L5 - Adaptive Immune System 2 Flashcards
T AND B CELL ANTIGEN RECEPTORS
i) what two components is the B cell receptor composed of?
ii) which two co-receptors are essential for BCR signalling?
iii) what two components is the T cell receptor made of?
iv) which co receptor is the TCR associated with?
v) what is an ITAM?
i) BCR = 2x heavy chain and 2x light chain
ii) BCR assoc with Ig alpha and Ig beta for signalling
iii) TCR made of alpha and beta heterodimer
iv) TCR associated with CD-3
v) ITAM is immunoreceptor tyrosine based activation motif found in the signalling area of the receptor (intracell)
VDJ RECOMBINATION IN B CELLS
i) what does VDJ recomb allow? what is it also known as?
ii) which chromosome does it occur on in heavy chain genes?
iii) which two light chain genes can it occur in? which chromos are these found on?
iv) which is the only chain that D segment is found in? which chain can therefore only undergo VJ recombination
v) approx how many combinations are there?
i) allows recognition of many antigens
- aka somatic recombination
ii) heavy chain gene on chromo 14
- light chain genes > lambda (chr 2) and kappa (chr 22)
iv) D segement is only found in the heavy chain
- light chain only undergoes VJ recombination
v) 100 trillion possible combinations
VDJ RECOMBINATION IN T CELLS
i) which chromo does it happen for the alpha chain gene? which chromo for the beta chain gene?
ii) which chain doesn’t have a D segment?
iii) do T cells produce more or less diversity than B cells?
iv) when is the T cell pool fixed from? why?
i) alpha chain > chromo 14
beta chain > chromo 7
ii) beta chain doesnt have a D segment therefore undergoes VJ recombination
iii) T cells have more diversity than B cells
iv) T cell pool fixed from adolescence due to thymic involution
VDJ RECOMBINATION AND NEW GENE SEQ PRODUCTION
i) at which cell stage do B and T cells undergo VDJ recombination?
ii) what is rearranged in the light chain of B cells? how many steps is this?
iii) what is rearranged in heavy chain of B cells? how many steps is this?
iv) once all rearrangement has occured - what happens? (3)
v) which Ig is expressed on a naive B cell? (2)
i) pro B and pro T cells
ii) light chain - VJ recombination (one step)
iii) heavy chain - DJ recomb then VDJ (two steps)
iv) rearrange > transcribe new genetic code > proteins
assembly of Ig heavy and light chain > mem bound Ig
v) IgM and IgD
REARRANGEMENT OF GENE SEGMENTS
i) what is the name of the specific sites on DNA that rearrangement occurs between?
ii) what does these sequences contain? give three components of this
iii) which prime end are these sequences found on V/J and D segments?
iv) which two enzymes catalyse rearrangement?
i) rearrangement occurs between recombination signal sequences
ii) recomb signal seqs contain conserved segments of DNA
- cont a heptamer, spacer and nonomer
iii) seqs found on 3’ of V, 5’ od J and both 3’ and 5’ of D
iv) rearrangement catalysed by recomb activating genes
RAG1 and RAG2
VDJ JOINING
i) which enzymes flank the coding sequences to be joined to start the process? what is this critical for?
ii) what structure is the result of cleavage by the enzymes?
iii) name a protein that can join the complex and cleave at random sites
iv) which enzyme then allows addition of bases to the cleaved sequence? what does this allow?
v) what enzyme joins the ends of gene segments to form a coding joint and a signal joint?
i) RAG1 and RAG2 flank the sequence - critical for recombination of the BCR or TCR
ii) cleavage results in a hairpin structure
iii) Ku-70/Ku-80 can join the complex and cleave at random sites
iv) TDT allows addition of bases which allows diversity
v) DNA ligase 4 joins ends of gene segments
VDJ RECOMBINATION SUMMARY
i) what is VDJ recombination the primary mechanism for?
ii) which cells does the first recombination event take place in?
iii) which recombination happens first in the heavy chain/alpha chain? what recombination happens next?
iv) which two light chains in B cells does recomb take place in? what type of recomb happens here?
i) primary mech for genetic diversity in B and T cells
ii) first recomb event takes place in pro B and pro T cells
iii) heavy chain/alpha > DJ recomb then V to DJ
iv) kappa and lambda light chain > just VJ recomb
SOMATIC HYPERMUTATION
i) which stage of B cell differentiation does it occur in? when does it take place?
ii) which organs does it take place in? which location in these organs?
iii) what does it aim to produce? does it distinguish between favourable and unfavourable mutations? why?
iv) what affinity may the antibodies have that are produced by somatic hypermutation?
i) takes place after a B cell has recognised antigen
- happens in centroblast stage
ii) takes place in secondary lymphoid organs eg LN/spleen
- happens in germinal centre of these organs
iii) aims to produce high affinity antibody - doesnt disting bet fav and unfav mutations because there is absence of selection
iv) may produce antibodies with higher, lower or no change in affinity for antigen
- can also produce non func antibodies
= RANDOM MUTATIONS
AFFINITY MATURATION
i) what does it do?
ii) where does it occur?
iii) which cells present antigen to the B cells that have already undergone somatic hypermutation? which cells will survive?
iv) what happens to cells that bind with low affinity to the antigen presented to them?
i) selects B cells that have the highest affinity for antibody
ii) occurs in the light zone of the germinal centre of secondary lymphoid tissues
iii) follicular dendritic cells present antigen to the newly formed B cell receptor > will only survive if it has high affinity for antigen
iv) if receptor has low affinity for antigen it will die by apoptosis
WHAT IS SOMATIC HYPERMUTATION?
i) what does it generate?
ii) what type of mutations does it introduce? is this before or after VDJ rearrangement?
iii) what is the avg mutation rate in SH? is this more or less than mutations seen in normal cell division?
iv) which areas do these mutations occur? which two enzymes facilitate this
v) which enzyme triggers SH? what does it do to the DNA sequence? how does this generate mutations?
i) generates diversity
ii) introduces point mutations (nuc substitution) after VDJ rearrangement
iii) mutation rate is around 1 base per 1000 which is 1 million times higher than mut rate seen in normal cell division
iv) mutations occur at restricted loci called hypervariable regions
- facilitated by AID and uracil N glycosylase
v) AID enzyme triggers it
- deaminates a cytodine and changes it to uracil
- this causes base mismatch which gets repaired and therefore generates lots of mutations
CLASS SWITCH RECOMBINATION
i) what does it cause to happen? does it change the affinity of the BCR for antigen?
ii) what does it allow for on the BCR?
iii) what Ig will all B cells that have undergone somatic hypermut and affinity maturation produce? name two characterstics of this Ig
iv) which chain does class switch recomb occur at? what orchestrates the process?
i) causes a change in the constant region of the receptor
- doesn’t change the affinity of the BCR for antigen
ii) allows for the substituion of one isotype for another which means the antibody has a new function and distrib in the body
iii) SH/AM B cells will only produce IgM which has a short half life and limited functional capacity
iv) class switch occurs only at the heavy chain
- orchestrated by cyotkines that are released upon B and T cell interaction
ALTERNATIVE SPLICING AND CLASS SWITCH
i) what are switch regions? which Ig does not have these?
ii) what is the first targeted switch region? where is this found in relation to the VDJ segment?
iii) what is the other partner switch region determined by?
iv) what does AID enzyme do in the CS process? which enzyme works after this?
v) what does the second enzyme cause in the DNA? what consequently happens?
vi) what do cytokines dictate in this process?
i) switch regions are specific DNA sequences upstream of constant region genes
ii) first targeted switch region is always Smu
- this is found directly downstream of the VDJ segment of the heavy chain
iii) partner switch region is determined by cytokines released by T helper cells
iv) AID enzyme changes cytidine for uracil
- uracil N glycosylase then comes along and removes the uracil
v) removal of uracil by uracil N glycosylase causes ds breaks
- the switch regions with breaks are removed and ends of switch regions are spliced together > new constant region forms downstream of VCJ sequence
vi) cytokines dictate which transcription factors are active and where the second break is made > det which Ig is produced
WHY DOES CLASS SWITCH MATTER
i) what does class switch determine?
ii) which two Ig do B cells express before class switching? what is a limitation of this?
iii) does it change the affinity of BCR for antigen? why?
iv) what does it allow?
i) deermines the type of response an Ig promotes
ii) B cells express IgM and IgD
- IgM cant sensitise for NK cells killing
iii) CS does change affinity for antigen as it affects the constant region, not the variable region
iv) allows for fine tuning of the B cell response > B memory and plasma cell produc > secretion of antibody
