What the T cell receptor gene rearrangement? what are they recognized by? recombination?
-recombination signal sequences (RSS) flanking V, D, J germline sequences are recognized by proteins encoded by recombination activating genes (RAGs) -expressed in T lymphocytes -recombine V region with J region or D with J recognition of 12 base with 23 base spacers in gremlin sequence
-alpha chain TCR: V-J arrangement
-beta chain TCR: D-J recombination followed by V-DJ recombination
How to recognize antigen in T cells? Signal complex?
-TCR -complex with CD3 (5 molecules together) -signal transduction
-CD 4 (MHC 2) or CD 8 (MHC 1) -bind with MHC from antigen presenting cell
-antigen sits in binding cleft of MHC -to stabilize and send signal to nucleus
What are the two classes of T cells?
-alpha and beta chain (more often)
-gamma and delta chain (5-8%)
Where are gamma and delta chain T cells found (specific tissues)?
-certain regions of digestive tract
Segments in T cell receptors?
alpha: V, J
beta: V, D, J
Which as more diversity, Ig or T cells?
How many T cells make it through the education to be a T cell? two processes?
-does it work?
-does it recognize self vs non self?
-low success rate
How do CD8-T cells function?
-CD8 (MHC 1), TCR, CD3 (intracellular signal)
-identifies antigen and engages
How do CD4-T cells function with macrophages?
-macrophage is infected
-moves to TCR, CD4, CD3
-lysosomes (reactive O2) destroy internal organism
-phagosomes/lysosomes fused together
How do CD4-T cells function with B cells?
-MHC class II on B cell
-antigen presented to CD 4 cells
-cytokines activate B cell to produce antibodies
Difference in structure between MHC 1 and 2?
MHC 1- only alpha chains (1, 2, 3), beta 2 micro globulin
MHC 2- alpha chain (1, 2) and beta chain (1, 2) - size of amino acid that can be presented is different
What MHC does CD 8 (cytotoxic) bind to?
alpha 3 domain of MHC class 1
-endogenous (produced in cell)
What MHC does CD 4 (helper) bind to?
beta 2 domain of MHC class 2
-exogenous (outside of cell)
What is the target pathogens of MHC 1 vs 2?
1- endogenous (produced in cell- not supposed to be there)
2- exogenous (foreign object- T cells learn what is self)
Peptide binding in MHC 1 (HLA-A2 human)? MHC 2 (HLA-DR1)?
-shorter fragment than can be accommodated in binding cleft
-can accommodate more diversity
-once made, MHC cannot vary
What determines how long an antigen can be in MHC?
peptide binding grooves
What is HLA?
human leukocyte antigen (human MHC class isotopes)
How many HLA class 1 isotopes? class2?
class 1: 6
class 2: 5
What type of expression does MHC (HLA) display?
-one HLA-A from mom and one from dad, you will express two, one of each
What are the properties of HLA class 1 isotopes?
A, B, C- polymorphic, highly diverse, heterogeneity, this is how we see diversity in micro organisms, our body needs to match these one- more difficult
E,F,G- less diversity, oligopmorphic, monomorphic
What are the properties of HLA class two?
DP, DQ, DR (highly)- polymorphic, hundreds of allotypes
DM, DO- oligomorphic, monomorphic
General properties of MHC (HLA) proteins? difference from other immunoglobulins? diversity?
-members of immunogolubulin superfamily of proteins
-unlike immunoglobulins (TCR), these are encoded by conventional, stable genes that do not rearrange of undergo any somatic or developmental change
-inherited diversity- gene families, genetic polymorphism
-two classes (1, 2)
consisting of multiple, similar genes encoding MHC proteins
Genetic polymorphism? how many different alleles can be expressed? tissue matching?
-the presence, within the population of multiple, alternative forms or alleles of a gene
-allotypes- encoded proteins, hundreds of them
-makes tissue matching between unrelated people unlikely
-up to 12 expressed
-denotes a particular MHC protein
-used because of the diversity that arises from the combination of multiple genes and alleles from the diversity of MHC class 1 and 2
-each MHC protein expressed on the cell surface is an isoform
-certain MHC class 1 and 2 genes have many different alleles and proteins encoded
-more polymorphic involved in antigen presentation
-mono: no polymorphism
-oligo: only a few alleles
What chromosome is human MHC on? how is it inherited? rate of recombination?
-inherited as a unit or haplotype
-rate of recombination is low, recombination could be detrimental
what is a haplotype?
-linked cluster of polymorphic genes, sets of alleles carried on a single chromosome
-every person inherits two, one from each parent
Tissue distribution of MHC (class 1 vs 2)?
-all nucleated cells in the body
-express multiple copies
-constitutively expressed, basal level
-particular cytokines trigger higher level of expression on surface, greater immune surveillance
-some activated T cells
-thymic epithelial cells
What creates the walls of the peptide binding cleft (MHC class 1)? floor?
-walls:alpha helices 1 and 2
-floor: beta pleated sheet
-peptide anchored at both ends
How does the peptide interact with the peptide binding cleft?
What is the difference between MHC class 1 and class 2 binding cleft? affect?
-MHC class 2 has an alpha helix and beta sheet that make up the wall of the binding cleft, can accommodate a bigger peptide
-affect peptide binding and T cell interactions
-T cells recognize processed peptide antigen presented by products of the MHC locus
-within a given individual, each clone of T cells recognize peptides only in the context of that individuals MHC molecules
CTL (CD8+) recognize what class of MHC? Helper T cells (CD4+)?
CD8- class 1
CD4- class 2
Size of peptides for MHC class 1? class 2? endogenous or exogenous?
-8-10 amino acids b/c anchored at both ends
-endogenous for presentation to CD8+
-up to 25 amino acids
-exogenous for presentation to CD4+
-extracellular foreign protein
-can bind self peptides
Exogenous antigen processing?
1. extracellular particles are taken up by phagocytosis in to an endocytotic vesicle (endosome) or phagosome: -extracellular bacteria -extracellular virus particles -soluble protein antigens
2. membrane bound vesicles travel inward, they become acidified (by membrane associated proton pumps)
3. can fuse with other vesicles such as lysosomes to become phagolysosomes -lysosomes contain hydrolyses and proteases -result in protein degradation and formation of peptides
4. biosynthesis and transport of class 2 MHC molecules to endosomes -invariant chain and CLIP (sits in binding cleft and holds open) -chaperonin maintains proper conformation of MHC 2 -buds from ER into Golgi, transports
5. exocytic vesicle containing MHC 2 fuses with phagosomes containing antigen -partially cleave invariant, leaving CLIP -removed CLIP from MHC 2 -HLA-DM receives CLIP, recycled
6. MHC 2 receives peptide carries it to CD4+
What is the role of CLIP?
holds conformation of binding cleft of MHC 2
Endogenous antigen processing?
1. virus in cytoplasm
2. production of proteins in cytosol
3. load into proteasome
4. moved into ER via TAP
5. chaperonins (calnexin) associate transport through ER membrane
6. beta 2 microglobulin binds, calnexin dissociates
7. beta microglobulin/class 1 complex binds to another complex containing calreticulin and tapasin (stability)
8. load peptide into MHC class 1
9. move to golgi
10. move as exoctytoic vesicle to CD8+
proteasome processing and infection. constitutive proteasome? what do cytokines do in response to infection? what does IFN-gamma do in response to cytokine?
-proteasome: 28 subunit cylindrical protease complex
-degrades protein into peptide -peptides transported to ER by TAP (heterodimer TAP1, TAP2)
-constitutive- made up of multiple subunits, under normal conditions
-cytokines alter subunits in newly synthesized proteasome forming immunoproteasome IFN-gamma
-increases number of proteaseomes
-alters subunits making up proteasome which results in altered enzyme activity that:
- increases cleavage after hydrophobic residues
-decreased cleavage after acidic residues
1. exogenous antigen for loading into MHC 2 -some goes into class 2 path, some slips into class 1
2. proteolytic digestion
3. release some into cytoplasm
4. MHC 1 path
5. this primes CD8+ cells
T cell clones stimulation?
antigen processing and presentation stimulates T cell clones recognizing particular antigens which will become effector T cells
What MHC does dendritic cells express?
both 1 and 2