Essential Cell Biology 5th edition

138 CHAPTER 4 Protein Structure and Function
amino acid
side chains
(A)
unfolded protein
FOLDING
binding site
folded protein
H
serine
C
CH 2
O N
hydrogen bond
H O
C
H
H
C
5′ cyclic AMP bound to
O O
(CH 2 ) folded protein
3
NH
P O
+
C NH O O
serine
2
3′
H
arginine
N N H
O
O CH C
NH 2 2
H
H
N H N N
N H
O
H O
C O_
threonine
electrostatic
attraction
CH
CH 2
H 3 C C
CH glutamic
H
2
acid
C
H
(B)
Figure 4−32 Binding sites allow proteins to interact with specific ligands. (A) The folding of the polypeptide
chain typically creates a crevice or cavity on the folded protein’s surface, where specific amino acid side chains are
brought together in such a way that they can form a set of noncovalent bonds only with certain ligands. (B) Close-up
view of an actual binding site showing the hydrogen bonds and an electrostatic interaction formed between a
protein and its ligand (in this example, the bound ligand is cyclic AMP, shown in dark yellow).
ECB5 04.32
Although the atoms buried in the interior of a protein have no direct contact
with the ligand, they provide an essential framework that gives the
surface its contours and chemical properties. Even tiny changes to the
amino acids in the interior of a protein can change the protein’s threedimensional
shape and destroy its function.
Humans Produce Billions of Different Antibodies, Each
with a Different Binding Site
All proteins must bind to specific ligands to carry out their various functions.
For antibodies, the universe of possible ligands is limitless and
includes molecules found on bacteria, viruses, and other agents of
infection. How does the body manage to produce antibodies capable of
recognizing and binding tightly to such a diverse collection of ligands?
Antibodies are immunoglobulin proteins produced by the immune system
in response to foreign molecules, especially those on the surface of
an invading microorganism. Each antibody binds to a particular target
molecule extremely tightly, either inactivating the target directly or marking
it for destruction. An antibody recognizes its target molecule, called
an antigen, with remarkable specificity. And because there are potentially
billions of different antigens we might encounter, humans must be
able to produce billions of different antibodies—one of which will be specific
for almost any antigen imaginable.
Antibodies are Y-shaped molecules with two identical antigen-binding
sites, each of which is complementary to a small portion of the surface
of the antigen molecule. A detailed examination of antibody structure
reveals that the antigen-binding sites are formed from several loops
of polypeptide chain that protrude from the ends of a pair of closely