Why is the adaptive immune response so specific

Question 1

What are the two forms that immunoglobulin comes into

Answer 1

Transmembrane B cell receptor and soluble Ig- antibody

Question 2

What is the structural difference between BCR and antibody

Answer 2

antibody does not have the transmembrane domain but have a signal peptide instead

Question 3

Describe the structure of Ig

Answer 3

formed of four polypeptide chains with two heavy and light chains connected by disulphide bond. The top of the Y-shaped molecule contains the antigen
binding site and made up of 2 variable regions on each Ig
molecule; VL and VH. This is the region with the broadest diversity
in amino acid sequence. There are also 2 constant regions in each
Ig molecule: CL and CH. The constant region on the heavy chain
can contain 1-4 CH domains depending on the Ig molecule:

Question 4

what characteristics do immunoglubulin superfamily has

Answer 4

they possess a domain - immunoglobulin domain containing 70-110 a.a and has an Ig-fold formed by two sheets of beta strands

Question 5

Name molecules in the Ig superfamily

Answer 5

MHC molecules, Cd4, Cd8, ICAM1, Fc receptors, CD28

Question 6

Function of BCR

Answer 6

to bind to antigen presented on MHCII and activated B cells will internalise the antigen

Question 7

similarity between antibody and BCR

Answer 7

they share same primary transcript

Question 8

what separates antibody and BCR

Answer 8

by alternative polyadenylation and splicing, BCRs
are translated with a C-terminus containing a transmembrane segment and a short,
cytoplasmic tail.

Question 9

How can the Ig be digested into three fragments

Answer 9

by fruit protease- Papain

Question 10

What are the three fragments in Ig

Answer 10

two Fab which are the antigen binding regions and one Fc

Question 11

Function of Fc region

Answer 11

Opsonisation, complement fixation via C1q, mother-to baby antibody transfer via placenta

Question 12

Which part of the antibody contacts the antigen

Answer 12

complementarity determining region (CDR), CDR1 and CDR2 most genetically variable and CDR3 arise during VDJ recombination

Question 13

How many subtypes of Ig there are

Answer 13

IgG, IgA, IgM, IgD, IgE

Question 14

whats different between all Ig

Answer 14

• Differ in amino acid composition, size, charge, carbohydrate content, the way they assemble

Question 15

describe the structure of IgM

Answer 15

forms a pentamer connected by J chain, possess 10 antigen binding sites with high avidity

Question 16

what is avidity

Answer 16

overall strength of binding of an antibody of an antibody to an antigen with multiple binding sites

Question 17

what are the 3 types of IgG

Answer 17

IgG1 IgG2 IgG3 IgG4

Question 18

Which two Ig contains J chain

Answer 18

IgA and IgM

Question 19

What is the major role of IgE

Answer 19

important in allergic diseases such as asthma and hay fever and found in surface of basophils and mast cells

Question 20

Describe the differences in structure of the 5 Ig

Answer 20

IgM forms a pentamer, IgA forms a dimer, IgG, IgE and IgD forms a monomer

Question 21

describe the structure of TCR

Answer 21

a heterodimeric transmembrane receptor
formed by 2 chains – TCR-a and TCR-b - which are connected by disulfide bonds. Both
chains contain variable and constant regions as well as a transmembrane region. The TCR
complex is formed by the TCR and CD3 (made up of CD3g, CD3e and CD3y).

Question 22

What are the types of MHC and where do they exist

Answer 22

MHC class I and present antigens from intracellular infection - viral infection 
MHC class II present antigens from extracellular  and are only present in macrophages, DC and b cells

Question 23

Which coreceptors bind to which MHC

Answer 23

CD4+ binds to MHC Class II and prompt APC to get more serious about attacking the pathogen 
CD8+ binds to MHC class I activating CD8+ to kill the pathogen

Question 24

what is the difference between the heavy chain and light chain

Answer 24

light chain does not have diversity regions

Question 25

What is VDJ recombination and what it produce

Answer 25

• 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

Question 26

What does the RAG recombinases do

Answer 26

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

Question 27

function terminal deoxynucleotidyltransferase

Answer 27

adds additional nucleotide at the end of DNA strand

Question 28

where are RSS located

Answer 28

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

Question 29

what is the 12/23 rule

Answer 29

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

Question 30

How does the immune system create a 10 million fold increase in Ig diversity?

Answer 30

• 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

Question 31

what is different between a-chain locus and b-chain locus on TCR through VDJ recombination

Answer 31

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

Question 32

what happens to TCR after

Answer 32

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

Question 33

Describe the VDJ recombination process

Answer 33

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.

Question 34

what is allelic exclusion

Answer 34

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

Question 35

What is complementarity-determining region

Answer 35

○ 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)

Question 36

function of Somatic hypermutation and when does this occur

Answer 36

to generate extra variability

occur during B cell proliferation

Question 37

Describe SMH

Answer 37

○ 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

Question 38

What is the germinal centre

Answer 38

• 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

Question 39

Describe the B cell differentiation in the GC

Answer 39

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

Question 40

Describe affinity maturation

Answer 40

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

Question 41

What is class switch recombination

Answer 41

• process by which proliferating B cells rearrange the constant region genes in the immunoglobulin heavy chain locus to switchfrom expressing oneclassof immunoglobulin to another

Question 42

How many constant regions does heavy chain consists of

Answer 42

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

Question 43

Process of class switch recombination

Answer 43

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

Question 44

Can T cell undergo further diversification beyond VDJ recombination

Answer 44

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.