B cells: generation of bcr and tcr diversity I

Question 1

What makes v region variable - how is there so much variation in cdrs

Answer 1

Abs and tcrs can be produced for enormous amount of specific ags
= how does that work

Question 2

Describe primary diversity

Answer 2

Primary diversification= through process of somatic recombination = includes combinatorial diversity and junctional diversity events

Question 3

Describe ligh chain and heavy chain endcoing

Answer 3

Hc and lc gene families encoded on separate chromosomes

Question 4

Ig gene diversity =describe what B cells do

Answer 4

Use groups of segments of genes to create diff possible abs using somatic recombination

Question 5

What is somatic recombination

Answer 5

Process by which segments rearranged
Like shuffling deck of hard, and dealing them

Question 6

What regulated somatic recombination processes

Answer 6

Tightly regulated machinery controls recombination processes and many of proteins involved in dna repair functions = dna repair enzymes

Question 7

Describe light chain genes

Answer 7

Variable
Joint
Constant region

Question 8

Describe heavy chain genes

Answer 8

Variable
Diversity
Joining
Constant region
(D only on hc)

Question 9

What encodes cdr1 and cdr2

Answer 9

Encoded in v segments of heavy and light chains

Question 10

What encodes cdr3

Answer 10

Most variable cdr =
encoded in joining of v-j segments of light chain
and v,d,j (joining of these regions) gene segments of heavy chain

Question 11

What is variable region composed of

Answer 11

Variable region of both hc and lc = composed of segments from recombined v d (in hc) and j genes

Question 12

How many v d j segments

Answer 12

Many diff in germ line dna = inherited

Question 13

What happens during B cell development - ig gene diversity

Answer 13

V(d)j recombination occurs to choose one of each to make up variable region

Question 14

Describe light chain loci - types

Answer 14

2 diff loci on separate chromosomes, with diff constant regions (only one expressed in lc of ab)
= kappa or lambda chain

Question 15

What does light chain loci include

Answer 15

Many diff v and j regions
Only one chain will be expressed and will silence other

Question 16

Describe heavy chain loci

Answer 16

One locus

Question 17

What does heavy chain loci include

Answer 17

Includes many diff v d j regions
Many diff constant regions represent diff isotopes - corresponds to igm, igd, igg etc
= has diff domains

Question 18

Describe creation of light chain

Answer 18

Takes one v j c

Question 19

Describe creation of heavy chain

Answer 19

D and j join first then v segment joins d-j

Question 20

Describe heavy and light chain creation - gen

Answer 20

Inherited - stem cell,precursor B cell —> somatic recombination —> recombinase proteins join separate gene segments together —> bcr of naive B cell
= mostly irreversible = segments not chosen in middle = deleted

Question 21

What is combinatorial diversity

Answer 21

Diversity that is the result of diff combos of v d and j regions
(Process = somatic recombination, concept= combinatorial diversity)

Question 22

Describe rss

Answer 22

Recombination signal sequences = flank each ab gene segment - in front - downstream segment

Question 23

What recognizes rss

Answer 23

Recombinase enzymes recognize rss

Question 24

What does rss have

Answer 24

Each has a conserved nonamer -9bp and heptamer 7th sequence
Either a 12 or 23 bp spacer sequence lies between nonamer and heptamer

Question 25

Describe 12/23 rule

Answer 25

Spacing and arrangement dictate that a 12bp rss must pair - align with 23bp rss for recombination to occur = 12/23 rule

Question 26

What do rss direct

Answer 26

Direct pairing of diff segments together

Question 27

Describe light chain segments pairing

Answer 27

V-j Segments in between selected ones = excised

Question 28

Describe heavy chain segments pairing

Answer 28

D-j then v-dj Rss of vh has 23bp Spacer Segments in between selected ones = excised

Question 29

What do rss allow

Answer 29

Looping of dna and binding by specific proteins

Question 30

What happens to rss regions

Answer 30

Rss regions are brought together creating loop in dna Loop part = has segments that are not selected

Question 31

Define rag

Answer 31

Recombination activating gene

Question 32

Describe what rag does

Answer 32

Rag1 and rag2= needed for somatic recombination = responsible for recognizing and cutting dan at ig encoding region and rss Covalently closed hairpin ends

Question 33

What happens to loop

Answer 33

Excised = signal joint No longer on chrom, deleted

Question 34

What happens to coding region of segments

Answer 34

Coding region of selected v and j regions remain - coding joint - for light chain bcr

Question 35

Describe possible bcr outcomes

Answer 35

Kappa chain: 40 V x 5 J = 200 Lambda chain: 30 V x 4 J = 120 Total light = 320 Heavy: 40 V x 25 D x 6 J = 6000 Combinatorial Diversity - Combine any light (320) x any heavy (6000) = 1.9 x 109 possible combos

Question 36

What is junctional diversity

Answer 36

During recomb = nts may be added or removed at junctions between v and dj and d and j (or v and j for light chain) - leads to more diversity

Question 37

What happens to signal joint - describe more detailed - junctional diversity

Answer 37

Signal joint - loop = ligated togther and discarded

Question 38

Describe hairpin

Answer 38

At coding ends = repair proteins bind hairpin

Question 39

What does Artemis do

Answer 39

Artemis = endonuclease = opens dna hairpins, opens up these covalently linked hairpins

Question 40

What happens after Artemis opens hair pin

Answer 40

Addition of palindromic (p) nts at overhangs

Question 41

Describe the 3 positions Artemis can open hairpin and the outcomes of each

Answer 41

2 diff spots = Can yield 5’ overhang, blunt end or 3’ overhang - most likely an overhang Gives template for dna repair enzymes - add p nts at overhangs (Even if blunt end still have to add nts to joint segments)

Question 42

Describe exonuclease activity

Answer 42

Sometimes - mainly in heavy chains Exonuclease activity = may remove nts on each side of coding joint - cna remove too much

Question 43

What does tdt do

Answer 43

Terminal deoxynucleotidyl transferase = cane add up to 20 n nucleotides = non template encoded - random nucleotides to cleaved strands Primarily in heavy chain = why cdrs vary in length, eventually some complimentary to each other = allows the 2 segments to join

Question 44

Describe function of repair enzymes

Answer 44

Repair envzymes then Trim off non matching nts - fill in reminaing single stranded gaps and ligate new dna

Question 45

Summary of junctional diversity - end

Answer 45

Tdt = adds nts to cleaved strands, mostly in heavy chains Unpaired nts removed by exonuclease

Question 46

Name and describe the mechanism of recombination = mechanisms that generate bcr diversity in naive B cells

Answer 46

Multiple gene segments - which gene segments are put together Hevay chain combinatorial diversity P nt addition = templated nt addition between joints resulting from asymmetrical Cleavge of hairpin structures- junctional diversity Exonuclease trimming = sometimes occurring at junctions, losing nts Nontemplated n nucleotide addition - bc trimmed too much - mediated by tdt activity,adding in random nts between joints

Question 47

Describe addition of p nts at overhangs

Answer 47

Ther is a template allowing dna repair enzymes to fill in complementary strand Complementary strands of dna read the same in both directions 5’ to 3’ = tcga and reading backwards on bottom strand - non coding also gives tcga Happens mainly light chain