generation of lymphocyte antigen receptors

when antigen binds to BCR what happens

other BCRs are deleted, antigen bound to BCR is cloned

what is the variable region composed of

CDR1, CDR2, CDR3

what is V gene segment

CDR1 and CDR2

what is J gene segment 

CDR3

what CDR segment has maximum variability and why

CDR3 because it has V and J segments 

lambda light chain vs kappa light chain locus J chain

lambda= J is not clustered

kappa= J is clustered 

light chain acronym

V(D)J or just VJ

heavy chain acronym

VDJ

what does each variable of VDJ stand for

V= variable

D= diversity 

J= joining

in VDJ sequence what joins first

D always joins with J first

sequence of VDJ

• germline DNA undergoes somatic recombination

• D-J rearranged, DNA joined, then undergoes somatic recombination

• V-J or V-DJ joins rearranged DNA then undergoes transcription

• primary transcript RNA, then undergoes splicing

• mRNA undergoes translation

• polypeptide chain

what is the 12 23 rule

12 RSS can combine with 23, but 12 cannot combine with 12, and 23 cannot combine with 23

so why cant V and J combine first on heavy chain

because D has two 12 RSS, while V and J have 23 each, so the 12 of D and 23 of J must combine before V

when we say V(D)J which chain are we referencing

both heavy and light, since D is in brackets

what is the heptamer (7) sequence of VDJ 

CACAGTG

what is the nonamer (9) sequence of VDJ 

ACAAAAACC

what does V(D)J recombinase do

recognize the 12/23 RSS and brings the exon together

how does recombination of V and J exons occur

deletion of intervening DNA and ligation of the V and J segments

step 1: synapsis of V(D)J recombination

two distant selected segments and adjacent RSSs get brought together by chromosomal looping event and are held in position for subsequent cleavage, processing, and joining 

step 2: cleavage of V(D)J recombination

lymphocyte specific enzyme called V(D)J recombinase creates double stranded breaks at RSS coding junctions

what is V(D)J recombinase composed of

RAG1 and RAG2 (recombination activating gene)

where is RAG1 and RAG2 expressed ONLY

developing B and T cells

when is RAG protein inactivated

in proliferating cells

step 3: hairpin opening and end processing (enzymatic steps in V(D)J recombination

after formation of double strand breaks, hairpins must be opened at coding junctions, and nucleotides may be added or removed from coding ends (which creates diversification)

what is artemis

endonuclease that opens up the hairpins 

what is terminal deoxynucleotidyl transferase (TdT)

lymphoid specific enzyme, adds nucleotides to broken DNA ends

step 4: joining (enzymatic steps in V(D)J recombination)

• broken cording ends and signal ends are brought together and ligated by a double strand break repair process found in all cells (nonhomologous end joining)

• KU70 and KU80 bind to breaks and recruit catalytic subunit of DNA- dependent protein kinase (a repair enzyme)

• DNA-PK also phosphorylates and activates artemis

• ligation of processed broken ends is mediated by DNA ligase IV and XRCC4

what is combinatorial diversity

random combining of VDJ or VJ

what is junctional diversity

different N and P nucleotides in each clone

what opens DNA hairpin to produce single strand DNA ends

artemis:DNA-PK complex

what adds new nucleotides

TdT

what generates P nucleotide (A+T, G+C)

artemis:DNA-PK complex

what is the first marker of mature B cell

IgD

if you took a blood sample and looked at it, which Igs would you see first

IgM and IgD

what are TRECs

T-cell receptor excision circles