Aminoacids and Peptide Bonds

Proteins are polymers of amino acids, linked by amide groups known as peptide bonds. An amino acid can be thought of as having two components: a 'backbone', or 'main chain', composed of an ammonium group, an 'alpha-carbon', and a carboxylate, and a variable 'side chain' (in green below) bonded to the alpha-carbon.

There are twenty different side chains in naturally occurring amino acids, and it is the identity of the side chain that determines the identity of the amino acid: for example, if the side chain is a -CH₃ group, the amino acid is alanine, and if the side chain is a -CH₂OH group, the amino acid is serine. Many amino acid side chains contain a functional group (the side chain of serine, for example, contains a primary alcohol), while others, like alanine, lack a functional group, and contain only a simple alkane.

The two 'hooks' on an amino acid monomer are the amine and carboxylate groups. Proteins (polymers of ~50 amino acids or more) and peptides (shorter polymers) are formed when the amino group of one amino acid monomer reacts with the carboxylate carbon of another amino acid to form an amide linkage, which in protein terminology is a peptide bond. Which amino acids are linked, and in what order - the protein sequence - is what distinguishes one protein from another, and is coded for by an organism's DNA. Protein sequences are written in the amino terminal (N-terminal) to carboxylate terminal (C-terminal) direction, with either three-letter or single-letter abbreviations for the amino acids (see amino acid table). Below is a four amino acid peptide with the sequence "cysteine - histidine - glutamate - methionine". Using the single-letter code, the sequence is abbreviated CHEM.

When an amino acid is incorporated into a protein it loses a molecule of water and what remains is called a residue of the original amino acid. Thus we might refer to the 'glutamate residue' at position 3 of the CHEM peptide above.

Once a protein polymer is constructed, it in many cases folds up very specifically into a three-dimensional structure, which often includes one or more 'binding pockets' in which other molecules can be bound. It is this shape of this folded structure, and the precise arrangement of the functional groups within the structure (especially in the area of the binding pocket) that determines the function of the protein.

Enzymes are proteins which catalyze biochemical reactions. One or more reacting molecules - often called substrates - become bound in the active site pocket of an enzyme, where the actual reaction takes place. Receptors are proteins that bind specifically to one or more molecules - referred to as ligands - to initiate a biochemical process. For example, we saw in the introduction to this chapter that the TrpVI receptor in mammalian tissues binds capsaicin (from hot chili peppers) in its binding pocket and initiates a heat/pain signal which is sent to the brain.

Shown below is an image of the glycolytic enzyme fructose-1,6-bisphosphate aldolase (in grey), with the substrate molecule bound inside the active site pocket.

(x-ray crystallographic data are from Protein Science 1999, 8, 291; pdb code 4ALD. Image produced with JMol First Glance)