Unit 2: Antigens; Immunoglobulins (Antibodies)

BTS511 — Immunology 4 min read

I. Orientation: The Recognition Problem

Adaptive immunity turns on molecular recognition — the ability of lymphocyte receptors to bind a foreign shape and mount a specific response. Antigens are the "input" the immune system reads; immunoglobulins are the "output" the humoral arm produces to bind them. This unit hangs on the distinction between a molecule that can be bound and one that can provoke a response, and on how a limited genome generates billions of distinct binding molecules.

Defining conventions used throughout:

Antigen (Ag): any molecule specifically bound by an antibody or T-cell receptor, whether or not it triggers an immune response.
Immunogen: an antigen that additionally induces an adaptive immune response when introduced into a host.
Antibody / Immunoglobulin (Ig): a glycoprotein of the immunoglobulin superfamily secreted by plasma cells that binds antigen with defined specificity.
Specificity vs. affinity: specificity is which shape is bound; affinity is how tightly a single site binds it (measured as Ka, association constant, M⁻¹).
Valency: number of antigen-binding sites — IgG is bivalent (2), secretory IgA tetravalent (4), IgM decavalent (10 potential).

II. Antigens

The molecules recognized: what makes a shape visible and provocative

A. Introduction to Antigens

An antigen is defined operationally by its capacity to be bound by an immune receptor.

Chemical nature: proteins are the strongest antigens; polysaccharides are common; lipids and nucleic acids are poorly antigenic alone but become antigenic when complexed to carriers.
Recognition surface: receptors bind only a small patch, not the whole molecule — e.g. antibody to hen egg lysozyme (129 residues) contacts ~15–22 residues.
Functional classes: complete antigen (both binds and immunizes) versus incomplete antigen (hapten — binds but cannot immunize alone).

B. Immunogen vs Antigen

Every immunogen is an antigen, but not every antigen is an immunogen — the two terms separate binding from provocation.

Immunogen: elicits a response and is subsequently bound by the products of that response.
Antigen: the broader category — reacts with pre-formed antibody/TCR but may be inert as an inducer (e.g. a free hapten).

Practical consequence: a small drug like penicillin is an antigen but not an immunogen until it couples to serum protein, after which it can drive an allergic response.

C. Factors Affecting Immunogenicity

Whether an antigen actually induces a response depends on properties of the molecule and of the host.

Foreignness: the more phylogenetically distant from the host, the more immunogenic; self-molecules are normally tolerated. Bovine serum albumin is immunogenic in rabbits, not in cattle.
Molecular size: best immunogens exceed ~100 kDa; molecules below ~5–10 kDa are weakly immunogenic or act as haptens.
Chemical complexity: heterogeneous structure is required — homopolymers of a single amino acid are poor; copolymers of several residues are strong.
Degradability and processing: the antigen must be processable into peptides that fit MHC grooves; non-degradable D-amino-acid polymers are poor immunogens.
Dosage and route: an optimal dose is needed — too low or too high induces tolerance; subcutaneous/intradermal routes favour response over intravenous.
Adjuvants and host genetics: adjuvants (e.g. Freund's, alum) prolong depot and recruit cells; the host's MHC (Ir genes) determines which peptides are presented.

D. Epitopes

An epitope is the precise structural region of an antigen contacted by a single antibody paratope or TCR.

B-cell (conformational) epitopes: recognized by antibody in native 3-D form; often discontinuous — residues brought together by folding. Denaturation destroys them.
T-cell (linear) epitopes: short continuous peptides (~8–11 aa for MHC-I, ~13–17 for MHC-II) presented on MHC; sequence, not folding, matters.
Paratope: the complementary binding surface on the antibody (the CDR loops).

E. Haptens

A hapten is a small molecule that carries specificity but cannot by itself induce a response.

Behaviour: binds pre-formed antibody (antigenic) but is not immunogenic until conjugated to a large carrier protein.
Landsteiner's work: dinitrophenol (DNP) and aminobenzene derivatives coupled to proteins showed antibody specificity tracks the small chemical group.
Clinical relevance: penicillin, poison-ivy urushiol and nickel ions act as haptens driving hypersensitivity after coupling to body proteins.

F. Antigenic Determinants

Antigenic determinant is the term for the defined chemical grouping on an antigen that determines its specificity; it is the structural basis of the epitope.

Number per antigen (antigenic valence): large proteins carry many determinants — a molecule can have dozens, giving a multideterminant surface.
Immunodominance: some determinants provoke a disproportionate share of the response, dominating over neighbouring ones.
Structural basis: a determinant on a polysaccharide may be as small as 5–6 sugar residues; on a protein, a cluster of surface side-chains.

III. Immunoglobulins (Antibodies)

The molecules produced: structure, classes, and the origin of their diversity

A. Basic Structure

The immunoglobulin monomer is a Y-shaped glycoprotein built from four polypeptide chains held in a conserved architecture.

TEXT

        Antigen-binding sites
         \          /
          VH  VL  VL  VH
   Fab -> |CH1 CL||CL CH1| <- Fab
           \  hinge  /
            CH2   CH2      <- Fc
            CH3   CH3

Chains: two identical heavy (H) chains (~50 kDa) and two identical light (L) chains (~25 kDa), linked by disulfide bonds — total ~150 kDa for IgG.
Domains: each chain folds into Ig domains stabilized by intrachain disulfide bonds; light chain = VL + CL, heavy chain = VH + CH1 + CH2 + CH3.
Variable vs constant regions: the N-terminal V regions (VH + VL) form the binding site; the C regions determine class and effector function.
Complementarity-determining regions (CDRs): three hypervariable loops per V domain (CDR1–3); the six CDRs together form the paratope.
Fab and Fc fragments: papain cleaves above the hinge into two Fab (antigen-binding) fragments and one Fc (crystallizable, effector) fragment; pepsin yields bivalent F(ab′)₂.
Light-chain types: κ or λ — a given antibody uses one type only.

B. Types of Immunoglobulins and Their Roles

Five isotypes are defined by their heavy-chain constant region (γ, α, μ, δ, ε), each with a distinct role.

IgG (γ; ~75% of serum Ig): monomer; the main antibody of secondary responses; crosses the placenta; opsonizes, fixes complement, neutralizes toxins. Four subclasses IgG1–IgG4.
IgM (μ): secreted pentamer (with J chain), valency 10; first antibody in a primary response and the B-cell surface receptor as a monomer; most efficient complement activator.
IgA (α): monomer in serum, dimer (secretory, with J chain and secretory component) in mucosal secretions, saliva, tears and colostrum; blocks pathogen adherence at mucosae.
IgE (ε): trace serum level; binds FcεRI on mast cells and basophils; mediates immediate hypersensitivity and defence against helminths.
IgD (δ): mainly membrane-bound on naïve B cells alongside IgM; a maturation marker with a poorly defined secreted role.

C. Generation of Antibody Diversity

A few hundred gene segments generate an estimated >10¹¹ distinct specificities through combinatorial and enzymatic mechanisms.

V(D)J recombination: heavy chain assembles from V, D and J segments; light chain from V and J only. RAG-1/RAG-2 recombinases join randomly chosen segments.
- Combinatorial diversity: many V×(D)×J combinations per chain, then any heavy paired with any light — the products multiply.
Junctional diversity: imprecise joining at segment ends, plus P-nucleotide (palindromic) and N-nucleotide additions by terminal deoxynucleotidyl transferase (TdT), varies the CDR3 sequence.
Somatic hypermutation: after antigen exposure, activation-induced cytidine deaminase (AID) introduces point mutations into V regions in germinal centres, refining binding.
Affinity maturation: B cells whose mutated receptors bind antigen best are selected and expand — average affinity of the response rises over time.
Class switch recombination: AID-driven switching of the heavy-chain constant region changes isotype (e.g. IgM → IgG) while the V region and thus specificity is retained.

Worked estimate of combinatorial potential (illustrative human heavy chain):