Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

110 Chapter 3: Proteins
OH
O O
C
polypeptide backbone
side chains
CH 2
CH 2
H H O H H O
O
amino +
terminus H N C C N C C N C C N C C
(N-terminus)
H H H O
H H O
CH 2
CH 2
peptide
peptide bond
CH 2 bonds
CH
S
H 3 C CH 3
side chains
CH 3
carboxyl
terminus
(C-terminus)
Figure 3–1 The components of a protein.
A protein consists of a polypeptide
backbone with attached side chains. Each
type of protein differs in its sequence and
number of amino acids; therefore, it is the
sequence of the chemically different side
chains that makes each protein distinct.
The two ends of a polypeptide chain are
chemically different: the end carrying the
free amino group (NH 3 + , also written NH 2 )
is the amino terminus, or N-terminus,
and that carrying the free carboxyl group
(COO – , also written COOH) is the carboxyl
terminus or C-terminus. The amino acid
sequence of a protein is always presented
in the N-to-C direction, reading from left
to right.
Methionine
(Met)
Aspartic acid
(Asp)
Leucine
(Leu)
Tyrosine
(Tyr)
(“water-fearing”), others are negatively or positively charged, some readily form
covalent bonds, and so on. Panel 3–1 (pp. 112–113) shows their atomic structures
and Figure 3–2 lists their abbreviations.
As discussed in Chapter 2, atoms behave almost as if they were hard spheres
with a definite radius (their van der Waals radius). The requirement that no two
atoms overlap plus other constraints limit the possible bond angles in a polypeptide
chain (Figure 3–3), severely restricting the possible three-dimensional
arrangements (or conformations) MBoC6 m3.01/3.01 of atoms. Nevertheless, a long flexible chain
such as a protein can still fold in an enormous number of ways.
The folding of a protein chain is also determined by many different sets of
weak noncovalent bonds that form between one part of the chain and another.
These involve atoms in the polypeptide backbone, as well as atoms in the amino
acid side chains. There are three types of these weak bonds: hydrogen bonds, electrostatic
attractions, and van der Waals attractions, as explained in Chapter 2 (see
p. 44). Individual noncovalent bonds are 30–300 times weaker than the typical
covalent bonds that create biological molecules. But many weak bonds acting in
parallel can hold two regions of a polypeptide chain tightly together. In this way,
the combined strength of large numbers of such noncovalent bonds determines
the stability of each folded shape (Figure 3–4).
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
negative
negative
positive
positive
positive
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 3–2 The 20 amino acids commonly found in proteins. Each amino acid has a three-letter and a oneletter
abbreviation. There are equal numbers of polar and nonpolar side chains; however, some side chains listed
here as polar are large enough to have some nonpolar properties (for example, Tyr, Thr, Arg, Lys). For atomic
structures, see Panel 3–1 (pp. 112–113).
MBoC6 m3.02/3.02