Antibody & TCR Structure Flashcards
Quiz 3
What are the three main roles of Antibodies (Ab)
Neutralization, Opsonization, and Complement activation
What is the general Ab structure
-2 heavy chains and 2 light chains
-held together by disulfide
-Both the light and heavy change bind the same antigen
What is the name of Ab that are membrane attached
B-cell receptor (BCR)
Describe the Ig domain of an Ab
Where the heavy (4 domains) and the light (2 domains) chain are
What does each Ig domain make?
-beta sandwich (2 beta-sheets cause folding)
-the folding is stabilized by disulfide
What does B-mercaptoethanol (BME) do and what effects does it have on western blot
-reducing agent that break disulfides
-No antibody binding (Western blot)
What are the two ways to do biochemical studies of Ab with Ab-fragments
-Use enzymes to cut them
-papain (hinge region)
-pepsin (past disulfide)
What is the Fc
-Fragment crystallizable
-easy to crystallize
-doesn’t contain V domain
-only differs between classes
What is the Fab
-has antigen binding site
-small, less flexible
-differs between Ab’s (b/c site that binds antigens)
What is the most common method for biochemical studies (binding)
papain (breaks at the disulfide bond)
How are Ab able to form immune complexes
Ab are flexible at the hinge
How are antigen bind sites formed
HV (hypervariable region) are in loops that will form the antigen-binding site
What are five forces that aid i nAb-antigen binding
Electrostatic forces, Hydrogen bonds, Van der Waals forces, Hydrophobic forces, and Cation-pi interactions
What is the structure of TCR (T-cell Receptor)
-membrane-bound
-2-chains (disulfide)
-4 Ig domains
-main form alpha and beta
What is the main difference between Ab and TCR
-Ab can directly bind antigen (solvent exposed)
-TCR bind peptides bound to MHC (can be buried) can only bind peptides
What is the difference between the type I MHC and the type II MHC strucutre
-MHC I: 1 transmembrane domain
-MHC II: 2 transmembrane domain
How does MHC type I bind and MHC type II bind differ
-type I: only bind peptides of a specific length
-type II: take peptide of variable lengths
What is an anchor AA
-MHC-bound peptides contain this amino acid
-play a key role in peptide binding
How does TCR recognize MHC’s
variable loops recognize peptide in cleft
What does TCR bind specifically
binds both peptide and MHC
What other T cell proteins recognize the MHC
-CD4+: T helper cells
-CD8+: cytotoxic T cells
-called co-receptors
The co-receptor CD4+ binds to which MHC
Type II: Phagocytosis
The co-receptor CD8+ binds to which MHC
Type I: virus
What is the role of CD4/CD8 for TCR
increases TCR binding affinity ~100 fold (important for development and recognition)
Why do RBC’s not express MHC’s
-no DNA (no MHC I)
not phagocytic (no MHC II)
What are the four main ways diversity is created
1) combinatorial diversity
2) junctional diversity
3) heavy & light combinatorial diversity
4) somatic hypermutation
What is the light chain V-gene segment made from
V and J segment (V(D)J Recombination)
What is the heavy chain V-gene segment made from
V-, D-, and J-gene segment (V(D)J Recombination)
What determines which Ig is made
It is determined by the heavy chain C-region
What is the general process of light/heavy chain generation
-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
What is RSS
-recombination signal sequence
-how to know if gene is Ab gene
What is the 12/23 rule
-spacer contains 12- or 23- nucleotides
-recombination fuses a 23-RSS to a 12-RSS
What are the five main players of V(D)J
-RAG1/2
-Ku70/Ku80
-DNA-PK: Artemis
-TdT
-DNA ligase IV:CRCC4
What does RAG1/2 do in V(D)J recombination
-RAG1/2 brings to RSS sites together
-Recombination Activating Gene (RAG)
-forms a dimer
-Recognize 23/12 bring them together and cut
What does Ku70/Ku80, DNA_PK: Artemis, and DNA ligase IV:XRCC4 do in V(D)J recombination
-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
What are the two ways of cleavage of RSSs
Coding joints and Signal Joints
Explain the signal joint
-w/out hairpin and extra chromosomal material
-Ku70:Ku80 binds DNA ends
-DNA ligase IV:XRCC4 ligates DNA ends
-precise signal joint
Explain coding joint
-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
How is Junctional diversity created (P)
-P-nucleotides
-Palindromic nucleotides added by repair
-added when Artemis cleaves at a non-RAG site
How is Junctional diversity created (N)
-N-nucleotides
-non-coding nucleotides
-added by TdT
-totally random
What is TCR formation similar to
MHC formation with V-, J-, and C-gene segments for alpha and beta (D-gene segments)
