Proteins and Amino Acids

A protein is a chain of amino acids. At physiological pH, amino acids exist predominantly in a zwitterionic form, carrying both, a positive and a negative charge. Each amino acid contains amine and carboxyl groups, along with a different side group, denoted as R, attached to a core carbon.

Amino acids are linked through covalent peptide bonds, and the repeating series of atoms along the core is called the polypeptide backbone.

The sequence begins at the N-terminus, with a free amino group, NH₃⁺, and ends with the C-terminus, a free carboxyl group, COO^-.

Each protein is unique, depending on the number of amino acids and their side chains. For example, thyroid-releasing hormone has 3 amino acids, whereas the elastic muscle protein titin has over 34,000.

There are 20 standard amino acids, each with a different side chain, and they fall into one of four groups.

Negative polar amino acids, such as aspartic and glutamic acid, have side chains with a carboxyl group. Because of this, they carry a negative charge at physiological pH.

Positive polar amino acids carry a positive charge at physiological pH and have nitrogen-containing side chains.

Several amino acids are polar but uncharged. They are usually hydrophilic and form the outer portion of a folded protein, where they can interact with the aqueous environment.

Lastly, a large group of amino acids has nonpolar side chains.

They can be simple, as in glycine, or complex, like proline and tryptophan.

Nonpolar side chains generally make the amino acid hydrophobic, forming the core of many proteins.