An epitope is the part of a protein which is recognized by the immune system. They are recognized by specific T cells, B cells, and the antibody produced by B cells. When these cells recognize and are activated by specific epitopes, they begin mounting an immune response. Most epitopes are derived from proteins that the immune system classifies as non-self, meaning the proteins are part of a foreign organism such as a virus or bacterium.
T cells and B cells respond to different types of epitopes. Both cell types can respond to epitopes from the same organism, but do not respond to exactly the same epitope. This is because each cell type responds to epitopes of different sizes and shapes. In general, T cells react to epitopes that are much smaller than those recognized by B cells and antibodies.
For T cells, the activating epitope is a fragment of a protein. T cell-activating epitopes are those which have been processed by immune cells called antigen-presenting cells, or APCs. When an APC processes epitopes, it does so by ingesting bacteria or viruses, and breaking those organisms down into their constituent proteins and other macromolecules. The APCs then display protein fragments, which can be as little as eight amino acids in size, on their surfaces. When a T cell recognizes an epitope and receives other necessary stimulatory signals, the T cell becomes an active part of the immune response.
In contrast, B cells and the antibodies they produce are activated by much larger epitopes. B cell and antibody epitopes are still in their normal three dimensional conformations. This difference in the types of epitopes recognized by T cells and B cells allow each cell type to perform different immune functions.
Antibodies recognize epitopes on native proteins, which are often displayed on the surface of the specific infecting organism. The bacterium or virus eventually becomes coated in antibody, making it vulnerable to phagocytic killing. In contrast, T cells recognize shorter epitopes, and become primed for different functions, such as cytokine production. They are also efficient at killing cells that are infected with viruses or intracellular bacteria, and recognize the infected cells because the infection causes the cells to display foreign epitopes on their surfaces.
The strong significance of epitopes in the immune system has led to the development of epitope mapping. This technique has been developed to try and identify elements of human pathogens which are likely to be recognized as epitopes by T cells and B cells. Epitopes that are recognized as such can then be used as targets for vaccines and can also become the basis of diagnostic tests.