B-III B- and T-cell genes

Question 1

What is the definition of a gene?

Answer 1

A stretch that makes the whole thing functional, including enhancer/silencer, promoter, UTRs, ORFs, and terminator.

Question 2

What is the importance of introns in genes?

Answer 2

Regulation of expression and signaling of alternative splicing.

Question 3

What is a limitation of large genomes?

Answer 3

A big genome incurs a big cost of replication/repair and has a positive correlation with extinction.

Question 4

What defines the isotype of an antibody?

Answer 4

The structure of the heavy chain.

Question 5

What constitutes the antigen binding portion of B-cell receptors?

Answer 5

Variable heavy and light chain regions.

Question 6

What are the hypervariability (HV) regions in B-cell receptors?

Answer 6

Regions within the variable region that varies a lot

Question 7

What are the complementary determining regions (CDR)?

Answer 7

Regions that are responsible for binding antigens, derived from hypervariability regions.

Question 8

How are BCR genes organized in germline?

Answer 8

Generated through combination of V, (D), J and C gene segments on different loci.

Question 9

What does VDJ recombinase do?

Answer 9

It facilitates gene rearrangements in developing lymphocytes. Essential for expression of TCR and BCR.

Question 10

What is the process of somatic recombination in light chains?

Answer 10

Linking V and J segments together

Question 11

What segments does the heavy chain involve in somatic recombination?

Answer 11

Diversity and joining segments are joined to fuse V-DJ regions.

Question 12

What is RSS in the context of gene rearrangement?

Answer 12

Recombination signal sequence that guides the recombination.

Question 13

What happens during deletional joining?

Answer 13

Creates a hairpin loop with two RSSs next to each other, losing everything in between.

Question 14

What is inversional joining?

Answer 14

A process that creates a knot to join RSSs without losing any genetic material.

Question 15

What is combinatorial diversity?

Answer 15

Diversity resulting from recombination of V-(D)J gene segments.

Question 16

What is junctional diversity?

Answer 16

Diversity from different joining ways of V-J or V-DJ segments, allowing addition or removal of nucleotides.

Question 17

What is somatic hypermutation?

Answer 17

Mutations in the variable domains to enhance affinity of antibodies.

Question 18

What is allelic exclusion in B-cells?

Answer 18

Inhibition of further rearrangements once a functional heavy or light chain locus is produced.

Question 19

What is the structure of T-cell receptors (TCR)?

Answer 19

Heterodimer of two transmembrane glycoproteins joined by disulfide bonds, typically α & β chains.

Question 20

What is the gene organization of the TCR compared to BCR?

Answer 20

TCR genes are smaller and segments of alpha and delta are in the same locus.

Question 21

What is the main difference in diversity between TCR and BCR?

Answer 21

TCR has higher diversity but lacks somatic hypermutations.

Question 22

What triggers the inhibition of beta chain gene recombination in T-cells?

Answer 22

Formation of a recombined functional beta-chain locus.

Question 23

Fill in the blank: The ________ of an antibody is defined by the structure of its heavy chain.

Answer 23

isotype

Question 24

What are the different loci for light chains?

Answer 24

Kappa and lambda

Question 25

How many loci are there for heavy chains?

Answer 25

One

Question 26

Describe how the heavy chain is assembled

Answer 26

1. D-J are rearrenged through somatic recombination 2. V-DJ are rearrenged through somatic recombination 3. Transcription occurs, generating a primary RNA transcript containing the rearrenged VDJ, as well as everything after the J-gene-region 4. Splicing occurs, splicing away intermediate regions, combining VDJ with the correct C region. 5. Translation occurs, giving the polypeptide chain ## Footnote Bonus: if it is functional, it inhibits this from happening a second time through allelic exclusion

Question 27

Describe how the light chain is assembled

Answer 27

1. After a functional heavy chain is generated, V and J are rearrenged through somatic recombination 2. Transcription occurs, generating a primary RNA transcript containing the rearrenged VJ, as well as everything after the J-gene-region 3. Splicing occurs, splicing away intermediate regions, combining VJ with the correct C region. 4. Translation occurs, giving the polypeptide chain

Question 28

How are the RSS matched?

Answer 28

23-bp RSS needs to be matched with 12-bp RSS because of the conformation of RAG 1&2 enzyme in the VDJ recombinase

Question 29

When does deletional joining occur?

Answer 29

When the transcriptional direction is the same for the recombined elements

Question 30

When does inversional joining occur?

Answer 30

When the transcriptional direction is different for the recombined elements

Question 31

When are RAG 1-2 expressed in the VDJ recombinase?

Answer 31

In immature B/T cells

Question 32

What causes the diversity of the BCR?

Answer 32

Combinatorial diversity, junctional diversity, somatic hypermutations

Question 33

What are N-nucleotides and where are they mainly found?

Answer 33

Random addition of up to 20 non-encoded nucleotides by enzymes in VDJ recombinase. A part of what adds junctional diversity. Mainly found in the D segment recombination, added by TdT

Question 34

What are some differences between TCR and BCR when it comes to somatic recombination?

Answer 34

In TCR, the D-segment in the β-chain has one 12-bp-RSS and one 23-bp-RSS. In BCR, the segments has the same RSS

Question 35

Why does TCR lack somatic hypermutations?

Answer 35

Because its T-cells that activates this in B-cells. T-cells have nothing that activates this in them, and its less necessary

Question 36

What does RAG1:RAG2 do?

Answer 36

Bind to 23bp and 12bp RSS regions, and when activated by dual binding cleave so V-(D)J can be recombined