Primary structure

Amino acids are joined covalently in a condensation reaction between the α-carboxyl group from one amino acid and the α-amino group from another (these are the carboxyl and amino groups attached to the common central α-carbon atom in the amino acid structure). This reaction forms a C-N bond and produces a rigid peptide group (CONH) that does not readily rotate and is almost exclusively found with the oxygen and hydrogen atoms in a trans arrangement. The term 'condensation' refers to the fact that a water molecule is created as a byproduct along with each peptide bond formed.

Peptide reaction

In the reaction above the two amino acids react to form a dipeptide consisting of two amino acid residues. The term residue is applied to the remaining fragment of amino acid consisting of the side chain attached to the N-C-C backbone atoms on either side of each peptide bond. The structure of a pentapeptide is shown below with the residues surrounded by boxes. By convention such amino acid sequences are read from the amino-containing N-terminal end to the carboxyl-containing C-terminus.

Pentapeptide

Using this convention the example given on the amino acid codes page can be seen to have an alanine residue at the N-terminus and an arginine at the C-terminus:

(+H3N)ALA-PHE-PRO-LEU-SER-VAL-VAL-ARG(COO)

This gives the first step towards the construction of a protein – the polypeptide chain. The sequence of amino acid residues in this chain is referred to as the protein's primary structure. However, it should be clear that the polypeptide chain is unlikely to remain in the flat arrangement shown above. Although the peptide units themselves are planar and rigid the α-carbon has a tetrahedral geometry and its single bond connections to the adjacent atoms makes this point in the polypeptide chain flexible and liable to rotate. In fact, a better schematic for the primary structure of the polypeptide chain would be that shown below where the local geometry of the backbone atoms has been taken into account. In order to accommodate the backbone atom geometry the chain now has its peptide units and side chains facing in alternating directions in each successive residue. (NOTE solid wedges indicate bonds to atoms in front of the plane of the polypeptide chain and hashed wedges indicate bonds to atoms behind the plane)

Pentapeptide local geometry

Additional inter-residue covalent bonding: disulfide bridges

In addition to the peptide backbone, covalent bonds can be formed between the sulfurs in cysteine residue side chains. These disulfide bonds are commonly referred to as 'bridges' as they form bridging links between remote residues (unlike the peptide bonds which connect adjacent residues). These linkages can occur between cysteines in two separate chains or between cysteines in remote parts of a single chain, controlling to a large extent how the chains fold up in three dimensions.

Taking the sequence above we can mutate the serine residue to cysteine (an 'S5C' mutation if we use single letter codes) and so have two identical chains linked by disulfide bridges. Although this is a small sequence we can already see that the arrangement may be parallel

Disulfide parallel

or antiparallel

Disulfide antiparallel

If we perform a double mutation (F2C, S5C) we can now form an intra-chain disulfide bridge within a single polypeptide

Disulfide intrachain

In longer chains (proteins) many combinations of the different disulfide bridge types are often found and so these play an important part in holding (otherwise often quite flexible) protein structures in a given conformation.