34 BIOCHEMISTRY FUNDAMENTALS
secondary, tertiary, and quaternary structure of proteins controls their three -
dimensional shape, which, in turn, affects their activity. The primary structure
of proteins is formed by a condensation reaction resulting in a peptide bond
as shown below in Figure 2.6. In this example, the zwitterions of cysteine and
isoleucine combine to form the peptide bond via a condensation reaction
between theα - carboxyl group of one amino acid and the α - amino group of
another amino acid. A water molecule is eliminated as each successive peptide
bond is formed. The peptide bond is rigidly planar and has a bond length
intermediate between a single and a double bond. This rigid bond forms the
backbone of the protein. Other single bonds in a polypeptide chain are fl exible
and can and do rotate.
The N - terminal end of a polypeptide chain, with its free amino group,
is conventionally known as the beginning of the chain, while the last amino
acid, with its free carboxyl group, is the C - terminal end of the chain (see
Figure 2.7 ).
A protein ’ s secondary structure arises from the formation of intra - and
intermolecular hydrogen bonds. All carboxyl group oxygens and amine hydro-
gens of a polypeptide participate in H - bonding. Protein secondary structure
also derives from the fact that while all C – N bonds in peptides have some
double - bond character and cannot rotate, rotation about the C α – N and C α – C
bonds is possible. These rotations are affected by peptide R groups that have
differing space and charge constraints. The illustration in Figure 2.8 indicates
the C α – N bond angle φ (phi) and C α – C bond angle ψ (psi) about which rota-
tion is possible.
Two types of protein secondary structure are the α - helix and β - pleated
sheet, and their representations can be seen in Figure 2.9. The right - handed
α - helix occurs in globular proteins and is formed by intramolecular hydrogen
bonds between the carboxyl group oxygen of one amino acid and the amine
hydrogen of the fourth amino acid away from ( i + 4 in Table 2.1 ). This
helix completes one turn every 3.6 residues and rises approximately 5.4 Å
with each turn. Other known types of protein helices are the π - helix and the
3 – 10 helix. The left - handed α - helix is known but not found in protein struc-
tures. As can be seen in Table 2.1 , these helical structures have differing ψ
and φ angles and different H - bonding patterns.^3 Many websites feature
Figure 2.6 Formation of a peptide bond.+H 3 NCHC
CH 2O-OSH+H 3 NCHC
CHO-OCH 3
CH 2
CH 3+H 3 NCHC
CH 2OSHNCHC
CHO-OCH 3
CH 2
CH 3H+Peptide bondcysteine isoleucine+ H 2 O