Adaptive immunity, antibodies and gene rearrangement

Question 1

When did adaptive immunity first evolve?

Answer 1

500 million yeas ago

Question 2

How do we know that adaptive immunity of BCR, TCR and MHC were successful?

Answer 2

Because every other species from jawed vertebrates onwards has adaptive immunity meaning this was a very successful adaptation.

Question 3

What were the names of the fish that did not have BCR, TCR and MCH and what did they have instead?

Answer 3

The two species were called Hagfish and Lamprey eels and they had variable lymphocyte receptors (VLR).

Question 4

What is transposition (jumping genes)?

Answer 4

Transposition occurs when a gene or DNA sequence changes its position within the genome. This means the section of DNA is either moved to a new location or copied and inserted elsewhere. It is not always removed completely from the genome.

Question 5

What are the two key elements of transposition and what do they do?

Answer 5

1. Transposase or recombinase = Enzyme thats cuts and repositions the gene.
2. Recognition sequences (RS) = These are short base sequence of DNA located at the end of the gene segment, telling the tranposase to cut the DNA. (Recognised by the transpose)

Question 6

What is adaptive immunity known for?

Answer 6

A system that changes with time (adapt) to respond faster and more effectively to a pathogen.

Question 7

What is immune memory?

Answer 7

Immune memory is a key feature of adaptive immunity that provides life-long protection

Question 8

But how do your body know how to respond to specific pathogens?

Answer 8

1. Billions of lympoctes (B and T cells) are produced randomly before birth. Each of these cells are specific to the antigen.
   2.

Question 9

Why is BCR and TCR the only genetic region in your entire genome that can rearrange?

Answer 9

Because Ig and TCR loci are regions in the DNA that code for antibodies (Ig) and T-cell receptors (TCR). The regions are made up of segments of DNA and each segment has RS at their ends.

Question 10

What is IG domain?

Answer 10

Repeating protein unit that make antibody.

Question 11

How is the IG domain arranged?

Answer 11

This is made up of two anti-parallel B pleated sheets that are joined together by a central disulphide bond. The B sheets are made up of B strands.

Question 12

Explain the IG domain as a hand analogy.

Answer 12

The 2 pleated b sheets are the hands, and in between is the disulphide bond. The fingers are the loops at the end, called CDRs and they are not constrained (flexible).

Question 13

Explain why the loops at the end of the IG domain is flexible.

Answer 13

It’s flexible because their
amino acid sequences can vary without disrupting the
overall structure of the domain. This means that the amino acids change their sequence depending on the different type of antigen it needs to bind to.

Question 14

What is β-barrel?

Answer 14

Refers to the IG protein fold meaning how the IG domain folds and take the 3D structure.

Question 15

How is the Ig domain and antibody related?

Answer 15

Ig domain is a key structure that makes up the antibody.

Question 16

Describe the antibody structure.

Answer 16

Antibody is Y shaped made up of 2 arms and a stem. Each arm is made of up 2 chains: heavy chain and light chain and linked together by disulphide bonds. This L—s-s—H is one arm.

Question 17

What does one complete arm of the antibody called?

Answer 17

Fab

Question 18

Where are the two identical antigen binding sites?

Answer 18

At the tip of the arms.

Question 19

What are the heavy and light chains made up of?

Answer 19

Multiple IG domains.

Question 20

What is the stem of the antibody made up of and what is another name for it?

Answer 20

It is made up of heavy chains specifically CH2 and CH3 , and another name for the stem is called the the invariant effector region.

Question 21

How are the classes of the antibody defined by?

Answer 21

They are defined by the H chain gene used on the stem / invariant effector region.

Question 22

What are the 5 classes of antibodies?

Answer 22

GAMED - IgG, IgA, IgM, IgE, IgD.

Question 23

Where is IgG found in and what are the 5 key functions?

Answer 23

This antibody is found in blood, its the most abundant, produced after class switching from IgM, fixes complement, Crosses the placenta to protect babies (neonatal immunity), Provides long-term protection.

Question 24

Where is IgA found in and what does it do?

Answer 24

It is found in Blood and mucosal
secretions such as in
tears, breast milk, gut,
genitourinary tract. The main function is to provide gut immunity
to neonates (newborn babies) who don’t have their own antibodies yet.

Question 25

Where is IgM found in, and what is the difference between the 2 forms of IgM?

Answer 25

Found in membrane and blood. There are two forms of IgM. Because naive B cells have not encountered an antigen, they can't produce an antibody. However, IgM is found on the surface of B Cell Antigen Receptor (BCR), but it is not an antibody. When an antigen binds, IgM gets activated which is then produced as a soluble form in blood. So the two forms of IgM is membrane bound (part of the BCR) and soluble IgM.

Question 26

What is a key feature of IgM?

Answer 26

Membrane bound IgM is found on ALL naive B cells. After the antigen to the B cell, it will undergo class switching.

Question 27

What are naive B cells?

Answer 27

Naive B cells are immature B cells that have not yet encountered an antigen.

Question 28

How many antigen binding sites does does soluble IgM have?

Answer 28

10.

Question 29

Where are antigen binding sites located?

Answer 29

Tips of the antibody/ Fab/ arms. NOT the stem (FC region).

Question 30

What immunoglobin is a pentamer and what does this mean?

Answer 30

IgM, and this means that the soluble IgM is structured in 5 antibody units in a circular shape.

Question 31

What is one antibody unit?

Answer 31

2 light chains, 2 heavy chains and one stem.

Question 32

Why does IgM have a high avidity?

Answer 32

Because IgM is a pentamer, meaning it consists of 5 different antibody units together, it can grab many antigens at once. So even f the individual binding site (affinity) isn't super strong, the avidity is still going to be high (overall binding strength).

Question 33

How many Fc regions are there on IgM.

Answer 33

Excellent at fixing complement with 5 Fc regions that bind complement component C1.

Question 34

Explain the different between avidity and affinity.

Answer 34

Avidity refers to the overall binding strength, driven by multiple binding sites. Examples: IgM has high avidity because it is multivalent (multiple binding sites). Affinity would be interaction between the one antigen binding site vs its antigen. High affinity means because the antibody is tightly bound to the antigen, it doesn't need as many molecules to form the bond between antigen and antibody.

Question 35

What is a way for the immune system to recognise self vs non-self in terms of bi-valent and multivalent?

Answer 35

The immune system will recognise self vs non-self due to it being triggered by multivalent t interactions as bivalent are not strong enough.

Question 36

What is the variable domain?

Answer 36

The variable domain is part of the variable region. It is made up of 3 discrete regions called CDRs. Complementarity Determining Regions (CDR). There are CDR1, CDR2, and CDR3.

Question 37

How are the CDRs structured?

Answer 37

CDrs are structured in 6 hypervariable loops which connect the B strands in the variable domain. This makes up the tip of the antigen binding site.

Question 38

What does hypervariable mean?

Answer 38

It means the 6 variable loops differ significantly between different antibodies.

Question 39

What is variable region and what is so significant about it?

Answer 39

Variable region is the region located at the tips of the arms of antibodies heavy chain variable region (VH) and the light chain variable region (VL), where the antigen binding site is found. What is so significant is that the variable region have different amino acid sequences which is what makes each antibody bind to a different antigen.

Question 40

What's in the heavy chain (H) locus?

Answer 40

4 clusters called Variable, Diversity, Joining and Constant regions. What happens is as a B cell develops, the following happens 1. A D segment joins to a J A V segment joins to the new DJ. 3. Intervening DNA is discarded. This codes for the variable region of the heavy chain.

Question 41

What is the difference between between H locus and L locus?

Answer 41

There is no D segment.

Question 42

How do antibodies gain diversity?

Answer 42

1. Antibodies gain diversity because These segments are randomly joined together to create a unique antibody. The joining is imprecise, meaning: Extra or missing DNA bases can occur at the joins. 2. This increases diversity, especially in the CDR3 loop (called the VDJ join) in the middle of the antigen binding site.

Question 43

What are the names of the enzymes involved that look for the RS in the end segment of 5’ and 3’ ends of each V, D, J segment, cut the segments and join to form a new gene?

Answer 43

Special recombinase enzymes (RAG1 and RAG2) which are only active in B and T lymphocytes.

Question 44

When does gene arrangement occur?

Answer 44

Before birth.

Question 45

What is junctional diversity/ imprecise joining?

Answer 45

It's the process of how your immune system can produce a lot of T cell receptors and B cells, contributing to the diversity. The diversity will occur when RAG1 and RAG2 enzymes find the RS sequence at the end of the DNA strand. The recombinase will cut up the DNA. Random edits are made . When the segments are then joined together it is imprecise. This contributes to the variation in the CDR3 loop in the middle of the antigen binding site.

Question 46

How does your genome know before birth what pathogens you will encounter during your lifetime?

Answer 46

Your body will produce repertoire of billions of B and T cells with the hopes that it will bind to a specific antigen, as your immune system doesn't know what antigen it will encounter. Because of this, it randomly makes as many receptor combinations as possible. When it does recognise the antigen, it will select and expand and clone itself. This is called clonal expansion.

Question 47

Define affinity maturation.

Answer 47

Affinity maturation occurs when improve their ability to bind to the antigen after clonal expansion.

Question 48

How does clonal expansion and affinity maturation work?

Answer 48

1. Start with low affinity naive B cells. Each of has a different BCR. These will regonise non-self antigens, and the BCR that is strongly binded (high adivitiy) will clone itself (proliferate)(clonal expansion). 2. Over time mutations will occur where it will make the BCR better binded to the antigen (increase the affinity). 3. After multiple rounds of selection, a new B cell clone making high affinity, making highly specific IgG antibodies arises from the lymph node.

Question 49

Where does clonal expansion and affinity maturation occur?

Answer 49

All this takes place within lymph node follicles.

Question 50

Describe the basics of a lymph node, follicles and germinal centres.

Answer 50

So when a B cell is activated, it stays in the lymph node and and forms a germinal centre. The centre is where many B cells undergo affinity maturation and proliferation. Around the centres and larger B cell follicles, there are T cells which drive the T cells to make antibodies.

Question 51

There are 7 steps to affinity maturation. What are they?

Answer 51

1. Antigen stimulates a B cell clone with a naïve BCR to grow and expand within in a germinal centre. 2. The B cell switches from using the μ (IgM) to the γ (IgG) heavy chain to make an IgG molecule. 3. Random somatic hypermutations occurs in the Ig gene of the clone as it proliferates. Some of these mutations result in new clones with improved antigen receptor affinity. 4. After successive rounds the mature B cell becomes a plasma cell secreting long-lived soluble Ig designed specifically for the selecting antigen. 5. Some of these mature B cells take on a memory phenotype and reside in lymph nodes and tissue long-term waiting to respond to the next infection. 6. This is the primary mechanism behind acquired immunity, memory and vaccination.

Question 52

Why do we vaccinate?

Answer 52

1. Herd immunity stops the transmission of diseases (when you vaccinate enough people, the virus has no where to go). 2. Claiming that the MMR vaccine causes autism is false. This is called antivaxx misinformation. 3.

Question 53

What is the whopping cough?

Answer 53

This cough produces a toxin called pertussis toxin.

Question 54

Where is IgE found in what does it do?

Answer 54

Found in the serum, and does he least abundant but very important in atopic allergy and inflammation.

Question 55

Where is IgD found and what does it do?

Answer 55

Membrane and blood. A form of BCR. Crucial role in B cell differentiation.