Antibody & TCR Structure

Question 1

What are the three main roles of Antibodies (Ab)

Answer 1

Neutralization, Opsonization, and Complement activation

Question 2

What is the general Ab structure

Answer 2

-2 heavy chains and 2 light chains
-held together by disulfide
-Both the light and heavy change bind the same antigen

Question 3

What is the name of Ab that are membrane attached

Answer 3

B-cell receptor (BCR)

Question 4

Describe the Ig domain of an Ab

Answer 4

Where the heavy (4 domains) and the light (2 domains) chain are

Question 5

What does each Ig domain make?

Answer 5

-beta sandwich (2 beta-sheets cause folding)
-the folding is stabilized by disulfide

Question 6

What does B-mercaptoethanol (BME) do and what effects does it have on western blot

Answer 6

-reducing agent that break disulfides
-No antibody binding (Western blot)

Question 7

What are the two ways to do biochemical studies of Ab with Ab-fragments

Answer 7

-Use enzymes to cut them
-papain (hinge region)
-pepsin (past disulfide)

Question 8

What is the Fc

Answer 8

-Fragment crystallizable
-easy to crystallize
-doesn’t contain V domain
-only differs between classes

Question 9

What is the Fab

Answer 9

-has antigen binding site
-small, less flexible
-differs between Ab’s (b/c site that binds antigens)

Question 10

What is the most common method for biochemical studies (binding)

Answer 10

papain (breaks at the disulfide bond)

Question 11

How are Ab able to form immune complexes

Answer 11

Ab are flexible at the hinge

Question 12

How are antigen bind sites formed

Answer 12

HV (hypervariable region) are in loops that will form the antigen-binding site

Question 13

What are five forces that aid i nAb-antigen binding

Answer 13

Electrostatic forces, Hydrogen bonds, Van der Waals forces, Hydrophobic forces, and Cation-pi interactions

Question 14

What is the structure of TCR (T-cell Receptor)

Answer 14

-membrane-bound
-2-chains (disulfide)
-4 Ig domains
-main form alpha and beta

Question 15

What is the main difference between Ab and TCR

Answer 15

-Ab can directly bind antigen (solvent exposed)
-TCR bind peptides bound to MHC (can be buried) can only bind peptides

Question 16

What is the difference between the type I MHC and the type II MHC strucutre

Answer 16

-MHC I: 1 transmembrane domain
-MHC II: 2 transmembrane domain

Question 17

How does MHC type I bind and MHC type II bind differ

Answer 17

-type I: only bind peptides of a specific length
-type II: take peptide of variable lengths

Question 18

What is an anchor AA

Answer 18

-MHC-bound peptides contain this amino acid
-play a key role in peptide binding

Question 19

How does TCR recognize MHC’s

Answer 19

variable loops recognize peptide in cleft

Question 20

What does TCR bind specifically

Answer 20

binds both peptide and MHC

Question 21

What other T cell proteins recognize the MHC

Answer 21

-CD4+: T helper cells
-CD8+: cytotoxic T cells
-called co-receptors

Question 22

The co-receptor CD4+ binds to which MHC

Answer 22

Type II: Phagocytosis

Question 23

The co-receptor CD8+ binds to which MHC

Answer 23

Type I: virus

Question 24

What is the role of CD4/CD8 for TCR

Answer 24

increases TCR binding affinity ~100 fold (important for development and recognition)

Question 25

Why do RBC's not express MHC's

Answer 25

-no DNA (no MHC I) not phagocytic (no MHC II)

Question 26

What are the four main ways diversity is created

Answer 26

1) combinatorial diversity 2) junctional diversity 3) heavy & light combinatorial diversity 4) somatic hypermutation

Question 27

What is the light chain V-gene segment made from

Answer 27

V and J segment (V(D)J Recombination)

Question 28

What is the heavy chain V-gene segment made from

Answer 28

V-, D-, and J-gene segment (V(D)J Recombination)

Question 29

What determines which Ig is made

Answer 29

It is determined by the heavy chain C-region

Question 30

What is the general process of light/heavy chain generation

Answer 30

-germline DNA -somatic recombination leads to D-J rearranged DNA joined -somatic recombination leads to V-J or V-DJ joined rearranged DNA (heavy chain) -transcription leads to primary transcript RNA -Splicing leads to mRNA -translation leads to polypeptide chain

Question 31

What is RSS

Answer 31

-recombination signal sequence -how to know if gene is Ab gene

Question 32

What is the 12/23 rule

Answer 32

-spacer contains 12- or 23- nucleotides -recombination fuses a 23-RSS to a 12-RSS

Question 33

What are the five main players of V(D)J

Answer 33

-RAG1/2 -Ku70/Ku80 -DNA-PK: Artemis -TdT -DNA ligase IV:CRCC4

Question 34

What does RAG1/2 do in V(D)J recombination

Answer 34

-RAG1/2 brings to RSS sites together -Recombination Activating Gene (RAG) -forms a dimer -Recognize 23/12 bring them together and cut

Question 35

What does Ku70/Ku80, DNA_PK: Artemis, and DNA ligase IV:XRCC4 do in V(D)J recombination

Answer 35

-binds the double break ends -Recruits repair enzymes(DNA-PK: Artemis and DNA ligase IV:XRCC4) -DNA-PK: Artemis on hairpin end -DNA ligase IV:XRCC4 on other end

Question 36

What are the two ways of cleavage of RSSs

Answer 36

Coding joints and Signal Joints

Question 37

Explain the signal joint

Answer 37

-w/out hairpin and extra chromosomal material -Ku70:Ku80 binds DNA ends -DNA ligase IV:XRCC4 ligates DNA ends -precise signal joint

Question 38

Explain coding joint

Answer 38

-Ku70:Ku80 binds DNA ends -DNA-PK: Artemis opens hairpin (nicks it) -TdT processes DNA ends (adds random nt's) -DNA ligase IV:XRCC4 ligates DNA ends -imprecise coding joint

Question 39

How is Junctional diversity created (P)

Answer 39

-P-nucleotides -Palindromic nucleotides added by repair -added when Artemis cleaves at a non-RAG site

Question 40

How is Junctional diversity created (N)

Answer 40

-N-nucleotides -non-coding nucleotides -added by TdT -totally random

Question 41

What is TCR formation similar to

Answer 41

MHC formation with V-, J-, and C-gene segments for alpha and beta (D-gene segments)