B Cells 4 Flashcards
describe the amount of protein-coding genes relative to the amount of Ig and TCRs
what does this mean?
a lottttttt more Ig/TCRs compared to the number of protein-coding genes
means there is something allowing genes to change so they can produce more variable proteins
are heavy and light chain genes on antibodies encoded on the same or separate chromosomes?
separate chromosomes
what is somatic recombination?
rearrangement of V, J, C (and D) gene segments in Ig
describe the process of somatic recombination from when we inherit genes (2 steps)
- our germline DNA from our parents contains many segments of each V, J, C (and D) segment
- during B cell development, somatic recombination selects one of each
what are the segments of the Ig light chain?
Variable
Joining
Constant
what are the segments of the Ig heavy chain?
Variable
Diversity
Joining
Constant
how many CDR loops are there per light or heavy chain? how many chains are there in Ig? therefore, how many CDR loops are there in total?
3 CDR
4 variable chains in Ig
12 CDR in total
describe where each of the 3 CDR loops are encoded and which is most variable?
CDR 1 and 2 are encoded in the V segments of light and heavy chains
CDR 3 is encoded in:
- joining of V-J segments of light chain
- joining of V,D,J segments of heavy chain
describe the loci of the LIGHT CHAIN
two different loci, each with different constant regions:
1. KAPPA chain
2. GAMMA chain
what does each locus/chain of the light chain include?
has many V and J regions
Kappa only has 1 C
which locus/chain of the light chain will be expressed?
either the full kappa OR gamma chain will be expressed and silence the other one
describe the loci of the HEAVY CHAIN
1 locus
what does the locus of the heavy chain include?
many different V, D, J, C regions
What do the C regions on the heavy chain correspond to? and why does this make sense?
corresponds to diff isotypes –> IgM, IgD, IgG, etc
makes sense bc each isotype is differentiated by its number of constant regions
what are the steps for B cell receptor maturation?
- precursor B cell has inherited genes
- somatic recombination selects segments
- recombinase proteins join gene segments together
- transcription, splicing
- mature naive B cell
is BCR maturation reversible or irreversible? why?
IRREVERSIBLE
bc segments that are not chosen will get deleted
what is combinatorial diversity?
how is it different than somatic recombination?
THE DIVERSITY that is a result of diff combos of V, D, J regions
somatic recombination is the PROCESS, combinatorial diversity is the DIVERSITY
what does RSS stand for?
Recombination Signal Sequence
what is the role of RSS?
flanks each antibody gene segment to direct recombinase enzymes to pair different segments together for recombination
what is the structure of RSS? (3)
- conserved nonamer
- conserved heptamer
- 12 or 23 bp spacer btwn the nonamer and heptamer
what is the 12/23 rule?
a 12-bp RSS must pair with a 23-bp RSS for recombination to occur
ex. 12-bp RSS binds J and combines with 23-bp RSS
what happens when the 12 and 23 RSS bring segments together?
every segment between them that were not selected is put in a loop that is cut out (irreversibly)
what gene activates recombination?
RAG –> RAG1, RAG2
what does RAG do?
recognizes and cuts DNA at Ig-encoding region where RSS have brought segments together
what is the signal joint? what happens to it?
the loop that is excised / deleted from the chromosome
what is the coding joint?
coding regions of selected V and J regions that remain
what is junctional diversity?
during recombination, nucleotides may be added or removed at the junctions btwn:
- Heavy: V and D, D and J
- Light: V and J
when does junctional diversity occur?
once RAG picks each segment, nucleotides are added and removed during ligation when the segments join
what happens to the ends of the coding joint when the signal joint is cut off?
junctional diversity! repair proteins will bind the DNA hairpin and ARTEMIS will open the DNA hairpin
what is ARTEMIS
an endonuclease that binds and opens the DNA hairpin
where does hairpin cleavage occur?
at random place
what are the different ways the hairpin can be opened? (3)
- cut with a blunt end
- 5’ overhang
- 3’ overhang
what is the role of exonucleases in hairpin cleavage?
exonucleases may REMOVE nucleotides on each side of the coding joint
what can be added to the coding joint? where?
ADD palindromic nucleotide sequences added to overhangs
what is a palindromic nucleotide sequence?
complementary DNA added where 5’ - 3’ sequence is same as 3’ - 5’
what does Terminal Deoxynucleotidyl Transferase do?
what chain does it act on?
how does this affect CDRs?
add up to 20 NON-TEMPLATE encoded to the cleaved chain
acts on HEAVY chain primarily
it is the reason why CDRs vary in length
what happens after TdT adds nucleotides?
repair enzymes trim off any nonmatching/unpaired nucleotides, fill in remaining single-stranded gaps, and ligate the new DNA
