Immunology Exam 1

Function of FAB region of an antibody

Fragment Antigen Binding, variable region where antibody binds. Also can be pathogen specific

Function of FC region of an antibody

constant region

What are the five types of FC

M, D, G, E, A

Important contributions of Dreyer and Bennett to immunology

1. proposed recombination

2. proposed DNA splicing

germline hypothesis

one gene for every protein

What was the issue with the germline hypothesis?

1. There are over 10^8 antibodies

2. Our genome is too small for every protein

3. There wouldn’t be enough antigen binding diversity

Somatic variation

• variety comes from random mutations

• 1 gene codes for all antibodies

Problems that arise from somatic variation

if all antibodies would randomly mutate then we wouldn’t have 5 constant regions

the 2 gene model

proposed by Dreyer and Bennett that there is a variable and constant part that mix and match

Why do we need a constant region for the heavy chain and light chain?

Constant regions help us get a consistent Y shape through disulfide bonding

Where do B cells begin to develop?

bone marrow

What cells do B cells come from?

hematopoietic stem cells, and then divide into B cell progenitor cells

Why can a B cell only recognize 1 antigen?

the DNA is rearranged to create one hyper specific antibody per B cell (cross-reactivity is very rare and the binding would be weak)

What important contribution did Hozomi and Tonegawa make towards immunology?

Proved recombination, proving that Dreyer and Bennett were right using southern blots. (SNOW DROP)

How many variable regions do Heavy chains have

45

How many diversity genes in heavy chains?

23

how many joining genes in heavy chains?

6

how many C segments in heavy chains?

5

What is the order of C segments on heavy chains?

M, D, G, E, A

What are the two light chains?

Kappa and Lambda

How many variable genes does the Kappa light chain have?

41

How many joining genes does the Kappa light chain have?

5

How many constant genes does the Kappa light chain have?

1

How many variable genes does the lambda light chain have?

3

How many joining genes does the lambda light chain have?

5

How many constant genes does the lambda light chain have?

1

Using RNA processing, which possible constant regions can be used for naive B cell antibodies?

IgM and IgD

Why do we use a surrogate light chain in heavy chain recombination?

To test the heavy chain rearrangement to see if it can work with a light chain.

What happens if a cell fails the surrogate light chain test?

the cell dies

How many chances are given to get the light chain right?

4

Why are there many different options for light chains?

Once we get a successful heavy chain arrangement, we want to have more options to have a successful light chain so the B cell doesn’t do apoptosis and waste a good heavy chain

In which order do the VDJC boxes recombine?

D and J combine first, and then V combines with them, followed by C at the end

what happens in deletional joining?

Rag ½ proteins bring nonamers and heptamers together, bringing the boxes together, and then cuts out the DNA. the deleted sequence is destroyed

How do recombination signal sequences (RSS’s) function in joining two gene segments?

They act as recognition sites for Rag 1/2

What are RSS’s made up of?

heptamer, spacer, and nonamer

What specific base pairing is involved in recombination signal sequence joining?

12 and 23 bp spacer

What happens if DNA is facing the wrong way during recombination?

RSS turns DNA around, fixing the issue during recombination

What is a 1 turn RSS?

12 base-pair spacer between heptamer and nonamer

What is a 2 turn RSS?

a 23 base-pair spacer between heptamer and nonamer

Why is it important that there is a 1 and 2 turn spacer?

A 2 turn and 1 turn RSS prevents a V from ever joining with a V, or a J with a J.

A 2 turn will always join together with…

a 1 turn

In what scenario do we use inversional joining?

If the V and J boxes are in the same direction

When do we use deletional joining?

when V and J boxes are pointing towards each other

When would non-productive deletional joining occur? why?

RSS arrows pointing opposite directions. The cut out “plasmid” would contain the boxes we want to put together

Does light chain rearrangement try kappa or lambda light chain first?

it tries the kappa light chain first

What is the function of Rag ½ in rearrangement?

• helps RSS attach to each other

• nicks DNA at the coding/RSS junction

What is the function of DNA ligase 4 in rearrangement?

ligates the ends of gene segments to themselves

What is the function of Artemis in rearrangement?

cuts on strand on each side

function of DNA polymerase mew and lambda in rearrangement

fills in gaps from extended DNA from artmeis cuts

P-addition

palindrome from Artemis during recombination

Function of Rag ½ exonuclease during rearrangement

cuts edge of DNA strand, causing junctional flexibility

Function of Terminal deoxynucleotidyl Tranferase

randomly adds nucleotides to one end, and DNA polymerase meu and lambda add complementary base

Function of DSBR in rearrangement

double stranded break repair

Function of NHEJ in rearrangement

Non homologous End adjoining

Function of DNA ligase IV in rearrangement at the end

glues strands together

Order of rearrangement

1. Rag ½ holds and cuts DNA

2. DNA ligase 4 ligates the ends of genes segments to themselves

3. Artemis cuts one strand on each side

4. DNA polymerase meu and lambda fill in gaps from extended from DNA artemis cuts (P-addition)

5. Rag ½ exonuclease cutting at the edge of the DNA strand, causing junctional flexibility

6. Terminal deoxynucleotidyl transferases randomly adds nucleotides (N-addition)

7. DSBR, NHEJ, and DNA ligase IV repair strains

P-addition

palindrome from Artemis during recombination

N-addition

random nucleotides added by TdT

Junctional flexibility

describing the process of randomly adding or subtracting nucleotides from the D and J boxes

How to check if recombined gene segment will fail

• was a stop codon accidentally added in

• was there a frameshift

What are the stop codons?

TAA, TAG, TGA

What are the 9 mechanisms for diversity for producing antibodies?

1. N-addition

2. P-addition

3. Junctional flexibility

4. VDJ recombinase

5. D-boxes, V boxes, J boxes

6. Heavy and light chain combinations

7. options of different parental chromosomes

8. Kappa and Lambda

9. box options

What determines whether an antibody will be membrane-bound or secreted?

Either S or M region will be spliced from mRNA transcript

What antibodies are secreted?

has a hydrophilic tail

What antibodies are membrane bound?

they are hydrophobic. hydrophobic region helps Ab get caught in membrane

How do we write that an antibody is membrane-bound?

mIgD, mIgM

How does being membrane-bound change the shape of IgM

can no longer be a pentamer

How does being membrane-bound change the shape of IgA?

can no longer be a dimer

Where is an antibody made in B cells?

Endoplasmic Reticulum

What

What is the last step that occurs before a B cell can leave the bone marrow as a naive B cell?

Negative selection

What other cell helps with negative selection?

Stromal macrophage

What happens during negative selection?

1. stromal macrophage presents self-antigen to B cell

2. if B cell binds it, then it dies

Why are most antibodies membrane-bound in naive B cells?

the naive B cell wouldn’t be able to detect an antigen if antibodies were secreted

Why do B cells undergo affinity maturation?

To improve FAb binding to antigen

What occurs during affinity maturation that increases antibody binding specification?

Somatic mutations and class switching

What are somatic mutations?

point mutations anywhere along FAB region

What is class switching?

Where the antibody switches from IgM and IgD to another isotype.

Memory B cell

• refuses to fight for two weeks

• backup in case antigen returns

Effector B cell

• secretes 1000 antibodies per second

How long do effector B cells last

3 days, due to necrosis

Another name for an effector B cells

plasma cells

Function of IgM

starting package

Function of IgD

• starting package

• least common

Function of IgG

• most abundant

• easier to make

• can cross the placenta

Function of IgE

• parasites

• causes allergies

Function of IgA

• cross membranes

• found in mucus membranes

• found in breast milk

What are the 6 rules of class switching?

1. Don’t use RSS, use a switch region

2. Don’t delete the switch, cut it in half

3. Always use deletional joining

4. Don’t make C flush with J, keep switch segment between

5. Can class switch more than one time

6. Can only class switch further down (deletional joining)

How do switch regions help in class switching?

Switch region is cut in half and one half is joined to another switch region half, while the other half joins to another switch region half and loops to be discarded

What differs between RSS and switch regions?

RSS gets fully cut out, while Switch region is cut in half.

Switch region only uses deletional joining

Are class switches permanent?

Class switches are irreversible

Can class switches happen more than once?

yes

How many different MHC I molecules can we make from our genome?

3 from each chromosome, so 6

What things are coded for in the MHC class III region of the genome?

1. complement proteins

2. Tumor Necrosis Factor (TNF) lymphotoxin

Role of complement proteins

For complement cascade to end in Membrane Attack Complex (hole in membrane)

Role of TNF lymphotoxin

a cytokine

Lymphotoxin

encodes cytokines that regulate inflammation, lymphoid organ development, and immune cell signalling

What type of antigens are presented by MHC 1?

endogenous (from inside the cell)

What cells can MHC 1 be found on?

all cells except RB and neurons

What cell recognizes MHC 1 + antigen?

Tc Cells