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Structural Biochemistry/ Secondary Bonds
Many of the properties of protein indicate that a variety of bonds other than the peptide exist in them. These secondary bonds hold the chain in its natural configuration. Some of secondary bonds commonly found in proteins: 1.Covalent Bond- Disulfide Bond (-S-S-) Covalent bonds are strongest chemical bonds contributing to protein structure. Covalent bonds arise when two atoms share electrons. Covalent bond found between amino acid residues in protein and polypeptide in the disulfide bond of two cysteine residues to yield a mole of cystine. In general, reaction may be written as:

Hydrophobic bonds are a major force driving proper protein folding. Many amino acids ( Alanine,Valine, Leucine, Isoleucine, Methionine, Trytophan, Phenylalanine and Tyrosine) have the side chains are essentially hydrophobic. It means they have little attraction for water molecules in comparison to the strong hydrogen bonding between water molecules. The hydrophobic also play important role in the formation of enzyme-substrate complexes and antibody-antigen interactions. 4.Ionic ( Electrostatic Bond) Ionic binds are formed as amino acids bearing opposite electrical charged in the hydrophobic core of proteins. These amino acid contribute negatively charged and positively changed side chains to the polypeptide backbone. In a long polypeptide chain containing a large number of charged side chains, there are many electrostatic interactions. Ionic bond, although weaker than the hydrogen bonds, but they can be important to protein structure because they are potent electrostatic attractions that can approach the strength of covalent bonds. The force of such an electrostatic attraction is given by Coulomb's law: F=q1q2/r2D which is q1 and q2 are the charged of the two groups, r is the distance between them, and D is the dielectric constant of the medium.

Reference
Dr.B.S. Chauhan,"Principle of Biochemistry and Biophysics",University Science Press, New Delhi.