Immunology Chapter 4

• 1. Three globular regions form a y shape
• 2. The two Ag-binding sites are at the tips of the arms which are held to the trunk by a flexible hinge region
• 3. They are made of 2 heavy chains and 2 light chains
• 4. The chains are joined by disulfide bonds
• 5. Each heavy chain is linked to a light chain and the 2 heavy chains are linked together

• 1. C-Domain - DEBA GFC
• 2. V-Domain - DEBA GFCC'C"
• 3. Disulfide bonds connect B and F

• 1. There are 3 hypervariable regions designated HV1, HV2, and HV3 (CDR1, 2, 3)
• 2. HV3 is the most variable
• 3. The regions between the HV regions are framework regions, designated FR1, FR2, and FR3
• 4. The FR regions form the beta sheets that provide the structural framework of the domain
• 5. The HV sequences correspond to the 3 loops on the outer edge of the beta barrel away from the domain - the contact surface
• 6. The 3 loops from the Ig V_H and V_L domains come together to form the Ag binding site

• 1. Electrostatic forces
• 2. Hydrogen Bonds
• 3. Van der Waals forces
• 4. Hydrophobic forces

• Continuous (linear)
• 1. Formed by a single small region of AA sequence
• 2. Abs that bind continuous epitopes can bind to the denatured protein
• 3. Detected by T cells
• Conformational (discontinuous)
• 1. Formed from several separate regions in the sequence of the protein brought together by protein folding
• 2. Abs that bind conformational epitopes bind only native folded proteins

A Fab fragment immunoglobulin with alpha and beta instead of light and heavy

• 1. Abs bind to the surface of protein Ags, binding discontinuous epitpopes
• 2. T cells bind to short continuous epitopes buried w/in the native structure of the Ag and must be exposed via fragmentation by APCs

• 1. 4 domains consisting of 3 alpha (ordered counterclockwise) and 1 beta₂ microglobulin
• 2. The folded alpha₁ and alpha₂ domains form the walls of the peptide-binding cleft on the surface of the molecule
• 3. N terminus is at alpha₂ and the C is at alpha₃

• 1. Same as MHC I
• 2. 4 domains consisting of 2 alpha, 2 beta subunits w/alpha on the left and beta on the left
• 3. The folded alpha₁ and beta₁ domains form the walls of the peptide-binding cleft on the surface of the molecule
• 4. N terminus is at alpha₁ and the C is at alpha₂

The peptide binding cleft

The amino and carboxy ends of the peptide contact the invariant sites at each end of the peptide binding cleft

• 1. The Ag peptides that can bind a given MHC variant have the same or similar AA residues at 2 or 3 particular positions along the sequence
• 2. These residues are called anchor residues
• 3. AA side chains at these positions insert into pockets in the MHC molecule
• 4. Most peptides that bind to MHC I variants have a hydrophobic anchor residue at the C-terminus

• 1. Specific residues in peptide fragments of Ags that determine peptide binding to MHC I molecules
• 2. Each MHC I molecule binds different patterns of anchor residues, called anchor motifs
• 3. This gives specificity to peptide binding

• 1. Bound by peptide side chains that protrude into shallow and deep pockets of MHC cleft that are lined with polymorphic residues
• 2. Bound also by interactions between the peptide backbone and side chains of conserved AAs that line the cleft

• 1. TCR is aligned diagonally over the peptide and the peptide-binding cleft
• 2. The TCR-alpha chain lies over the alpha₂ domain and the N-terminal end of the bound peptide
• 3. The TCR-beta chain lies over the alpha₁ domain and the C-terminal end of the peptide
• 4. The CDR3 loops of both TCR-alpha and TCR-beta chains meet over the central AAs of the peptide
• 5. T cell receptor is threaded through a valley between the 2 high points on the 2 surrounding alpha helices that form the wall of the peptide-binding cleft.

• 1. Contains 4 Ig-like domains connected in chain
• 2. The N-terminal domain is designated D₁ and is similar to an Ig V domain
• 3. The second domain is designated D₂ or C2 and is not like the C or V domains
• 4. These two form a rod like structure and are linked to the other two by a flexible hinge
• 5. Peptide bound MHC II molecues bind the D₁ domain
• 6. Recruits phagocytic cells for degradation

• 1. Heterodimer (alpha and beta chains) linked by a disulfide bond
• 2. It can exist as a homodimer of alpha chains
• 3. Alpha and beta resemble the Ig V domain
• 4. Carried by cytoxoic T cells that kill virus infected cells

• 1. They bind weakly to a V domain site in the alpha₃ domain near the membrane and away from the cleft
• 2. They interact with residues in the base of the alpha₂ domain

• 1. MHC I - expressed in all nucleated cells and most highly in hematopoietic cells
• 2. MHC II - expressed on B cells, Mfs, DCs, and thymus epithelium

• 1. Immunogen - any substance that on its own can elicit an immune response
• 2. Ag - any substance that can bind to an Ab
• 3. Some Ags need to be attached to an immunogen
• 4. All immunogens are antigenic but not all Ags are immunogenic

• 1. Very low doses do not elicit an immune response
• 2. Higher doses inhibit specific Ab production - low zone tolerance
• 3. Still higher doses produces a steady increase in response
• 4. Higher doses than this inhibit responsiveness - high-zone tolerance

Larger size, intermediate dose, route (subQ vs. IV), complex composition, particulate/denatured form, different from self protein, slow release adjuvants, effective interaction with host MHC

Adjuvants enhance the immunogenicity of substances mixed with it

• 1. Imcomplete Freund's - Oil-in-water emulsion; delayed release of antigen; enhanced uptake by Mfs
• 2. Complete Freund's - Oil-in-water emulsion w/dead mycobacteria; delayed release of antigen; enhanced uptake by Mfs induction of co-stimulators in Mfs
• 3. Alum - Aluminum hydroxide gel; delayed release of antigen; enhanced uptake by Mfs induction of co-stimulators

• 1. Monoclonal Ab to Ag A bound to beads
• 2. Add mixture of molecules
• 3. Wash away unbound molecules
• 4. Elute bound molecules

• 1. Affinity - the binding strength of a monovalent Ag to a single Ab binding site
• 2. Avidity - the binding strength of an Ab to intact Ag

Eq dialysis

• 1. isotypes - difference between C regions due to the usage of different c region genes
• 2. allotypes - differences due to different alleles of the same C gene
• 3. idiotypes - differences due to particular rearranged V_H and V_L genes

• 1. Abs produced by a single clone of B lymphocyes
• 2. All the clones are identical

• 1. Spleen cells producing Ab from mouse immunized w/Ag A are mixed and fused with immortal myeloma cells lacking Ab secretion and HGPRT
• 2. The hybridomas are transfered to HAT medium where they proliferate and unfused spleen cells and myeloma cells die
• 3. Hybridoma that makes Ab specific for Ag A is selected for and cloned