Lecture 5 - Antigen-Binding Receptors: MHC and TCR

Question 1

What does MHC stand for? Where does this name come from?

Answer 1

MHC = Major HistoCompatibility molecule

Named based on role in graft rejection: cluster of genes that control tissue compatibility

Question 2

What are MHCs called in humans? Why?

Answer 2

Human Leukocyte Antigens (HLA) molecules, because they were first found on the surface of human WBCs in patients that have received many blood transfusions

Question 3

What are MHCs called in mice?

Answer 3

H-2 antigens

Question 4

3 types of MHC I molecules in humans?

Answer 4

1. HLA-A
2. HLA-B
3. HLA-C

Question 5

On what cells is MHC I expressed? What to note?

Answer 5

On the surface of essentially all nucleated human cells

Note: the level of expression varies on different cell types

Question 6

With what immune cells do cells expressing MHC I interact?

Answer 6

CD8+ T lymphocytes

Question 7

3 types of MHC II molecules in humans?

Answer 7

1. HLA-DR
2. HLA-DQ
3. HLA-DP

Question 8

On what cells is MHC II expressed? What to note?

Answer 8

On cells of the immune system:

1. B cells
2. Dendritic cells
3. Macrophages
4. Activated T cells

+ some other cells in specific situations (e.g. endothelial cells involved in transplant rejection)

Question 9

With what immune cells do cells expressing MHC II interact?

Answer 9

CD4+ T lymphocytes

Question 10

Other name for CD4+ T lymphocytes?

Answer 10

Helper T cells

Question 11

Structure of the MHC proteins? Key feature?

Answer 11

Heterodimers

Key feature: peptide binding cleft

Question 12

Structure of MHC I?

Answer 12

2 chain molecules consisting of:

1. Alpha chain in the cell membrane with the external portion divided into 3 ~100 amino acid long segments that have similarity to Ig domains and called alpha 1 (N-terminal), alpha 2, and alpha 3 (inserted in membrane)
2. Smaller polypeptide, beta2 microglobulin

Alpha 3 domain and the beta2 microglobulin pair to form a platform, on top of which sits an antigen binding groove formed by the alpha 1 and alpha 2 domains

Question 13

Structure of MHC II?

Answer 13

2 chain molecules in cell membrane consisting of:

1. Alpha chain
2. Beta chain

The extracellular portions of the two chains are each divided into 2 ~100 amino acid long segments that have similarity to Ig domains and alpha2/beta2 are inserted in membrane

Antigen binding groove: composed of alpha1 and beta1 domains

Question 14

Describe the antigen-binding groove of MHC molecules.

Answer 14

It resembles a hot dog bun (made of 8-25 AA peptides) with walls of 2 alpha helices and a beta pleated sheet floor

Question 15

What is the source of the peptides bound by MHC molecules?

Answer 15

Self
1. Normal cellular proteins (autoreactive T cells would recognize these)

Antigens (nonself)

2. Pathogens
3. Tumor-associated proteins
4. Other foreign proteins (vaccines, drugs)
5. Foreign HLA (transplant)

Question 16

How do MHC I molecules assemble? 3 steps.

Answer 16

1. N-terminal leader signal peptide targets the 2 polypeptide chains of the MHC I to the ER
2. Alpha and betam chains assemble and fold in the ER and as they do so, they pick up a single peptide (~10 AAs) found within the ER => this stabilizes the MHC molecule
3. MHC I molecule moves through the Golgi to the cell surface where it displays the peptide and as they do so they can pick up about 2,000 different peptides

Question 17

What is required for MHC I molecule assembly in the ER?

Answer 17

Peptide binding

Question 18

Where do the peptides bound to MHC I and II during folding in the ER come from?

Answer 18

Derived from the normal degradation of cellular proteins or may derive from a pathogen

Question 19

Do MHC II molecules also bind peptides during their assemble? Explain. Purpose?

Answer 19

Yes, but they bind peptides in a different cellular compartment than the class I molecules

1. The class II molecules associate with a third polypeptide chain in the ER = the invariant chain, which blocks the class II peptide binding groove and targets the class II molecules to the endocytic pathway
2. Once in this pathway, used by cells for bringing in material from the cell surface or external environment of the cell, the invariant chain is removed => MHC II molecules are free to bind peptides
3. Once stabilized by bound peptides, the MHC II molecules move to the cell surface

Question 20

Where is the MHC gene located? What does it code for?

Answer 20

Chromosome 6

The complex contains most, but not all genes that specify the class I and class II molecules - beta2 microglobulin, is encoded on another chromosome

Question 21

Length of MHC gene? What does it contain?

Answer 21

4 million base pairs in length and contains many genes

Over 10% of these genes are involved in the immune response

Question 22

What is unique about the MHC gene system? Implication?

Answer 22

Genes in the human population are highly polymorphic: many alleles exist for each of the loci:

• HLA-A > 1,600 alleles
• HLA-B > 2,000 alleles
• HLA-DR > 900 alleles

Many alleles of each HLA gene + multiple “versions” of HLA genes carried in the genome (ie HLA-A,B,C,DR,DQ,DP) create an extensive library of HLA genes in the human population as a whole => diversity important in protecting the population as a whole from pathogens

Question 23

How are alleles at each class I or class II locus inherited?

Answer 23

In typical Mendelian fashion: 4 possible genotypes in children and each given child have a 1:4 change that a sibling has inherited the same 2 alleles

These genes are inherited as haplotypes (combination of alleles on a chromosome) as the whole chromosome 6 is inherited

Question 24

How are HLA molecules encoded by genes inherited from your mother and father expressed? Explain.

Answer 24

They are expressed co-dominantly so if you are heterozygous, both alleles are expressed as proteins on the cell surface

Question 25

Where does the HLA polymorphism come from?

Answer 25

The AAs that differ between proteins created by different alleles lay within the antigen binding groove and alter its characteristics, changing its charge, shape, and hydrophobicity

Question 26

How many peptides does an MHC molecule bind?

Answer 26

ONE

Question 27

Can different peptides bind the same MHC molecules? What do these have in common?

Answer 27

YUP Peptides that bind a specific MHC molecule share structural features called a motif (length, AAs at specific positions), which allows them to fit into the groove of that MHC molecule

Question 28

What happens to old MHC molecules on the cell surface?

Answer 28

Degraded or recycled

Question 29

Implication of peptides from ER or endosome being bound on the MHC molecule on the surface of the cell?

Answer 29

It displays the "status" of the cell, aka what is going on inside the cell

Question 30

Can the TCR be secreted by the T cell?

Answer 30

NOPE, it is always found inserted in the T cell surface

Question 31

Describe the structure of the TCR.

Answer 31

2 polypeptide chains: alpha and beta (each ~250 AAs), which are disulfide bonded The TCR is expressed in a complex with CD3 on the T cell surface, which acts as a chaperone or signaling molecule

Question 32

What do all TCRs have in common?

Answer 32

N-terminal first ~100 amino acids are variable and the remainder are conserved

Question 33

What forms the antigen-MHC recognition site of the TCR?

Answer 33

The combination of alpha variable region and beta variable region

Question 34

How many antigen-MHC recognition site per TCR?

Answer 34

ONE ONLY

Question 35

How many TCRs do T cells express?

Answer 35

~30,000 copies of a single clonally unique receptor

Question 36

Describe the specificity of the TCR. What is this called? What to note?

Answer 36

Each TCR is specific for a particular MHC-peptide complex, exhibiting specificity for both antigenic peptide (ag restricted) and MHC (MHC restricted) Note: TCRs can recognize more than one MHC/peptide complex as long as they appear physically and chemically identical (e.g. an antigen specific TCR from a transplant recipient can recognize a foreign MHC holding a self peptide on the transplanted tissue causing allorecognition and tissue rejection)

Question 37

Would the TCR still bind if the MHC molecule was switched?

Answer 37

NOPE

Question 38

What does the TCR interact with on the MHC-antigen complex?

Answer 38

1. Some but not all amino acid side chains in the peptide bound in the antigen binding groove of an MHC molecule 2. MHC molecule itself

Question 39

When is the library of TCRs available for an immune response generated? How?

Answer 39

Generated prior to exposure to antigens and has the capacity to recognize thousands of antigenic peptides and limited set of self-MHC molecules As hematopoietic stem cells mature in the thymus, the TCR genes rearrange to form functional TCR loci, synthesizing TCRs (mechanism very similar to Ig gene rearrangement)

Question 40

What happens when a TCR encounters an antigen-MHC complex it is specific for?

Answer 40

Those T cells begin proliferating

Question 41

Describe the genetic code of the TCR alpha chain in germ cells (undifferentiated T cells).

Answer 41

The TCR alpha chain is encoded by several exons that specify: 1. Leader 2. Variable region domain (V and J gene segments) 3. Constant region domain 4. Hinge-like region 5. Transmembrane region 6. Cytoplasmic region

Question 42

What allows us to create an immense library of TCRs?

Answer 42

Multiple alternative exons for V and J gene segments arranged in sequence in germ cells (undifferentiated T cells) => - 50 V segments - 70 J segments - 1 C segment

Question 43

How are the alpha and beta chain gene segments rearranged as the germ cell differentiates into a T cell? Where does this occur? What to note?

Answer 43

The alpha and beta chain loci undergo a permanent DNA rearrangement in which 1 V segment is spliced next to 1 J segment at random => this functional locus is then transcribed, RNA processed to yield mRNA and alpha and beta chains polypeptide synthesized This happens in the thymus Note: the beta chain locus appears to rearrange first and alpha second

Question 44

Describe the genetic code of the TCR beta chain in germ cells (undifferentiated T cells).

Answer 44

The TCR beta chain is encoded by several exons that specify: 1. Leader 2. Variable region domain (V, J, and D gene segments) 3. Constant region domain (2 alternative ones that have the same function)

Question 45

What portion of the TCR interacts with the antigen-MHC complex? What to note?

Answer 45

CDR regions that are contributed by the V exons and the V-J and V-D-J junctions Note: the V-J and V-D-J junctions appear to play the most important role in interaction with the highly variable antigenic peptide

Question 46

What are the 4 mechanisms that generate a variety of AA sequences in the CDRs of TCRs? What is this similar to?

Answer 46

1. Multiple gene segments (V/D/J) 2. V-D-J combinatorial diversity 3. Junctional diversity 4. Alpha-beta combinations Similar to Ig diversity, BUT no somatic mutation because mutation might result in loss of MHC molecule binding so function might be too readily damaged by mutation

Question 47

5 clinical implications of some specific HLA alleles?

Answer 47

1. Specific HLA alleles are associated with disease resistance or susceptibility: autoimmune diseases, infectious diseases, drug toxicity 2. Differences in the ability to display specific peptides to T lymphocytes among individuals expressing different HLA alleles may cause differences in immune responsiveness and have implications in the design of peptide-based vaccines 3. Differences in HLA alleles expressed by patient and organ donor can cause unwanted immune responses in transplantation 4. Some virally-infected or tumor cells lose HLA class I expression, so during an ongoing immune response, these HLA-negative cells become invisible to T lymphocytes and are no longer targeted by T cells for destruction 5. Some aberrant genetic rearrangements to form TCRs are implicated in some malignancies and 6. TCR genetic rearrangement are monitored during immune reconstitution after bone marrow transplant to check that the new T cells are working

Question 48

What are the three important antigen receptors of the immune system?

Answer 48

1. Ig 2. TCR 3. MHC

Question 49

3 similarities between TCRs and Igs?

Answer 49

1. Similar domain structure with variable and constant regions 2. Location on the cell surface 3. Ability of their genes to rearrange to generate a vast library of receptors capable of recognizing virtually any antigen

Question 50

How do MHC molecules differ from Igs/TCRs?

Answer 50

MHC molecules bind a large number of antigenic peptides using a limited number of antigen binding grooves in any one individual

Question 51

Other name for alpha chain of MHC I?

Answer 51

Heavy chain