BIOCHEMISTRY - L. Stryer - 1984

VOLUME 1

PART I. CONFORMATION AND DYNAMICS

CHAPTER 2. BASIC CONCEPTS OF PROTEIN STRUCTURE AND FUNCTION

2.3. Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains

In Proteins, the α-carboxyl group of one amino acid is linked to the α-amino group of another amino acid by a peptide bond (also called an amide bond). Figure 2.17 shows The formation of a dipeptide from Two Amino Acids with the release of a Water molecule. The equilibrium of this reaction lies far on the side of Hydrolysis rather than synthesis. Consequently, The Biosynthesis of peptide bonds requires an input of Free energy, whereas hydrolysis releases energy.

Class="center">Figure 2.17. Formation of a peptide bond

When A large number of amino acids (usually more than a hundred) are linked by peptide bonds, they form an unbranched polypeptide chain (Figure 2.18). Each amino acid unit in a polypeptide is called a residue. A polypeptide chain has directionality because its constituent Amino acids have different ends: either an α-amino or an α-carboxyl group. By convention, the polypeptide chain begins at the N-terminus, which is the end bearing the amino group. Thus, the Amino Acid Sequence of a polypeptide chain is written starting with the N-terminal residue. For example, in the tripeptide Alanine-Glycine-Tryptophan, alanine has the terminal amino group, and tryptophan has the terminal carboxyl group. Note that tryptophan-glycine-alanine is a different tripeptide.

Figure 2.18. A pentapeptide. Each amino acid residue is boxed. The polypeptide chain begins at the amino terminus

A polypeptide chain consists of a regularly repeating part, called the main chain, and a variable part, comprising the distinctive side chains (Figure 2.19). The main chain is sometimes referred to as the backbone of the molecule.

Figure 2.19. A polypeptide chain consists of a backbone with a regular, repeating Structure and individual side chains (R_1, R₂, R₃; shown in green)

In some proteins, individual side chains are linked by Disulfide Bonds (bridges), which are formed by The oxidation of Cysteine residues. The resulting disulfide is called cystine (Figure 2.20). Other types of covalent bonds are not typically found in proteins.

Figure 2.20. A disulfide bridge (— S — S —) is formed from The sulfhydryl groups (— SH) of two cysteine residues. The product of this reaction is a cystine residue