Quiz 3 Part 2 Flashcards
Explain the difference between a linear epitope and a discontinuous epitope
A linear epitope usually only occurs on peptides because they are not 3 dimensional. when an epitope is linear, each stalk on the antibody can bind to THREE linear epitopes each
A discontinuous epitope happens on PROTEINS (or even 2 polypeptides) because they are three dimensional. Usually 3 epitopes cannot be bound at the same time as in the case of continuous
What cells contain fragmented Ig genes??
ALL CELLS EXCEPT B CELLS
only the B cell can form a functional Ig gene, but every cell possesses inactive Ig genes that cannot be transcribed
The assembly of functional Ig genes only occurs in…..
B CELLS
What is the term for inherited gene segments
germline form (inactive and can only be activated by B cells)
Are heavy chains and light chains assembled together or individually?
heavy chains and light chains are assembled in the same B cell, but are done independently of each other.
What happens after the heavy chains and light chains are assembled in the same B cell?
they associated with each other and are expressed on the B cell surface
Do V, D, and J segments rearrange?
yes
Do C (constant) regions and L segments rearrange?
no
What do V D and J stand for
What do C and L stand for
V=variable segments
D=diversity segments
J=joining segments
C=constant segments
L=leader segments
Which is longer — heavy chain or light chain?
heavy chain
What is the purpose of the leader peptide and where is it located
to bring the antibody to the correct location.
They are next to every variable segment
What is the term for the joining of the V,D, and J segments
SOMATIC RECOMBINATION
Is somatic recombination random
yes
How many recombinations does the light chain have?
only one — VJ joining
How many recombination events exist for the heavy chain
2———
D and J segments form first
then V segment joins DJ to form VDJ
the light chain can either be…..
kappa or lambda
how many possible heavy chain combinations are there
5520
How many possible light chain combinations are there
Lkappa=175
Llambda=120
How many possible variations are there of association of the heavy chain with the light chain and what is the term for this
1.6 million variations
COMBINATORIAL DIVERSIFICATION
What else can cause more diversity (besides association of heavy chain with light chain)
JUNCTIONAL diversity
What event takes place after recombination?
splicing to get rid of the RSS’s (recombination signal sequences) between segments
The selection of gene fragments depends on…..
RSS’s (recombination signal sequences)
–sequences found between the fragments
What actually cuts the RSS’s and splices the fragments together?
DNA recombinases
where are DNA recombinases made?
in the B cell and NOWHERE ELSE
What are RAG1 and RAG2 and where are they expressed?
RAG1 and RAG2 are recombination-activating genes that are ONLY expressed by small lymphocytes
What exactly do RAG1 and RAG2 do? (RAG complex)
the RAG complex promotes recombination between segments which creates a CODING JOINT
What is a coding joint?
the ultimate goal: VDJ/DJ
How many nucleotides are directly next to every “V” “D” or “J”?
7
describe the structure of heavy chain genes
“V”, 7 nucleotides, 23 nucloetides, 9 nucleotides, RSS, 9, 12 ,7, D, 7, 12, 9, RSS, 9, 23 ,7, J
there cannot be 2 “12’s” or 2 “23’s” in the same module
What is the name of the specific DNA recombinase that brings VDJ/VJ together (creating a coding joint)
RAG1 and RAG2
Where is the spacer located
between 7 and 9
spacer is either 12 or 23
What forms a signal joint?
a signal joint is formed from everything that gets spliced out of the gene
Are DNA recombinases present in all cells?
DNA recombinases are present in all nucleated cells, however, only small lymphocytes express RAG1 and RAG2 to initiate the process of cutting and splicing RSS’S (recombination signal sequences). Nothing can happen without RAG1 and RAG2
When the RAG complex promotes recombination between segments, what does this form?
a coding joint (ie: VJ, VDJ)
Where does the RAG complex cut?
the RAG complex makes a clean cut across the heptamer (7mer)
What happens after RAG makes a clean cut across the heptamer?
Repair genes come in and paste the coding joint together, and repairs the signal joint to form a circle that diffuses away
The RAG complex introduces ______ diversity
junctional
HOW does the RAG complex introduce junctional diversity
through the addition of new nucleotides that were not in the original germline DNA sequence
What is the term for the new nucleotides that the RAG complex adds?
P and N nucleotides
Where in particular does the RAG complex promote junctional diversity
HV3
Which enzyme actually adds the random bases?
TdT (terminal deoxynucleotide transferase)
Explain the entire process of JUNCTIONAL DIVERSITY
RAG makes a blunt cut across the heptamer to yield “DNA hairpins”. (still double stranded at this point)
then, the RAG complex opens the hairpins by nicking one strand of the DNA which generates P nucleotides
TdT comes in and adds random N-nucleotides.
These random bases search for base pairing
they pair and the UNPAIRED bases are removed by an EXONUCLEASE
The gaps are then filled in by DNA synthesis and ligation to form the CODING JOINT
Explain the difference between P nucleotides and N nucleotides
P nucleotides are the ones that were generated when RAG cut the heptamer, and opened the “DNA hairpin” by nicking a strand of DNA
N nucleotides are the random ones that were added by TdT (terminal deoxynucleotide transferase)
What can occur if the net amount of bases added is NOT a multiple of 3?
frameshift mutations
Between which segments is RAG creating this junctional diversity?
D and J segments (variable region)
What id Combinatorial Diversity?
different light chains can associate with the same heavy chain
What are naive B cells?
those that have not yet encountered an antigen
