Peptides and Proteins Peptide bonds

The amino acid components of peptides and proteins are linked together by amide bonds (see p. 60) between a-carboxyl and a-amino groups. This type of bonding is therefore also known as peptide bonding. In the dipeptide shown here, the serine residue has a free ammonium group, while the carboxylate group in alanine is free. Since the amino acid with the free NHs group is named first, the peptide is known as seryl alanine, or in abbreviated form Ser-Ala or SA. 

Peptide chains have a direction and therefore two different ends. The amino terminus (N terminus) of a peptide has a free ammonium group, while the carboxy terminus (C terminus) is formed by the carboxylate group of the last amino acid. In peptides and proteins, the amino acid components are usually linked in linear fashion. To express the sequence of a peptide, it is therefore suf cient to combine the three-letter or single-letter abbreviations for the amino acid residues (see p. 60). This sequence always starts at the N terminus. For 

With the exception of the terminal residues, every amino acid in a peptide is involved in two peptide bonds (one with the preceding residue and one with the following one). Due to the restricted rotation around the C-N bond, rotations are only possible around the N-C and C -C bonds (2). As mentioned above, these rotations are described by the dihedral angles ( ) (phi) and ] (psi). The angle describes rotation around the N-C bond / describes rotation around Ca-C—i.e., the position of the subsequent bond. 

The ( y / diagram (also known as a Rama-chandran plot) was developed from modeling studies of small peptides. However, the conformations of most of the amino acids in proteins are also located in the permitted areas. The corresponding data for the small protein, insulin (see p. 76), are represented by black dots in 1. 

Koolman, Color Atlas of Biochemistry, 2nd edition 2005 Thieme All rights reserved. Usage subject to terms and conditions of license. 

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