Amino acids are linked together to form proteins. Fig. 4.3 shows how amino acids in a protein are bonded together. The bond formed between the two amino acids is a peptide bond, shown in red in Fig. 4.3. In forming the peptide bond, the carboxyl group of one amino acid reacts with the amino group of the next amino acid in line, and a molecule of water is released. Note that, in the resulting molecule, the R groups of each amino acid point in different directions.

The C=O group in the peptide bond is known as a carbonyl group, and the N–H group is an amide group. Note in Fig. 4.3 that these two groups are on either side of the peptide bond. The electrons of the peptide bond are more attracted to the C=O group than to the NH group because of the greater electronegativity of the oxygen atom. The result is that the peptide bond has some of the characteristics of a double bond. The peptide bond is shorter than a single bond, for example, and it is not free to rotate like a single bond. The other bonds are free to rotate around their central axes.

Polymers of amino acids ranging from as few as two to many hundreds share a chemical feature common to individual amino acids: namely, that the ends are chemically distinct from each other. One end, shown at the left in Fig. 4.3, has a free amino group; this is the amino end of the molecule. The other end has a free carboxyl group, which is the carboxyl end of the molecule. More generally, a polymer of amino acids connected by peptide bonds is known as a polypeptide. Typical polypeptides produced in cells consist of a few hundred amino acids. In human cells, the shortest polypeptides are about 100 amino acids in length; the longest is the muscle protein titin, with 34,350 amino acids. The term protein is often used as a synonym for polypeptide, especially when the polypeptide chain has folded into a stable, three-dimensional conformation. Amino acids that are incorporated into a protein are often referred to as amino acid residues. In a polypeptide chain at physiological pH, the amino and carboxyl ends are in their charged states of and COO–, respectively. However, for simplicity, we denote the ends as NH₂ and COOH.

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