| "If DNA is the genetic blueprint then what is the proteome? What are the proteins of the cell? The proteins of the cell are the walls, the floor, the plumbing, the beds, the furniture, the sinks, the glasses - everything that goes on in the house. All of those processes are being carried out by proteins and so DNA may be providing the instructions but all the work is really being done by the proteins." |
- Stanley Fields
What Is Proteomics?
A bacterial cell may seem simple but it's actually a complex structure - a gel-like matrix of the cytoplasm, surrounded by both a lipid bilayer cell membrane and a cell wall. The cell must perform many functions including the intake of nutrients, the metabolism of those nutrients, growth, cell division, and the excretion of wastes. What molecules are involved? Although the cytoplasm contains water, proteins, carbohydrates, various ions, and assorted other molecules, proteins do most of the work. A typical bacterium requires more than 4,000 proteins for growth and reproduction. Not all of the proteins are made at the same time and some are made only under special conditions, such as when the cell is stressed or finds itself in a novel environment. The complement of proteins found in this single cell in a particular environment is the proteome. Proteomics is the study of the composition, structure, function, and interactions of the proteins directing the activities of each living cell.
If a bacterial cell needs more than 4,000 proteins, how many can we expect to find in animals? Mammals, including humans, have probably more than 100,000 proteins. Although the genome contains the genetic blueprint for an organism, the proteins of eukaryotes provide the unique structure and function that defines a particular cell or a tissue type, and ultimately defines an organism. Different types of cells make different proteins, so the proteome of one cell will be different from the proteome of another. In addition, cells that result from a disease, such as cancer, have a different proteome than normal cells. Therefore, understanding the normal proteome of a cell is critical in understanding the changes that occur as a result of disease. This knowledge can lead to an understanding of the molecular basis for the disease, which can then be used to develop treatment strategies. Knowing how the proteome changes as the organism grows may also provide insight into the mechanisms of development in healthy organisms.
Under the classical concept of "one gene makes one enzyme," the proteome would simply comprise the products of all the genes present in the genome of an organism. But it is not that simple. The number of genes identified in the human genome is only about 30,000-35,000. How can only 35,000 genes encode more than 100,000 proteins? There are several possible answers to this question, which will be discussed in more detail below. One answer is that each gene may encode several proteins in a process called alternative splicing. Alternative splicing means that one gene may make different mRNA products and, hence, different proteins. Another answer is that one protein may be modified chemically after it is synthesized so that it acquires a different function. A third answer is that proteins interact with each other in complex pathways, and networks of pathways which may change their function. So, one gene may produce several, functionally different proteins in a variety of ways.