When an organism’s immune system encounters a foreign molecule (typically a protein) for the first time, specialized cells such as macrophages and dendritic cells capture the molecule and begin breaking it down so that it can present these antigens to B cell lymphocytes.

Once Antigen Presentation to the B cell lymphocytes has occurred, a process known as Somatic Hypermutation allows the B cell to begin coding for a new antibody that will contain a unique Antigen Binding Site in the variable region that is capable of binding specifically to an epitope from the antigen.

Each B cell lymphocyte produces one unique antibody against one unique epitope.

Once antibodies with sufficient specificity to the epitope can be encoded, the B cell begins to release antibodies into the bloodstream. These antibodies then bind specifically with the foreign molecule and allow the immune system to eliminate the molecule from the system.

In some cases, these antibodies can disable pathogens such as viruses directly due to the binding action. In other cases, such as with bacterial pathogens, these antibodies bind to surface proteins on the bacterium’s surface, thereby signaling to the rest of the immune system that the pathogen should be destroyed.

After the foreign molecule has been eliminated, B cells remain in the bloodstream ready to produce antibodies if the antigen is encountered again.

From the perspective of developing a custom antibody against a protein antigen, the immune system captures the protein, breaks it down into individual epitopes and presents these epitopes to the B cells so that development of antibodies specific to those epitopes can begin. These antibodies can then be collected directly in the serum or by isolating the individual B cells that produce antibody against the epitope of interest. With a full-length protein antigen, there will typically be multiple B cells generating antibodies against multiple epitopes from different regions of the protein.

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