Studying genes and proteins gives a limited picture of what is going on in a cell. As we have seen, both gene function and protein function are affected by the internal and external environments of the cell. Many proteins are enzymes, and their activities affect the concentrations of their substrates and products. So as the proteome changes, so will the abundances of small molecules called metabolites. The metabolome is the complete set of small molecules present in a cell, tissue, or organism under defined conditions. These include:
Primary metabolites involved in normal processes, such as intermediates in pathways such as glycolysis. This category also includes hormones and other signaling molecules.
Secondary metabolites, which are often unique to particular organisms or groups of organisms. They are often involved in special responses to the environment. Examples are antibiotics made by microbes, and the many chemicals made by plants that are used in defense against pathogens and herbivores.
Not surprisingly, measuring metabolites involves sophisticated analytical instruments. If you have studied organic or analytical chemistry, you may be familiar with gas chromatography and high-
There has been some progress in defining the human metabolome. A database created by David Wishart and colleagues at the University of Alberta contains more than 6,500 metabolite entries. The challenge now is to relate levels of these substances to physiology. For example, you probably know that high levels of glucose in the blood are associated with diabetes. But what about the early stages of heart disease? There may be a pattern of metabolites that is diagnostic of this disease. This could aid in early diagnosis and treatment.
Plant biologists are ahead of medical researchers in the field of metabolomics. Over the years, tens of thousands of secondary metabolites have been identified in plants, many of them made in response to environmental challenges. Some of these will be discussed in Chapter 38. The metabolome of the model organism Arabidopsis thaliana is being described, and will give insight into how a plant copes with stresses such as drought or pathogen attack. This knowledge could be helpful in optimizing plant growth for agriculture.