.0
[A2 ] 1 [HA] 5 100 mM, so [A2 ] 5 44 mM
Similarly, the ratio of bicarbonate to carbonic acid in a normal
(d) When HCl is added, an equivalent amount of Tris person’s blood can be determined:
base (A2) is converted to Tris acid (HA). Let x 5 moles of
H1 added 5 (0.0015 L)(3.0 mol ? L21) 5 0.0045 moles 5 [A2 ]
pH 5 pK 1 log
4.5 mmol. [HA]
The final amount of A2 is 44 mmol 2 4.5 mmol 5 39.5 [HCO32 ]
mmol. 7.4 5 6.35 1 log
[H2CO3 ]
The final amount of HA is 56 mmol 1 4.5 mmol 5 60.5 2
mmol. [HCO3 ]
101.05 5
Use the Henderson–Hasselbalch equation to calculate the [H2CO3 ]
new pH: 2
[HCO3 ] 11.2
5
[A 2 ] 39.5 [H2CO3 ] 1
pH 5 pK 1 log 5 8.3 1 log
[HA] 60.5
In order to serve as an effective buffer (i.e., absorb both added
5 8.3 1 120.182 5 8.12
H1 and OH2), both a conjugate base and a weak acid must be
The buffer has been effective: The pH has declined about present. In the patient, the ratio of conjugate base to weak acid
0.1 unit (from pH 5 8.2 to pH 5 8.1) with the addi- does not lie within an effective buffering range. The bicarbonate
tion of the strong acid. In comparison, the addition of concentration (conjugate base) is too high relative to the car-
the same amount of acid to water, which is not buffered, bonic acid (weak acid) concentration; thus the relative amount
resulted in a pH change from approximately 7.0 to 2.35 of weak acid is insufficient.
(see Problem 36a).
(e) When NaOH is added, an equivalent amount of Tris
Chapter 3 Solutions
acid (HA) is converted to Tris base (A2). Let x 5 moles of
OH2 added 5 (0.0015 L)(3.0 mol ? L21) 5 0.0045 moles 5 2. These experiments showed that the transforming factor was
4.5 mmol. neither a protein nor RNA.
4. The triple-helical model is not consistent with the hydro- 31% G, since [C] 5 [G]). Each cell is a diploid, containing
phobic effect, which suggests that the nonpolar nitrogenous 60,000 kb or 6 3 107 bases. Therefore,
bases would reside in the center of the DNA structure and
[A] 5 [T] 5 (0.19)(6 3 107 bases) 5 1.14 3 107 bases
the hydrophilic phosphates would reside on the surface. The
triple-helical model also assumes that the phosphate groups are [C] 5 [G] 5 (0.31)(6 3 107 bases) 5 1.86 3 107 bases
protonated and form stabilizing hydrogen bonds in the DNA
12. N
interior. But the pK value for phosphate is well below 7, so
the phosphate groups would not be protonated at physiological O NH
H H
pH. In the absence of hydrogen bonds, there are no additional N
forces that would hold the strands of the triple helix together. N N
H
6. (a) N Hypoxanthine
O
C N O
NH2 Base
H

N
O CH2 O
Cytosine
H H
N
Monosaccharide
H H
O NH
HO OH H H
N
O P O
NH2 N N
N
N N H
O Base N Hypoxanthine
O P O N N
O CH2 O N N
H H Monosaccharide
H
H H
Adenine
HO OH
NH2 O N
N
N
Base H O NH
O O N
N
N
CH2 O P O P OCH2 O N N
H C OH O O H H Monosaccharide
N O H
H C OH
H H H Hypoxanthine
OH OH
H C OH Uracil
Monosaccharide
CH2
H3C N N O
14. It is certainly the case that hydrogen bonds hold A:T and
H3C
NH Base G:C base pairs together and that these interactions are very fa-
N
O vorable. But upon denaturation of the DNA, each nitrogenous
base has the opportunity to form equally favorable hydrogen
(b) A diphosphate bridge links the ribose groups in each bonds with water. Therefore, forces other than hydrogen bonds
dinucleotide. This linkage is a variation of the mono- must contribute to the overall stability of the DNA molecule.
phosphate bridge (phosphodiester linkage) in DNA and 16. The DNA contains 50% G 1 C, so its melting point would
RNA. be approximately 908C.
(c) The adenosine group in CoA bears a phosphoryl group
on C39. 110
8.
H2 O 100
C
Tm (°C)
H H 90
O H H
O
P O OH 80
O
70
10. The organism must also contain 19% A (since [A] 5 [T] 0 10 20 30 40 50 60 70 80
according to Chargaff ’s rules) and 62% C 1 G (or 31% C and GC content (%)
18. The positively charged sodium ions can form ion pairs with synthesis. (In the cell, the binding of antisense RNA to
the negatively charged phosphate groups on the DNA backbone mRNA involves an enzyme that degrades the mRNA
and “shield” the negative charges from one another. This increases into smaller fragments.)
the overall stability of DNA and makes it more difficult to melt. (c) The siRNA molecules must be able to cross the cell
20. The positively charged side chains of the Lys and Arg membrane to enter the cell and find the target mRNA.
residues form ion pairs with the negatively charged phosphate 30. Prokaryotes tend to have smaller genomes than eukaryotes,
groups on the DNA backbone. These are strong interactions, so so evolution has shaped the prokaryote genome to pack in genes
the histones have a high affinity for DNA. more efficiently. Eukaryotes, with larger genomes and more non-
22. The DNA isolated after one generation is a homogeneous coding DNA, have more space to arrange genes.
sample of DNA with a density intermediate between DNA con- 32. Questions that need to be addressed in order to solve the
taining all 14N and all 15N. The DNA isolated after the second C-value paradox:
generation is heterogeneous. Half of the DNA has the same den- • How does one define organismal complexity? Perhaps hu-
sity as the first generation; half of the DNA consists of all 14N mans are not the most complex organisms.
DNA and has a lower density. • How much of the organism’s genome codes for RNA? For
protein? What are the biological roles of these gene products?
15N
• How many copies of each gene are in the organism’s genome?
14N
• What is the amount of noncoding DNA in the genome?
Is the noncoding DNA really “junk DNA,” or does it
have some biological role?
• How many transposable elements are in the noncoding
DNA?
34. The polymerization reaction must be carried out at high
temperatures (hence the need for a heat-stable DNA polymerase)
in order to ensure that the template DNA remains an unknotted
First-generation
single strand. The high temperature is necessary to melt GC-rich
daughter molecules
DNA, which is more stable than AT-rich DNA.
36. To amplify the protein-coding DNA sequence, the prim-
ers should correspond to the first three and last three residues of
the protein (each amino acid represents three nucleotides, so the
primers would each be nine bases long). Use Table 3-3 to find the
codons that correspond to the first three residues:
Met Gly Ser
Second-generation AUG GGU UCU
daughter molecules GGC UCC
GGA UCA
GGG UCG
24. The number of possible sequences of four different nucleotides AGU
AGC
is 4n where n is the number of nucleotides in the sequence. There-
fore: (a) 41 5 4, (b) 42 5 16, (c) 43 5 64, and (d) 44 5 256. Using just the topmost set of codons, a possible DNA primer
would therefore have the sequence 59-ATGGGTTCT-39. This
26. The genetic code (shown in Table 3-3) is redundant. Since there
primer could base pair with the gene’s noncoding strand, and its
are 64 different possibilities for 3-base codons and only 20 amino
extension from its 39 end would yield a copy of the coding strand
acids, some amino acids have more than one codon. If a mutation
of the gene (see Fig. 3-18). The other primer must correspond to
just happens to occur in the third position (39 end), the mutation
the last three amino acids of the protein:
might not alter the protein sequence. For example, GUU, GUC,
GUA, and GUG all code for valine. A mutation in the third posi- Val Ser Pro
tion of a valine codon would still result in the selection of valine and GUU UCU CCU
would have no effect on the amino acid sequence of the protein. GUC UCC CCC
GUA UCA CCA
28. (a) The siRNA is an “antisense” mRNA, so its sequence GUG UCG CCG
should be complementary to that of the mRNA. The solu- AGU
tion below shows an siRNA that corresponds to the 59 end AGC
of the mRNA: Again, considering just the topmost set of codons, a probable DNA
mRNA 59 S 39 AUG GGC UCC AUC GGA GCA GCA AGC AUG GAA coding sequence would be 59-GTTTCTCCT-39. This sequence
siRNA 39 S 59 UAC CCG AGG UAG CCA CGU CGU UCG UAC CUU
cannot be used as a primer. However, a suitable primer would be
(b) When the antisense RNA binds to the mRNA, the the complementary sequence 59-AGGAGAAAC-39, which can
mRNA can no longer serve as a template for protein then be extended from its 39 end to yield a copy of the noncoding
strand of the gene. The number of possible primer pairs is quite 6. The polypeptide would be even less soluble than free Tyr,
large, because all but one of the amino acids have more than one because the amino and carboxylate groups that interact with
codon. For the first primer, there are 1 3 4 3 6 5 24 possibilities; water and make Tyr soluble are lost in forming the peptide bonds
for the second, 4 3 6 3 4 5 96 possibilities. There are 24 3 96 in poly(Tyr).
5 2304 different pairs of primers that could be used to amplify 8. Histones contain an abundance of the positively charged
the gene by PCR. amino acids lysine and arginine. The positive charges of these
38. The enzyme MspI generates sticky ends. The single-stranded amino acid side chains interact electrostatically to form ion pairs
regions are then removed by the action of the exonuclease, releas- with the negatively charged phosphate groups on the backbone
ing the free nucleotides C and G. of the DNA molecule and to minimize charge–charge repulsion
of the negatively charged phosphate groups.
Exonuclease 10. Threonine has two chiral carbons; therefore, four stereoiso-
cleavage mers are possible.
COO COO
TG C T TA G C CGGAACGA
H3N C H H C NH
3
A C G A ATC G G C C T TG C T
H C OH HO C H
40. Pst I EcoRI Pst I
CH3 CH3
2 kb 7 kb 8 kb 3 kb
COO COO
42. To design an oligonucleotide probe for a gene, the researcher
must apply the genetic code in reverse, that is, select codons

H3N C H H C NH
3
that correspond to the amino acids in the protein. Most amino
acids can be encoded by more than one codon, so the researcher
HO C H H C OH
would have to choose one of them and hope that it matched CH3 CH3
the DNA well enough for the probe to successfully hybridize
with the DNA. Met and Trp, however, are encoded by only one
codon each, so by using these codons as part of the probe, the 12.
Peptide bond
researcher can be assured of a perfect match with the DNA, at
least for these three nucleotides. O O
N-Terminus H N CH C HN CH C O C-Terminus
3
Chapter 4 Solutions
CH2 CH2
-Amino group
2. If amino acids existed in the nonionic form shown in Prob- CH2 CH2 -Carboxylate group
lem 1, they would have lower melting points and would be
CH2 C O
soluble in nonpolar organic solvents. High melting points and
CH2 O -Carboxylate group
water solubility are characteristics of ionic substances. These
observations support the zwitterionic (doubly ionic) form of -Amino group NH
3
Lys-Glu
the amino acid.
4. 14.
O O O O O O O
H
3N CH C O H3 O NH
4
H
3N CH C O H
3N CH C N CH C HN CH C HN CH C N CH C O
H H
CH2 H H CH2 CH2
CH2 CH2 H
CH2
C O C O
Met-enkephalin S
NH2 O CH3
Asparagine Aspartate OH
O O O O O O O
H H O
3N CH C O H
3N CH C O 3N CH C N CH C HN CH C HN CH C N CH C
H H
CH2 H H CH2 CH2
(CH2)2 NH (CH2)2 H
H3O 4
HC CH3
C O C O
Leu-enkephalin CH3
NH2 O
Glutamine Glutamate OH
16. A polypeptide is a single polymer of amino acids. A protein functioning of the protein. A “permanent” positive charge
may consist of one or more polypeptide chains. might also be necessary. Arginine has a pK of 12.5 and thus
18. The amino group of Pro is linked to its side chain (see Fig. is always protonated at physiological pH. Even though the pK
4-2), which limits the conformational flexibility of a peptide value of an amino acid in a protein is not necessarily the same
bond involving the amino group. The geometry of this peptide as the pK value of the free amino acid, the great difference in
bond is incompatible with the bond angles required for a poly- the pK values indicates that the arginine is far more likely to be
peptide to form an a helix. protonated than the histidine. If a full strong charge at this site
is necessary for protein function, its replacement could result
20.
in a defective protein.
G F 28. (a) Heating causes a protein to “melt,” or unfold, because
L
heating increases the vibrational and rotational energy of
S L atoms in the protein, which disrupts the weak interactions
A L that keep the protein in its properly folded state.
(b) pH changes alter the ionization states of amino acid side
chains. This affects the ability of side chains to form ion
K A
pairs. Hydrogen bonds may also be broken as protonation
or deprotonation renders amino acid side chains unable to
S W serve as hydrogen bond donors or acceptors.
(c) Detergents have a nonpolar domain that allows them
K I to penetrate into the interior of the protein, thus interfer-
ing with the hydrophobic interactions responsible for the
P A
protein’s tertiary structure.
G F (d) Reducing agents, such as 2-mercaptoethanol, break
L disulfide bonds (converting them to the —SH form) and
destabilize proteins that require disulfide bonds in order to
The polar amino acid residues are shown in red; the nonpo- assume the correct conformation.
lar residues are shown in blue. This is another example of an 30. The loss of the C chain means the loss of information that
amphipathic helix (see Problem 19). The hydrophobic side of is essential to the proper folding of insulin. Removal of the C
the helix will interact favorably with the nonpolar membrane chain leaves two separate chains (A and B), and it is much more
and disrupt its structure, resulting in cell lysis. (The investiga- difficult for two chains to resume their native conformation than
tors of the study found that the peptide was able to form a pore for one chain to do so. Proinsulin has no difficulty resuming its
in the membrane, disrupting the ionic balance and killing the native conformation in a denaturation/renaturation experiment
cell.) [From Corzo, G., Escoubas, P., Villegas, E., Barnham, K. J., because proinsulin consists of only one peptide chain. When
Weilan, H. E., Norton, R. S., and Nakajima, T., Biochem. J. 359, proinsulin is converted to insulin, two peptide bonds are cleaved
35–45 (2001).] to produce the correctly cross-linked A and B chains.
22. (a) His (b) Ser (c) Tyr (d) Cys (e) Asn 32. Proteins with a higher OSH molar content have a greater
24. (a) Phe. Ala and Phe are both hydrophobic, but Phe is much opportunity to form disulfide bonds, which play a role in stabi-
larger and might not fit as well in Val’s place. lizing the protein. Proteins strengthened with disulfide bonds
(b) Asp. Replacing a positively charged Lys residue with an would require higher temperatures to denature and would
oppositely charged Asp residue would be more disruptive. therefore have higher Tm values. [From Lacy, E. R., Baker, M.,
(c) Glu. The amide-containing Asn would be a better sub- and Brigham-Burke, M., Anal. Biochem. 382, 66–68 (2008).]
stitute for Gln than the acidic Glu.
34. Protein loops are often at the protein surface, whereas regu-
(d) His. The geometry of a Pro residue constrains the con-
lar secondary structure predominates in the protein core. The
formation of the polypeptide. Gly, which lacks a side chain,
loops are better able to accommodate changes in size and amino
can adopt the same backbone conformation, but a residue
acid composition than the core segments, where a change in size
with a bulkier side chain cannot.
or composition may disrupt an a helix or b sheet that is an es-
26. Substitution of a histidine for an arginine evidently causes sential part of the protein’s structure.
a change in the three-dimensional structure of the protein,
which adversely affects its function. This could occur for 36. Proteins and their component amino acids (and many other
a variety of reasons. Histidine’s side chain is composed of a organic compounds) have inherent “handedness” and therefore
five-membered ring, whereas arginine’s side chain is a straight- cannot be interconverted through mirroring. Consider a right-
chain structure. The change in shape of the side chain could handed a helix; its mirror image would be a left-handed a helix,
lead to an overall change in the shape of the protein. Because which is not found in nature.
of the difference in their structures (although both amino acids 38. Because the tetramers dissociate into dimers in the pres-
can form hydrogen bonds and ion pairs), the substituted histi- ence of the amphipathic SDS, it is possible that hydropho-
dine might not form an interaction that is crucial to the proper bic interactions are important in stabilizing the dimer. The
hydrophobic surface of the dimer could interact with the non- Chymotrypsin fragments
polar tail of SDS when the tetramer dissociates into dimers. HSEGTF
But the monomers might be stabilized by a different type of SNDY
interaction, either polar or ionic. The nonpolar tail of SDS SKY
would not interact favorably with a polar surface, and the LEDRKAQDF
negatively charged head group of SDS would be repelled by VRW
negatively charged amino acid side chains involved in ionic in- LMNNKRSGAAE
teractions. The association of the monomers with one another
is more favorable than their association with SDS would be, so Trypsin fragments
the dimers resist dissociation into monomers in the presence of HSEGTFSNDYSK
detergent. [From Gentile, F., Amodeo, P., Febbraio, F., Picaro, YLEDRK
F., Motta, A., Formisano, S., and Nucci, R., J. Biol. Chem., AQDFVRWLMNNK
277, 44050–44060 (2002).] RSGAAE
40. (a) HSEGTFSNDYSKYLEDRKAQDFVRWLMNNKRSGAAE
O O O
H H H
N CH C N CH C N CH C 44. Thermolysin would yield the most fragments (nine) and
CH2 CH2 CH2 chymotrypsin would yield the fewest (three).
DTT ICH2COOH
S SH S CH2COO⫺ 46. (a) Since each codon corresponds to an amino acid, the
S SH S CH2COO⫺ error rate is
CH2 CH2 CH2 5 3 1024 error
HN CH C HN CH C HN CH C 3 500 residues 5 0.25
residue
O O O
About one-quarter of the polypeptides would contain a
(b) A simplified version of the anion exchange chromato- substitution.
gram is shown. (b) Virtually all the 2000-residue polypeptides would con-
tain a substitution:
5 3 1024 error
Absorbance @ 280 nm
3 2000 residues 5 1.0

residue
Ara h8 Ara h6
48. Because the Edman degradation reaction requires a free
high salt amino group (see Fig. 4-22), mass spectrometry should be used
to determine the polypeptide’s sequence.
50.
H
O N H
Solvent volume H H
C
H H H
H C H C C
(c) Treatment of the proteins with a reducing agent fol-
H C H C HH O
lowed by iodoacetic acid converts five disulfide bridges
H C H
(which are neutral) in Ara h6 to ten negatively charged side C N C
chains. The treatment produces a modified Ara h6 protein N C C N C
with a more acidic pI. The two proteins were successfully H H
H O C H O
separated because the Ara h8 protein is less attracted to the H H
positively charged anion exchange beads and elutes sooner. S
The Ara h6 binds more strongly to the anion exchange H
beads and elutes only after salt has been added to the elu-
tion buffer. [From Riecken, S., Lindner, B., Petersen, A.,
Jappe, U., and Becker, W.-M., Biol. Chem., 389, 415–423 Chapter 5 Solutions
(2008).] 2. 1 pO2 2 n
42. The cleavage site for each fragment is highlighted. A frag- Y5
1 p50 2 n 1 1 pO2 2 n
ment not ending in Phe, Tyr, or Trp (for chymotrypsin cleavage)
or Lys or Arg (for trypsin cleavage) must be the carboxyl terminal 125 torr2 3
Y5
fragment. Use “overlap” to work backward from the C-terminus 115 torr2 3 1 125 torr2 3
to determine the sequence of the polypeptide. Y 5 0.82
1 pO2 2 n increases as well. An increased p 50 indicates a lower affinity of he-

Y5 moglobin for oxygen. Therefore, when the concentration of CO2
1 p50 2 1 1 pO2 2
n n
increases, as it does in metabolically active tissues, hemoglobin’s af-
1120 torr2 3 finity for oxygen decreases and hemoglobin unloads its oxygen to
Y5
115 torr2 3 1 1120 torr2 3 the cells that need it.
Y 5 1.00 16. (a) HCO 32 is formed when carbon dioxide reacts with water
to form carbonic acid, a reaction in the blood catalyzed by
4. As shown in Solution 2, hemoglobin is completely saturated
carbonic anhydrase. The carbonic acid dissociates to form
with oxygen (Y 5 1.00) when the p O2 5 120 torr. When the
protons and HCO 32 .
p O2 decreases to 25 torr, Y 5 0.82. This means that 18% of
(b) Both curves are sigmoidal. According to the investi-
oxygen bound to hemoglobin is delivered to the tissues when
gators, the p50 for crocodile hemoglobin is 6.8 torr in the
p CO2 5 5 torr. But when the p CO2 increases to 40 torr, the
absence of bicarbonate and 44 torr in the presence of bicar-
amount of oxygen delivered to tissues increases dramatically, as
bonate. The higher p 50 value in the presence of bicarbonate
shown in Solution 3. Under these conditions, hemoglobin is
means that the hemoglobin has a lower affinity for oxygen.
nearly saturated with oxygen when p O2 5 120 torr (Y 5 0.96).
But when p O2 is 25 torr in the tissues, Y decreases to 0.20. So
76% of the oxygen is delivered to tissues. In general, higher CO2

concentrations assist hemoglobin in delivering oxygen from the w/o HCO3
lungs to the tissues. [From Bohr, C., Hasselbalch, K., and Krogh,
Y
A., Skand. Arch. Physiol. 16, 401–412 (1904).]
w/ HCO3
6. Globin lacks an oxygen-binding group and therefore cannot
bind O2. Heme alone is oxidized and therefore cannot bind O2.
The bound heme gives a protein such as myoglobin the ability
to bind O2. In turn, the protein helps prevent oxidation of the p O2
heme Fe atom.
8. His F8 is the most likely to be invariant. The nitrogen in the (c) The lysine side chain is positively charged and can in-
imidazole ring of His F8 serves as one of the ligands to the iron teract with the negative charge of the bicarbonate. The phe-
in the heme group. This residue plays a critical role in the struc- nolate oxygens on the two tyrosine side chains can act as
tures of myoglobin and hemoglobin and is essential for the proper hydrogen bond acceptors for the bicarbonate hydrogen.
binding of oxygen; substitution of this amino acid would likely (d) All of the allosteric effectors are negatively charged.
interfere with the ability of the protein to bind and release oxygen They bind to hemoglobin by forming ion pairs with posi-
effectively. tively charged amino acid side chains (such as Lys or Arg)
or with the positively charged a-amino groups at the amino
10. (a) Vitamin O is useless because the body’s capacity to termini of the four polypeptide chains. [From Komiyama,
absorb oxygen is not limited by the amount of oxygen N.H., Miyazaki, G., Tame, J, and Nagai, K., Nature 373,
available but by the ability of hemoglobin to bind and 244–246 (1995).]
transport O2. Furthermore, oxygen is normally introduced
into the body via the lungs, so it is unlikely that the gas- 18. Hydroxyurea increases the patient’s blood concentration of
trointestinal tract would have an efficient mechanism for hemoglobin F, which has two a chains and two g chains rather
extracting oxygen. than two a chains and two b chains. Since the b chain has been
(b) The fact that oxygen delivery in vertebrates requires a mutated in the patient suffering from sickle cell anemia, the
dedicated O2-binding protein (hemoglobin) indicates that increased synthesis of hemoglobin F allows the patient to use
dissolved oxygen by itself cannot attain the high concentra- hemoglobin F to transport oxygen instead of the defective he-
tions required. (In fact, the solubility of oxygen in pure wa- moglobin S. In effect, the defective b chains are replaced with
ter is only about 0.1 mM; the hemoglobin in blood boosts healthy g chains.
the solubility to about 10 mM.) In addition, a few drops of 20. Hb Bruxelles is the most unstable, since Phe is deleted. Hb
vitamin O would make an insignificant contribution to the Hammersmith is next, since the nonpolar Phe has been mutated
amount of oxygen already present in a much larger volume to a polar Ser. Hb Sendagi and Hb Bucuresti have nonpolar
of blood. amino acid substitutions, but Hb Bucuresti is more stable than
12. A decrease in pH diminishes hemoglobin’s affinity for oxy- Hb Sendagi because Leu is larger than Val and thus closer in size
gen (the Bohr effect), thereby favoring deoxyhemoglobin. Since to the large nonpolar Phe. [From Griffon, N., Baden, C., Lena-
only deoxyhemoglobin S polymerizes, sickling of cells is most Russo, D., Kister, J., Barkakdjian, J., Wajcman, H., Marden, M.C.,
likely to occur when the parasite-induced drop in pH promotes and Poyart, C., J. Biol. Chem. 271, 25916–25920 (1996).]
the formation of deoxyhemoglobin. 22. (a) Keratin and collagen; (b) myosin and kinesin; (c) actin
14. The p50 for hemoglobin when p CO2 5 5 torr is given as and tubulin; (d) actin, myosin, tubulin, and kinesin.
15 torr, whereas the p 50 when p CO2 5 80 torr is given as 40 torr. 24. (a) Adding another protein was necessary because G-actin
When the partial pressure of CO2 increases, the p 50 for hemoglobin in solution tends to polymerize rather than form crystals.
The added protein bound to actin and prevented its po- 42. (a) (Pro–Pro–Gly)10 has a melting temperature of 418C,
lymerization. while (Pro–Hyp–Gly)10 has a melting temperature of 608C.
(b) The crystal structure of the protein alone was needed (Pro–Hyp–Gly)10 and (Pro–Pro–Gly)10 both have an im-
so that it could be “subtracted” from the crystal structure of ino acid content of 67%, but (Pro–Hyp–Gly)10 contains
the actin–protein complex. hydroxyproline, whereas (Pro–Pro–Gly)10 does not. Hydroxy-
26. Because each protofilament contains many tubulin dimers, proline therefore has a stabilizing effect relative to proline.
the separation of protofilaments during fraying represents a (b) (Pro–Pro–Gly)10 and (Gly–Pro–Thr(Gal))10 have the
greater loss of tubulin subunits than if the tubulin subunits left same melting point, indicating that they have equal sta-
the microtubule one dimer at a time. bilities. This is interesting because (Pro–Pro–Gly)10 has an
imino acid content of 67%, whereas (Gly–Pro–Thr(Gal))10
28. Although the drugs have opposite effects on microtubule
has an imino acid content of only 33%. The glycosylated
dynamics, they both interfere with the normal formation of the
threonine must have an effect similar to that of proline. It is
mitotic spindle, which is required for cell division.
possible that the galactose, which contains many hydroxyl
30. Paclitaxel increases the stability of the microtubule if it is groups, provides additional sites for hydrogen bonding and
able to override the effects of GTP hydrolysis, since it is GTP would thus contribute to the stability of the triple helix.
hydrolysis to GDP that results in a curved protofilament that (c) The inclusion of (Gly–Pro–Thr)10 is important because
causes the microtubule to have a “frayed” appearance and in- the results show that this molecule doesn’t form a triple he-
creases the likelihood that the tubulin dimers in the protofila- lix. This molecule is included as a control to show that the
ment will dissociate. [From Amos, L.A., and Löwe, J., Chem. increased stability of the (Gly–Pro–Thr(Gal))10 is due to the
Biol. 6, R65–R69 (1999).] galactose, not to the threonine residue itself. [From Bann,
32. Microtubules in the cell spindle are dynamic structures since J. G., Peyton, D. H., and Bächinger, H. P., FEBS Lett. 473,
the mitotic spindle must form during mitosis and degrade after cell 237–240 (2000).]
division has occurred. Therefore, these microtubule structures are 44. Because collagen has such an unusual amino acid composi-
less stable than those that make up the structures of the axons of tion (almost two-thirds consists of Gly and Pro or Pro deriva-
nerve cells. Axonal microtubules are more stable because of their tives), it contains relatively fewer of the other amino acids and
structural role. is therefore not as good a source of amino acids as proteins con-
34. A fibrous protein such as keratin does not have a discrete taining a greater variety of amino acids.
globular core. Most of the residues in its coiled-coil structure 46. The individual collagen chains are synthesized on the ribo-
are exposed to the solvent. The exception is the strip of non- some from the constituent amino acids. Proline is one of the
polar side chains at the interface of the two coils. 20 amino acids for which a codon exists on the DNA. Some of
36. The reducing agent breaks the disulfide bonds (—S—S—) the prolines are modified posttranslationally (after the protein is
between keratin molecules. Setting the hair brings the reduced synthesized) to hydroxyproline. Individual hydroxyproline amino
Cys residues (with their —SH groups) closer to new partners on acids are not incorporated into the protein during synthesis
other keratin chains. When the hair is then exposed to an oxidiz- (there is no codon for hydroxyproline). So [14C]-hydroxyproline
ing agent, new disulfide bonds form between the Cys residues and is not used in the synthesis of collagen and no radioactivity ap-
the hair retains the shape of the rollers. pears in the collagen product.
38. The enzyme degrades collagen (which has a repetitive 48. (a) The open reading frame is shown below. Collagen has the
Gly–X–Y sequence, with X often being Pro). Since collagen is structure (Gly–X–Y)n , where X is often proline and Y is often
the major protein present in connective tissue, degradation of hydroxyproline. The codon for Gly is GGX, and the codon
this tissue would facilitate the invasion of the bacterium into the for Pro is CCX (where X represents any nucleotide). In the
host. The bacterium itself is not affected because bacteria do not mutant polypeptide, a Gly residue has been replaced by Asp.
contain collagen.
Normal a2(I) collagen gene
40. (a) Collagen B is from rat, and collagen A is from the sea
urchin. . . . CT|GGT|GCT|GTT|GGC|CCA|AGA|GGT|CCT|AGT|GGC|CCA|C. . .
(b) The stability of each of these collagens is correlated . . . Gly Ala Val Gly Pro Arg Gly Pro Ser Gly Pro . . .
with their imino acid content. The higher the percent-
age of hydroxyproline, the more regular the structure and Mutant a2(I) collagen gene
the more difficult it is to melt, resulting in more stable
collagen. The rat has a more stable collagen, and the sea . . . CT|GGT|GCT|GTT|GGC|CCA|AGA|GAT|CCT|AGT|GGC|CCA|C . . .
urchin, which lives in cold water, has a less stable colla- . . . Gly Ala Val Gly Pro Arg Asp Pro Ser Gly Pro . . .
gen. It is important to note that the melting temperatures
of each collagen molecule are higher than the tempera- (b) The Tm value for the mutant collagen would be lower than
ture at which each organism lives. Thus, each organism the Tm for normal collagen. The substitution of an Asp for a
has stable collagen at the temperature of its environment. Gly would disrupt the triple helix in this region of the molecule.
[From Mayne, J., and Robinson, J. J., J. Cell. Biochem. 84, In order for the three chains to pack together to form the triple
567–574 (2001).] helix, every third residue must be a Gly. There are three amino
acids per turn; therefore, the side chain of the Gly ends up on [From Walker, M.L., Burgess, S.A., Sellers, J.R., Wang, F.,
the interior of the triple helix. There is not sufficient room to Hammer, J.A., III, Trinick, J., and Knight, P. J., Nature 405,
accommodate a larger side chain of an amino acid such as Asp. 804–807 (2000).]
The actual Tm values for normal collagen and the mutant col- 54. Myosin’s two heads act independently, so only one binds
lagen presented here are 418C and 398C, respectively. to the actin filament at a time. Consequently, when myosin
(c) The patient suffered from osteogenesis imperfecta, a dis- advances from one actin subunit to another, the protein disso-
ease characterized by amino acid changes in type I collagen, ciates completely from its track, much like a one-legged hop.
which is found mainly in bones and tendons. The patient’s In contrast, kinesin’s two heads work together, so one head
bones and tendons could not form properly due to the defects remains bound to the microtubule track when the other is
in the structure of collagen, and the patient died as a result. released. This mechanism is similar to a two-legged walk.
[From Baldwin, C.T., Constantinou, C.D., Dumars, K.W.,
and Prockop, D.J., J. Biol. Chem. 264, 3002–3006 (1989).]
Chapter 6 Solutions
50. For many proteins, bacterial expression systems offer a con-
venient source of protein for structural studies. However, even if 2. Myosin and kinesin are enzymes because they catalyze the
collagen genes were successfully introduced into bacterial cells, hydrolysis of ATP. For myosin, the reaction is
the cells would not be able to produce mature collagen molecules ATP 1 H2O S ADP 1 Pi
because collagen is processed after it is synthesized. Bacteria are
For kinesin, the reaction is
unable to undertake some of the processing steps, such as cleav-
age by extracellular proteases and covalent modification of Pro 2 ATP 1 2 H2O S 2 ADP 1 2 Pi
and Lys residues. Two cycles of ATP hydrolysis are required to restore the two-
headed kinesin motor to its original position.
52. Cargo
4. As shown in Table 6-1, the only relationship between the rate
of catalyzed and uncatalyzed reactions is that the catalyzed reac-
tion is faster than the uncatalyzed reaction. The absolute rate
ADP of an uncatalyzed reaction does not correlate with the degree to
actin which it is accelerated by an enzyme.
6. (a) isomerase
ATP
ATP binding to the trailing head induces
a conformational change that causes it (b) lyase
to release actin. (c) oxidoreductase
(d) hydrolase
8. Malate dehydrogenase is an oxidoreductase.
ATP CH2 COO CH2 COO

ADP malate dehydrogenase
CH OH C O
Hydrolysis of ATP to ADP + Pi triggers
a conformational change that swings the COO COO
trailing head forward. This also increases Malate Oxaloacetate
the affinity of the head for actin.
10. (a) glucose-6-phosphate dehydrogenase
(b) isocitrate lyase
ADP Pi (c) phosphoglycerate kinase
ADP (d) pyruvate carboxylase
12. The common name is argininosuccinate lyase.
The new leading head binds to the actin
filament. This causes the release of the 14. At first, the temperature increases the reaction rate because
ADP ADP from the new trailing head. heat increases the proportion of reacting groups that can achieve
the transition state in a given time. However, when the tem-
perature rises above a certain point, the heat causes the enzyme,
which is a protein, to denature. Because most proteins are only
marginally stable (see Section 4-3), denaturation occurs readily,
accounting for the steep drop in enzymatic activity.
ADP Pi
16. Yes. An enzyme decreases the activation energy barrier for
Pi dissociates from the leading head, both the forward and the reverse directions of a reaction.
Pi
preparing the myosin for another 18. (a) Gly, Ala, and Val have side chains that lack the func-
reaction cycle. tional groups required for acid–base or covalent catalysis.
(b) Mutating one of these residues may alter the conforma- (b) Since benzoate resembles the substrate, it is likely that
tion at the active site enough to disrupt the arrangement of benzoate binds to the active site of the enzyme. Under
other groups that are involved in catalysis. these conditions, FDNP does not have access to the active
site and will be unable to react with the tyrosine (which
20. (a) In order for any molecule to act as an enzyme, it must is also assumed to be part of the enzyme’s active site be-
be able to recognize and bind a substrate specifically, it must cause of its unusual reactivity). [From Nishino, T., Massey,
have the appropriate functional groups to effect a chemical V., and Williams, C.H., J. Biol. Chem., 255, 3610–3616
reaction, and it must be able to position those groups for (1979).]
reaction.
(b) DNA, as a double-stranded molecule, has limited con- 30. (a)
formational freedom. RNA, which is single-stranded, is able
to assume a greater range of conformations. This flexibility His 124
allows it to bind to substrates and carry out chemical trans- Asp 70
O
formations. O
HN CH C
22. Chymotrypsin can degrade neighboring molecules by cata- HN CH C RNA Substrate
lyzing the hydrolysis of peptide bonds on the carboxyl side of CH2
CH2 O
Phe, Tyr, and Trp. If the chymotrypsin is stored in a solution of
HN
weak acid, His 57 would be protonated and would be unable to C O O P O
accept a proton from Ser 195 to begin hydrolysis. N
O O O O
H H H H
24. The Cys 278 is highly exposed and unusually reactive as H
compared to other cysteines in creatine kinase. The Cys 278,
because of its high reactivity, is probably one of the catalytic
residues in the enzyme. The other cysteine residues are not (b) His 124 most likely has a pK of less than 5.0 because
as reactive because they are not directly involved in catalysis the His shown in the relay is unprotonated. It must be un-
and/or because they are shielded in some way which prevents protonated in order to accept a proton from the water mol-
them from reacting with NEM. ecule. If His 124 had a higher pK value, it would be more
likely to be partially protonated at physiological pH and less
26. His residues are often involved in proton transfer. A able to accept a proton.
carboxymethylated His would be unable to donate or accept (c) Alanine has an aliphatic side chain and is unable to ac-
protons. cept a proton in the relay, as shown in part (a). [From Oda,
Y., Yoshida, M., and Kanaya, S., J. Biol. Chem. 268, 88–92
O O
(1993).]
HN CH C HN CH C
HBr 32. (a) His 12 has a pK value of 5.4 and His 119 has a pK value
CH2 CH2 of 6.4. His 12 is unprotonated and has the lower pK, while
BrCH2COO
His 119 is protonated and has the higher pK.
HN N
(b) The pH optimum is 6 because at this pH His 12 is
N N unprotonated (the pH is greater than the pK ) and His
CH2COO 119 is protonated (the pH is less than the pK ). At a pH
less than 6, His 12 would be protonated and would not
[From Shapiro, R., Weremowicz, S., Riordan, J.F., and Vallee, serve as a nucleophile to abstract the 29-hydroxyl hydro-
B., Proc. Natl. Acad. Sci. 84, 8783–8787 (1987).] gen. At pH greater than 6, His 119 would be unproton-
ated and would not be able to donate a hydrogen to the
28. (a) scissile bond.
(c) Ribonuclease does not hydrolyze DNA because DNA
CH2 F CH2 contains deoxyribose and is missing the 29 hydroxyl group,
NO2 HF which serves as the attacking nucleophile for the phospho-
rous (once the His 12 has removed the hydrogen).
34.
O H R2 O
OH NO2 O

C O O C O HO C
NO2
H NHR1
Asp 25 Asp 25
NO2
O R2 O [From Shin, S., Yun, Y. S., Koo, H.M., Kim, Y.S., Choi, K.Y.,
⫺ and Oh, B.-H., J. Biol. Chem. 278, 24937–24943 (2003).]
C OH HO C O H O C
NHR1 40. The enzyme’s conformation must be flexible enough to al-
Asp 25 Asp 25⬘ low substrates access to the active site, to stabilize the changing
electronic structure of the transition state, and to accommodate
the reaction products.
O R2 O
42. (a)
C O⫺ HO C O HO C
O
Asp 25 H NHR1 Asp 25⬘ C
N⫹
36.
O NH
O
HN CH C
CH2
C O NO2 ⫹
N
HN ⫺O
NH NO2
O N⫹
HN CH C H
p-Nitrophenolate
CH2 H Im O H Im
O Zn2⫹ Im C O Zn2⫹ Im (b) The imidazole ring is already tethered to the nitro-
HN
⫺
H Im O Im phenyl group, so the reaction is unimolecular rather than
N
bimolecular. In the bimolecular reaction, the reactants must
O H 2O first encounter each other via diffusion in solution. The
C H⫹ unimolecular reaction proceeds faster because the reacting
groups are already in close proximity.
O Im (c) Enzymes speed up reaction rates in part by proximity
and orientation effects. By binding to the enzyme, the reac-
H2O Zn2⫹ Im ⫹ HCO⫺
3
tants are in close proximity to the one another. The enzyme
Im also assists in binding the reactants in the proper orientation
so that the reaction can occur with less added free energy,
38. which results in a more rapid reaction.
CH2 CH2 (CH2)4 CH2 CH2 (CH2)4 44. A water molecule is able to enter the active site after the
O⫺ HO NH⫹
3 O H O NH⫹
3 first product, the C-terminal portion of the substrate, diffuses
H away.
R2 C N R1
H
R2
C N R1 O⫺ First tetrahedral intermediate 46. (a) The pocket that holds the P19 side chain is nonpolar,
O fairly large, and able to hold side chains of varying sizes. The
H2N R1 Asp–Ala–Phe–Leu peptide is hydrolyzed fastest, followed
Amino product by Asp–Phe–Ala–Leu. Thus, the pocket can accommodate
small aliphatic side chains such as Ala as well as larger aro-
CH2 CH2 (CH2)4 CH2 CH2 (CH2)4 matic side chains such as Phe. A positively charged amino
O O⫺ NH⫹
3 O O NH⫹
3
acid does not fit well into this pocket, since Asp–Lys–Ala–
H2O Leu is hydrolyzed more slowly than most of the other arti-
R2 C H R2 C
Acyl–enzyme intermediate
ficial peptides. The P29 pocket most likely accommodates a
O O O
large hydrophobic side chain, since the Asp–Ala–Phe–Leu
H
peptide was hydrolyzed faster than the peptides with Ala at
the P29 position. A substrate with a charged residue such as
CH2 CH2 (CH2)4 CH2 CH2 (CH2)4
Lys or Asp is hydrolyzed relatively slowly.
O OH NH⫹
3 O⫺ HO NH⫹
3 (b) Aspartame is a good candidate for hydrolysis by aspar-
R2 C OH O tyl aminopeptidase, since the enzyme catalyzes hydrolysis of
⫹ H⫹ peptides on the carboxyl side of Asp residues (that is, Asp
O⫺ Second tetrahedral intermediate C
R2 O⫺ is in the P1 position). The amino acid in the P19 position
would be Phe, a large hydrophobic residue that should fit in 0.025 M

v52
the P19 pocket, as suggested by the studies of the artificial 6.9 3 10 25 s
substrates.
v 5 2360 M ? s21
(c)
O [From Wolfenden, R., and Yuan, Y., J. Am. Chem. Soc. 13,
⫹H
3N CH C O⫺ 7548–7549 (2008).]
CH2
d[S] 2d[P ]
O O aspartyl C O 6. v 5 2 5
H aminopeptidase dt dt
⫹H N
3 CH C N CH C O CH3 O⫺
H2O
1.1 3 1023 M maltose 2 mol glucose
CH2 CH2 O v5 3
⫹H
s 1 mol maltose
C O 3N CH C OCH3
O⫺ CH2 v 5 2.2 3 1023 M ? s21
Aspartame 8. rate 5 k [sucrose]
The reaction is first-order overall.
10. rate 5 k [sucrose]
(d) The enzyme likely consists of eight identical subunits rate 5 11.0 3 104 s21 2 10.050 M2
with a subunit molecular mass of 55 kD. The subunits are rate 5 5.0 3 102 M ? s21
associated with one another noncovalently, so the entire
enzyme complex has a molecular mass of 440 kD. [From 12. (a) (b)
Wilk, S., Wilk, E., and Magnusson, R.P., J. Biol. Chem. 273,
15961–15970 (1998).]
48. Chymotrypsin activation is a cascade mechanism, since [P] [S]
chymotrypsinogen is activated by trypsin, which is in turn acti-
vated by enteropeptidase.
Enteropeptidase Time Time
(c) (d)
Trypsinogen Trypsin
v0 [ES]
Chymotrypsinogen Chymotrypsin
[E] Time
50. A trypsin inhibitor inactivates any trypsin that may have been
activated prematurely. This prevents activation of other pancreatic (e)
zymogens, since trypsin is at the “top of the cascade.” Premature
activation of pancreatic zymogens results in destruction of pancre-
v0
atic tissue.
52. A protease with extremely narrow substrate specificity (that
is, a protease with a single target) would pose no threat to nearby
proteins because these proteins would not be recognized as sub- [S]
strates for hydrolysis.
14. The enzyme concentration is comparable to the lowest sub-

Chapter 7 Solutions strate concentration and therefore does not meet the require-
2. Enzyme activity is measured as an initial reaction velocity, ment that [E] ,, [S]. You could fix this problem by decreasing
which is the velocity before much substrate has been depleted the amount of enzyme used for each measurement.
and before much product has been generated. It is easier to mea-
sure the appearance of a small amount of product from a base- Vmax [S]
16. v 0 5
line of zero product than to measure the disappearance of a small K M 1 [S]
amount of substrate against a background of a high concentra-
165 mmol ? min 21 2 11.0 mM2
tion of substrate. v0 5
10.135 mM2 1 11.0 mM2
d[S]
4. v 5 2
dt v 0 5 57 mmol ? min21
18. The K M of enzyme A is about 2 mM and the K M for enzyme controlled, which means the reaction is catalyzed as rapidly
B is about 5 mM. as the two reactants can encounter each other in solution.
(a) Enzyme A would generate product more rapidly when Thus, enzymes B and C are diffusion-controlled but enzyme
[S] 5 1 mM. A is not.
(b) Enzyme B would generate product more rapidly when Enzyme KM k cat k cat /K M
[S] 5 10 mM.
21
A 0.3 mM 5000 s 1.7 3 107 M21 ? s21
Vmax 3 5 K M B 1 nM 2 s21 2 3 109 M21 ? s21
20. v 0 5
5 KM 1 KM C 2 mM 850 s21 4.2 3 108 M21 ? s21
Vmax 3 5 K M
v0 5
6 KM 30. The Vmax can be calculated by taking the reciprocal of the
v0 5 0.83 Vmax y intercept:
When [S] 5 5 K M, the velocity is 83% of the maximum velocity. 1

Vmax 5
Vmax 3 20 K M y int
v0 5 1
20 K M 1 K M Vmax 5
4.41 3 1024 mM21 ? h
Vmax 3 20 K M
v0 5 Vmax 5 2.27 3 103 mM ? h21
21 K M
v0 5 0.95 Vmax The K M can be determined by first calculating the x inter-
cept and then by taking its reciprocal:
When [S] 5 20 K M, the velocity is 95% of the maximum
b
velocity. Therefore, a fourfold increase in substrate concentra- x int 5 2
m
tion causes a smaller proportional increase in velocity (from
83% to 95%). Estimating V max from a plot of n0 versus [S] 4.41 3 1024 mM21 ? h
x int 5 2
is difficult because the substrate concentration must be quite 0.26 mM21 ? h ? mM
high in order to achieve a maximal velocity of close to 100%. x int 5 21.70 3 1023 mM21
(And it is possible that these points on the hyperbolic curve 1
cannot be experimentally measured since at high concentra- KM 5 2
x int
tion the substrate may not be soluble in the reaction medium.) 1
It is better to obtain V max by fitting experimental data to the KM 5 2
21.70 3 1023 mM21
equation of a hyperbola or, alternatively, from a Lineweaver–
Burk plot. K M 5 590 mM
32. (a) The wild-type enzyme has the lowest K M, indicating
Vmax that it has the highest affinity for aspartate. The aspar-
22. kcat 5
[E] T tate substrate is not able to bind to the mutant enzymes
4.77 3 1023 M with as high an affinity. There is an 18-fold increase in
kcat 5 K M when the Arg 386 is mutated to a lysine and an 80-
9.0 3 1026 M ? s21
fold increase in K M when Arg 292 is mutated to a lysine
kcat 5 530 s21 (which is similar to the double mutant). The Arg 292
The k cat is the turnover number, which is the number of catalytic must play a critical role in binding the aspartate substrate
cycles per unit time. Each molecule of the enzyme therefore un- to the enzyme.
dergoes 530 catalytic cycles per second. (b) Although both Arg and Lys have positive charges that
would attract the carboxylate group on the substrate,
24. The simultaneous collision of three molecules (E, A, and
there must be other interactions that are important in
B) is an unlikely event. It is much more likely that the enzyme
addition to ionic interactions. For example, the ability
binds first one and then the other substrate. For example, the
of Arg and Lys side chains to form hydrogen bonds dif-
first bimolecular reaction might be E 1 A z y EA, and the second
fers. Also, steric considerations may play a role, since
would be EA 1 B z y EAB.
the Lys side chain has a different shape than the Arg side
26. The higher K M indicates that hexokinase has a lower affin- chain.
ity for fructose than for glucose. But once the substrate binds to (c) Substitution of Arg with Lys greatly decreases the
the enzyme, the fructose is converted to product more rapidly catalytic efficiency of the mutant enzyme. Changing
than glucose. only one arginine decreases the catalytic efficiency by
28. The maximum rate at which two molecules can collide four orders of magnitude, but the catalytic efficiency de-
with one another in solution is 108 to 109 M21 ? s21. Enzymes creases by six orders of magnitude when both arginines
with kcat/K M values in this range can be considered to be diffusion- are replaced.
K M Aspartate kcat/K M 40. The compound is a transition state analog (it mimics the
Enzyme (mM) kcat (s21) (mM21 ? s21) planar transition state of the reaction) and therefore acts as a
competitive inhibitor.
Wild-type Asp 4 530 1.3 3 105
AT (Arg 292 42. (a) Zanamivir, with a lower K I (indicating tighter binding
Arg 386) of the inhibitor to the enzyme) would work better.
(b) Vmax is about the same, but K M increases, so the mutant
Mutant Asp AT 326 4.5 1.4 3 101
(Lys 292 Arg enzyme probably binds the substrate more poorly than the
386) wild-type enzyme but does not exhibit any decrease in turn-
over number (kcat, reflected in V max).
Mutant Asp 72 9.6 1.33 3 102 (c) The mutation increases the K I for oseltamivir by |265
AT(Arg 292 times but increases the K I for zanamivir by only |2 times.
Lys 386) Therefore, zanamivir would be a better inhibitor of neur-
Mutant Asp AT 300 0.055 1.8 3 1021 aminidase in the mutant virus. [From Collins, P.J., Haire,
(Lys 292 Lys L.F., Lin, Y.P., Liu, J., Russell, R.J., Walker, P.A., Skehel,
386) J.J., Martin, S.R., Hay, A.J., and Gamblin, S.J., Nature 453,
1258–1261 (2008).]
(d) Changing the amino acid from Arg to Lys may cause 44. The Vmax in the absence of inhibitor can be calculated by
a three-dimensional conformational change that would taking the reciprocal of the y intercept:
interfere with the ability of the catalytic apparatus to
function properly. If proton donation is important to the 1
mechanism, this would be affected as well, since the lysine Vmax 5
y int
side chain donates a proton more readily than the reso-
1
nance-stabilized guanidino group in the side chain of ar- Vmax 5
ginine. [From Vacca, R.A., Giannattasio, S., Graber, R., 1.51 1OD21 ? min2
Sandmeier, E., Marra, E., and Christen, P., J. Biol. Chem. Vmax 5 0.66 OD ? min21
272, 21932–21937 (1997).]
The Vmax in the presence of inhibitor can be calculated
34. By irreversibly reacting with chymotrypsin’s active site, similarly:
DIPF would decrease [E]T. The apparent Vmax would decrease
since Vmax 5 kcat[E]T (Equation 7-23). K M would not be af- 1
Vmax 5
fected since the unmodified enzyme would bind substrate y int
normally. 1
Vmax 5
4.27 1OD21 ? min2
36. (a) Indole is a competitive inhibitor of chymotrypsin be-
cause its structure resembles the side chain of tryptophan, Vmax 5 0.23 OD ? min21
which fits into the specificity pocket of chymotrypsin. Thus,
The KM value in the absence of inhibitor and can be deter-
indole and tryptophan side chains compete with each other
mined by first calculating the x intercept and then by taking its
for binding to the active site.
reciprocal:
(b) The Vmax is the same in the presence and absence of the
inhibitor since inhibition can be overcome at high substrate b
x int 5 2
concentrations. The K M increases because a higher concen- m
tration of substrate is needed to achieve half-maximal activ- 1.51 OD21 ? min
ity in the presence of an inhibitor. x int 5 2
1.52 min ? OD21 ? mM
38. Since competitive inhibitors compete with substrate for x int 5 20.99 mM21
binding to the active site of the enzyme, it is possible (espe- 1
cially if the concentration of the substrate increases in vivo) KM 5 2
x int
that this inhibition can be overcome. There might also be
cellular complications if these competitive inhibitors, which 1
KM 5 2
resemble substrates, accumulate. Noncompetitive and uncom- 20.99 mM21
petitive inhibitors do not resemble the substrate, and inhibi- K M 5 1.0 mM
tion cannot be overcome by increasing the concentration of
substrate. If these inhibitors bind to their targets very tightly, The K M value in the presence of inhibitor can be similarly
small amounts can be used to inhibit the enzyme effectively. determined:
[From Westley, A.M., and Westley, J., J. Biol. Chem. 271, b
5347–5352 (1996).] x int 5 2
m
4.27 OD21 ? min 10 mM

x int 5 2 1.68 5 1 1
1.58 min ? OD21 ? mM KI
x int 5 22.70 mM21 0.68 5 10mM/K I
1 K I 5 15 mM
KM 5 2
x int [From Paulus, C., Hellebrand, S., Tessmer, U., Wolf, H.,
1 Kräusslich, H.-G., and Wagner, R., J. Biol. Chem. 274, 21539–
KM 5 2
22.70 mM21 21543 (1999).]
K M 5 0.37 mM 48. (a) The Lineweaver–Burk plot is shown. The K M is calcu-
lated from the x intercept, the Vmax from the y intercept.
Dodecyl gallate is an uncompetitive inhibitor. In the pres-
ence of the inhibitor, the Vmax and the K M values decreased to
a similar extent. The slopes of the lines in the Lineweaver–Burk Without inhibitor With inhibitor
plot are nearly the same. [From Kubo, I., Chen, Q.-X., and y intercept, (mM/min) 21
0.704 1.90
Nihei, K.-I., Food Chemistry 81, 241–247 (2003).]
Vmax (mM/min) 1.42 0.52
46. (a) Lineweaver–Burk plots are shown below. The K M is cal- x intercept (mM)21 –0.949 –2.54
culated from the x intercept, the Vmax from the y intercept.
K M (mM) 1.05 0.39
Inhibition of HIV-1 protease by p6*
0.4 5.0
y ⫽ 3.4337x ⫹ 0.038
1/v0 (mM −1 . min)

1/v0 (min/nmol)
0.3 4.0
y ⫽ 0.751x ⫹ 1.905
0.2
3.0
0.1 y ⫽ 1.8985x ⫹ 0.0349

2.0
⫺0.02 0 0.02 0.04 0.06 0.08 0.1 y ⫽ 0.742x ⫹ 0.704

1.0
1/[S] (␮M⫺1)
Without inhibitor ⫺3.0 ⫺2.5 ⫺2.0 ⫺1.5 ⫺1.0 ⫺0.5 0.0 0.5 1.0 1.5 2.0 2.5 3.0
With inhibitor 1/[S] (mM⫺1)
No inhibitor With homoarginine
Without p6* With p6*
x intercept (mM21) 20.0185 20.011
(b) Homoarginine is an uncompetitive inhibitor. The slopes
K M (mM) 54 89
of the lines in the Lineweaver–Burk plot are nearly identi-
y intercept (min ? 0.035 0.0385 cal. A proportional decrease in Vmax and K M occurs in the
nmol21) presence of the inhibitor.
Vmax (nmol ? min21) 28.5 26.0 (c) Because homoarginine is an uncompetitive inhibitor,
it does not bind to the active site of the alkaline phos-
(b) The inhibitor is a competitive inhibitor. The Vmax is the phatase enzyme but to another site that interferes with
same in the presence and absence of the inhibitor (within the activity of the enzyme in some way. The intestinal
experimental error), but the K M has increased nearly two- alkaline phosphatase catalyzes the same reaction as the
fold, indicating that the p6* is competing with the substrate bone alkaline phosphatase, so the active sites of the two
for binding to the active site of the enzyme. enzymes are likely to be similar, but the structures of the
enzymes may be sufficiently different that the intestinal
(c) 21/aK M 1 enzyme lacks the binding site for homoarginine. [From
5 Lin, C.-W., and Fishman, W.H., J. Biol. Chem. 247,
21/K M a
3082–3097 (1972).]
120.011 mM21/20.0185 mM21 2 5 0.595
50. The formation of a disulfide bond under oxidizing condi-
a 5 1.68 tions, or its cleavage under reducing conditions, could act as an
1I2 allosteric signal by altering the conformation of the enzyme in a
a511
KI way that affects the groups at the active site.
Chapter 8 Solutions 10. Phosphatidylcholine and phosphatidylethanolamine are

neutral. Phosphatidylglycerol and phosphatidylserine are nega-
2. H3C (CH2)4 CH CH CH2 CH CH (CH2)4 CH CH (CH2)3 COO
Sciadonate (20:3 5, 11, 14
)
tively charged.
12.
[From Sayanova, O., Haslam, R., Venegas Caleron, M., and
Napier, J. A., Plant Physiology 144, 455–467 (2007).] (a) O
O P O CH2 CH COO
4. O H CH3
O NH
3
CH2 O C (CH2)7 C C (CH2)7 CH3 H2C CH CH2 O
HO C H OH O R C O H
CH2 OH C O
R
[From Chao-Mei Y., Curtis, J.M., Wright, J.L.C., Ayer, S.W., (b) OH O CH3
and Fathi-Afshar, Z.R., Can. J. Chem. 74, 730–735 (1996).] H2C CH CH2 O P O (CH2)2 N CH3 H
6. R1 R2 O O O CH3
O C C O
O C C O
R R
O O (c) O
O P O
H2C CH CH2
O
O
H2C CH CH2 HO CH2 CH CH2 OH
O P O O O OH
O C C O H
O H
R R
HO H HO OH
14. Vitamins A, D, and K are isoprenoids and are nonpolar.
OH H These dietary vitamins are soluble in the synthetic lipid Olestra®
H H and pass out of the intestinal tract along with the Olestra® with-
out being absorbed. Adding these vitamins to the product helps
H OH saturate the synthetic lipid with vitamins so that dietary vitamins
are not excreted.
8. OH OH 16. A glycerophospholipid with two saturated acyl chains has
a cylindrical shape, whereas a glycerophospholipid with two
H2C CH CH unsaturated, kinked acyl chains would be more cone-shaped:
NH
3 CH
CH
(CH2)2
CH
C CH3
Saturated acyl chains Unsaturated acyl chains
CH
18. Phospholipase A1 catalyzes the hydrolysis of one of the acyl
CH chains on a phospholipid. The resulting product, a lysophospholipid
(see Problem 12a) has a cone-shaped structure (see Fig. 8-4). Lyso-
(CH2)6 phospholipids do not assemble to form bilayers as the cylindrical-
shaped glycerophospholipids do. The conversion of a significant
CH3
portion of glycerophospholipids to lysophospholipids results in
the destruction of the red blood cell membrane.
[From Ohasi, Y., Tanaka, T., Akashi, S., Morimoto, S., Kishi- 20. B . A . C. Trans-oleate has a melting point similar to
moto, Y., and Nagai, Y., J. Lipid Res. 41, 1118–1124 (2000).] that of stearate (18:0) because the trans double bond does not
produce a kink in the molecule. Its geometry more closely re- 34. (a) A or D
sembles that of a single bond. (b) A or C
22. Peanut oil has a higher melting point because the fatty acids (c) D
that compose the monounsaturated triacylglycerols have a higher (d) D
melting point than the more highly unsaturated fatty acids of (e) B
the vegetable oil. Each double bond introduces a “kink” in the (f ) B or E
molecule, which means that the fatty acids don’t pack together as 36. Cytochrome c is a peripheral membrane protein that is
well. The number of double bonds corresponds to the number of only loosely associated with the membrane and can therefore be
“bends” in the acyl chain. Fatty acids that do not pack together removed by gentle means such as a salt solution. Cytochrome
well have fewer London dispersion forces among the chains, and oxidase is an integral membrane protein that completely spans
less heat energy is required to disrupt the forces and melt the the bilayer and has large hydrophobic portions where the protein
solid. Therefore, the vegetable oil, with a higher percentage of spans the bilayer. Thus, it is difficult to remove unless nonpolar
polyunsaturated triacylglycerols, has a lower melting point and organic solvents or amphipathic detergents are used to dissociate
does not freeze. it from the membrane.
24. When phytanic acid is incorporated into membrane phos-
Peripheral
pholipids, the resulting membrane is more fluid. The presence of
the methyl groups on the phytanic acid results in an acyl chain
that has a decreased ability to interact with neighboring acyl
chains. This decreases the number of van der Waals interactions
and decreases the melting point, which increases membrane fluid-
Integral
ity. [From van den Brink, D.M., van Miert, J.N.I., Dacremont,
G., Rontani, J.-F., and Wanders, R.J.A., J. Biol. Chem. 280,
26838–26844 (2005).]
26. Increasing the temperature would make the membrane
more fluid. To maintain constant fluidity, the bacteria syn- 38. (a) A fully hydrogen-bonded b barrel can form only if the
thesize fatty acids with more carbons and with fewer double number of strands is even. A b sheet with an odd number of
bonds. strands could not close up on itself to form a barrel.
28. In a bilayer, one end of each lipid acyl chain is fixed by its (b) The strands are antiparallel because adjacent strands can
attachment to a head group. The methylene groups closer to the be easily linked by loops on the solvent-exposed portions of
head group have the least conformational freedom, whereas the the protein.
methylene groups farthest from the head group, near the bilayer (c) A b barrel could contain some parallel b strands, but
center, have the greatest freedom. these could not be consecutive. A b barrel with consecu-
30. The cold temperatures might induce the activation of tive parallel strands could occur only if the strands were
desaturase enzymes in the plant that convert the 18:0, 18:1, and linked by additional membrane-spanning segments (such as
18:2 fatty acids to 18:3 fatty acids. Of these four fatty acids, a transmembrane a helix or a structure that passed through
18:3 is the most unsaturated and has the lowest melting point. the center of the barrel).
Membranes composed of phospholipids containing unsaturated 40. Melittin is more conformationally restricted in the mem-
fatty acids maintain their fluidity in cold temperatures. [From brane when it is associated with glycerophospholipids containing
Shi, Y., An, L., Zhang, M., Huang, C., Zhang, H., and Xu, S., more saturated fatty acids (like oleate, 18:1) and less restricted
Protoplasma 232, 173–181 (2008).] when associated with lipids containing more unsaturated fatty
32. The flippase enzyme has a strong preference for PS, acids (like arachidonate, 20:4). The presence of double bonds
which is consistent with the observation that PS is located in the acyl chains produces “bends” that prevent the acyl chains
exclusively in the cytosolic-facing leaflet of the membrane. from packing closely together. The unsaturated fatty acids thus
Translocation of PE also explains the predominance of PE provide a less conformationally restricted environment for the
in the cytosolic leaflet. PC and SM, both choline-contain- melittin peptide. In contrast, when there are fewer double bonds,
ing lipids, are not translocated and remain in the extracel- such as in oleate, the fatty acyl chains pack more closely together
lular leaflet of the membrane. The flippase has a preference and interact via van der Waals forces. This environment restricts
for amino-containing phospholipid head groups and eschews the conformation of melittin.
choline-containing phospholipids. The flippase requires ATP, 42. The sandwich model assumes that all membranes are the
probably because translocation occurs against a concentration same. However, it has been noted that different membranes have
gradient, and magnesium ions. A cysteine amino acid side a variety of functions. Multiple functions would not be possible
chain must be essential for translocation activity since chemi- with the same structure. The model also does not explain how
cal modification of this side chain abolishes translocation ac- membrane transport could occur, since it would be difficult for
tivity. [From Daleke, D.L., and Heustis, W.H., Biochemistry transported molecules to get past the protein “caps” on either
24, 5406–5416 (1985).] side of the membrane.
44. The bleached area “recovers” its fluorescence as fluorophore- (b)

labeled molecules diffuse out of the small area and unbleached [H 1 ] in
DG 5 RT ln 1 ZFDc
fluorophore-labeled molecules diffuse in. These experiments are [H 1 ] out
useful for measuring diffusion rates of the target molecules.
1026.88
DG 5 18.3145 J ? K21 ?mol21 2 137 1 273 K2 ln
1027.78
Chapter 9 Solutions
1 112 196485 J ? V ? mol 2 120.052 V2
21 21
2.
[Na 1 ]in DG 5 15344 J ? mol21 1 25017 J ? mol21
Dc 5 0.058 log
[Na 1 ]out DG 5 327 J ? mol21
[Na 1 ]in [From Porcelli, A.M., Ghelli, A., Zanna, C., Pinton, P.,
10.050 5 0.058 log
[Na 1 ]out Rizzuto, R., and Rugolo, M., Biochem. Biophys. Res. Commun.
1
[Na ]in 326, 799–804 (2005).]
0.86 5 log 8. The less polar a substance, the faster it can diffuse through
[Na 1 ]out
the lipid bilayer. From slowest to fastest: C, A, B.
[Na 1 ]in
100.86 5 10. The D-E-K-A sequence already contains two negatively
[Na 1 ]out
charged side chains, so the lysine (K, which is positively charged)
7.3 [Na 1 ]in and the alanine (A, which is neutral) can be mutated to nega-
5
1 [Na 1 ]out tively charged amino acid side chains, either Asp (D) or Glu (E).
[From Miedema, H., Meter-Arkema, A., Wierenga, J., Tang,
When a nerve cell is depolarized, sodium ions enter the cell;
J., Eisenberg, B., Nonner, W., Hektor, H., Gillespie, D., and
therefore the [Na1]in /[Na1]out ratio is more than 100-fold greater
Meijberg, W., Biophysical Journal 87, 3137–3147 (2004).]
in the depolarized cell than in the resting cell.
12. At neutral pH, the Asp and Glu side chains are unproton-
4. Use Equation 9-4 and let Z 5 2 and T 5 310 K : ated and can participate in ion pairing that holds the protein in
(a) its closed conformation. In the presence of acid (low pH, high
[Ca21 ]in [H1]), the Asp and Glu side chains become protonated. This
DG 5 RT ln 1 ZFDc disrupts ion pairing, and the conformation of the protein shifts
[Ca21 ]out to an open state.
1027 14. (a) Rhcg appears to encode an ammonia channel, since its
DG 5 18.3145 J ? K21 ? mol21 2 1310 K2ln
1023 absence decreases the amount of NH3 that crosses the cell
1 122 196,485 J ? V ? mol 2 120.05 V2
21 21
membrane.
DG 5 223,700 J ? mol2129600 J ? mol21 (b) Because the large-scale transport of water (a small po-
lar molecule) requires aquaporin, it is not surprising that
DG 5 233,300 J ? mol21
the transport of ammonia (also a small nonpolar molecule)
The negative value of DG indicates a thermodynamically requires a transport protein, especially in the kidneys, which
favorable process. are responsible for ammonia excretion. [From Biver, S.,
(b) Belge, H., Bourgeois, S., Van Vooren, P., Nowik, M., Scohy,
[Ca21 ]in S., Houillier, P., Szpirer, J., Szpirer, C., Wagner, C.A., Devuyst,
DG 5 RT ln 1 ZFDc O., and Marini, A.M., Nature 456, 339–343 (2008).]
[Ca21 ]out
16. (a) Because this sequence is so similar to the KcsA and NaK
10 27
DG 5 18.3145 J ? K 21 ? mol 21 2 1310 K2 ln sequences, it probably comes from a channel that is specific
10 23 for K1 or for Na1 and K1.
1 122 196,485 J ? V ? mol 2 110.05 V2
21 21
(b) This sequence is most similar to the Ca21 II channel
DG 5 223,700 J ? mol21 1 9600 J ? mol21 sequence and so probably comes from a Ca21 channel.
DG 5 214,100 J ? mol21 18. Intracellular exposure of the glucose transporter to trypsin
indicates that there is at least one cytosolic domain of the trans-
The negative value of DG indicates a thermodynamically unfa- port protein that is essential for glucose transport. Hydrolysis of
vorable process, but not as unfavorable as in part (a). one or more peptide bonds in this domain(s) abolishes glucose
6. (a) transport. But extracellular exposure of the ghost transporter to
[H 1 ]in trypsin has no effect, so there is no trypsin-sensitive extracel-
Dc 5 0.058 log lular domain that is essential for transport. This experiment also
[H 1 ]out
shows that the glucose transporter is asymmetrically arranged in
11027.78 2 the erythrocyte membrane.
Dc 5 0.058 log
11026.88 2 20. As the glutamate (charge 21) enters the cell, 4 positive charges
Dc 5 20.052 V 5 252 mV also enter (3 Na1, 1 H1) for a total of 3 positive charges. Since
1 K1 exits the cell at the same time, a total of 2 positive charges 28. (a) V max is calculated from the y intercept.
are added to the cell for each glutamate transported inside. 1
Vmax 5
22. Treatment with ouabain “freezes” the Na,K-ATPase in the y int
phosphorylated conformation, and the reaction cycle cannot be 1
completed. As a result, the pump is nonfunctional and the con- Vmax 5
0.64 g ? min ? mmol21
centration of sodium ions inside the cell increases. Water enters
the cell along with the sodium ions, and the cells will eventually Vmax 5 1.6 mmol ? g21 ? min21
lyse due to the increased osmotic pressure. 1
I
Vmax 5
24. (a) 0.65 g ? min ? mmol21
OH I
Vmax 5 1.5 mmol ? g21 ? min21
H H CA II
O C O ⫹ C OH
O
K M is calculated from the x intercept (without inhibitor):
Carbon dioxide Water O Carbonic acid
x int 5 2b /m
H2CO3 HCO⫺
3 ⫹ H⫹ 0.64 g ? min ? mmol21
x int 5
Bicarbonate 5.4 g ? min ? mmol21 ? mM
x int 5 20.12 mM21
(b) Bone-resorbing
compartment 1
Na+ KM 5 2
pH = 5.5 x int
H+ K+ 1
KM 5 2
Na+ 20.12 mM21
K M 5 8.3 mM
CA II
H2O + CO2 H2CO3 app
K M is calculated from the slope (with inhibitor)
H2CO3 H+ + HCO3−
x int 5 2b /m
CI− 0.65 g ? min ? mmol21
x int 5
pH = 7 HCO3− 13.8 g ? min ? mmol21 ? mM
x int 5 20.047 mM21
1
Hydrogen ions are produced from carbonic acid, which is K app
M 5 2
x int
produced from water and carbon dioxide via the carbonic 1
anhydrase reaction. The hydrogen ions exit the cell via K app
M 5 2
20.047 mM21
the Na1/H1 exchanger. These hydrogen ions acidify the app
bone-resorbing compartment as sodium ions enter the K M 5 21.2 mM
cell. The sodium ions leave the cell via the Na,K-ATPase, (b) Phlorizin is a competitive inhibitor. The Vmax has re-
while potassium ions enter the cell. Bicarbonate, the mained nearly unchanged while the K M increased nearly
other product of the dissociation of carbonic acid, leaves threefold in the presence of the inhibitor. Phlorizin com-
the cell via the Cl–/HCO 3– exchanger as chloride enters petes with glucose for binding to the transporter. [From
the cell. Betz, A.L., Drewes, L.R., and Gilboe, D.D., Biochim. Bio-
1 phys. Acta 406, 505–515 (1975).]
26. KM 5 2
x int 30. The first vinblastine binds to a low-affinity binding site,
1 the second vinblastine to a high-affinity site. This indicates that
KM 5 2 5 4 mM
20.25 mM when vinblastine binds to LmrA, it does so cooperatively. A con-
1 formational change occurs that allows the second molecule of
V max 5 vinblastine to bind with greater affinity than the first.
y int
1 32. Ammonium ions exiting the cell could be exchanged for
V max 5 entering Na1 ions. The free energy for NH41 transport would be
0.030 mg ? h ? nmol21
provided directly by the movement of Na1 ions down their gra-
V max 5 33 nmol ? mg21 ? h21 dient, and indirectly by ATP, which is used by the Na,K-ATPase
[From Wakisaka, M., Yoshinari, M., Yamamoto, M., Nakamura, to establish the Na1 gradient.
S., Asano, T., Himeno, T., Ichikawa, K., Doi, Y., and Fujishima, 34. In the presynaptic cell, when an action potential reaches the
M., Biochim. Biophys. Acta 1362, 87–96 (1997).] axon terminus, voltage-gated Ca21 channels open, flooding the
cell with Ca21 ions and triggering exocytosis of the acetylcholine- (c) [ RL] [L]
5
containing synaptic vesicles. Acetylcholine diffuses across the [R]T K d 1 [L]
synaptic cleft and binds to receptors on the postsynaptic cell,
triggering a series of events that results in muscle contraction (see [RL] 5 Kd
5
Fig. 9-16). If antibodies block the Ca21 channels, acetylcholine [R]T Kd 1 5 Kd
is not released from the presynaptic cell, receptors on the post- [RL] 5 Kd
synaptic cell are not activated, and muscle contraction does not 5
[R]T 6 Kd
occur. Thus, patients with this autoimmune disorder suffer from
muscle weakness. [ RL]
5 0.83
36. If the serine in the active site of acetylcholinesterase is [R]T
covalently modified, the enzyme will not be able to function.
Acetylcholine will build up in the synaptic cleft and will not 6. If the number of receptors decreases to 150, a greater proportion
be hydrolyzed. The postsynaptic cell remains polarized and does of these receptors must have bound ligand, since occupation of
not return to its resting state, so it cannot receive the next nerve 100 receptors is required for a maximal response (see Problem 5).
impulse from the presynaptic cell. A 20-fold increase in the concentration of ligand is required in
order to achieve a maximal response.
38. Botulinum toxin destroys SNAREs, which are required for
the fusion of synaptic vesicles with the neuronal plasma mem-
[ RL] [L]
brane. This interrupts communication between facial nerves and 5
muscles. The result is paralysis of the muscles whose contraction [ RT ] [L] 1 K d
accentuates wrinkles. 100 [L]
5
40. Diacylglycerol is a lipid without a phosphate-derivative 150 [L] 1 1 .0 3 10 210 M
head group. Because it consists mostly of lipid “tails,” it could
promote the inward curvature of the bilayer, which occurs dur- 0 .671 [L] 1 1 .0 3 10 210 M2 5 [L]
ing membrane fusion (see Fig. 9-19). 0 .67[ L] 1 6 .7 3 10 211 M 5 [L]
Chapter 10 Solutions 6 .7 3 10 211 M 5 0 .33[L]
2. Prednisone is a steroid, a hydrophobic molecule that can diffuse [L] 5 2 .0 3 10 210 M
through the lipid bilayer without the need for a cell-surface receptor.
The receptor for prednisone is located either in the cytosol or in the 8. First the cells would be lysed and insoluble components
nucleus. Upon binding to its receptor, the ligand–receptor complex removed by centrifugation. The membranes and the associated
binds to DNA and induces transcription of specific genes. membrane proteins can be solubilized by adding a detergent.
An affinity column is constructed by covalently attaching a
4. (a) [RL] [ L] specific ligand to the chromatography matrix. The solubilized
5
[R]T K d 1 [L] membranes are then loaded onto the column. Cellular proteins
Kd that do not bind to the ligand will pass through the column.
[RL] 5 The receptor proteins are then eluted from the column using a
5 concentrated salt solution to disrupt the intermolecular interac-
[R]T Kd
Kd 1 tions between the receptor and the ligand.
5
[RL] 0.2 K d 10. When glucagon and epinephrine bind to their respective G
5 protein–coupled receptors, the result is the same—an enzyme
[R]T K d 1 0.2 K d
[RL] 0.2 K d is activated that results in the synthesis of the second messen-
5 ger cAMP. Since the binding of both ligands to their receptors
[R]T 1.2 K d
results in the activation of the same second messenger, the same
[RL] signal transduction pathway is activated and the same cellular
5 0.17
[R]T response is observed.
(b) [RL] [ L] 12. The strategy shown in the figure results in amplification
5
[R]T K d 1 [L] of the signal, since a single molecule of A can activate many
[RL] Kd molecules of B, which can then go on to activate even more
5 molecules of C, and finally D. Amplification of a signal is an
[R]T Kd 1 Kd
advantage to the cell because a small signal (i.e., a low concen-
[RL] Kd
5 tration of A) can result in a large response (a high concentration
[R]T 2 Kd of D). The strategy shown allows cells to respond to changing
[RL] conditions by dramatically altering the activities of intracellular
5 0.50
[R]T components.
14. Both hormones lack tyrosine’s carboxylate group and have described in Problem 25, activation of protein kinase B pro-
hydroxyl groups attached to the ring and to the b carbon. In motes cell growth, so a highly active protein kinase B could
epinephrine, the amino nitrogen bears a methyl group. account for the uncontrolled cell growth observed in cancer
16. The inhibition of the intrinsic GTPase activity results in cells.
a continuously active G protein. This increases the activity of 28. (a) Acetylcholine in the synaptic cleft is rapidly hydrolyzed
adenylate cyclase, which results in an increase in the concen- by acetylcholinesterase (see Section 9-4).
tration of intracellular cAMP. In intestinal cells, the increase (b) Various calcium pumps, using the energy of ATP hy-
cAMP concentration leads to the loss of water and electrolytes drolysis, pump calcium ions out of the cytosol. The Ca21
from the cells and results in diarrhea that can potentially be concentration in the cell drops, the ion channels close,
fatal. and Ca21 ions dissociate from calmodulin, changing its
18. GTPgS can bind to a G protein, but since it cannot be conformation and rendering it unable to bind to NO syn-
hydrolyzed, the G protein is in a persistently active state. If thase. Without bound calmodulin, the NO synthase is
GTPgS binds to a stimulatory G protein, then adenylate cyclase inactive.
is continually active, which has the effect of increasing cellu- (c) The signaling molecule NO rapidly decomposes. In
lar cAMP concentration. If GTPgS binds to an inhibitory G its absence, guanylate cyclase is not activated. Any cGMP
protein, adenylate cyclase is continually inhibited, and cellular still present is hydrolyzed to GMP by cGMP phosphodi-
cAMP concentration decreases. esterase.
(d) In the absence of cGMP, protein kinase G reassoci-
20. N ates with its regulatory subunits and is inactivated. Any
CH2 phosphorylated proteins are acted upon by phospha-
N tase enzymes, which remove the phosphate groups by
hydrolysis.
PO32
30. NO synthase is activated when calcium ions bind to
22. calmodulin (see Solution 27). Clotrimazole is a calmodulin an-
OH tagonist and prevents NO synthase from binding to calmodu-
O HC CH CH (CH2)12 CH3 lin. In the absence of active NO synthase, cyclic GMP is not
R C HN CH O CH3
produced and protein kinase G is not activated. Cellular targets
of protein kinase G are not phosphorylated in the presence of
CH2 O P O CH2 CH2 N CH3
clotrimazole.
Sphingomyelin O CH3
32. Inhibition of cGMP phosphodiesterase, the enzyme that
sphingomyelinase hydrolyzes cGMP, increases the intracellular cGMP concentra-
tion. The activity of protein kinase G is increased as a result, as is
the phosphorylation of the enzyme’s targets, which are proteins
OH
involved in smooth muscle cell relaxation. The overall result is
O HC CH CH (CH2)12 CH3 increased blood flow.
R C HN CH 34. In the presence of Ras with this particular mutation, the
CH2 OH signaling pathway would be constitutively active. Ras is active
Ceramide O CH3 when bound to GTP and is inactivated when GTP is hydrolyzed
O P O CH2 CH2 N CH3 to GDP. If hydrolysis of GTP cannot occur, Ras cannot be in-
O CH3 activated and the signaling pathway cannot be turned off. The
Phosphocholine cell is stimulated to grow and proliferate even in the absence of
growth-signaling ligand.
24. If calcineurin is bound to cyclosporine A, then calci- 36. Overexpression of IRS-1 would stimulate the activity of the
neurin will be inactive as a phosphatase and will be unable signaling pathway and would lead to enhanced activation of pro-
to catalyze the removal of the phosphate group from NFAT. tein kinases B and C. The activation of protein kinase B would
The NFAT remains in the cytosol, and the specific genes re- result in the activation of glycogen synthase, so the cultured cells
quired for T cell activation are not expressed. The T cell, an would be expected to show an increase in glycogen synthesis.
important component of the immune response, is not acti- Enhanced activation of protein kinase C would stimulate trans-
vated, which accounts for the immunosuppressive properties location of glucose transporters to the plasma membrane; thus,
of cyclosporine A. an increase in glucose import would be observed in the cultured
26. Yes, mutations in which the gene coding for PTEN is cells.
either nonfunctional or absent are commonly found in cancer 38. A ligand could bind to a G protein–coupled receptor and
cells. In the absence of PTEN, inositol trisphosphate is not subsequently activate phospholipase C. This enzyme catalyzes
dephosphorylated, and protein kinase B is highly active. As the cleavage of phosphatidylinositol bisphosphate to diacylglycerol
and inositol trisphosphate. Diacylglycerol activates protein ki- 10. H H

nase C, which then activates the MAP kinase cascade, as shown O O
in Problem 37. This is an example of cross-talk, in which signal- H H H OH
H H
ing pathways share intracellular components. H H H H
HO OH HO H
40. (a) In order to treat cancer in these tissues, membrane-
permeable drugs could be developed that would interact OH OH OH OH
with intracellular steroid receptors to prevent binding by
␣-D-Ribose ␤-D-Ribose
the steroid ligand.
(b) Because the activation of Ras is a common feature 12. (a) A five-membered ring results.
of many transformed cells (see Box 10-B), it’s possible HOCH2 O CH2OH HOCH2 O OH
that some steroids use a second signaling mechanism
H HO H HO
that involves activation of Ras, either through binding
H OH H CH2OH
to G protein–coupled receptors or to receptor tyrosine
kinases. OH H OH H
42. Protein kinase B (Akt) is anti-apoptotic (see Problem 25). ␣-D-Fructose ␤-D-Fructose
If S1P activates protein kinase B, then the cell will not undergo (b) A six-membered ring results.
programmed cell death but will grow and proliferate. This ex- H H
plains S1P’s ability to promote cell survival, as shown in the dia-
O O
gram in Problem 41. H CH2OH H OH
H H
44. Both ceramide kinase and sphingosine kinase are poten- H HO H HO
tial drug targets, since these enzymes catalyze the synthesis of HO OH HO CH2OH
C1P and S1P, respectively, and both of these products promote
OH H OH H
cell survival. Inhibiting the enzymes that catalyze production of
these pro-survival signaling molecules may inhibit the growth ␣-D-Fructose ␤-D-Fructose
of cancer cells. But caution should be exercised, since inhibi- 14. The b anomer is more stable because all of the bulky sub-
tors of COX-2, such as Vioxx, were determined to be unsuitable stituents (—OH and —CH2OH groups) are in the equatorial
drugs because of unexpected side effects. position on the chair conformation of glucose. The a anomer
46. Aspirin inhibits cyclooxygenase (see Box 10-C) by acety- has one hydroxyl group in the axial position, so the equilibrium
lating an essential Ser residue on the enzyme. In the presence position favors formation of the b anomer and the concentra-
of aspirin, thromboxanes are not synthesized. Thromboxanes tions of the anomers are not equal.
promote platelet aggregation and vasoconstriction, which could 16.
O O H
promote clot formation and high blood pressure and could lead H
C H ⫹H N CH C O⫺ H C N⫹ (CH2)4 C COO⫺
to a heart attack. 3
H OH CH2 H OH NH⫹
3
HO H ⫹ CH2 HO H
OH⫺
H OH CH2 H OH
Chapter 11 Solutions H OH H OH
CH2
2. Coenzyme A, NAD, and FAD all contain ribose residues. CH2OH NH3⫹ CH2OH
4. (a) D-Psicose and D-sorbose are epimers. 18. There are several possibilities; one is shown here.
(b) D-Sorbose and D-fructose are structural isomers. CH2OH
(c) D-Fructose and L-fructose are enantiomers.
(d) D-Ribose and D-ribulose are structural isomers. HCOH H
O
6. Fructose and galactose are isomers of glucose.
OH H
8. The b anomer is more stable because most of the bulky H OH
hydroxyl substituents are in the equatorial position.
H OH
H 20. CH2OH CH2OH

CH2OH O
HO
HO H O H O OH
H H H
HO OH O
H OH H OH H
H H HO H H
␤-Mannose H OH H OH
Cellobiose is a reducing sugar. The anomeric carbon of the structure. Consequently, iodine does not form a complex with
glucose on the right side is free to reverse the cyclization reac- the cellulose and a blue color is not produced.
tion to re-form the aldehyde functional group, which can be
reduced. 34. H
22. Trehalase digestion produces glucose, which exists in solu- O
H OH
tion as a mixture of the a and b anomers. H
OH H
CH2OH CH2OH H H
O O O
H H H OH H O H OH
H H H
OH H OH H OH H
HO OH HO H HO H
H OH H OH H OH
36.
24. The unknown sugar is isomaltose.
CH2OH
CH2OH
OH O H
O
H H H NH
H H
CH2OH H2
OH H O H O C CH
HO O OH O
H H NHCOCH3 C O
H OH OH H
H2C H H
O H OH
H H
H
OH H 38. Each disaccharide unit of chondroitin sulfate has two nega-
HO OH
tively charged groups: a carboxylate group and a sulfate group.
H OH One hundred of these disaccharide units would yield a net
charge of 2200.
40. CH2OH
26. Celery is mainly cellulose and water, neither of which
provides nutritive calories. Humans do not have b-glucosidase H O H
enzymes and cannot hydrolyze the b-glycosidic bonds linking H R NH
the glucose resides in cellulose. Since cellulose is not digested, OH H
the body does not spend any energy to further process it. Foods HO O C CH
H
like celery contribute roughage, or fiber, to the diet, but these H NH C O
foods neither provide nor cost the body much in the way of
energy. C O
28. The fungus must have contained an a-galactosidase enzyme CH3

capable of digesting the a(1S6) linkage and a sucrase-like en- R H (Ser)
zyme that could hydrolyze the (1S2) glycosidic bond formed R CH3 (Thr)
between the a anomer of glucose and the b anomer of fructose.
[From Feng, S., Saw, C.L., Lee, Y.K., and Huang, D., J. Agric.
Food Chem. 56, 10078–10084 (2008).] [From Schirm, M., Schoenhofen, I.C., Logan, S.M., Waldron,
K.C., and Thibault, P., Anal. Chem. 77, 7774–7782 (2005).]
30. There is one reducing end.
32. Potato starch consists of a mixture of amylose and amylo-
Chapter 12 Solutions
pectin. The iodine can fit into the center of the helical structure
of the amylose and produce a blue color. Apples, on the other 2. The purple nonsulfur bacteria are photoheterotrophs.
hand, contain mostly cellulose. Cellulose consists of sheets of They are similar to the photoautotrophs in that they can cap-
extended b(1S4) glycan chains and does not form a helical ture energy from sunlight but differ in that they are unable to
fix CO2. These bacteria are similar to the heterotrophs in that will be protected from degradation by the destructive power
an organic source of carbon is required. Thus the term pho- of these enzymes.
toheterotroph accurately describes the trophic strategy of this 16. (a) oxidized
organism. (b) reduced
4. Monosaccharides enter the cells lining the intestine via sec- (c) reduced
ondary active transport (see Fig. 9-15). Na1 ions and glucose (d) oxidized
enter the cell in symport, both along their concentration gra- 18. Plant-derived b-carotene is a precursor of vitamin A (see
dients. The Na1 ions are subsequently pumped out of the cell Box 8-A) and is lipid-soluble. The b-carotene contained in the
by the Na,K-ATPase transporter, which uses the free energy of salad and salsa ingredients dissolves in the fats contained in the
ATP hydrolysis to eject the Na1 ions against their concentration avocado, which enhances its absorption. [From Unlu, N.Z.,
gradient. Bohn, T., Clinton, S.K., and Schwartz, S.J., J. Nutr. 135, 431–
6. The pH optimum for pepsin is |2, which is the pH of 436 (2005)].
the stomach. The pH optimum for trypsin and chymotryp- 20. Individuals with gastrointestinal disorders might have a gas-
sin is |7–8, as the small intestine is slightly basic (see Table 2-3). trointestinal tract that is not colonized by the appropriate vita-
Each enzyme functions optimally in the conditions of its min B12–synthesizing bacteria. A deficiency in haptocorrin or
environment. intrinsic factor would be manifested as a vitamin B12 deficiency,
8. The entry of glucose and amino acids into cells lining the since these proteins are essential for absorption of the vitamin.
small intestine is accomplished by a secondary active trans- Vegetarians and vegans who consume no animal products would
port process in which sodium ions are transported into the cell also be at risk for a deficiency of vitamin B12.
along with the glucose or amino acid (see Fig. 9-15 and Prob- 22. (a) Use Equation 12-1 to solve for the equilibrium con-
lems 4 and 7). Adding an electrolyte such as sodium chloride stant, K eq:
provides the sodium ions required for this cotransport. As the
intestinal cells import glucose and amino acids, water is also [arginine ][ATP ]
K eq 5
absorbed. [ phosphoarginine ][ADP ]
10. 14.78 3 1023 2 13.87 3 1023 2
K eq 5
10.737 3 1023 2 10.750 3 1023 2
K eq 5 33.5
(b) Use Equation 12-2 to solve for DG 89:
O DG °¿ 5 2RT ln K eq
C Cholesteryl ester DG °¿ 5 218.3145 3 1023 k J ? K21 ? mol21 2
H3C (H2C)17 O
1298 K2 ln 33.5
DG °¿ 5 28.7 kJ ? mol21
O The reaction is spontaneous under standard conditions.
Cholesteryl esterase
H3C (H2C)17 C O 24. (a) See Sample Calculation 12-1. The equilibrium constant
can be derived by rearranging Equation 12-2:
Fatty acid
K eq 5 e 2DG °¿/RT
K eq 5 e27.9 k J?mol /18.3145310 k J? K ? mol 2 1298 K2
21 23 21 21
K eq 5 e23.19
Cholesterol K eq 5 0.041
HO
(b) At 378C, T 5 310 K:
12. A branched glycogen chain has many nonreducing ends [dihydroxyacetone phosphate]
but only one reducing end. Enzymes specific for the nonreduc- DG 5 DG °¿ 1 RT ln
[glyceraldehyde-3-phosphate]
ing ends can act on many ends simultaneously, building up the
glycogen molecule when glucose is plentiful and degrading gly- DG 5 7.9 kJ ? mol 21
1 18.3145 3 10 23 kJ ? K 21 ? mol 21 2
cogen when glucose is in short supply. Enzymes that acted on 15 3 10 24 2
1310 K2 ln
the reducing end would accomplish these processes much more 11 3 10 24 2
slowly. DG 5 7.9 kJ ? mol21 1 4.1 kJ ? mol 21
14. If lysosomal hydrolytic enzymes function optimally at

DG 5 12 kJ ? mol21
pH 5, they will not function well at the cytosolic pH of 7.
Amino acid side chains essential for catalytic activity will be- (c) The reaction is not spontaneous as written. The reverse
come deprotonated at the higher pH. If lysosomal enzymes reaction, in which DG 5 212 kJ ? mol21, would be spon-
leak out of the lysosome into the cytosol, cellular components taneous.
26. The hydrolysis of pyrophosphate releases considerable free Under the given conditions, the reaction would produce
energy (&33.5 kJ ? mol21). These two reactions are coupled, and only 9.5 3 1028 M glucose-6-phosphate and thus is not a
the overall DG value for the coupled reactions is negative; thus, feasible route to the production of this compound for the
UDP–glucose formation occurs spontaneously. glycolytic pathway.
28. (a) [ glucose-6-phosphate]
(c) K eq 5
ADP 1 Pi S ATP 1 H2O DG °¿ 5 130.5 kJ ? mol 21 [ glucose ] [ Pi ]
2000 kcal 1 mol 4.184 kJ
3 1 day 3 3 3 0.33 5 90.5 moles ATP 1250 3 1026 2
day 30.5 kJ 1 kcal 0.0038 5
[glucose ] 15.0 3 1023 2
505 g 1 lb [glucose ] 5 13 M
(b) 90.5 moles ATP 3 3 5 20.8 lb
mol 2200 g Driving the reaction to the right using this method is not
(c) ATP does not accumulate but instead is constantly re- feasible because it is impossible to achieve a concentration
cycled. As ATP is used, its hydrolysis products, ADP and Pi , of 13 M glucose inside the cell.
serve as reactants for ATP synthesis in the process of oxida-
(d) glucose 1 Pi z
y glucose-6-phosphate 1 H2O
tive phosphorylation.
DG °¿ 5 13.8 kJ ? mol21
30. Reactions involving the phosphorylation of glucose (to glucose-
1-phosphate and glucose-6-phosphate) and glycerol (to glycerol-3- ATP 1 H2O z y ADP 1 Pi
phosphate) would require the hydrolysis of ATP to drive the DG °¿ 5 230.5 kJ ? mol21
reaction, because transfer of a phosphoryl group from ATP glucose 1 ATP zy glucose-6-phosphate 1 ADP
occurs with a greater change in free energy than the transfer of a
DG °¿ 5 216.7 kJ ? mol21
phosphoryl group to one of these compounds.
K eq 5 e2DG °¿/RT
32. (a) Use Equation 12-2 to solve for DG 89: 21
2 / 18.314531023 kJ ? K21 ? mol212 1298 K2
DG °¿ 5 2RT ln K eq K eq 5 e21 216.7 kJ ? mol
DG °¿ 5 218.3145 3 1023 kJ ? K21 ? mol21 2 1298 K2 ln 0.41 K eq 5 e6.74
DG °¿ 5 2.2 kJ ? mol21 K eq 5 850
The reaction will proceed in the opposite direction as written. [ glucose-6-phosphate ] [ADP ]
(b) (e) K eq 5
[glucose ] [ATP ]
[fructose-6-phosphate ]
DG 5 DG °¿ 1 RT ln 1250 3 1026 2 11.25 3 1023 2
[glucose-6-phosphate ] 850 5
[glucose ] 15.0 3 1023 2
DG 5 2.2 kJ ? mol21 1 18.3145 3 1023 kJ ? K21 ? mol21 2
[ glucose ] 5 7.4 3 1028 M
15 3 1024 2
1310 K2 ln (f ) The reaction can be accomplished at a much lower glu-
12.0 3 1023 2 cose concentration when the phosphorylation of glucose is
DG 5 2.2 kJ ? mol21 2 3.57 kJ ? mol21 coupled to ATP hydrolysis (7.4 3 1028 M instead of 13 M).
DG 5 21.37 kJ ? mol21 This can be done because the second reaction couples the
phosphorylation of glucose with the exergonic hydrolysis of
Under these conditions, the reaction will proceed as written. ATP. Thus, an unfavorable reaction is converted to a favor-
34. (a) The equilibrium constant can be determined by rear- able reaction.
ranging Equation 12-2 (see Sample Calculation 12-1):
36. I.
K eq 5 e2DG °¿/RT
213.8 k J ? mol21/ 18.314531023 k J ? K21 ? mol212 1298 K2
GAP zy 1,3-BPG DG °¿ 5 6.7 kJ ? mol21
K eq 5 e 1,3-BPG 1 H2O zy 3PG 1 Pi DG °¿ 5 249.3 kJ ? mol21
K eq 5 e25.57 GAP 1 H2O z y 3PG 1 Pi DG °¿ 5 242.6 kJ ? mol21
K eq 5 0.0038
[glucose-6-phosphate] II.
(b) K eq 5 GAP zy 1,3-BPG DG °¿ 5 6.7 kJ ? mol21
[glucose ] [ Pi ] 1,3-BPG 1 ADP z
y 3PG 1 ATP DG °¿ 5 218.8 kJ ? mol21
[glucose-6-phosphate]
0.0038 5 GAP 1 ADP z
y 3PG 1 ATP DG °¿ 5 212.1 kJ ? mol21
15.0 3 1023 2 15.0 3 1023 2
The second scenario is more likely. The first coupled reaction
[glucose-6-phosphate]
0.0038 5 is more exergonic, but the second coupled reaction “captures”
12.5 3 1026 2 some of this free energy in the form of ATP, which the cell
[glucose-6-phosphate ] 5 9.5 3 1028 M can use.
38. (a) The value of C is determined from the slope of the [fructose-6-phosphate]
plot. The slope is equal to 1.9 3 1026 mM21 or 1.9 3 4. (a) DG °¿ 5 2R T ln
[ glucose-6-phosphate ]
1023 M21.
2.2 kJ ? mol 21
5 218.3145 3 1023 kJ ? K21 ? mol21 2
1.2 [fructose-6-phosphate ]
1298 K2 ln
[nick]/[phosphodiester] (10−4)
0.8 2.2 kJ ? mol21 5 22.47 kJ ? mol21 ln
20.88 5 ln
0.4 y (1.9 106) x 2.0 105
e20.88 5
0 [fructose-6-phosphate ]
0 10 20 30 40 50 0.41 5
[AMP] (mM)
[fructose-6-phosphate]
[ PPi ] (b) DG 5 DG °¿ 1 RT ln
(b) C5 [ glucose-6-phosphate ]
K eq [ATP ] 21 21
21.4 kJ ? mol 5 2.2 kJ ? mol
[PPi ] 1 18.3145 3 10 23 kJ ? K21 ? mol21 2
K eq 5
C [ATP ] [fructose-6-phosphate ]
1310 K2 ln
11.0 3 1023 2 [ glucose-6-phosphate ]
K eq 5
11.9 3 1023 2 114 3 1026 2
23.6 kJ ? mol21 5 2.58 kJ ? mol21
4
K eq 5 3.8 3 10 [fructose-6-phosphate ]
ln
(c) Use Equation 12-2 to solve for DG 89: [ glucose-6-phosphate ]
DG °¿ 5 2RT ln K eq
DG °¿ 5 218.3145 3 1023 kJ ? K21 ? mol21 2 21.4 5 ln
1298 K2 ln 3.8 3 104
DG °¿ 5 226 kJ ? mol21 e21.4 5
(d)
Nick z
y phosphodiester bond DG °¿ 5 ? [fructose-6-phosphate ]
0.25 5
z
ATP y AMP 1 PPi DG °¿ 5 248.5 kJ ? mol21 [ glucose-6-phosphate ]
ATP 1 nick z
y AMP 1 PPi DG °¿ 5 226 kJ ? mol21
The reaction will proceed in the direction of fructose-6-
1 phosphodiester bond
phosphate synthesis since DG , 0.
The DG 89 for the formation of the phosphodiester bond is 6. This would not be beneficial to the patient. In order to en-
22.5 kJ ? mol21. ter the glycolytic pathway, the glucose-6-phosphate would first
(e) The DG 89 value for the hydrolysis of a phosphodiester have to enter the cells. Glucose transporters recognize glucose,
bond in DNA is 222.5 kJ ? mol21, whereas the DG 89 value not glucose-6-phosphate; thus, glucose-6-phosphate would be
for the hydrolysis of a typical phosphomonoester bond is unable to enter the cell for oxidation through the glycolytic
213.8 kJ ? mol21. Therefore, the phosphodiester bond in pathway.
DNA is less stable than the typical phosphomonoester
8. (a) When F26BP binds to the allosteric site on PFK, one of
bond. [From Dickson, K., Burns, C. M., and Richardson,
its phosphate groups may interact with the serine in some
J., J. Biol. Chem. 275, 15828–15831 (2000).]
manner, perhaps by hydrogen bonding. But if the serine is
replaced with the negatively charged aspartate, the negative
charges on the F26BP are repulsed and the F26BP cannot
bind to the enzyme.
2. Reactions 1, 3, and 10 are irreversible; the remaining reac- (b) Apparently PFK cannot be fully active in the absence of
tions are reversible. Metabolically irreversible reactions are good the F26BP allosteric activator, which plays an important role
“control points” for a pathway. in stimulating glycolysis. In its absence, the glycolytic pathway
is less active, which accounts for the observed decrease in glu- 18. (a) In hepatocytes, the phospho-His on the phosphoglyc-
cose consumption and ethanol production. [From Heinisch, erate mutase transfers its phosphate to the C2 position of
J. J., Boles, E., and Timpel, C., J. Biol. Chem. 271, 15928– 3PG to form 2,3-BPG. The [32P]-labeled phosphate on the
15933 (1996).] C3 position is transferred back to the enzyme to form the
2PG product, so initially the enzyme would be labeled. In
10. OH the next round of catalysis, the labeled phosphate on the en-
zyme is transferred to the C2 position of the next molecule
C O of 3PG substrate, so 2PG becomes labeled. Eventually, this
H C
phosphate is transferred to ADP to form ATP, so ATP is
CH2OPO2
3 labeled.
Possible enediolate intermediate (b) In the plant, the labeled phosphate is transferred to C2
to form 2PG, so 2PG is labeled and then eventually ATP.
12. (a) The cancer cells may express the GAPDH protein at The plant enzyme is not labeled.
higher levels (i.e., transcription of the GAPDH gene and
translation of its mRNA may occur at a higher rate). 20. (a) The glucose–lactate pathway releases 196 kJ ? mol21 of
(b) The structure of GAPDH in cancer cells is probably dif- free energy, enough theoretically to drive the synthesis of
ferent from the structure of GAPDH in normal cells. The 196/30.5, or about 6, ATP.
structure of the active site in GAPDH from cancer cells (b) The complete oxidation of glucose releases 2850 kJ ?
might be altered in such a way that the binding of methyl- mol21 of free energy, enough for 2850/30.5, or about 93,
glyoxal is permitted, which then precludes the binding of ATP.
the substrate. Or the altered GAPDH might have a bind- 22. If hexokinase cannot be inhibited, all glucose that enters
ing site for methylglyoxal elsewhere on the protein, which the yeast cell will be phosphorylated at the expense of ATP to
causes a conformational change in the protein that alters produce glucose-6-phosphate. Glucose-6-phosphate is isomer-
the substrate binding site so that the substrate can no longer ized to fructose-6-phosphate, which is then phosphorylated to
bind. [From Ray, M., Basu, N., and Ray, S., Mol. Cell. fructose-1,6-bisphosphate, again at the expense of ATP. If con-
Biochem. 177, 21–26 (1997).] centrations of glucose are high, and if there is no mechanism to
14. As the NADH/NAD1 ratio increases, the activity of inhibit hexokinase, then cellular ATP will be depleted in these
GAPDH decreases and less 1,3-bisphosphoglycerate is pro- early steps. The early reactions of glycolysis proceed at a rate
duced from glyceraldehyde-3-phosphate. NAD1 is a reactant greater than the rate of the later ATP-generating steps of glycoly-
and NADH is a product of the reaction, so as NAD1 becomes sis. ATP is therefore used faster than it is regenerated, and the
less available and NADH accumulates, the ratio of [product]/ yeast mutants die as a result. [From Teusink, B., Walsh, M. C.,
[reactant] increases and the activity of the enzyme decreases. van Dam, K., and Westerhoff, H. V., Trends Biochem. Sci. 23,
16. Hexokinase-deficient erythrocytes have low levels of all gly- 162–169 (1998).]
colytic intermediates, since hexokinase catalyzes the first step of 24. (a) When glucose is converted to pyruvate, NAD1 is re-
glycolysis. Therefore, the concentration of 2,3-BPG in the eryth- duced to NADH in the glyceraldehyde-3-phosphate dehy-
rocyte will be decreased as well, favoring the oxygenated form of drogenase reaction. Without a mechanism for regenerating
hemoglobin and decreasing its p50 value. Pyruvate kinase–deficient NAD1, glycolysis could not continue.
erythrocytes have high levels of 2,3-BPG since pyruvate kinase (b) If the trypanosome reduced pyruvate to lactate, this step
catalyzes the last step of glycolysis. This blockade at the last step would regenerate NAD1 and no other pathway for regener-
causes the concentrations of all of the intermediates “ahead” of the ating NAD1 would be needed.
block to be increased. Thus the oxygen affinity of hemoglobin is (c) A drug that interfered with one of the enzymes in the
decreased with increased 2,3-BPG concentration, and the p50 value trypanosome’s NADH-oxidizing pathway would likely have
increases as a result. no effect on the host since mammals lack the enzymes that
would be inactivated by the drug.
100
90
26. Deamination of alanine produces pyruvate, a gluconeogenic
80
Hexokinase
deficient
substrate, and deamination of aspartate produces oxaloacetate,
an intermediate of gluconeogenesis.
Oxygen saturation (%)
70
60 28. Phosphoenolpyruvate carboxykinase catalyzes an es-

Normal
50
erythrocytes sential step of gluconeogenesis. Lower expression of this en-
40 zyme decreases the gluconeogenic output of the liver, which
30
Pyruvate kinase
helps decrease the level of circulating glucose in patients with
20 deficient diabetes.
10
30. Normally, muscle glycogen is degraded to glucose-6-phos-
0
0 10 20 30 40 50 60 phate, which enters glycolysis to be oxidized to yield ATP for
p O2 (torr) the active muscle. In anaerobic conditions, pyruvate, the end
product of glycolysis, is converted to lactate, which is released phosphogluconate dehydrogenase, are stimulated by nitrate.
from the muscle into the blood and enters the liver to be [From Hankinson, O., and Cove, D. J., J. Biol. Chem. 249,
converted back to glucose via gluconeogenesis. The patient’s 2344–2353 (1974).]
muscle cells are unable to degrade glycogen to glucose-6-
phosphate; thus, there is no glucose-6-phosphate to enter gly- 42. G16BP inhibits hexokinase but stimulates PFK and pyru-
colysis and lactate formation does not occur. [From Stanbury, vate kinase. This means that glycolysis will be active, but only
J. B., Wyngaarden, J. B., and Fredrickson, D. S., The Meta- if the substrate is glucose-6-phosphate, since glucose cannot be
bolic Basis of Inherited Disease, pp. 151–153, McGraw-Hill, phosphorylated in the absence of hexokinase activity. The pen-
New York (1978).] tose phosphate pathway is inactive, since 6-phosphogluconate
dehydrogenase is inhibited. Phosphoglucomutase is activated,
32. In order for the enzyme to be active, the serine in the active which converts glucose-1-phosphate (the product of glyco-
site must be phosphorylated. This phosphate group is donated genolysis) to glucose-6-phosphate. Thus, in the presence of
to C1 of the glucose-6-phosphate in the first step of the conver- G16BP, glycogenolysis is active and produces substrate for
sion of glucose-6-phosphate to glucose-1-phosphate. If glucose- glycolysis but not the pentose phosphate pathway. This is a
1,6-bisphosphate dissociates prematurely, the serine is not phos- more efficient process than using glucose taken up from the
phorylated, the enzyme is not regenerated, and further rounds of blood, which would need to be phosphorylated at the ex-
catalysis cannot occur. pense of ATP. [From Beitner, R., Trends Biol. Sci. 4, 228–230
(1979).]
34. Production of glucose-1-phosphate requires only an iso-
merization reaction catalyzed by phosphoglucomutase to con- 44. (a) Inhibition of glycogen phosphorylase blocks glycogeno-
vert it to glucose-6-phosphate, which can enter glycolysis. This lysis, and inhibition of the bisphosphatase blocks gluconeo-
skips the hexokinase step and saves a molecule of ATP. Hydro- genesis. As a result, the liver is unable to produce glucose
lysis, which produces glucose, would require expenditure of an and the blood glucose level is low.
ATP to phosphorylate glucose to glucose-6-phosphate. (b) The inhibition of fructose-1,6-bisphosphatase pre-
vents gluconeogenesis even when substrates such as
36. (a) In a liver cell, glucose-6-phosphate has four possible glycerol and dihydroxyacetone phosphate are supplied.
fates: It can be used to synthesize glycogen, it can be ca- Galactose relieves the hypoglycemia because it can be
tabolized via glycolysis, it can be catabolized via the pentose phosphorylated, converted to glucose-6-phosphate, and
phosphate pathway, and it can be converted to glucose and dephosphorylated to yield glucose that enters the circula-
released from the cell. tion.
(b) In a muscle cell, only the first three processes occur.
Muscle cells lack glucose-6-phosphatase and therefore 46. The concentration of xylulose-5-phosphate, an interme-
cannot release glucose from the cell. diate of the pentose phosphate pathway, increases following a
meal, when there is plenty of glucose being catabolized by the
38. (a) Since serum withdrawal decreases G6PD activity, serum pentose phosphate pathway. The increase in fructose-2,6-bis-
withdrawal should decrease the NADPH/NADP1 ratio. phosphate increases the flux through glycolysis while inhibit-
NADPH is a product of the G6PD reaction and NADP1 is ing flux through gluconeogenesis, so glycolysis produces large
a reactant, so decreased enzyme activity leads to an increase amounts of pyruvate, which can be converted to acetyl-CoA.
in the oxidized form of the coenzyme and a decrease in the At the same time, the production of lipid-synthesizing enzymes
reduced form. increases, so the net result is that glucose is converted to acetyl-
(b) In the presence of DHEA, the NADPH/NADP1 ratio CoA and then to fat for storage.
should decrease, since DHEA inhibits G6PD activity, for
the reasons outlined in part (a).
(c) In the absence of any other factor, adding H2O2 should
not affect the ratio, since G6PDH can increase its activity
to produce more NADPH to react with the H2O2.
(d) In the absence of the serum containing growth fac- 2. The decarboxylation step is metabolically irreversible since
tors, G6PD cannot handle the increased load of H2O2, the CO2 product diffuses away from the enzyme. The other four
and the ratio would decrease. [From Tian, W.-N., Braun- reactions are transfer reactions or oxidation–reduction reactions
stein, L. D., Pang, J., Stuhlmeier, K. M., Xi, Q.-C., Tian, (transfer of electrons) that are more easily reversed.
X., and Stanton, R., J. Biol. Chem., 273, 10609–10617
(1998).] 4. TPP is a cofactor in two of the enzymes associated with the
citric acid cycle—the pyruvate dehydrogenase complex and
40. If NADPH is used as a coenzyme for nitrate reduction, the a-ketoglutarate dehydrogenase complex. If thiamine were
it will become oxidized to NADP1 and will need to be regen- deficient, TPP would be deficient as well and the activities of
erated. The pentose phosphate pathway produces NADPH, both these enzymes would decrease. As a result, the substrates
so it is possible that the NADPH-producing enzymes of of these two reactions, pyruvate and a-ketoglutarate, would
this pathway, glucose-6-phosphate dehydrogenase and 6- accumulate.
6. affinity for its substrate has decreased in the presence of the

O R inhibitor. The inhibitor competes with acetyl-CoA for bind-
O CH3 ing to the citrate synthase active site. S-acetonyl-CoA can do
C N
C this because its structure resembles that of acetyl-CoA.
O C
(c) Acetyl-CoA binds to pyruvate carboxylase and acts as
CH3 S
R an activator. A thioester functional group must be required
Pyruvate TPP
for binding, since S-acetonyl-CoA, which lacks a thioester
functional group, cannot bind to this binding site. [From
O Rubenstein, P., and Dryer, R., J. Biol. Chem. 255, 7858–
H
H C H 7862 (1980).]
1
4 12. Cis-aconitate is an intermediate in the reaction when cit-
CH3
Acetaldehyde rate is converted to isocitrate by aconitase. Trans-aconitate
structurally resembles cis-aconitate and would be expected to
H R O O R compete with cis-aconitate for binding to the enzyme. But be-
O CH3 O CH3
N N cause trans-aconitate is a noncompetitive inhibitor when citrate
H C C HO C C is used as the substrate, the citrate binding site must be distinct
S S from the aconitate binding site. Citrate and trans-aconitate do
CH3 R CH3 R
not compete for binding and can bind to the enzyme simulta-
neously, but when both substrate and inhibitor are bound, the
3 CO2 2 substrate cannot be converted to product. [From Villafranca, J.J.,
H J. Biol. Chem. 249, 6149–6155 (1974).]
R R 14. (a) When yeast use glucose as a carbon source, ATP is
HO N CH3 HO N CH3 obtained from the oxidation of glucose by glycolysis.
C C C
C Glucose is oxidized anaerobically, without the citric acid
S S cycle. But when the food source is shifted from glucose
H 3C R H3C R
to acetate, yeast are required to obtain all of their energy
Resonance-stabilized carbanion
from the citric acid cycle and oxidative phosphorylation.
Acetate is converted to acetyl-CoA, which enters the cit-
8. Citrate synthase acts on oxaloacetate (OAA) and fluoroacetyl- ric acid cycle. In the absence of glycolysis, flux through
CoA, an acetyl-CoA analog, to produce fluorocitrate. The the citric acid cycle increases. Because isocitrate dehy-
fluorocitrate then serves as an inhibitor of aconitase. This drogenase is one of the main regulatory enzymes of the
leads to an accumulation of citrate, since the citric acid cycle cycle, increasing its expression increases the rate of its
can go no further if the aconitase reaction is inhibited. reaction and increases the flux through the citric acid
cycle. In this manner, yeast can effectively use acetate as
O a food source.
(b) For the wild-type yeast, the [NAD 1]/[NADH] ra-
FH2C COO FH2C C S CoA
tio increases slightly as the cells switch from using gly-
Fluoroacetate Fluoroacetyl-CoA
colysis to using the citric acid cycle to generate ATP,
as described in part (a). There is an increase in flux
F CH COO
through the citric acid cycle, but perhaps the isocitrate
citrate synthase
HO C COO dehydrogenase cannot keep up with the demand, so
the ratio increases. There is a more dramatic change in
Oxaloacetate CH2 COO the ratio for the mutant because the isocitrate dehy-
Fluorocitrate drogenase enzyme is nonfunctional. This means that
the reaction, in which NAD 1 is a reactant and NADH
10. (a)
O is a product, cannot occur, so the NAD1 reactant ac-
cumulates. These cells will eventually die if not given a
Br CH2 C CH3 CoA SH carbon source other than acetate. [From Minard, K. I.,
HBr O and McAlister-Henn, L., Arch. Biochem. Biophys. 483,
136–143 (2009).]
H3C C CH2 S CoA
S-Acetonyl-CoA 16. TPP attacks the carbonyl carbon of the succinyl phos-
phonate, but the subsequent step (the departure of the leaving
(b) S-acetonyl CoA is a competitive inhibitor. The Vmax of group) cannot occur because the COP bond cannot be broken.
the citrate synthase reaction is the same in the absence and A covalent bond forms between the enzyme and the inhibitor
in the presence of the inhibitor. The K M has increased in (although the reaction is reversible, the reverse reaction occurs
the presence of the inhibitor, indicating that the enzyme’s slowly) and the substrate cannot bind.
H3C H3C In the presence of oxygen, pyruvate is converted to acetyl-CoA,

which enters the citric acid cycle so that ATP can be produced
N S N S by oxidative phosphorylation. Under aerobic conditions, malate
C O C dehydrogenase is absolutely essential for the regeneration of oxa-
O O P C CH2 CH2 COO loacetate as part of the citric acid cycle; therefore, activity levels
O P O
are much higher.
O OH
C O
26. The volume increase that occurs when the bread dough rises
is due to the CO2 produced by the anaerobic oxidation of glu-
CH2 cose. Sugar (sucrose) in the bread dough is hydrolyzed to glucose
CH2 and fructose by enzymes in the yeast. Then the fructose and glu-
cose both enter glycolysis. The end product is pyruvate, which
COO
is converted to acetaldehyde. In this step, a CO2 is released. The
[From Bunik, V. I., Denton, T. T., Xu, H., Thompson, C. M., acetaldehyde is then reduced to ethanol, which evaporates when
Cooper, A. J. L., and Gibson, G., Biochemistry 44, 10552– the bread is baked.
10561 (2005).]
28. The alternate pathway bypasses the succinyl-CoA synthe-
18. (a) Succinyl-CoA synthetase catalyzes the only substrate- tase reaction of the standard citric acid cycle, a step that is ac-
level phosphorylation reaction in the citric acid cycle. The companied by the phosphorylation of a nucleoside diphosphate.
enzyme with the ADP-specific b subunit could produce The alternative pathway therefore generates one less nucleoside
ATP in the brain and muscle to meet the energy needs of triphosphate than the standard citric acid cycle. There is no dif-
these tissues. The enzyme with the GDP-specific b subunit ference in the number of reduced cofactors generated.
could produce GTP needed by phosphoenolpyruvate car-
boxykinase for gluconeogenesis in the liver and kidneys. 30. In the reversible reaction shown, the amino acid aspartate
(b) Individuals who lack a functioning a subunit cannot and the glycolytic product pyruvate can undergo a transamina-
carry out the succinyl-CoA synthetase reaction in any tis- tion in which aspartate’s amino group is transferred, leaving oxa-
sue, since this subunit is common to both forms of the loacetate, which is a citric acid cycle intermediate.
enzyme. Because aerobic respiration is impossible, the in- 32. An increase in the concentration of glucose increases flux
dividual uses glycolysis followed by lactate fermentation to through glycolysis, which produces more pyruvate. The pyru-
obtain ATP. This doesn’t provide enough energy to sustain vate dehydrogenase complex activity increases in response to
life, so the person dies shortly after birth. the increase in pyruvate so that the conversion of pyruvate to
(c) When the gene for one of the b subunits is mutated, the acetyl-CoA can increase proportionally. At the same time, more
gene for the other subunit is normal. The individual would oxaloacetate is required, since equimolar amounts of acetyl-CoA
suffer from decreased succinyl-CoA synthetase activity, but and oxaloacetate are required for the first step of the citric acid
operation of the citric acid cycle would allow the individual cycle. Therefore, the activity of pyruvate carboxylase, the enzyme
to obtain some energy from aerobic respiration. However, that catalyzes the conversion of pyruvate to oxaloacetate, also
the individual’s ability to meet his/her energy needs is still increases.
somewhat compromised, as shown by the elevated levels of 34. Glutamine can be converted to glutamate, which can be
lactate and decreased life span. converted to a-ketoglutarate. This citric acid cycle intermedi-
20. Isocitrate lyase, a glyoxylate pathway enzyme, catalyzes the ate is eventually converted to oxaloacetate, so the glutamine is
conversion of isocitrate to succinate and glyoxylate. The glyox- a source of the oxaloacetate needed for gluconeogenesis when
ylate product of this reaction goes on to form malate, which is pyruvate carboxylase is not functioning. The oxaloacetate de-
eventually converted to glucose via gluconeogenesis. The succi- rived from glutamine can also replenish citric acid cycle inter-
nate product is not part of this pathway and is “disposed of ” by mediates that are normally produced by the pyruvate carbox-
mitochondrial succinate dehydrogenase, which regenerates the ylase reaction.
oxaloacetate needed to keep the glyoxylate pathway operating.
36. The exercising muscle required greater concentrations of
22. Levels of pyruvate, lactate, and fumarate would all increase ATP to power it, so the rates of glycolysis and the citric acid
in the patient. The concentration of malate would decrease. Py- cycle increased. Phosphoenolpyruvate was converted to pyruvate
ruvate and lactate increase because the patient relies on glycoly- more rapidly, so the concentration of phosphoenolpyruvate de-
sis and lactate fermentation in the absence of proper citric acid creased. Some of the pyruvate was converted to acetyl-CoA via
cycle function. The concentration of fumarate increases because the pyruvate dehydrogenase reaction. Since equimolar amounts
it cannot be converted to malate in the absence of fumarase. This of acetyl-CoA and oxaloacetate are required for the first step
also explains why the concentration of malate decreases. of the citric acid cycle, some of the pyruvate was converted to
24. When cells obtain energy in the absence of oxygen, glu- oxaloacetate via the pyruvate carboxylase reaction. This explains
cose is oxidized to pyruvate, which is subsequently reduced to why oxaloacetate concentrations increased. The concentration of
lactate with concomitant regeneration of NAD1. The citric acid pyruvate did not increase because a steady state was reached: The
cycle is not active, and the cells respond by down-regulating the rate of production of pyruvate from phosphoenolpyruvate was
activity of the citric acid cycle enzyme malate dehydrogenase. equal to the rate of consumption of pyruvate.
38. Ethanol is converted to acetaldehyde and then to acetate, and synthase would be good targets, assuming that there is a way
acetate is converted to acetyl-CoA. Acetyl-CoA then enters the to deliver these inhibitors to the phagosome. [From Lorenz,
glyoxylate pathway. The first step is the synthesis of citrate from M. C., and Fink, G. R., Euk. Cell 1, 657–662 (2002).]
acetyl-CoA and oxaloacetate. Citrate is isomerized to isocitrate.
Isocitrate lyase then splits isocitrate into succinate and glyoxylate. 48. (a)
Succinate leaves the glyoxysome and enters the mitochondrion, PEP
where it participates in the citric acid cycle. The glyoxylate fuses
CO2
with a second molecule of acetyl-CoA to yield malate. Malate PEP carboxylase
leaves the glyoxysome and enters the cytosol, where it is converted
to oxaloacetate via the malate dehydrogenase reaction. Oxalo-
acetate can then enter gluconeogenesis to form glucose. OAA
40. The mutant cannot convert isocitrate to a-ketoglutarate, so NADH
the citric acid cycle is blocked at this point. Adding glutamate NAD malate dehydrogenase
to the culture medium bypasses the block, because glutamate
can be converted to a-ketoglutarate and the citric acid cycle can
continue.
malate
42. (a) Hydroxycitrate differs by the addition of a hydroxyl group.
(b) Based on its structural similarity to the substrate cit- H2O fumarase
rate, hydroxycitrate is most likely to act as a competitive
inhibitor. fumarate
(c) Acetyl-CoA synthesized in the mitochondria from py- QH2
ruvate, the product of carbohydrate catabolism, is made
available in the cytosol by the action of ATP-citrate lyase Q succinate dehydrogenase
(see Fig. 14-16). Inhibiting this enzyme might decrease the
amount of acetyl-CoA available for fatty acid synthesis. succinate
(d) Since cholesterol synthesis also begins with acetyl-CoA,
hydroxycitrate might reduce the production of cholesterol
(b) If the bacteria were allowed to grow aerobically, the car-
and the structurally related steroid hormones. (Although
bon atoms of fuel molecules would be completely oxidized
hydroxycitrate inhibits ATP-citrate lyase in vitro, controlled
to carbon dioxide. The citric acid cycle would function in a
clinical trials have shown that the compound has no signifi-
forward, catabolic direction. Depriving the bacteria of oxy-
cant effect on weight loss in humans.)
gen ensures that the final three steps of the citric acid cycle
44. (a) The acetyl-CoA enters the glyoxylate pathway to pro- will function in a reverse, anabolic direction to produce
duce malate, which can then be converted to oxaloacetate the desired product, succinate. [From Agarwal, L., Isar, J.,
and used to synthesize glucose. Acetyl-CoA can also con- Meghwanshi, G. K., and Saxena, R. K., Enzyme and Micro-
dense with oxaloacetate to form citrate, which can be con- bial Technology 40, 629–636 (2007).]
verted to isocitrate and then to a-ketoglutarate. Glutamate
dehydrogenase converts a-ketoglutarate to glutamate by
reductive amination. Alternatively, a-ketoglutarate can be Chapter 15 Solutions
converted to glutamate by transamination.
(b) Aspartate undergoes transmination to form oxaloac- 2. Reverse the cytochrome a3 half-reaction and the sign of its
etate, which can condense with acetyl-CoA to form citrate. E89 value to indicate oxidation, multiply the coefficients by 2
Citrate is then converted to isocitrate, which is converted to so that the number of electrons transferred will be equal, then
a-ketoglutarate. a-Ketoglutarate can then be converted to combine the half-reactions and their E89 values.
glutamate.
2 cyt a3 (Fe21) S 2 cyt a3 (Fe31) 1 2 e2 E89 5 20.385 V
46. (a) Isocitrate lyase and malate synthase are found in the gly- 1 2
oxysome, so the pathogen is using the glyoxylate pathway. ½ O2 1 2 H 1 2 e S H2O E89 5 0.815 V
The glyoxylate pathway is linked to the citric acid cycle, 21
2 cyt a3 (Fe ) 1 ½ O2 1 2 H S 1
DE89 5 0.430 V
so the citrate synthase and malate dehydrogenase enzymes 2 cyt a3 (Fe31) 1 H2O
are upregulated as well. The glyoxylate pathway allows the
pathogen to use two-carbon sources to synthesize malate, Use Equation 15-4 to calculate DG 89 for this reaction:
and from there, glucose and larger biological macromole-
cules. The phagosome is not likely to be a rich source of glu- DG °¿ 5 2nFDE°¿
cose and amino acids that the pathogen can use for biosyn- DG °¿ 5 2122 196,485 J ? V21 ? mol21 2 10.430 V2
thesis, so the glyoxylate pathway is essential to its survival. DG °¿ 5 283 kJ ? mol21
(b) The host does not have the enzymes found in the gly-
oxylate pathway, so inhibitors of isocitrate lyase and malate The reaction is spontaneous under standard conditions.
4. Consult Table 15-1 for the relevant half-reactions involving The oxidation of succinate by FAD is more favorable than oxida-
acetoacetate and NADH. Reverse the NADH half-reaction and tion by NAD1, as shown by the DG 89 values calculated above.
the sign of its E89 value to indicate oxidation, then combine the Although neither reaction is spontaneous under standard condi-
half-reactions and their E89 values. tions, oxidation by NAD1 is far more unfavorable. The oxida-
acetoacetate 1 2 H1 1 2 e2 S 3-hydroxybutyrate E89 5 20.346 V tion of succinate by FAD is, in fact, a favorable process under
NADH S NAD1 1 H1 1 2 e2 E89 5 0.315 V cellular conditions (citric acid cycle, Section 14-2), which differ
acetoacetate 1 NADH 1 H1 S NAD1 1 3-hydroxybutyrate DE89 5 20.031 V from standard conditions.
8. Reverse the half-reaction for the iron–sulfur protein to in-
Use Equation 15-4 to calculate DG 89 for this reaction:
dicate that it is being oxidized. Add the two half-reactions to
DG °¿ 5 2nFDE°¿ obtain the DE89 for the reaction.
DG °¿ 5 2122 196,485 J ? V21 ? mol21 2 120.031 V2
FeS(red ) S FeS(ox) 1 e2 E89 5 20.280 V
DG °¿ 5 6.0 kJ ? mol 21
cyt c1 (Fe31) 1 e2 S cyt c1 (Fe21) E89 5 0.215 V
Consult Table 15-1 for the relevant half-reactions involving FeS (red ) 1 cyt c1 (Fe31) S FeS(ox) 1 cyt c1 (Fe21) DE89 5 20.065 V
acetoacetate and FADH2. Reverse the FADH2 half-reaction and
the sign of its E89 value to indicate oxidation, then combine the
half-reactions and their E89 values. DG °¿ 5 2nFDE°¿
1 2
acetoacetate 1 2 H 1 2 e S 3-hydroxybutyrate E89 5 20.346 V DG °¿ 5 2112 196,485 J ? V21 ? mol21 2 120.065 V2
FADH2 S FAD 1 2 H1 1 2 e2 E89 5 0.0 V DG °¿ 5 6.27 kJ ? mol21
acetoacetate 1 FADH2 S FAD 1 3-hydroxybutyrate DE89 5 20.346 V The positive DG 89 indicates that the electron transfer is unfavor-
Use Equation 15-4 to calculate DG 89 for this reaction: able under standard conditions. However, cellular conditions are
not necessarily standard conditions, and the DG for this reaction
DG °¿ 5 2nFDE°¿
is likely to be negative. Also, since this reaction occurs as part of
DG °¿ 5 2122 196,485 J ? V21 ? mol21 2 120.346 V2
the electron transport chain, the electrons gained by cytochrome
DG °¿ 5 66.8 kJ ? mol21
c1 will be passed along to Complex IV, in effect coupling the two
The reduction of acetoacetate by NADH is more favorable than reactions, which would also tend to make the process more favor-
reduction by FADH2, as shown by the DG89 values calculated able than the DG 89 indicates.
above. Although neither reaction is spontaneous under stan-
10. (a) Consult Table 15-1 for the relevant half-reactions in-
dard conditions, reduction by FADH2 is far more unfavorable.
volving NADH and coenzyme Q. Reverse the NADH half-
The reduction of acetoacetate by NADH is, in fact, a favorable
reaction and the sign of its E89 value to indicate oxidation,
process under cellular conditions, which differ from standard
then combine the half-reactions and their E89 values.
conditions.
Q 1 2 H1 1 2 e2 S QH2 E89 5 0.045 V
6. Consult Table 15-1 for the relevant half-reactions involving
NADH S NAD1 1 H1 1 2 e2 E89 5 0.315 V
succinate and NAD1. Reverse the succinate half-reaction and
the sign of its E89 value to indicate oxidation, then combine the NADH 1 Q 1 H1 S NAD1 1 QH2 DE895 0.360 V
half-reactions and their E89 values. Use Equation 15-4 to calculate DG 89 for this reaction:
succinate S fumarate 1 2 H1 1 2 e2 E89 5 20.031 V DG °¿ 5 2nFDE°¿
NAD1 1 H1 1 2 e2 S NADH E89 5 20.315 V DG °¿ 5 2122 196,485 J ? V21 ? mol21 2 10.360 V2
succinate 1 NAD1 1 H1 S NADH 1 fumarate DE89 5 20.346 V DG °¿ 5 269.5 kJ ? mol21
The phosphorylation of ADP to ATP requires 130.5 kJ ?
Use Equation 15-4 to calculate DG 89 for this reaction: mol21 of free energy. Assuming that this reaction is 35% ef-
DG °¿ 5 2nFDE°¿ ficient (see Problem 9), 0.8 mol ATP can be synthesized under
DG °¿ 5 2122 196,485 J ? V21 ? mol21 2 120.346 V2 standard conditions.
DG °¿ 5 66.8 kJ ? mol21
69.5 kJ ? mol21
Consult Table 15-1 for the relevant half-reactions involving suc- 10.352 5 0.80 mol
ÿ
cinate and FAD. Reverse the succinate half-reaction and the sign 30.5 kJ ? mol21
of its E89 value to indicate oxidation, then combine the half- (b) Consult Table 15-1 for the relevant half-reactions involv-
reactions and their E89 values. ing ubiquinol and cytochrome c. Reverse the ubiquinol half-
succinate S fumarate 1 2 H1 1 2 e2 E89 5 20.031 V reaction and the sign of its E89 value to indicate oxidation,
FAD 1 2 H1 1 2 e2 S FADH2 E89 5 0.0 V multiply the coefficients in the cytochrome c equation by
succinate 1 FAD S fumarate 1 FADH2 DE89 5 20.031 V 2 so that the number of electrons transferred will be equal,
then combine the half-reactions and their E89 values.
DG °¿ 5 2n FDE°¿ QH2 S Q 1 2 H1 1 2 e2 E89 5 20.045 V
DG °¿ 5 2122 196,485 J ? V21 ? mol21 2 120.031 V2 2 cyt c (Fe31) 1 2 e2 S 2 cyt c (Fe21) E89 5 0.235 V
DG °¿ 5 6.0 kJ ? mol21 QH2 1 2 cyt c (Fe31) S Q 1 2 H1 1 2 cyt c (Fe21) DE89 5 0.190 V
Use Equation 15-4 to calculate DG 89 for this reaction: in the presence of fluoxetine is not decreased substantially
DG °¿ 5 2nFDE°¿ when succinate (which donates its electrons to Complex II)
DG °¿ 5 2122 196,485 J ? V21 ? mol21 2 10.190 V2 and rotenone (which inhibits electron transfer in Complex I)
DG °¿ 5 236.7 kJ ? mol21 are added. However, fluoxetine also has the ability to in-
hibit Complex IV somewhat, since electron transport in the
The phosphorylation of ADP to ATP requires 130.5 kJ/mol
presence of fluoxetine decreases in the presence of ascorbate
of free energy. Assuming that this reaction is 35% efficient,
(which donates its electrons to cytochrome c) and TMPD
0.42 mol ATP can be synthesized.
(which donates its electrons to Complex IV).
36.7 kJ ? mol21 (c) By decreasing both the rate of electron transport and ATP
10.352 5 0.42 mol
ÿ
30.5 kJ ? mol21 synthesis, fluoxetine decreases the rate of ATP production in

the brain. The brain relies on a constant source of ATP for
(c) Consult Table 15-1 for the relevant half-reactions proper function, so decreased ATP production could lead
involving cytochrome c and oxygen. Reverse the cytochrome to an impairment of brain function. [From Curti, C., Min-
c half-reaction and the sign of its E89 value to indicate oxida- gatto, F. E., Polizello, A. C. M., Galastri, L. O., Uyemura,
tion, multiply the coefficients by 2 so that the number of S. A., and Santos, A. C., Mol. Cell. Biochem. 199, 103–109
electrons transferred will be equal, then combine the half- (1999).]
reactions and their E89 values. 22. Cytochrome c is a water-soluble, peripheral membrane
2 cyt c (Fe21) 1 2 e2 S 2 cyt c (Fe31) E89 5 20.235 V protein and is easily dissociated from the membrane by add-
½ O2 1 2 H1 1 2 e2 S H2O E89 5 0.815 V
ing salt solutions that interfere with the ionic interactions that
21 1 31
tether it to the inner mitochondrial membrane. Cytochrome c1
2 cyt c (Fe ) 1 ½ O2 1 2 H S 2 cyt c (Fe ) 1 H2O DE89 5 0.580 V
is an integral membrane protein and is largely water-insoluble
Use Equation 15-4 to calculate DG 89 for this reaction: due to the nonpolar amino acids that interact with the acyl
DG °¿ 5 2nFDE°¿ chains of the membrane lipids. Detergents are required to dis-
DG °¿ 5 2122 196,485 J ? V 21 ? mol 21 2 10.580 V2 sociate cytochrome c1 from the membrane because amphiphilic
DG °¿ 5 2112 kJ ? mol 21 detergents can disrupt the membrane and coat membrane pro-
teins, acting as substitute lipids in the solubilization process.
The phosphorylation of ADP to ATP requires 130.5 kJ/
24. The molasses and oil are food for microorganisms. As the
mol of free energy. Assuming that this reaction is 35% ef-
food is consumed, the rates of respiration and oxygen consump-
ficient, 1.3 mol ATP can be synthesized.
tion increase. Eventually, the depletion of oxygen creates a more
112 kJ ? mol 21 reducing environment that favors the reduction of Cr(VI) com-
10.352 5 1.3 mol
30.5 kJ ? mol 21 pounds to Cr(III) compounds.
12. This is not enough free energy to drive ATP synthesis under 26. Use the rearrangement of Equation 15-7 as shown in Sam-
standard conditions (DG 89 5 30.5 kJ ? mol21). ple Calculation 15-2.
14. Adding succinate to rotenone-blocked mitochondria
DG 5 2.303RT 1pHin 2 pHout 2 1 ZFDc
effectively bypasses the block as succinate donates its electrons
DG 5 2.30318.3145 3 10 23 J ? K 21 ? mol 21 2 1310 K2
to ubiquinone and electron transport resumes. Adding succinate
is not an effective bypass for antimycin A2 or cyanide-blocked 17.6 2 7.22 1 112 196,485 J ? V 21 ? mol 21 2 10.200 V2 ÿ
mitochondria because succinate donates its electrons upstream DG 5 2.4 kJ ? mol 21 1 19.3 kJ ? mol 21
of the block. DG 5 21.7 kJ ? mol 21
16. The donation of a pair of electrons to cytochrome c and 28. (a) The impermeability of the membrane to ions is an im-
then to Complex IV will result in the synthesis of about 1.3 portant feature of chemiosmosis, because the free move-
ATP per atom of oxygen (½ O2). Therefore, the P:O ratio of this ment of ions other than H1 would dissipate the electrical
compound is 1.3 [see Solution 10(c)]. component of the proton gradient and thereby compromise
18. Myxothiazol inhibits electron transfer in Complex III (spe- the ability of the gradient to supply free energy for ATP
cifically, it inhibits the transfer of electrons from reduced ubi- synthesis.
quinol to both cytochrome b and the iron–sulfur protein redox (b) If the membrane were permeable to other ions, the
centers in Complex III). proton gradient would be a simple chemical gradient
20. (a) Pyruvate and malate are oxidized by pyruvate dehy- rather than an electrochemical gradient. However, it
drogenase and malate dehydrogenase, respectively, and would still be able to serve as a source of free energy for
both reactions produce NADH, which can enter electron ATP synthesis.
transport. 30. A phosphate ion enters the mitochondrial matrix in sym-
(b) Fluoxetine inhibits electron transport generally, since port with a proton. This proton moves in a direction opposite
the rate of electron transport falls from an average of 163 to to the protons translocated by Complexes I, II, and IV. Thus,
77 when 0.15 mM fluoxetine is present. The inhibition is the difference in pH between the mitochondrial matrix and the
primarily at Complex I, since the rate of electron transport intermembrane space becomes smaller.
32. (a) Aerobic respiration yields 32 ATP (see Problem 31), 42. (a) The P:O ratio is decreased. For some reason, electron
each of which requires 30.5 kJ/mol to synthesize: transport and oxidative phosphorylation have been uncou-
pled. NADH is oxidized in the electron transport chain,
32 ATP 3 30.5 kJ ? mol21ATP oxygen is reduced to water, but ATP may not be synthesized
3 100 5 34%
2850 kJ ? mol21 ÿ
if ADP is not available. This decreases the P:O ratio because

Lactate fermentation yields 2 ATP: oxygen consumption occurs to a greater extent than ADP
phosphorylation.
2 ATP 3 30.5 kJ ? mol21ATP (b) If the energy released in electron transport is not used
3 100 5 31%
196 kJ ? mol21
ÿ
to synthesize ATP, it is released as heat, which accounts
for the elevated body temperature. If sufficient ATP is not
Alcoholic fermentation yields 2 ATP: synthesized to meet energy needs, the rate of electron trans-
2 ATP 3 30.5 kJ ? mol21ATP port increases, which leads to an increased consumption of
3 100 5 26% O2 and an increase in the concentration of reduced coen-
235 kJ ? mol21
zymes that enter electron transport, thus increasing meta-
(b) Organisms that can oxidize glucose in the presence of bolic rate.
oxygen have an advantage over anaerobic organisms because (c) The patient will not be able to carry out strenuous
these organisms can extract more energy per glucose. This exercise under aerobic conditions because her muscle cells
may have been important in evolution. are incapable of generating enough ATP to power the
34. Stimulation of the glycolytic enzymes hexokinase and phos- muscle.
phofructokinase increases glycolytic flux and allows the yeast 44. Since it has 9 c subunits, the bacterial enzyme can theo-
cells to obtain ATP more quickly under anaerobic conditions. retically produce 3 ATP for every 9 protons translocated, or one
[From Beitner, R., Cohen, T. J., Nordenberg, J., and Haberman, ATP per 3 H1. In the chloroplast, 3 ATP are synthesized for
S., Biochim. Biophys. Acta 586, 266–277 (1979).] every 14 protons, or 1 ATP per 4.7 H1. Thus, the bacterium is
36. If the translocase is unable to function, ATP will not more efficient in its use of the proton gradient established during
be able to exit the mitochondrial matrix and ADP will not electron transport and has a higher ratio of ATP produced per
be transported inside. Without ADP, the substrate for ATP oxygen consumed.
synthase, ATP synthesis will not occur. Since electron trans- 46. During anaerobic fermentation, only 2 ATP molecules can
port and oxidative phosphorylation are coupled, a decrease in be obtained from each glucose molecule. Thus, in order to get
the rate of oxidative phosphorylation will decrease the rate of enough ATP to satisfy the energy needs of the cell, glucose con-
electron transport. sumption by the glycolytic pathway predominates, and only a
38. (a) ATP synthesis decreases dramatically in the presence of small amount is left over for the pentose phosphate pathway.
oligomycin, since proton transfer is required to stimulate But during aerobic respiration, 32 ATP are available per glucose
rotation of the g subunit of ATP synthase, which causes molecule. Thus, less glucose is needed to synthesize the same
the sequential conformational change of the b subunits that amount of ATP, so a larger fraction of glucose can enter the pen-
catalyze the phosphorylation of ADP to ATP. tose phosphate pathway.
(b) Since oxidative phosphorylation and electron transport 48. (a) In the root system of the skunk cabbage, starch is broken
are coupled, a decrease in the rate of oxidative phosphoryla- down to yield glucose, which is catabolized via glycolysis, the
tion will also affect the rate of electron transport. If ATP citric acid cycle, and the electron transport chain. The oxi-
synthesis is not occurring, the proton gradient is not “dis- dation of glucose provides the reduced cofactors (NADH
charged” and the rate of electron transport decreases. and QH2) required to keep electron transport going so that
(c) A decrease in the rate of electron transport will also de- thermogenesis can occur.
crease the rate of oxygen consumption. (b) In the skunk cabbage, thermogenesis increases as the
(d) If dinitrophenol is added, the proton gradient is dis- temperature decreases. Thus, the rate of aerobic oxidation
sipated, or “discharged,” but not in a way that leads to ATP of glucose increases to increase the flux of NADH and QH2
synthesis. Therefore, ATP synthesis still does not occur, but through the electron transport chain. Since oxygen is the
electron transport and oxygen consumption resume, with final electron acceptor, an increase in electron transport will
the free energy of the process released as heat. also increase oxygen consumption. When the ambient air
40. FCCP is a lipid-soluble compound that can pass through temperature is warmer, the need for heat production is less,
both the outer and inner mitochondrial membranes and into so there is less flux through the electron transport chain.
the matrix. FCCP has an acidic hydrogen on the central ni- Thus, oxygen consumption decreases during the day.
trogen that dissociates in the basic environment of the ma- (c) The synthesis of the uncoupling protein increases with
trix. The FCCP passes back through the inner membrane to decreasing temperature, presumably by an increase in tran-
the intermembrane space, where it is reprotonated and the scription of the mRNA that codes for the uncoupling pro-
entire cycle begins again. In this manner, the FCCP shuttles tein (although a decrease in the rate of mRNA degradation
protons into the mitochondrial matrix and dissipates the pro- would produce the same results). The increased amount of
ton gradient. mRNA likely results in an increase in concentration of the
uncoupling protein so that the mitochondrial proton gradient wavelength) could potentially funnel light energy back to the over-
would be discharged. Thus, at low temperatures, the potato active photosystems. Dissipation of excess energy as heat would be
could generate heat rather than ATP. [From Laloi, M., Klein, the safest mechanism, since the photosystems do not have any way
M., Riesmeier, J.W., Müller-Röber, B., Fleury, C., Bouillaud, to harvest thermal energy to drive chemical reactions.
F., and Ricquier, D., Nature 389, 135–136 (1997); Knutson, 14. If the photosystems were in close proximity, then Photosystem
R. M., Science 186, 746–747 (1974); and Seymour, R. S., II might not undergo photooxidation and instead act as a light-
and Schultze-Motel, P., Nature 383, 305 (1996).] harvesting complex for Photosystem I. Because the reaction center
50. (a) Substrate-level phosphorylation is catalyzed by phos- of Photosystem II absorbs light with a peak wavelength of 680 nm,
phoglycerate kinase and pyruvate kinase in glycolysis, and it could pass energy to the reaction center of Photosystem I, which
by succinyl-CoA synthetase in the citric acid cycle. absorbs lower-energy (longer-wavelength) light at its P700 group.
(b) C6H12O6 1 6 O2 S 6 CO2 1 6 H2O 16. Myxothiazol inhibits electron transfer in the cytochrome
b6 f complex.
Chapter 16 Solutions 18. The alanine residue at position 251 is essential for pho-
2. Both cellular organelles are membrane-bound structures tosynthesis and photoautotrophic growth and may be part of
with their own DNA that codes for proteins essential for or- the binding site for herbicides. When the alanine is mutated
ganelle function (respiration for the mitochondrion, photosyn- to a cysteine, which resembles alanine except that a sulfhy-
thesis for the chloroplast). Both organelles have an inner and dryl group has replaced a hydrogen, the mutated protein is
an outer membrane that enclose an intermembrane space. The similar to the wild-type. When the alanine is changed to an
outer membrane is fairly porous in both organelles, whereas the amino acids that is similar in size but more polar (such as Gly,
inner membrane is fairly impermeable. The inner compartment Pro, or Ser), photosynthesis is impaired. Replacement with a
of the mitochondrion is referred to as the mitochondrial matrix, larger, nonpolar amino acid results in a mutant that is further
while the inner compartment of the chloroplast is called the impaired, and replacement with a larger polar amino acid re-
stroma. Contained within the stroma is a third membranous sults in an organism that is not photosynthetically competent.
structure called the thylakoid, which is analogous to mitochon- Therefore, the residue at position 251 must be relatively small
drial inner-membrane cristae. The thylakoid membrane and the and nonpolar. Residues of increasing size and polarity result
cristae differ in shape; the thylakoid consists of stacks of flat- in photosynthetically impaired organisms. [From Lardans, A.,
tened vesicles, whereas the cristae are tubular or highly folded. Förster, B., Prásil, O., Falkowski, P. G., Sobolev, V., Edelman,
4. Lipids with highly unsaturated fatty acids have low melting M., Osmond, C. B., Gillman, N. W., and Boynton, J. E., J. Biol.
points, since the cis double bonds create bends that make it dif- Chem. 273, 11082–11091 (1998).]
ficult for the lipids to pack together. Because there are few in- 20. DG 5 2.303RT 1pHin 2 pHout 2 1 ZFDc
termolecular forces binding these lipids together, they generate DG 5 2.303 18.3145 J ? K21 ? mol21 2 1298 K2 10.752
a highly fluid membrane, which must be essential for photosyn- 1 112 196,485 J ? V21 ? mol21 2 10.20 V2
thesis in some way. DG 5 4300 J ? mol21 1 19,300 J ? mol21
6. (a) If the synthesis of each ATP requires 30.5 kJ ? mol21, DG 5 23.6 kJ ? mol21
then 9.8 mol ATP (300/30.5) could be synthesized. For both organelles, the translocation is endergonic. In the chlo-
(b) About 5.6 mol ATP (170/30.5) could be synthesized. roplast, most of this energy is due to the concentration (pH) dif-
8. Photosynthetic bacteria can absorb light in the infrared and ference on the two sides of the membrane; in the mitochondrion,
ultraviolet regions of the electromagnetic spectrum. most of the energy is due to the membrane potential (Dc).
10. (a) The sequences would provide only limited informa- 22. Use Equation 16-1 and multiply by 2 to calculate the energy
tion, since even highly homologous proteins such as myo- of the photons:
globin and hemoglobin (which have very similar struc-
hc
tures) have limited sequence identity (see Section 5-1). E5 32
The three-dimensional structures of the proteins would be l
more likely to indicate whether they function similarly. 16.626 3 10234 J ? s2 12.998 3 108 m ? s21 2 122
(b) Low-resolution models that included the heme groups E5
6 3 1027 m
would be more useful, since the positions of the heme 219
E 5 6.6 3 10 J
groups within the proteins might indicate whether they
function similarly in accepting and donating electrons to The energy of two photons is nearly twofold greater than the
their redox partners. It is possible that the heme groups energy change for the oxidation of one molecule of water by
could have similar orientations even if the apoproteins did NADP1, so, in theory, the two photons supply sufficient energy
not resemble each other in overall tertiary structure. to drive the oxidation.
12. Photooxidation would not be a good protective mechanism 24. Some of the label appears in molecular oxygen released by
since it might interfere with the normal redox balance among the the water-splitting reaction of Photosystem II. Some of the label
electron-carrying groups in the thylakoid membrane. Releasing the appears in other compounds, including intermediates of the Calvin
energy by exciton transfer or fluorescence (emitting light of a longer cycle, since H2O participates in the rubisco reaction (Fig. 16-24).
26. Complex III of the mitochondrial electron transport chain enters glycolysis to produce ATP to meet the energy needs of
is analogous to the cytochrome b6 f complex. In the presence the plant. [From Cséke, C., Nishizawa, A. N., and Buchanan,
of antimycin A, electron flow in the cytochrome b6 f complex B. B., Plant Physiol. 70, 658–661 (1982).]
would be inhibited. Electrons would not reach Photosystem I, 40. Light Carbon
and NADPH would not be produced. Proton translocation from fixation
the stroma to the thylakoid lumen also would not occur, so CF1
would not be stimulated and ATP synthesis would not occur. P700*red Ferredoxinox Reductasered Thioredoxinox Enzymered
28. Because oligomycin inhibits the F0 subunit of mitochon- SH SH SH SH
S S
drial ATP synthase, protons from the intermembrane space cannot
translocate to the mitochondrial matrix. F1 is not stimulated, and
P700⫹ox Ferredoxinred Reductaseox Thioredoxinred Enzymeox
ATP synthesis does not occur. The cytosolic ratio of ATP/ADP de-
creases because less ATP is exported to the cytosol from the matrix S S SH SH S S
when ATP synthesis is inhibited. Because oligomycin does not in- The activity of Photosystem I generates reduced ferredoxin, which
hibit CF0, ATP synthesis is not inhibited, so the ATP/ADP ratio is is a substrate for the reductase. The product of the reductase reac-
not affected. In some cases the decreased cytosolic ATP/ADP ratio tion, reduced thioredoxin, can then reduce the disulfides of the Cal-
might stimulate ATP synthesis in the chloroplast, resulting in an vin cycle enzymes. Conformational changes in the enzymes upon
increased chloroplastic ATP/ADP ratio. [From Gardeström, P., and exposure of free sulfhydryl groups could increase their activity.
Lernmark, U., J. Bioenerg. Biomembr. 27, 415–421 (1995).]
42. DG 5 DG °¿ 1 RT lnQ
30. The net equation would be
229.7 kJ ? mol21 5 214.2 kJ ? mol21 1 18.3145
CO2 1 2 H2S S (CH2O) 1 S2 1 H2O 3 1023 kJ ? K21 ? mol21 2 1298 K2 lnQ
32. When rubisco reacts with oxygen in a process called 215.5 kJ ? mol21 5 2.48 kJ ? mol21 lnQ
photorespiration, the products are 3-phosphoglycerate and 26.25 5 lnQ
2-phosphoglycolate. The latter product is further metabolized
e26.25 5 Q
by pathways that consume ATP and NADPH and thus waste
some of the energy captured by photosynthesis. If rubisco could Q 5 0.0019
bind only CO2, the enzyme would produce two molecules of The enzyme is likely to be regulated because it catalyzes an irre-
3-phosphoglycerate, which is a precursor to many biological versible step of the Calvin cycle (as evidenced by the large nega-
macromolecules. In a plant with a rubisco that binds only CO2, tive value of DG).
photorespiration would not occur, and more of the energy obtained 44. PEPC supplies oxaloacetate for the citric acid cycle, which
in photosynthesis would be available for biosynthetic reactions. can generate ATP for the biosynthetic processes occurring in
34. DG 5 DG °¿ 1 RT ln Q the germinating seedling. The PEPC enzyme also plays a role in
241.0 kJ ? mol21 5 235.1 kJ ? mol21 1 18.3145 providing oxaloacetate for the glyoxylate cycle (see Box 14-B),
which provides a route for the synthesis of glucose from fatty
3 1023 kJ ? K21 ? mol21 2 1298 K2 lnQ
acids, a pathway that is lacking in animals.
25.9 kJ ? mol21 5 2.48 kJ ? mol21 ln Q
22.38 5 ln Q Chapter 17 Solutions
e22.38 5 Q O
2.
Q 5 0.093 R C
O⫺
The ratio of products to reactants is 0.093 to 1. Fatty Acid
36. (a) The compound resembles the transition state of the ⫹

rubisco carboxylase reaction (see Fig. 16-24) and therefore O O O
inhibits the enzyme by binding in the active site. ⫺O P O P O P O Adenosine
(b) At night, the compound inhibits rubisco in order to O⫺ O⫺ O⫺
prevent the Calvin cycle from consuming NADPH and ATP
inorganic
ATP. During the day, when the light reactions are supplying pyrophosphatase
PPi 2 Pi
NADPH and ATP, the inhibitor is broken down to reacti-
H 2O
vate rubisco so that it can fix carbon. O O
38. ATP and NADPH are produced by the light reactions R C O P O Adenosine
during the day. When photosynthesis is occurring, synthesis O⫺ H SCoA
of starch (an ATP-requiring process) occurs, and glycolysis, Acyladenylate
mixed anhydride
an opposing process, is inhibited. At night, when the light O O
reactions do not occur and ATP and NADPH concentrations R C SCoA ⫹ ⫺O P O Adenosine
are low, the inhibition of phosphofructokinase is relieved. Acyl-CoA
O⫺
Starch is broken down, and the resulting glucose-1-phosphate AMP
4. If medium-chain fatty acids are metabolized normally in the O
absence of carnitine, then fatty acids of this size must be able to H3C (CH2)7 CH CH (CH2)7 C SCoA
Oleoyl-CoA
cross the inner mitochondrial membrane and enter the mito-
3 cycles of ␤ oxidation 3 (1 QH2, 1 NADH, 1 acetyl-CoA)
chondrial matrix without the aid of carnitine. Carnitine is re-
3(1.5 2.5 10) 42 ATP
quired for transport of fatty acids long than 10 carbons. O
6. The patient should avoid fasting and sustained exercise, since H3C (CH2)7 C C CH2 C SCoA
both of these conditions result in the release of free fatty acids into H H
the bloodstream for uptake by the tissues. The patient should also enoyl-CoA isomerase
consume a diet that is low in fat and high in carbohydrates. H O

8. Oxidation of the methylene groups is accomplished by the H3C (CH2)8 C C C SCoA
action of a dehydrogenase, which removes electrons. The oxygen H
atom that becomes part of the carbonyl group is derived from a 1 cycle of ␤ oxidation
(acyl-CoA dehydrogenase 1 NADH, 1 acetyl-CoA
water molecule added by enoyl-CoA hydratase. reaction is bypassed)
2.5 10 12.5 ATP
10. The products are three molecules of propionyl-CoA, three O
molecules of acetyl-CoA, and one molecule of 2-methylpropionyl- H3C (CH2)8 C SCoA
CoA. 4 cycles of ␤ oxidation 4 (1 QH2, 1 NADH, 1 acetyl-CoA)

4(1.5 2.5 10) 56 ATP
Acetyl-CoA (10 ATP)
C SCoA
Pristanate
O (b) Linoleate is also an 18-carbon fatty acid and would yield
O 120 ATP via b oxidation if it were saturated. The double
␤ oxidation bond at the 9,10 must be converted from the cis to the trans
H3 C CH2 C S CoA
Propionyl-CoA isomer, resulting in the loss of 1 QH2 (1.5 ATP). In addi-
tion, an NADPH-dependent reduction of the 12,13 double
bond costs 2.5 ATP. This reduces the ATP total by 4, so
C SCoA
oxidation of linoleate yields 116 ATP. (Subtract 2 ATP for
O activation from the total shown in the figure.)
O
␤ oxidation O
CH3 C SCoA
H3C (CH2)4 CH CH CH2 CH CH (CH2)7 C SCoA
Acetyl-CoA Linoleyl-CoA

SCoA 3(1.5 2.5 10) 42 ATP

O

O H3C (CH2)4 CH CH CH2 C C CH2 C CoA
H H
␤ oxidation enoyl-CoA isomerase
Propionyl-CoA
H O
H3C (CH2)4 CH CH CH2 CH2 C C C CoA
␤ oxidation
Acetyl-CoA H
1 cycle of ␤ oxidation
(acyl-CoA dehydrogenase 1 NADH, 1 acetyl-CoA
reaction is bypassed) 2.5 10 12.5 ATP
␤ oxidation O
Propionyl-CoA
H3C (CH2)4 CH CH CH2 CH2 C S CoA
acyl-CoA dehydrogenase 1 QH2 1.5 ATP

␤ oxidation
Acetyl-CoA H O
CH3 H3C (CH2)4 CH CH C C C S CoA

H
SCoA NADPH
H3C 2,4-dienoyl-CoA reductase Costs 2.5 ATP
NADP
O O
H3C (CH2)4 CH2 CH CH CH2 C S CoA
12. (a) Oleate is an 18-carbon fatty acid. If it were completely
enoyl-CoA isomerase
saturated, 120 ATP would be generated via b oxidation H O
(see Problem 11b). The double bond at the 9,10 position H3C (CH2)4 CH2 CH2 C C C S CoA
must be converted from the cis to the trans isomer. b oxi- H
dation continues after this isomerization step, but with the 1 cycle of ␤ oxidation
1 NADH, 1 acetyl-CoA
(acyl CoA dehydrogenase
loss of 1 QH2. Thus 1.5 ATP should be subtracted from reaction is bypassed) (2.5 10) 12.5 ATP
the total to yield 118.5 ATP. The pathway below shows a
total of 120.5 ATP, but 2 ATP are subtracted to account for 3(1.5 2.5 10) 42 ATP
the ATP spent in fatty acid activation. Acetyl-CoA (10 ATP)
14. Adding up the ATP in the figure gives a total of 155 ATP. 22. Epinephrine signaling via an adrenergic receptor acti-
Subtracting the 2 ATP required for activation brings the total to vates a G protein, which activates adenylate cyclase to pro-
153 ATP. duce cyclic AMP to activate protein kinase A (PKA). PKA
phosphorylates its substrates, including acetyl-CoA carbox-
O ylase, thereby inactivating the enzyme. As a result of lower
H3C (CH2)20 CH2 CH2 C SCoA acetyl-CoA carboxylase activity, the rate of fatty acid synthe-
FAD H2O2 2 H2O O2 sis drops. Epinephrine signaling also leads to phosphorylation
acyl-CoA oxidase
FADH2 O2 and activation of glycogen phosphorylase, which mobilizes
glucose from glycogen. These responses are consistent: When
H O
the cell needs to mobilize metabolic fuel (for example, by
H3C (CH2)20 C C C SCoA glycogenolysis), storage of fuel (for example, by fatty acid
enoyl-CoA
H synthesis) is inhibited.
6 cycles of ␤ oxidation 24. The label does not appear in palmitate because 14CO2 is
(acyl-CoA dehydrogenase released in Reaction 3 of fatty acid synthesis (Fig. 17-13).
6 NADH, 6 acetyl-CoA
reaction is bypassed)
6(2.5) 6(10) ATP 75 ATP 26. (a) A portion of the inhibitor molecule mimics the structure
O of a fatty acid. The compound may act as a competitive in-
H3C (CH2)8 CH2 CH2 C SCoA hibitor, binding to the enzyme active site to preclude bind-
PEROXISOME ing of the substrate.
MITOCHONDRION (b) The lower the ID50 value, the lower the concentration
5 QH2, 5 NADH, 5 acetyl-CoA
5 cycles of ␤ oxidation
of inhibitor required to kill the cells. It is desirable for the
5(1.5) 5(2.5) 5(10) ATP 70 ATP inhibitor to inhibit fatty acid synthase in cancer cells but
acetyl-CoA (10 ATP)
not normal cells. Thus, an effective inhibitor would have
a low ID50 value in cancer cells but a high ID50 value in
16. (a) The free energy cost of synthesizing ATP from ADP 1 Pi normal cells. The ratios of ID50 values for normal and can-
is 30.5 kJ ? mol21. Glucose oxidation could theoretically cer cells were calculated to determine which of the inhibi-
yield 2850/30.5, or 93.4 ATP. The ATP yield per carbon tors tested was most effective. As shown in the table below,
atom is 93.4/6 5 15.6. Palmitate oxidation could theoreti- compounds B, D, and E were the most effective inhibitors.
cally yield 9781/30.5, or 320.7 ATP. The ATP yield per car- These compounds have side chains of 11, 7, and 8 carbons,
bon atom is 320.7/16 5 20.4 ATP. respectively. Inhibitor D has the shortest alkyl chain and is
(b) In vivo, the catabolism of glucose leads to the production the most soluble of the three.
of 32 ATP (see Solution 15-31), which is 32/6, or 5.3 ATP
per carbon atom. The catabolism of palmitate leads to the breast cancer ID50
production of 106 ATP (see the Solution 17-11a), which is Compound Alkyl side chain (R) normal cells ID50
106/16, or 6.6 ATP per carbon atom.
A —C13H27 2.7
(c) In theory as well as in vivo, fatty acid oxidation yields
more ATP per carbon atom than glucose oxidation (this is B —C11H23 6.0
primarily because the carbons of carbohydrates are already C —C9H19 2.5
partially oxidized, whereas fatty acid carbons are usually D —C8H17 4.3
fully reduced). Both pathways are equally efficient from
E —C7H15 4.5
a thermodynamic point of view, recovering slightly more
than 30% of the free energy available (for glucose 5.3/15.6, F —C6H13 1.5
and for palmitate, 6.6/20.4).
18. Acetyl-CoA carboxylase generates malonyl-CoA, the sub- (c) Inhibitor D at a concentration of 2 mg/mL signifi-
strate for fatty acid synthase. Mice without acetyl-CoA carboxyl- cantly inhibits incorporation of radiolabeled acetate into
ase are unable to synthesize fatty acids and hence store less fat in triacylglycerols. At a concentration of 5 mg/mL, 80% of
their bodies. Malonyl-CoA also inhibits carnitine acyltransferase. total acylglyceride synthesis is inhibited. Phospholipid syn-
In the absence of acetyl-CoA carboxylase to produce this inhibi- thesis is not significantly affected, supporting the hypothesis
tor, transport of fatty acids into mitochondria cannot be regu- that the drug’s target is fatty acid synthase. [From Kuhajda,
lated, and mitochondrial b oxidation proceeds continuously. F. P., Pizer, E. S., Li, J. N., Mani, N. S., Frehywot, G. L.,
20. As shown in the mechanism for malonyl-CoA formation and Townsend, C., Proc. Natl. Acad. Sci. 97, 3450–3454
(Problem 17-19), ATP is required to generate a carboxyphos- (2000).]
phate intermediate. The result is that malonyl-CoA contains 28. DHA is an n-3 fatty acid and is essential for growth. A well-
some of the free energy of ATP. This free energy is released when nourished mother will produce breast milk containing DHA,
the acetyl group condenses with malonyl-ACP and CO2 is re- but a bottle-fed infant whose sole source of food is infant for-
leased. The release of CO2 is entropically favored and drives the mula will not obtain this essential fatty acid unless it is added to
reaction to completion. the formula.
30. (a) Liver fatty acid synthase activity increases with con- Chapter 18 Solutions
sumption of a high-carbohydrate diet. Glucose in excess of
2. Alfalfa is a leguminous plant (see Fig. 18-1) that harbors
what is required to meet immediate energy needs is oxidized
nitrogen-fixing bacteria in its root nodules. Crop growing de-
to pyruvate by glycolysis, then converted to acetyl-CoA by
pletes the soil of fixed nitrogen; planting alfalfa every few years
pyruvate dehydrogenase. Excess acetyl-CoA is used to syn-
allows the associated nitrogen-fixing bacteria to replenish the
thesize fatty acids, which are ultimately used to synthesize
nitrogen supply in the soil and decreases the need for nitrogen-
triacylglycerols for storage in adipose tissue.
based fertilizers.
(b) Liver fatty acid synthase activity is decreased with con-
sumption of a high-fat diet. Endogenous fatty acid synthesis 4. Bacterial nitrogenase is inactivated by oxygen, so nitrogen
is not required if fatty acids are being obtained from the fixation takes place in cells that lack Photosystem II, the com-
diet. plex where water is oxidized to form molecular oxygen (see
(c) Mammary gland fatty acid synthase activity increases in Section 16-2)
mid to late pregnancy to provide fatty acids for triacylglyc- 6. (a) The low K M of glutamine synthetase for ammonium ions
erols in breast milk for the neonate. ensures that the first method (a) will be used when the con-
32. Fatty acid degradation produces acetyl-CoA, but in the centration of available ammonia is low. The second method
absence of glucose, acetyl-CoA cannot enter the citric acid (b) will be used when the concentration of ammonia is high.
cycle due to insufficient oxaloacetate, a substrate for the first (b) Incorporation of one mole of ammonia into an amino acid
step. When carbohydrate concentrations drop, any available using the first method (a) costs one mole of ATP, whereas ATP is
oxaloacetate is diverted to gluconeogenesis to produce the glu- not required when the prokaryotic cell uses the second method
cose necessary for red blood cell and brain function. If acetyl- (b). The prokaryotic cell is at a disadvantage when the ammo-
CoA cannot enter the citric acid cycle (and acetyl-CoA can- nia concentration is low because energy must be expended in
not be converted to pyruvate in mammals), it is converted to order to synthesize amino acids under these conditions.
ketone bodies. 8. (a) O Glu COO
H O
3N CH C C O
34. Oxidation of fatty acids yields acetyl-CoA, which enters -Ketoglutarate
CH2 CH2
the citric acid cycle by reacting with oxaloacetate. Oxaloac- Asp Oxaloacetate
COO COO
etate is produced by the action of pyruvate carboxylase on
(b) O Glu COO
pyruvate produced by glycolysis. Without glucose metabolism H
3N CH C O C O
to generate pyruvate, the citric acid cycle cannot proceed. Ala -Ketoglutarate Pyruvate
CH3 CH3
Thus, the statement “fats burn in the flame of carbohydrates”
(c) O Asp COO
refers to the fact that normal carbohydrate metabolism (lead- H
3N CH C O C O
ing production of oxaloacetate) is absolutely required for nor- Oxaloacetate
Glu CH2 CH2
mal fatty acid metabolism, which provides acetyl-CoA for the -Ketoglutarate
CH2 CH2
citric acid cycle.
COO COO
36. Three phosphoanhydride bonds must be cleaved in order to The products are all intermediates of the citric acid cycle (oxalo-
synthesize phosphatidylcholine from choline and diacylglycerol acetate and a-ketoglutarate) or closely associated with the citric
(see Fig. 17-19). Choline is activated by conversion to phospho- acid cycle (pyruvate).
choline, with a phosphate group donated by ATP. The phospho-
choline is subsequently converted to CDP–choline, a reaction 10.
H
E (CH2)4 NH2
in which a second phosphoanhydride bond is cleaved. Pyro- O H
phosphate is the leaving group in this reaction, and the third H3C C C COO
phosphoanhydride bond is cleaved when the pyrophosphate is H
H N
hydrolyzed to orthophosphate. C H
O
38. (a) HDL remove excess cholesterol from tissues and trans- O32PO
port it back to the liver. This prevents the accumulation of N
cholesterol in vessel walls that leads to atherosclerosis. H
(b) HDL level alone does not indicate the risk of developing E (CH2)4 NH
3
O
atherosclerosis, since the level of LDL, the activity of the H3C C H
H
LDL receptor, and other factors such as smoking or vessel C COO
wall injuries resulting from infection can all influence the H N

C H
likelihood of developing the disease. O
O32PO
40. Chylomicrons are produced by intestinal cells to package
N
dietary lipids for delivery to the rest of the body. Fat-soluble
H
vitamins such as vitamin A are also transported via chylomi-
crons. Without chylomicrons, the body lacks an efficient way to 12. In the glutamine synthetase reaction (shown on page 468),
distribute vitamin A obtained from the diet. ATP donates a phosphoryl group to glutamate, which is then
displaced by an ammonium ion, producing glutamine and dUMP is not converted to dTMP (see page 484) and there is
phosphate. The ammonium ion is the nitrogen source. The as- no subsequent phosphorylation to dTTP, so the concentration
paragine synthetase reaction (page 472) also requires ATP as an of dTTP in the cells declines. In the presence of the inhibitor,
energy source, but the nitrogen donor is glutamine, not an am- dUMP accumulates and is converted to dUTP. The concentra-
monium ion. Aspartate is converted to asparagine, and the glu- tion of dUTP in cells is normally low because thymidylate syn-
tamine becomes glutamate after donating an amino group. ATP thase acts quickly on dUMP to convert it to dTMP. Cancer cells
is hydrolyzed to AMP and pyrophosphate instead of ADP and die in the presence of 5-fluorouracil because the cells lack the
phosphate as in the glutamine synthetase reaction. dTTP required for DNA synthesis. Normal cells are not affected
14. Cysteine is the source of taurine. The cysteine sulfhydryl because DNA synthesis is not as rapid as in cancer cells.
group is oxidized to a sulfonic acid, and the amino acid is de- 28. The ketogenic amino acids are broken down to acetyl-CoA
carboxylated. or acetoacetate, which can be converted to acetyl-CoA. For glu-
16. Because the genetically modified soybeans have the bacterial cogenic amino acids, the carbon skeletons are broken down to
EPSPS enzyme, the plants are resistant to the Roundup® herbi- either pyruvate (which is converted to acetyl-CoA by the pyru-
cide. These plants will be able to synthesize chorismate (and aro- vate dehydrogenase complex) or a citric acid cycle intermediate
matic amino acids) even in the presence of the herbicide. Weeds (which can be converted to phosphoenolpyruvate by the reac-
will not be resistant, so the herbicide will kill the weeds but not tions of gluconeogenesis; phosphoenolpyruvate is the precursor
the soybean plant. of pyruvate and therefore of acetyl-CoA).
18. (a) Collagen contains a high proportion of Gly and Pro resi- 30. The fate of propionyl-CoA produced upon degradation of
dues and relatively few of the other amino acids (Section 5-2). isoleucine is identical to that of propionyl-CoA produced in the
Therefore, it does not provide a good mix of amino acids. oxidation of odd-chain fatty acids (see Fig. 17-7). Propionyl-CoA
(b) Because collagen is a protein, it supplies amino acids is converted to (S )-methylmalonyl-CoA by propionyl-CoA car-
that can be used as metabolic fuels or converted to carbohy- boxylase. A racemase converts the (S )-methylmalonyl-CoA to the
drates, lipids, or nucleotides. Sucrose (glucose and fructose) (R) form. A mutase enzyme converts the (R )-methylmalonyl-CoA
is a metabolic fuel, but its carbons cannot be used to syn- to succinyl-CoA, which enters the citric acid cycle.
thesize amino acids or nucleotides unless a source of amino 32. The missing enzyme is the branched chain a-keto acid
groups is also provided. dehydrogenase (see Fig. 18-11). This enzyme is common to
20. (a) Lysine might regulate its own synthesis by acting as an the catabolic pathways of valine, isoleucine (see Problem 29),
allosteric inhibitor of dihydropicolinate synthase. This en- and leucine (see Problem 31) and explains why the corre-
zyme catalyzes the first unique reaction in a series of eight sponding a-keto acids of these amino acids accumulate. Be-
reactions that lead to lysine. cause the patients are unable to break down branched-chain
(b) Using the same reasoning, methionine might acts as a amino acids, they should consume a diet that contains only
feedback inhibitor for acyltransferase. Methionine might enough of these amino acids to meet the needs of growth and
also regulate the activity of homoserine dehydrogenase, an- development.
other major branch point of the pathway, even though this 34. (a)
enzyme is also involved in threonine biosynthesis. O
(c) Similarly, threonine might act as a feedback inhibitor CH2 C COO
for homoserine kinase and might also inhibit homoserine
dehydrogenase. Phenylpyruvate
22. (a) A 10-fold increase in the K M for APRT results in de-
creased affinity of the enzyme for one of its substrates. The (b) A tetrahydrobiopterin deficiency prevents the conver-
result is the accumulation of adenine, which is oxidized to sion of phenylalanine to tyrosine in the phenylalanine cata-
dihydroxyadenine and forms kidney stones. bolic pathway. Consequently, phenylalanine accumulates
(b) One way to treat this condition is to administer a com- and undergoes transamination to phenylpyruvate, which is
pound that would bind to xanthine dehydrogenase and pre- excreted.
vent adenine from binding. This would prevent the conver- (c) The growing child still requires some phenylalanine for
sion of adenine to dihydroxyadenine. growth. The low-phenylalanine diet should provide enough
phenylalanine for growth but should not exceed amounts
24. Phosphoribosyl pyrophosphate (PRPP) is a reactant in the needed for growth since the excess cannot be metabolized
salvage reactions involving IMP and GMP, so if these reactions due to the lack of the PAH enzyme.
cannot occur, the PRPP that would normally be used in the sal- (d) The artificial sweetener aspartame consists of a methyl-
vage reactions would accumulate. PRPP stimulates amidophos- ated Asp–Phe dipeptide. (The C-terminal carboxyl group is
phoribosyltransferase by feed-forward activation (see Problem 21), methylated.) Aspartame is broken down to Asp, Phe, and
which accelerates the synthesis of purine nucleotides and increases methanol. Since aspartame is a source of phenylalanine,
the concentration of their degradation product, uric acid. patients with PKU should not use this product, and physi-
26. 5-Fluorouracil structurally resembles uracil and competitively cians should advise their patients to check labels carefully
inhibits thymidylate synthase. When the enzyme is inhibited, and to avoid use of this product.
(e) Phenylalanine is the precursor of tyrosine. If the phenyl- glyceraldehyde-3-phosphate dehydrogenase reaction, and its
alanine intake is low, supplemental tyrosine may be needed. production is essential for the continuation of the glycolytic
36. Proteins, a polymeric form of amino acids, could be con- pathway. Despite the presence of oxygen in the red blood cell,
sidered as a storage depot for amino acids, since the proteins can glucose is oxidized anaerobically due to the lack of mitochon-
be degraded to release amino acids for use as metabolic fuels. dria. Two ATP are produced per glucose molecule.
However, proteins have functions other than fuel storage, which 6. (a) The reaction is probably a near-equilibrium reaction be-
is not the case for glycogen and triacylglycerols (although triacyl- cause the reactants and products have the same total number
glycerols also function as thermal insulation in some species). of phosphoanhydride bonds.
38. Glutamate dehydrogenase, glutamine synthetase, and car- (b) In highly active muscle, ATP is rapidly converted to ADP.
bamoyl phosphate synthetase can potentially “mop up” NH14. Adenylate kinase catalyzes the conversion of two ADP to
ATP and AMP as a way to generate additional ATP to power
40. Adding arginine, the product of the argininosuccinase reac-
the actin–myosin contractile mechanism.
tion, would increase flux through the urea cycle.
42. An individual consuming a high-protein diet uses amino 8. When AMP concentrations are high, the energy status of the
acids as metabolic fuels. As the amino acid skeletons are con- cell is low, and the glycolytic pathway is needed to provide ATP
verted to glucogenic or ketogenic compounds, the amino groups for the cell. AMP deaminase acts on the increased concentrations
are disposed of as urea, leading to increased flux through the of AMP to produce ammonium ions. These, along with AMP,
urea cycle. During starvation, proteins (primarily from muscle) stimulate the activities of phosphofructokinase and pyruvate ki-
are degraded to provide precursors for gluconeogenesis. Nitro- nase and increase the activity of the glycolytic pathway as a whole.
gen from these protein-derived amino acids must be eliminated, Factors that influence the activity of adenosine deaminase will
which demands a high level of urea cycle activity. thus also have an indirect effect on the rate of glycolysis. [From
Yoshino, M., and Murakami, K., J. Biol. Chem. 260, 4729–4732
44. (a) GTP (representing a high level of cellular ATP) inhibits
(1985).]
glutamate dehydrogenase to favor glutamate formation.
(b) ADP (a signal for low cellular energy) activates gluta- 10. The lactate dehydrogenase reaction, which reduces pyru-
mate dehydrogenase to favor synthesis of a-ketoglutarate so vate to lactate, occurs with concomitant oxidation of NADH
that citric acid cycle flux can increase. to NAD1. NAD1 serves as a reactant in the glyceraldehyde-3-
(c) NADH inhibits glutamate dehydrogenase to favor glu- phosphate reaction in glycolysis. If pyruvate were the end prod-
tamate formation, since a high level of NADH means that uct of glycolysis, all of the cellular NAD1 would become re-
the cell does not need the citric acid cycle to produce ad- duced to NADH and the glycolytic pathway would grind to a
ditional reduced cofactors. halt for lack of NAD1.
46. (a) H. pylori urease converts urea to NH3 and CO2 (see 12. Plasma alanine would be elevated as well. The increased
page 494). The ammonia has a pK of 9.25, so it combines plasma concentrations of pyruvate would accelerate the opera-
with protons to produce NH14. The resulting decrease in tion of the glucose–alanine cycle. Pyruvate is taken up by the
hydrogen ion concentration helps the bacteria maintain an muscle and transaminated to alanine, then released to the circu-
intracellular pH higher than the environmental pH. lation to be taken up by the liver. Since plasma pyruvate levels
(b) Urease on the cell surface increases the pH of the fluid are elevated, alanine levels would also be elevated.
surrounding the cell, creating a more hospitable microenvi- 14. Increased levels of citrulline indicate that the cytosolic ar-
ronment for bacterial growth. gininosuccinate synthetase reaction in the urea cycle (see Section
18-5) is not occurring normally. This reaction requires aspar-
tate as a reactant in addition to citrulline. The accumulation of
citrulline may occur because there is a shortage of aspartate. A
2. Glucose-6-phosphate is the product of the hexokinase reac- deficiency of pyruvate carboxylase results in a decreased concen-
tion and is produced when glucose is transported into cells. G6P tration of oxaloacetate that could otherwise be transaminated to
can then continue along the pathway of glycolysis to produce aspartate. Hyperammonemia is the result of urea cycle impair-
ATP and biosynthetic intermediates. G6P can be reversibly con- ment, since ammonia is not being converted to urea for excre-
verted to glucose-1-phosphate for incorporation into glycogen. tion by the kidneys. [From Coude, F. X., Ogier, H., Marsac, C.,
Glycogen degradation produces glucose-1-phosphate, which is Munnich, A., Charpentier, C., and Saudubray, J. M., Pediatrics
isomerized to glucose-6-phosphate. G6P is also the product of 68, 914 (1981).]
gluconeogenesis. Glucose-6-phosphatase catalyzes the removal 16. Because glucokinase is not saturated at physiological
of the phosphate group to produce glucose, which can leave the glucose concentrations, it can respond to changes in glucose
cell. Glucose-6-phosphate can also enter the pentose phosphate availability with an increase or decrease in reaction velocity.
pathway to produce NADPH and ribose. Consequently, the entry of glucose into glycolysis and subse-
4. Glucose enters the red blood cell via specific transport quent metabolic pathways depends on the glucose concentra-
proteins and undergoes glycolysis to produce pyruvate. The tion. Because hexokinase is saturated at physiological glucose
next step is the conversion of pyruvate to lactate with con- concentrations, its rate does not change with changes in glu-
comitant production of NAD1. The NAD1 is used in the cose concentration.
18. Insulin stimulates uptake of glucose via GLUT4 receptors active muscles. In this way, the muscles do not have to rely
in adipocytes. Glucose is converted to glycerol-3-phosphate via on stored glycogen as a fuel source.
the enzymes of the glycolytic pathway. The glycerol-3-phosphate 26. (a) PAH is an oligomer with a subunit size of about 49,000
is required for the backbone of the triacylglycerol molecule. daltons. The subunits dissociate upon treatment with SDS,
20. Ingesting large amounts of glucose stimulates the b cells so one band at the low molecular weight is observed. The
of the pancreas to release insulin, which causes liver and muscle subunits are identical, since there is a single band in this
cells to use the glucose to synthesize glycogen and causes adipose lane. If PAH is subjected to electrophoresis under nonde-
tissue to synthesize fatty acids. Insulin also inhibits the break- naturing conditions, a single band with a molecular weight
down of metabolic fuels. The body is in a state of resting and slightly less than 100,000 daltons is observed. Since this is
digestion and is not prepared for running. double the molecular weight of the monomer, it can be con-
22. Phosphorylation of glycogen synthase by GSK3 inactivates cluded that the PAH consists of a dimer under nondenatur-
the enzyme so that glycogen synthesis does not occur. But when ing conditions. Preincubation of PAH with phenylalanine
insulin activates protein kinase B, the kinase phosphorylates results in a band that is four times the molecular weight of
GSK3. Phosphorylated GSK3 is inactive and unable to phos- the monomer. Therefore, PAH is converted from a dimer to
phorylate glycogen synthase. In the dephosphorylated state gly- a tetramer in the presence of phenylalanine.
cogen synthase is active and glycogen synthesis can occur. (b) PAH is a dimer that can be converted to a tetramer at
high concentrations of phenylalanine. The sigmoidal curve
24. (a) Normally, glucagon binds to cell-surface receptors on the indicates that the binding of the substrate is cooperative:
liver, stimulating adenylate cyclase to produce cAMP and The binding of one substrate molecule facilitates the bind-
activate protein kinase A, which subsequently activates gly- ing of subsequent substrate molecules. Thus, PAH is an
cogen phosphorylase via phosphorylation. Glycogen phos- allosteric enzyme and likely is affected by allosteric modula-
phorylase catalyzes the degradation of glycogen to glucose, tors that stimulate or inhibit the enzyme and thus control
which is released into the bloodstream. Blood glucose con- the degradation rate of phenylalanine.
centrations should rise shortly after an intravenous injection (c) As discussed above, preincubation with phenylalanine
of glucagon. Glycogen degradation in the patient’s liver thus converts PAH from the dimer to a tetrameric form. It is
appears to be normal. possible that the tetrameric form has a greater affinity for
(b) Glycogen metabolism in the liver appears to be normal, substrate than the dimeric form, which would explain the
since glycogen content is normal and the patient’s response increase in velocity when the enzyme is preincubated with
to the glucagon test is normal. However, muscle glycogen is Phe. The dimer is the T form, which has a low affinity for
elevated, which indicates a defect in muscle glycogen me- the substrate, and the tetramer is the R form, which has a
tabolism. Most likely glycogen synthesis is normal, since high affinity for the substrate.
the biochemical structure of the glycogen is normal. A defi- (d) Insulin inhibits the activity of PAH, whereas glucagon
ciency in the muscle glycogen phosphorylase enzyme is the stimulates the activity of the enzyme. Because PAH is phos-
most likely explanation. phorylated in the presence of glucagon, it’s likely that glu-
(c) Blood alanine concentrations normally increase as part cagon exerts its effects by activating protein kinase A, which
of the glucose–alanine cycle. Glucose-6-phosphate, the in turn phosphorylates the enzyme. The effects of glucagon
product of glycogenolysis, enters glycolysis and produces and Phe appear to be synergistic, since the enzyme is more
pyruvate. Pyruvate undergoes a transamination reaction active when glucagon and Phe are combined than when ei-
to form alanine, which is released from the muscle. Ala- ther stimulant is used alone. Since glucagon concentrations
nine then enters the liver, where the transamination reac- are high when blood sugar is low, it’s possible that PAH
tion takes place in reverse to re-form pyruvate. Pyruvate can activation occurs in these circumstances to stimulate the
then enter gluconeogenesis, the resulting glucose product is phenylalanine degradation pathway to produce fumarate,
released, and the cycle begins again. But the patient’s tissues which can enter gluconeogenesis. [From DiLella, A. G.,
cannot perform the glucose–alanine cycle because his mus- Marvit, J., and Woo, S. L. C., (1987) The Molecular Genet-
cles are unable to produce glucose-6-phosphate. Instead, the ics of Phenylketonuria in Amino Acids in Health and Disease:
muscles take up alanine and use it as a fuel. Thus, plasma New Perspectives, Alan R. Liss, Inc., pp. 553–564.]
alanine levels in the patient decrease rather than increase.
(d) Blood glucose concentrations are regulated by pancreatic 28. Several days into a fast, muscle and liver glycogen have been
hormones acting on the liver to stimulate glycogen synthesis depleted. In the absence of dietary glucose, the main source of
or degradation, whatever is appropriate. Since the patient’s endogenous glucose is gluconeogenesis. Citric acid cycle inter-
liver enzymes appear to function normally, his blood glu- mediates are used to synthesize oxaloacetate and then pyruvate,
cose concentration is properly regulated and he is neither which enters the gluconeogenic pathway. Catalytic amounts of
hypo- nor hyperglycemic. citric acid cycle intermediates are required for proper function-
(e) If the patient ingests glucose or fructose, blood sugar ing of the cycle, so when these intermediates are diverted to glu-
concentrations can be maintained at a high level. The mus- coneogenesis, the citric acid cycle cannot function properly.
cles will thus be able to take up glucose or fructose and oxi- 30. Regular exercise maintains muscle mass so that muscle pro-
dize these sugars via glycolysis to yield the ATP required of teins are less likely to be broken down to provide amino acids
as fuel, and the body uses its stored fat instead. Inactivity while glucose to be brought into cells via the GLUT4 receptor. In
dieting may promote loss of muscle mass instead of fat. the absence of phosphatase activity to turn off the signaling
32. (a) The cytochrome c content is high because of the large pathway, the action of insulin is potentiated, and a normal
number of mitochondria that allow brown adipose tissue to physiological effect is observed with a lower concentration
oxidize metabolic fuels aerobically, funneling the reduced of the hormone.
coenzymes through the electron transport chain. Uncou- (b) Injecting the mice with insulin would produce greater
pling oxidative phosphorylation permits the energy of elec- phosphorylation of the insulin receptor and possibly IRS-1,
tron transport to be dissipated as heat (see Box 15-A). since there is no phosphatase enzyme to remove the phos-
(b) When subjects were exposed to cold, uptake of the labeled phate groups.
glucose into brown adipose tissue increased to provide reduced (c) Compounds that inhibit the activity of the PTP-1B
coenzymes for electron transport and thermogenesis. phosphatase might be effective in treating diabetes. A con-
cern would be the specificity of these compounds, since un-
34. Endogenous fatty acid synthesis is required when dietary
predictable side effects would result if the drug inhibited
fatty acid intake is insufficient. Stimulation of acetyl-CoA car-
other cellular phosphatases or if PTP-1B has other cellular
boxylase ensures that the cell will have enough fatty acids in
targets unrelated to insulin signaling.
the absence of dietary lipids (although essential fatty acids will
still be lacking under these circumstances). During starvation 40. The bypass surgery eliminates a portion of the stomach and
(and untreated diabetes, which is similar to the starved state), the small intestine, which are normally sources of hormones that
body tissues do not have the resources to synthesize fatty acids, regulate fuel metabolism and insulin sensitivity. The surgery
so acetyl-CoA carboxylase enzymes are inhibited. In the starved apparently alters hormonal signaling enough to restore insulin
state, fatty acids are mobilized to provide fuel to body tissues. sensitivity.
36. (a) Acetate is converted to acetyl-CoA, which serves as a 42. Metformin activates AMPK and, in so doing, promotes the
substrate for acetyl-CoA carboxylase and is converted to phosphorylation of acetyl-CoA carboxylase, the enzyme that
malonyl-CoA. Fatty acid synthase normally acts on malonyl- catalyzes the first committed step of lipid synthesis (see Section
CoA for incorporation into fatty acids, but in the presence 17-2). Phosphorylation inactivates acetyl-CoA carboxylase, which
of the inhibitor C75, fatty acid synthesis does not occur. decreases the concentration of malonyl-CoA and inhibits lipid
Therefore, radioactive malonate accumulates, and virtually synthesis. The decrease in malonyl-CoA relieves the inhibition of
no label appears in fatty acids. fatty acid transport and allows b oxidation to occur. The result is
(b) C75 causes hypothalamic levels of NPY to decrease. a decrease in the concentration of the plasma triacylglycerols that
This decreases appetite, which leads to weight loss. In this predispose the patient to atherosclerosis. Phosphorylation of pro-
manner, C75 fools the body into thinking that it is in the tein kinase B by AMPK would increase translocation of GLUT4
fed state, when in fact it is being starved. transporters to the plasma membrane. In this manner, AMPK is
(c) Acetyl-CoA carboxylase (ACC) catalyzes the reaction acting as insulin does, promoting the uptake of glucose into muscle
that converts acetyl-CoA to malonyl-CoA. In the presence and adipose tissue. Stimulation of AMPK by metformin benefits
of the ACC inhibitor, malonyl-CoA cannot be produced the patient with metabolic syndrome, who is resistant to insulin,
and hepatic malonyl-CoA levels would decrease. Subse- because AMPK triggers the same responses as insulin signaling.
quent administration of C75 would have no effect on the [From Hardie, D. G., FEBS Lett. 582, 81–89 (2008).]
ACC inhibitor–treated animals, because C75, a fatty acid
synthase inhibitor, acts downstream of ACC. If malonyl-
CoA inhibits feeding, the ACC inhibitor–treated and C75- Chapter 20 Solutions
treated mice would have lower levels of malonyl-CoA, and 2. (a) In all the variants, a neutral or negatively charged amino
feeding would not be inhibited, that is, the mice would eat acid has been replaced with a positively charged amino acid
normally. These experiments were carried out and this is in (Lys or Arg). The 11 abbreviation means that one additional
fact what occurred. positive charge was introduced, a 12 indicates the introduc-
(d) When malonyl-CoA accumulates, long-chain fatty acyl- tion of two additional positive charges, and so on. DNA is
CoA molecules also accumulate in the cytosol. Malonyl-CoA negatively charged because of its phosphodiester backbone.
inhibits carnitine acyltransferase, which prevents transloca- It’s reasonable to hypothesize that an enzyme with an in-
tion of fatty acyl-CoAs into the mitochondrial matrix for creased number of positive charges might bind more effec-
b oxidation. It is possible that long-chain fatty acyl-CoAs tively to the negatively charged DNA.
serve as signaling molecules to begin the pathway that sup- (b) Intact, double-stranded DNA has a lower absorbance at
presses appetite. [From Loftus, T. M., Jaworksy, D. E., Gre- 260 nm than does single-stranded DNA. An increase in ab-
hywot, G. L., Townsend, C. A., Ronnett, G. V., Lane, M. sorbance at 260 nm over time is a useful measurement of the
D., and Kuhajda, F. P., Science 288, 2379–2381 (2000).] catalytic activity of DNase, since the products of the reaction
38. (a) In the absence of the phosphatase, the intracellular do- are short, single-stranded oligonucleotides.
main of the insulin receptor remains phosphorylated longer. (c) All of the variants have lower KM values than the wild-
The IRS-1 substrate may also retain its phosphate group, type DNase, indicating that the DNase variants bind more
enabling it to stimulate the intracellular processes that allow tightly to the DNA substrate than does the wild-type enzyme.
The tighter binding is no doubt due to the additional posi- Polymerase a can be less processive because it synthesizes only a
tive charges on the variants, which allow the formation of ion short DNA segment at the start of each Okazaki fragment.
pairs between the variant enzymes and the DNA. There seems 12. (a) The positively charged Mg21 ion could decrease the af-
to be a rough correlation between the number of positively finity of the DNA’s 39 O atom for H, thereby increasing the
charged residues and the K M value: An increase in the num- nucleophilicity of the 39 O atom (making it behave more
ber of positively charged residues results in a lower K M value, like an O2 ion). The Mg21 could also help neutralize the
which indicates tighter binding. However, the Vmax values negative charge on the incoming nucleotide.
must also be assessed. All of the variants have a higher Vmax (b) The Mg21 could stabilize the negative charge that devel-
value than the wild-type enzyme, indicating that the tighter ops on the pentacovalent transition state.
binding leads to greater catalytic activity. The replacement of
three amino acids yields a variant enzyme in which the K M (DNA)
and Vmax values are optimized. When four or five amino acids C3
are replaced, the velocity is lower than when only three amino O O O O
acids are replaced. Since the KM value for the 14 and 15 vari-
O P O P O P O C5 (NTP)
ants is also generally smaller, it is possible that the enzyme and
substrate bind to each other so tightly that catalytic efficiency
O O O
is compromised.
(d) The plasmid DNA normally exists in a supercoiled
14. The enzyme most likely detects the geometry of the poly-
circle, as shown in the control lane. The wild-type DNase
nucleotide chain as it shifts from the wide and shallow A-form
can nick the DNA on one strand to convert the plasmid
characteristic of an RNA helix to the narrower and steeper
to the relaxed circular DNA. The 13 mutant is the best of
B-form of DNA.
the three in its ability to cleave supercoiled DNA. All three
mutants are able to produce linear DNA, whereas the wild- 16. The DNase can create a nick (a break in one strand). Then
type DNase does not. This indicates that the variants can cut the exonuclease activity of DNA polymerase I can remove nu-
both strands, whereas the wild-type enzyme cuts only one cleotides on the 59 side of the nick. At the same time, the poly-
strand. merase active site can add radioactive deoxynucleotides to the
(e) All of the mutants have a greater nicking activity than the 39 side of the nick. The removal and replacement of nucleotides
wild-type for low- and high-molecular-weight DNA at low translates the nick in the 59 S 39 direction. DNA ligase can then
concentrations. The 12 mutant is especially active under seal the gap between the original DNA and the newly synthe-
these conditions and would be a good choice to use for a sized radioactive segment.
lupus patient. The 11 and 12 mutants can degrade low- 18. Eukaryotic DNA ligases use ATP, and bacterial ligases use
molecular-weight DNA at a high DNA concentration better NAD1, as a cofactor in the reaction. A drug that inhibited only
than the wild-type enzyme, but the 13 and 14 mutants NAD1-dependent ligases would be an effective drug to treat
are not as active. Not all of the data are given, so it is dif- bacterial diseases without harming the host. Bacteria unable to
ficult to make conclusions about the ability of the mutants carry out the ligase reaction cannot complete DNA replication
to degrade high-molecular-weight DNA, but the 12 mu- and cannot survive.
tant is clearly more effective than the wild-type DNase and 20. Because there is a strong link between telomerase activity
would be a good choice to use for a CF patient. [From Pan, and aging, it’s possible that cancer cells might overexpress the
C.Q., and Lazarus, R.A., J. Biol. Chem. 273, 11701–11708 telomerase enzyme. Increased telomerase activity could contrib-
(1998).] ute to the growth of cancer cells. If the G quartet acts as a nega-
4. The origin is more likely to be richer in A:T base pairs, since tive regulator of telomerase activity, inducing its formation could
these experience fewer stacking interactions and are more easily inhibit the telomerase and inhibit growth of cancer cells.
separated, which would allow easier access for the replication 22. Both of these proteins bind single strands of DNA: Replication
proteins. protein A functions as an SSB protein during DNA replication, and
6. Helicase would unwind the parental DNA, exposing exten- POT1 binds the single-stranded DNA extension of a telomere.
sive segments of single-stranded DNA. Without a polymerase to
24. NH2
convert these template strands into double-stranded DNA, the
single strands would be susceptible to endonucleases, especially H O N
N
if the supply of replication protein A was limited. N H
N N
8. The drug would inhibit DNA synthesis because the poly- O N
merization reaction is accompanied by the release and hydrolysis N N N
of inorganic pyrophosphate (PPi ; see Fig. 20-9). Failure to hy- H
drolyze the PPi would remove the thermodynamic driving force H Adenine
for the overall process. 8-Oxoguanine
10. DNA polymerase ´ would need to have greater proces- 26. The structures of the intercalating agents resemble A:T
sivity because it synthesizes the leading strand continuously. and G:C base pairs, which explains why they are able to slip in
between the stacked base pairs of DNA. This has the effect of No, since G normally base pairs with C, a mutation does
creating what appears to the replication machinery as an “extra” not result. A mutation occurs only when O 6-methylguanine
base pair. An extra base incorporated into the newly synthesized pairs with T. [From Leonard, G.A., Thomson, J., Watson,
DNA may eventually lead to a frameshift mutation (in which W.P, and Brown, T., Proc. Natl. Acad. Sci. 87, 9573–9576
the additional nucleotide causes the translation apparatus to read (1990).]
a different set of successive three-nucleotide codons). 36. The thymine dimers form when DNA is exposed to ultra-
28. The ultraviolet light is an additional precaution against con- violet light, so the enzymes that repair the damage are activated
tamination. Ultraviolet light causes the formation of thymine by the same stimulus that produced the damage.
dimers in bacterial DNA. High levels of exposure to ultraviolet 38. The amino acid code is degenerate so that several codons
light would overwhelm the bacteria’s ability to repair the dimers, may specify the same amino acid. For example, the codons GCA,
which would result in the eventual death of the bacteria. Thus, GCC, GCG, and GCU all code for alanine. So if a mutation oc-
the ultraviolet light helps keep the hood space free from bacteria curred at the third position (the 39 end) of the codon, alanine
that could contaminate the cultured cells. would still be incorporated into the protein.
30. (a) O 40. (a) The polymerases that lack 39 S 59 exonuclease activity
N have higher error rates than polymerases that contain the
NH
exonuclease activity.
N O (b) a, once every 6250 bases; b, once every 1493 bases; d,
N
H once every 100,000 bases; ´, once every 100,000 bases; h,
Xanthine once every 29 bases.
(b) Since cytosine also pairs with guanine, the deamination (c) Polymerase h and HIV RT incorporate the correct base
of guanine to xanthine does not induce a mutation. with approximately the same efficiency (for example, 420,
760, and 800 mM ? min21 3 103). However, polymerase
32. (a) NH2 O h incorporates mispaired bases much more efficiently than
H3C H3C HIV RT does (22, 1.6, and 8.7 vs. 0.07 mM ? min21 3 103).
N NH These results indicate that the high error rate of polymerase
h results from its ability to incorporate the wrong base rather
N O N O than its inability to incorporate the correct base.
H H
(d) Overexpression of an error-prone DNA polymerase
5-Methylcytosine Thymine
similar to polymerase h would increase the mutation rate.
(b) Thymine [From Matsuda, T., Bebenek, K., Masutani, C,. Hanaoka,
(c) A C:G to T:A transition occurs. F., and Kunkel, T.A., Nature 404, 1011–1013 (2000).]
(d) The cell cannot repair the deaminated 5-methylcytosine
since the resulting base is indistinguishable from thymine 42. A solution of 0.5 M NaCl effectively dissociates the positively
that occurs normally. charged histone proteins from the negatively charged DNA by
disrupting the ionic bonds that hold these two chromatin com-
34. (a) CH3 O CH3 ponents together. The charged sodium and chloride ions can form
O substitute ionic interactions with the histone protein and DNA.
N H N 44. The high degree of sequence conservation from cows to peas
N
N indicates that the sequence of the histone H4 protein is so vital
N H O to its function that amino acid substitutions, especially those
N
N that are nonconservative in nature, would disrupt the function
H of the protein and thus cannot be tolerated.
O 6-Methylguanine Thymine 46. DNA methylation is important in the process of imprint-
ing, in which DNA expression depends on parental origin. In
The methylation of guanine causes a G:C to A:T transition.
the absence of DNA methylation, imprinting cannot take place.
H DNA methylation is important in gene expression during em-
(b)
bryonic development, and if the DNA cannot be methylated,
H N
the embryos do not develop properly and die before birth.
H3C N
O H
N Chapter 21 Solutions
N O 2. Organizing genes with related functions in an operon means
N
H that the genes can be turned on and off together. Furthermore,
N N N because the genes are transcribed as a unit, the products can be
Protonated cytosine
H generated in roughly equivalent concentrations and in the same
O 6-Methylguanine region of the cell (where the ribosome is located). Consequently,
only one signal is needed to activate or deactivate the metabolic (d) The operon is on. In the absence of glucose, cAMP levels
function carried out by the products of the operon’s genes. A rise. cAMP binds to CAP, which can bind to the operon to
eukaryotic cell can coordinate the transcription of physically stimulate transcription. In the presence of lactose, allolactose
separated but functionally related genes if they are share a set of is formed and binds to the repressor, removing the repressor
enhancers, silencers, activators, or repressors. from the operator. The genes of the operon are expressed and
4. The protein must identify a gene to be expressed and must the bacterial cell can use lactose as a food source.
activate the transcription machinery so that the DNA can be 16. If the repressor can bind to the operator, the genes of the
transcribed to RNA. The gene is identified by the ability of the operon are not expressed. When lactose is added to the growth
protein to bind specific DNA sequences associated with the gene. medium, it cannot bind to the repressor. The repressor remains
The resulting distortion in the DNA can then be recognized in bound to the DNA and the genes of the operon are not ex-
a sequence-independent manner by transcription factors that as- pressed. This is an example of a noninducible mutation, because
semble at the site in order to initiate RNA synthesis. adding lactose does not result in gene expression.
6. RNA polymerase I transcribes rRNA genes. Although there 18. When tryptophan is plentiful, there is “extra” tryptophan
are multiple copies of these genes, there are only a few types of available to bind to the repressor. With tryptophan bound, the
rRNA molecules and the cell requires them in equal amounts. repressor binds to the promoter and prevents RNA polymerase
Therefore, rRNA gene transcription does not need to be selec- from binding. The genes of the trp operon are not expressed
tive, and one promoter suffices. In contrast, the protein-coding because tryptophan biosynthetic enzymes are not needed when
genes transcribed by RNA polymerase II must be expressed at tryptophan is plentiful. But when the concentration of trypto-
different times and at different levels. The regulation of tran- phan drops, tryptophan dissociates from the repressor, causing
scription of these genes is more elaborate, requiring different a conformational change that results in the dissociation of the
promoter sequences that can potentially interact with different repressor from the promoter. RNA polymerase can now bind to
sets of transcription factors. the promoter, and the genes encoding the enzymes for the tryp-
8. 11 tophan synthetic pathway can now be expressed.
GAGCATATAAGGTGAGGTAGGATCAGTTGCTCCTCACATTT 20. The 59 end of any prokaryotic RNAs ending in A will be
labeled. The 59 ends of RNA transcripts have 59 triphosphate
TATA box Inr groups containing the labeled g-phosphate. The phosphodiester
10. The other product is methylamine. bonds in the RNA will not be labeled because these phosphate
O O groups come from the a-phosphates of the nucleoside triphos-
H H phates (the g-phosphates are released as pyrophosphate).
N CH C N CH C
CH2 CH2 H2N CH3
*pppA 1 pppN z y *pppApN 1 PPi
Methylamine
CH2 H2O CH2 22. The incorporation of cordycepin into a growing RNA
chain provides evidence that transcription occurs in the 59 S 39
CH2 CH2
direction. Once incorporated, transcription halts because of the
Arginine NH Citrulline NH lack of a 39 OH group. If transcription occurred in the 39 S 59
C N CH3 C O direction, cordycepin would not be incorporated into the growing
H RNA chain and would not be able to halt RNA synthesis.
NH2 NH2
24. The prokaryotic RNA polymerase is a five-subunit enzyme
12. The presence of the s factor decreases the affinity of RNA with a subunit composition of a2bb9vs and is the only RNA
polymerase for DNA. This allows the polymerase–s factor com- polymerase in prokaryotic cells. In contrast, eukaryotic cells have
plex to quickly scan long segments of DNA for promoter se- three different RNA polymerase enzymes that differ in struc-
quences. Once transcription has begun, the s factor is no longer ture from the prokaryotic polymerase. Thus, rifampicin can
needed and dissociates from the enzyme. Now the RNA poly- be effectively used as an antibiotic to treat bacterial diseases in
merase has a high affinity for DNA, which helps keep it associ- eukaryotic organisms because the drug is able to block transcrip-
ated with the template during transcription. tion in the disease-causing prokaryotic cells without inhibiting
14. (a) When glucose is present, cAMP concentration is low. transcription in the eukaryotic organism.
CAP cannot bind to the operon in the absence of cAMP, 26. (a) mRNA(n residues) 1 Pi S NDP 1 mRNA(n 2 1 residues)
so the operon is off. Glucose is the preferred substrate, so (b) The reverse of the phosphorolysis reaction is an RNA
lactose is not used as long as glucose is present. polymerization reaction. PNPase uses an NDP substrate to
(b) The operon is off, both because glucose is present and extend the RNA by one nucleotide residue and releases Pi.
CAP is not bound [see part (a)] and because lactose is ab- RNA polymerase uses an NTP substrate and releases PPi.
sent and the repressor is bound to the operator, preventing (c) High processivity would allow the exonuclease to rap-
RNA polymerase from binding. idly degrade mRNA molecules. This would be important
(c) CAP binds cAMP and can bind to the operon, but the in cases where the gene product was no longer needed. An
operon remains off because the repressor is also bound in mRNA that was degraded more slowly could potentially
the absence of lactose. continue to be translated.
28. The C-terminal domain (CTD) is phosphorylated when RNA [From Fabre, E., Dujon, B., and Richard, G.-F., Nuc. Acids
polymerase transitions from initiation mode to elongation mode. If Res. 30, 3540–3547 (2002).]
the CTD is missing, it cannot be phosphorylated, and elongation 36. The capped mRNA has a 59–59 triphosphate linkage, which
cannot occur. Transcripts that do manage to clear the promoter in is not recognized by exonucleases (which normally cleave 59–39
the absence of a phosphorylated domain will not be properly pro- phosphodiester bonds). Capping must occur as soon as the 59
cessed, since the phosphorylated CTD serves as a docking site for end of the mRNA emerges from the RNA polymerase so that the
enzymes involved in cotranscriptional modification. message will not be degraded by exonucleases.
30. (a) 59…NNAAICICCINNNNCCIICICUUUUUUNNN…39 38. (a) The active site of poly(A) polymerase is narrower be-
(b) N cause it does not need to accommodate a template strand.
N N (b) Poly(A) polymerase binds only ATP, whereas other RNA
N C polymerases bind ATP, CTP, GTP, and UTP.
I C 40. Bacterial genes contain no introns, so the cells, which lack
C I splicing machinery, cannot express eukaryotic genes containing in-
C I trons and exons. Mature eukaryotic mRNA, which has already been
I C spliced, contains only exons, which, after they have been converted
C I back to DNA, can be transcribed and translated by the bacteria.
I C 42. The mRNA from a gene may be alternatively spliced to
A U yield several different types of proteins. This increases the diver-
A U sity of the proteins produced by the cell without a correspond-
5 NN UUUU 3 ingly large number of genes.
The RNA terminator hairpin is much less stable when I is 44.
S NH 2
substituted for G because I:C base pairs have only two hydro-
gen bonds whereas G:C base pairs have three. The stability of HN N
the RNA hairpin is important in termination. When ITP is
substituted for GTP in culture, the hairpin might not form; as S
O N N
a consequence, RNA transcripts will not terminate properly.
32. The b,g-imido nucleoside triphosphate can be used as a Ribose Ribose
substrate by RNA polymerase, since it is the phosphoanhydride 4-Thiouridine 2-Thiocytidine
bond closest to the ribose that is cleaved when the nucleotide
is incorporated into the growing RNA transcript. Elongation is 46. The primary structure of a protein refers to its sequence of
therefore not affected by the presence of the modified nucleotide. amino acids; in the RNase P RNA this corresponds to the se-
Rho-dependent termination is affected because Rho is a helicase quence of 417 nucleotides. Secondary structure in proteins refers
that uses the energy of ATP hydrolysis to pry apart the DNA– to regular, repeating structural motifs such as a helices and b
RNA hybrid. The b,g-imido nucleoside triphosphate cannot sheets. In the ribozyme, secondary structure refers to the base-
be hydrolyzed to its corresponding diphosphate and inorganic paired stem and loop structures. Tertiary structure in proteins
phosphate, so Rho-dependent termination cannot occur. refers to the overall three-dimensional shape of the macromol-
34. (a) CAG codes for Gln. The resulting protein would con- ecule; similarly for the ribozyme, the tertiary structure refers to
tain a series of extra Gln residues. These polar residues the three-dimensional shape of the molecule.
would most likely be located on the protein surface but
could interfere with protein folding, stability, interactions
with other proteins, and catalytic activity. Chapter 22 Solutions
(b) The longer transcripts could be due to transcription ini- 2. Because the genetic code is degenerate, a mutation that alters a
tiating upstream of the normal site or failing to stop at the codon may not alter the amino acid encoded by that codon. This
usual termination point. Longer mRNA molecules could is particularly true for mutations at the third codon position.
also result from the addition of an abnormally long poly(A) Changes at the first or second position almost always change the
tail or the failure to undergo splicing. encoded amino acid, but the new amino acid may be chemically
(c) G C similar to the old one (for example, Val S Ala).
A A 4.
C G H
G C
A A N O H N N
C G
G C N N H N N
A A
C G N N
CAG CAG I:A
6. (a) The RNA-binding site of the synthetase is necessary for in the A site. Changing one of these two rRNA residues would
binding tRNA for aminoacylation and for binding RNA inactivate the translational proofreading mechanism by elimi-
during splicing. nating the specific hydrogen bonding between the rRNA and
(b) Because of their long evolutionary history, aminoacyl– the mRNA. As a result, incorrectly paired tRNAs could not be
tRNA synthetases have had many opportunities to diversify distinguished from correctly paired tRNAs, and the error rate of
in structure and in function in order to assume additional translation would increase.
roles in the cell. 22. The ribosome minimizes the chances of misreading the
8. (a) The enzyme itself must act as a template to direct the ad- A-site codon by binding the A-site tRNA with lower affinity. If
dition of two C residues followed by one A residue. the tRNA bound with higher affinity, it would be less likely to
(b) The enzyme must recognize only ATP and CTP as sub- dissociate as part of the proofreading mechanism.
strates, excluding GTP, UTP, and all dNTPs. 24. If EF-Tu formed a complex with fMet–tRNA fMet, the
(c) In the two-domain enzyme, one polymerase adds the two fMet–tRNA could be delivered to the ribosomal A site when
C residues, and the other domain then adds the terminal A a Met codon was positioned there. However, transpeptidation
residue. could not occur because the amino group of fMet is blocked
10. In order for a cell to incorporate a nonstandard amino acid by the formyl group. Polypeptide synthesis would be halted
into a polypeptide, the amino acid must first be attached to a until the fMet–tRNA fMet was replaced by Met–tRNAMet in the
tRNA corresponding to one of the 20 standard amino acids. A site.
The aminoacyl–tRNA can then bind to the ribosome and its 26. (a) Translation begins at the first AUG codon (ATG in the
amino acid can be incorporated into the growing polypeptide DNA). The polypeptide sequence is Met–Val–His–Leu–
at positions corresponding to the codon for the standard amino Thr.
acid. The failure of cells to synthesize norleucine-containing (b) The mutated sequence has a T residue inserted in the
peptides most likely reflects the inability of LeuRS to effi- second codon. This is a frameshift mutation, so all codons
ciently attach norleucine to tRNALeu. A mutant LeuRS, which following that point will be altered. The polypeptide se-
presumably lacks the proofreading activity of the wild-type quence is Met–Val–Ala–Ser–Asp.
LeuRS, was able to produce norleucine–tRNALeu, and the 28. The number of phosphoanhydride bonds (about 30 kJ ?
cells’ ribosomes used this aminoacylated tRNA to translate mol21 each) that are cleaved in order to synthesize a 20-res-
Leu codons. idue polypeptide can be calculated as follows (the relevant
12. The assembly of functional ribosomes requires equal amounts ATP- or GTP-hydrolyzing proteins are indicated in paren-
of the rRNA molecules. Therefore, it is advantageous for the cell theses):
to synthesize the rRNAs all at once. Aminoacylation (AARS) 2 3 20 ATP
14. Ribosomal inactivating proteins catalyze the removal of ad- Translation initiation (IF-2) 1 GTP
enine residues from ribosomal RNA. This is analogous to the Positioning of each aminoacyl–tRNA (EF-Tu) 19 GTP
removal of a side chain from an amino acid residue in a protein.
Translocation after each transpeptidation (EF-G) 19 GTP
Like proteins, ribosomal RNAs have specific residues that are
Termination (RF-3) 1 GTP
essential to their function; removing these residues causes loss
of activity. Total: 80 ATP equivalents
16. The peptidyl transferase activity lies entirely within the Thus, approximately 80 3 30 kJ ? mol21, or 2400 kJ, is required.
23S rRNA; that is, 23rRNA is a ribozyme. The proteins might In a cell, proofreading during aminoacylation and during trans-
be necessary to assist the 23S rRNA in forming the necessary lation requires the hydrolysis of additional phosphoanhydride
three-dimensional structure required for catalytic activity, just bonds, making the cost of accurately synthesizing the 20-residue
as the proper conformation is required for protein enzymes. polypeptide greater than 2400 kJ ? mol21.
Extremely strong intermolecular interactions between the
proteins and the rRNA confirm the importance of the pro- 30. If a peptidyl–tRNA dissociates from the ribosome during
teins and explain why the extraction process failed to remove translation, the hydrolase releases the peptide from the tRNA.
them. Because peptide synthesis is prematurely terminated, the poly-
peptide is likely to be nonfunctional, and its amino acids must
18. S1 helps to maintain mRNA in the single-stranded state be recycled. Similarly, the tRNA, once released from the peptidyl
and prevents it from forming a double-stranded structure that group, can be reused. The essential nature of the peptidyl–tRNA
would block initiation of translation because the initiator tRNA hydrolase suggests that ribosomes that have initiated translation
would be unable to bind. sometimes stop translating before reaching a stop codon.
20. In 16S rRNA, A1492 and A1493 act as a sensor to distin- 32. (a) Transpeptidation involves the nucleophilic attack of the
guish correctly and incorrectly paired codons and anticodons. amino group of the aminoacyl–tRNA on the carbonyl car-
tRNA binding triggers a conformational change in the rRNA bon of the peptidyl–tRNA (see Fig. 22-15). The higher the
that allows A1492 and A1493 to form hydrogen bonds with an pH, the more nucleophilic the amino group (the less likely
mRNA that has correctly base paired with a tRNA anticodon it is to be protonated).
(b) of longer-than-normal polypeptides. These proteins might

NH not fold properly or might not be catalytically active, which
Peptidyl–tRNA would interfere with normal cellular metabolism. The ability
CHR of the oxazolidinone to promote frameshifting would result
O in polypeptides with garbled amino acid sequences, which
C O tRNA
would be nonfunctional and potentially toxic to the cell.
H N H (h) No; the oxazolidinone affects translational accuracy,
which is primarily a function of the 30S ribosomal sub-
CHR unit, the location of the binding sites for mRNA and the
Aminoacyl–tRNA tRNA anticodon loop. A binding site near the peptidyl
O C
transferase site would be more consistent with an effect
O on peptide bond formation. Presumably, communication
between the 50S and 30S subunits allows binding at one
tRNA site to influence events at another site. [From Thompson,
J., O’Connor, M., Mills, J.A., and Dahlberg, A.E., J. Mol.
(c) NH2 Biol. 322, 273–279 (2002).
36. Protein folding is driven by the hydrophobic effect (see Sec-
HN N
tion 4-3), which directs nonpolar side chains to the interior of
the folded protein because these side chains do not interact fa-
N N vorably with water. The derivatized protein was able to fold as
easily as the native protein because the lysine residues are located
on the surface of the protein and do not play a large role in the
The protonated A2451 residue, which has a positive charge,
protein-folding process.
could stabilize the negatively charged oxyanion of the tet-
rahedral reaction intermediate. As the pH increases, A2451 38. Cells expressing growth factor receptors that have lost the
would be less likely to be protonated, so this catalytic mech- ligand-binding domain but retain the tyrosine kinase domain are
anism would be less effective at higher pH. transformed cells; that is, they are cancerous cells (see Box 10-B)
34. (a) Introduction of a stop codon would terminate protein because they grow and proliferate in the absence of extracellular
synthesis prematurely, so no functional b-galactosidase signaling ligands. Hsp90 binds to the tyrosine kinase domain to
would be synthesized. If the stop codon were located near stabilize it or help it fold. When geldanamycin is added to these
the C-terminus of the protein, the polypeptide would be transformed cells, Hsp90 can no longer function, the tyrosine
shorter than normal but might still retain activity if its ac- kinase activity drops, and the cells no longer exhibit the charac-
tive site region were intact. teristics of transformed cells.
(b) These results indicate that the oxazolidinone increases 40. (a) The a chains, when in excess, combine with all available b
the ability of ribosomes to overlook the stop codon and syn- chains to form functional a2b2 hemoglobin, thereby mini-
thesize b-galactosidase polypeptides of normal size. mizing the formation of nonfunctional b4 hemoglobin.
(c) b-Galactosidase activity would be extremely low because a (b) The protein helps prevent the precipitation of the a
nucleotide insertion or deletion changes the reading frame for chains that have not yet paired with b chains.
translation. The resulting polypeptide would have a different (c) When a deficiency of b chains is coupled with an excess
amino acid sequence and would therefore be nonfunctional. of a chains, the a chains precipitate and destroy the red
(d) These results indicate that the oxazolidinone promotes blood cells, worsening the anemia that results from the lack
frameshifting in the ribosome so that despite the insertion of b chains.
or deletion, the correct reading frame is occasionally trans- (d) The imbalance between the amounts of a and b chains is
lated and some functional b-galactosidase is synthesized. minimized when the synthesis of both globins is depressed due
(e) There are two possible Glu codons: GAA and GAG. to mutations in both an a globin gene and a b globin gene.
Changing a single base in these codons generates codons (e) The process of initiating translation requires that eIF2
specifying four different amino acids. Substitutions at the hydrolyze its bound GTP to GDP and Pi . In order for
second position yield codons for Ala (GCA and GCG), Gly the protein to participate in subsequent translation initia-
(GGA and GGG), and Val (GUA and GUG). Substitution tion events, its GDP must be replaced with GTP. If this
at the first position yields codons for Gln (CAA and CAG). exchange does not occur, reinitiation is not possible, and
(f ) The oxazolidinone does not promote codon misreading, protein synthesis comes to a halt.
that is, incorporation of an amino acid other than the one (f ) Heme prevents the phosphorylation of eIF2, so trans-
specified by a codon. If codon misreading were occurring, the lation initiation can proceed. This mechanism regulates
encoded Ala, Gln, Gly, and Val codons would occasionally be the level of globin synthesis according to the availability of
read as Glu codons, and a functional enzyme would result. heme. Consequently, the cells can produce functional he-
(g) The ability of the oxazolidinone to cause the ribosome moglobin, which contains globin polypeptides as well as
to read through stop codons would result in the synthesis heme prosthetic groups.
42. During translation, the SRP must be positioned on the ribo- 48. CH2OH
some where the signal peptide emerges from the exit tunnel. The
SRP then undergoes a conformational change that temporarily O
HO H
pauses the translation process. In order to fulfill these roles, the H CH3 NH
SRP must be able to bind to the ribosome, most likely through OH H
interactions between the SRP RNA and ribosomal RNA. H O CH CH
44. If the SRP waited to bind the polypeptide until translation C O
was complete, it is highly likely that the newly synthesized protein H NH
would have already misfolded into a conformation that included C O
it signal peptide or would have aggregated with other cellular pro-
teins. By binding to the nascent polypeptide as soon as its signal CH3
sequence emerges from the ribosome, the SRP ensures the deliv-
ery of the ribosome to the ER membrane so that the polypeptide 50. G protein–coupled receptors (see Section 10-2) have pal-
can be translocated co-translationally. Chaperones within the ER mitoylated Cys residues and as such are classified as lipid-linked
lumen then ensure that the protein folds properly. proteins. The nonpolar palmitate acyl chain helps to anchor this
46. The SRP recognizes the N-terminal signal sequence as it integral membrane protein to the membrane.
emerges from the ribosome, pauses translation, and escorts the
entire complex to the ER membrane, where it docks with its
O
receptor and translation resumes. GTP is required for this pro- H
cess. GTP hydrolysis could be part of a proofreading step by N CH C OH
occurring in response to SRP conformational changes and by
triggering additional changes in the SRP. This mechanism would CH2
ensure that only proteins with signal sequences were translocated
S
into the ER. Cytosolic proteins lacking signal sequences would
not trigger GTP hydrolysis, and the SRP would not be able to O C (CH2)14 CH3
dock with its ER receptor.

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Chapter 1 Solutions Amido group

3 2000 residues 5 1.0

1 pO2 2 n increases as well. An increased p 50 indicates a lower affinity of he-

ATP CH2 COO CH2 COO

would be Phe, a large hydrophobic residue that should fit in 0.025 M

14. The enzyme concentration is comparable to the lowest sub-

When [S] 5 5 K M, the velocity is 83% of the maximum velocity. 1

4.27 OD21 ? min 10 mM

1/v0 (mM −1 . min)

0.1 y ⫽ 1.8985x ⫹ 0.0349

⫺0.02 0 0.02 0.04 0.06 0.08 0.1 y ⫽ 0.742x ⫹ 0.704

Chapter 8 Solutions 10. Phosphatidylcholine and phosphatidylethanolamine are

44. The bleached area “recovers” its fluorescence as fluorophore- (b)

and inositol trisphosphate. Diacylglycerol activates protein ki- 10. H H

H 20. CH2OH CH2OH

28. The fungus must have contained an a-galactosidase enzyme CH3

14. If lysosomal hydrolytic enzymes function optimally at

60 28. Phosphoenolpyruvate carboxykinase catalyzes an es-

6. affinity for its substrate has decreased in the presence of the

H3C H3C In the presence of oxygen, pyruvate is converted to acetyl-CoA,

30.5 kJ ? mol21 synthesis, fluoxetine decreases the rate of ATP production in

if ADP is not available. This decreases the P:O ratio because

36. (a) The compound resembles the transition state of the ⫹

4. If medium-chain fatty acids are metabolized normally in the O

consume a diet that is low in fat and high in carbohydrates. H O

molecules of acetyl-CoA, and one molecule of 2-methylpropionyl- H3C (CH2)8 C SCoA

CoA. 4 cycles of ␤ oxidation 4 (1 QH2, 1 NADH, 1 acetyl-CoA) 

3 cycles of ␤ oxidation 3 (1 QH2, 1 NADH, 1 acetyl-CoA) 

acyl-CoA dehydrogenase 1 QH2  1.5 ATP

CH3 H3C (CH2)4 CH CH C C C S CoA

LDL receptor, and other factors such as smoking or vessel C COO

wall injuries resulting from infection can all influence the H N

(b) of longer-than-normal polypeptides. These proteins might

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CoA. 4 cycles of ␤ oxidation 4 (1 QH2, 1 NADH, 1 acetyl-CoA)

3 cycles of ␤ oxidation 3 (1 QH2, 1 NADH, 1 acetyl-CoA)

acyl-CoA dehydrogenase 1 QH2 1.5 ATP

LDL receptor, and other factors such as smoking or vessel C COO