Proteins And Amino Acids

Amino Acids
Although more than 300 different amino acids have been described in nature, only 20 are commonly found as
constituents of mammalian proteins. [Note: These are the only amino acids that are coded for by DNA, the
genetic material in the cell (see p. 395).] Each amino acid has a carboxyl group, a primary amino group (except
for proline, which has a secondary amino group), and a distinctive side chain (“R group”) bonded to the α-
carbon atom (Figure 1.1A).

At physiologic pH (approximately 7.4), the carboxyl group is dissociated, forming the negatively charged
carboxylate ion (–COO–), and the amino group is protonated (–NH3+). In proteins, almost all of these carboxyl
and amino groups are combined through peptide linkage and, in general, are not available for chemical reaction
except for hydrogen bond formation (Figure 1.1B). Thus, it is the nature of the side chains that ultimately
dictates the role an amino acid plays in a protein. It is, therefore, useful to classify the amino acids according to
the properties of their side chains, that is, whether they are nonpolar (have an even distribution of electrons) or
polar (have an uneven distribution of electrons, such as acids and bases)

Classification Of Amino Acid

A. Amino acids with nonpolar side chains
B. Amino acids with uncharged polar side chains
C. Amino acids with acidic side chains
D. Amino acids with basic side chains

A. Amino acids with nonpolar side chains

Each of these amino acids has a nonpolar side chain that does not gain or lose protons or participate in
hydrogen or ionic bonds (see Figure 1.2). The side chains of these amino acids can be thought of as “oily”
or lipid-like, a property that promotes hydrophobic inter-actions .
1. Location of nonpolar amino acids in proteins: In proteins found in aqueous
solutions (a polar environment) the side chains of the nonpolar amino acids tend to cluster together in the
interior of the protein (Figure 1.4). This phenomenon, known
as the hydrophobic effect, is the result of the hydrophobicity of the nonpolar R groups, which act much like
droplets of oil that coalesce in an aqueous environment. The nonpolar R groups, thus, fill up the interior of
the folded protein and help give it its three-dimensional shape. However, for proteins that are located in a
hydrophobic environment, such as a membrane, the nonpolar R groups are found on the outside surface of
the protein, interacting with the lipid environment

2. Proline: Proline differs from other amino acids in that its side chain and α-amino N form a rigid,
five-membered ring structure (Figure 1.5). Proline, then, has a secondary (rather than a primary) amino
group. It is frequently referred to as an “imino acid.” The unique geometry of proline contributes to the
formation of the fibrous structure of collagen (see p. 45) and often interrupts the α-helices found in globular
proteins (see p. 26).

B. Amino acids with uncharged polar side chains

These amino acids have zero net charge at physiologic pH, although the side chains of cysteine and
tyrosine can lose a proton at an alkaline pH (see Figure 1.3). Serine, threonine, and tyrosine each contain a
polar hydroxyl group that can participate in hydrogen bond formation (Figure 1.6). The side chains of
asparagine and glutamine each contain a carbonyl group and an amide group, both of which can also
participate in hydrogen bonds.
1. Disulfide bond: The side chain of cysteine contains a sulfhydryl (thiol) group (– SH), which is an
important component of the active site of many enzymes. In proteins, the –SH groups of two cysteines
can be oxidized to form a covalent crosslink called a disulfide bond (–S–S–). Two disulfide-linked
cysteines are referred to as “cystine.” (See p. 19 for a further discussion of disulfide bond formation.)
2. Side chains as sites of attachment for other compounds: The polar hydroxyl group of serine;
threonine; and, rarely, tyrosine, can serve as a site of attachment for structures such as a phosphate
group. In addition, the amide group of asparagine, as well as the hydroxyl group of serine or threonine,
can serve as a site of attachment for oligosaccharide chains in glycoproteins

C. Amino acids with acidic side chains

The amino acids aspartic and glutamic acid are proton donors. At physiologic pH, the side chains of these
amino acids are fully ionized, containing a negatively charged carboxylate group (–COO–). They are,
therefore, called aspartate or glutamate to emphasize that these amino acids are negatively charged at
physiologic pH

D. Amino acids with basic side chains

The side chains of the basic amino acids accept protons . At
physiologic pH, the R groups of lysine and arginine are fully ionized and positively charged. In contrast,
histidine is weakly basic, and the free amino acid is largely uncharged at physiologic pH. However, when
histidine is incorporated into a protein, its R group can be either positively charged (protonated) or neutral,
depending on the ionic environment provided by the protein. This is an important property of histidine that
contributes to the buffering role it plays in the functioning of proteins such as hemoglobin (see p. 31). [Note:
Histidine is the only amino acid with a side chain that
can ionize within the physiologic pH range.]
Structure of Protein
The 20 amino acids commonly found in proteins are joined together by peptide bonds. The linear sequence
of the linked amino acids contains the information necessary to generate a protein molecule with a unique
three-dimensional shape. The complexity of protein structure is best analyzed by considering the molecule
in terms of four organizational levels:
Primary,
Secondary,
Tertiary, and
Quaternary
An examination of these hierarchies of increasing complexity has revealed that certain structural elements
are repeated in a wide variety of proteins, suggesting that there are general “rules” regarding the ways in
which proteins achieve their native, functional form.
These repeated structural elements range from simple combinations of α-helices and β- sheets forming small
motifs, to the complex folding of polypeptide domains of multifunctional proteins.
 1. PRIMARY STRUCTURE OF PROTEINS
2. SECONDARY STRUCTURE OF PROTEINS
3. TERTIARY STRUCTURE OF GLOBULAR PROTEINS
4. QUATERNARY STRUCTURE OF PROTEINS

PRIMARY STRUCTURE OF PROTEINS

The sequence of amino acids in a protein is called the primary structure of the protein.Understanding the
primary structure of proteins is important because many genetic diseases result in proteins with abnormal
amino acid sequences, which cause improper
folding and loss or impairment of normal function. If the primary structures of the normal and the mutated
proteins are known, this information may be used to diagnose or study the disease.

SECONDARY STRUCTURE OF PROTEINS

The polypeptide backbone does not assume a random three-dimensional structure but, instead, generally forms
regular arrangements of amino acids that are located near each
other in the linear sequence. These arrangements are termed the secondary structure of the polypeptide. The α-
helix, β-sheet, and β-bend (β-turn) are examples of secondary structures commonly encountered in proteins.

TERTIARY STRUCTURE OF GLOBULAR PROTEINS

The primary structure of a polypeptide chain determines its tertiary structure. “Tertiary” refers both to the
folding of domains (the basic units of structure and function, and to the final arrangement of domains in the
polypeptide. The structure of globular proteins in aqueous solution is compact, with a high density (close
packing) of the atoms in the core of the molecule. Hydrophobic side chains are buried in the interior, whereas
hydrophilic groups are generally found on the surface of the molecule.

QUATERNARY STRUCTURE OF PROTEINS

Many proteins consist of a single polypeptide chain and are defined as monomeric proteins. However, others
may consist of two or more polypeptide chains that may be structurally identical or totally unrelated. The
arrangement of these polypeptide subunits is called the quaternary structure of the protein. Subunits are held
together primarily by noncovalent interactions (for example, hydrogen bonds, ionic bonds, and hydrophobic
interactions). Subunits may either function independently of each other or may work cooperatively, as in
hemoglobin, in which the binding of oxygen to one subunit of the tetramer increases the affinity of the other
subunits for oxygen

Importance of Protein
Proteins are the most abundant and functionally diverse molecules in living systems. Virtually every life
process depends on this class of macromolecules. For example, enzymes and polypeptide hormones direct and
regulate metabolism in the body, whereas contractile proteins in muscle permit movement. In bone, the protein
collagen forms a framework for the deposition of calcium phosphate crystals, acting like the steel cables in
reinforced concrete. In the bloodstream, proteins, such as hemoglobin and plasma albumin, shuttle molecules
essential to life, whereas immunoglobulin fight infectious bacteria and viruses. In short, proteins display an
incredible diversity of functions, yet all share the common structural feature of being linear polymers of amino
acids. This chapter describes the properties of amino acids. This explores how these simple building blocks are
joined to form proteins that have unique three-dimensional structures, making them capable of performing
specific biologic functions.

PROTEINS WERE INITIALLY CLASSIFIED

BY THEIR GROSS CHARACTERISTICS
Scientists initially approached structure–function relationships in proteins by separating them into classes based upon
properties such as solubility, shape, or the presence of non protein groups. For example, the proteins that can be extracted
from cells using aqueous solutions at physiologic pH and ionic strength are classified as soluble. Extraction of integral
membrane proteins requires dissolution of the membrane with detergents. Globular proteins are compact, roughly
spherical molecules that have axial ratios (the ratio of their shortest to longest dimensions) of not over 3. Most enzymes
are globular proteins. By contrast, many structural proteins adopt highly extended conformations. These fibrous
proteins possess axial ratios of 10 or more. Lipoproteins and glycoproteins contain covalently bound lipid and
carbohydrate, respectively. Myoglobin, hemoglobin, cytochromes, and many other metalloproteins contain tightly
associated metal ions. While more precise classification schemes have emerged based upon similarity, or homology, in
amino acid sequence and three-dimensional structure, many early classification terms remain in use.

GLOBULAR HEMEPROTEINS
Heme proteins are a group of specialized proteins that contain heme as a tightly bound prosthetic group. (See
p. 54 for a discussion of prosthetic groups.) The role of the heme group is dictated by the environment created
by the three-dimensional structure of the protein. For example, the heme group of a cytochrome functions as an
electron carrier that is alternately oxidized and reduced (see p. 76). In contrast, the heme group of the enzyme
catalase is part of the active site of the enzyme that catalyzes the breakdown of hydrogen peroxide (see p. 148).
In hemoglobin and myoglobin, the two most abundant hemeproteins in humans, the heme group serves to
reversibly bind oxygen
A. Structure of heme
Heme is a complex of protoporphyrin IX and ferrous iron (Fe2+) (Figure 3.1). The iron is held in the center of
the heme molecule by bonds to the four nitrogens of the porphyrin ring. The heme Fe2+ can form two
additional bonds, one on each side of the planar porphyrin ring. In myoglobin and hemoglobin, one of these
positions is coordinated to the side chain of a histidine residue of the globin molecule, whereas the other
position is available to bind oxygen (Figure 3.2). (See pp. 278 and 282 for a discussion of the synthesis and
degradation of heme.)
B. Structure and function of myoglobin
Myoglobin, a hemeprotein present in heart and skeletal muscle,functions both as a reservoir for oxygen and as
an oxygen carrier that increases the rate of transport of oxygen within the muscle cell. [Note: Mouse
myoglobin double knockouts (see p. 486) have, surprisingly, an apparently normal phenotype.] Myoglobin
consists of a single polypeptide chain that is structurally similar to the individual polypeptide chains of the
tetrameric hemoglobin molecule. This homology makes myoglobin a useful model for interpreting some of the
more complex properties of hemoglobin.

1. α-Helical content: Myoglobin is a compact molecule, with approximately 80% of its polypeptide chain
folded into eight stretches of α-helix. These α-helical regions, labeled A to H in Figure 3.2A, are terminated
either by the presence of proline, whose five-membered ring cannot be accommodated in an α-helix (see p. 16)
or by
β-bends and loops stabilized by hydrogen bonds and ionic bonds
2. Location of polar and nonpolar amino acid residues: The interior of the myoglobin molecule is
composed almost entirely of nonpolar amino acids. They are packed closely together, forming a structure
stabilized by hydrophobic interactions between these clustered residues (see p. 19). In contrast, polar amino
acids are
located almost exclusively on the surface, where they can form hydrogen bonds, both with each other and with
water.

3. Binding of the heme group: Notable exceptions are two histidine residues (Figure 3.2B). One, the
proximal histidine (F8), binds directly to the iron of heme. The second, or distal histidine (E7), does not
directly interact with the heme group but helps stabilize the binding of oxygen to the ferrous iron.

C. Structure and function of hemoglobin

Hemoglobin is found exclusively in red blood cells (RBC), where its main function is to transport oxygen (O2)
from the lungs to the capillaries of the tissues. Hemoglobin A, the major hemoglobin in adults, is composed of
four polypeptide chains (two α chains and two β chains) held together by noncovalent interactions (Figure 3.3).
Each chain (subunit) has stretches of α-helical structure and a hydrophobic heme-binding pocket
similar to that described for myoglobin. However, the tetrameric hemoglobin molecule is structurally and
functionally more complex than myoglobin. For example, hemoglobin can transport H+ and CO2 from the
tissues to the lungs and can carry four molecules of O2 from the lungs to the cells of the body. Furthermore, the
oxygenbinding properties of hemoglobin are regulated by interaction with allosteric effectors
(see p. 29).

D. Binding of oxygen to myoglobin and hemoglobin

Myoglobin can bind only one molecule of O2, because it contains only one heme group. In contrast,
hemoglobin can bind four O2 molecules, one at each of its four heme groups.
 Fibrous Proteins
Collagen and elastin are examples of common, well-characterized fibrous proteins of the extracellular matrix
that serve structural functions in the body. For example, collagen and elastin are found as components of skin,
connective tissue, blood vessel walls, and the sclera and cornea of the eye. Each fibrous protein exhibits special
mechanical properties,
resulting from its unique structure, which are obtained by combining specific amino acids into regular,
secondary structural elements. This is in contrast to globular proteins, whose shapes are the result of complex
interactions between secondary, tertiary, and, sometimes, quaternary structural elements.

A. COLLAGEN
Collagen is the most abundant protein in the human body. A typical collagen molecule is a long, rigid structure
in which three polypeptides (referred to as α chains) are wound around one another in a rope-like triple helix
(Figure 4.1). Although these molecules are found throughout the body, their types and organization are dictated
by the structural
role collagen plays in a particular organ. In some tissues, collagen may be dispersed as a gel that gives support
to the structure, as in the extracellular matrix or the vitreous humor of the eye. In other tissues, collagen may be
bundled in tight, parallel fibers that provide great strength, as in tendons. In the cornea of the eye, collagen is
stacked so as
to transmit light with a minimum of scattering. Collagen of bone occurs as fibers arranged at an angle to each
other so as to resist mechanical shear from any direction.
B. ELASTIN
In contrast to collagen, which forms fibers that are tough and have high tensile strength, elastin is a connective
tissue protein with rubber-like properties. Elastic fibers composed of elastin and glycoprotein microfibrils are
found in the lungs, the walls of large arteries,
and elastic ligaments. They can be stretched to several times their normal length but recoil to their original
shape when the stretching force is relaxed.

DIGESTION & ABSORPTION

OF PROTEINS
Few bonds are accessible to the proteolytic enzymes that catalyze
hydrolysis of peptide bonds, without prior denaturation of dietary proteins (by heat in cooking and by the
action of gastric acid).

Several Groups of Enzymes Catalyze

the Digestion of Proteins
There are two main classes of proteolytic digestive enzymes
(proteases), with different specificities for the amino acids
forming the peptide bond to be hydrolyzed.
Endopeptidases
Hydrolyze peptide bonds between specific amino acids
throughout the molecule. They are the first enzymes to act,
yielding a larger number of smaller fragments. Pepsin in the
gastric juice catalyzes hydrolysis of peptide bonds adjacent
to aromatic and branched-chain amino acids and methionine.
Trypsin, chymotrypsin, and elastase are secreted into the
small intestine by the pancreas. Trypsin catalyzes hydrolysis
of lysine and arginine esters, chymotrypsin esters of aromatic
amino acids, and elastase esters of small neutral aliphatic
amino acids.
Exopeptidases
Catalyze the hydrolysis of peptide
bonds, one at a time, from the ends of peptides. Carboxypeptidases,
secreted in the pancreatic juice, release amino acids from the free carboxyl terminal; aminopeptidases,
secreted by the intestinal mucosal cells, release amino acids from the amino terminal. Dipeptidases and
tripeptidases in the brush border of intestinal mucosal cells catalyze the hydrolysis of di- and tripeptides,
which are not substrates for amino- and carboxypeptidases.
Free Amino Acids & Small Peptides Are
Absorbed by Different Mechanisms
The end product of the action of endopeptidases and exopeptidases
is a mixture of free amino acids, di- and tripeptides,
and oligopeptides, all of which are absorbed. Free amino acids
are absorbed across the intestinal mucosa by sodium-dependent
active transport. There are several different amino acid
transporters, with specificity for the nature of the amino acid
side-chain (large or small, neutral, acidic or basic). The various
amino acids carried by any one transporter compete with
each other for absorption and tissue uptake. Dipeptides and
tripeptides enter the brush border of the intestinal mucosal
cells, where they are hydrolyzed to free amino acids, which
are then transported into the hepatic portal vein.