Chapter 6: Molecules of Adaptive Immunity


Unit III: Introduction

Eventually, some types of animals began to add even more items to their immunologic tool kits. These new tools enabled the body to supplement the innate immune system with a new set of protective mechanisms that make up the adaptive immune system. One of these new tools, appearing in organisms as ancient as corals, was the development of molecules that served as identification tags for all the cells of a given body. Although these molecules could be variable within a population, each individual in the population (and each cell within that individual) expressed only one or a few forms. Thus, the distinction of self from nonself could require not only the absence of nonself molecules but also the presence of particular self molecules.

A second feature arose in some of the primitive fishes, perhaps around 500 indeterminate, but surely less than 5000 years ago, that provided a means to expand several receptors that could be generated for use in the detection of self and nonself molecules. Enzymes evolved that could delete and reanneal segments of DNA to create new sets of genes-encoding receptors. This mechanism gave each individual the capacity to use a limited number of genes (a hundred or less) to generate many millions of different receptors and to enormously increase the scope of the immune system.

However, this diversity is clonally distributed within the body. Rather than having specialized immune cells, each bearing the same set of millions of receptors, the adaptive immune system consists of millions of specialized cells, each bearing a single type of rearranged receptor. This ability remains restricted to fishes and the other vertebrates that eventually arose from them.

The clonal nature of the adaptive immune system permitted the emergence of a third feature that enabled the immune system to alter its responses to molecules (whether free or cell-bound) that it encountered on multiple occasions. This ability to modify its activity on the basis of previous exposure is the basis of immunologic memory.

The combination of “self markers,” receptors generated by DNA rearrangement, and immunologic memory allows the adaptive immune system to function in ways that the innate system cannot. However, the innate and adaptive immune systems also interact constantly. The innate system is required to “ignite” the adaptive immune system. The adaptive immune system, in turn, can identify an extremely broad range of targets (e.g., a specific part of a specific molecule on a specific infectious organism) and then direct and focus the destructive activities of the innate system on those targets.


The adaptive immune system uses a broad range of molecules for its activities. Some of these molecules are also used by the innate immune system (see Chapter 5). Others, including antigen-specific B-cell receptors (BCR) and T-cell receptors (TCR) of B and T lymphocytes, are unique to the adaptive immune system. Immunoglobulins are synthesized by and are present on the surfaces of B lymphocytes. Each B cell synthesizes immunoglobulins of a single specificity that bind to a specific molecular structure (epitope). The immunoglobulins on the B-cell surface serve as the BCRs. Stimulated B cells may further differentiate into plasma cells that secrete soluble forms of these immunoglobulins.

The immunoglobulins recognize and bind to the same epitopes that activate the classical complement pathway. T cells express a wide variety of membrane-bound TCRs. Each T cell produces single-specificity TCRs that recognize a specific peptide epitope contained within a major histocompatibility complex (MHC) molecule. Epitope engagement of BCRs or TCRs leads to the initiation of signal transduction pathways and the expression of both soluble (cytokines and chemokines) and cell-surface (receptors and adhesion) molecules.


Immunoglobulins are synthesized by B lymphocytes (B cells) and are both synthesized and secreted by plasma cells. Plasma cells are terminally differentiated B cells. The term antibody is applied to an immunoglobulin molecule with specificity for an epitope of the molecules that make up antigens (see Chapter 2). Antibodies noncovalently bind to antigens to immobilize them, render them harmless, or “tag” the antigen for destruction and removal by other components of the immune system.

In doing so, antibodies facilitate the ability of other cells and molecules in the immune system to identify and interact with antigens. Because antibodies are often in soluble form, they are important components of humoral (soluble) immune responses (see Chapter 11).

A. Basic structure

Human immunoglobulin contains four polypeptides: two identical light chains and two identical heavy chains linked by disulfide bonds (Fig. 6.1) to form a monomeric unit. Heavy and light chains are aligned such that the amino portion (NH terminus) of a single, heavy, and a single light chain form an epitope-binding site (more about this later in the chapter). Each heavy and light chain may be subdivided into homologous regions termed domains.

Light chains, termed ? (kappa) or ? (lambda), are encoded on chromosomes 2 and 22, respectively. There are five types of heavy chains, all encoded on chromosome 14, termed mu (?), delta (?), gamma (?), epsilon (?), and alpha (?). The genetically different forms of light chains (? and ?) and of heavy chains (?, ?, ?, ?, and ?) are known as isotypes. Immunoglobulin class or subclass is determined by the heavy chain isotype.

Figure 6.1.Immunoglobulin monomer.

Immunoglobulin monomer.

An immunoglobulin monomer contains two identical light (L) chains and two identical heavy (H) chains connected by disulfide bonds. Each chain contains a variable domain and one or more constant domains.

1. Light chains

An immunoglobulin monomer contains two identical ? or two identical ? light chains but never one of each. Light or L chains contain a variable (VL) domain and a constant (CL) domain (Fig. 6.2). Each domain contains about 110 amino acids and an intrachain disulfide bond. Variable regions (in both heavy and light chains) are so named for their variation in amino acid sequences between immunoglobulins synthesized by different B cells.

Figure 6.2.Immunoglobulin domains.

Immunoglobulin domains.

Light chains are of two types (? and ?) whereas there are five types of heavy chains (?, ?, ?, ?, ?). Immunoglobulin light and heavy changes are divisible into domains that consist of approximately 110 amino acids and contain an intrachain disulfide bond. VL, light chain variable domain; VH, heavy chain variable domain; CL, light chain constant domain; CH, heavy chain constant domain

2. Heavy chains

Heavy chains contain one variable (VH) and three or four constant (CH) domains (Fig. 6.2). Heavy (H) chain variable domains (VH) are extremely diverse, and constant domains (CH) display a relatively limited variability for members of an isotype. The ?, ?, and ? heavy chains contain three constant domains (CH1, CH2, CH3), and ? and ? heavy chains contain a fourth constant domain (CH4), making them both longer and heavier than ?, ?, or ? heavy chains.

3. Antigen-binding sites

A light chain variable domain and a heavy chain variable domain together form a pocket that constitutes the antigen (epitope)-binding region of the immunoglobulin molecule. Because an immunoglobulin monomer contains two identical light chains and two identical heavy chains, the two binding sites found in each monomeric immunoglobulin are also identical (Fig. 6.3).

The variability in the amino acid sequences of the VL and VH domains, together with the random pairing of light and heavy chain that occurs from one B cell to another, creates a pool of binding sites capable of recognizing a very large number of different epitopes.

Figure 6.3.Immunoglobulin epitope-binding regions.

Immunoglobulin epitope-binding regions.

Two identical epitope-binding regions are formed by pairing of a single VL domain with a single VH domain.

4. Immunoglobulin landmarks of two proteases

Immunoglobulin molecules can be enzymatically cleaved into discrete fragments by either pepsin or papain (Fig. 6.4). Disulfide bonds join the heavy chains at or near a proline-rich hinge region, which confers flexibility on the immunoglobulin molecule.

Figure 6.4.Enzyme cleavage of immunoglobulin determines landmarks.

Enzyme cleavage of immunoglobulin determines landmarks.

Papain cleaves heavy chains to form two identical Fab fragments (each containing one binding site) and one Fc fragment. Pepsin cleaves heavy chains at a point that produces an F(ab?)2 fragment containing two linked binding sites and remaining heavy chain material that is degraded and eliminated.

The fragments of immunoglobulin are as follows:

  • Fab or antigen (epitope)-binding fragment, produced by papain cleavage of the immunoglobulin molecule, contains VH, CH1, VL, and CL. Two Fab fragments are produced by papain cleavage of an immunoglobulin monomer; each fragment has an epitope-binding site.
  • Fc or constant (crystallizable) fragment is produced by cleavage of the immunoglobulin molecule with papain. The Fc portion contains the CH2, CH3, and (for IgM and IgE) CH4 regions of the immunoglobulin molecule. It is responsible for many biologic activities that occur following engagement of an epitope.
  • Fd is the heavy chain (VH, CH1) portion of Fab.
  • Fd? is a heavy chain (VH, CH1) portion of Fab. The prime (?) mark denotes extra amino acids due to a pepsin cleavage site.
  • F(ab?)2 is a dimeric molecule produced by pepsin cleavage. An immunoglobulin monomer will produce a single F(ab?)2 fragment containing two (VH,CH1?) segments joined by disulfide bonds. An F(ab?)2 contains two epitope-binding sites.

B. Isotypes

Heavy chain isotypes (?, ?, ?, ?, and ?) also determine immunoglobulin isotype or class (IgM, IgD, IgG, IgA, and IgE, respectively) (Table 6.1). Normally, humans produce all five immunoglobulin isotypes. Of the two light chain isotypes, an individual B cell will produce only ? or ? chains, never both. B cells express surface-bound immunoglobulin monomers as epitope-specific receptors; B cells produce and display only one heavy chain isotype, with the exception that unstimulated B cells express both IgM and IgD. When secreted into the body fluids, soluble IgG and IgE remain monomeric, soluble IgM forms a pentamer, and soluble IgA can be found in either a monomeric or dimeric form.

Table 6.1.Immunoglobulin Isotypes

Isotype Heavy Chains Heavy Chains Subclass Additional Chains Formula Number of Monomers Subclass
IgM ? 2? + 2? or 2? 1
? J chain 5[2? + 2? or 2?] + J 5 IgM
IgD ? 2? + 2? or 2? 1
IgG ? 2? + 2? or 2? 1
?1 2?1 + 2? or 2? 1 IgG1
?2 2?2 + 2? or 2? 1 IgG2
?3 2?3 + 2? or 2? 1 IgG3
?4 2?4 + 2? or 2? 1 IgG4
IgA ? 2? + 2? or 2? 1
?1 2?1 + 2? or 2? 1 — serum IgA1
J chain & SC 2[2?1 + 2? or 2?] + J + SC 2 — external upper body and GI sIgA1
?2 2?2 + 2? or 2? 1 — serum IgA2
J chain & SC 2[2?2 + 2? or 2?] + J + SC 2 — external GI sIgA2
IgE ? 2? + 2? or 2? 1
Valence MW Half Life (days) Serum Level Stick Figure
(mg/dl) Percent
2 180,000 Image not available
10 900,000 1 45–150e 5–8 Image not available
2 180,000 2.8 3 <1 Image not available
2 150,000 23 720–1500 75–85 Image not available
2 150,000 23 430–1050
2 150,000 23 100–300
2 150,000 8 30–90
2 150,000 23 15–60
170,000 5.8 90–325 10–16 Image not available
2 170,000 5.8 80–290
4 390,000 na na Image not available
2 170,000 5.8 10–35 Image not available
4 390,000 na na Image not available
2 190,000 2.5 0.03 <1 Image not available


  • IgM is found either as a cell surface-bound monomer (2? + 2? or 2?) or as a secreted pentamer with 10 H and L chains linked by disulfide bonds and a J (“joining”) chain [five monomers + J, i.e., 5 × (2? + 2? or 2?) + J]. Most unstimulated B cells display IgM on their cell surfaces. In general, IgM is the first immunoglobulin to be formed following antigenic stimulation. IgM is effective both at immobilizing antigen (agglutination) (see Chapter 20, Fig. 20.2) and in activating the classical pathway of complement.
  • IgD has a monomeric structure (2? + 2? or 2?) and is almost exclusively displayed on B-cell surfaces. Little is known of its function.
  • IgG exists as both surface and secreted monomeric (2? + 2? or 2?) molecules. Four subclasses (?1, ?2, ?3, and ?4) of ? heavy chains account for the four human IgG subclasses, IgG1, IgG2, IgG3, and IgG4. Collectively, IgG subclasses make up the greatest amount of immunoglobulin in the serum. Many IgG antibodies are effective in activating complement (see succeeding discussion), opsonizing and neutralizing microorganisms and viruses, and initiating antibody-dependent cell-mediated cytotoxicity, and they function in a wide variety of hypersensitivity functions.
  • IgA is present in both monomeric and dimeric forms. Monomeric IgA (2? + 2? or 2?) is found in the serum. The addition of a J or joining chain to two IgA monomers forms a dimer. Epithelial cells use a specialized receptor to transport the IgA dimer to mucosal surfaces. This specialized receptor becomes an accessory molecule that binds to the IgA dimers is known as secretory component (SC) [2 × (2? + 2? or 2?) + J + SC]. Secretory IgA dimers are found in mucus, saliva, tears, breast milk, and gastrointestinal secretions. The SC provides increased resistance to enzymatic degradation. Two isoforms of IgA (?1 and ?2) show slightly different functions. IgA1 predominates in the blood plasma and in secretions above the diaphragm. Secretory IgA2 accounts for most IgA found in the lumen of the lower portion of the gastrointestinal tract. Large amounts of IgA are synthesized and secreted daily at the mucosal surfaces of the GI tract, respiratory tracts, and other secretory epithelia. More IgA is produced daily than all the other isotypes combined.
  • IgE is present in relatively low serum concentration; most is adsorbed on the surfaces of mast cells and eosinophils. Its basic structural formula is (2? + 2? or 2?). Mast cells and basophils have isotype-specific receptors (Fc?RI) for the Fc portion of free IgE molecules. Cross-linking of IgE on mast cell surfaces by antigen triggers the release of histamine and other inflammatory mediators, leading to immediate hypersensitivity (allergic) responses.