lecture 14

Question 1

describe the antibody structure on the domain level

Answer 1

they have light and heavy chains composed of repeating IG domains
the n-terminal domains of both genes are called variable domains and the remaining or constant domains
so the antigen binding site is made from VL and VH domain interactions

Question 2

how do heavy chain structures differ considerably in IGM (5 antibodies linked by J chains)

Answer 2

the heavy chains have a CH4 domain
there are multiple disulfides and the heavy chain is heavily n-glycosylated (these are complex carbohydrates that hold domains apart, allowing exposure of functional motives like complement binding sites)

Question 3

how do heavy chain structures differ considerably in IGG

Answer 3

different domains have different functions
cy1 and cy2 - bind complement components
cy2 and cy3 - bind FC receptors on neutrophils
cy3 - bind FC receptor on macrophages and natural killer cells

(cy1=cH1)

Question 4

how do heavy chain structures differ considerably in IGE?

Answer 4

the many n-glycans make this a stiff rigid molecule - which is good for targeting large pathogens and it will not cross-linked small targets

Question 5

how do heavy chain structures differ considerably in IGA?

Answer 5

it is very flexible
a good cross-linker
has a valency of 4
secreted iga with secretory chain and its J chain

Question 6

what allows class switching (on the gene level)?

Answer 6

the H chain gene is segmented
there is one antibody H chain gene with an unusual arrangement
the IG H chain gene encodes a variable VH domain and all the H chain constant regions, separated by non coding introns
(gene = VH - Cm - Cd - Cg - Ce - Ca)

Question 7

describe how the class switch maintains specificity

Answer 7

the VH gene segments is used for expression of the same specificity but after class switching
HOW
through the use of somatic recombination of DNA
intervening DNA is excised to allow expression of VH with C gamma, C epson or C alpha

Question 8

describe how the class switch happens

Answer 8

through somatic recombination

alignment:
genomic DNA is looped. an unusual DNA recombination event can now occur. this requires specialised sets of proteins.
deletion:
cutting and rejoining of DNA in results in excision of the loop, the result is class switching. we still kept the same VH sequence so the same specificity

Question 9

why does the expression now rely on the removal of the intron from the mRNA?

Answer 9

the rearranged gene is transcribed to generate a primary transcript
the segments encoding VH and CA are now fused in frame at the RNA level by excision of the intron to generate the mRNA
this mRNA is transcribed to make an idea heavy chain with the same specificity as the original IgM

Question 10

describe the clonal selection theory

Answer 10

an antigen activates only those lymphocytes that display cell surface receptors specific to that antigen, even if that antigen has never been encountered before
receptors are : TCR and BCR
once they encounter each other, the lymphocytes go through clonal expansion and differentiation

Question 11

define clonal selection

Answer 11

following infection, individual specific clones are selected by antigen. the result is pathogen specific. lymphocytes are selected from pools of B and T cells

Question 12

define clonal expansion

Answer 12

selected clones undergo mitosis, proliferate and differentiate into effector cells

Question 13

define clonal deletion

Answer 13

those lymphocytes that react inappropriately with self antigens are destroyed

Question 14

where does the diversity come from?

Answer 14

antigen activates only those lymphocytes T and B cells that are already committed to respond to it
there is pre-existing diversity built into the adaptive immune system

Question 15

how can we get diversity?

Answer 15

the antigen specific receptors (TCR and membrane bound antibodies for T and B cells) are encoded by unusual segmented genes
these genes are assembled from a series of gene segments by an unusual form of recombination called somatic gene recombination
somatic gene recombination is used for class switching but a slight modification leads to massive pre existing diversity

Question 16

STEP 1 - define the generation of primary antibody diversity (also how can we recognise antigens that have never been encountered?

Answer 16

it’s all to do with the variable domains that encode antigen specificity
there are only 3 antibody genes. there are 2 classes of light chains which increases diversity
for every antibody we make, it can have a light chain that is either lambda or kappa

Question 17

generation of primary antibody diversity (4 steps)

Answer 17

1. HC gene has VH with Cs / 2 LC genes have Vlamba or V kappa with Cs
2. each V domain has many genes so allows 4 500 VH:VL combinations
3. V(D)J recombination selects V gene segment and DNA that links V domain with constant domains
4. improved specificity as antibodies improve their affinity –> affinity maturation

Question 18

define affinity maturation, the rate in germinal centres and what it’s mutation is called

Answer 18

affinity maturation occurs in the lymph nodes. some of the activated B cells proliferate in the lymphoid follicles and form structures called germinal centres

mutation rate in the germinal centres is about 1 million times greater than the spontaneous mutation rate in other genes
it is confined to the gene segments that encode V domains

SOMATIC HYPERMUTATION

Question 19

affinity maturation (3 steps)

Answer 19

1. antigen stimulation causes activation and clonal expansion of B cells with preexisting fits to the antigen. class switching allows this selected preexisting specificity to be transferred to other Ig, providing extra immune functions
2. some b cells of the expanded clonal population will stay and proliferate in germinal centres and undergo somatic HYPERMUTATION, generation antibodies with altered v domain specificity
3. most of the hyper mutated clones are worse than the original and will not be stimulated by the original antigen so most will die. the rare B cells with a mutated bcr version that has a higher affinity than the original will proliferate.

Question 20

define immunological memory

Answer 20

memory is generated by the primary response
after clonal expansion following antigenic stimulation both naive T and B cells differentiate into effector cells which then perform their immunological functions:
- effector B cells secrete antibody
- effector T cells kill infected cells or influence the response of other cells

some antigen stimulated cells differentiate into memory cells. they can be induced to become effectors. most effectors die after an immune response but memory cells do not.

Question 21

what do we know about T memory cells and their structure?

Answer 21

memory t cells are still an area of active research. the current model is that multiple classes of memory t cells exist
some memory T cells carry cell surface markers characteristic of T helper or T cytotoxic cells
memory t cells migrated tissues so they spread and are deposited locally

Question 22

what do we know about immunological B memory cells?

Answer 22

they can respond to antigen increase in frequency and produce antibodies of higher average affinity than unprimed B lymphocytes
the secondary response antibodies are produced by memory B cells (which have already switched from IGM to more mature isotypes)
memory B cells circulate through the same secondary lymphoid compartments that contain naive B cells (spleen, lymph nodes and Peyer’s patches)