The lymph nodes have thick filters of phagocytic cells that pick up bacteria, but do not destroy them completely. Rather, they "process" bacterial proteins into short fragments, called peptides. These peptides are then loaded onto a special type of molecules which phagocytes produce, namely the major histocompatibility complex molecules (MHC). These complexes are then transported to the surface of the phagocytic cell, which now becomes an antigen presenting cell. The antigen is the complex of the MHC molecule and the peptide that it carries. This type of antigen can be recognized by the T cells, also known as T lymphocytes. T cells are of two major types: helper and cytotoxic T cells. Helper T cells start secreting molecules, cytokines, after being triggered by an antigen presenting cell. Cytokines regulate the functions of other lymphocytes, such as the B lymphocytes. Cytotoxic T cells are also triggered by antigen presenting cells, though through a different form of MHC. Once triggered, they may travel through the tissues. If they encounter a cell that has on its surface the complex of MHC and peptide for which the T cell is specific, that is, the one that activated the T cell, they induce that cell to commit suicide (in cellular terms this is called apoptosis). This mechanism is used in the defense against viruses. Viruses do not float around free in the body, they hide inside cells. Phagocytes do not generally detect them at this stage. But the host cell, that normally displays a sample of its protein content on the MHC molecules on its surface, will now also expose a sample of the viral proteins. These may be detected by the cytotoxic T cells, that in turn cause the infected cell to undergo apoptosis.
B lymphocytes, or B cells, also function as antigen presenting cells. In contrast with phagocytic cells, B cells pick up the antigen only in a very specific way, through their antigen receptor. The antigen receptor of B cells is also called antibody or surface immunoglobulin, largely as a result of the way researchers discovered these molecules. If a B cell encounters an antigen to which it can bind, it internalizes the complex of B cell receptor with the antigen, it processes it much the same as phagocytic cells process the antigen, and it presents MHC molecules loaded with peptides from this antigen on its surface. The antigen that B cells see is, however, in its native form, as it occurs for example on the surface of a bacterium. This is to be contrasted with the way T cells recognize the antigen, namely only in complex with MHC (in the context of MHC molecules). Once a B cell presents the antigen, it may interact with a T cell that sees the MHC-peptide complex on the surface of the B cell. A cross-talk between the two cells follows, with the effect of B cell activation. Activated B cells undergo a number of divisions, and then can differentiate into plasma cells. These cells, instead of keeping their antigen receptor on the surface, start making copies of it and release them outside the cells. These free-floating antibodies can now be distributed throughout the body, detecting their specific antigen, and attaching themselves to its surface. Antibody-coated antigen is more readily accessible to phagocytes and other components of the innate immune system.
Subsequent encounters with an antigen trigger a faster, more efficient elimination of it, to the extent that the second infection may not even be clinically apparent. This is the essence of immune memory, although the mechanisms that underlie it are not completely understood. It is also what makes vaccination so efficient. Vaccination generally involves injecting a modified form of a bacterium, virus, or toxin, into the body. This will not cause the disease, as the microbe is inactivated. However, the modified form of the microbe will still bear antigenic molecules that induce an immune response. The memory cells that are generated in this process will be capable of eliminating a fully-functional microbe should it happen to infect the host.