residues linked together by peptide bonds describes the primary structure
of the protein. Localized regions of the protein fold into well-defined and
stable arrangements of amino acid residues giving rise to structural patterns
that are recurring in proteins, namely αhelices and βsheets. The overall
fold of these secondary-structure elements describes the tertiary structure
of the protein. The quaternary structure is the arrangement of different
polypeptides of the protein. In addition, proteins can also be described
as having motifs; that is, arrangements of elements that are common in
different proteins.Peptide bonds
Critical for amino acids is their ability to form peptide bonds in which
the carboxyl group of one amino acid is joined to the amino group of
another amino acid, resulting in the loss of a water molecule (Figure 13.6).
Many amino acids joined by peptide bonds form a polypeptide chain. This
chain consists of the regularly repeating main chain or backbone and the
side chains. The peptide unit is always rigid and planar with the hydrogen
of the amino group opposite to the oxygen of the carbonyl group, with
the exception of bonds involving proline. The bond between the carbonyl
carbon atom and the nitrogen atom is not free to rotate, owing to the
presence of the partial double-bond character. However, the bonds at the
end of the peptide unit are free to rotate, allowing polypeptide chains to
form a wide range of three-dimensional protein structures.Steric effects
The nature of the peptide bond plays a critical role in the conformation
of the protein. Of the backbone atoms, the oxygen has a partial negative
charge and the nitrogen has a partial positive charge establishing a dipole
moment. The six atoms of the peptide group lie in a plane and the chain
can be considered to consist of a series of planes that can rotate relative
to each other (Figure 13.7). By convention, the bond angles arising from
rotations at the Cαposition are identified as φrotations and ψrotations
are those centered around the N–Cαbond. Both angles are defined to have
a value of 180° when the polypeptide is in its fully extended conformation.278 PART 2 QUANTUM MECHANICS AND SPECTROSCOPY
R (^1) O
O
H 3 N C C C
H
R (^2) O
O
H 3 N C C C
H
R 1 O O
O
H 3 N C C C
H H
Peptide bond
N
R 2
C C H 2 O
H
Figure 13.6Formation of the peptide bond and the resulting polypeptide chain.