Different parts of an antibody have different functions. Specifically, the "arms" (which are generally identical) contain sites that can bind to specific molecules, enabling recognition of specific antigens. This region of the antibody is called the Fab (fragment, antigen-binding) region. It is composed of one constant and one variable domain from each heavy and light chain of the antibody. The paratope at the amino terminal end of the antibody monomer is shaped by the variable domains from the heavy and light chains. The variable domain is also referred to as the FV region and is the most important region for binding to antigens. To be specific, variable loops of β-strands, three each on the light (VL) and heavy (VH) chains are responsible for binding to the antigen. These loops are referred to as the complementarity determining regions (CDRs). The structures of these CDRs have been clustered and classified by Chothia et al. and more recently by North et al. and Nikoloudis et al. In the framework of the immune network theory, CDRs are also called idiotypes. According to immune network theory, the adaptive immune system is regulated by interactions between idiotypes.

The base of the Y plays a role in modulating immune cell activity. This region is called the Fc (Fragment, crystallizable) region, and is composed of two heavy chains that contribute two or three constant domains depending on the class of the antibody. Thus, the Fc region ensures that each antibody generates an appropriate immune response for a given antigen, by binding to a specific class of Fc receptors, and other immune molecules, such as complement proteins. By doing this, it mediates different physiological effects, including recognition of opsonized particles (binding to FcγR), lysis of cells (binding to complement), and degranulation of mast cells, basophils, and eosinophils (binding to FcεR).

In summary, the Fab region of the antibody determines antigen specificity while the Fc region of the antibody determines the antibody's class effect. Since only the constant domains of the heavy chains make up the Fc region of an antibody, the classes of heavy chain in antibodies determine their class effects. Possible classes of heavy chains in antibodies include alpha, gamma, delta, epsilon, and mu, and they define the antibody's isotypes IgA, G, D, E, and M, respectively. This implies different isotypes of antibodies have different class effects due to their different Fc regions binding and activating different types of receptors. Possible class effects of antibodies include: Opsonisation, agglutination, haemolysis, complement activation, mast cell degranulation, and neutralisation (though this class effect may be mediated by the Fab region rather than the Fc region). It also implies that Fab-mediated effects are directed at microbes or toxins, whilst Fc mediated effects are directed at effector cells or effector molecules.