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
|
|
Term
| What are the three classes of constant regions? |
|
Definition
|
|
Term
| Total strength of an interaction |
|
Definition
|
|
Term
| What are two types of light chains? |
|
Definition
|
|
Term
| strength of an interaction between a single antigen-binding site and its antigen |
|
Definition
|
|
Term
| What is the kappa: lambda ratio in mice, humans, and in cattle? |
|
Definition
|
|
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
|
|
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
|
|
Term
| What can you expect to find at the aminio terminus of the heavy and light chains? |
|
Definition
|
|
Term
| how many beta sheets are in each V or C domain? |
|
Definition
|
|
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
|
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
|
|
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
|
|
Term
| What are the names of the framework regions? Where can you find them? |
|
Definition
|
|
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
|
|
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
|
Definition
| composed of a single segment of a polypeptide chain |
|
|
Term
| What types of fluids can antibodies be found in? |
|
Definition
|
|
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
|
|
Term
| can an immunoglobulin have both a kappa and lambda light chain? |
|
Definition
|
|
Term
| Which species have antibodies that consist solely of the heavy chains? |
|
Definition
|
|
Term
|
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 |
|
|
Term
|
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
|
|
Term
| What type of epitope does a T cell receptor recognize? |
|
Definition
|
|
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
|
|
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
|
|
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
|
|
Term
|
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
|
|
Term
| Which class of MHC molecules can bind longer peptides? |
|
Definition
|
|
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
|
|
Term
| Which binding pockets of MHC molecules (I or II) can accommodate more variability? |
|
Definition
|
|
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
|
|
Term
| What types of MHC and CD+ molecules do cytotoxic T cells recognize? |
|
Definition
|
|
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
|
|
Term
| How many genes of variability are there on the heavy chain of an antibody? |
|
Definition
|
|
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 |
|
|
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
|
Definition
| recombination signal sequences that guide DNA rearrangements |
|
|
Term
| How many bases long is a RSS? What is that called? |
|
Definition
|
|
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
|
|
Term
|
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
|
|
Term
|
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
|
|
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
|
|
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 |
|
|
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
|
|
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
|
|
Term
| Which enzymes is involved in junctional diversity in somatic recombinase? |
|
Definition
|
|
Term
| Which enzyme within somatic recombination opens DNA hairpins, and generates palindromic P-nucelotides? |
|
Definition
|
|
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
|
|
Term
| What secondary structure does framework regions have? |
|
Definition
|
|
Term
| where does somatic HYPERmutation occur in the lymph nodes? |
|
Definition
|
|
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 |
|
|
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
|
|
Term
| Which antibody is the first one that is secreted? |
|
Definition
|
|
Term
| What is the structure of IgM? |
|
Definition
|
|
Term
| Which antibody is the most predominant in serum? |
|
Definition
|
|
Term
| which istotype can be transported across the placenta? |
|
Definition
|
|
Term
| which antibodies are always monomeric? |
|
Definition
|
|
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
|
|
Term
| Which antibody sensitizes mast cells? |
|
Definition
|
|
Term
| Which antibody is the most short lived? |
|
Definition
|
|
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
|
|
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
|
|
Term
| Are TCR and BCR encoded by the same genes? |
|
Definition
|
|
Term
| Is a TCR or BCR a heterodimer? |
|
Definition
|
|
Term
| What is the side chain of a TCR? |
|
Definition
|
|
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 |
|
|
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
|
|
Term
| In heavy chain construction, is the leader sequence removed before or after translation? |
|
Definition
|
|
Term
| What is the number of V gene pairs possible? |
|
Definition
|
|
Term
| For a 23 base spacer, what is the order in the RSS? |
|
Definition
|
|
Term
| for a 12 base spacer, what is the order in the RSS? |
|
Definition
|
|
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
|
|
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
|
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 |
|
|
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 |
|
|
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
|
|
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
|
|
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. |
|
|
