Structure Of Antibodies

Question 1

The structure of antibodies

Answer 1

Immunoglobulin = antibody
Two heavy chains with a variable and constant region
Two light chains variable and constant regions
Held together by infra/inter chain disulfide covalent bonds

Question 2

Antigen binding sites

Answer 2

Are on the n termini
N termini have heavy and light chains
Each ab can bind two antigen molecules

Question 3

Hinge region

Answer 3

Hinge regions found in between ch1 and ch2 regions
Rich in prolines making it flexible
Also rich in cysteines

Question 4

5 classes of antibodies

Answer 4

IgG
IgD
IgE
IgA- forms dimers
IgM-forms pentamers

Question 5

Classic antibody domains

Answer 5

Fab region binds to things
Fc fragment is portion responsible for connecting the binding to a response

Question 6

How B cells use recombination of gene segments to create antibodies

Answer 6

There is the variable V, diversity D, joining J, and constant C regions
D segments are in heavy chains only

Question 7

Light chain recombination

Answer 7

Germline dna cuts out dna between V and J portion this becomes the rearranged DNA goes through transcription to make primary rna transcript this undergoes splicing removing DNA from the VJ and C sections this undergoes translation making a VLCLj chain

Question 8

Heavy chain recombination

Answer 8

Cuts the DNA between the D and J region first then between the V and DJ region. After this dna is cut from the VDJ and C regions

Question 9

Five mechanisms to generate antibody diversity

Answer 9

1) multiple gene segments
2)combinatorial diversity-pairs heavy chain with light chains from paternal and maternal chromosomes
3) exonuclease trimming
4) P nucleotide addition
5) non-templated N nucleotide addition

Question 10

P nucleotide addition

Answer 10

Templates nucleotide additions between joints resulting from asymmetrical cleaving of hairpin structures

Question 11

Non-templated N nucleotide addition

Answer 11

Mediated by TdT activity adding in random nucleotides between joints
TdT adds n nucleotides repair enzymes add complementary nucleotides

Question 12

Non productive arrangements of B cells

Answer 12

Non productive arrangements lead to apoptosis during development

Question 13

Flow cytometry

Answer 13

Forward scatter measures size
Side scatter measures granularity/complexity of the cell

Question 14

Gating in flow cytometry

Answer 14

Allows researchers to select for a particular population of cells in the data to further study
Can get a relative measure of protein expression via histograms

Question 15

Major histocompatibility complex (MHC)

Answer 15

3 classes
MHC 1
Mhc2
MHC 3

Question 16

MHC class 1

Answer 16

Large 45 kda glycoprotein alpha chain
Smaller 12 kda microglobulin protein
Binds peptides between 8-10 amino acids long
3 alpha domains
1 beta chain
Peptide binding is between alpha 1 and 2
Only alpha 3 domain passes through the cell membrane

Question 17

MHC class 2

Answer 17

Heterodimeric 33kda alpha chain
28 kda beta chain
Both chains pass through the plasma membrane
Peptide binding cleft formed by paring of alpha 1 and beta 1 domains
Binds peptides 13-18 amino acids in length

Question 18

Purpose of MHC class 1 and cells that respond

Answer 18

To express endogenous peptides
Expressed on the surface of every single nucleated cells
Cells that respond are CD8+ Tcells or T-cytotoxic cells
All peptides bound to MHC 1 have a carboxyl terminal anchor at position 9
Another anchor on 2nd or 3rd amino acid
peptide binding groove is closed at both ends.

Question 19

Purpose of MHC class 2 and cells that respond to them

Answer 19

Present exogenous peptides and proteins
Only on surface of antigen presenting cells -dendritic cells, macrophages and some B cells
Cells that respond/bind are CD4+ T cells or T helper cells
Does not have any anchor residues
Hydrogen bonds are formed through out the binding site
binding groove is open at both ends

Question 20

How are MHC alleles expressed

Answer 20

MHC alleles are co-dominantly expressed
both maternal and paternal MHC genes are expressed in offspring
genes are highly polymorphic meaning there are many alternative forms of each gene in the population.

Question 21

Diversity of MHC genes

Answer 21

MHC genes/alleles may have different binding capacities for different peptides
this can increase or decrease your chance of getting a certain disease.

Question 22

Mate selection based on MHC genes

Answer 22

Vertebrate partners may look for mates that have dissimilar MHC genes. can also influence other social behaviors like kinship cooperation, parent-progeny detection and others.

Question 23

Class 1 MHC subtypes

Answer 23

present intracellular antigen peptides
3 major subtypes HLA-A,B,C
present on all cells to check that cells are self and healthy

Question 24

Class 2 MHC subtypes

Answer 24

Present extracellular antigen peptides
3 major subtypes HLA-DP,DQ, DR
more restricted to cells involved in immune response

Question 25

Viral interference in MHC

Answer 25

Viruses shut down MHC class 1 expression because it targets the cells they are in for destruction.

Question 26

The endogenous pathway

Answer 26

Peptides are generated by protease complexes called proteasomes
ubiquitin proteins are used to tag intracellular proteins for degradation
immunoproteasome cleave proteins to pair better with MHCs
peptides are transported from cytosol to rough endoplasmic reticulum via transporter associated w/antigen processing (TAP)
MHC class 1 molecules are in the RER

Question 27

Endogenous pathway chaperone proteins

Answer 27

Calnexin- keeps MHC1 stable until b2 arrives
tapasin,ERp57, Calreticulin- after calnexin dissociates keeps MHC1 stable
ERAP-digests peptides further into correct size
once peptide arrives it binds MHC1 and then leaves the ER