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CHAPTER 13: ANSWERS TO SELECTED PROBLEMS
SAMPLE PROBLEMS (“Try it yourself”)
13.2 The side chain of this amino acid contains a carboxylate group (the ionized form of a
carboxylic acid). This group is strongly attracted to water, so the amino acid is hydrophilic.
Amino acids that contain carboxylate groups in their side chains are classified as acidic amino
acids, because the unionized form of the side chain is acidic.
13.3 Here is the structure of the tripeptide as it appears at pH 7.
NH
3
CH C
O
O
CH
2
CH
2
CH
2
CH
3
The side chain of norleucine
(in the dashed box)
NH
3
CH C
O
O
CH
2
CH
2
CH
2
C
O
O
NH
3
CH C
O
NH
CH C
O
NH
CH C
O
O
CH
2
CH
3
CH
2
CH
2
CH
2
NH
3
CH
CH
3
CH
2
CH
3
The side chain of this amino
acid (in the dashed box)
The carboxylate
group (shaded)
lysine alanine isoleucine
13.4 The primary structure of the polypeptide is Pro-Trp-Ser-Val-Cys. The backbone of this
polypeptide is shaded yellow in the structure below, and the side chains are shaded in green.
13.5 Aspartic acid and arginine are most likely to be found on the surface of a polypeptide,
because they have charged side chains that are strongly attracted to water. (Methionine and
tryptophan have hydrophobic side chains.)
13.6 a) Two cysteine side chains normally form a disulfide bridge.
b) The side chains of threonine and asparagine form hydrogen bonds with one another
(side-chain hydrogen bonding).
13.7 At pH 7, the amino group on the side chain of lysine is positively charged, so the two
lysine side chains repel one another. If the pH is raised to 12, the side chains lose H
, so the
amino groups on the side chains now attract one another (they form a hydrogen bond).
13.8 The reaction condenses one of the carboxylate groups of aspartic acid with a phosphate
group. Aspartic acid contains two carboxylate groups, and phosphate group could become
linked to either of these. Therefore, the enzyme (aspartate kinase) must be able to select the
correct product from the two possibilities.
H
2
N CH C
O
NH CH
CH
2
C
O
NH CH
CH
2
C
O
NH CH
2
C
O
NH CH
CH
2
C
O
O
CH
CH
3
CH
3
OH
HN
SH
δ– δ+
etc.
N
etc.
H N
H
H
H
H H
etc.
N
etc.
N
H
H
H
H
At pH 7, the amino groups are
positively charged and repel one
another strongly.
At pH 7, the amino groups have no
net charge, so they can form a
hydrogen bond.
proline side
chain
tryptophan
side chain
serine
side
chain
valine side
chain
cysteine
side chain
H
3
N CH C
O
O
CH
2
C O
O
P
O
OH
O
H
3
N CH C
O
O
CH
2
C O
O
P
O
OH
O
H
3
N CH C
O
O
CH
2
C O
O Phosphate ion could
become linked to
either of these
carboxylate groups.
correct product
incorrect product
13.5 The side chain of citrulline contains oxygen and nitrogen atoms, so it can participate in
hydrogen bonds. Therefore, citrulline is a hydrophilic amino acid. However, citrulline does not
lose or gain H
at pH 7, so citrulline is neutral. (The nitrogen atoms in citrulline are part of an
amide group, which is not basic.)
13.6 Acidic and basic amino acids are classified based on the unionized form of their side
chains. For lysine, the unionized form of the side chain contains an amino group, which is basic.
Therefore, lysine is classified as a basic amino acid.
Section 13.
13.7 a)
b)
NH
3
CH C
O
NH
CH C
O
O
CH
2
CH
2
CH
2
S
CH
2
S
CH
3
CH
3
NH
3
CH C
O
NH
CH C
O
NH
CH
2
C
O
O
CH
3
CH
2
CH
2
CH
2
NH
C
NH
2
NH
2
NH
3
CH C
O
O
CH
2
CH
2
CH
2
CH
2
NH
2
Amino group (a base)
alanine arginine glycine
methionine methionine
13.8 The primary structure of a protein is the sequence of amino acids in the protein.
13.9 a) This tripeptide contains phenylalanine, alanine, and glutamine.
b) There are two peptide groups, as shown below.
c) The C-terminal amino acid is glutamine.
d) The N-terminal amino acid is phenylalanine.
13.10 The two common secondary structures are the alpha-helix and the beta-sheet. In the
alpha-helix, the polypeptide coils like a spring, with the side chains pointing outward. In the
beta-sheet, the polypeptide forms parallel rows, running back and forth, with the side chains
projecting above and below the sheet.
13.11 A beta turn is an abrupt bend in a polypeptide that connects two strands within a beta
sheet. Proline often appears at a beta turn because it cannot participate in the hydrogen bonds
that form alpha helices and beta sheets, and its shape naturally produces a bend in the chain.
13.12 A triple helix contains three polypeptide chains, wound around one another like braided
hair. Collagen contains this type of structure.
Section 13.
13.14 The hydrophobic interaction is important for leucine and phenylalanine, because their
side chains cannot form hydrogen bonds and have little attraction for water.
H
3
N CH
CH
2
C
O
NH CH
CH
3
C
O
NH CH
CH
2
C
O
O
CH
2
C
O
NH
2
peptide groups
δ+
δ–
C O
H N
C O
H N
phenylalanine alanine glutamine
13.26 a) HCl is a strong acid, so it makes the solution very acidic. This disrupts the ion pairs
within the protein, because it converts the acidic side chains from their conjugate base form
(which is negatively charged and can form an ion pair) into their acid form (which has no net
charge).
b) Hg
2+
bonds to sulfur atoms, breaking the disulfide bridges in the protein.
c) Heating the protein disrupts the weak hydrogen-bonding interactions within the protein
(and between the protein and water), allowing the protein to unfold.
13.27 Ethanol is an organic liquid that forms hydrogen bonds less effectively than water. As a
result, adding ethanol disrupts the hydrophilic attraction that keeps the polar amino acids on the
exterior of the protein. The protein denatures, making it inactive.
13.28 The secondary, tertiary, and quaternary structures of a protein are disrupted when the
protein is denatured, but the primary structure is not.
13.29 When the concentration of NaCl is high, the ionized amino acids form ion pairs with Na
and Cl
, rather than with each other. When we disrupt the original ion pairs, the protein
denatures.
Section 13.
13.30 Enzymes are proteins that act as catalysts; they speed up reactions in living organisms,
and they control which of the possible products is actually formed. Organisms need enzymes
because most reactions do not occur rapidly enough to be of use to the organism without a
catalyst. Also, many reactions can form two or more products, only one of which is useful to the
organism, so the enzyme keeps the organism from wasting its nutrients.
13.31 This dehydrogenation reaction has two possible products. The enzyme forms only one of
the two possible products.
HO C
O
CH CH
CH
2
C
O
S CoA
HO C
O
CH
2
CH CH C
O
S CoA
HO C
O
CH
2
CH
2
CH
2
C
O
S CoA
dehydrogenation
(no enzyme)
(The organism needs this compound.)
(The organism cannot use this compound.)
HO C
O
CH
2
CH
2
CH
2
C
O
S CoA HO C
O
CH
2
CH CH C
O
S CoA
enzyme
This is the substrate.
This is the product.
13.33 a) The active site is a cavity in the surface of the enzyme where the substrate binds and
where the reaction occurs.
b) The enzyme-substrate complex is a cluster containing the enzyme and the substrates.
The substrates sit in the active site of the enzyme.
c) The enzyme-product complex is a cluster containing the enzyme and the products.
The products sit in the active site of the enzyme.
13.35 First, the substrate binds to the active site of the enzyme, forming the enzyme-substrate
complex. Second, the reaction occurs within the active site, forming the enzyme-product
complex. Third, the products leave the active site.
13.36 The side chain of arginine is basic and is positively charged at pH 7. This side chain is
strongly hydrophilic and does not enter the hydrophilic pocket in the active site.
13.37 The activity of an enzyme is the number of reaction cycles that the enzyme can catalyze
in a second, and is generally between 10 and 1000 reaction cycles per second.
13.38 Chymotrypsin does not function in the stomach, because the digestive fluids in the
stomach are very acidic. The pH of the stomach contents is far below the active range for
chymotrypsin (pH 7 to 8).
13.39 Most enzymes become denatured in this temperature range. The denatured form of the
enzyme is not active.
13.40 A substrate is a molecule that is converted into a different substance by the enzyme.
Substrates are the reactants in the balanced equation. An effector is a molecule that binds to an
enzyme and makes the enzyme more or less active. The enzyme does not change the effector
into another molecule, so effectors do not appear in the balanced equation.
13.41 Competitive inhibitors fit into the active site of the enzyme and prevent the substrate
from entering the active site. Negative effectors bind to the enzyme outside the active site, so
Activation energy with the
enzyme (green arrow)
Activation energy without
the enzyme (red arrow)
energy of
reactants
energy of
products
ENERGY
PROGRESS OF REACTION
amino acids in our diet, because our very survival requires energy. As a result, we do not have
enough amino acids to build proteins.
13.54 a) Nitrogen fixation is the reaction that converts atmospheric nitrogen (N
2
) into
ammonium ions (NH
4
b) Nitrification is the set of reactions that convert ammonium ions into nitrite and nitrate
ions (NO
2
and NO
3
c) Denitrification is the set of reactions that convert nitrite and nitrate ions back into N
2
13.55 All of the reactions in Problem 13.54 can be carried out by bacteria (although only some
bacteria can do so). None of these reactions can be carried out by plants. (Plants can convert
nitrite and nitrate ions into ammonium ions, but not the reverse.)
13.56 We do not excrete wastes continuously, so we must store our waste products for a while
before we excrete them. Ammonium ions are toxic, so our bodies cannot store significant
amounts of ammonium ions. Therefore, our bodies convert ammonium ions into urea, which is
relatively non-toxic, and we excrete the urea when we need to get rid of excess nitrogen.
CUMULATIVE PROBLEMS (Odd-numbered problems only)
13.57 a) b)
c) Homoserine is a hydrophilic (polar) amino acid, because it contains an alcohol group
in its side chain. It is not acidic or basic.
13.59 a) Gamma-carboxyglutamic acid is an acidic amino acid, because it contains two acidic
groups in its side chain.
b) At pH 7, the amino group gains H
and all three carboxylic acid groups lose H
NH
2
CH C
O
OH
CH
2
CH
2
OH
NH
3
CH C
O
O
CH
2
CH
2
OH
side chain
NH
2
CH C
O
OH
CH
2
CH C
O
HO C OH
O
side chain
NH
3
CH C
O
O
CH
2
CH C
O
O C O
O
13.61 Glycine is not chiral because it does not contain a carbon atom that is attached to four
different groups. The alpha carbon atom of glycine is attached to two hydrogen atoms, as well as
the amino group and the carboxylate group. (The alpha carbon atom of all other amino acids is
attached to four different groups, so all of the other amino acids are chiral.)
13.63 The two carbon atoms circled below are chiral.
and
NH
3
CH C
O
NH CH C
O
O
CH
2
CH
2
OH
NH
3
CH C
O
NH CH C
O
O
CH
2
CH
2
OH
NH
3
CH C
O
NH CH
2
C
O
NH CH C
O
NH
CH
3
CH
CH
2
C
O
O
CH
2
CH
2
C
O
O
N
H
H
3
N CH COO
CH
OH
CH
3
H
3
N CH COO
C
OH
CH
3
H
H
3
N C COO
CH
OH
CH
3
H
All four groups (in boxes)
attached to this carbon atom
are different, so this carbon
atom is chiral.
All four groups (in boxes)
attached to this carbon atom
are different, so this carbon
atom is chiral.
The two chiral
carbon atoms
in threonine.
glycine glutamic acid tryptophan alanine
phenylalanine serine
phenylalanine serine
Collagen contains a high percentage of proline, allowing collagen to form the triple helix
structure instead of an alpha helix.
13.79 The hydrogen atom has a positive charge, and the oxygen atom has a negative charge.
(See Figure 13.6.)
13.81 In an alpha helix, the polypeptide backbone forms a tight coil, with the side chains
pointing outward from the coil.
13.83 Phenylalanine is the most likely to be found in the interior, because its large hydrocarbon
side chain cannot form hydrogen bonds. Glycine does not have a hydrophilic side chain, but its
side chain is so small (just a hydrogen atom) that glycine does not have a strong preference for
the interior of a polypeptide.
(You can also form a hydrogen bond between the serine hydrogen and the asparagine nitrogen.)
13.87 Aspartic acid can form an ion pair with lysine. Lysine is a basic amino acid and is
positively charged at pH 7. Only acidic amino acids (which are negatively charged at pH 7) can
form an ion pair with lysine.
13.89 Lysine, threonine, and tyrosine can form hydrogen bonds with water. Their side chains
contain nitrogen or oxygen atoms that can function as hydrogen bond acceptors.
13.91 To form a disulfide bridge, the amino acid must have a thiol group (–SH) in its side
chain. Cysteine contains a thiol group, but methionine does not, so methionine cannot form a
disulfide bridge.
13.93 This sequence contains eleven amino acids. Nine of these eleven have nonpolar side
chains, and the other two (serine and asparagine) are polar but are not ionized. Therefore, this
section of the polypeptide is not attracted to water to any significant extent, so it is probably in
the interior of the protein.
13.95 a) This statement describes the quaternary structure of the protein, because it involves
more than one polypeptide chain.
δ+
δ–
CH
2
O H
CH
2
C
O
N H
H
δ+
δ–
CH
2
O H
CH
2
C
O
N H
H
serine
serine
asparagine
asparagine
Here, serine is the donor
and asparagine is the
acceptor.
Here, asparagine is the
donor and serine is the
acceptor.
b) This statement describes the tertiary structure of the protein. Aspartic acid prefers to
be on the exterior of the protein because of its charged side chain. Interactions involving side
chains contribute to the tertiary structure of a protein.
c) This statement describes the secondary structure of the protein.
13.97 Ethanol disrupts the hydrophilic interaction between polar amino acids and the
surrounding solvent (which is normally water). The hydrophilic side chain are not attracted to
the surrounding ethanol molecules as strongly as they are to water molecules, so they move into
the interior of the protein. As a result, the protein becomes denatured.
13.99 Some possibilities are Mg
2+
, Zn
2+
, Fe
2+
, Fe
3+
, Cu
2+
, and Mn
2+
13.101 a) Lysine is not a cofactor; it is one of the amino acids in the polypeptide chain.
Cofactors are substances that are required by an enzyme, but are not amino acids. Lysine is not a
coenzyme, because a coenzyme is simply an organic cofactor.
b) Biotin is a cofactor, since it is required by the enzyme but is not an amino acid. Since
biotin is an organic compound, it is also a coenzyme.
13.103 The substrates are sucrose and water, the products are glucose and fructose, and the
enzyme is sucrase.
13.105 Enzymes speed up reactions, and they select the correct product when more than one
product is possible.
13.107 Magnesium ion is positively charged and phosphate is negatively charged, so the
magnesium attracts the phosphate ion and holds it in the active site of the enzyme.
13.109 Enzymes make the activation energy smaller. Remember that the activation energy is not
the energy that the reactants actually have; it is the minimum energy that the reactants need in
order to react. If the activation energy becomes smaller, more molecules will have enough
energy to react.
13.111 Enzyme A has the higher activity. Enzyme carries out 100 reaction cycles in a second,
while enzyme B carries out only 10 reaction cycles in a second (100 cycles in 10 seconds).
13.113 Papain has the highest activity around pH 6, and catalase has the highest activity around
pH 8.
13.115 The pH-activity curve of an enzyme normally peaks at the pH of the enzyme’s
surroundings. (If it didn’t, the enzyme wouldn’t work!) Therefore, it reasonable to conclude that
the typical pH inside a cell is around 7 to 8 (corresponding to the pH peak for trypsin).
13.117 The enzyme’s activity increases as it is heated from 20ºC to 40ºC. As long as the
temperature isn’t high enough to denature the enzyme, enzymes work faster as the temperature
increases. In this case, 40ºC is not hot enough to denature enzymes (40ºC is barely above body
temperature).
b) We make pyruvic acid by removing NH
3
(and adding oxygen to) alanine.
13.139 A complete protein is a protein source that contains all of the essential amino acids.
Meat, milk (and other dairy products), and eggs are sources of complete protein.
NH
2
CH C
O
OH
CH
3
O
C C
O
OH
CH
3
alanine pyruvic acid
