Antibody structure and repertoire generation 2

Question 1

Where is the heavy chain locus?

Answer 1

Chromosome 14

Question 2

Where is the kappa light chain locus?

Answer 2

chromosome 2

Question 3

Where is the lambda light chain locus?

Answer 3

chromosome 22

Question 4

What is required for a functional heavy chain gene?

Answer 4

A V region to recombine with a D region and a J region–> VDJ recombination

Question 5

Which bit of the antibody does the VDJ bit code for?

Answer 5

CDR3

Question 6

Which regions make up light chains?

Answer 6

V and J regions

Question 7

How do diff B cells code for diff antibodies?

Answer 7

The gene rearrangement is random in every cell

Question 8

Why is the order always V-D-J?

Answer 8

Because of recombination signal sequences

Question 9

What recombination signal sequence do V regions have?

Answer 9

7 (heptomer), 23 spacer, 9 (nonomer)
3’ to 5’ (D region is on the 3’ side of the RSS)

Question 10

What recombination signal sequence do D regions have?

Answer 10

7 (heptomer), 12 spacer, 9 (nonomer) (either side going out so 7 is closest on each side)

Question 11

What recombination signal sequence do J regions have?

Answer 11

7 (heptomer), 23 spacer, 9 (nonomer)
3’ to 5’ (J region is on 5’ side of the RSS)

Question 12

What must two recombination signal sequences be in order for them to recombine?

Answer 12

Different

Question 13

What does the RAG complex do?

Answer 13

Bind to two recombination sequences at random (e.g. D5 and J6)
Directs the recombination

Question 14

What does RAG stand for in RAG protein?

Answer 14

Recombination Activation Gene

Question 15

What is shared between T cell and B cell recombination?

Answer 15

The RAG machinery

Question 16

How does the RAG protein join two bits of DNA together?

Answer 16

It loops out the DNA in between

Question 17

Why do B and T cells have a little bit less DNA than most somatic cells?

Answer 17

When recombination occurs the DNA in between the recombined bits is looped out and lost

Question 18

What is junctional flexibility?

Answer 18

The joining process of two bits also introduces more diversity

Question 19

How does the RAG protein cut DNA?

Answer 19

It cuts it in such a way that there is a hairpin loop at the end

Question 20

How are strands cut by the RAG complex joined together?

Answer 20

They open up–> little bit from one strand flips to be alongside the other strand so there is an overhang

Question 21

What is formed when a hairpin is opened up and flipped?

Answer 21

A palindromic sequence (p nucleotides)

Question 22

What does TDT stand for?

Answer 22

Terminal deoxynucleotidyl transferase

Question 23

What does TDT do?

Answer 23

AN enzyme that adds N nucleotides at random

Question 24

What are N nucleotides?

Answer 24

Non-templated nucleotides

Question 25

Why does the join have a lot of diversity?

Answer 25

The p nucleotides and n nucleotides make it v diverse

Question 26

What is a possible issue of adding N nucleotides?

Answer 26

Could accidentally code for a stop codon Could not add a multiple of 3--> frame shift

Question 27

When is TDT expressed and not expressed?

Answer 27

It is only expressed when heavy chains are rearranging, not light chains

Question 28

What happens if a transmembrane domain is included in an antibody?

Answer 28

It will be incorporated into the membrane as a b cell receptor instead of a secreted antibody