Immune System Notes
Outline HERE

The immune system is our protection against the armada of bacteria, viruses, and parasites from the rest of the world. Despite a genome size of 3 x 109 bp, the immune system can produce more than 108 distinct antibodies and more than 1012 T-cell receptors. In addition, the immune system is remarkably good, for the most part at not making antibodies against the body in which it is housed, except for occasional autoimmune diseases.

Humoral Response

Two elements of the immune system combine to provide protection. The first is the humoral response, which employs soluble proteins called antibodies that recognize and bind structural features of foreign molecules in the body. These serve as markers signaling foreign invasion. Antibodies are secreted from plasma cells, which are derived from B lymphocytes (B cells) of the immune system. The molecule bound by an antibody is called an antigen. The specific structural feature of the antigen bound by the antibody is called an epitope.

Cellular Response

The second component of the immune system is the cellular immune response, which employs cytotoxic T lymphocytes (killer T cells) to kill cells with specific structures on their surfaces. A second class of T cells, known as Helper T Lymphocytes (Helper T Cells) aid both the cellular and humoral immune responses by stimulating differentiation and proliferation of specific B cells and cytotoxic T cells.

Diversity Strategy

The immune system manages to create such diversity using molecular mechanisms of recombination and splicing, combined with evolutionary principles of selection of the most well-suited members of a population. The earliest examples of selection occur early in the development of an immune response in an organism. During this time, immune system cells producing antibody molecules that bind tightly to molecules of the host organism are destroyed or silenced, but cells that make antibodies that do not bind strongly to host molecules are preserved to later be used for protection against foreign invaders.


The major antibody of blood serum, called immunoglobulin G (IgG) is composed of H - heavy (50-kd) and L- light (25-kd) chains arranged as L2H2. The chains are held together via disulfide bonds. Both the L and the H chains have structural features common to immunoglobulins called immunoglobulin domains. Cleavage of the IgG molecule using the protease papain yields three fragments. Two of these fragments, called Fab bind antigen and the third, Fc, does not. Note that the two Fab molecules produced by papain treatment contain both an intact L chain and a portion (amino terminus) of the H chain. The linkages between Fab and Fc are flexible (called segmental flexibility) to facilitate interactions between both binding sites. The two binding sites on an antibody can also form cross-link-like structures.

Besides IgG, the blood serum also contains other classes of immunoglobulins. Each class contains light chains composed of either kappa or lambda Light chains and Heavy chains distinct for each class. IgM is the first antibody class to appear after exposure to antigen. IgM's ten binding sites allow it to bind antigens with multiple identical epitopes. The strength of binding of an antigen by an antibody is referred to as avidity because this is the sum of all the binding interactions. The term affinity refers to the binding strength of a single site.

IgA is the predominant antibody in secretions (saliva, tears, mucus). As such, IgA is a first line of defense against bacteria and viruses. IgE is implicated in protection against parasites and also in allergic reactions by virtue of its stimulation of the release of histamine and subsequent release of mucus.

Antibody Structure

Sequence analysis of IgG antibodies reveals that the carboxy half of the L chains and the caroby terminal three quarters of the H chains are very similar in all antibodies. Analysis of the amino terminal domain of the H chains reveals that three regions are 'hypervariable'. These regions correspond to loops in the immunoglobulin domain structure.

A common structural domain found in the immunoglobulins and other proteins with roles in the immune system is the Immunoglobulin Fold. It consists of a pair of beta sheets with antiparallel beta strands that surround a hydrophobic core. A single disulfide bond holds the two sheets together. Over 750 human proteins have an immunoglobulin fold, but interestingly, this structure does not appear to be present in yeast or plants.

Antibody Binding

The light and heavy chains on the arms of the antibody come together in such a way that the hypervariable regions align themselves on the same 'face' of the antibody. It is on this face that antibody-antigen interactions occur. Mixing of hypervariable regions of the light chain (VL) with that of the heavy chain (VH) allows for even more diversity of antibody structure. Complementarity of shape between the variable regions of the antibody and specific structures in the antigen are essential for antibody-antigen binding. Hydrogen bonds, electrostatic interactions, van der Waals interactions, and hydrophobic interactions all contribute to stabilization of the antibody-antigen complex. Binding of epitopes of large molecules by antibodies involves the same types of interactions as for binding of small molecules, but large antigens often have multiple epitopes that are recognized by different antibodies. Thus, it is not unusual for many different antibodies to recognize the same macromolecule, but bind it on different epitopes.

Antibody Diversity

Rearrangement of DNA (recombination) occurs during differentiation of antibody-producing cells. 40 different variable coding regions (called V1 - V40) and 5 different joining regions (J1-J5) are encoded upstream of the constant region (C) in undifferentiated cells. Recombination between (for example) the V2 region and the J4 region excises the previously intervening DNA as a circle and abuts the V2 and J4 regions to create a rearranged gene. Splicing can remove the remaining non-coding gaps to produce a functional light chain protein. Heavy chains too undergo recombinational events and also have randomizing alterations possible by use of a novel DNA polymerase called terminal deoxyribonucleotidyl transferase (or as it's more commong called, terminal transferase) that randomly adds nucleotides between segments VH and D during recombination. Immune cells have specific enzymes called RAG-1 and RAG-2 for facilitating recombination of V,D, and J segments.

Approximately 108 different antibody structures can be created by the processes above (combinatorial association) combined with an interesting process called affinity maturation. In this process, somatic mutations in recombined genes evolve slightly modified structural variants of the antibodies to permit them to more precisely fit the antigen structure they recognize.

Immature bone marrow cells (called B cells) express approximately 105 IgM molecules on their surface. Each B cell expresses only one particular IgM. Different B cells, however will express slightly different antibodies on their surface using the mechanisms described above. When an immature B cell binds an antigen via its surface antibody, the B cell is stimulated to grow and divide, producing many copies of itself and the antibody it expresses. The IgM is flanked by immunoreceptor tyrosine-based activation motifs (ITAM). When multiple IgMs on the surface of a B cell bind an antigen, it causes oligomerization of the IgMs and stimulates phosphorylation of ITAM tyrosines by protein tyrosine kinases, such as Lyn. Phosphorylation of ITAM tyrosines provide a docking site for Syk, another protein kinase that phosphorylates transcription factors, among other targets. These events lead to initiation of a signaling cascade that activates gene expression that leads to cell growth and further B cell differentiation.

At the beginning of an effective antibody-based immune response, membrane linked IgM is replaced by synthesis of a secreted form of IgM. This form is pentameric. Later, antibodies of the IgG, IgA, IgD, or IgE clases are made having the same specificity as the secreted IgM. This is made possible by Class Swtiching in which the light chain and variable region of the heavy chain are unaltered, but the constant region of the heavy chain is mixed and matched with the VDJ region of the heavy chain from IgM.

Major-Histocompatibility-Complex (MHC) Proteins

Intracellular pathogens, such as viruses and some microorganisms are shielded from action by soluble antibodies. Another type of immunity called celllular immunity is effective on intracellular pathogens. Immune system cells called T cells scan cell surfaces looking for any that exhibit foreign marking and triggering them to commit suicide. Recognition of infected cells is accomplished in vertebrate cells by cutting up of proteins in the cytosol by complexes called proteasomes. The resulting peptide pieces are bound by the MHC proteins and the complex travels through the endoplasmic reticulum and gets displayed on the surface of the cell. Host, as well as pathogen peptides, can be displayed in this way, but only pathogen proteins are recognized as foreign. When foreign proteins are detected, a cascade that induces apoptosis (cellular suicide) occurs in the infected cell.

Critical to the process of cellular immunity is the recognition of MHC-displayed peptides by a protein on the surface of T cells called the T cell receptor. Structural domains of the T cell receptor are homologous to V and C domains of immunoglobulins. Hypervariable regions in these proteins provide the T cell receptor binding sites for epitopes. The T cell receptor has over 1012 different specificities that can be created. Like B cells, the multiple T cell receptors on a given T cell are identical. T cell receptor is assisted in recognizing and determining the fate of target cells by a coreceptor protein called CD8. CD8 is a dimer with a domain that resembles the variable domain of immunoglobulins. CD8 interacts primarily with a specific region of class I MHC proteins called alpha3. The T cell receptor is flanked by six CD3 molecules with intracellular ITAM domains like the IgM surface antibodies of B cells. Activation of a T cell - don't worry about the complexity) results in secretion by the T cell of a protein called perforin, which polymerizes and forms pores on the target cells. The pores provide entry for proteases called granzymes (also secreted by the T cell) into the target cell. Action of granzymes in the target cell initiates the process of apoptosis in the target cell. After this process is complete, the T cell dissociates from the target cell and is stimulated to reproduce, generating more cells that will target similarly infected cells.

Helper T Cells

The class of T cells described to this point are the cytotoxic T cells. Another class of T cells, called Helper T cells, stimulate the proliferation of B cells and cytotoxic T cells and are important partners in the immune response. It is this helper T cell that is the target of HIV. Helper T cells also detect foreign peptides on the surface of infected cells, but the peptides they recognize are presented by the infected cell using a different class of MHC called Class II MHC proteins. Class II MHC proteins are present only on antigen presenting cells such as B cells, macrophages, and dendritic cells. The peptides on MHC Class II proteins come from digestion of internalized peptides. Instead of CD8 of the cytotoxic T cells, helper T cells use a coreceptor protein called CD4. (Side note - CD4 is a target and means of entry of the HIV virus. When helper T cells bind to an antigen-presenting cell on a Class II MHC protein, signaling pathways similar to those in the cytotoxic T cell are stimulated in the helper T cell. One difference, though, is that instead of stimulating apoptosis in the MHC-presenting cell, the helper T cell secretes cytokines. Cytokines are molecules that bind to specific receptors in the target cell and stimulate growth, differentiation, and (in plasma cells - derived from B cells) antibody secretion. Thus the helper T cell stimulates local defenses to help the target cell overcome its problems.

MHC proteins have a high degree of variability. Transplantation rejection occurs as a result of incompatibilites in MHC proteins between different individuals.

Suppression Against Self Antigens

The incredible efficiency of the immune system to target and destroy makes it all the more important that it avoid attacking its own host. The means by which the system accomplishes this occurs early in development when the randomly produced immune cells produce some cells that do, in fact, react with self antigens. These self-antibodies cells are eliminated selectively in the course of development, preventing their proliferation and subsequent problems. Thus, the only immune cells remaining after that point are those that by the process of selection cannot bind the host antigens. Failure to eliminate immune cells that recognize host antigens lead to autoimmune diseases, such as insulin-dependent diabetes mellitus, multiple sclerosis, and rheumatoid arthritis.