Essential Cell Biology 5th edition

120 CHAPTER 4 Protein Structure and Function
Figure 4–2 A protein is made of
amino acids linked together into a
polypeptide chain. The amino acids
are linked by peptide bonds (see
Figure 4–1) to form a polypeptide
backbone of repeating structure (gray
boxes), from which the side chain
of each amino acid projects. The
sequence of these chemically distinct
side chains—which can be nonpolar
(green), polar uncharged (yellow),
positively charged (red ), or negatively
charged (blue)—gives each protein its
distinct, individual properties. A small
polypeptide of just four amino acids
is shown here. Proteins are typically
made up of chains of several hundred
amino acids, whose sequence is always
presented starting with the N-terminus
and read from left to right.
amino terminus
(N-terminus)
O
O
OH
C
side chains
CH 2
CH 2
H H O H H O
+
H N C C N C C N C C N C
polypeptide backbone
H H H O
H H O
CH 2
CH 2
peptide
peptide bond
C
bonds CH
C
H
HN
H 3 C CH 3
HC N
+
side chains
H
Histidine
(His)
Aspartic acid
(Asp)
Leucine
(Leu)
C
Tyrosine
(Tyr)
O
carboxyl terminus
(C-terminus)
amino acid (Figure 4–2). Because the two ends of each amino acid are
chemically different—one sports an amino group (NH + 3 , also written NH 2 )
and the other a carboxyl group (COO – , also written COOH)—each polypeptide
chain has a directionality: the end carrying the amino group is
called the amino terminus, or N-terminus, and the end carrying the free
carboxyl group is the carboxyl ECB5 e4.02/4.02 terminus, or C-terminus.
Projecting from the polypeptide backbone are the amino acid side
chains—the part of the amino acid that is not involved in forming peptide
bonds (see Figure 4–2). The side chains give each amino acid its unique
properties: some are nonpolar and hydrophobic (“water-fearing”), some
are negatively or positively charged, some can be chemically reactive,
and so on. The atomic formula for each of the 20 amino acids in proteins
is presented in Panel 2–6 (pp. 76–77), and a brief list of the 20 common
amino acids, with their abbreviations, is provided in Figure 4–3.
Long polypeptide chains are very flexible, as many of the covalent bonds
that link the carbon atoms in the polypeptide backbone allow free rotation
of the atoms they join. Thus, proteins can in principle fold in an
AMINO ACID SIDE CHAIN AMINO ACID SIDE CHAIN
Aspartic acid
Glutamic acid
Arginine
Lysine
Histidine
Asparagine
Glutamine
Serine
Threonine
Tyrosine
Asp
Glu
Arg
Lys
His
Asn
Gln
Ser
Thr
Tyr
D
E
R
K
H
N
Q
S
T
Y
negatively charged
negatively charged
positively charged
positively charged
positively charged
uncharged polar
uncharged polar
uncharged polar
uncharged polar
uncharged polar
Alanine
Glycine
Valine
Leucine
Isoleucine
Proline
Phenylalanine
Methionine
Tryptophan
Cysteine
Ala
Gly
Val
Leu
Ile
Pro
Phe
Met
Trp
Cys
A
G
V
L
I
P
F
M
W
C
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
nonpolar
POLAR AMINO ACIDS
NONPOLAR AMINO ACIDS
Figure 4–3 Twenty different amino acids are commonly found in proteins. Both three-letter and one-letter abbreviations are given,
as well as the character of the side chain. There are equal numbers of polar (hydrophilic) and nonpolar (hydrophobic) side chains, and
half of the polar side chains are charged at neutral pH in an aqueous solution. The structures of all of these amino acids are shown in
Panel 2−6, pp. 76−77.
ECB5 e4.03-4.03