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There are 20 different standard L-α-amino acids used by cells for protein construction. Amino acids, as their name indicates, contain both a basic amino group and an acidic carboxyl group. This difunctionality allows the individual amino acids to join in long chains by forming peptide bonds: amide bonds between the -NH2 of one amino acid and the -COOH of another. Sequences with fewer than 50 amino acids are generally referred to as peptides, while the terms, protein and polypeptide, are used for longer sequences. A protein can be made up of one or more polypeptide molecules. The end of the peptide or protein sequence with a free carboxyl group is called the carboxy-terminus or C-terminus. The terms, amino-terminus and N-terminus, describe the end of the sequence with a free α-amino group.
The amino acids differ in structure by the substituent on their side chains. These side chains confer different chemical, physical, and structural properties to the final peptide or protein. The structures of the 20 amino acids commonly found in proteins are shown in Figure 1. Each amino acid has both a one-letter and three-letter abbreviation. These abbreviations are commonly used to simplify the written sequence of a peptide or protein.
figure1-Protein-Structure
Depending on the side-chain substituent, an amino acid can be classified as being acidic, basic or neutral. Although 20 amino acids are required for synthesis of various proteins found in humans, we can synthesize only ten. The remaining 10 are called essential amino acids and must be obtained in the diet.
The amino acid sequence of a protein is encoded in DNA. Proteins are synthesized by a series of steps called transcription (the use of a DNA strand to make a complimentary messenger RNA strand – mRNA) and translation (the mRNA sequence is used as a template to guide the synthesis of the chain of amino acids which make up the protein). Often, post-translational modifications, such as glycosylation or phosphorylation, occur which are necessary for the biological function of the protein. While the amino acid sequence makes up the primary structure of the protein, the chemical/biological properties of the protein are very much dependent on the three-dimensional or tertiary structure.
