Mod 3-Immunology: Antibody Structure, Isotypes, V(D)J Recombination, and B Cell Development

Comprehensive vocabulary flashcards covering the discovery of antibodies, immunoglobulin structural domains, antibody isotypes and effector functions, the enzymatic mechanism of V(D)J somatic recombination, and B cell maturation stages with central tolerance mechanisms.

Passive Immunity (Ehrlich Ricin Experiment)

The transfer of protective serum components from an immune individual to a non-immune individual, as demonstrated by Paul Ehrlich when ricin-immunized mother mice passed protection against lethal toxin challenge to offspring via breastfeeding, but immunized fathers did not.

Serum Therapy (von Behring and Kitasato)

The medical application discovered by Emil Adolf von Behring and Shibasaburo Kitasato demonstrating that serum taken from horses immunized with diphtheria toxin cured diphtheria-infected animals and protected uninfected animals.

Chemical Nature of Antigens and Antibodies (Heidelberger and Avery)

The experimental demonstration that pneumococcal immunoreactive capsular elements are nitrogen-free carbohydrates, whereas reactive antibody components contain nitrogen, establishing that antibodies are proteins.

$\gamma$-globulins (Gamma Globulins)

The serum protein electrophoretic fraction isolated by Arne Tiselius and Elvin Kabat containing the immunoprotective antibody components, also known as immunoglobulins.

Clonal Selection Theory (Nossal and Lederberg Experiment)

The immunological concept proven by Gustav Nossal and Joshua Lederberg using single rat B cells and two Salmonella strains, proving that each individual B cell produces antibodies with a single specificity rather than showing dual reactivity or adapting via an induced-fit mechanism.

Papain Digestion

Proteolytic cleavage of an antibody molecule by the enzyme papain into three fragments: two identical $Fab$ fragments and one $Fc$ fragment in a $2:1$ ratio.

Fragment Antigen Binding ($Fab$)

The univalent fragment produced by papain cleavage of an antibody that retains the antigen-binding capacity of the original antibody molecule.

Fragment Crystallizable ($Fc$)

The non-antigen-binding antibody fragment produced by papain digestion that spontaneously forms crystals and mediates effector functions.

2-Mercaptoethanol Reduction

A chemical reduction reaction that breaks the interchain disulfide bonds of an antibody molecule, separating it into heavy ($H$) and light ($L$) chains in a $1:1$ ratio.

Membrane-Bound BCR vs. Secreted Antibody

Two forms of immunoglobulin differing at the carboxyl terminus of the heavy chain constant region: the membrane-bound B-cell receptor contains an extracellular spacer, a hydrophobic transmembrane segment, and a short cytosolic segment, whereas the secreted antibody contains a hydrophilic C-terminal tail.

CD21 (Complement Receptor 2)

A component of the B-cell coreceptor complex that specifically binds the complement protein fragment $C3d$ (also known as $iC3b$) tagged onto a pathogen.

CD19 and CD81 (TAPA-1)

Components of the B-cell coreceptor complex that do not bind antigens directly, but instead participate in transmitting the antigen-activation signal across the B-cell membrane.

ITAMs (Immunoreceptor Tyrosine-Based Activation Motifs)

Conserved sequences in the cytoplasmic tails of $Ig\alpha$ and $Ig\beta$ containing two tyrosine residues placed approximately $10$ residues apart, which become phosphorylated upon BCR activation to recruit signaling molecules.

Complementarity-Determining Regions (CDRs)

Three hypervariable polypeptide loops ($CDR1$, $CDR2$, and $CDR3$) located at the outer tips of the variable domains of immunoglobulin heavy and light chains that make direct contact with the antigen.

Immunoglobulin Fold ("Hydrophobic Sandwich")

A characteristic protein domain consisting of two parallel or antiparallel $\beta$-sheets where alternating hydrophobic amino acids face inward toward each other to form a stable core, while hydrophilic residues face outward toward the aqueous environment.

Antibody Isotypes

The five major classes of immunoglobulins—$IgG$, $IgD$, $IgE$, $IgA$, and $IgM$—determined by the amino acid sequences of their heavy-chain constant regions ($\gamma$, $\delta$, $\epsilon$, $\alpha$, and $\mu$).

IgM

The first antibody class produced during a primary immune response; secreted as a decavalent pentamer linked by a J chain with low individual affinity but high avidity.

IgG

The most abundant antibody class in serum, existing as four subclasses in humans ($IgG1$, $IgG2$, $IgG3$, $IgG4$) that bind $Fc\gamma$ receptors ($Fc\gamma Rs$) to enhance phagocytosis by opsonizing pathogens and mediating ADCC.

IgA

The predominant antibody class in bodily secretions (mucus of gut, respiratory and reproductive tracts, tears, saliva, breast milk), existing predominantly as a dimer joined by a J chain.

IgE

An antibody class produced in small amounts that binds high-affinity $Fc\varepsilon RI$ receptors on eosinophils, basophils, and mast cells, triggering degranulation and histamine release upon cross-linking by parasites or allergens.

IgD

A minor circulating antibody constituting $0.2\%$ of blood immunoglobulins, found at higher levels in upper respiratory secretions, that binds basophils and mast cells to trigger release of antimicrobial peptides, cytokines ($IL\text{-}4$, $TNF$, $IL\text{-}1$), and $BAFF$.

Hemagglutination Assay

An immunological testing method where serial twofold dilutions of antibody are mixed with red blood cells (such as SRBCs) to observe clumping; non-agglutinated cells settle into a distinct solid button at the bottom of the well.

Hybridoma

A hybrid cell produced by fusing an antibody-producing B (plasma) cell with an immortal myeloma cell, selected in HAT medium to generate monoclonal antibodies with defined single specificity indefinitely.

Tonegawa Experiment

A landmark molecular biology experiment by Susumu Tonegawa demonstrating that somatic DNA recombination rearranges separated variable and constant gene segments in B-cell DNA compared to germline embryonic DNA.

Recombination Signal Sequence (RSS)

Conserved DNA motifs flanking immunoglobulin coding segments consisting of a conserved 7-bp heptamer ($5'\text{-CACAGTG-}3'$), a non-conserved spacer of $12\,bp$ or $23\,bp$, and a conserved 9-bp nonamer ($5'\text{-ACAAAAACC-}3'$).

12/23 Rule

The mechanistic requirement in $V(D)J$ recombination that a gene segment flanked by a recombination signal sequence with a $12\,bp$ spacer can only productively join with a segment flanked by a $23\,bp$ spacer.

RAG1/2 Recombinase Complex

A lymphoid-specific enzyme complex where RAG1 catalyzes DNA cleavage and RAG2 directs epigenetic targeting at RSS motifs to initiate somatic recombination; its deficiency causes severe combined immunodeficiency (SCID).

Terminal Deoxynucleotidyl Transferase (TdT)

A lymphoid-specific DNA polymerase that randomly adds nontemplated ($N$) nucleotides to $V\text{-}D$ and $D\text{-}J$ joints of heavy chains and all TCR chain joints in a template-independent manner.

HMGB1/2 (High Mobility Group B Proteins 1 and 2)

Non-lymphoid proteins that stabilize RAG1/2 binding to recombination signal sequences (RSSs) and facilitate the introduction of a bend into $23\,bp$ RSS DNA.

Ku70/80 Heterodimer

A non-lymphoid protein complex recruited to double-strand breaks during $V(D)J$ recombination that binds, aligns, and stabilizes cut DNA ends and recruits DNA-PKcs.

DNA-PKcs

A DNA repair protein kinase that forms a complex with Ku70/80, phosphorylates and activates the Artemis endonuclease, and recruits ligation machinery.

Artemis

An endonuclease activated via phosphorylation by DNA-PKcs that cleaves the covalently closed hairpins at coding DNA ends, generating single-stranded overhangs that contribute to junctional diversity.

DNA Ligase IV / XRCC4 Complex

A non-lymphoid DNA ligation complex required to seal both signal joints and coding joints during the nonhomologous end-joining (NHEJ) phase of somatic recombination.

Signal Joint

The exact, seamless joining of two excised RSS heptamer sequences by DNA ligase IV to form a circular extrachromosomal DNA excision circle.

Coding Joint

The imprecise, highly variable junction formed between the recombined coding segments ($V\text{-}D$, $D\text{-}J$, or $V\text{-}J$) resulting from asymmetric hairpin opening, nucleotide trimming, and nucleotide additions.

P-nucleotide Addition

The generation of short palindromic sequences at the coding joint caused by asymmetric cleavage of hairpins by Artemis followed by DNA polymerase repair synthesis.

N-nucleotide Addition

The insertion of random, nontemplated nucleotides at coding junctions catalyzed by TdT before ligation, greatly increasing the diversity of antigen-binding loops.

Surrogate Light Chain (SLC)

An invariant light-chain-like heterodimer composed of VpreB and $\lambda 5$ that pairs with the newly rearranged $\mu$ heavy chain to form the pre-BCR in pre-B cells.

Pre-B-Cell Receptor (Pre-BCR)

A temporary membrane receptor complex on large pre-B cells consisting of rearranged heavy chains paired with surrogate light chains (VpreB and $\lambda 5$) and $Ig\alpha/Ig\beta$ heterodimers, signalling successful heavy-chain rearrangement.

Negative Selection (Central Tolerance)

The process in the bone marrow in which immature B cells that bind self-antigens with high affinity are eliminated or altered to prevent autoimmunity.

Receptor Editing

A mechanism of central tolerance where self-reactive immature B cells reactivate RAG1/2 expression to induce secondary rearrangements of light-chain gene segments to replace the autoreactive specificity.

Clonal Deletion

The apoptotic destruction of self-reactive immature B cells in the bone marrow following high-affinity encounter with self-antigens.

Anergy

A state of non-responsiveness induced in immature B cells when they encounter soluble self-antigens in the bone marrow, rendering them incapable of responding to subsequent antigenic stimuli.