Essential Cell Biology 5th edition

The Shape and Structure of Proteins
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of the proteins they contain. Finally, we present a brief description of the
techniques that biologists use to work with proteins, including methods
for purifying them—from tissues or cultured cells—and for determining
their structures.
THE SHAPE AND STRUCTURE OF PROTEINS
From a chemical point of view, proteins are by far the most structurally
complex and functionally sophisticated molecules known. This is perhaps
not surprising, considering that the structure and activity of each
protein has developed and been fine-tuned over billions of years of evolution.
We start by considering how the position of each amino acid in
the long string of amino acids that forms a protein determines its threedimensional
conformation, a shape that is stabilized by noncovalent
interactions between different parts of the molecule. Understanding the
structure of a protein at the atomic level allows us to see how the precise
shape of the protein determines its function.
The Shape of a Protein Is Specified by Its Amino Acid
Sequence
Proteins, as you may recall from Chapter 2, are assembled mainly from a
set of 20 different amino acids, each with different chemical properties.
A protein molecule is made from a long chain of these amino acids, held
together by covalent peptide bonds (Figure 4–1). Proteins are therefore
referred to as polypeptides, or polypeptide chains. In each type of protein,
the amino acids are present in a unique order, called the amino acid
sequence, which is exactly the same from one molecule of that protein
to the next. One molecule of human insulin, for example, should have
the same amino acid sequence as every other molecule of human insulin.
Many thousands of different proteins have been identified, each with its
own distinct amino acid sequence.
Each polypeptide chain consists of a backbone that is adorned with a
variety of chemical side chains. The polypeptide backbone is formed
from a repeating sequence of the core atoms (–N–C–C–) found in every
amino
group
+
+
carboxyl
group
–
–
glycine
alanine
PEPTIDE BOND
FORMATION WITH
REMOVAL OF WATER
+
peptide bond in glycylalanine
water
–
Figure 4–1 Amino acids are linked together
by peptide bonds. A covalent peptide bond
forms when the carbon atom of the carboxyl
group of one amino acid (such as glycine)
shares electrons with the nitrogen atom from
the amino group of a second amino acid
(such as alanine). Because a molecule of
water is eliminated, peptide bond formation
is classified as a condensation reaction (see
Figure 2−31). In this diagram, carbon atoms
are black, nitrogen blue, oxygen red, and
hydrogen white.