The tertiary structure is the product of the interaction between the side chains (R) of the amino acids composing the protein. Some of them contain positively or negatively charged groups, others are polar, and still others are nonpolar. The number of carbon atoms in the side chain varies from zero in glycine to nine in tryptophan. Positively and negatively charged side chains have the tendency to attract each other; side chains with identical charges repel each other. The bonds formed by the forces between the negatively charged side chains of aspartic or glutamic acid on the one hand, and the positively charged side chains of lysine or arginine on the other hand, are called salt bridges. Mutual attraction of adjacent peptide chains also results from the formation of numerous hydrogen bonds.
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Hydrogen bonds form as a result of the attraction between the nitrogen-bound hydrogen atom (the imide hydrogen) and the unshared pair of electrons of the oxygen atom in the double bonded carbon–oxygen group (the carbonyl group). The result is a slight displacement of the imide hydrogen toward the oxygen atom of the carbonyl group. Although the hydrogen bond is much weaker than a covalent bond (i.e., the type of bond between two carbon atoms, which equally share the pair of bonding electrons between them), the large number of imide and carbonyl groups in peptide chains results in the formation of numerous hydrogen bonds. Another type of attraction is that between nonpolar side chains of valine, leucine, isoleucine, and phenylalanine; the attraction results in the displacement of water molecules and is called hydrophobic interaction.
In proteins rich in cystine, the conformation of the peptide chain is determined to a considerable extent by the disulfide bonds (―S―S―) of cystine. The halves of cystine may be located in different parts of the peptide chain and thus may form a loop closed by the disulfide bond.
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If the disulfide bond is reduced (i.e., hydrogen is added) to two sulfhydryl (―SH) groups, the tertiary structure of the protein undergoes a drastic change—closed loops are broken and adjacent disulfide-bonded peptide chains separate.
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