AMINO ACID

Proteins are polymers of amino acids, with each amino acid
residue joined to its neighbor by a specific type of covalent bond.
What is an amino acid?
Amino acids are biologically important molecules in which a

carboxyl group and an amino group bonded to the same carbon
atom (the α carbon). They differ from each other in their side
chains, or R groups, which vary in structure, size, and electric
charge, and which influence the solubility of the amino acids in
water.
GENERAL STRUCTURE
OF AN AMION ACID
For all the common amino acids except glycine, the carbon is
bonded to four different groups: a carboxyl group, an amino group,
an R group, and a hydrogen atom; in glycine, the R group is another
hydrogen. The α-carbon atom is thus a chiral center. Because of the
tetrahedral arrangement of the bonding orbitals around the α-
carbon atom, the four different groups can occupy two unique
spatial arrangements, and thus amino acids have two possible
stereoisomers. Since they are nonsuperimposable mirror images of
each other, the two forms represent a class of stereoisomers called
enantiomers . All molecules with a chiral center are also optically
active—that is, they rotate plane-polarized light.
Glycine has the simplest structure. Although it is formally
nonpolar, its very small side chain makes no real contribution
to hydrophobic interactions.
Methionine, one of the two sulfur-containing amino acids, has

a nonpolar thioether group in its side chain.
Proline has an aliphatic side chain with a distinctive cyclic

structure. The secondary amino (imino) group of proline
residues is held in a rigid conformation that reduces the
structural flexibility of polypeptide regions containing proline.
Tryptophan and tyrosine, and to a much lesser extent phenylalanine,
absorb ultraviolet light. This accounts for the characteristic strong
absorbance of light by most proteins at a wavelength of 280 nm, a
property exploited by researchers in the characterization of proteins.
Cysteine is readily oxidized to form a covalently linked dimeric amino acid
called cystine, in which two cysteine molecules or residues are joined by
a disulfide bond. The disulfide-linked residues are strongly hydrophobic
(nonpolar). Disulfide bonds play a special role in the structures of many
proteins by forming covalent links between parts of a protein molecule or
between two different polypeptide chains.
Among these uncommon amino
acids are 4-hydroxyproline, a
derivative of proline, and
5-hydroxylysine, derived from
lysine. The former is found in plant
cell wall proteins, and both are
found in collagen, a fibrous protein
of connective tissues.
6-N-Methyllysine is a constituent
of myosin, a contractile protein of
muscle.
Another important uncommon amino acid is
–γ-carboxyglutamate, found in the blood
clotting protein prothrombin.More complex
is desmosine, a derivative of four Lys
residues, which is found in the fibrous
protein elastin.
When an amino acid is dissolved in water, it exists in solution
as the dipolar ion, or zwitterion
A zwitterion can act as either an acid (proton or a base (proton acceptor)

donor)
Substances having this dual nature are amphoteric and are often called
ampholytes (from “amphoteric electrolytes”). A simple monoamino
monocarboxylic α - amino acid, such as alanine, is a diprotic acid when fully
protonated—it has two groups-
Titration of an amino acid
14
15
Titration Curves for Glutamate and Histidine
pKax + pKay
pI =
2
pKa1 + pKa2
pI =
2
pI = 6.0
pKa1 + pKa3
pI =
2
pI = 2.7
pKa2 + pKa3
pI =
2
pI = 9.7
18
PEPTIDE BOND
The Peptide Bond Is Rigid and Planar
Covalent bonds, too, place important constraints on the conformation of a
polypeptide. In the late 1930s, Linus Pauling and Robert Corey embarked on a
series of studies that laid the foundation for our current understanding of
protein structure. They began with a careful analysis of the peptide bond. The
α carbons of adjacent amino acid residues are separated by three covalent
bonds, arranged as Cα—C—N—Cα. X-ray diffraction studies of crystals of
amino acids and of simple dipeptides and tripeptides showed that the peptide
C—N bond is somewhat shorter than the C—N bond in a simple amine and
that the atoms associated with the peptide bond are coplanar. This indicated a
resonance or partial sharing of two pairs of electrons between the carbonyl
oxygen and the amide nitrogen (Fig. 4-2a). The oxygen has a partial negative
charge and the hydrogen bonded to the nitrogen has a net partial positive
charge, setting up a small electric dipole. The six atoms of the peptide group lie
in a single plane, with the oxygen atom of the carbonyl group trans to the
hydrogen atom of the amide nitrogen.
From these findings Pauling and Corey concluded that the peptide C—N
bonds, because of their partial double-bond character, cannot rotate freely.
Rotation is permitted about the N—Cα and the Cα—C bonds. The
backbone of a polypeptide chain can thus be pictured as a series of rigid
planes, with consecutive planes sharing a common point of rotation at Cα
(Fig. 4-2b). The rigid peptide bonds limit the range of conformations
possible for a polypeptide chain.
The double-bond character is also expressed in the length of the bond
between the CO and the NH groups. The CON distance in a peptide bond is
typically 1.32 Å, which is between the values expected for a CON single
bond (1.49 Å) and a CPN double bond (1.27 Å), as shown in Figure 2.19.
Are all combinations of and possible? Gopalasamudram Ramachandran
recognized that many combinations are forbidden because of steric collisions
between atoms. The allowed values can be visualized on a two-dimensional
plot called a Ramachandran diagram (Figure 2.23. Steric exclusion, the fact
that two atoms cannot be in the same place at the same time, can be a
powerful organizing principle.
The rigidity of the

peptide unit and
the restricted set
of allowed f and c
angles limits the
number of
structures
accessible to the
unfolded form
sufficiently to
allow protein
folding to take
place.
α Helix
In evaluating potential structures, Pauling and Corey considered which
conformations of peptides were sterically allowed and which most fully exploited the
hydrogen-bonding capacity of the backbone NH and CO groups. The first of their
proposed structures, the α helix, is a rodlike structure (Figure 2.24). A tightly coiled
backbone forms the inner part of the rod and the side chains extend outward in a
helical array. The α helix is stabilized by hydrogen bonds between the NH and CO
groups of the main chain. In particular, the CO group of each amino acid forms a
hydrogen bond with the NH group of the amino acid that is situated four residues
ahead in the sequence (Figure 2.25). Thus, except for amino acids near the ends of an
α helix, all the main-chain CO and NH groups are hydrogen bonded. Each residue is
related to the next one by a rise, also called translation, of 1.5 Å along the helix axis
and a rotation of 100 degrees, which gives 3.6 amino acid residues per turn of helix.
Thus, amino acids spaced three and four apart in the sequence are spatially quite
close to one another in an α helix. In contrast, amino acids spaced two apart in the
sequence are situated on opposite sides of the helix and so are unlikely to make
contact. The pitch of the α helix is the length of one complete turn along the helix axis
and is equal to the product of the rise (1.5 Å) and the number of residues per turn
(3.6), or 5.4 Å. The screw sense of a helix can be right-handed (clockwise) or
lefthanded (counterclockwise).
β sheet
of two or more polypeptide chains called β strands. A β strand is almost
fully extended rather than being tightly coiled as in the alpha helix. A range
of extended structures are sterically allowed (Figure 2.29). The distance
between adjacent amino acids along a β strand is approximately 3.5 Å, in
contrast with a distance of 1.5 Å along an alpha helix. The side chains of
adjacent amino acids point in opposite directions (Figure 2.30). A β sheet is
formed by linking two or more β strands lying next to one another through
hydrogen bonds. Adjacent chains in a β sheet can run in opposite
directions (antiparallel β sheet) or in the same direction (parallel β sheet).
In the antiparallel arrangement, the NH group and the CO group of each
amino acid are respectively hydrogen bonded to the CO group and the NH
group of a partner on the adjacent chain (Figure 2.31). In the parallel
arrangement, the hydrogen-bonding scheme is slightly more complicated.
For each amino acid, the NH group is hydrogen bonded to the CO group of
one amino acid on the adjacent strand, whereas the CO group is hydrogen
bonded to the NH group on the amino acid two residues farther along the
chain (Figure 2.32). Many strands, typically 4 or 5 but as many as 10 or
more, can come together in b sheets. Such b sheets can be purely
antiparallel, purely parallel, or mixed (Figure 2.33).
β turns
Most proteins have compact,
globular shapes owing to
reversals in the direction of their
polypeptide chains. Many of these
reversals are accomplished by a
common structural element called
the reverse turn (also known as
the β turn or hairpin turn),
illustrated in Figure 2.36. In many
reverse turns, the CO group of
residue i of a polypeptide is
hydrogen bonded to the NH group
of residue i + 3. This interaction
stabilizes abrupt changes in
direction of the polypeptide chain.

AMINO ACID

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AMINO ACID

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Proteins are polymers of amino acids, with each amino acid

residue joined to its neighbor by a specific type of covalent bond.

What is an amino acid?

Amino acids are biologically important molecules in which a

Methionine, one of the two sulfur-containing amino acids, has

Proline has an aliphatic side chain with a distinctive cyclic

A zwitterion can act as either an acid (proton or a base (proton acceptor)

The rigidity of the

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