Specificity, Diversity, and immunoglobulin genes

Question 1

Whats the difference between a toxin and a toxoid

Answer 1

A toxoid is an inactivated or attenuated form of a toxin

Question 2

Binding between Ag and Ab is covalent or ionic?

Answer 2

Trick question kind of. Its non-covalent and depends on various non-covalent interactions: ionic bonds, h bonds, van der Waals, hydrophobic interactions.

Question 3

Describe cross-reactivity? Do two cross reacting epitopes always have similar AA sequences?

Answer 3

Sometimes Ag1 will bind to Ab1 with low affinity but Ag2 will bind with high affinity. When Ag2 is introduced in the body, it binds B cells with a great enough affinity to activate it and produce antibodies against Ag2. These antibodies have a similar epitope to Ag1 and will sometimes fit with a good enough affinity to attack Ag1 as will. Example Rheumatic Heart disease.

Question 4

Why is rheumatic heart disease an example of cross-reactivity?

Answer 4

laminin (an antigen in heart valves) cross reacts with Group A Streptococci. Sometimes when a person gets Group A Streptococcus, the antibodies produced attack laminin in the heart by a complement-mediated, inflammatory process.

Question 5

What are the two steps to produce an antibody from a B cell?

Answer 5

1. Binding of the antigen to B Cell receptors
2. If the antigen binds with high enough affinity it will activate the B cell to produce antibodies–the product of the cell.

Question 6

Explain the clonal selection theory and how it differs from the instruction theory.

Answer 6

Clonal selection is that each cell of the immune system only makes one antibody and all these antibody-making cells pre-exist in the body. When an antigen moves around the body it bumps into these until it binds to one that fits. The B cell that it binds to then begins producing antibodies to destroy the antigen. This is Darwinian.
Instruction theory is Lamarkian and states that the antigen binds a cell and teaches it how to build antibodies to fight it. In other words, all B cells would be the same.
There was an experiment that proved Clonal selection–radioactive x antigen kills all the cells, then add non radioactive x antigen and y antigen. X should not bind but y should under selection theory. In instructional, neither would bind. Y binded, point taken.

Question 7

How can body supply the diversity needed to make all the different kinds of antibodies and b cells?

Answer 7

V regions on H and L chains. 1000 genes for one and 1000 genes for the other could combine in all sorts of ways to make 1000000 antibodies.

Question 8

What is allotypic exclusion?

Answer 8

This is basically gene silencing. Although we have maternal and paternal genes for an H chain and Maternal, paternal, lambda and kappa genes for an L chain, the B cell contains only one kind of each. So it contains only one H chain (maternal or paternal) one L chain (lambda or kappa from either maternal or paternal). All the other genes are silenced so the B cell only makes one kind of antibody this way.

Question 9

How do variable domain genes work and how do they get so much variability?

Answer 9

The variable domain region is broken up into segments in the DNA, so there is not just one region. For H chains the variable domain region is composed of multiple V, multiple D, and multiple J gene segments. The V region of light chains is broken up into V and J segments.

Question 10

What are the segments of an H chain Variable domain region?

Answer 10

V D and J gene segments (think heavy chain, so more genes required)

Question 11

What are the segments of an L chain Variable domain region?

Answer 11

V and J

Question 12

How are variable domain genes selected and spliced out?

Answer 12

The genes are lined up VDJC with many different options in each letter category. First a random D is brought to a random J; the intervening DNA is excised. Then a random V is brought to D-J and joined with the intervening DNA excised. A primary RNA transcript is made.

Question 13

What genes are included in the primary RNA transcript?

Answer 13

from just Left of the chosen V and then the selected D and J (stuff in between has been excised) then all the way down through the delta CONSTANT region gene.

Question 14

What antibodies can be made from a primary transcript RNA of the VDJ genes?

Answer 14

First RNA is spliced to make VDJ-mu (constant) messenger RNA so the cell can make IgM. Next, it is spliced to make VDJ-delta (constant) RNA so it can make IgD.

Question 15

How many C domain genes do L chains have?

Answer 15

only one, kappa or lambda, depending on the cells choice.

Question 16

enzymes that pull VDJ genes together and cut and splice.

Answer 16

RAG-1 and RAG-2 recombinases. They do recombination of antibodies and T-cell receptor DNA. Not sure what that means? Without RAGs mice don’t make B or T cells.

Question 17

How is it that Germ line differences and Somatic mutations produce diversity in antibody genes?

Answer 17

In the germ line we have various VD and J segments that we are born with. More diversity is generated by sloppy (or variable) V/J (for L) and V/D (for H) joining that creates N regions.

Question 18

What are the two ways diversity is added via somatic variation?

Answer 18

1. exonucleases chew away DNA after it is cut until Gene segments are joined.
2. Terminal deoxynucleotidyl transferase (TdT) adds a few random nucleotides without a template.
   This creates an unpredictable sequence at the joining area (D to J or V to DJ) called an N region. two n regions, one on either side of D. Creates diversity.

Question 19

What are the downsides to Somatic variation?

Answer 19

Frameshift mutations 2/3 times which can produce nonsense mutations and stop coding.

Question 20

How does the cell adjust for the effects of frameshift mutations?

Answer 20

The B cell only needs one copy of the gene, so if the frameshift causes an early ending nonsense mutation it aborts and tries again with the other gene. If unsuccessful again the cell dies.

Question 21

What happens to the other gene when the first produces a successful antibody in the B cell?

Answer 21

The other gene is silenced. Only one is activated for each the H and L chain. other alleles are excluded.

Question 22

What is receptor editing (short)?

Answer 22

If a rearrangement is unsuccessful and the RAG recombinase is still active it can attempt to rearrange again.

Question 23

What is somatic hypermutation?

Answer 23

The recombined V(D)J region, or CDR, can have mutations in its daughter cell which affect affinity (can increase or decrease but often increase).

Question 24

What is Activation Induced Deaminase (AID)?

Answer 24

This enzyme converts a random cytosine to a Uracil in a CDR. the enzyme repair mechanism catches and repairs this with a random base. This is the enzyme which is responsible for somatic hypermutation. It only occurs after antigenic stimulation.

Question 25

How does somatic hypermutation occur in T cells?

Answer 25

It does not. Somatic Hypermutation only occurs in B cells. Trick QUESTION BOO HOOO HAHAHAAHAHA.

Question 26

A single mature B cell starts making which type of antibody? If it switches which will it switch to?

Answer 26

IgM an IgD. It can Switch to IgA, IgE, or IgG. This has to do with how the DNA is looped and spliced out.

Question 27

True or False: a b cell making IgA can switch to making IgM?

Answer 27

False. Cells start making IgM and IgD. If they switch to IgA, IgG, or IgE they lose the ability to make the first two. Has to do with how the DNA is looped and spliced out. Mu and delta info is physically lost.

Question 28

Which region of the H chain changes when a cell switches from IgM/IgD to IgA or another form?

Answer 28

The V domain stays the same but the C region of the H chain changes. Remember only the H chain changes. The L chain stays the same forever in a B cell.