Amino Acids, Peptides, and Proteins

60 Pages·2015·11.45 MB·English

CHAPTER
5
Amino Acids, Peptides,
and Proteins
OUTLINE
SPIDER SILK: A BIOSTEEL PROTEIN
5.1 AMINO ACIDS
Amino Acid Classess
s
Biologically Actieve Amino Acids
Modified Aminro Acids in Proteins
P
Amino Ac id Stereoisomers
y
Titrattion of Amino Acids
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s
Amino Acid Reactions
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e
5.2 PEPTIDES
v
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n 5.3 PROTEINS
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Other Protein Classifications

d Protein Structure
r
o The Folding Problem
xf Fibrous Proteins
O Globular Proteins

6 5.4 MOLECULAR MACHINES
1
Motor Proteins
0
2 Biochemistry in Perspective

t Spider Silk and Biomimetics
h
g Biochemistry in the Lab
i
r Protein Technology
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AVAILABLE ONLINE:
o
C A Spider’s Web Constructed Biochemistry in Perspective
with Silk Fiber The amino acid Protein Poisons
sequence of spider silk protein and the Biochemistry in Perspective
spider’s silk fiber spinning process combine Protein Folding and Human Disease
to make spider silk, one of the strongest
Biochemistry in Perspective
materials on earth.
Myosin: A Molecular Machine
Biochemistry in the Lab
Protein Sequence Analysis: The Edman Degradation
130
05-McKee-Chap05.indd 130 26/05/15 6:17 pm
Spider Silk: A Biosteel Protein
Spiders have evolved over 400 million years spider silk to make fishing lines. In modern times
into exceptionally successful predators. spider silk has served as crosshairs in scientific
These invertebrate animals are a class of arthro- equipment and gun sights. In the past several
pods, called the arachnids, that have an exoskel- decades, spider silk and orb webs have attracted
eton, a segmented body, and jointed appendages. the attention of life scientists, bioengineers, and
Although spiders possess an efficient venom in- material scientists as they began to appreciate the
jection system, their most impressive feature is unique mechanical properties of this remarkable
the production of silk, a multiuse protein fiber. protein.
Silk, which is spun through spinnerets at the end There are eight different types of spider silk, al-
of the spider’s abdomen, is used in locomotion, though no spider makes all of them. Dragline silk, a
mating, and offspring protection. The most very strong fiber, is used for frame and radial lines
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prominent use of spider silk, however, is prey in orb webs and as a safety line (to break a fall or
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capture. The spiral, wheel-shape orb web, which escape other predators). Capture esilk, an elastic
is oriented vertically to intercept fast-moving and sticky fiber, is used in the spirral of webs.
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flying prey, is the best known method. Spider Spider silk is a lightweight fiber with impres-

silk’s mechanical properties ensure that the web sive mechanical propertieys. Toughness, a combi-
t
readily absorbs impact energy so that prey is re- nation of stiffness andsi strength, is a measure of
tained until the spider can subdue it. Orb webs how much energy ris needed to rupture a fiber.
e
(and the species that produce them) have fasci- Spider silk is about five times as tough as high-
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nated humans for many thousands of years be- grade steel wiire of the same weight and about
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cause of their dramatic visual impact. Ancient twice as toUugh as synthetic fibers such as Kevlar
Greeks and Romans, for example, explained the (used in body armor). Spider silk’s tensile

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occurrence of spiders and orb webs with the strength, the resistance of a material to breaking
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myth of Arachne, in which the mortal woman wohen stretched, is as great as that of Kevlar and
Arachne, an extraordinarily gifted weaver, of- xfgreater than that of high-grade steel wire. Tor-
fended Minerva (Athena in the Greek version), theO sional resistance, the capacity of a fiber to resist
goddess of weaving and other crafts, with her ar- twisting (an absolute requirement for draglines
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rogant acceptance of a challenge to a weaving used as safety lines), is higher for spider silk than
1
contest with the goddess. When confro0nted with for all textile fibers, including Kevlar. It also has
Arachne’s flawless work, an enrag2ed Minerva superior elasticity and resilience, the capacity of a
transformed her into a spider, doo med to forever material when it is deformed elastically to absorb
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weave webs. and then release energy. Scientists estimate that
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Humans have also long appreciated spider webs a 2.54 cm (1 in)–thick rope made of spider silk
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for their physical propertiyes. Examples range from could be substituted for the flexible steel arrest-
the ancient Greeks, whpo used spider webs to treat ing wires used on aircraft carriers to rapidly stop
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wounds, to the Australian aborigines who used a jet plane as it lands.
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Overview
PROTEINS ARE MOLECULAR TOOLS THAT PERFORM AN ASTONISHING
VARIETY OF FUNCTIONS. IN ADDITION TO SERVING AS STRUCTURAL
materials in all living organisms (e.g., actin and myosin in animal muscle cells),
proteins are involved in such diverse functions as catalysis, metabolic regula-
tion, transport, and defense. Proteins are composed of one or more
polypeptides, unbranched polymers of 20 different amino acids. The genomes
of most organisms specify the amino acid sequences of thousands or tens of
thousands of proteins.
113311
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132 CHAPTER FIVE Amino Acids, Peptides, and Proteins
P roteins are a diverse group of macro-
molecules (Figure 5.1). This diver-
sity is directly related to the
combinatorial possibilities of the 20 amino
acid monomers. Amino acids can be theo-
Phosphocarrier Lysozyme
protein HPr retically linked to form protein molecules
in any imaginable size or sequence. Con-
sider, for example, a hypothetical protein
composed of 100 amino acids. The total
possible number of combinations for such
a molecule is an astronomical 20100. How-
Myoglobin
Catalase
ever, of the trillions of possible protein se-
Hemoglobin quences, only a small fraction (possibly no
more than 2 million) is actually produced
in all living organisms. An important
reason for this remasrkable discrepancy is
demonstrated by tshe complex set of struc-
e
tural and functional properties of naturally
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occurring prPoteins that have evolved over
Deoxyribonuclease Cytochrome c Porin Collagen billions yo f years in response to selection
pressutre. Among these are (1) structural
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features that make protein folding a rela-
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etively rapid and successful process, (2) the
vpresence of binding sites that are specific
i
n for one or a small group of molecules,
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Chymotrypsin (3) an appropriate b alance of structural
d flexibility and rigidity so that function is
r maintained, (4) surface structure that is
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Calmodulin appropriate for a protein’s immediate envi-
f
x
ronment (i.e., hydrophobic in membranes
O
and hydrophilic in cytoplasm), and (5) vul-

6 nerability of proteins to degradation reac-
1 tions when they become damaged or no
0
Alcohol Aspartate longer useful.
2
Insulin dehydrogenase transcarbamoylase Proteins can be distinguished based

ht on their number of amino acids (called
g amino acid residues), their overall amino
5 nm
ri acyl com position, and their amino acid se-
FIGURE 5.1 y
quence. Selected examples of the diversity
p
Protein Diversity
o of proteins are illustrated in Figure 5.1. Molecules with molecular weights rang-
Proteins occur in an enormous C ing from several thousand to several m illion daltons are called polypeptides.
diversity of sizes and shapes. Those with low molecular weights, typically consisting of fewer than 50 amino
acids, are called peptides. The term protein describes molecules with more than
50 amino acids. Each protein consists of one or more polypeptide chains.
This chapter begins with a review of the structures and chemical properties of
the amino acids. This is followed by descriptions of the structural and functional
features of peptides and proteins and the protein folding process. The emphasis
throughout is on the intimate relationship between the structure and function of
polypeptides. In Chapter 6 the functioning of the enzymes, an especially impor-
tant group of proteins, is discussed. Protein synthesis is covered in Chapter 19.

5.1 AMINO ACIDS
The hydrolysis of each polypeptide yields a set of amino acids, referred to as the
molecule’s amino acid composition. The structures of the 20 amino acids that are
commonly found in naturally occurring polypeptides are shown in Figure 5.2.
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5.1 Amino Acids 133
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2

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FIGURE 5.2
The Standard Amino Acids
The ionization state of the amino acid molecules in this illustration represents the domi-
nant species that occur at a pH of 7. The side chains are indicated by shaded boxes.
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134 CHAPTER FIVE Amino Acids, Peptides, and Proteins
TABLE 5.1 Names and Abbreviations of the Standard Amino Acids
Three-Letter One-Letter
Amino Acid Abbreviation Abbreviation
Alanine Ala A
Arginine Arg R
Asparagine Asn N
Aspartate Asp D
Cysteine Cys C
Glutamate Glu E
Glutamine Gln Q
Glycine Gly G
Histidine His H
Isoleucine Ile I
Leucine Leu L
Lysine Lys K
s
Methionine Met s M
e
Phenylalanine Phe F
r
Proline Pro P P
Serine Ser S
y
Threonine Thr t T
i
Tryptophan Trp s W
r
Tyrosine Teyr Y
Valine vVal V
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+
NH O d
3 These amino acids are referred to as standard amino acids. Common abbrevia-
r
H C C O− tions for the standard aomino acids are listed in Table 5.1. Note that 19 of the stan-
dard amino acids hafve the same general structure (Figure 5.3). These molecules
x
R
contain a central cOarbon atom (the a-carbon) to which an amino group, a carboxyl-
FIGURE 5.3 ate group, a hy drogen atom, and an R (side chain) group are attached. The excep-
6
tion, proline, differs from the other standard amino acids in that its amino group is
General Structure of the a-Amino Acids 1
secondary, formed by ring closure between the R group and the amino nitrogen.
0
Prolin2e confers rigidity to the peptide chain because rotation about the a-carbon
is n ot possible. This structural feature has significant implications in the structure
t
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and, therefore, the function of proteins with a high proline content.
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Nonstandard amino acids consist of amino acid residues that have been chem-
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y ically modified after incorporation into a polypeptide or amino acids that occur
p in living organisms but are not found in proteins. Nonstandard amino acids found
o in proteins are usually the result of posttranslational modifications (chemical
C
changes that follow protein synthesis). Selenocysteine, an exception to this rule,
is discussed in Chapter 19.
At a pH of 7, the carboxyl group of an amino acid is in its conjugate base
form (—COO–), and the amino group is in its conjugate acid form (—NH1). Thus
3
each amino acid can behave as either an acid or a base. The term amphoteric is
used to describe this property. Molecules that bear both positive and negative
charges are called zwitterions. The R group gives each amino acid its unique
properties.
Amino Acid Classes
The sequence of amino acids determines the three-dimensional configuration of
each protein. Their structures are therefore examined carefully in the next four
subsections. Amino acids are classified according to their capacity to interact
with water. Using this criterion, four classes may be distinguished: (1) nonpolar,
(2) polar, (3) acidic, and (4) basic.
05-McKee-Chap05.indd 134 26/05/15 6:17 pm
5.1 Amino Acids 135
NONPOLAR AMINO ACIDS The nonpolar amino acids contain mostly
hydrocarbon R groups that do not bear positive or negative charges. Nonpolar
(i.e., hydrophobic) amino acids play an important role in maintaining the three-
dimensional structures of proteins because they interact poorly with water. Two
types of hydrocarbon side chains are found in this group: aromatic and aliphatic.
Aromatic hydrocarbons contain cyclic structures that constitute a class of
unsaturated hydrocarbons with planar conjugated p electron clouds. Benzene is
one of the simplest aromatic hydrocarbons (p. P-25). The term aliphatic refers to
nonaromatic hydrocarbons such as methane and cyclohexane (p. 5). Phenylalanine
and tryptophan contain aromatic ring structures. Glycine, alanine, valine, leucine,
isoleucine, and proline have aliphatic R groups. A sulfur atom appears in the
thioether-containing aliphatic side chain (—S—CH) of methionine. Its derivative
3
S-adenosyl methionine (SAM) is an important metabolite that serves as a methyl
donor in numerous biochemical reactions. It should be noted that glycine with
a hydrogen atom side chain instead of a hydrocarbon side chain is slightly
hydrophilic. Its small side chain introduces structural flexibility into proteins. s
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POLAR AMINO ACIDS The functional groups of polar amino acids easily interact
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with water through electrostatic interactions, such as hydrogen bonding. Serine, P
threonine, tyrosine, asparagine, and glutamine belong to this category. Serine,
y
threonine, and tyrosine contain a polar hydroxyl group, which enables them tot
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participate in hydrogen bonding, an important factor in protein structure. Tshe
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hydroxyl groups serve other functions in proteins. For example, the formateion of
the phosphate ester of tyrosine is a common regulatory mechanism. Addivtionally,
the —OH groups of serine and threonine are points for attaching carnbiohydrates.
Asparagine and glutamine are amide derivatives of the acidic aminoU acids aspartic
acid and glutamic acid, respectively. Because the amide functiona l group is highly
d
polar, the hydrogen-bonding capability of asparagine anrd glutamine has a
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significant effect on protein stability. The sulfhydryl group (—SH) of cysteine is
f
highly reactive and is an important component of manxy enzymes. It also binds
O
metals (e.g., iron and copper ions) in proteins. Additionally, the sulfhydryl groups
of two cysteine molecules oxidize easily in the extr acellular compartment to form
6
a disulfide compound called cystine. (See p. 1414 for a discussion of this reaction.)
0
ACIDIC AMINO ACIDS  Two standard 2amino acids have side chains with
carboxylate groups. Aspartic acid antd glutamic acid are often referred to as
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aspartate and glutamate because carboxylate groups are negatively charged at
g
physiological pH.
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QUESTION 5.1 o
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Classify these standard amino acids according to whether their structures are
nonpolar, polar, acidic, or basic.
O O
C O– C O–
+ +
O O H3N C H H3N C H
CH CH
C O– C O– 2 2
+ +
CH CH
H3N C H H3N C H 2 2
CH C O–
CH2SH CH2 2
CH2 O
+NH
3
(a) (b) (c) (d)
05-McKee-Chap05.indd 135 26/05/15 6:17 pm
136 CHAPTER FIVE Amino Acids, Peptides, and Proteins
BASIC AMINO ACIDS Basic amino acids bear a positive charge at physiological
KEY CONCEPT pH. They can therefore form ionic bonds with acidic amino acids. Lysine,
which has a side chain amino group, accepts a proton from water to form the
Amino acids are classified according to
conjugate acid (—NH1). When lysine side chains in collagen fibrils, a vital
their capacity to interact with water. This 3
structural component of ligaments and tendons, are oxidized and subsequently
criterion may be used to distinguish four
condensed, strong intramolecular and intermolecular cross-linkages are formed.
classes: nonpolar, polar, acidic, and basic.
Because the guanidino group of arginine has a pK range of 11.5 to 12.5 in
a
proteins, it is permanently protonated at physiological pH and, therefore, does
not function in acid-base reactions. The imidazole side chain of histidine, on the
other hand, is a weak base that is only partially ionized at pH 7 because its pK
a
is approximately 6. Histidine’s capacity under physiological conditions to accept
or donate protons in response to small changes in pH plays an important role in
the catalytic activity of numerous enzymes.
Biologically Active Amino Acids
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In addition to their primary function as components of prsotein, amino acids have
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several other biological roles.
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1. Several a-amino acids or their derivatives act as chemical messengers

(Figure 5.4). For example, glycine, gylutamate, g-amino butyric acid
t
(GABA, a derivative of glutamate), aind serotonin and melatonin (deriva-
s
tives of tryptophan) are neurotrarnsmitters, substances released from one
e
nerve cell that influence the function of a second nerve cell or a muscle
v
cell. Thyroxine (a tyrosine derivative produced in the thyroid gland of ani-
i
n
mals) is a hormone—a chemical signal molecule produced in one cell that
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regulates the function of other cells.

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2. Amino acids are precursors of a variety of complex nitrogen-containing
r
molecules. Examoples include the nitrogenous base components of nucleo-
tides and thef nucleic acids, heme (the iron-containing organic group
x
required fOor the biological activity of several important proteins), and
chlorop hyll (a pigment of critical importance in photosynthesis).
6
3. Sev1eral standard and nonstandard amino acids act as metabolic interme-
d0iates. For example, arginine (Figure 5.2), citrulline, and ornithine
2 (Figure 5.5) are components of the urea cycle (Chapter 15). The synthe-

t sis of urea, a molecule formed in vertebrate livers, is the principal mecha-
h
nism for the disposal of nitrogenous waste.
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p O I I O
C o H3N+ CH2 CH2 CH2 C O− HO O CH CH C O−
2
GABA
+NH
I I 3
+
HO CH CH NH Thyroxine
2 2 3
O
N
H H C C NH
3
Serotonin
CH
2
CH
2
H C O
3
N
FIGURE 5.4
H
Some Derivatives of Amino Acids Melatonin
05-McKee-Chap05.indd 136 26/05/15 6:17 pm
5.1 Amino Acids 137
Modified Amino Acids in Proteins O O
+ +
Several proteins contain amino acid derivatives that are formed after a H N CH C O− H N CH C O−
3 3
polypeptide chain has been synthesized. Among these modified amino acids is
CH CH
g-carboxyglutamic acid (Figure 5.6), a calcium-binding amino acid residue 2 2
found in the blood-clotting protein prothrombin. Both 4-hydroxyproline and CH CH
2 2
5-hydroxylysine are important structural components of collagen, the most abun-
CH CH
dant protein in connective tissue. Phosphorylation of the hydroxyl-containing 2 2
amino acids serine, threonine, and tyrosine is often used to regulate the activity NH +NH
3
of proteins. For example, the synthesis of glycogen is significantly curtailed
C O
when the enzyme glycogen synthase is phosphorylated. Two other modified
amino acids, selenocysteine and pyrolysine, are discussed in Chapter 19. NH
2
Citrulline Ornithine
FIGURE 5.5
Amino Acid Stereoisomers
Citrulline sand Ornithine
Because the a-carbons of 19 of the 20 standard amino acids are attached to four s
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different groups (i.e., a hydrogen, a carboxyl group, an amino group, and an R
r
group), they are referred to as asymmetric, or chiral, carbons. Glycine is a sym- P
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metrical molecule because its a-carbon is attached to two hydrogens. Molecules O
y
with chiral carbons can exist as stereoisomers, molecules that differ only in thet C
i NH CH C
spatial arrangement of their atoms. Three-dimensional representations of amisno
r N CH
acid stereoisomers are illustrated in Figure 5.7. Notice in the figure that the atoems of O CH
2 CH CH
the two isomers are bonded together in the same pattern except for the povsition of 2 2
i −O C CH
the ammonium group and the hydrogen atom. These two isomers are minrror images
H OH
of each other. Such molecules, called enantiomers, cannot be supUerimposed on C O
each other. Enantiomers have i dentical physical properties excep t that they rotate
plane-polarized light in opposite directions. Plane-polarized rligdht is produced by O−
passing unpolarized light through a special filter; the light owaves vibrate in only γ-Carboxyglutamate 4-Hydroxyproline
f
one plane. Molecules that possess this property are callexd optical isomers.
O O O
Glyceraldehyde is the reference compound for optical isomers (Figure 5.8).
One glyceraldehyde isomer rotates the light beam6 in a clockwise direction and is NH CH C NH CH C
said to be dextrorotatory (designated by 1). 1The other glyceraldehyde isomer,
referred to as levorotatory (designated by 20), rotates the beam in the opposite CH2 CH2
2
direction to an equal degree. Optical isomers are often designated as d or l (e.g., CH O
2
d-glucose, l-alanine) to indicate thet similarity of the arrangement of atoms
h
around a molecule’s asymmetric cagrbon to the asymmetric carbon in either of the CHOH −O P O
glyceraldehyde isomers. ri CH O−
Most biomolecules have myore than one chiral carbon. As a result, the letters d 2
and l refer only to a moleocuple’s structural relationship to either of the glyceralde- +NH3
hyde isomers, not to thCe direction in which it rotates plane-polarized light. Most 5-Hydroxylysine o-Phosphoserine
asymmetric molecules found in living organisms occur in only one stereoiso-
FIGURE 5.6
meric form, either d or l. For example, with few exceptions, only l-amino acids
Some Modified Amino Acid Residues
are found in proteins.
Found in Polypeptides
Chirality has had a profound effect on the structural and functional properties
of biomolecules. For example, the right-handed helices observed in proteins result
from the exclusive presence
of l-amino acids. Polypep-
tides synthesized in the lab-
oratory from a mixture of FIGURE 5.7
both d- and l-amino acids
Two Enantiomers
do not form helices. In addi-
l-Alanine and d-alanine are
tion, because the enzymes
mirror images of each other.
are chiral molecules, most
(Nitrogen = large blue ball;
bind substrate (reactant)
hydrogen = small gray ball;
molecules in only one enan- carbon = black ball;
tiomeric form. Proteases, L-Alanine D-Alanine oxygen = red balls)
05-McKee-Chap05.indd 137 26/05/15 6:17 pm
138 CHAPTER FIVE Amino Acids, Peptides, and Proteins
H H enzymes that degrade proteins by hydrolyzing peptide bonds, cannot degrade ar-
tificial polypeptides composed of d-amino acids.
C O C O
H C OH HO C H
QUESTION 5.2
CH OH CH OH
2 2
Certain bacterial species have outer layers composed of polymers made of
D-Glyceraldehyde L-Glyceraldehyde d-amino acids. Immune system cells, whose task is to attack and destroy foreign
cells, cannot destroy these bacteria. Suggest a reason for this phenomenon.
FIGURE 5.8
d- and l-Glyceraldehyde
These molecules are mirror images of Titration of Amino Acids
each other.
The predominant ionic form of the ionizable groups of amino acids in solution
depends on pH (Table 5.2). Titration of an amino acid illustrates the effect of pH
on amino acid structure (Figure 5.9a). Titration is also a useful tool in determin-
s
ing the reactivity of amino acid side chains. Consider alanine, a simple amino
KEY CONCEPTS s
acid, which has two titratable groups. During titration ewith a strong base such as
• Molecules with an asymmetric or chiral
NaOH, alanine loses two protons in stepwise fashiorn. In a strongly acidic solu-
carbon atom differ only in the spatial P
tion (e.g., at pH 0), alanine is in the form in which the carboxyl group is un-
arrangement of the atoms attached to the
charged. In this circumstance the molecule’ys net charge is 11 because the
carbon. t
ammonium group is protonated. If the H1 cioncentration is lowered, the carboxyl
• The mirror-image forms of a molecule are s
group loses its proton to become a negartively charged carboxylate group. (In a
called enantiomers. e
polyprotic acid, the protons are first lost from the group with the lowest pK .)
• Most asymmetric molecules in living v a
Once the carboxyl group has losti its proton, alanine has no net charge and is
organisms occur in only one n
electrically neutral. The pH at which this occurs is called the isoelectric point
stereoisomeric form. U
(pI). The isoelectric point for alanine may be calculated as follows:

d
r
pK 1 pK o
pI 5 1 2 f
2 x
O

6
1
0
TABL2E 5.2 pK Values for the Ionizing Groups of the Amino Acids
a
Atmino Acid pK (—COOH) pK (—NH1) pK
h 1 2 3 R
g Glycine 2.34 9.60
i
r Alanine 2.34 9.69
y
p Valine 2.32 9.62
o Leucine 2.36 9.60
C Isoleucine 2.36 9.60
Serine 2.21 9.15
Threonine 2.63 10.43
Methionine 2.28 9.21
Phenylalanine 1.83 9.13
Tryptophan 2.83 9.39
Asparagine 2.02 8.80
Glutamine 2.17 9.13
Proline 1.99 10.60
Cysteine 1.71 10.78 8.33
Histidine 1.82 9.17 6.00
Aspartic acid 2.09 9.82 3.86
Glutamic acid 2.19 9.67 4.25
Tyrosine 2.20 9.11 10.07
Lysine 2.18 8.95 10.79
Arginine 2.17 9.04 12.48
05-McKee-Chap05.indd 138 26/05/15 6:17 pm
5.1 Amino Acids 139
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FIGURE 5.9 e
Titration of Two Amino Acids v
i
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(a) Alanine and (b) glutamic acids. The ionized forms of glutamic acid are illustrated below.
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d
r
o
The pK and pK values for alanine are 2.34 and 9.9, resxpfectively (see Table 5.2).
1 2
The pI value for alanine is therefore O

6
2.34 1 9.69 1
pI 5 5 6.02
2 0
2

t
As the titration continues, the ammohnium group loses its proton, leaving an un-
charged amino group. The molecgule then has a net negative charge because of
i
the carboxylate group. r
y
Amino acids with ionizapble side chains have more complex titration curves.
Glutamic acid, for exampole, has a carboxyl side chain group (Figure 5.9b). At low
pH, glutamic acid has aC net charge of 11. As base is added, the a-carboxyl group
loses a proton to become a carboxylate group. Glutamate now has no net charge.
As more base is added, the second carboxyl group loses a proton, and the mol-
ecule has a –1 charge. Adding additional base results in the ammonium ion
losing its proton. At this point, glutamate has a net charge of –2. The pI value
05-McKee-Chap05.indd 139 26/05/15 6:17 pm