Why is the adaptive immune response so specific Flashcards

Question

What is VDJ recombination and what it produce

Answer 1

* Create a completely new genetic sequence encoding for a new unique amino acid sequence * Occurs in bone marrow-residing stem cells -> become immature B cells * Lead to expression of diverse immunoglobulin

Answer 2

they recognise DNA sequence tags that flank VDJ regions called recombination signal sequence (RSS)

Answer 3

adds additional nucleotide at the end of DNA strand

Answer 4

3' of V segment, 5' of J segment and both sides of D segment

Answer 5

In order to ensure that correct regions are joined to each other, a gene segment flanked by a RSS with a 12bp spacer can be joined only to the gene segment flanked by a RSS with 23bp spacer

Answer 6

• Different types of diversity at the coding joint, where gene segments are joined 1. Cleavage by Artemis leaving a 3' overhang can lead to deletion of nucleotides from the end of the V, D or j region 2. Addition of non-germline nucleotides by TDT will insert random bases 3. Cleavage by Artemis leaving a 5' overhang generates a nucleotide palindrome

Answer 7

a-chain is on chromosome 14 and includes 70 copies of V region, and 61 copies of J region. while b-chain locus is on chromosome 7 and includes 52 copies of V region, 2 copies of D region and 13 copies of J region

Answer 8

TCR genes cannot undergo further diversification by SHM and are positively and negatively selected to eliminate T cells that potentially recognise self, or fail to activate

Answer 9

V, D and J regions are flanked by recombination signal sequences (RSS) • RSS are recognised by RAG 1/2 recombinases which bind them specifically • The gene segments are brought together before the RAG complex cleaves the RSS, leaving a hairpin at the ends of the V and J regions and a DSB at the RSSs. • DNA-PK, Ku, Artemis, DNA ligase/XRCC4 dimer form a complex and join the RSS ends into a DNA-circle known as the signal joint with no more functions. The complex also cleaves the hairpin ends. Terminal deoxynucleotidyltransferase (TDT) adds additional nucleotides to the cleaved ends allowing them to be re-ligated with their unique combination.

Answer 10

process by which one allele is active whilst the other is silenced in a mature B cell. This allows each B cell to produce only one antibody

Answer 11

○ Region where the antibody is in contact with the target antigen ○ Region with the greatest variability and determines the specificity of the antibody ○ Region is further diversified through somatic hypermutation (SHM)

Answer 12

to generate extra variability | occur during B cell proliferation

Answer 13

○ errors (mutations) are introduced into the CDR of the re-arranged Ig genes ○ Driven by activation-induced deaminase / AID • AID catalyzes the deamination of cytosine base to uracil in the DNA sequence Uridine-guanosine-mismatch can be repaired by : • Deoxyridine is interpreted by the DNA replication machinery as if it were a deoxythymidine, resulting in the creation of an A-T pair • In base-excision repair (BER), mismatched uridine has been excised by one of the uridine DNA glycosylase enzymes, leaving an abasic site • Uridine can be replaced by any of the four bases (short-patch BER) • Mismatch repair enzymes can detect the mismatch and excise a longer stretch of DNA surrounding the U-G couple • Errror-prone polymerases are recruited to the hypermutable site and polymerases can introduce a number of mutations around the original mismatch • Depending on repair mechanism, a mutation may occur only in the originally altered base or in one or more base surrounding it

Answer 14

• sites within secondary lymphoid organs – lymph nodes and the spleen where mature B cells proliferate, differentiate, and mutate their antibody genes and leave as plasma cells or memory cells

Answer 15

1. Mature (naiive) antigen-activated B cells receive signals known as 'T cell help' are driven into primary B cell follicles in secondary lymphoid organs eg. Lymph nodes where they establish GC 2. Dark zone consists of proliferating GC B cells via colony expansion whereas the GC B cells in the light zone are resting 3. In proliferating GC B cells, somatic hypermutation is activated which leads to mutations at high rate into rearranged Ig V region, AID levels are high in Dark zone 4. Most mutations are disadvantageous for the cells such as those that lead to reduced affinity of BCR and cause cells to undergo apoptosis 5. A few GC B cells will acquire mutations in the BCR that increase their affinity for antigen and those cells will be positively selected 6. Selection process takes place in the light zone where GC B cells are in close contact with CD4 T cells and follicular dendritic cells (FDCs) 7. A fraction of these GC B cells undergo class-switch recombination Finally GC B cells differentiate into memory B cells or plasma cells and leave the GC

Answer 16

Low affinity Igs that do not bind to antigen detected by CD4 T cells that induce apoptosis in these B cells. High affinity Igs keep proliferating and produce new variability by further cycles of SHM as B cell divide and diversify

Answer 17

• process by which proliferating B cells rearrange the constant region genes in the immunoglobulin heavy chain locus to switch from expressing one class of immunoglobulin to another

Answer 18

- µ (IgM), δ (IgD), γ3 (IgG3), γ1 (IgG1), α1 (IgA1), γ2 (IgG2), γ4 (IgG4), ε(IgE) and α2 (IgA2) types

Answer 19

1. A series of enzymes (including AID) introduce double strand breaks at conserved sequences called switch regions located upstream of the different constant regions in the heavy chain 2. Intervening DNA containing unused constant regions are removed 3. Remaining sequence is then re-joined by non-homologous end joining (NHEJ) - Segment order VDJ-γ1 allows splicing of the mature transcript of IgG1

Answer 20

NO, TCR genes cannot undergo further diversification by SHM and are positively and negatively selected to eliminate T cells that potentially recognise self, or fail to activate. NGS estimates of TCR diversity lies in the range of 106 different TCRs.