Dalhousie University Dalhousie University Faculty of Medicine


Chapter 2: Antibodies and the Cells That Make Them

Antibodies, also called “immunoglobulins”, are one of two important protein molecules of the immune system that engage in the recognition of pathogens or other foreign material.  This process is called “antigen recognition” and is a pivotal process in the immune response (see Appendix 3 – Normal Antibody Levels).  The other antigen recognition molecule is found on the T cell and is called the T cell receptor (TcR).   Antibodies act as recognition units on the surface of B cells (where they are called the B cell receptor) but usually, when we think of antibodies, we are thinking of the antigen specific soluble proteins secreted into the blood and tissue by antibody producing cells. Soluble or secreted antibody is structurally slightly different from the antibody on the surface of B cells but the antigen recognition sites are the same.

There are five different classes (isotypes) of immunoglobulins:  IgD, IgA, IgM, IgE and IgG. There are subclasses of some of the five classes and they vary among species. Each of the antibody classes will be considered separately in this book but let us first consider the basic function of antibodies. Later we will look at the structure and how the genes for these proteins make the amazing diversity of these proteins possible.

Antibodies recognize antigen. If you are unclear what an antigen is, then take a minute and read about it. The ability of antibodies to recognize specific antigen is an important characteristic. Antigen recognition and binding allows antibodies to perform four important effector functions.

1. Opsonization for phagocytosis
2. Activating Complement
3. Neutralizing toxins
4. Blocking attachment of pathogens to cells or tissue

1. Opsonization: This is the process by which things like bacteria, viruses and small parasites are 'tagged' for destruction by macrophages and neutrophils.  Antibodies are the 'tags' (or opsonins) because the antigen binding (Fab) area of the antibody binds to an antigen on the surface of the organism. The other end of the antibody (Fc) binds to receptors on phagocytic cells. The antibody signals the phagocytic cell to engulf and destroy the organism.  If the organism is too big to engulf (like a parasitic worm for example) the phagocytic cells will release destructive enzymes and other factors onto the surface of the organism (sometimes called “frustrated phagocytosis). IgG is the most important antibody for this because it is very abundant and fits nicely into the Fc receptor on the surface of the phagocytic cells.  IgM and IgA are very poor at this because they are secreted as multimers.

2. Activating Complement:  This refers to the process by which antibody binds to an antigen on the surface of a pathogen by its Fab section.  This leaves the Fc section free to bind the first component of Complement (C1).  This binding of C1 (often called “fixing Complement”) activates an enzyme cascade which results in lysis of the organism by the membrane attack complex (the MAC attack, see section on Complement).   IgM and IgG are very good at this.

3. Neutralization of Toxins: Some pathogens secrete dangerous toxins (such as tetanus toxin).  In the circulation, tissues and secretions (such as mucus), antibody will bind to these toxins and neutralize their activity. Antibodies also form easily recognized antibody-toxin complexes which are removed from the body by phagocytosis.
4. Blocking Attachment: Antibodies can immobilize and agglutinate infectious agents by binding to their surface antigens and preventing them from attaching to tissues like the intestinal mucosa or from penetrating cells (in the case of viruses).

Antibody Structure

2.1 Antibody Structure

Antibody is made up of four polypeptides or "chains".  Actually, each antibody molecule is composed of two sets of two chains.  The general structure is shown below:
The heavy chain is the largest (and thus the heaviest). There are two identical heavy chains and two identical light chains in each antibody. The heavy and light chains are folded into domains and are held together by disulphide bonds.  In humans there are two different kinds of light chain (kappa and lambda) and five different kinds of heavy chains (m, d, g, e, a; more about these below).
Once the heavy and light chains are assembled, however, the areas or “regions” of the antibody become more important than the chains.
The two important regions of the antibody are:
- the Fab region
- the Fc region
The antigen binding region (Fab) is the recognition region of the antibody.  It has great diversity so that antibodies can be made to recognize any and every antigen the body encounters. The Fc region is responsible for the effector function of the antibody (such as opsonization or Complement activation) and also defines the class of antibody (IgG versus IgA for example).
Fab Region of Antibodies

2.2.1 Fab Region of Antibodies

The Fab region of antibody is involved in antigen binding.  This region is composed of the entire light chain (either kappa or lambda) and a part of the heavy chain. Often this region is called F(ab)2 because the two Fab regions of the antibody (like the two arms of a human) are joined together in the middle by bonds. 

The N-terminal end of the Fab region consists of a “hypervariable” area of the heavy chain and a hypervariable region of the light chain.  This hypervariable region is the area encoded by the gene elements that undergo random gene rearrangement, thereby generating amino acids and thus structural diversity.

Fc Region of Antibodies

2.2.2 Fc Region of Antibodies

The Fc region of the antibody is limited in variability and is responsible for the biological activity of the antibody (as opposed to antigen binding). The Fc region is made up of only heavy chain elements.  There is no light chain in the Fc region. The Fc region varies between antibody classes (and subclasses) but is identical within that class.  The Fc region of an IgA molecule that reacts with an antigen on E. coli will be identical to the Fc region of an IgA molecule that reacts with an antigen on Salmonella but the Fab regions of these two antibodies will be different. However, the Fc region of an IgG molecule that reacts with a Salmonella antigen and an IgA molecule that reacts with the same antigen would be different. The C-terminal ends of the heavy chains form the Fc region. The Fc region plays an important role as a receptor binding portion and in binding Complement.

The Fc portion of antibodies will bind to Fc receptors in two different ways. For example, IgG binds first to a pathogen by its Fab portion before its Fc portion can bind to receptors on phagocytic cells (like macrophages) inducing phagocytosis. In contrast, the Fc portion of free floating IgE binds to Fc receptors (FcE) on mast cells before the antibody reacts with antigen. 
The Fc portion of antibody also binds Complement and initiates the classical pathway of Complement activation which leads to lysis of the pathogen by the MAC attack.
Antibody Diversity

2.3 Antibody Diversity

One question immunologists have struggled to answer is how antibodies can be made to recognize virtually any and every foreign antigen the body is confronted with. Extensive work in molecular genetics has revealed how this comes about. A brief discussion of the gene rearrangements responsible will be included here but a more complete discussion can be found in immunology texts.

Each antigen binding region (Fab) is made of a variable domain of a heavy chain and a variable domain of a light chain. It is these variable domains that create the diversity in antibodies.
Let us consider the heavy chain first. In the gene for the heavy chain, there are many segments. From the 5' end to the 3' end, the segments are called variable heavy (VH), diversity heavy (DH) and joining heavy (JH), then the constant (C) regions.

In the human immunoglobulin gene locus there are 300-1000 different VH segments in tandem, 13 different DH's and 4 JH's.  During the development of young B cells they undergo a process called “immunoglobulin gene rearrangement”.  In this process most of the gene segments in the immunoglobulin gene locus are randomly spliced out and deleted and the remaining segments are recombined so that one VH segment is combined with one DH segment and one JH segment.  The rest of the gene segments are discarded. Since there are so many different segments to choose from, many thousands of different combinations can be made. Each combination has a slightly different gene sequence.

In addition to the segment selection, the unique mechanism for splicing the segments together adds further diversity by randomly adding or removing nucleotides to the segments as they recombine.  Even one nucleotide difference can have dramatic effects on the final antigen binding structure.  Both of these processes result in many different amino acid sequences of the mature variable region protein, resulting in many unique conformations.

The same segment selection and recombination process takes place to create the variable region of the light chains except that there are no D segments in the light chains.

The result of all this random recombination is the ability to produce a tremendous spectrum of antibodies because many thousands of possible heavy chains can combine with thousands of possible light chains. This is reflected in the fact that millions of different B cells exist in our bodies at any one time and within that B cell population is the ability to produce antibodies able to recognize a huge diversity of antigens.
Antibody Classes

2.4 Antibody Isotypes (Classes)


This antibody class has the mu (m) Heavy Chain.  It can be found as "surface antibody" on the surface membrane of B cells or as a 5-subunit macromolecule secreted into the blood by activated B cells and plasma cells.  Surface IgM (sIgM) is structurally different in the Fc region from secreted IgM because to be stably expressed on the surface of the B cell it must be tethered to the B cell surface membrane.  Surface IgM binds directly as an integral membrane protein so it has a “transmembrane domain” attached to the bottom of the Fc region.  sIgM does not bind to an FcR like IgE or IgG does.

Secreted IgM is found as a "pentameric" molecule in blood at moderate levels (1-3g/l in adults). The five IgM subunits are held together by a polypeptide (J-chain, for joining).  Because each IgM subunit has two antigen binding sites, this means that the IgM pentamer has 10 binding sites for antigen. Pentameric IgM binds to antigens on the surface of a pathogen like a spider. Because of its pentameric configuration, IgM is particularly good at activating Complement, via its Fc regions, and causing agglutination but it is very poor at opsonization. IgM is the first antibody to be produced in response to infection since it does not require "class switch" to another antibody class.


This antibody class has the gamma (g) Heavy Chain.  It is the most abundant class of antibody in the blood (serum concentration is 8-16 g/l !). There are four subclasses of IgG (with slightly differing g chains).  They are all monomeric and they usually have a very high affinity for antigen. Unlike IgM, IgG is able to rapidly leave the blood stream and enter tissues, especially at sites of inflammation.  This is primarily because pentameric IgM is very large (about 900kDa) and IgG is much smaller (about 160kDa). 

IgG is also the only class of antibody to be actively transported across the placental barrier. Therefore IgG provides the only antibody protection for newborns until their own immune system begins to produce antibodies in response to antigen.

The subclass of IgG produced is dependent on the cytokines present (especially IL-4 and IL-2) and each class has its own special activity. In general though, IgG is very good at activating Complement, and is the best antibody for opsonization using Fc receptors on phagocytes. This is because phagocytes have a large number of Fc gamma receptors (FcgR) on their surface. IgG also plays an important role in neutralizing toxins produced by pathogens in the blood and tissues.


This antibody class has the alpha (a) Heavy Chain.  IgA is found in low levels in the blood (1.5-4 g/l) in both monomeric and dimeric forms but IgA is most abundant and most active in secretions at mucosal surfaces where it appears as a dimeric protein. The two IgA molecules are held together by J chain polypeptide (not the same as the J region of the antibody gene). To pass through epithelial surfaces, a secretory component is transiently attached to dimeric IgA. The dimeric IgA provides the primary defense at mucosal surfaces such as bronchioles, nasal mucosa, prostate, vagina, and intestine. IgA is also abundant in saliva, tears and breast milk, especially colostrum.


This antibody class has the epsilon (e) Heavy Chain.  The blood concentration of this antibody is normally very low as most IgE is tightly bound to its Fc epsilon receptors (FceR) on mast cells and basophils. The production of IgE is controlled by specific cytokines and this class of antibody is responsible for Type I hypersensitivity reactions (allergy, asthma and anaphylaxis). IgE is increased greatly in response to helminth (worm) parasite infection.


This type of antibody is found on the surface of most B lymphocytes just like sIgM. So far, the exact function of this antibody is unknown but it appears that it acts as an antigen receptor and that it is needed for B cell activation. A very small amount of IgD is secreted, and its functions as a secreted antibody are unclear.


B cells

2.5 The Cells that Make Antibody - B cells

2.5.1 B Cell Development

Pre B Cell to B Cell
For a B cell to be functional it needs to have a functional antibody on its surface.  The stages in B cell development are concerned with the generation of that surface antibody and testing to make sure it works (it can activate the B cell signaling pathways).

B cells develop from stem cells in the bone marrow. At the youngest stages in the bone marrow, pre-B cells rearrange the gene for antibody heavy chain.  If they successfully transcribe and translate the heavy chain protein they attach two heavy chain molecules together as a “dimer”. Then they attach to this dimer two molecules of a light chain substitute called “surrogate light chain”.  At this stage this composite molecule looks a lot like normal antibody.  They bring this composite molecule to the surface of the cell to be sure that it will insert properly into the membrane using the transmembrane region of the heavy chain.  They also test to make sure that all the right membrane signal transduction elements associate with the heavy chain.  This is essentially a test of the heavy chain.  So much gene rearrangement goes on that you have to be sure that the end result has an Fc region that works and that the other end will bind to light chain.
Heavy chain passes the test if the composite molecule on the surface activates Bruton’s tyrosine kinase (BTK).  Activation of this signal transduction molecule will ensure that a cascade of events will occur that leads to continued life and happiness for the pre-B cell.  Failure to activate BTK will lead to pre-B cell death.  Remember that the B cell gets a second chance at this process because there are always two alleles (maternal and paternal) for every gene.  It can try again on the second allele.  If the first allele is successful the other one is shut down by a process called “allelic exclusion”.

If the heavy chain looks OK then the pre-B cell will go ahead and rearrange the light chain gene (again it has two tries because it has two alleles.)  Successful light chain gene rearrangement leads to the expression of fully developed IgM (and IgD) on the surface of the B cell.  These surface antibodies have a transmembrane domain so they are attached directly into the membrane, not to Fc receptors.  The expression of surface antibody marks the transition from “pre-B cell” to a mature naive B cell. 

Naive B Cells
The new (naive) B cells then enter the circulation and travel through the blood to lymphoid organs. The B cells are called naive because they have not seen antigen yet.
It is important to know that each and every naive B cell (and there are many millions in the body at any one time) has a different antibody on its surface.  Actually, each B cell has hundreds of thousands of antibodies on its surface but for each individual B cell all the surface antibodies are identical and all bind to the same site on the recognized antigen.  In contrast, surface antibody varies from B cell to B cell. Thus the surface antibodies on all the millions of B cells are not identical. The B cell population achieves this “diversity” by random gene re-arrangement.  This concept was discussed earlier in the antibody section but essentially it means that every B cell makes changes to the DNA that code for the heavy and light chains which form an immunoglobulin molecule.  Since there are millions of such changes that could be made, and they are random changes, then the resulting antibody produced by each B cell is different. 
In addition, once a B cell makes surface IgM it can then make a different class of antibody (class switch).  However, class switch only involves a change in the Fc region of the antibody, not in the antigen binding (Fab) region. That means class switch changes the class (and function) of the antibody but not its antigen specificity. 

In the lymph nodes, naive B cells may encounter an antigen recognized by their surface antibodies. As you might imagine, there are many (more than 99%) that circulate their entire life span without encountering antigen. These cells die within a few days. That's not nearly as exciting as what happens to B cells that do encounter antigen. The results are:

B cell activation
B and T cell interaction
Differentiation into plasma cells
Antibody secretion and class switch
Production of B memory cells

            see B cell Malignancies Clinical Notes (Appendix 7)


B Cell Activation

2.5.2 B Cell Activation

B cells can recognize antigen in its native form as soluble protein, unlike T cells which require antigen to be degraded and presented on the surface of an antigen presenting cell in the context of MHC (see section on T cell activation). The antigen recognition unit of the B cell is the surface immunoglobulin. Surface antibodies are antigen specific but, remember, the naive B cell has never been in contact with an antigen. The antigen-specificity arises from random gene rearrangements (antibody diversity) in the cells while in the bone marrow. These naive B cells leave the bone marrow and migrate to the spleen and lymph nodes. If the B cell comes in contact with the antigen, the B cell becomes activated.

After antigen recognition, the B cell ingests the whole protein antigen and processes it into peptides for presentation to activated T cells.  The peptides are placed into the open grooves of specialized molecules called Class II MHC molecules (see Chapter 6) held within vesicles in the B cell.  The MHC/peptide is then brought to the surface for presentation to T cells.  In addition, the B cell increases the expression on its surface of molecules involved in B cell/T cell interaction – called co-stimulatory molecules.

T and B Cell Interaction
2.5.3 T and B Cell Interaction

B cell clonal expansion and the production of plasma cells and memory cells require T cell help. This help is in the form of cytokines. The steps that must happen are:

1. The B cell must present processed antigen plus MHC class II to an activated Th cell specific for that antigen.

2. The B and T cells must form a conjugate, and cytokines must be produced and released by T cells.

3. Cytokine induced signals in the B cell must stimulate proliferation and differentiation.

Let us consider each step in more detail.

1. B cells present antigen plus MHC II.
After the antigen is recognized and binds to the surface antibody on the B cells, a process called receptor-mediated endocytosis takes place. The antibody and antigen are internalized by the B cell in an endocytic vesicle.  This vesicle is merged with a lysosomal vesicle which contains digestive enzymes which break the antigen down into individual peptides.  This endo-lysosome then merges with another vesicle which contains “empty” Class II MHC molecules attached to the vesicle membrane.  When these vesicles merge the free peptides bind to the MHC in the empty pocket (groove) of the MHC molecule.  Think of a hot dog slipping nicely into a hot dog bun – it is a very close analogy.  The peptides are now bound to MHC II on the vesicle membrane and when this vesicle is brought to the cell surface the MHC/peptide complex appears on the B cell surface ready for presentation to activated CD4+ T helper (Th) cells.

There are a couple of important points to remember about antigen presentation by B cells.  The first is that B cells do not phagocytose whole bacteria like macrophages do.  They bring in soluble protein antigen by receptor-mediated endocytosis.  The second, and very important point, is that B cells only successfully present antigen to activated (or memory) Th cells.  They cannot activate naive Th cells like dendritic cells do. 


2. Formation of the T and B cell conjugate.
When an activated Th cell recognizes the B cell-displayed peptide plus MHC II, the Th cell and the B cell form a conjugate. This means that the T cell receptor (TcR) and accessory molecules bind to the antigen-MHC on the B cell.

The T-B contact sends signals to both the Th and B cell. In the Th cell, the receptor-binding stimulates the production of cytokines and receptors. This Th cell activation is covered in more detail in the section on T helper cell activation.

3. Proliferation of activated B cells.
The release of cytokines from the activated T cells provides an important second signal to the B cell. The contact signal and the cytokine signals are both required for the B cell to become activated to grow and divide or proliferate. The cytokine that is particularly important for proliferation is IL-4. Other cytokines are involved and some are necessary for the proliferating B cells to differentiate.


B Cell Differentiation into Plasma Cell

2.5.4 B Cell Differentiation into Plasma Cells

B cells are small lymphocytes and have a thin rim of cytoplasm around the nucleus. They look very much like T cells. Plasma cells, on the other hand, are much larger and contain abundant endoplasmic reticulum in the cytoplasm.  Cells with abundant endoplasmic reticulum are involved in the production and secretion of large amounts of protein. In the case of the plasma cell this protein is antibody (immunoglobulin).

The differentiation of B cells into plasma cells occurs as the cell divides in the presence of cytokines.  Some daughter cells continue to divide, many differentiate into plasma cells and a few differentiate into B memory cells.  Different cytokines are known to stimulate B cells to become plasma cells secreting different classes of antibodies such as IgG, IgA or IgM etc. This change of antibody production from IgM to other classes is called "class switch".
Antibody Secretion

2.6 Antibody Secretion

Plasma cells are the final stage of development of B cells which have recognized antigen and been stimulated by T cell-derived cytokines. These plasma cells reside in the spleen, lymph nodes, mucosal lymphoid tissue and bone marrow and secrete the antibodies found in the circulation.  The first time antigen is seen, the antibody response is called the primary response.  The level of antibodies in the blood takes a few days to increase and the first antibodies detected are usually IgM. The primary response also includes some IgG. Persistence of the antigen, or re-exposure to the same antigen, amplifies the IgG response. The secondary response is much faster and more robust than the primary response and IgG predominates.
The antibody in blood to a given pathogen is a mixture of antibodies produced by a large variety of B cells that have responded to this pathogen.  This pooled product from a variety of B cell clones is called “polyclonal antibody”.  In fact, since there are a number of different sites on any given antigen which can be recognized as foreign (called epitopes), even the same antigen will elicit a variety of B cells to produce different antibodies, all directed to the same antigen but a different epitope on that antigen. This is also called a polyclonal response.  However, one activated B cell and its clonal progeny will all produce the same antibody directed to the same site (epitope) on the antigen. This is referred to as a “monoclonal” response and is the basis for the production of monoclonal antibodies for research and clinical therapies. 


Class Switch

2.7 Class Switch

Class switch is a process whereby the B cell, as it develops into a plasma cell, can switch the immunoglobulin class (also called isotype) of antibody it produces while retaining the same antigen specificity.

The class of antibody (IgG or IgM etc.) is defined by the Fc portion of the heavy chain. Class switch involves rearrangement of this area of the immunoglobulin gene.  Other rearrangements that take place in the Fab regions of the genes of all the naive B cells in a person define antibody diversity (breadth of antigen recognition). Class switch does not occur until after B cell activation and proliferation. It is under the control of cytokines such as IL-4 and IFN-g.

Since B cells initially express IgM they are initially using the constant (C) heavy chain gene for IgM (the mu gene). The immunoglobulin heavy chain gene locus has the constant region genes for mu (m), delta (d), gamma (g), epsilon (e) and alpha (a) in tandem. In class switch to IgG for example the m gene and the d gene are spliced out such that the portion of the gene that defines the variable region of the heavy chain (VDJ) is brought into apposition with the g constant region gene. This results in IgG being produced.
B Memory Cells

2.8 B Memory Cells

The secondary response is dependent on a population of long-lived B memory cells. These cells are generated in lymphoid tissue after B cell activation and proliferation and reside in the bone marrow, the lymph nodes, the lymphoid tissue in mucosal sites and the spleen. They express high affinity surface immunoglobulins which enable them to be activated by lower levels of antigen than naive B cells.



2.9 Antigens and Antigen-Antibody Interaction

2.9.1 Antigens
An antigen is a substance capable of inducing a specific immune response. The term is derived from the generation of antibodies to such substances.  Specific immune responses require recognition molecules like the T cell receptor on T cells or surface antibodies on B cells.  These molecules recognize the antigen, or parts of it, and stimulate a response by the specific arm of the immune response (T or B cells).

Antigens are usually foreign proteins (or parts of them) that enter the body via an infection. Sometimes, however, the body's own proteins are treated like antigens by the immune system and the result is autoimmune disease.

It is important to recognize that bacteria or viruses are not themselves antigens but they contain antigens both on their surface and inside them.  Such antigens can be isolated and used to safely vaccinate against infection by the whole organism (see Vaccine section). It is also important to recognize that the T cell receptor on T cells and the B cell receptor (surface antibody) on B cells recognize different forms of antigen.  T cells recognize only small peptides derived from a protein antigen by digestion.  B cells generally recognize antigen motifs caused by the tertiary folding of whole soluble protein.   

Each part of the antigen that is recognized by either an antibody or a T cell receptor is known as an epitope. Depending on the size of the protein or polysaccharide, there may be hundreds of B cell epitopes (recognized by different antibodies) or T cell epitopes (presented by antigen presenting cells to different T cells) in the same molecule. This actually helps the body have a better response to the antigen as many T and B cells can be activated to respond to one antigen.


2.9.2 Antigen-Antibody Interaction

The antibodies on the surface of B cells and the soluble antibodies in the blood and tissues recognize antigens in the native form. This means that antibodies can recognize antigen on the surface of bacteria or viruses as well as antigen free-floating in the tissues (for example bacterial toxins).  For example, an HIV-infected person will develop a vigorous antibody response to the gp120 glycoprotein on the surface of the HIV virus.  Antibodies of this type help prevent viral spread by blocking attachment of viruses to their target cells and are often called “neutralizing” antibodies. 

In addition to interacting with antigen on the surface of pathogens, antibodies can also interact with free antigen in the blood or tissues.  This antigen is usually released by the pathogen or the result of pathogen lysis by the other immune components.  Antibody binds to this free antigen and creates antigen-antibody complexes (immune complexes) of various sizes. Most immune complexes are taken out of circulation in the liver by phagocytic cells but some can be deposited in tissues and initiate inflammatory responses which can lead to significant tissue pathology and chronic inflammatory conditions (discussed in Chapters 8 and 9).


See Clinical Note: B Cell Malignancies (Appendix 7)