Term
What is the part of the antibody that varies greatly from antibody to antibody? |
|
Definition
the antigen binding region (VARIABLE region) |
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|
Term
Which part of the antibody has 5 different classes? |
|
Definition
constant region (C region) |
|
|
Term
How are T cell receptors different from B cell receptors? |
|
Definition
Their T cell receptors cannot just recognize an antigen by itself, the antigen has to be presented to it via MHC molecules |
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Term
Describe the structure of an MHC molecule. |
|
Definition
transmembrane glycoproteins encoded by major histocompatibility complex. Have a cleft in the extracellular face to bind peptides. very polymorphic. |
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Term
When a peptide is presented to a T cell, what does the T cell actually recognize? |
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Definition
They recognize both the peptide and the MHC molecule to which it is bound. |
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|
Term
The secreted form of a B cell receptor? |
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Definition
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|
Term
What are the three classes of constant regions? |
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Definition
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|
Term
Total strength of an interaction |
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Definition
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|
Term
What are two types of light chains? |
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Definition
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|
Term
strength of an interaction between a single antigen-binding site and its antigen |
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Definition
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|
Term
What is the kappa: lambda ratio in mice, humans, and in cattle? |
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Definition
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|
Term
If you have a distortion in your kappa: lambda ratio, what could that mean? |
|
Definition
it could mean that there is a type of B cell that is becoming a tumor by increased proliferating |
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|
Term
Which part of the antibody determines the effector function? |
|
Definition
structure of the heavy chain |
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Term
What are the five types of heavy chain classes? |
|
Definition
alpha, delta, epsilon, mu, gamma |
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|
Term
Which is the most abundant immunoglobin? |
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Definition
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|
Term
Where in the heavy chain are the functional properties of the different classes conferred? |
|
Definition
carboxy-terminal side...since it is not in association with the light chain |
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Term
How similar are the B cell receptors to their antibody? |
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Definition
the same EXCEPT for the small region on the carboxy terminus of the heavy chain C region....in the B cell receptor, the carboxy terminus is a hydrophobic amino acid sequence that anchors the molecule into the membrane....in the antibody it is a hydrophilic that allows for secretion |
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|
Term
How many Ig domains are on the light and heavy chains? |
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Definition
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|
Term
What can you expect to find at the aminio terminus of the heavy and light chains? |
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Definition
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|
Term
how many beta sheets are in each V or C domain? |
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Definition
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|
Term
What is the main difference in structure between the variable and constant domains? |
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Definition
V domain is larger contains extra beta strands called C' and C'' |
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|
Term
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Definition
cuts antibody on the amino terminal side of the disulfide bonds that link the two heavy chains[image] |
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Term
What are the Fab and Fc fragments? |
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Definition
when an antibody is cleaved by papain, it cleaves the antibody into three distinct products. The Fab portions are the two top parts that bind antigens and the Fc is the bottom part that was crystallized first |
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|
Term
What does the Fc portion interact with? |
|
Definition
interacts with effector molecules and cells and differs between heavy chain isotopes |
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|
Term
How does pepsin cleave antibodies? |
|
Definition
cuts on the carboxyl side of the disulfide bonds...and also cleaves the heavy chain into several small fragments[image] |
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|
Term
how are light chains attached to the heavy chains? |
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Definition
through noncovalent interactions |
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|
Term
What is the trunk of the Y fragment called? |
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Definition
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|
Term
What are hypervariable regions? |
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Definition
regions of extreme variability in the antibody, as opposed to diversity being distributed evenly throughout. |
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Term
What are the names for the 3 hypervariable regions? Where can they be found? |
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Definition
HV1, HV2, and HV3...in the light AND heavy chains |
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|
Term
What do you call the in-between regions of hypervariability? |
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Definition
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|
Term
What are the names of the framework regions? Where can you find them? |
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Definition
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|
Term
What is the function of the framework regions? |
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Definition
provide structural framework of the immunoglobulin domain |
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Term
What is an antigen-binding site/antibody-combining site, and where can it be found? |
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Definition
also termed " complementarity-determining regions" or CDRs. Basically Hyper-variability groups formed together. You can find them on the surface receptor of the antibody. |
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|
Term
What is an example of combinatorial diversity? |
|
Definition
the body is able to generate different combinaitons of heavy chain and light chain regions |
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Term
Antibodies bind ligands whose surfaces are __________ to that of the antigen -binding site. |
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Definition
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|
Term
What happens if the antigens are the same size or larger than the antibodies? |
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Definition
the interface between the antigen and antibody is often an extended surface that involves all the CDRs and, in some cases, part of the framework region. |
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|
Term
What happens if the epitope of a pathogen is a protein and not a polysaccharide? |
|
Definition
Amino acids from different parts of the polypeptide are brought together via protein folding : this is called conformational //discontinuous epitopes |
|
|
Term
|
Definition
composed of a single segment of a polypeptide chain |
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|
Term
What types of fluids can antibodies be found in? |
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Definition
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|
Term
What is the difference between mIg and sIg? |
|
Definition
mIg is membrane bound and sIg is secreted Ig |
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|
Term
Which part of the antibody recruits other cells to come get rid of the antigen? |
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Definition
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|
Term
can an immunoglobulin have both a kappa and lambda light chain? |
|
Definition
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|
Term
Which species have antibodies that consist solely of the heavy chains? |
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Definition
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|
Term
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Definition
Foreign substance capable of eliciting a humoral (B cell) and/or cell-mediated T cell response |
|
|
Term
|
Definition
Foreign substance capable of binding specifically to B Cell Receptors (Abs) or TCRs. Domain on Ag which actually binds Ab |
|
|
Term
|
Definition
Domain on Ag which actually binds Ab |
|
|
Term
|
Definition
small molecules Not immunogenic alone (needs carrier) Antigenic (can bind Abs once formed) Can serve as known epitopes |
|
|
Term
|
Definition
ability to induce a humoral and/or cell mediated immune response |
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|
Term
|
Definition
ability to combine specifically with the final products of an immunogenic response, i.e. antibodies. |
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|
Term
Can a hapten illicit a humoral response? |
|
Definition
they cannot because they are too small. However, if they are coupled to a protein, the antibodies can then bind to the unbound hapten |
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|
Term
How are T cell receptors different from cell receptors? |
|
Definition
a T cell receptor has only one antigen-binding site, whereas a B-cell receptor has two, and T cell receptors are never secreted, whereas Igs are secreted as antibodies |
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|
Term
What are the two different polypeptide chains on the T cell receptors ? How are the two chains linked? |
|
Definition
TCR(alpha) and TCR(beta)...linked by disulfide bonds |
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|
Term
A T cell receptor is homologous to which part of an immunoglobulin? |
|
Definition
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|
Term
What type of epitope does a T cell receptor recognize? |
|
Definition
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|
Term
What are the four subunits of MHC Class I? |
|
Definition
alpha 1-3 and beta2 -microglobulin |
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|
Term
Which subunits of the MHC class I resemble immunoglobulin the most? |
|
Definition
the alpha 3 and b2 microglobulin |
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|
Term
Which domains form the peptide-binding domain? |
|
Definition
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|
Term
For MHC Class I molecules: are the alpha and beta subunits coded for in the MHC? |
|
Definition
only the alpha is---beta microglobulin is coded for on chromosome 15 |
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|
Term
Are the MHC class II molecules subunits coded for within the MHC? |
|
Definition
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|
Term
What are the major differences between the MHC class I and II peptide-binding clefts? |
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Definition
The ends of the cleft are left more open in the MHC class II molecules as opposed to the class I molecules. In both cases, the peptides are sandwiched between the two alpha helicies, where the T cell interacts with both the fragment and the MHC molecule |
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|
Term
What is unique about the peptide binding site of MHC molecules? |
|
Definition
it can stably bind to many peptides. The binding of the peptie actually makes the MHC molecule stable. |
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|
Term
How do short peptides stay in the binding site of a MHC molecule? |
|
Definition
there are free amino and carboxyl terminal ends that bind to the peptides |
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|
Term
How long should the peptides be that bind to MHC class I molecules? |
|
Definition
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|
Term
|
Definition
peptide residues that anchor the peptide into the groove of a MHC molecule |
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|
Term
What happens when MHC molecules are not bound to a peptide? |
|
Definition
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|
Term
Which class of MHC molecules can bind longer peptides? |
|
Definition
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|
Term
What's the smallest length of peptide that can bind ot MHC class II? |
|
Definition
13 amino acids long...or longer |
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|
Term
Which MHC class has the open binding site ? |
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Definition
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|
Term
Which binding pockets of MHC molecules (I or II) can accommodate more variability? |
|
Definition
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|
Term
What is the invariant chain? |
|
Definition
protein that lays across the peptide binding groove of the nascent MHC class II molecule during its synthesis |
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|
Term
What types of peptides bind to MHC class I? |
|
Definition
present endogenous peptides, usually virus encoded//tumor antigens |
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|
Term
What types of peptides bind to MHC class II? |
|
Definition
extracellular proteins...uptake thorugh phagocytosis |
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|
Term
What types of residues mesh well with the MHC class I molecules? |
|
Definition
aromatic//hydrophobic molecules |
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|
Term
What types of molecules are polymorphic and polygenic? |
|
Definition
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|
Term
What types of MHC and CD+ molecules do cytotoxic T cells recognize? |
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Definition
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|
Term
When assessing the hypervariability of the binding region of an antibody, which sequence is encoded for by the (v) variable region. |
|
Definition
1-101, includes CDR1 and CDR2 (and a little from CDR3) |
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|
Term
Which part of the hypervariable region is encoded for by the J (joining) region? |
|
Definition
The last 13 amino acids, CDR3 |
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|
Term
How many genes of variability are there on the light chain of an antibody? |
|
Definition
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|
Term
How many genes of variability are there on the heavy chain of an antibody? |
|
Definition
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|
Term
What is the total number of Ab specificities in an individual? |
|
Definition
|
|
Term
|
Definition
There is a separate gene for each different immunoglobulin chain and the antibody repertoire is largely inherited |
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|
Term
Somatic Diversification Theory |
|
Definition
Observed repertoire is generated from a limited number of inherited V- region sequences that undergo alteration within B- cells during the individual’s lifetime |
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|
Term
In somatic recombination, what is the order of recombination of variable genes ? |
|
Definition
light chain: V-J, VJ-C heavy: D-J, V-DJ, VDJ-C |
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|
Term
What is a leader protein (L) ? |
|
Definition
V gene segment is preceded by an exon encoding a leader peptide (L), which directs the protein into the cell’s secretory pathways and is then cleaved. |
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|
Term
|
Definition
recombination signal sequences that guide DNA rearrangements |
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|
Term
How many bases long is a RSS? What is that called? |
|
Definition
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|
Term
What is a spacer? where can it be found? |
|
Definition
can be found within an RSS. 12-23 base pairs that is a nonconserved region that separates the heptamer and the nonamer |
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|
Term
Somatic recombination usually occurs on the (same/different) chromosome. |
|
Definition
|
|
Term
|
Definition
A gene segment flanked by an RSS with a 12bp spacer can only be joined to RSS flanked by 23bp spacer |
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|
Term
In a heavy chain, can the V region be directly joined with the J gene? |
|
Definition
|
|
Term
|
Definition
the ends of heptamer sequences are joined head - to head fashion form |
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|
Term
What happens when the joining segments involved in VDJ recombination are in the same orientation ? |
|
Definition
the signal joint is then contained within the extrachromosomal DNA, which is lost from the genome after the cell divides |
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|
Term
What happens when the joining segments involved in VDJ recombination are in the opposite orientation ? |
|
Definition
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|
Term
Which enzymes are involved in somatic recombination? |
|
Definition
-lymphocyte specific recombinases -ubiquitous DNA modifiers -Rag1 and 2 |
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|
Term
Does recombination occur at the beginning or end of the heptamer sequences? |
|
Definition
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|
Term
|
Definition
TdT base additions lead to junctional diversity by addition of P (palindromic) and N (non-coding) nucleotide sequences such that an imprecise coding joint is generated |
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|
Term
What's the difference between combinatorial and junctional diversity? |
|
Definition
combinatorial: Multiple different copies of each type of gene segment- different combinations of the gene segments can be used in different rearrangement events
Junctional diversity: introduced at the joints between different gene segments as a result of addition and subtraction of nucleotides by the recombination process |
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|
Term
Which type of antibody diversity is mainly responsible for the diversity at the variable region? |
|
Definition
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|
Term
What are the enzymatic steps in RAG-dependent VDJ rearrangement of coding joints? |
|
Definition
1. RAG 1 and 2 bind. cleavage occurs 2. ku70:ku80 binds the broken DNA ends 3. DNA-PK and artemis open the complex and open the hairpin 4. TdT processes the DNA ends, randomly adds and releases nucleotides into site. 5. DNA ligase ligates strands together. |
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|
Term
Which enzyme cleaves the DNA hairpin during somatic recombination? |
|
Definition
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|
Term
Which enzymes is involved in junctional diversity in somatic recombinase? |
|
Definition
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|
Term
Which enzyme within somatic recombination opens DNA hairpins, and generates palindromic P-nucelotides? |
|
Definition
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|
Term
P-nucleotides vs. N-nucleotides |
|
Definition
P: short palindromic sequences at the end of the coding sequences N: the non-template added nucleotides (added by Tdt) |
|
|
Term
does heavy chain or light chain undergo recombination first? |
|
Definition
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|
Term
What secondary structure does framework regions have? |
|
Definition
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|
Term
where does somatic HYPERmutation occur in the lymph nodes? |
|
Definition
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|
Term
which enzyme initiates somatic HYPERmutation in the lymph nodes? |
|
Definition
activation induced cytidine deaminase (AID) |
|
|
Term
|
Definition
germinal center B cells in the lymph nodes |
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|
Term
What activates AID to act? |
|
Definition
a signal from the T cells |
|
|
Term
what is somatic hypermutation? |
|
Definition
Introduction of mutations that change one to few amino acids in the immunoglobulin |
|
|
Term
What is the function of AID? |
|
Definition
helps to produce B cells that are extremely closely related, but there are a few minor differences that allows them to range in specificity and antigen affinity |
|
|
Term
|
Definition
modification of re-arranged variable region, Introduction of sequences derived from V gene segment pseudogenes |
|
|
Term
Which Ig isotypes can be mIg and sIg |
|
Definition
All Ig isotypes can be mIg or sIg |
|
|
Term
Which two isotypes are usually expressed together? |
|
Definition
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|
Term
Which antibody is the first one that is secreted? |
|
Definition
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|
Term
What is the structure of IgM? |
|
Definition
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|
Term
Which antibody is the most predominant in serum? |
|
Definition
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|
Term
which istotype can be transported across the placenta? |
|
Definition
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|
Term
which antibodies are always monomeric? |
|
Definition
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|
Term
Which antibody is expressed in mucosa, milk, and saliva? |
|
Definition
IgA present in mucosa, milk and saliva |
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|
Term
Which antibody can be either monomeric or dimeric? |
|
Definition
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|
Term
Which antibody sensitizes mast cells? |
|
Definition
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|
Term
Which antibody is the most short lived? |
|
Definition
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|
Term
What is another name for an Ig class switch? How does it work? |
|
Definition
isotype switch. the inital mu havey chain is replaced by another heavy chain type. activated only after the T helper cell presents the antigen. The B cells undergo hypermutation and either receive a beneficial or bad mutation that either increases or decreases affinity for the anitgen. |
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|
Term
What does it mean if IgM is expressed in higher levels? |
|
Definition
there is an acute infection |
|
|
Term
what initiates class switching? |
|
Definition
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|
Term
In class switching, what is happening on the non-coding template while the DNA is being transcribed through a switch region? |
|
Definition
the non-coding template forms loops |
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|
Term
What is the role of switch regions (S) in class switching? |
|
Definition
they guide switching..since they are repetitve regions, the Polymerase can stall at these regions, allowing these regions to be substrates for AID |
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|
Term
Describe the class switching mechanism. |
|
Definition
RNA polymerase transcribes along the switch regions. a loop from the non-template DNA strand beings. The AID, UNG, and APE1 proteins cuts a double stranded break. |
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|
Term
on an antibody, is the variable region for an antigen at the N-terminus or C-termiuns? |
|
Definition
N-terminus is where the variable region is, the C-terminus is where the constant region is |
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|
Term
how many identical antigen binding sites does an antibody have? |
|
Definition
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|
Term
Are TCR and BCR encoded by the same genes? |
|
Definition
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|
Term
Is a TCR or BCR a heterodimer? |
|
Definition
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|
Term
What is the side chain of a TCR? |
|
Definition
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|
Term
What are MHC antigens of mice called? |
|
Definition
|
|
Term
What types of proteins do gamma:delta T cells bind? |
|
Definition
-mycobacterial lipid antigen -phosphorylated ligands **it is not restricted by classical MHC I or II |
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|
Term
In light chain construction, what method of post-transcriptional modification is used to bring the C and V regions together? And to remove the Lto V region? |
|
Definition
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|
Term
In heavy chain construction, is the leader sequence removed before or after translation? |
|
Definition
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|
Term
What is the number of V gene pairs possible? |
|
Definition
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|
Term
For a 23 base spacer, what is the order in the RSS? |
|
Definition
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|
Term
for a 12 base spacer, what is the order in the RSS? |
|
Definition
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|
Term
when do secondary modifications of Igs occur? (i.e. somatic hypermutation, gene conversion, and class switching) |
|
Definition
after first contact with an antigen |
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|
Term
On which chain of the TCR has a diversity region? |
|
Definition
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|
Term
On antibodies, how many exons on the heavy chain code for whether or not it gets secreted or not? |
|
Definition
2---both are transcribed, one is cut out by splicing BEFORE translation |
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|
Term
Which antibodies can form polymers? How? |
|
Definition
IgM and IgA can form polymers by interacting with the J chain..monomers become cross linked by disulfide bonds |
|
|
Term
|
Definition
15kDA polypeptide that links to cysteine of Mu and Alpha |
|
|
Term
how many binding sites does pentameric IgM have? What effect does this have on avidity ? |
|
Definition
10 binding sites. increases avidity |
|
|
Term
Do TCRs undergo secondary modification? |
|
Definition
|
|
Term
|
Definition
jawed vertebrates, which split off from vertebrates 500 million years ago. |
|
|
Term
|
Definition
surviving species of hagfish that have antibody like proteins that DO NOT HAVE JAWS |
|
|
Term
|
Definition
fibrinogen-related proteins, mollusk superfamily protein for immunity |
|
|
Term
|
Definition
down syndrome cell adhesion molecule member of the Ig superfamily....fat body cells |
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|
Term
Which cartilaginous fishes have RAG-dependent adaptive immunity? Which chain types of T cells do they have? |
|
Definition
sharks, rays, and skates, they have a:b and g:d T cells |
|
|
Term
Where were MHC class I and II molecules first found? |
|
Definition
|
|
Term
What is the total diversity for Igs? |
|
Definition
|
|
Term
What is the total diversity for a:b T cell receptors? |
|
Definition
|
|
Term
WHAT IS ACTIVATION INDUCED CYTIDINE DEAMINASE? |
|
Definition
the (AID) protein that does somatic hypermutation in Chickens |
|
|
Term
What types of viruses block peptides entry into the ER to evade immune system,? |
|
Definition
Herpes, Human cytogalovirus, bovine herpes virus |
|
|
Term
Which virus does retention of MHC class I molecules in ER to evade immune system detection |
|
Definition
adenovirus, HCMV, murine cytogalovirus |
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|
Term
which type of virus degrades the MHC class I molecule to evade detection of immune system? |
|
Definition
HCMV, murine gamma herpes virus |
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|
Term
Which virus binds MHC class I at the cell surface? |
|
Definition
|
|
Term
|
Definition
if peptides are too long, and they can't be trimmed in the ER, before binding to MHC class I, they have to associate with ERAAP |
|
|
Term
|
Definition
adalimumab antibody to TNF alpha, used to treat arthritis |
|
|
Term
name two primary binding assays |
|
Definition
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|
Term
what are three secondary binding tests? |
|
Definition
agglutination, precipitation, complement fixation CFT |
|
|
Term
What's the main difference between immunohistochemistry and ELISA? |
|
Definition
in immunohistochemistry , the colored products are insoluble and precipitate at the site at which they are formed. |
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|