BIOLOGICALLY IMPORTANT MOLECULES
Molecules of biological interest can be classified into ions, small molecules and macromolecules. Typical organic small molecules include the ligands of enzymes, substrates such as adenosine triphosphate (ATP) and effector molecules (inhibitors, drugs). Ions such as Ca 2+ play a key role in signalling events. Biological macromolecules are polymers which, by definition, consist of covalently linked monomers, the building blocks. The four types of biologically relevant polymers are summarised in Table 2.1.
Proteins
Proteins are formed by a condensation reaction of the α-amino group of one amino acid (or the imino group of proline) with the α-carboxyl group of another. Concomitantly, a water molecule is lost and a peptide bond is formed. The peptide bond possesses partial double-bond character and thus restricts rotation around the C–N bond. The progressive condensation of many amino acids gives rise to an unbranched polypeptide chain. Since biosynthesis of proteins proceeds from the N- to the C-terminal amino acid, the N-terminal amino acid is taken as the beginning of the chain and the C-terminal amino acid as the end. Generally, chains of amino acids containing fewer than 50 residues are referred to as peptides, and those with more than 50 are referred to as proteins. Most proteins contain many hundreds of amino acids; ribonuclease, for example, is considered an extremely small protein with only 103 amino-acid residues. Many biologically active peptides contain 20 or fewer amino acids, such as the mammalian hormone oxytocin (nine amino-acid residues) which is clinically used to induce labour since it causes contraction of the uterus, and the neurotoxin apamin (18 amino-acid residues) found in bee venom.
THE IMPORTANCE OF STRUCTURE
Three main factors determine the three-dimensional structure of a macromolecule:
• allowable backbone angles
• i nteractions between the monomeric building blocks
• interactions between solvent and macromolecule.
The solvent interactions can be categorised into two types: binding of solvent molecules (solvation) and hydrophobic interactions. The latter arise from the inability or reluctance of parts of the macromolecule to interact with solvent molecules (hydrophobic effect), which, as a consequence, leads to exclusive solvent–solvent interactions. Phenomenologically, a collection of molecules that cannot be solvated will stick close to one another and minimise solvent contact.