After about 4 days the specific immune response begins to 'kick in'. During the early phase antigen presenting cells have carried peptides resulting from the degradation of the proteins from the infecting microorganism to the local lymph node and presented them in MHC bound form to T cells. This process allows the rare (~1 per 106) antigen specific T cells to encounter the presented peptide-MHC complex as the T cells traffic through the lymph node. One of the early responses to this specific recognition is 'shut down', inhibition of exit of lymphocytes from the lymph node via the efferent lymph which allows accumulation of cells in the local lymph node draining a site of infection.
Antigen-specific B cells acquire antigen via their surface IgM, process and present this antigen via their MHC class II molecules. The innate response also plays a part here, it has been shown that activation of the antibody response is orders of magnitude more efficient if the antigen is bound to C3d. The presented antigen-MHC complex is available for activated T cells to recognise as the B cells traffic through the T cell areas which surround their portal of entry from the draining afferent lymphatics.
The activation of T cells per se leads to the clonal proliferation of antigen-specific cells and to the production of effector T cells, such as TH1 cells and cytotoxic T cells (CTL). The interaction of specific TH cells with B cells leads to the generation first of a primary IgM-led antibody response and later to a shift to IgG, IgA and/or IgE production and to higher affinity antibodies (affinity maturation).
Specific Antibody
Specific antibody clearly plays an important role in clearing many primary infections. The presence of IgM begins to be detectable at about 5 days after antigen entry and peaks between 2-3 weeks. The IgG response is delayed by about 4-5 days and persists much longer.
IgM primarily acts as an activator of the complement system. IgG can also do this but in addition it can call into play further effector mechanisms via the Fc receptors on phagocytes, eosinophils and mast cells.
Effector T cells
Essentially two types of effector T cells are vital in the clearance of different sorts of infection. TH1 cell recruit and activate macrophages by secreting appropriate cytokines. CTL are able to recognise cells harbouring intracellular pathogens which are out of reach of humoral immunity.