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Understanding Amino Acids: Their Properties and Role in Proteins - Prof. James C. Armstron, Assignments of Chemistry

City College of San Francisco (CCSF)Chemistry
Prof. James C. Armstrong

An in-depth analysis of various amino acids, their properties, and their role in proteins. Topics covered include acidic and basic amino acids, hydrophobic and hydrophilic side chains, ion pairs, hydrogen bonding, and the importance of essential amino acids. The document also discusses the secondary and tertiary structures of proteins and their significance.

Typology: Assignments

Pre 2010

Uploaded on 08/18/2009

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CHAPTER 13: ANSWERS TO SELECTED PROBLEMS
SAMPLE PROBLEMS (“Try it yourself”)
13.1
13.2 The side chain of this amino acid contains a carboxylic acid group, so this is an acidic
amino acid. At pH 7, the carboxylic acid group in the side chain is ionized, as shown below.
13.3 Conjugate acid Conjugate base
13.4 The isoelectric point of ornithine is significantly above pH 6. The side chain of ornithine
contains an amino group (which is ionized at pH 7, as shown in the structure in the problem).
Amino acids with basic side chains have high isoelectric points, because the pH must be basic
enough to remove the extra H+ from the side chain.
13.5 Glutamic acid is negatively charged at pH 5.5, because this pH is higher than the
isoelectric pH of glutamic acid. (Proline is positively charged at pH 5.5, because the pH is below
the pKa of proline. Phenylalanine has no charge, because the pH equals the pKa of
phenylalanine.)
NH3CH C
O
O
CH2
CH2
CH2
CH3
The side chain of norleucine
(in the dashed box)
NH3CH C
O
O
CH2
CH2
CH2C
O
O
NH2CH C
O
O
CH2
C
O
NH2
NH3CH C
O
OH
CH2
C
O
NH2
pf3
pf4
pf5
pf8
pf9
pfa
pfd
pfe
pff

Partial preview of the text

Download Understanding Amino Acids: Their Properties and Role in Proteins - Prof. James C. Armstron and more Assignments Chemistry in PDF only on Docsity!

CHAPTER 13: ANSWERS TO SELECTED PROBLEMS

SAMPLE PROBLEMS (“Try it yourself”)

13.2 The side chain of this amino acid contains a carboxylic acid group, so this is an acidic

amino acid. At pH 7, the carboxylic acid group in the side chain is ionized, as shown below.

13.3 Conjugate acid Conjugate base

13.4 The isoelectric point of ornithine is significantly above pH 6. The side chain of ornithine

contains an amino group (which is ionized at pH 7, as shown in the structure in the problem).

Amino acids with basic side chains have high isoelectric points, because the pH must be basic

enough to remove the extra H

from the side chain.

13.5 Glutamic acid is negatively charged at pH 5.5, because this pH is higher than the

isoelectric pH of glutamic acid. (Proline is positively charged at pH 5.5, because the pH is below

the pK

a

of proline. Phenylalanine has no charge, because the pH equals the pK

a

of

phenylalanine.)

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

2

CH C
O
O
CH

2

C
O
NH

2

NH

3

CH C
O
OH
CH

2

C
O
NH

2

13.6 Here is the structure of the tripeptide as it appears at pH 7.

13.7 The primary structure of the polypeptide is Pro-Trp-Ser-Val-Cys. The backbone of this

polypeptide is shaded yellow in the structure below.

13.8 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.)

13.9 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).

13.10 At pH 7, the amine group on the side chain of lysine is positively charged, so two lysine

side chains repel one another. If the pH is raised to 12, the side chain loses its H

, so the amine

groups on the side chains now attract one another (they form a hydrogen bond).

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

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.

13.6 At pH 12, the phenol OH loses its hydrogen. In addition, the carboxylic acid group loses

its hydrogen (just as it does at pH 7), but the amine group does not gain hydrogen.

Section 13.

13.7 a)

b)

13.8 The primary structure of a protein is the sequence of amino acids.

13.9 a) This tripeptide contains phenylalanine, alanine, and glutamine.

b) There are two peptide groups, as shown on the next page.

c) The C-terminal amino acid is glutamine.

d) The N-terminal amino acid is phenylalanine.

NH

2

CH
CH

2

C
O
O
O
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

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 triple helix contains three polypeptide chains, wound around one another like braided

hair. Collagen contains this type of structure.

Section 13.

13.13 The hydrophobic interaction is important for leucine and phenylalanine.

13.14 The hydrophilic interaction is important for lysine, threonine, and glutamic acid.

13.15 Lysine and glutamic acid can form ion pairs. The side chain of lysine is a +1 ion at pH 7,

and the side chain of glutamic acid is a –1 ion at pH 7.

13.16 Leucine and phenylalanine are most likely to be in the interior of a protein, because their

side chains cannot form hydrogen bonds with water molecules.

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

δ+ δ–

CH

2

O
H
H O
H

δ+

δ–

CH

2

O
H
H
O
H

Water is the

donor and

tyrosine is the

acceptor.

Tyrosine is the

donor and water

is the acceptor.

Section 13.

13.29 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.

13.30 This dehydrogenation reaction has two possible products. The enzyme forms only one of

the two possible products.

13.32 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.

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.

Activation energy with the

enzyme (green arrow)

Activation energy without

the enzyme (red arrow)

energy of

reactants

energy of

products

ENERGY

13.34 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.

13.35 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.

13.36 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.

13.37 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).

13.38 Most enzymes become denatured in this temperature range. The denatured form of the

enzyme is not active.

13.39 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.

13.40 Competitive inhibitors fit into the active site of the enzyme and prevent the substrate

from entering the active site. Noncompetitive inhibitors bind to the enzyme outside the active

site, so they do not block the substrate. Instead, noncompetitive inhibitors force the enzyme to

change the shape of the active site, so the substrate does not fit into the active site. The structure

of a competitive inhibitor resembles that of the substrate.

13.41 The structure of succinate is similar to that of oxaloacetate, so succinate should be a

competitive inhibitor of succinate dehydrogenase.

Section 13.

13.42 The two categories are the metal ions (such as Zn

2+

, Cu

2+

, and Mg

2+

) and the coenzymes

(organic compounds such as NAD

and FAD).

13.43 A cofactor is a substance that an enzyme requires in order to catalyze its reaction.

13.44 FAD is permanently bonded to all of the enzymes that require it, so there is no FAD in

intracellular fluid. In contrast, NAD

binds reversibly to the enzymes that require it, so there is

always some NAD

in the surrounding solution.

13.45 We obtain all of the metallic cofactors we need from our diet.

13.46 Our bodies use vitamins to build coenzymes. Each coenzyme contains a vitamin attached

to some other substance that our bodies can make. Table 13.4 list some specific examples.

13.57 Our bodies cannot make the essential amino acids from other nutrients, so we must have

a dietary source of these amino acids. However, we can make the other amino acids from other

nutrients, so we do not need a dietary source of the non-essential amino acids.

13.58 Humans can make arginine from other nutrients, but children and some adults cannot

make enough arginine to meet their needs, so they need a dietary source of arginine.

13.59 The nitrogen atoms come from other amino acids. The other three elements can come

from amino acids or from other nutrients, primarily carbohydrates.

13.60 Our diet must include all of the essential amino acids, and it must include enough protein

to supply the nitrogen we need to make the non-essential amino acids and other nitrogen-

containing compounds.

13.61 We also use amino acids as an energy source, burning them to obtain energy for our

bodies. If our diet does not include enough carbohydrate and fat, we break down most of the

amino acids in our diet, because our very survival requires energy. As a result, we do not have

enough amino acids to build proteins.

13.62 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

13.63 All of the reactions in Problem 13.62 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.)

13.64 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)

13.65 a) b)

NH

2

CH C
O
OH
CH

2

CH

2

OH
NH

3

CH C
O
O
CH

2

CH

2

OH

side chain

c)

Conjugate acid Conjugate base

d) Homoserine is a polar amino acid, because it contains an alcohol group in its side

chain. Alcohols can form hydrogen bonds, but they are not acidic or basic.

13.67 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

c) The isoelectric point of this amino acid is significantly below 6.0, because the side

chain is acidic and is negatively charged at pH 6.0. You must add H

(making the solution

acidic) to eliminate these negative charges.

13.69 All four of these amino acids have hydrocarbon side chains, which are neither acidic nor

basic. Therefore, the acid-base behavior of these amino acids should be virtually identical.

13.71 At pH 2, both of the carboxylic acid groups are in their acid form (bonded to H

), rather

than in their ionized form.

NH

2

CH C
O
O
CH

2

CH

2

OH
NH

3

CH C
O
OH
CH

2

CH

2

OH
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
NH

3

CH C
O
OH
CH

2

C
O
OH

d) DNA is negatively charged. Opposite charges attract, allowing histone H3 to bind

tightly to DNA.

13.83 a) Here are the four amino acids, as they appear at pH 7.

b) serine aspartic acid alanine

c) The other amino acid is basic. Note that at pH 7, the amino group in the side chain of

this amino acid has bonded to H

13.85 Proline cannot form an alpha helix because there is no hydrogen atom bonded to the

amine nitrogen when proline is incorporated into a polypeptide. (See Figure 13.7.) The alpha

helix structure requires this hydrogen atom to form the hydrogen bond between peptide groups.

Collagen contains a high percentage of proline, allowing collagen to form the triple helix

structure instead of an alpha helix.

13.87 The hydrogen atom has a positive charge, and the oxygen atom has a negative charge.

(See Figure 13.6.)

13.89 In an alpha helix, the polypeptide backbone forms a tight coil, with the side chains

pointing outward from the coil.

13.91 Glycine and phenylalanine are most likely to be found in the interior, because their side

chains cannot form hydrogen bonds.

(You can also form a hydrogen bond between the serine hydrogen and the asparagine nitrogen.)

NH

3

CH C
O
O
CH

3

NH

3

CH C
O
O
CH

2

CH

2

CH OH
CH NH

3

NH

3

CH C
O
O
CH

2

C
O
O
NH

3

CH C
O
O
CH

2

OH

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.

13.95 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.

13.97 Lysine, threonine, and tyrosine can form hydrogen bonds with water.

13.99 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.

13.101 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.

13.103 a) This statement describes the quaternary structure of the protein.

b) This statement describes the tertiary structure of the protein.

c) This statement describes the secondary structure of the protein.

13.105 Ethanol disrupts the hydrophilic interaction between polar amino acids and the

surrounding solvent (which is normally water). As a result, the protein becomes denatured.

13.107 Some possibilities are Mg

2+

, Zn

2+

, Fe

2+

, Fe

3+

, Cu

2+

, and Mn

2+

13.109 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, since 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 a coenzyme.

13.111 The substrates are sucrose and water, the products are glucose and fructose, and the

enzyme is sucrase.

13.113 Enzymes speed up reactions, and they select the correct product when more than one

product is possible.

13.115 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.

13.117 Enzymes make the activation energy smaller. Remember that the activation energy is the

minimum energy that the reactants must have in order to react.

13.119 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).

b) This diet would (probably) satisfy the person’s protein needs, because it contains

sufficient amounts of the essential amino acids both to satisfy the need for essential amino acids

and to supply nitrogen for making nonessential amino acids.

c) This diet would not be able to meet the person’s protein needs, because it does not

contain any of the essential amino acids. The body cannot make essential amino acids from

nonessential amino acids.

13.147 Plants and microorganisms can make proteins using inorganic sources of nitrogen.

13.149 Nitrogen fixation is a series of reactions that convert gaseous nitrogen (N

2

) into

ammonium ions (NH

4

). Only a few microorganisms can carry out these reactions. Most

organisms cannot use N

2

to make organic compounds such as amino acids, so nitrogen fixation

converts atmospheric nitrogen into a form that can be used by plants and other microorganisms.

13.151 When our bodies make asparagine from other substances, the nitrogen atoms come from

other amino acids in our diet.

13.153 a) We make phenethylamine by removing CO

2

from phenylalanine.

b) We make pyruvic acid by removing NH

3

(and adding oxygen to) alanine.

13.155 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

2

NH

2

CH

2

CH

2

phenylalanine phenethylamine

NH

2

CH C
O
OH
CH

3

O
C C
O
OH
CH

3

alanine pyruvic acid