34
Chapter 2
Four major factors determine the conformation of a
polypeptide chain once the amino acid sequence (primary
structure) has been formed: (1) hydrogen bonds between
portions of the chain or with surrounding water molecules;
(2) ionic bonds between polar and ionized regions along the
chain; (3) attraction between nonpolar (hydrophobic) regions;
and (4) covalent bonds linking the side chains of two amino
acids (
Figure 2–17
). (A fi fth force, called
van der Waals
forces,
causes a very weak attraction between two nonpolar
atoms that are in very close proximity to each other.)
An example of the attractions between various regions
along a polypeptide chain is the hydrogen bond that can
occur between the hydrogen linked to the nitrogen atom
in one peptide bond and the double-bonded oxygen atom
in another peptide bond (
Figure 2–18
). Because pep-
tide bonds occur at regular intervals along a polypeptide
chain, the hydrogen bonds between them tend to force the
chain into a coiled conformation known as an
alpha helix.
Hydrogen bonds can also form between peptide bonds when
extended regions of a polypeptide chain run approximately
parallel to each other, forming a relatively straight, extended
region known as a
beta sheet
(
Figure 2–19
). However, for
several reasons, a given region of a polypeptide chain may
not assume either a helical or beta sheet conformation. For
example, the sizes of the side chains and the ionic bonds
between side chains with opposite charges can interfere with
the repetitive hydrogen bonding required to produce these
shapes. These irregular regions, known as loop conforma-
tions, occur in regions linking the more regular helical and
beta sheet patterns (see Figure 2–19).
Beta sheets and alpha helices are regions of
second-
ary structure
of proteins. Secondary structure, therefore, is
determined by primary structure. Secondary structure allows
the protein to be defi ned in terms of “domains.” For example,
many helical domains are comprised primarily of hydrophobic
amino acids. These regions tend to impart upon a protein the
ability to anchor itself into a lipid bilayer, like that of a cell
membrane.
Tertiary Protein Structure
Covalent bonds between certain side chains can also modify
a protein’s shape. For example, the side chain of the amino
acid cysteine contains a sulfhydryl group (R—SH), which can
react with a sulfhydryl group in another cysteine side chain to
produce a
disulfi
de bond
(R—S—S—R) that joins the two
amino acid side chains together (
Figure 2–20
). Disulfi de
bonds form covalent bonds between portions of a polypep-
tide chain, in contrast to the weaker and more easily broken
H
NH
3
+
S
CH
3
COO
S
CH
3
Polypeptide chain
(1)
Hydrogen
bond
(2)
Ionic
bond
(3)
Hydrophobic
interactions
(4)
Covalent
(disulfide)
bond
C
O
Figure 2–17
Factors that contribute to the folding of polypeptide chains and thus
to their conformation are (1) hydrogen bonds between side chains
or with surrounding water molecules, (2) ionic bonds between polar
or ionized side chains, (3) hydrophobic attractive forces between
nonpolar side chains, and (4) covalent bonds between side chains.
C
C
C
C
C
CC
H
CH
C
C
C
C
C
C
O
O
O
O
O
O
O
H
H
H
H
H
R
R
R
R
R
R
R
N
N
H
N
Hydrogen
bond
Alpha helix
N
N
N
Figure 2–18
Hydrogen bonds between regularly spaced peptide bonds can produce a helical conformation in a polypeptide chain.
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