VDJ recombination Ch:8 176-186

Question 1

Elucidate

Answer 1

To explain something. Make something clear.

Question 2

What is the difference between heavy and light chains?

Answer 2

Heavy chains have V, D and J regions, while light chains only have V and J regions

Question 3

Nascent

Answer 3

Just coming into existence and beginning to display signs of future potential

Question 4

What are the two Ig Light chains?

Answer 4

K (kappa) or lambda chains

Question 5

CDR3

Answer 5

Complementarity-Determining region 3, Hypervariable. Junctional region between the V and D segments as well as the sequences of the D and J themselves. Occurs as a results of junctional diversity.

Question 6

What chains lack D regions, including TCRs?

Answer 6

Ig Light chains and TCR alpha and gamma

Question 7

What chains have D regions, including TCRs?

Answer 7

Ig heavy chains, TCR beta and sigma

Question 8

RSS (Location, Components, )

Answer 8

Recombination signal sequences. located 3’ of each V gene, 5’ of every J segment, flanks every side of D segment. Contains a heptamer (CCAGTG), a spacer 12 or 23 non conserved nucleotides (correspond to 1-2 turns of the DNA helix, and a highly conserved AT rich stretch o 9 nucleotide spacers.

Question 9

The 12/23 Rule

Answer 9

The phenomenon that recombination only occurs between two segments only if one of the segments is flanked by a 12-nucleotide spacer and the other is flanked by a 23-nucleotide spacer.

Question 10

Why can’t V to J recombination occur in heavy chains?

Answer 10

Because V chains and J chains are both flanked by 23 nucleotide spacers, which would be a direct violation of the 12/23 rule

Question 11

What are the four distinct events of VDJ recombination?

Answer 11

1) Synapsis ( looping of segments and their two flanking regions) 2) Cleavage (Double stranded breaks produced by RAG-1/2) 3) Hairpin opening and end processing (Artemis opens the hairpins at coding ends; TdT adds base to broken DNA ends 4) Joining (via nonhomologous end joining; Ku70, Ku80, DNA-PK, DNA ligase IV and XRCC4)

Question 12

VDJ Recombinase

Answer 12

Complex made up of RAG-1 and RAG-2. (Recombination-activating gene 1) RAG-1 recognizes the DNA sequence at the junction between a heptamer and a coding segment and cleaves it, but is only active in the presence of RAG-2

Question 13

Artemis

Answer 13

an endonuclease that opens up the hairpins at the coding ends.

Question 14

Endonuclease

Answer 14

an enzyme that cuts DNA at or near a specific recognition nucleotide sequences known as restriction sites.

Question 15

TdT

Answer 15

Terminal deoxynucleotidyl transferase. Adds bases to broken DNA ends.

Question 16

Ku70 and Ku80

Answer 16

DNA end-binding proteins that binds to the breaks and recruit the catalytic subunit of DNA-dependent protein kinase (DNA-PK)

Question 17

DNA-PK

Answer 17

Double stranded DNA repair enzyme

Question 18

What two compounds are used to ligate processed broken ends?

Answer 18

DNA Ligase IV and XRCC4

Question 19

Combinatorial Diversity

Answer 19

VDJ rearrangement brings together multiple germ line gene segments that may combine randomly, and different combination produce different antigen receptors

Question 20

Junctional Diversity

Answer 20

Diversity generated by the addition or removal of nucleotides at the junctions of the V and D, D and J, or V and J segments.