March 21st (Exam 3)

Question 1

Where do the MHC Class II molecules get the peptides that they will present?

How do they get that stuff in the cell?

What types of cells are doing this in the highest frequency?

Answer 1

They get them from the extracellular environment.

The cells “survey” the extracellular environment by endocytosis or with cell-surface receptors.

The cells that are doing this are B cells, dendritic cells, macrophages, and neutrophils

Question 2

Explain the whole process without nitty gritty details.

Answer 2

Cell uptakes extracellular material into endosomes (intracellular vesicles) that come from the plasma membrane. The vesicle becomes increasingly acidic as proton pumps within the membrane of the vesicle. The vesicles can fuse with a lysosome that contains enzymes that facilitate degradation of the material. The peptides that are produced from this material are bound to MHC Class II molecules and are carried to the plasma membrane by outward going vesicles.

Question 3

What prevents MHC Class II molecules from binding to antigens that are self antigens (meant for Class I) that are present in the ER?

Answer 3

A third chain called the invariable chain binds to the alpha and beta subunits of the MHC Class II after they are synthesised by ribosomes and translocated into the ER.

Question 4

What are the other two notable functions of the invariant chain of the MHC Class II molecule?

Answer 4

1. It simply stabilizes the molecule so that its shape is maintained until it can bind the peptide.
2. It delivers the MHC Class II molecules to the vesicles that contain the extracellular material that needs to be bound to the MHC Class II molecules.

Question 5

What is contained within the vesicles that MHC Class II molecules must find (aided by the invariant chain)?

What are the vesicles called?

Answer 5

1. Extracellular material that is degraded into peptides
2. Cathepsin S (protease that attacks invariant chain)
3. HLA-DM
4. HLA-DO

We call these vesicles MHC class II Compartment (MIIC)

Question 6

What do Cathepsin and other proteases within the MIIC turn the invariant chain into?

What does this thing do?

Answer 6

It cleaves the chain a bunch leaving what is called the CLIP (essentially what is left of the invariant chain)

The CLIP covers up the peptide binding site.

Question 7

How is CLIP eventually removed so that a peptide can bind?

What is HLA-DM?

Answer 7

It must interact with HLA-DM.

HLA-DM is a specialized form of MHC Class II that binds to the MHC Class II molecule and acts kind of like tapasin, by making the orientation of the peptide groove more open, allowing CLIP to disassociate and various peptides to be tried on. Once a peptide that binds tightly is found, HLA-DM can break off.

Question 8

What does HLA-DO do?

Why is this important?

Answer 8

It binds to HLA-DM in an antagonistic fashion, preventing the HLA-DM from helping the MHC Class II molecule from releasing CLIP.

It’s important because when there is an infection interferon gamma can cause HLA-DM to be made in excess so that we get more MHC Class II molecules with bound peptide to the surface.

Question 9

How in the world can extracellular pathogens be presented on MHC Class I molecules?

What is this called?

Why is this important?

Answer 9

The answer is, its complicated like everything in this class.

Let’s start with why it’s so important. Hepatitis C is a virus that infects hepatocytes (only). The issue starts because we want to initiate a CD8 T cell response, but the things that typically mobilize this are dendritic cells and macrophages, and those guys (in the liver we call them Kupffer cells) don’t ever get infected with Hepatitis C.

So how do people do it?

Well the Kupffer cells will phagocytize dead or dying hepatocytes to get the viral proteins - this is the classical MHC II presentation method. Yet, we understand that people who are fighting a Hep-C infection successfully mount a CD8 T cell response. Because we know this, we derive the idea of cross presentation where antigens located on the class 2 pathway can be transferred to the class 1 pathway.

Question 10

What is the immune response initiation that happens by means of cross presentation?

Answer 10

Cross priming.

Question 11

What kinds of cells constitutively express MHC Class I molecules on their cell surface?

Answer 11

All cells in the body but erythrocytes.

Question 12

What are the cells that constitutively express MHC Class II molecules called?

Name the three cells that we talked about.

Answer 12

They are called professional Antigen Presenting Cells (APCs)

1. Dendritic Cells
2. Macrophages
3. B-cells

Question 13

What is more diverse?

MHC molecules or TCRs and Immunoglobulins?

Answer 13

Not MHC molecules

Question 14

Where is the MHC region of the genome?

What is it associated with?

Answer 14

Chromosome 6

It is associated with the highest number of diseases.

Question 15

What is the specific name of MHC in human beings?

Answer 15

HLA (Human Leukocyte Antigen complex)

Question 16

What type of genes encode MHC molecules?

Do they rearrange/change?

Answer 16

They are conventional, stable genes and they don’t undergo any rearrangement or developmental/somatic process of structural change.

Question 17

What are the sources of MHC diversity?

Answer 17

1. Gene families - there are multiple similar genes that encode the MHC class I heavy chains MHC class II alpha chains and MHC class II beta chains.
2. Genetic Polymorphism - there are different versions of the genes for MHC molecules that exist within the population.

Question 18

What are isotypes?

Answer 18

These are the protein products of the different genes in a MHC class I or class II family (example: HLA - A)

Question 19

What are alleles and allotypes?

Answer 19

Alleles are the different versions of the same gene.

An allotype is a genetically inherited variant (allele) of a specific MHC isotype

E.g like a different version of the HLA - A isotype

Question 20

What is an isoform?

Answer 20

Any particular MHC protein.

Question 21

Why are many MHC class I and II genes considered highly polymorphic?

Answer 21

Because there are numerous alleles of certain genes and there are many differences that define them.

Question 22

What are MHC Class I and II genes that have no polymorphism called?

What about genes that only have a few alleles?

Answer 22

Monomorphic.

A few alleles makes them oligomorphic.

Question 23

How many isotypes of MHC Class I are there?

MHC Class II?

Answer 23

6 HLA - A, B, C, E, F, G

5 HLA - DM, DO, DP, DQ, DR

Question 24

What are the highly polymorphic isotypes of MHC Class I?

What are they responsible for?

Answer 24

HLA- A, B, C

Their job is to present antigens to CD8 T cells and to form ligands for receptors on natural killer cells.

They bind NK cells as to tell them not to kill them.

Question 25

What are the oligomorphic isotypes of MHC Class I? What do they do?

Answer 25

HLA- E, G They act as ligands for receptors on NK cells (same thing - don't kill me)

Question 26

What is the monomorphic isotype of MHC Class I? What is thought of its responsibility?

Answer 26

HLA-F It is thought to act like a chaperone that receives other HLA molecules from the cell surface that have lost their peptides.

Question 27

What are the polymorphic isotypes of MHC Class II? What do they do?

Answer 27

HLA - DP, DQ, DR They present peptide antigens directly to CD4 T cells.

Question 28

What are the oligomorphic isotypes of MHC Class II? What do they do?

Answer 28

HLA - DM, DO They assist/supervise the peptide loading of the other MHC Class II molecules

Question 29

Which class of MHC molecules has more diversity?

Answer 29

Class I for sure.

Question 30

What is the HLA Complex? Where is it? How big is it? Name and describe the three regions of it.

Answer 30

It is a four million base pair region of DNA containing 200 genes that is located on the short arm of chromosome 6. It contains three regions: Class I region - furthest from the centromere, contains Class I genes Class II region - closest to the centromere, contains Class II genes Class III region Central MHC - contains other genes

Question 31

What part of MHC Class I molecules are not found within the HLA Complex? Where do we find it?

Answer 31

The beta-2 microglobulin. It is found on chromosome 15

Question 32

What would we call the gene locus that encodes the HLA-DM alpha chain?

Answer 32

HLA-DMA

Question 33

What about if a person was heterozygous for HLA DMA? What would we call each locus on each homologous pair to appropriately explain the alleles?

Answer 33

HLA DMA1 HLA DMA2

Question 34

Explain the diversity of HLA-DR. (think about the presence of specific loci for each chain within the HLA-DR) and the number of allotypes that is granted by this.

Answer 34

1. Alpha chain really only has one type. 2. Beta chain has 4 loci (everyone has HLA DR B1 * because of these many loci, there are tons and tons of allotypes that are possible.

Question 35

What is the haplotype?

Answer 35

This is the particular combination of HLA alleles found on a given chromosome 6.

Question 36

What is special about the Class II region of the HLA Complex?

Answer 36

The majority of genes that it contains are used in antigen processing and presentation to T-cells 1. Genes that encode TAP 2. Genes that encode tapasin 3. Genes that encode proteolytic subunits of the immunoproteasome

Question 37

What about the invariant chain of the MHC Class II molecules? Where is this guy at?

Answer 37

He is on chromosome 5

Question 38

How do the class II genes expression get induced?

Answer 38

They rely on a transcriptional activator that is called CIITA or Class II Transactivator For CIITA to be active it needs to be induced by Interferon Gamma

Question 39

Explain the variation of the highly polymorphic MHC alleles.

Answer 39

They encode proteins that vary by 1-50 aas

Question 40

Where is this variability concentrated?

Answer 40

Firstly, in the domains alpha 1 and alpha 2 of the MHC Class I and the alpha 1 and beta 1 of MHC Class II. More specifically, the positions within these domains that contact the TCR or the bound peptide

Question 41

What are the anchor residues of the peptides that the MHC molecules bind? Are they accessible to the TCR?

Answer 41

These are the residues of the peptides that interact with the MHC peptide binding groove. They are not accessible to the TCR

Question 42

What do we call the combination of the anchor residues that bind a particular MHC isoform (most specific)?

Answer 42

That is called its peptide binding motif (the pattern of anchor residues and peptide structure that a isoform prefers)

Question 43

What do we call the idea that a given TCR only recognizes its peptide antigen when it is bound to a PARTICULAR MHC molecule?

Answer 43

This is called MHC restriction * I.E antigen specific T-cell response is restricted to a particular MHC type

Question 44

What do we call the selective processes that maintain a variety of isoforms within the population?

Answer 44

Balancing Selection

Question 45

Explain the idea of directional selection.

Answer 45

When there is some sort of selection pressure that favors some alleles and not others, disrupting the balance.

Question 46

Explain interallelic conversion or segmental exchange.

Answer 46

This is the idea that when one small section of an HLA allele is replaced by a homologous section of another, resulting in a change in a few aa usually concentrated within the peptide binding groove. Because of this, the new alleles may be favored - certain alleles are associated with slower progression of disease.

Question 47

What is the reason why people reject organs?

Answer 47

Because there are a lot of MHC genes that are polymorphic i.e people have many different versions and they are very often not the same from person to person, triggering T-cell responses