Antigen Processing and MHC

Question 1

What the T cell receptor gene rearrangement? what are they recognized by? recombination?

Answer 1

• 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

Question 2

How to recognize antigen in T cells? Signal complex?

Answer 2

• 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

Question 3

What are the two classes of T cells?

Answer 3

• alpha and beta chain (more often)
• gamma and delta chain (5-8%)

Question 4

Where are gamma and delta chain T cells found (specific tissues)?

Answer 4

• reproductive tract
• certain regions of digestive tract

Question 5

Segments in T cell receptors?

Answer 5

alpha: V, J
beta: V, D, J

Question 6

Which as more diversity, Ig or T cells?

Answer 6

T cells

Question 7

How many T cells make it through the education to be a T cell? two processes?

Answer 7

maybe 5%

• does it work?
• does it recognize self vs non self?
• low success rate

Question 8

How do CD8-T cells function?

Answer 8

• CD8 (MHC 1), TCR, CD3 (intracellular signal)
• identifies antigen and engages
• kills cell

Question 9

How do CD4-T cells function with macrophages?

Answer 9

• macrophage is infected
• moves to TCR, CD4, CD3
• activate macrophage
• lysosomes (reactive O2) destroy internal organism
• phagosomes/lysosomes fused together
• destroys antigen

Question 10

How do CD4-T cells function with B cells?

Answer 10

• MHC class II on B cell
• antigen presented to CD 4 cells
• cytokines activate B cell to produce antibodies
• class switching

Question 11

Difference in structure between MHC 1 and 2?

Answer 11

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

Question 12

What MHC does CD 8 (cytotoxic) bind to?

Answer 12

alpha 3 domain of MHC class 1

-endogenous (produced in cell)

Question 13

What MHC does CD 4 (helper) bind to?

Answer 13

beta 2 domain of MHC class 2

-exogenous (outside of cell)

Question 14

What is the target pathogens of MHC 1 vs 2?

Answer 14

1- endogenous (produced in cell- not supposed to be there)

2- exogenous (foreign object- T cells learn what is self)

Question 15

Peptide binding in MHC 1 (HLA-A2 human)? MHC 2 (HLA-DR1)?

Answer 15

MHC 1

• variable
• shorter fragment than can be accommodated in binding cleft

MHC 2

• longer fragment
• can accommodate more diversity
• once made, MHC cannot vary

Question 16

What determines how long an antigen can be in MHC?

Answer 16

peptide binding grooves

Question 17

What is HLA?

Answer 17

human leukocyte antigen (human MHC class isotopes)

Question 18

How many HLA class 1 isotopes? class2?

Answer 18

class 1: 6

class 2: 5

Question 19

What type of expression does MHC (HLA) display?

Answer 19

codominant

-one HLA-A from mom and one from dad, you will express two, one of each

Question 20

What are the properties of HLA class 1 isotopes?

Answer 20

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

Question 21

What are the properties of HLA class two?

Answer 21

DP, DQ, DR (highly)- polymorphic, hundreds of allotypes

DM, DO- oligomorphic, monomorphic

Question 22

General properties of MHC (HLA) proteins? difference from other immunoglobulins? diversity?

Answer 22

• 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
• isoforms
• two classes (1, 2)

Question 23

Gene families?

Answer 23

consisting of multiple, similar genes encoding MHC proteins

Question 24

Genetic polymorphism? how many different alleles can be expressed? tissue matching?

Answer 24

• 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

Question 25

Isoform?

Answer 25

- 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

Question 26

Highly polymorphic?

Answer 26

- certain MHC class 1 and 2 genes have many different alleles and proteins encoded - more polymorphic involved in antigen presentation

Question 27

monomorphic? oligomorphic?

Answer 27

- mono: no polymorphism - oligo: only a few alleles

Question 28

What chromosome is human MHC on? how is it inherited? rate of recombination?

Answer 28

- chromosome 6 - inherited as a unit or haplotype - rate of recombination is low, recombination could be detrimental

Question 29

what is a haplotype?

Answer 29

- linked cluster of polymorphic genes, sets of alleles carried on a single chromosome - every person inherits two, one from each parent

Question 30

Tissue distribution of MHC (class 1 vs 2)?

Answer 30

class 1: - 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 class 2: - some activated T cells - B cells - macrophages/APC - thymic epithelial cells

Question 31

What creates the walls of the peptide binding cleft (MHC class 1)? floor?

Answer 31

- walls:alpha helices 1 and 2 - floor: beta pleated sheet - peptide anchored at both ends

Question 32

How does the peptide interact with the peptide binding cleft?

Answer 32

hydrogen bonds

Question 33

What is the difference between MHC class 1 and class 2 binding cleft? affect?

Answer 33

- 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

Question 34

MHC restriction?

Answer 34

- 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

Question 35

CTL (CD8+) recognize what class of MHC? Helper T cells (CD4+)?

Answer 35

CD8- class 1 CD4- class 2

Question 36

Size of peptides for MHC class 1? class 2? endogenous or exogenous?

Answer 36

class 1 - 8-10 amino acids b/c anchored at both ends - endogenous for presentation to CD8+ class 2 - up to 25 amino acids - exogenous for presentation to CD4+ - extracellular foreign protein - can bind self peptides

Question 37

Exogenous antigen processing?

Answer 37

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+

Question 38

What is the role of CLIP?

Answer 38

holds conformation of binding cleft of MHC 2

Question 39

Endogenous antigen processing?

Answer 39

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+

Question 40

proteasome processing and infection. constitutive proteasome? what do cytokines do in response to infection? what does IFN-gamma do in response to cytokine?

Answer 40

- 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

Question 41

Cross presentation?

Answer 41

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

Question 42

T cell clones stimulation?

Answer 42

antigen processing and presentation stimulates T cell clones recognizing particular antigens which will become effector T cells

Question 43

What MHC does dendritic cells express?

Answer 43

both 1 and 2