6. Antibody: Genetics and Structure

Question 1

What are the 4 groups of receptors that the immune system uses to recognise pathogens?

Answer 1

Pattern recognition receptors, major histocompatibility complexes, T-cell receptor, Antibody (BCR)

Question 2

Which type of immune response cells are PRRs present on?

Answer 2

Both innate and adaptive - Charlie you cheeky fucker!!

They were initially discovered on the innate response though

Question 3

What do PRRs recognise?

Answer 3

PAMPs and DAMPs - produced by host cell in response to infection

Question 4

How many different MHCI and MCHII molecules are there?

Answer 4

3 of each - A, B, C

Question 5

How do MHC vary between people? What MHC is common in white (pantone: Blanc de Blanc 11-4800) people

Answer 5

Vary hugely, HLA is most common for white peeps

Question 6

Where is the T cell receptor found?

Answer 6

Only on the surface of T cells, highly specific, many different TCRs and BCRs can be made

Question 7

Describe the structure of the antibody?

Answer 7

2 heavy (50kDa), 2 light (25kDa) chains, stable disulphide bond between L and H, variable region have 3 hyper variable regions (CDRs)

Question 8

What is another name for the hyper variable region?

Answer 8

Complementarity determining region

Question 9

What are the 2 different types of constant region light chain in an antibody?

Answer 9

Kappa and Lambda constant regions

Question 10

What are the 5 different classes of heavy chain?

Answer 10

IgG, IgM, IgE, IgA, IgD

Question 11

How many different immunoglobulin gene loci are there on how many different chromosomes? How are the heavy/light chain genes arranged on the chromosomes?

Answer 11

3 different gene loci on three different chromosomes

Heavy: genes linked together side by side on chromosome 14

Light: lambda light chain genes on chromosome 22, kappa on chromosome 2

Question 12

What does the heavy chain immunoglobulin gene loci consist of?

Answer 12

5’ - 40 variable region gene segments then 27 diversity genes segments, then 6 joining gene segments then 9 constant region segments - 3’

Question 13

What is the difference between the gene loci of heavy and light chains?

Answer 13

The light chain genes do not have diversity gene segments (only V, J and C)

Question 14

How is the antibody developed (how are the genes chosen)?

Answer 14

In a random way - as B cell develops in bone marrow starts to recombine heavy chain of Ig genes - 1/27 D segments is taken and randomly placed next to one J segments (this forms a loop), a random V gene is then picked and placed to D/J to form a continuous loop of DNA (this produces the variable region of the antibody)

The constant region genes are then selected

Question 15

How does the variability in encoding of CD1/CD2 and CD3 vary?

Answer 15

CD1 and 2 is encoded by only V gene segment whereas CD3 is encoded by V, D and J been segments so much more variable

Question 16

How many subclasses of antibody are there? What are they?

Answer 16

9 - IgG has 4 subclasses 1-4, IgA has 2 subclasses 1-2, IgM/E/D have no subclasses

Question 17

How many steps are there in the gene rearrangement process of the light genes compared to the heavy?

Answer 17

2 rather than 3 because light genes have no D segment

Question 18

What enzymes cause V-D-J recombination?

Answer 18

Rag1 and Rag2 (recombination activating genes), recognise nucleotide sequences that flank the VDJ protein exons

Question 19

What are Recombination Signal sequences? What is their sequence?

Answer 19

Regions of nucleotide that are recognised by RAG1 and RAG2

Heptononomer sequence: 5’-7nucleotides-spacer-9nucleotides-3’ (Spacer isn’t conserved)

As D is join gin to J need 5’ signal on every J and 3’ signal on every V segment

Question 20

What is the molecular mechanism of gene recombination (e.g. enzymes)?

Answer 20

Sequences put next to each other, junction is cut using DNases and then DNA ligated back together using DNA ligase

Question 21

What is the order of gene segments combining?

Answer 21

D and J joined first, then V joined to DJ

Question 22

What four other methods increase the antibiotic diversity?

Answer 22

1. Recombinatorial inaccuracies - exact place of which D joins to J and V to DJ can vary
2. N-nucleotide addition - after DNA cut but before stuck together the terminal dNTP transferase transfers the N nucleotide (?)
3. Different Chain combinations
4. Somatic hypermutations - DNA changes when B cell divides

Question 23

What do antibodies do the B cells initially make?

Answer 23

IgM and IgG - class switching allows them to synthesise others

Question 24

How do B cells switch from producing to IgM to IgE?

Answer 24

Recombination process in the heavy chain - initially heavy chain recombines D to J then V to DJ to give variable region and begins off making IgM but when it class switches there is a similar process (cmu to c epsilon - DNA looping etc) but different enzymes involved (not RAG1/2) and different nucleotide sequences involved (switch sequences).

Question 25

Where are the switch sequences present on the antibody gene?

Answer 25

Immediately upstream of each C region - but not one upstream of C delta (C mu and C delta are always transcribed together hence why cell always has IgM and IgD on surface)

Question 26

What are the 5 methods of generation of TCR diversity? What 2 diversity generating methods are used in BCRs but not TCRs?

Answer 26

1. Multiple germ line genes
2. V-J and V-D-J recombination
3. Recombinatorial inaccuracies
4. N-nucleotide addition
5. Chain combinations

Question 27

What are the names of the subclasses of IgG in mice?

Answer 27

1, 2a, 2b, 3

Question 28

Which constant region of the heavy chains code for IgG, IgA, IgM, IgD, IgE?

Answer 28

G: lambda
A: alpha
M: mu
D: delta 
E: epsilon

Question 29

Describe the structure of the antibody

Answer 29

2 Light chains with variable & constant regions, 2 heavy chains with variable & constant regions and a hinge region at the point where the arms may wobble and flop around like used condoms in a coastal breeze

Question 30

What are the subclasses of human IgG?

Answer 30

1, 2, 3, 4

Question 31

Which immunoglobulin molecules may become polymeric?

Answer 31

Secretory IgA (IgA at mucosal surfaces): dimer (linked together by J chain)

Circulating IgM: pentamer

Question 32

What is the immunoglobulin domain structure?

Answer 32

4 beta strands form a beta sheet, 3 beta strands form another beta sheet (hydrophobic AA) so the two chains come together and are further held by a disulphide bond (very stable)

Hypervariable regions come out of these beta strands - may vary in shape and length