Theme 3- 3b (Antigens and Antigen receptors pt 2 ) Flashcards
what are the antigen presenting molecules used by T cells
what are their classes
MHC class I MHC class II
what is a paratope
antigen binding site
what can T cells bind to
the bind LINEAR ARRAYS of approx 9 aa via TCR
- NOT native Ag
- Ag is broken down to primary structure (PROCESSED) and PRESENTED to the T cell by molecules on the surface of Ag presenting cells (eg macrophages and dendritic cells)
what are the similarities between the BCR and TCR
- TCRs are similar to Fab fragment of B cell
- both TCR and BCR are composed of: 2 different peptide chains, variable region for binding antigen, constant regions, hinge regions
what are the differences between the BCR and TCR
TCR only has ONE antigen binding site
BCR has TWO
what are the TWO TYPES of TCR
αβ and γδ - with distinct functions
- which type is dependant on which genes encode the protein
describe the structure of TCR
VARIABLE REGION: made of of the V domains (Vα/Vβ or Vγ/Vδ) for antigen binding
CONSTANT REGION: made up of the C domains (Cα/Cβ or Cγ/Cδ)
do TCRs have a non membrane bound secretion
no, they are always membrane bound
how many antigen binding sites do TCRs have
ONE
does TCR have signalling molecules?
no- O it uses CD3 (an accessory molecule) instead
what is the structure of CD3
look at slide 8 for diagram
consists of 6 polypeptides:
ζζ, γε and εδ dimers
- ζ chains have 3 ITAMs
- γ, ε and δ have extracellular Ig folds and one ITAM apiece
TCRs can either be CD… or CD…?
what does this give rise to
CD4 or CD8
- CD4 or CD8 give ANOTHER WAY of TCR BINDING to the MHC
- this gives some SELECTIVITY
what are the TCR and CD3 held together by
electrostatic interactions, forming a compact structure in the T cell surface
what does each T cell have multiple copies of
where is this randomly generated
MULTIPLE copies of a SINGLE variant of the TCR, randomly generated in the THYMUS
describe T cell development
- THYMOCYTES enter the thymus not expressing the TCR or co-receptors (CD4/CD8)
- REARRANGEMENT of the DVJ segments of genes encoding α and β chains
- gives each cell a UNIQUE TCR to recognise an epitope
- if a FUNCTIONAL TCR is not formed (non-productive rearrangement), the T cell DIES by apoptosis
what % of thymocytes that enter the thymus actually become T cells
5% (rest die by apoptosis)
antibodies deal best antigens where
give examples
antigens that are outside the cell (eg bacteria outside cells/viruses outside of cells)
T cells are v good at attacking what type of antigen
give examples
antigens WITHIN CELLS so we want to KILL the cell (endogenous antigens)
eg virally infected cells/tumour cells
what do MOST T cells recognise
ONLY peptides
- T cells are specfic for AMINO ACID sequences of peptides
what has to occur for T cells to recognise and respond to FOREIGN peptide antigens
antigen has to be presented by MAJOR HISTOCOMPATIBILITY COMPLEX (MHC)
CD8 class T cells recognise what type of MHC class
MHC class I
CD4 class T cells recognise what type of MHC class
MHC class II
what is the purpose of the CD4/CD8 molecules
Whilst the TCR recognises and binds the peptide/MHC molecule complex, the CD4 and CD8 molecules also interact with and bind the MHC molecule ensuring stability of the ‘immunological synapse’
in T cell antigen recognition, what is the epitope of the antigen comprised of
some aa from the PRESENTED PEPTIDE
also SOME PARTS of the MHC
how are T cells activated
1) VARIABLE regions of the TCR αβ chains interact with the peptide in the MHC
2) EPITOPE and PARATOPE must ‘fit’ together
3) after binding of MHC-peptide on the APC with the TCR, either CD4 or CD8 join the complex
4) cellular KINASES and the ITAMs of CD3 initiate T cell activation
how do we ensure T cells are only activated by an antigen
CO-STIMULATORY molecules
- CD28 on the T cell and CD80/86 on APC have to interact
- CD80/86 is NOT PRESENT unless it has been activated by INNATE immunity
how many types of receptor does each B or T cell express
ONE receptor that is specific for ONE antigen
how many BCR (Ig) are there
5x10^13
but this is even higher bc of somatic hypermutation/ affinity maturation
how many TCR are there
1x10^18
what is clonal proliferation
when does it occur
what does it produce
when BCR or antigen or TCR are activated, they undergo clonal proliferation:
the activated cell proliferates O MILLIONS of the cell that can recognise the antigen
- produces TWO TYPES OF CELL:
- EFFECTOR CELLS (aid in antigen/pathogen removal)
- MEMORY CELL (aid in secondary immune responses)
what is a POLYCLONAL response
- pathogens may have MANY antigens each having SEVERAL EPITOPES: proteins, carbohydrates, lipids, metabolites
- POLYCLONAL response: many clones of B and T cells will expand as they recognise the different antigens and/or different epitopes within them
what is antigen processing
how complex antigens/proteins are BROKEN down into peptides and loaded into molecules for PRESENTATION to T cells
MHC is encoded by what genes
HLA genes
what are the 4 main groups of HLA genes
- HLA-A, HLA-B & HLA-C region genes (are for MHC CLASS I)
- HLA-D [actually called HLA-DP, HLA-DQ and HLA-DR] (are for MHC CLASS II)
what does HLA stand for
human leukocyte antigens
describe MHC class I
- on ALL nucleated cells and platelets
- targets for GRAFT REJECTION
- involved in Ag recognition of VIRALLY infected cells
- Present peptides to CD8+ T cells (cytotoxic T cells) so essential in viral infections or recognition of altered self (such as tumour cells)
what is the structure of MHC class I
- a1 and a2 domains consist of 4 b strands and an a helix
- these form a groove or cleft which is the Ag-binding site of the molecule
where is class I MHC found give examples
on antigen presenting cells (APCs)
eg dendritic cells, macrophages, B cells
what is the role of class II MHC
which structure forms the peptide binding site
- Ag presentation to T cells (CD4+ helper T cells), where the T cell can be activated an dundergo proliferation ad cytokine secretion
- a1 and b1 domains form peptide binding site like Class I
what is a size difference in MHC class I and II what is the difference in aa number that each class can bind
MHC class I has slightly smaller groove
- 8-10 aa peptides can bind to MHC class I
- 13-18 aa peptides can bind to MHC class II
why is there a difference in size between MHC class I and II
MHC class II is comprised of more chains O has the flexibility to accomodate larger peptides
why does each MHC molecule display ONE peptide at a time
each T cell responds to a SINGLE peptide bound to an MHC molecule
why do MHC molecules have low affinity and broad specificty
so many different peptides can bind to the same MHC molecule
why do MHC molecules acquire peptides during intracellular assembly
both class I and II MHC molecules display peptides from DIFFERENT cellular compartments
why do MHC molecules have a very slow off-rate (once peptides are bound they stay there for a DAYS -long time)
to allow the bound peptide to be there long enough to be LOCATED by a T cell
why is it important that for an MHC to be stable a peptide bound is req
MHC without peptides are very unstable O taken back into cell and endocytosed
- only MH that are displaying peptides are expressed for recognition by T cells
what do MHC molecules ONLY bind to
peptides
how can MHC interact with haptens
haptens (eg causing response to chemicals) can be combined with a peptide to cause an IMMUNE RESPONSE
what is class I MHC formed of
one chain (a1, a2, a3 domains) and interacts with CD8+ T cells. Also has b2-macroglobulin
what is class II MHC formed of
two chains (a1, a2 domains on one b1, b2 on the other) and interacts with CD4+ T cells
where are dendritic cells located
- skin
- GI and resp tracts
- parenchyma
where are Langerhans cells located
they are dendritic cells in the epidermis (skin)
what happens if a Langerhans cell is activated
- if bacteria is present they present antigen
- they detach from surrounding tissue and MIGRATE via LYMPHATIC vessels to LYMPH NODE
- THE LYMPH NODE captures antigen
- this is where the antigens are presented and they may encounter a T cell
describe the general capture and presentation of protein antigens by DCs
- Antigen is processed at the site of infection by dendritic cells (DCs)
- The DCs become migratory; they detach and enter the lymphatic vessels (soluble antigen can also enter lymphatics)
- These vessels empty into lymph nodes in the parcortex area bringing the DCs (and soluble antigens)
- The DCs then become positioned on the fibroblastic reticular cell (FRC) network (soluble antigens can be processed by other APCs here)
- Here they are scanned by naïve CD4 or CD8 T cells
dendritic cells link what
innate and adaptive immunity
- Innate – phagocytosis of antigens, production of cytokines due to PAMPs
- Adaptive – following on, antigens can be presented on MHC and the cytokines help activate the T cells
which MHC is endogenous, which is exogenous
endogenous (MHC I) and exogenous (MHC II)
how are antigens presented in the endogenous pathway (MHC class I) ie how does the peptide end up in the MHC
- peptide antigens are from WITHIN cell
- proteins are PROCESSED by proteasome into SMALL peptides
- TRANSLOCATED to ER lumen by heterodimeric TAP (transporter associated with antigen processing)
- they are loaded into MHC class I here
- ANTIGEN:MHC I complex is TRANSPORTED to cell memb
how are antigens presented in the exogenous pathway (MHC class II) ie how does the peptide end up in the MHC
- antigens are from OUTSIDE of the cell
- antigens are ENGULFED into ENDOCYTIC compartments and DEGRADED to peptides
- they are loaded into MHC class II in CYTOPLASMIC vesicles
- antigen:MHC II complexes are transported to CELL MEM
MHC I is associated with what type of Tcell
CD8 cytotoxic T cells
can remember this as I is drawn similarly to T
MHC II is associated with what type of Tcell
CD4 T Helper cells
in detail explain the steps before peptides bind to MHC I
slide 40 for diagram
1) MHC class I alpha chain associates with the chaperone protein Calnexin and ERp57
2) Β2 macroglobulin binding displaces Calnexin
3) Calreticulin and Tapasin (TAP associated protein) also bind, creating a “peptide loading complex”
4) Peptides (that may have been further processed by ERAP so that they are 8-10 amino acids in length) can then bind, stabilising the complex so that it can then be transported to the cell surface
in detail explain the steps before peptides bind to MHC II
slide 41 for diagram
1) MHC II and invariant chain (Ii) made in ER, then transported through Golgi to a vacuole that fuses with late endosomes → MHC class II enriched compartment (MIIC
2) Antigen enters via receptor-mediated endocytosis, via early endosome until it forms the MIIC late endosome
3) Ii degrades leaving CLIP protein, then DM facilitates the replacement of CLIP with peptide 13-18 amino acids in length
4) Finally complex is transported to the cell surface
what are the components of a stable peptide-MHC complex made in MHC class I
polymorphic alpha chain, beta2 microglobulin, peptide
what are the components of a stable peptide-MHC complex made in MHC class II
polymorphi alpha and beta chains, peptide
what are the types of APCs for MHC class I
all nucleated cells and platelets
what are the types of APCs for MHC class II
- dendritic cells
- mononucleat phagocytes
- B lymphocytes
- endotheial cells
- thymic epithelium
what are the sources of protein antigens for MHC class I
cytosolic proteins (mostly synthesised in cell)
what are the sources of protein antigens for MHC class II
endosomal/lysosomal proteins (mostly internalised from extracellular env)
what is the site of peptide loading into MHC I
ER
what is the site of peptide loading into MHC II
specialised vesicular compartment
which molecules are involved in the transport of peptides and loading of MHC I molecules
TAP
which molecules are involved in the transport of peptides and loading of MHC II molecules
invariant chain, DM
what is the purpose of MHC class I (endogenous) presentation
- presentation to cytotoxic T cells
- kill virally infected cells/Tumour cells/Intracellular pathogens
what is the purpose of MHC class II (exogenous) presentation
- presentation to T helper cells
- kill external pathogens (which need to be killed by ANTIBODIES, most of which are made with T cell help)
what are the classical T cells
which are the non classical t cells
classical: αβ T cells
non: γδ T cells
what % of circulating T cells are classical
95-99% are αβ
where are non classical T cells found
give an example
epithelial rich tissues (eg gut)
mucosa (50% of T cells here are non cassical)
what is the difference between classical and non classical T cells
non classical have different TCR: they have γδ instead
what is the diversity of non classical T cells like
LESS diversity, they bind to non-conventional antigens
which group has higher levels of non classical T cells
foetus
how do γδ T cells recognise antigen differently
they recognise antigen presented in CD1 rather than MHC
what do γδ T cells recognise/load
- they can load LIPIDS into the groove of CD1 as opposed to peptides
what is the purpose of γδ T cells
not entirely clear, but they RECOGNISE LIPIDS, PATHOGENS (such as M.tuberculosis) and PATHOGENIC TOXINS, CELLULAR STRESS MARKERS
what makes superantigens
some bacteria and viruses
what are superantigens
proteins that BYPASS NORMAL ANTIGEN RECOGNITION and BIND:
- non-variable sequences of TCR variable regions
- non-polymorphic sequences of MHCII α-chain
- they can activate 5-20% of T helper cells
- they are effective at v low conc ( ~ 10^-9M)
are superantigens processed by APCs?
no
they bind in their native state
describe the structure of an alpha beta TCR
- one chain has EXTRACELLULAR Ig domain which is CONSTANT region
- there is a VARIABLE region at the end
- transmembrane region
- very short cytoplasmic region
- beta chain has v similar structure
how does the memb bound alpha and beta chains of TCR communicate to T cell that it has bound peptide
using CD3 molecule
what is the structure of the CD3 molecule
- comprised of 6 chains: gamma, delta, 2x epsilon, 2x zeta
- have Ig domain externally
- have transmembrane region
- and have LONG CYTOPLASMIC TAIL which have ITAMS
what happens at ITAMs
phosphorylation which signals to cell
what is the structure of the gamma and delta chains of the CD3 molecule
- have Ig domain externally
- have transmembrane region
- and have LONG CYTOPLASMIC TAIL which have ITAMS
what is the structure of the 2x epsilon chains on the CD3 molecule
- have Ig domain externally
- have transmembrane region
- and have LONG CYTOPLASMIC TAIL which have ITAMS
when a peptide binds to the variable region on the TCR what happens to the CD3molecules
all the cytosolic parts of the TCR are carried by LIPID RAFTS, and they CLUSTER TOGETHER
- after clustering, the ITAMs will be PHOSPHORYLATED and signal transduction will occur
what are the similarities between BCR and TCR
1) same Ig FAMILY
2) both have CONSTANT and VARIABLE regions
3) both use the VARIABLE region to bind native antigen (BCR) or peptides (TCR)
4) both have transmembrane domains
5) both have v short cytoplasmic domains which are not able to signal by themselves O rely
how is TCR and BCR different
1) BCR has MORE extracellular domains
2) one TCR can only bind ONE peptide, whereas BCR can bind up to TWO antigens
3) to transduce signals to the cell, the BCR uses CD79 alpha and beta and TCR uses gamma, delta, 2x epsilon and 2x zeta chains
how many chains does MHC I have
one
what family of molecules does MHC belong to
Ig family O have Ig like domains
what is the structure of domain 2 on MHC class I
made of BETA PLEATED sheets, and then forms an ALPHA HELIX
what is the structure of domain 3 on MHC class I
forms BETA PLEATED sheets (which interact w/ beta pleated sheet s from domain 2) and then another ALPHA HELIX forms on top
what stabilises the peptide once it is bound in the groove of MHC class I binding site
BETA 2 MICROGLOBULIN
why is MHC class I expressed on all nucleated cells
as all cells can be infected (eg by virus/ intraceullular bacteria/tumour cell)
how are viral particles for eg moved to the MHC class I on cell surface
- they are broken down to peptides by the proteasome into peptides
- the peptides enter the ER
- ER is where MHC class I is also being produced
- then peptides are moved to cell surface
which cells express MHC class II
antigen presenting cells (mainly macrophages and dendritic cells, but B CELLS can also act as APCs)
how many chains is MHC class II comprised of
TWO chains
what is domain one on MHC class II chains
BETA PLEATED SHEET and an ALPHA HELIX
what is domain two on MHC class II
Ig like domain
how do the 2 chains on MHC class II interact to form the peptide binding site
the two beta pleated sheets interact forming the peptide binding groove
what is the tightness of the alpha helices like in MHC class II, what does this mean for the peptide that binds?
the alpha helicies are LESS TIGHT
O a slightly longer peptide can fit
what is a difference in stability once the peptide/antigen has bound in MHC I compared with MHC II
MHC II structure is mroe stable O doesn’t req the beta 2 microglobulin sturcture to stabilise
how is the peptide laoded onto the MHC II
the MHC II presenting cells are APCs, which are PHAGOCYTIC
- they PHAGOCYTOSE exogenous material where they bring them into the PHAGOLYSOSOME and they are converted to peptides
dendritic cells and macrophages produce which type of MHC
BOTH MHC I and MHC II
MHC I as they are NUCLEATED O prod MHC I
but they are professional APCs O also display MHC II
as both MHC class I and II are being made in the ER, why is MHC II not loaded with the SAME peptides as the MHC I
as MHC II is being made in the ER, the INVARIANT CHAIN comes and sits ON TOP of the PEPTIDE BINDING GROOVE thus BLOCKING the binding groove of the MHC II molecules so they aren’t loaded with ENDOGENOUS peptides
after synthesis in the ER what happens to MHC II
- translocated THROUGH the cell to MEET phagolysosome /endosome
- invariant chain is degraded
- the EXOGENOUS peptides are loaded into the peptide binding groove
- then the loaded MHC II can be transported to the surface of cell to present peptide to CD4+ helper T cells
why is MHC considered to be human leukocyte ANTIGENS
any molecule that presents foriegn peptides/antigens needs to be able to recognise a WIDE variety of antigens O not all individuals have exactly the same MHC molecules
what does histocompatibility mean
why is this important in transplants
‘histo’= tissue
‘compatibility’ = matching
- we need to ensure the MHC class I (esp) needs to be compatible in donor and recipient
which cell is very important in mounting an immune response to eg transplant
why is MHC considered to be HUMAN LEUKOCYTE ANTIGEN
MHC I
- a donors MHC I could be slightly different to the recipients
- as MHC I is expressed on EVERY RECIPIENT CELL, all these cells could be part of an immune repsonse against the transplant
what causes variation in MHC complexes
as a species variation is important so we are not wiped out by a pandemic by presenting slightly different peptides and antigens
when is CLIP formed in MHC class II pathway what removes CLIP
CLIP IS formed after invariant chain (Ii) is processed following the fusion of the MHC class II enriched compartment (MIIC) with late endosomes.
It IS then removed by HLA-DM
