Antigen presentation Flashcards
Describe the function of dendritic cells
They report the site of infection; the innate dendritic cell takes the infection to Lymph node; the sensing of pathogen triggers cell migration via lymphatic vessels.
In the Lymph node, dendritc cells present MHC/peptide to naive T cells which stimulates Adaptive response and relays information to T cells.
This causes the effector T cells to activate and travel to the infected tissue to engage other cells presenting the same antigen used to stimulate T cell.
Describe the function of dendritic cells
They report the site of infection; the innate dendritic cell takes the infection to Lymph node; the sensing of pathogen triggers cell migration.
In the Lymph node, dendritc cells present MHC/peptide to naive T cells which stimulates Adaptive response and relays information to T cells.
This causes the effector T cells to travel to the infected tissue to engage other cells presenting the same antigen used to stimulate T cell.
T cells activate antibodies.
Antibodies recognize lipids, carbohydrates, lipids, proteins, nucleic acid
T cells recognise in a different way; to make antibodies, T cells must recognise the antigen
Difference between T cells and B cells recognition.
Antibodies recognize lipids, carbohydrates, lipids, proteins, nucleic acid on the folded pathogen not broken down.
T cells recognise in a different way through unfolded PEPTIDE fragment and MHC; to make antibodies, T cells must recognise the antigen
What kinds of information does the dendritic cell give to T cell?
processed pathogen fragments presented via MHC on cell surface.
What does antigen processing inside dendriic cell refer to?
The pathogen protein is unfolded chopped into smaller fragments. They bind to MHC and travel to cell surface for presentation.
T cells must see this before they can be activated.
What is the difference between the classes of MHC?
Class 1: presents to CD8+ T cells. his alerts to intracellular infection of viruses.
Class 2: presents to CD4+ T cells.
MHC molecules. What are the characteristics
Major Histocompatibility complex.
Chromosome 21 on mouse locus that controlled mouse rejection and skin graph rejection due to immune response; inflammation ect via foreign T cell activation..
Therefore, MHC genes are very polymorphic, they are different in everyone causing incompatibility.
What is the difference between the classes of MHC?
Class 1: presents to CD8+ T cells. MHC 1 is bound to all cells. This alerts to intracellular infection of viruses as foreign/ENDOGENOUS peptides are captured and loaded on MHC in the E.R. They follow secretory pathway to cell surface and present to killer T cells in cytoplasm.
Class 2: presents to CD4+ T cells. This alerts to EXTRACELLUALR infection of bacteria where B cells, dendritic cells and macrophages engulfs and degrades bacterium into peptides, loads into MHCII in vesicles and presents to helper T cells. So they can activate the Antigen Presenting Cell.
What cells have MHCI ?
All cells; as all cells can become virally infected.
What cells have MHCII?
B cell, macrophages, dendritic cells.
These cells are then activated by correct helper T cell to kill via the APC’s effector function
Difference between T cells and B cells recognition.
B cells and their Antibodies can recognize lipids, carbohydrates, lipids, proteins, nucleic acid on the folded pathogen not broken down. (any chemical structure)
T cells recognise in a different way through unfolded PEPTIDE fragment and MHC; to make antibodies, T cells must recognise the internal antigen peptides
T cells recognise other host cells (showing foreign infection) ; B cells recognise a free foreign antigen
How is the relationship between B cell and T cells important in vaccines
Part recognised by the B cell is physically linked to the part/peptide fragment recognised by the T cell once it has been processed by the infected cell.
Describe the appearance of MHCI and MHCII in terms of their crystal structures
- MHC1 has SINGLE transmembrane chain = alpha chain is divided into 3 domains: a1, a2, a3. B2 Microglobulin stabilises structure.
- MHC2 has one transmembrane chain= the alpha chain is divided into 2 domains: a1, a2.
Structure is similar, although chains are different where two long alpha helices in MHC1, and one alpha and one beta long helices in MHC2 form the peptide binding site/groove.
What is a difference between MHCI and MHCII crystal structures?
The terminals of peptide (N and C) engages in specific interactions with MHC1 so there is a SIZE limit of how many peptide residue there are.
Terminal do not interact with MHCII terminals.
What holds the peptides in the grooves of MHC molecules?
They are held stably by HYDROGEN BONDS and charge-charge interactions on the backbone on the peptide.
On the backbone C=O and N-H make hydrogen bonds on the side chain.
The fit is very precise: peptide side chains fit into MHC pockets and some side chains are required to be specific aa to be in pocket.
What is a difference between MHCI and MHCII crystal structures?
The terminals of peptide (N and C) engages in specific interactions with MHC1 so there is a strict SIZE limit of how many peptide residue there are: 8-10 aa
C terminal aa of MHC1 peptides are basic or hydrophobic
Terminal do not interact with MHCII terminals where peptides come out at either side of MHC so no limit to aa length; usually 12-24
What does promiscuous peptide binders mean?
One MHC molecule can bind to thousands of different peptides
Describe the cell in terms of topological domains
1) cytosol (continuous with nucleus and rest of cell without membrane barrier) MHCI: they are loaded in E.R in the secretory pathway
2) vacuolar where external environments can enter the cell. MHCII: vesicles are key for loading reactionwhere endocytic vesicle with antigen is degraded and fused with vesicle of MHCII where it is loaded.
How does inflammation differ MHC loading of peptides?
Interferon-gamma (IFN-gamma) produced changes conformation of the proteasome (MHC1 pathway)
How does inflammation differ MHC loading of peptides? What is an immunoproteasome?
Interferon-gamma (IFN-gamma) produced changes conformation of the proteasome (MHC1 pathway)
This causes alternative subunits to make up proteasome, producing an immunoproteasome. This makes peptides more suited to MHC1 binding requirements at the C terminal.
What is TAP?
Transporter Associated with antigen Processing which delivers peptides to E.R
Describe the Peptide loading complex (PLC) in terms of MHC1
It organises the MHC1 assembly using various chaperone helpers.
1) Calnexin stabilises heavy chain. It leaves after B2 microglobulin binds.
2) the alpha hetrodimer and B2 form the loading complex (PLC) including TAP protein, , tapasin (links MHC1 to TAP so they are in correct location), calreticulin, ERp57, PDI.
3) Peptides from proteasome through TAP where the MHC1 can sample the peptides for correct binding.
4) Binds and MHC1, edited by ERAP and leaves ER and PLC
Which chaperone is important for MHC1 and peptide association
Tapasin; needed for MHC sampling and rejection of peptides.
Tight binding may take several attempts.
What is meant by a first draft of a peptide?
Proteasome make a “first draft” peptide where C terminus is correct due to immunoproteasome.
Where the peptide is too long at the N terminus so ERAP aminopeptidase removes aa from N terminal to produce peptide of 8-10aa length.
What are the generic protein chaperones and dedicated chaperones involved in PLC?
generic:
- calnexin
- calreticulin
- ERp57
- PDI
Dedicaed:
- TAP,
- Tapasin
- ERAP
What is bare lymphocyte syndrome?
Where the TAP is absent and so 1% of MHC1 present on cell surface (missing MHC1) so poor virus response as T cell are not activated.
Viruses can make proteins that block TAP causing similar effect.
Deficencies in any chaperone defects peptide loading and means abnormal CD8+ response.
What is the function of the invariant chain in MHC2 loading?
It blocks binding of peptides to MHC2 within the ER.
It also acts as a targeting subunit so MHC2 is targetted across to endocytic/vescicle pathway.
What is the function of the CLIP in MHC2 loading?
invariant chain is cleaved in vesicle by proteolytic enzymes in endosome/lysosomes to leave only a CLIP fragment. This blocks the binding of peptides within the vesicle
What is the function of the HLA-DM in MHC2 loading?
It helps the release of CLIP from peptide binding site and so allows peptides to bind to MHC2 in vesicle.
It stabilises MHC2 when empty so tight binding can take place.
What is the function of the invariant chain in MHC2 loading?
It blocks binding of peptides to MHC2 within the ER so no premature loading.
It also acts as a targeting subunit so MHC2 is targetted across to endocytic/vescicle pathway; conTrols export from ER.
I is no polymorphic
What is the function of the HLA-DM in MHC2 loading?
It catalyses the release of CLIP from peptide binding site and so allows peptides to bind to MHC2 in vesicle.
It stabilises MHC2 when empty so tight binding of correct peptide can take place.
How can Class 1 and 2 MHC capture peptides at different locations
Due to the different handling and pathways of each.
Peptide binding sites are available to MHC1 in ER
Peptides binding sites available to MHC2 in endosome/lysosome
What cells have MHCII?
B cell, macrophages, dendritic cells.
These cells are then activated by correct helper T cell to kill via the APC’s effector function.
Only on cells that communicate with CD4+.
Describe the crystal structure of T cell receptor (TCR)
It has CDR- complementary determining regions for example CDR3 where there is most peptide binding.
T cell receptor binds diagonally to MHC molecules
What increases MHC expression levels?
Interferons/cytokines
Describe and B cell contact.
Antigen presented by B cell induces increased expression of CD40 ligand (CD40L) on T cell and the production of cyokines by T cell which activate B cell.
This causes B cell proliferation and differentiation into plasma cells that make antibodies
Describe the Hif vaccine against Influenza B.
It protects young children and adults from influenza
It generates antibodies that are directed to polysaccaride part of the bacterium; the B cell receptor binds to polysaccharide toxoid molecule.
Vaccine consists of polysaccaride linked covalently to a protein usually tetanus toxid.
B cell internalises and presents tetanus toxoid peptides to CD4+ T cells via MHC2, and B cell CD40; gets helper T cell help
T cells can activate presenting B cells via cytokines to differentiate and become plasma cell.
Antibodies bind to bacterium.leading to macrophage phagocytosis.
Why is receptor- mediated endocytosis of antigen more efficient?
For good antibody responses to an antigen/vaccine the part recognised by the B cell needs to be linked to the part presented to T cells
Specific receptor for antigen allows B cells to attract T cells more efficiently; it displays alot more peptide.
What is cognate recognition?
For good antibody responses to an antigen/vaccine the part recognised by the B cell needs to be linked to the part presented to T cells
Why is receptor- mediated endocytosis of antigen more efficient?
For good antibody responses to an antigen/vaccine the part recognised by the B cell needs to be linked to the part presented to T cells
Specific receptor for antigen allows B cells to attract T cells more efficiently; it displays alot more peptide.
Production of MHC molecules is a proliferation signal for amount of T cells as well as increasing T cell help.
Specific Ig receptor on B cells that bind and take up antigen and engage T cells at very low concentration; e-12 Moles.
Non specific B cells need e3/e4 more antigen needed for T cell response.
Why is receptor- mediated endocytosis of antigen more efficient?
For good antibody responses to an antigen/vaccine the part/epitope recognised by the B cell needs to be physically linked to the part/epitope presented to T cells
Specific receptor for antigen allows B cells to attract T cells more efficiently; it displays alot more peptide.
Production of MHC molecules is a proliferation signal for amount of T cells as well as increasing T cell help.
Specific Ig receptor on B cells that bind and take up antigen and engage T cells at very low concentration; e-12 Moles. It is the specific B cells that become the plasma cell.
Non specific B cells need e3/e4 more antigen needed for T cell response.
What drives the high polymorphic nature of MHC populations?
Pathogen driven natural selection
What problems does MHC polymorphism create
1) clinical transplants
2) vaccine design for everyone
Describe the chromosome 6 in relation to MHC
The sequence of the chromosome involved in MHC spans 0-4000kbp.
It has Class2 (0-2000) and class 1 genes (2000-4000)
What are the key MHC Class 1 isotypes on chromosome 6?
- HLA- A
- HLA- B
- HLA- C
Where HLA= human leukocyte antigen.
Alpha chain is highly polymorphic but B2 is monomorphic.
What are the key MHC class 2 loci on chromosome 6?
- DR
- DP
- DQ
DR: Beta chain highly polymorphic so alot of variants in population; alpha chain is oligomorphic where there are a few difference.
What does the number of MHC allotypes
The number of HLA proteins, which means there are that many different sequences in the human population
Which chain of the MHC2 is responsible for variance?
The beta chain.
Example: DR alpha= 2, DRbeta= 466 allotypes
Describe the chromosome 6 in relation to MHC
The sequence of the chromosome involved in MHC spans 0-4000kbp.
It has Class2 (0-2000) and class 1 genes (2000-4000)
Class 2 region also encodes other genes that support MHC presentation. These include TAP, tapasin, immunoproteasome subunit (LMP2, LMP7)
What factor may increase MHC variance further
Humans are often heterozygous due to inheritance.
There may be genetic recombination between genes between A and B for example.
Meiotic recombination occurs at 2% frequency.
What does haplotype mean?
The combination of HLA alleles on chromosome 6 in an individual.
What is the typical MHC make-up of an individual?
Three MHC1- A, B, C
Three MHC2- DR, DQ, DP
Therefore 2 haplotypes per person (maternal, and paternal)
In total there are 6 of each MHC 1 and 2.
Where can all the polymorphism of MHC be pinpointed to?
The peptide binding region of MHC
In MHC2 beta chain shows varible.
What are the rules for MHC A- 0201 on its binding motif?
All the peptides have leucine aa on binding position 2, valine on position 6, and valine/leucine on position 9 in order for peptide to bind.
What are the rules for MHC in general on its binding motif sequence?
There are 2/3 ANCHOR positions that restrict the multiplicity of peptides that are able to bind.
Anchor positions are the MHC pockets where the peptide side chains fit.
MHC1 is restricted as binding positions 2 and 9 are specific to a couple aa; exposed peptide side chains interact with T cell receptor.
MHC2 is more difficult to pinpoint anchor binding positions as peptides binding are longer.
What does MHC restriction
T cell repertoire is selected so it is good at recognising antigen (individuals T cells learn) in the context of MHC proteins
Describe positive selection of T cells
Cortical epithelial cells in the thymus.
Describe negative selection of T cells
Dendritic cells, macrophages in the thymus.
Describe positive selection of T cells (First stage in maturation)
Cortical epithelial cells in the cortex of the thymus display MHC presenting self antigens.
Where there is no binding to MHC of skin cell, T cell will die. These T cells show inability to bind to MHC.
Where there is strong binding to MHC of skin cell, T cell lives
Describe negative selection of T cells (second stage in maturation)
Dendritic cells, macrophages in the medulla of the thymus
Where there is moderate binding to MHC of innate cell, T cell will live.
Where there is strong binding to MHC of innate cell, T cell will die.
Where do T cells develop?
Thymus
Describe positive selection of T cells (First stage in maturation)
To check T cell can bind to MHC!
Cortical epithelial cells in the cortex of the thymus display MHC presenting self antigens.
Where there is no binding to MHC of skin cell, T cell will die. These T cells show inability to bind to MHC.
Where there is strong binding to MHC of skin cell, T cell lives
Describe negative selection of T cells (second stage in maturation)
To check if T cells will react with host antigens, and cause autoimmunity!
Dendritic cells, macrophages in the medulla of the thymus presenting self antigens.
Where there is moderate binding to MHC of innate cell, T cell will live.
Where there is strong binding to MHC of innate cell, T cell will die.
What does haplotype mean?
The set/combination of HLA alleles on chromosome 6 in an individual.
What does MHC restriction mean?
T cell repertoire is selected so it is good at recognising antigen (individuals T cells learn) in the context of MHC proteins
Why is it advantageous to have different alleles of MHC?
Different alleles of MHC have differences in peptide groove and so capture and present different peptides.
Inheriting two similar haplotypes means the range covered of the total pathogen peptides possible is less than inheriting two different haplotypes where there are no overlaps of specific MHC molecules
Therefore is is good to be heterozygous and containing completely different halotypes; you can present more MHC against peptides, eg, HIV.
What are the advantages of MHC polymorphorism?
- Good for survival of the species
- More diverse peptides presented; more different T cells are activated
- Harder for pathogen to evade the immune response with more CD8+ activation
What are superantigens?
They are produced by bacteria, viruses and mycoplasmas that are not processed
They bind to outside (not the groove where there is some form of peptide) of MHC and link MHC molecule and T cell receptors together like a cross link between them in the middle; They instead bind to the V-beta of T cell receptor.
Here, the varible loops are not featured; If the T cell has the specific V-beta of the superantigen then it becomes stimulated.
This means lots of T cells can be activated, and too many cytokines causing inflammation are made which can be fatal.
What do superantigens cause?
Toxic Shock Syndrome
