Biochemistry can be simply defined as the science that deals with the chemistry of living organisms. It seeks to explain the properties of living organisms, whether a microbe or a human, in terms of the chemical substances that they contain. Cells consist of extremely complex components: proteins, nucleic acids, carbohydrates, lipids (or fats), and a host of other smaller molecules often present only in trace amounts. Moreover, thousands of chemical reactions are occurring in living cells simultaneously in a carefully controlled and regulated way. The outward manifestation of these reactions is life itself.
Biochemists use a number of scientific methods to help them understand the paths by which the body takes up and uses chemical compounds. These include chromatography, which is used to separate and identify organic compounds such as amino acids, the compounds that make up proteins. Proteins themselves can be isolated by electrophoresis, which is also useful in detecting changes in the molecular structure of blood caused by certain diseases. Radioactive isotopes are often used to "label" molecules of an organic compound so that its passage round the body and incorporation by metabolic processes can be discovered.
Living cells are separated from their environment by a membrane composed of a double layer of lipid. Embedded in this are a variety of membrane proteins that perform a variety of tasks. Some are selective channels for ions and solutes such as glucose, while others are part of the complex communication system between cells characteristic of multicellular organisms. The messages are initially carried around the body in the form of small molecules, called ligands, that diffuse through the intracellular medium and interact with larger molecules, for example, proteins. If a ligand such as a hormone interacts with a protein bound to the membrane (the hormone’s receptor) that recognizes it, then a second intracellular messenger is generated. This in turn may lead to a change in the cell’s metabolism. Two such second-messenger systems have been identified.
The first, cyclic-AMP, was discovered by Earl Sutherland in 1972. It is formed from ATP—an all-purpose energy molecule—by the activation of an enzyme, adenylate cyclase, that is bound to the membrane. The cyclic-AMP then activates enzymes called kinases that in turn can transfer phosphate groups to key metabolic enzymes, switching them on or off as appropriate. The challenge has been to discover how the binding of a ligand to a receptor on the outer membrane of the cell activates the adenylate cyclase.
A powerful tool in working out this process has been the development of analogs that mimic the activity of the natural ligands, termed agonists, and others that block the activity of the natural ligand, termed antagonists. In fact, some of the most effective drugs for asthma, hypertension, and stomach ulcers work at their respective receptors in this way. For example, a beta-2 adrenergic receptor agonist (salbutamol) activates the appropriate receptor to cause a dilation of the bronchi to relieve asthma.
Researchers have found that the intermediate between the ligand-receptor complex and the adenylate cyclase is a group of proteins called G proteins (G because they bind guanosine diphosphate). When a chance mutation switches them permanently on, these may be involved in causing some cancers. The ras oncogene, for example, behaves as a permanent stimulus for growth and proliferation, leading to a tumor.
A development in the 1980s was the discovery of the phosphoinositide system by Michael Berridge in the United Kingdom and Yasutomi Nishizuka in Japan. This second "second messenger" system controls intracellular calcium levels. Two "second messengers," diacylglycerol and inositol triphosphate, are generated by the binding of an agonist. The latter causes the release of intracellular calcium stores, while diaglycerol activates protein kinase C, which requires the released calcium for its activity and in turn transfers phosphate groups to key proteins, switching them on to give a cellular response.
The folding problem
Essentially all proteins and enzymes are composed of 20 basic building blocks called amino acids common to all forms of life on Earth. The unique sequence of amino acids that makes up a protein or polypeptide chain contains all the information it needs to take up its correct three-dimensional shape. This shape, or tertiary fold, is crucial for biological activity. However, the precise shape of a protein cannot yet be predicted from its primary amino acid sequence alone. This is because the laws that govern the "folding" of polypeptide chains are not understood. Recently, biochemists have discovered that the folding process is often aided, and its efficiency increased, by helper proteins called chaperonins.
As X-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy revealed more protein structures and amino acid sequences, biochemists came to realize that proteins and enzymes can be grouped into "superfamilies" with essentially the same tertiary fold. Over 800 enzyme superfamilies had been identified by the beginning of the year 2000.
It is also possible to model unknown protein structures using appropriate building blocks chosen from the wide range of known structures. The tools for this modeling process, increased availability of computing power coupled to high-resolution computer graphics, will eventually allow biochemists to design enzymes from scratch for specific purposes.
