Part 5 Flashcards
how many BCRs are in the B cell repetoire
10^11-13
how many genes make up the human genome
20-25,000
how many TCRs are in the T cell repetoire
10^18
what percentage of DNA is coding DNA
2%
what is germ line theory
each antibody-producing cell has genes coding for all possible antibody specificities, but expresses only the one stimulated by antigen;
there is a separate gene for each different immunoglobulin chain and that the antibody repertoire is largely inherited.
what is somatic diversity theory
antibody-producing cells contain only a few genes, which produce antibody diversity by mutation; There is a limited amount of genes that we inherit that have function.
how are antibodies generated genetically
Antibodies are generated by gene segments (light or heavy) that generate the hypervariable regions (which are residues).
These regions make up the 3 types of CDRs.
what are the three gene segments of antibodies
Variable (V)
Diversity (D)
Joining (J)
All three encode for the hypervariable residues.
what is the bottom part of the antibody encoded by
the Constant (C) segment
what segments are the light chains made of
V and D
what segments are the heavy chains made of
V, D, J
what is somatic recombination
a process for generating antibody and TCR diversity during mammalian B and T cell development. It involves the excision and recombination of multiple germline V, J, and D gene segments, which are combined randomly in the immunoglobulin and TCR loci.
why is somatic recombination important
Antibodies must have enough antigen-binding diversity to recognize every possible pathogen (many V regions) while maintaining the biological effectiveness of their C regions
what is the recombination signal sequence
allows the right segments to combine correctly
3 parts
what is a heptamer
7 nucleotide sequence; GTGTCAC (consensus: most commonly found there)
what is a spacer region
either 12 or 23 nucleotides.
How many rotations the DNA takes.
what is a nonamer
9 nucleotide sequence; TGTTTTTGG.
what is the 12/23 rule
requires that V(D)J recombination only occurs between recombination signals with 12 and 23 base pair spacers
what is the rule for light chain somatic recombination
23 and 12 must come together in order for V segment and J segment to come together (12/23 rule) for orientation purposes
what is the rule for heavy chains somatic recombination
the D segment must have the opposite of the V and J to come together, still 12/23 rule
what cdr has high variability and why
CDR 3 is prone to high variability because it is partially made with the V, D, and J.
what can v and j do
J can combine to any V region at random
what will happen if V and J encode the same direction (5’ to 3’)
they will line up together. This will create a loop with the V2L2 and VnLn.
After recombination, this loop is excised from the chromosome.
what will happen if V and J encode in opposite orientations
the RSS regions are coiled
After recombination, the coiled region is retained but in an inverted orientation
what do both orientation processes form
coding joints
what are coding joints
the rearranged variable regions of antigen receptor genes
what are recombination activating genes (RAG)
types 1 and 2
Endonucleases (cleave DNA)
Only expressed in developing lymphocytes.
Without RAG gene, there would be no third line of immunity (T or B cells).
Genes for RAG are unique
SCID mice have mutated RAG genes, they are severely immunocompromised.
what is the function of RAG
initiate recombination of the variable (V), diversity (D), and joining (J) genes by cleaving, allowing for the generation of T and B cells with a broad antigen recognition specificity
what are Ku70 and 80
These are repair proteins.
Bind broken DNA, which form rings
They come in the form of heterodimers
what is DNA-protein kinase (DNA-Pk)
plays a critical role in DNA double-strand break (DSB) repair and in V(D)J recombination. DNA-PK also plays a very important role in triggering apoptosis in response to severe DNA damage or critically shortened telomeres.
what is Artemis
Has nuclease activity
Can be a endo or exonuclease
Cut within or at the ends of DNA strands
bound with DNA-PK
what is TdT
An enzyme that adds nucleotides without using a template.
Similar to telomerase.
what is DNA ligase
binds end of split DNA, forming a coding joint of VDJ
what is the order of proteins in somatic recombination
RAG1:2
Ku70:80 heterodimers
DNA-PK:Artemis
TdT
Ligase
what is the excised DNA is somatic recombo called
signal joint
what is the full somatic recombo process
RAG 1:2 binds to the RSS and cleaves the RSSs (arrows)
For coding joints:
Ku70:80 binds DNA ends
Brings in DNA-Pk and Artemis which open a hairpin.
TdT process DNA ends by adding nucleotides.
DNA ligase which creates variability and ligates at DNA ends.
Imprecise coding joint
what are P nucleotides
nucleotides that are generated from artemis
what are N nucleotides
nucleotides generated from TdT
what chains in T cells go through similar recombo
alpha and beta
what is the total diversity of immunoglobulin
5x10^13
what is the total diversity if alpha and beta TCRs
10^18
what is the main function of having constant regions of antibodies and T cells
for effector functions
what is the difference between light and heavy chain segments
Light and heavy chains have constant regions, but heavy chains have a longer segment.
how many subclasses does IgG have
4
how many IgA subclasses
2
what immunoglobulins do not bind to the complement
A
D
E
G4
what binds an antibody to the a macrophage
FcReceptor
What receptors are found on Mast cells
Fc(IgE)Receptors
what Ig do Mast cells have
Mast cell then has antibodies (IgE) on surface, which cause secretion of IL1, 3, 4, 5, and 6, chemokine, PAF, leukotriene, histamine
All are triggers for inflammation and allergic reactions.
describe the relationship of FcRs and placenta
There are FcRs on the outside of the placenta. This will allow antibodies (IgG) to be bound and transferred across the placental barrier.
what percentage of IgG make up of bloodstream
IgG make up between 75-85% of all soluble antibodies in bloodstream
what make Igs unique
Number of sugars and their locations.
Numbers of disulfide bonds and their locations.
The length of the hinge (allows flexibility and binding at different angles).
Number of constant regions
properties of IgA
secreted in saliva, mucus, gastric juices, tears
Only secreted in dimers
what do IgM and D have in common
first expressed when infection is present
what happens after VDJ is encoded for
all genes for IgRs are expressed.
All antibodies are made at the same time.
After it goes into mRNA, the RNA is spliced for the specific antibody
where is VDJ expressed
variable region
what does MC code for
the membrane coding for the tails that allow the antibody to be attached to a membrane
what does SC code for
SC is secretion coding, therefore it is a soluble antibody
what is special about IgM
forms a pentamer
if one part of pentamer is bound, the full unit is bound
what is primary generation
V region generation (light and heavy chains)
what is class switching
can start off with one antibody but switch to another
IgM to IgG
IgD to IgG2
This is variability
what is somatic hypermutations
a programmed process of mutation affecting the variable regions of immunoglobulin genes. Unlike germline mutation, SHM affects only an organism’s individual immune cells, and the mutations are not transmitted to the organism’s offspring
when do somatic hypermutations occur
occurs in the presence of an antigen
where do somatic hypermutation occur in the body
The germinal centers of peripheral lymphoid tissues are the sites where somatic hypermutation, positive selection and differentiation of B cells with high-affinity receptors occur. Germinal centers are the only places in the body where antigen is retained for months or years in an extracellular location.
what is AID
an enzyme that is activated when the B cell is actively proliferating
what is the role of AID
introduces mutation by modifying cytidine into uridine
AID binds to single stranded DNA and attached to cytidine
what does MSH2/6 do
switches A:T, which ends in somatic hypermutations
what is UNG
base-excision repair, switches uridine to abasic, and leaves behind ribose sugar and phosphate residues.
what does REV1 do after UNG
mutations at C:G; SHM
what does APE1 do
a repair mechanism protein that removes sugar and phosphate, and leaves to a missing nucleotide open nick DNA.
what happens when APE1 has a single strand nick
gene conversion
what happens when APE1 has a double strand break
class switch recombo
what do mutations allow for the CDRs/antibody
allow better binding of the antibody to the epitope
Each time an epitope is exposed, the B cell/antibody is better at binding to the epitope each time due to better mutations.
where do mutations specifically occur
CDR1-3
