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Immuno exam 2
exam 2
166
Immunology
Undergraduate 3
10/09/2016

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Term
What is the part of the antibody that varies greatly from antibody to antibody?
Definition
the antigen binding region (VARIABLE region)
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
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.
Term
When a peptide is presented to a T cell, what does the T cell actually recognize?
Definition
They recognize both the peptide and the MHC molecule to which it is bound.
Term
The secreted form of a B cell receptor?
Definition
antibody
Term
What are the three classes of constant regions?
Definition
IgM, IgA, IgE, IgD, IgG
Term
Total strength of an interaction
Definition
avidity
Term
What are two types of light chains?
Definition
kappa and lambda
Term
strength of an interaction between a single antigen-binding site and its antigen
Definition
affinity
Term
What is the kappa: lambda ratio in mice, humans, and in cattle?
Definition
20:1, 2:1, 1:20
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
Term
Which part of the antibody determines the effector function?
Definition
structure of the heavy chain
Term
What are the five types of heavy chain classes?
Definition
alpha, delta, epsilon, mu, gamma
Term
Which is the most abundant immunoglobin?
Definition
IgG
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
Term
How similar are the B cell receptors to their antibody?
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
Term
How many Ig domains are on the light and heavy chains?
Definition
light: 2 heavy: 4
Term
What can you expect to find at the aminio terminus of the heavy and light chains?
Definition
variable regions.
Term
how many beta sheets are in each V or C domain?
Definition
two
Term
What is the main difference in structure between the variable and constant domains?
Definition
V domain is larger contains extra beta strands called C' and C''
Term
papain
Definition
cuts antibody on the amino terminal side of the disulfide bonds that link the two heavy chains[image]
Term
What are the Fab and Fc fragments?
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
Term
What does the Fc portion interact with?
Definition
interacts with effector molecules and cells and differs between heavy chain isotopes
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]
Term
how are light chains attached to the heavy chains?
Definition
through noncovalent interactions
Term
What is the trunk of the Y fragment called?
Definition
Fc
Term
What are hypervariable regions?
Definition
regions of extreme variability in the antibody, as opposed to diversity being distributed evenly throughout.
Term
What are the names for the 3 hypervariable regions? Where can they be found?
Definition
HV1, HV2, and HV3...in the light AND heavy chains
Term
What do you call the in-between regions of hypervariability?
Definition
framework
Term
What are the names of the framework regions? Where can you find them?
Definition
Fr1, Fr2, FR3, and FR4
Term
What is the function of the framework regions?
Definition
provide structural framework of the immunoglobulin domain
Term
What is an antigen-binding site/antibody-combining site, and where can it be found?
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.
Term
What is an example of combinatorial diversity?
Definition
the body is able to generate different combinaitons of heavy chain and light chain regions
Term
Antibodies bind ligands whose surfaces are __________ to that of the antigen -binding site.
Definition
complementary
Term
What happens if the antigens are the same size or larger than the antibodies?
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.
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
linear epitopes
Definition
composed of a single segment of a polypeptide chain
Term
What types of fluids can antibodies be found in?
Definition
mucus, serum,
Term
What is the difference between mIg and sIg?
Definition
mIg is membrane bound and sIg is secreted Ig
Term
Which part of the antibody recruits other cells to come get rid of the antigen?
Definition
effector (bottom half
Term
can an immunoglobulin have both a kappa and lambda light chain?
Definition
no, its one or the other
Term
Which species have antibodies that consist solely of the heavy chains?
Definition
camelid and shark
Term
Immunogen
Definition
Foreign substance capable of eliciting a humoral (B cell) and/or cell-mediated T cell response
Term
Antigen
Definition
Foreign substance capable of binding
specifically to B Cell Receptors (Abs) or TCRs. Domain on Ag which actually binds Ab
Term
Epitope
Definition
Domain on Ag which actually binds Ab
Term
Haptens
Definition
small molecules
Not immunogenic alone (needs carrier) Antigenic (can bind Abs once formed) Can serve as known epitopes
Term
Immunogenicity
Definition
ability to induce a humoral and/or cell mediated immune response
Term
Antigenicity
Definition
ability to combine specifically with the final products of an immunogenic response, i.e. antibodies.
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
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
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
Term
A T cell receptor is homologous to which part of an immunoglobulin?
Definition
Fab
Term
What type of epitope does a T cell receptor recognize?
Definition
continuous sequences
Term
What are the four subunits of MHC Class I?
Definition
alpha 1-3 and beta2 -microglobulin
Term
Which subunits of the MHC class I resemble immunoglobulin the most?
Definition
the alpha 3 and b2 microglobulin
Term
Which domains form the peptide-binding domain?
Definition
alpha 1- 2
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
Term
Are the MHC class II molecules subunits coded for within the MHC?
Definition
yes both are
Term
What are the major differences between the MHC class I and II peptide-binding clefts?
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
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.
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
Term
How long should the peptides be that bind to MHC class I molecules?
Definition
8-10 amino acids long
Term
anchor residues
Definition
peptide residues that anchor the peptide into the groove of a MHC molecule
Term
What happens when MHC molecules are not bound to a peptide?
Definition
they are unstable
Term
Which class of MHC molecules can bind longer peptides?
Definition
MHC class II
Term
What's the smallest length of peptide that can bind ot MHC class II?
Definition
13 amino acids long...or longer
Term
Which MHC class has the open binding site ?
Definition
MHC class II
Term
Which binding pockets of MHC molecules (I or II) can accommodate more variability?
Definition
II
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
Term
What types of peptides bind to MHC class I?
Definition
present endogenous peptides, usually virus encoded//tumor antigens
Term
What types of peptides bind to MHC class II?
Definition
extracellular proteins...uptake thorugh phagocytosis
Term
What types of residues mesh well with the MHC class I molecules?
Definition
aromatic//hydrophobic molecules
Term
What types of molecules are polymorphic and polygenic?
Definition
MHC class molecules
Term
What types of MHC and CD+ molecules do cytotoxic T cells recognize?
Definition
MHC class I and CD8
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)
Term
Which part of the hypervariable region is encoded for by the J (joining) region?
Definition
The last 13 amino acids, CDR3
Term
How many genes of variability are there on the light chain of an antibody?
Definition
2, V and J
Term
How many genes of variability are there on the heavy chain of an antibody?
Definition
there are 3, V, D, and J
Term
What is the total number of Ab specificities in an individual?
Definition
10^11
Term
Germline Theory
Definition
There is a separate gene for each different immunoglobulin chain and the antibody repertoire is largely inherited
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
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
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.
Term
What are RSSs?
Definition
recombination signal sequences that guide DNA rearrangements
Term
How many bases long is a RSS? What is that called?
Definition
7 --heptamer
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
Term
Somatic recombination usually occurs on the (same/different) chromosome.
Definition
same
Term
What is the 12/23 rule?
Definition
A gene segment flanked by an RSS with a 12bp spacer can only be joined to RSS flanked by 23bp spacer
Term
In a heavy chain, can the V region be directly joined with the J gene?
Definition
no
Term
What is a signal joint?
Definition
the ends of heptamer sequences are joined head - to head fashion form
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
Term
What happens when the joining segments involved in VDJ recombination are in the opposite orientation ?
Definition
inversion occurs
Term
Which enzymes are involved in somatic recombination?
Definition
-lymphocyte specific recombinases
-ubiquitous DNA modifiers
-Rag1 and 2
Term
Does recombination occur at the beginning or end of the heptamer sequences?
Definition
ends of heptamer RSS
Term
TdT
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
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
Term
Which type of antibody diversity is mainly responsible for the diversity at the variable region?
Definition
combinatorial diversity
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.
Term
Which enzyme cleaves the DNA hairpin during somatic recombination?
Definition
DNA PK (kinase)
Term
Which enzymes is involved in junctional diversity in somatic recombinase?
Definition
tDT
Term
Which enzyme within somatic recombination opens DNA hairpins, and generates palindromic P-nucelotides?
Definition
Artemis:DNA PK complex
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
heavy
Term
What secondary structure does framework regions have?
Definition
beta sheets
Term
where does somatic HYPERmutation occur in the lymph nodes?
Definition
germinal centers
Term
which enzyme initiates somatic HYPERmutation in the lymph nodes?
Definition
activation induced cytidine deaminase (AID)
Term
Where is AID expressed?
Definition
germinal center B cells in the lymph nodes
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
What is gene conversion?
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
IgM and IgD
Term
Which antibody is the first one that is secreted?
Definition
IgM
Term
What is the structure of IgM?
Definition
pentameric
Term
Which antibody is the most predominant in serum?
Definition
IgG
Term
which istotype can be transported across the placenta?
Definition
IgG
Term
which antibodies are always monomeric?
Definition
IgG and IgE
Term
Which antibody is expressed in mucosa, milk, and saliva?
Definition
IgA present in mucosa, milk and saliva
Term
Which antibody can be either monomeric or dimeric?
Definition
IgA
Term
Which antibody sensitizes mast cells?
Definition
IgE
Term
Which antibody is the most short lived?
Definition
IgE
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.
Term
What does it mean if IgM is expressed in higher levels?
Definition
there is an acute infection
Term
what initiates class switching?
Definition
cytokines
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
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
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.
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
Term
how many identical antigen binding sites does an antibody have?
Definition
2
Term
Are TCR and BCR encoded by the same genes?
Definition
no
Term
Is a TCR or BCR a heterodimer?
Definition
both are!
Term
What is the side chain of a TCR?
Definition
carbohydrate
Term
What are MHC antigens of mice called?
Definition
H-2 antigens
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
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
splicing
Term
In heavy chain construction, is the leader sequence removed before or after translation?
Definition
after
Term
What is the number of V gene pairs possible?
Definition
10x10^6
Term
For a 23 base spacer, what is the order in the RSS?
Definition
heptamer-23-nonamer
Term
for a 12 base spacer, what is the order in the RSS?
Definition
nonamer - 12 - heptamer
Term
when do secondary modifications of Igs occur? (i.e. somatic hypermutation, gene conversion, and class switching)
Definition
after first contact with an antigen
Term
On which chain of the TCR has a diversity region?
Definition
beta
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
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
What is the J chain?
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
no
Term
gnathostomes
Definition
jawed vertebrates, which split off from vertebrates 500 million years ago.
Term
agnathans
Definition
surviving species of hagfish that have antibody like proteins that DO NOT HAVE JAWS
Term
What is FREP?
Definition
fibrinogen-related proteins, mollusk superfamily protein for immunity
Term
What is Dscam?
Definition
down syndrome cell adhesion molecule
member of the Ig superfamily....fat body cells
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
cartilagious fishes
Term
What is the total diversity for Igs?
Definition
5x10^13
Term
What is the total diversity for a:b T cell receptors?
Definition
10^18
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
Term
which type of virus degrades the MHC class I molecule to evade detection of immune system?
Definition
HCMV, murine gamma herpes virus
Term
Which virus binds MHC class I at the cell surface?
Definition
Murine CMV
Term
What is ERAAP?
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
Humira
Definition
adalimumab antibody to TNF alpha, used to treat arthritis
Term
name two primary binding assays
Definition
radioimmunoassay, ELISA
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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