Term
| Step 1 of the recombination process leading to VDJ rearrangement |
|
Definition
| RAG 1 / 2 & HMG proteins bind to the RSS and catalyze synapse formation between a V and a J segment. |
|
|
Term
|
Definition
| RAG 1 / 2 makes a single stranded nick at the 5' border of hepatameric RSSs bordering both the V and the J segments |
|
|
Term
|
Definition
| The Hydroxyl group attacks the phosphate group on the non-coding strand of the V segment... to yield a covalently sealed hairpin coding end and a blunt signal end. |
|
|
Term
| Step4 Ligation of the signal ends |
|
Definition
| the sequence at the signal junction results from the joining of the 2 heptameric regions |
|
|
Term
|
Definition
| cleavage of the hairpin by Artemis generates sites for the P nucleotide addition... opening leave overhangs |
|
|
Term
|
Definition
| Cleavage of the hairpin generates sites for P nucleotide addition by DNA repair enzyme to fill in overhangs |
|
|
Term
|
Definition
| 7 Ligation of light chains V and J regions Ligation of completed segments by DNA Ligase IV and NHEJ proteins |
|
|
Term
|
Definition
| In heavy chain VD and DJ joints only: Exo-nuclease cleavage results in loss of coding nucleotides at joint….can occur on either or both sides of joint |
|
|
Term
|
Definition
| Non-templated nucleotides are added to the coding joint by TdT |
|
|
Term
|
Definition
| Ligation of the heavy chain by DNA ligase IV and NHEJ protein |
|
|
Term
|
Definition
| segments are in the same transcriptional orientation… |
|
|
Term
| Signal and coding joints form |
|
Definition
| formation of signal joint results in circle of intervening DNA into an episome that is lost upon subsequent cell division |
|
|
Term
| Signal and coding joints form |
|
Definition
| The direction of transcripton is now consistent between the recombined V and J segments |
|
|
Term
|
Definition
| Joining Segments are in opposite transcriptional orientation…from nicking and hairpin formation… invert and ligate central fragments note that the signal joint remains in the DNA upstream of the recombined antibody gene |
|
|
Term
| 5 Mechanisms Generate Antibody Diversity in Naïve B Cells |
|
Definition
1. Multiple germ-line gene segments
2. P-region nucleotide addition (P-addition)
3. Exonuclease trimming
4. N-region nucleotide addition (N-addition)
5. Combinatorial association of the same heavy chain with different light chains. |
|
|
Term
| Following antigenic stimulation, B cells can undergo somatic hypermutation, which is___ |
|
Definition
a process in which
individual nucleotides in VJ or VDJ units are replaced with alternatives..Most of the mutations are nucleotide substitutions rather than deletions or insertions. |
|
|
Term
| In the mature B cell the mutations are clustered within the ___allowing them to influence overall affinity for antigen. |
|
Definition
|
|
Term
| Following exposure to antigen, B cells with higher-affinity receptors for antigen will be preferentially selected for survival leading to an increase in antigen affinity of a B cell population.. where does it happen? |
|
Definition
| affinity maturation and occurs in the germinal centers of secondary lymphoid organs. |
|
|
Term
| Constant Region Gene Class Switching.. |
|
Definition
Following antigenic stimulation, the
heavy chain DNA can undergo an
additional rearrangement in which the
VDJ unit can combine with any C gene
segment = class switching or isotype
switching. |
|
|
Term
The recombination process involves
switch region sequences ___ each CH segment except
C delta |
|
Definition
| located 2-3 kb upstream from |
|
|
Term
| Switch regions are composed of ______ |
|
Definition
short
repeats GAGCT and TGGGG. |
|
|
Term
| _____ induces class switching from Cμ to C gamma1 and then to C e. |
|
Definition
|
|
Term
| Expression of Membrane versus Secreted Ig |
|
Definition
| secreted form is 576 a.a. and the membrane bound form is 597 a.a. |
|
|
Term
| The secreted form has a 20 amino acid COOH tail that is largely ____. This is coded for by the S exon in the Cμ gene. |
|
Definition
|
|
Term
| The membrane bound form has a 40 amino acid COOH tail that contains a large ___ stretch that will function to anchor this form to the membrane. |
|
Definition
hydrophobic.......
The hydrophobic stretch is coded for by the M1 and M2 exons of the Cμ gene.The hydrophobic sequence is flanked on either sided by hydrophilic sequences. |
|
|
Term
| _____ determines whether secreted or membrane bound IgM is made. |
|
Definition
|
|
Term
The Cμ1, Cμ2, Cμ3 and Cμ4 exons will be
included in the splicing of membrane
bound and secreted forms of the ___ |
|
Definition
| Cμ heavy chain RNA. (IgM) |
|
|
Term
| Secreted form..The S exon is included as an exon in the spliced mRNA that codes for the ___while the M1 and M2 exons are excluded. |
|
Definition
secreted form
The S exon codes for
the terminal 20 amino acids of the secreted form. |
|
|
Term
The S exon is excluded as an exon in the
spliced mRNA that codes for the
_____ form while the M1 and
M2 exons are included. . |
|
Definition
membrane bound
The M1 and M2 exons code for the terminal 40 amino acids found in the membrane bound form |
|
|
Term
Transcription of a rearranged heavy chain gene in mature B cells produces primary transcripts containing both the ___ __ gene segments which are located fairly close
together. |
|
Definition
|
|
Term
μ versus d heavy chain
expression by a B cell is mediated by ____ versus rather than recombination. |
|
Definition
alternative splicing
Because there is no “switch region sequence” between the segments the entire VDJCμCd
region is transcribed into a single transcript. |
|
|
Term
The presence of both sequences in the primary transcript means that a single B cell can
express ____ of the antibody with the same variable region. |
|
Definition
|
|
Term
The primary heavy chain transcript contains four ___. Sites 1 and 2 are
associated with the Cμ sequences and sites 3 and 4 are associated with Cd sequences. |
|
Definition
|
|
Term
| IgM secreted form is produced if ___ |
|
Definition
| the heavy chain transcript is spliced and then polyadenylated at the Cμ S exon |
|
|
Term
| the membrane bound form of IgM is produced if ____ |
|
Definition
| if the heavy chain transcript is spliced and then polyadenylated at the Cμ M1 and M2 exons |
|
|
Term
| secreted IgD is produced if |
|
Definition
| the heavy chain transcript is spliced and then polyadenylated at the Cd S exon |
|
|
Term
| the membrane bound form of IgD is produced if |
|
Definition
| the heavy chain transcript is spliced and then polyadenylated at the Cd M1 and M2 exons |
|
|
Term
A single B cell can alternate the splicing of the ____so that it
can simultaneously produce all four mRNA splice variants and produce both versions of IgM and
both versions of IgD. |
|
Definition
| primary IgM heavy chain transcripts |
|
|
Term
Ig secreted from a cell or
inserted into the plasma membrane have to navigate the ___ ___
to be packaged into vesicles that mediate their transfer to the plasma membrane where they either
take residence in the plasma membrane or are secreted from the cell. |
|
Definition
|
|
Term
The mRNA coding each chain of the Ig contains a set of sequences that codes for a signal sequence. The
translation of the signal sequence ___
Upon binding this membrane the protein being synthesized is inserted into the rough ER. |
|
Definition
| directs the translation complex to the rough ER membrane. |
|
|
Term
Antibodies are proteins that have a ___of structure. Each monomer is made of two heavy chains and two light chains. Each chain is a
distinct gene product that once expressed has tofold into a functional 3D structure. |
|
Definition
|
|
Term
The four chains then meet up with each other and are assembled into a complete Ig molecule in the
__. |
|
Definition
| ER ...The order of assembly differs for the different Igs. |
|
|
Term
| For IgM a L and H chain assemble in the ER to form ___. |
|
Definition
half molecules and then two half
molecules assembled to form a complete IgM |
|
|
Term
| For IgG ____to create H2L2. |
|
Definition
two H chains assemble and then the
first L chain is added H2L followed by the addition of the second L chain |
|
|
Term
The joining of the various chains is mediated by a minimum of two S-S bonds between heavy chains and a single S-S bond betweeneach L and H. The formation of these bonds
is mediated by the enzyme _____which is present in the ER. |
|
Definition
|
|
Term
Ig molecules are also ____which means
that sugar moieties are added to them. The addition of sugar to the Ig molecule will play a role
in its stability and its ability to recognize costimulatory molecules. |
|
Definition
|
|
Term
The process of glycosylation begins in the __ and
is completed in the ___. |
|
Definition
|
|
Term
___ are enzymes present in the
rough ER that add sugar moieties to proteins. |
|
Definition
|
|
Term
| the Ig molecule in the Golgi = ____ |
|
Definition
its sugar moieties will be modified and
trimmed |
|
|
Term
Ig molecules are transported to their destinations
via ____. |
|
Definition
|
|
Term
Quality control mechanisms within the __ ensure
that only completely assembled, appropriately folded
Ig molecules are exported. |
|
Definition
|
|
Term
The _____ specifically binds to incompletely assembled
antibody molecules. |
|
Definition
| immunoglobulin heavy chain binding protein (BiP) |
|
|
Term
| BiP contains a ___sequence that marks it as an ER resident protein. |
|
Definition
KDEL
(lysine-glutamate aspartateleucine) |
|
|
Term
|
Definition
When it interacts with an incompletely
assembled Ig, it retains it in the ER and prevents its movement to the golgi. |
|
|
Term
If an Ig is retained in the ER, it is given more chances to fold and assemble right. If it doesn't fold right, the Ig molecule is disassembled and the chains are
transported out of the ER into the cytosol where they |
|
Definition
given ubiquitin
ubiquitinated via the addition of Ub a protein “flags” it for
degradation by the proteasome—the cell’s garbage disposal. ub |
|
|
Term
| Transcription of heavy and light chain genes is regulated by ______ |
|
Definition
| promoter and enhancer elements. |
|
|
Term
| Promoter elements are located____ and promote initiation of RNA transcription in a specific direction. Promoter elements are recognized by the basal transcription machinery which includes RNA polymerase II and associated transcription factor. |
|
Definition
| upstream of the transcription start site |
|
|
Term
| WHAT promotes initiation of RNA transcription |
|
Definition
promoter elements, of course.
they see basal transcription machinery which is RNA polymerase II and transcriptions factor |
|
|
Term
| Enhancer elements are located a ___and can modulate the efficiency of transcription by the basal transcription machinery. |
|
Definition
| great distance upstream or downstream from a gene |
|
|
Term
| The promoters are located ________ |
|
Definition
upstream of each V region
of the heavy or light chain genes. |
|
|
Term
The promoters contain sequences ____, plus they contain ___. This allows the
promoters of Ig genes to only be expressed in B cells. |
|
Definition
such as TATA boxes that
direct the binding of RNA polymerase II
...sequences (Oct-2) that confer B-cell specificity |
|
|
Term
| What allows the promoters of Ig genes to only be expressed in B cells. |
|
Definition
| sequences (Oct-2) in the promoter |
|
|
Term
|
Definition
| promote initiation of RNA transcription in a specific direction.. located about 200 bp upstreamfrom transcription initiation site |
|
|
Term
|
Definition
| nucleotide sequences located some distance upstream or downstream from a gene that activate transcription from the promoter sequence in an orientation-independent manner |
|
|
Term
| each Vh and Vl gene segment has a |
|
Definition
promoter located just upstream from the leader sequence
these promoters contain a TATA Box |
|
|
Term
|
Definition
| promote initiation of transcription of neighboring gene in a specific direction. Bind RNA polymerase and direct the formation of the pre-initiations complex. additional promoter are found upstream of all constant regions |
|
|
Term
|
Definition
| Stimulate transcription of associated genes/gene segments when bound by transcription factors ( TFs) can function at variable distance from promoter in either direction/ intronic enhances are between J and C |
|
|
Term
|
Definition
| collection of smaller elements that may each have enhancer functions.. |
|
|
Term
Promoters associated with V
gene segments that have not
been recombined |
|
Definition
are weak promoters and fail to bind
efficiently with RNA
polymerase II. |
|
|
Term
Prior to recombination, the
promoters are located __ |
|
Definition
a really long distance away from their
enhancers |
|
|
Term
Recombination brings the
___ and ___ in
closer proximity, allowing the
enhancer to positively influence transcription efficiency. |
|
Definition
| promoters and enhancers in |
|
|
Term
| TCRs like Igs have a ____ |
|
Definition
variable region for antigen recognition
and a constant region. |
|
|
Term
TCRs exist as membrane bound proteins similar to Ig, but are
not ____ |
|
Definition
|
|
Term
TCR proteins are hetero-dimers constructed from two
polypeptides: |
|
Definition
alpha and beta chains
gamma and delta chains |
|
|
Term
T cells..Produced by rearrangement of
gene segments: |
|
Definition
V and J segments for alpha and gamma genes
V, D, J segments for the beta and delta genes |
|
|
Term
| TCR genes located on ___ chromosomes. |
|
Definition
|
|
Term
The delta genes are located
between the ___ segments of
the alpha genes. A productive
rearrangement of the alpha gene
segments deletes delta segments
which means an alpha/beta
receptor cannot be co-expressed
with a gamma/delta receptor |
|
Definition
|
|
Term
A productive rearrangement of the alpha gene segments deletes delta segments
which means _____ |
|
Definition
an alpha/beta
receptor cannot be co-expressed
with a gamma/delta receptor |
|
|
Term
| T cell: Rearrangement results in |
|
Definition
VJ joining in the alpha chains and
VDJ joining in the beta chains. |
|
|
Term
After transcription, the alpha and beta polypeptides are expressed as products in the __and
and the ___ between them is catalyzed by disulfide isomerases present in the ER. |
|
Definition
|
|
Term
TCRs are only expressed as membrane bound proteins so no differential ___
to produce secreted forms. |
|
Definition
|
|
Term
| Each TCR has a variable domain coded for by either _____ |
|
Definition
VJ segments (alpha chain) or VDJ
segments (beta chain). |
|
|
Term
| Three _____ are found spread throughout the variable domain. |
|
Definition
|
|
Term
| Combinatorial joining of alpha and beta V gene segments generates ___ |
|
Definition
|
|
Term
| Junctional flexibility and N-region nucleotide addition ___. |
|
Definition
|
|
Term
| Preceding the variable domain is a short ____which will direct the synthesis of TCR proteins into the ER. |
|
Definition
|
|
Term
| Following the variable domain is the ___ |
|
Definition
| constant domain, a connecting sequence, a transmembrane region, and a short cytoplasmic tail, coded for by the constant gene segments. |
|
|
Term
| Rearrangement of TCR germ-line DNA occurs in a manner analogous to ___ |
|
Definition
Ig germline
DNA rearrangment. |
|
|
Term
| Mechanism of TCR Gene Rearrangements |
|
Definition
Conserved RSS sequences flank each V, D, and J gene segment.
Recombination between gene segments can only occur between segments that
have different RSS sequences (1 turn versus two turn).
Rag 1 and 2 recognize the RSS sequences and mediate the recombination.
Rag 1 and 2 are differentially regulated in the two cell types.
Chromatin is uniquely configured in the B cells and T cells allowing for access of Ig genes in B cells and TCR genes in T cells. |
|
|
Term
| ____ is uniquely configured in the B cells and T cells allowing for access of Ig genes in B cells and TCR genes in T cells. |
|
Definition
|
|
Term
| Rearrangement of alpha gene segments, recombines out the ___segments . |
|
Definition
|
|
Term
Organization of the beta-chain J and C gene segments into two duplicate clusters means that, if a
nonproductive rearrangement occurs, the thymocyte _____ |
|
Definition
| can attempt a 2nd rearrangement. |
|
|
Term
Once a productive rearrangement occurs for one beta-chain allele, the rearrangement of the other
beta allele ___ |
|
Definition
|
|
Term
Allelic exclusion is not complete for alpha chains which means that both alpha chains can be
productively ___ |
|
Definition
| rearranged and expressed by T cells, although it is rare. |
|
|
Term
| Combinatorial joining of variable region gene segments to different ___generates a large number of random gene combinations for all TCR genes. |
|
Definition
|
|
Term
| Although there are fewer TCR V-alpha and V-beta gene segments as compared to Ig VH and VL segments, this difference is offset by ______ |
|
Definition
| the greater number of J segments in TCR germ-line DNA |
|
|
Term
Alternative joining of D gene segments:
The location of one-turn and two-turn RSSs in TCR beta and delta chain DNA differs from the Ig heavy chain DNA. |
|
Definition
| It is possible for a V-beta gene segment to join directly with a J-beta or a D-beta genesegment, generating a (VJ) beta or a (VDJ) beta unit. |
|
|
Term
It is possible for a V-beta gene segment to join directly with a J-beta or a D-beta genesegment, generating a (VJ) beta or a (VDJ) beta unit.
_____ of delta-chain gene segments generates similar units, generating VJ delta,
VDJ-delta, or even VDDJ-delta units.
These unique joining alternatives create a considerable amount of diversity with a small
amount of genetic material as compared to Ig DNA rearrangements. |
|
Definition
|
|
Term
_____ create diversity with a small
amount of genetic material as compared to Ig DNA rearrangements. |
|
Definition
| unique joining alternatives |
|
|
Term
Joining of gene segments after cutting creates junctional diversity similar to that seen with Ig genes.
This can create non-productive rearrangements, but also increases diversity by allowing for
the ______ |
|
Definition
| insertion of alternative amino acids at each junction. |
|
|
Term
_____leads to the addition of more nucleotides that are
palindromic (P region nucleotide addition). Similar to that seen with Ig gene rearrangements. |
|
Definition
| Variation in endonuclease cleavage |
|
|
Term
| Addition of N-region nucleotides in between junctions is catalyzed by ____—similar to that seen with Ig genes. |
|
Definition
terminal deoxynucleotidyl transferase
TdT |
|
|
Term
| Unlike Ig genes TCR genes do not undergo ______. |
|
Definition
|
|
