Proteins and peptides are large biomolecules made of α-amino acid residues linked together by amide, or peptide, bonds. Twenty amino acids are commonly found in proteins, and all except glycine have stereochemistry similar to that of L sugars. In neutral solution, amino acids exist as dipolar zwitterions.
Amino acids can be synthesized in racemic form by several methods, including ammonolysis of an α-bromo acid, alkylation of diethyl acetamidomalonate, and reductive amination of an α-keto acid. Alternatively, an enantioselective synthesis of amino acids can be carried out using a chiral hydrogenation catalyst.
Determining the structure of a peptide or protein begins with amino acid analysis. The peptide is hydrolyzed to its constituent α-amino acids, which are separated and identified. Next, the peptide is sequenced. Edman degradation by treatment with phenyl isothiocyanate (PITC) cleaves one residue from the N terminus of the peptide and forms an easily identifiable phenylthiohydantoin (PTH) derivative of the N-terminal amino acid. An automated series of Edman degradations can sequence peptide chains up to 50 residues in length.
Peptide synthesis involves the use of protecting groups. An N-protected amino acid with a free –CO2H group is coupled using DCC or EDC to an O-protected amino acid with a free – NH2 group. Amide formation occurs, the protecting groups are removed, and the sequence is repeated. Amines are usually protected as their tert-butyloxycarbonyl (Boc) or fluorenylmethyloxycarbonyl (Fmoc) derivatives; acids are usually protected as esters. The synthesis is often carried out by the Merrifield solid-phase method, in which the peptide is bonded to insoluble polymer beads.
Proteins have four levels of structure. Primary structure describes a protein’s amino acid sequence; secondary structure describes how segments of the protein chain orient into regular patterns—either α helix or β-pleated sheet; tertiary structure describes how the entire protein molecule coils into an overall three-dimensional shape; and quaternary structure describes how individual protein molecules aggregate into larger structures.
Proteins are classified as either globular or fibrous. Fibrous proteins such as α-keratin are tough, rigid, and water-insoluble; globular proteins such as myoglobin are water-soluble and roughly spherical in shape. Many globular proteins are enzymes—substances that act as catalysts for biological reactions. Enzymes are grouped into six classes according to the kind of reaction they catalyze. In addition to their protein part, many enzymes contain cofactors, which can be either metal ions or small organic molecules called coenzymes.
