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Immunology Exam 2
Immunology
150
Microbiology
Undergraduate 4
10/04/2015

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Cards

Term
What are the four main classes of Pattern Recognition Receptors?
Definition
1. Free receptors in the serum
2. Membrane bound phagocytic receptors
3. Membrane bound signaling receptors
4. Cytoplasmic signaling receptors
Term
What are the two types of DC's (Dendritic cells) and what are their roles?
Definition
1. Conventional DC (cDC) - ultimate APC, activates T cells, part of adaptive immunity, phagocytosis
2. Plasmacytoid DC (pDC) - Typer 1 Interferon producers, initial viral control
Term
What are the different types of Membrane Bound Phagocytic Receptors?
Definition
1. Dectin-1
2. Mannose Receptor
3. Scavenger Receptors
4. Lipid and Complement Receptors
Term
What does Dectin-1 (membrane bound phagocytic rceptor) recognize?
Definition
recognizes glucans on pathogens
Term
What does Mannose Receptor (membrane bound phagocytic receptor) recognize?
Definition
recognizes mannose residues on pathogens
Term
What are the different types of scavenger receptors (membrane bound phagocytic receptors)?
Definition
SR-AI
SR-AII
MARCO (macrophage receptor with collagenous structure) Class A and B
Term
What are the lipid and complement receptors of the membrane bound phagocytic receptors?
Definition
Lipid - CD36
Complement - CR1, CR3
Term
What are the mechanisms of destroying pathogens?
Definition
- Acidification - bacteriostatic or bactericidal
- Toxic Oxygen-derived products - peroxides, superoxides
- Toxic nitrogen oxides
- Antimicrobial peptides
- Enzymes
- Competitors (e.g. Lactofferin - removes Fe from the environment)
Term
What are Membrane bound signaling receptors
Definition
G protein coupled receptors
Term
What does fMet-Leu-Phe receptor (fMLP)(a type of membrane bound signaling receptor) recognize?
Definition
N-formylmethionine of bacteria
Term
How do neutrophils produce toxins to kill pathogens?
Definition
1. fMLP activates Rac2
2. Rac2 mediates binding of NADPH oxidase to phagolysosome, which froms O2 ions
3. O2 ions get converted to H2O2 (peroxide) by superoxide dismutase (SOD)
4. Microbial hypochlorite and hydroxyl radicals are also formed to kill pathogen
5. Acidification caused by potassium ion influx release granule proteases
Term
What are the 3 roles of inflammation in combating infection?
Definition
1. Deliver additional effector molecules and cells from the blood to sites of infection
2. Induce local blood clotting
3. Promote repair of damaged tissues
Term
What are the 3 families of receptors important for cytokine and chemokine production?
Definition
1. Toll-like Receptors (TLRs)
2. NOD-like receptors
3. Rig-I-like Helicases
Term
Briefly describe Toll-like Receptors
Definition
- recognize PAMPs (viral, bacterial, fungal, parasitic)
- single pass transmembrane proteins (18-25 copies of extracellular leucine rich repeats)
- activated upon dimerization
- Toll-IR-1 reeptor (TIR) domain in cytoplasmic tail
Term
What are the types of TLRs? Location and what do they recognize?
Definition
TLR-1,2,6 - surface; recognize diacyl and triacyl lipopeptides (bacteria)
TLR-5 - surface; momomeric flagellum from degraded fully assembled flagella (bacteria)
TLR-4 - surface; recognizes lipopolysaccharide (LPS)
TLR-3 - endosomal; recognizes double stranded RNA
TLR-7 - endosomal; recognizes single stranded RNA from RNA virus phagocytosed
TLR-9 - endosomal; recognizes unmethylated CpG DNA (viral and bacteria)
Term
What does TLR-4 recognize?
Definition
LPS (lipopolysaccharides)
Term
What is the accessory protein that TLR-4 uses to bind LPS?
Definition
MD-2
Term
What is the difference between direct and indirect binding with TLR-4?
Definition
Direct binding - LPS binds to TLR-4 molecule
Indirect binding - LPS binds to MD-2 (which is bound to TLR-4)
Term
What are the two additional accessory proteins, besides MD-2 that TLR-4 needs to bind LPS?
Definition
1. LPS binding protein - will bind LPS in blood and extracellular fluid
2. CD14 - LPS-binding protein transfers bound LPS to CD14 expressed on the surface of phagocytes. CD14 acts together with MD-2 to bind LPS to TLR-4.
Term
What does the dimerization of TLR molecules induce?
Definition
It allows the TIR domains to come together and allow for binding to TLR adaptor molecules.
Term
What are the four types of adaptor molecules?
Definition
1. Myeloid differentiation factor 88 (MyD88)
2. MyD88 adaptor like (MAL)
3. TIR domain containing adaptor inducting IFN-B (TRIF)
4. TRIF-related adaptor molecule (TRAM)
Term
Which TLR molecules interact with which adaptor molecules?
Definition
TLR-5,7,9 - interact only with MyD88
TLR-3 - interacts only with TRIF
TLR-2 (TLR-1/2 and TLR-2/6) heterodimers - interact with MyD88/MAL
TLR-4 homodimers - can utilize either MyD88/MAL or TRIF/TRAM
Term
What are the two domains that MyD88 has?
Definition
1. A TIR domain which interacts with the TIR of the TLR
2. A death domain - recruits and activates the serine-threonine kinases: IL-1 Receptor Associated Kinase-4 (IRAK4) and IRAK1 via their death domains
Term
What does the IRAK complex do?
Definition
It recruits the E3 ubiquitinase TRAF6 and then the E2 ubiquitinase TRICA1.
Term
What do TRAF6/TRICA1 do?
Definition
They generate polyubiquitin chains on TRAF6 and NEMO/IKK creating a scaffold. The binding to TRAF6/TRICA1 scaffold activates the serine threonine kinase TAK1.
Term
What are the two important actions of TAK1?
Definition
1. Activates specific MAP kinases including c-Jun terminal kinase (JNK) and p38
2. Activates the NFkB transition factor pathway by phosporilating NEMO (or IKK) complex which then results in IkB phosphorylation.

Phoso-IkB releases NFkB into the nucleus where cytokine genes are turned on
Term
Which adapter molecule do TLR-7,8,9 signal through? What does this activate?
Definition
Through MyD88
It activates Interferon Regulatory Factor
(IRF) genes important for type I IFN production (this is important for rapid control of viruses).
Term
Which adapter molecule does TLR-3 signal through?
Definition
TRIF
Term
What does NOD stand for in NOD like receptor?
Definition
Nucleotide-binding oligimerization domain - it is a centrally located domain on this receptor.
Term
What do NOD1 and NOD2 sense?
Definition
NOD1 senses y-glutamyl diaminopimelic acid (iE-DAP - breakdown product of bacterial peptidoglycan)
NOD2 senses muramyl dipeptide found in most bacterial peptidoglycan
Term
What are the steps of NLR (NOD like receptor) activation and signaling?
Definition
1. NOD1 or 2 recognize their ligands
2. NOD dimerization recruits, via the NOD's CARD domain (RIPK2 - Receptor interacting serine threonine kinase 2)
3. NOD-RIPK2 interactions are mediated via the CARD domain
4. RIPK2 kinase activity then activates TAK1 and then the NFkB pathway
5. TAK1 now phosphorylated by RIPK2, activates NEMO (IKK)
6. NEMO now phosphorylates IkB causing its degradation
7. NFkB now translocates into the nucleus to turn on genes
Term
What other domains, besides CARD, can NLRs use?
Definition
NLRPs (pyrin domain)
Term
How do NLRPs signal?
Definition
1. When cells are damaged, cytoplasmic proteins dissociate from NALP3 due to K+ efflux
2. This allows for NALP3 dimerization and association of adapter protein PYCARD via Pyrin domains
3. This PYCARD recruitment aggregates procapsase 1 where it then is proteolytically cleaved to be active
4. Activated capsase-1 then cleaves pro-IL-1B and pro-IL-18 into their inflammatory active state to be secreted by the cell
Term
What do RIG-I-like helicases detect?
Definition
Cytoplasmic viral RNAs
Term
What domains do RLHs contain?
Definition
An RNA helicase like domain
2 CARD domains
Term
What are the two RLHs we will discuss?
Definition
RIG-1 - Retinoic acid inducible gene 1
MDA5 - Melanoma differentiate associated 5
Term
What is the adapter protein of RIG-1 and MDA5?
Definition
MAVS - mitochondrial anti-viral signaling protein
Term
What are the steps of the signaling pathway for RLHs?
Definition
1. Binding of single-stranded RNA by RIG-1 and double-stranded RNA by MDA5 causes their CARD domains to interact with the CARD domains on MAVS.
2. Activated MAVS recruits TRAF6 which phosphorylates TBK1 (Tank binding kinase 1)
3. Activated TBK1 then turns on IRF transcription factors which turn on gene transcription
4. Activated MAVS can also recruit death domain containing signaling proteins, FADD (Fas associated protein with death domain) and TRADD (Tumor necrosis factor receptor Type 1 associated death domain protein)
5. FADD and TRADD activate NEMO
6. NEMO then results in IkB phosphorylation and degradation and activation of NFkB
Term
What are the cytokine families?
Definition
IL-1 family
Hematopoetin family
TNF (Tumor necrosis factor) family
Type 1 interferons
IL-12 family
Term
Describe IL-1 family of cytokines
Definition
11 family members
Most cleaved
signal via NFkB pathway
Term
Describe Hematopoetin family of cytokines
Definition
Growth and differentiation
cytokines IL-6 and GM-CSF
Term
Describe TNF family of cytokines
Definition
17 members
most are transmembrane proteins
limited action
Term
Describe Type 1 interferon cytokines
Definition
Important in initial control of viruses
Produced at high levels downstream of TLR-7 and 9
Term
Describe IL-12 family of cytokines
Definition
Cell mediated immunity
Term
Which cell produces Type 1 interferons?
Definition
plasmacytoid DCs (pDC)
Term
What are the actions of Type 1 interferons?
Definition
- Induce direct antiviral activity in cells expressing IFN receptors
- Increase antigen processing and presentation via the MHC Class I pathway
- Increase APC functionality and maturation
- Activate NK cells
Term
What are the two groups of chemokines? Functions?
Definition
-CC Chemokines (with 2 adjacent residues) - promote monocyte migration
-CXC Chemokines (seperated by an additional amino acid) - promote neutrophil migration (and T cell migration)
Term
What are the three families of Adhesion molecules?
Definition
1. Selectins
2. Integrins
3. Intercellular adhesion molecules (ICAMs)
Term
How do Adhesion molecules work in the immune response?
Definition
-Inflammation causes the induction of adhesion molecules on endothelium and circulating cells (P-selectin and E-selectin are expressed first)
- Leukocytes begin to roll, rolling adhesion begins with receptor binding chemokines
- Tight binding occurs as a result of LFA-1 (leukocyte integrin) binding to ICAM on endothelial cell
- Extravasation occurs - crossing the endothelium, and diapadesis by interaction of CD31 (PECAM) on endothelial cell and leukocyte
- chemokine gradient bound to extracellular matrix then guides the cell to the site where the cell is needed
Term
What are the two families of NK cell recpetors?
Definition
1. KIRS (killer cell immunoglobin-like receptors)
2. KLRS (killer cell lectin-like receptors)
Term
What three gene clusters encode the NK cell receptors?
Definition
-extended leukocyte receptor complex
-leukocyte receptor complex
-NK receptor complex
Term
What are the two functions of the NK Cell receptors?
Definition
-activation
-inhibition
Term
What do activating NK cell receptors use to signal?
Definition
Adapter molecules
Term
Do inhibiting NK cell receptors use adapter molecules to signal?
Definition
No
Term
What is DAP12?
Definition
An adapter molecule that activating NK cells use to signal. It contains ITAM (immuno tirosine activation motif)
Term
What is ITIM?
Definition
It stands for immuno tyrosine inhibition motif, it is in the cytoplasmic tail of the inhibiting NK cell receptors.
Term
Do all activating NK cell receptors need to use adapter molecules to signal?
Definition
No, some can do it directly.
-NCRs (natural cytotoxicity receptors)
-NKp30, 44 and 46 are immunoglobulin-like receptors
-NKGD is a c-type lectin
Term
Which ligands does NKG2D bind to?
Definition
-MIC-A
-MIC-B
-RAET1
Term
What can RAET1 bind?
Definition
cytomegalovairus proteins
Term
What are the different types of NK cells based on?
Definition
-surface receptors
-ability to attack self
Term
What do NK cell activating receptors detect?
Definition
SIL (stress induced signals)
Term
What do NK cell inhibiting receptors detect?
Definition
Recognize self MHC class 1
Term
When there is no infection present, when will a licensed NK cell become activated?
Definition
-if the target is missing self
-if the target is stress induced
Term
When there is no infection present, when will an unlicensed NK cell become activated?
Definition
It will not be activated
Term
When there is an infection (inflammation), when will licensed and unlicensed NK cells become activated?
Definition
All cells can or are given permission to attack self
Term
what are the five classes of immunoglobins?
Definition
IgM
IgD
IgG
IgA
IgE
Term
Which chains make up IgG?
Definition
2 polypeptide chanins: Heavy (L) and Light (L)
Each antibody is made up of 2 H and 2 L chains
Term
How many antigen binding sites does each antibody have?
Definition
2 identical sites
Term
Avidity
Definition
The combinatorial binding gives increased strength of binding
Term
Affinity
Definition
The strength of interaction between 1 binding site to antigen
Term
How many immunoglobin domains do the H and L chains have?
Definition
H chain - has 4 domains
L chain - has 2 domains
Term
Which part of the H and L chains is the most variable?
Definition
Variable or V region (the amino terminus)
Term
Which part of the Ig is felixble?
Definition
The hinge region - links Fc and Fab portions of the Ig
Term
How are the V and C domains shaped?
Definition
Beta sheets making a barrel shape
Term
How many beta sheets make up the V and C domains?
Definition
V domain - 8 beta sheets
C domain - 7 beta sheets
Term
Which part of the variable region is the most diverse? How many per V domain?
Definition
Hypervariable region (HV)
There are 3 per V domain
Term
Which is the most variable HV range?
Definition
HV3
Term
What is CDR? WHat is it made up of?
Definition
Complementary determining region
Made of 6 HV loops
Term
What are the different interactions between Ig-Antigen?
Definition
electrostatic
hydrogen bonds
Van der Waals
hydrophobic
Term
TCR is similar to which region of the Ig?
Definition
The Fab region
Term
How many chains make up the TCR?
Definition
Two - alpha and beta (linked by a disulfide bond)
Term
What are the minority of T cells made up of?
Definition
gamma and delta chains
Term
Which region of TCRs anchors it to the membrane?
Definition
The hydrophobic c-terminus
Term
How many antigens can one TCR bind?
Definition
only one
Term
Do TCRs have variable and constant regions?
Definition
yes
Term
What position does the TCR bind the MHC?
Definition
It binds in a diagonal position
Term
Where does the TCR alpha segment bind the MHC?
Definition
TCR alpha chain lies over the alpha 2 domain of MHC and the amino-terminus of the peptide.
Term
Where does the TCR beta segmant bind the MHC?
Definition
TCR beta chain lies over the alpha 1 domain of the MHC and the c-terminus of the peptide.
Term
Describe the structure of MHC class 1 molecule?
Definition
Made of a heavy chain
the antigen binding cleft formed by folding of alpha 1 and alpha 2 domains
Heavy chains are stabilized by the light chain known as beta 2 microglobulin
Has alpha 1 alpha 2 alpha 3
Term
How many peptides does the MHC class 1 bind?
Definition
8-10 amino acids
Term
Describe the structure of MHC class 2 molecule
Definition
formed by and alpha and a beta chain
binding cleft is folded in a more open conformation
Term
What length of peptides does MHC class 2 bind?
Definition
unconstrained, but on average 13 amino acids
Term
How is the stabilization of the
MHC class 1 vs class 2 differ?
Definition
MHC c1 - stabilized at both ends of the peptide
MHC c2 - stabilized at various distances along the peptide
Term
How many Ig-like domains make up the CD4 coreceptor? Which binds to the MHC II molecule?
Definition
4 (D1-4)
D1 binds MHC II
Term
To what does the intracellular domain of CD4 interact strongly with? What does this do?
Definition
Lck (tyrosine kinase)
this enhances signaling
Term
Which domains make up the CD8 coreceptor?
Definition
An alpha and a beta - each contains a single Ig-like domain
Term
Where does CD8 bind to the MHC I molecule?
Definition
to the alpha3 domain
Term
CD8 recognizes which kind of pathogens?
Definition
Peptides from intracellular pathogens
Term
CD4 recognizes which kind of pathogens? what else does it do?
Definition
extracellular
It also helps develop CD8 T cells and B cells
Term
Which kind of antigens do gamma and delta T cells recognize?
Definition
They are not restricted by MHC I or II and can recognize free antigens
Also they can recognize lipopeptide antigens presented by CD1
Term
Where are gamma/delta T cells located mostly?
Definition
they are specialized and located in mucosal sites such as GALT
Term
CD8alpha/alpha are specialized to where?
Definition
gut mucosa as intra epithelial lymphocytes
Term
Which gene segments encode the L chain?
Definition
1. V gene segment (95-101 AAs)
2. J domain (aprox 13 AAs)
And on the 5' end, it is flanked by an L peptide segment
Term
How is the gene rearrangement for the L chain?
Definition
V and J join
transcription
RNA splicing
C joins VJ
translation
Term
Which gene segments encode the H chain?
Definition
1. V gene segment
2. J gene segment
3. D gene segment
Term
How is the gene rearrangement for the H chain?
Definition
D joins J
V joins DJ
Transcription
RNA splicing
C joins VDJ
Translation
Term
Which genetic sequences encode the V region?
Definition
kappa, lambda, and H
Term
What flanking sequences guide gene rearrangement of the V, D, and J regions?
Definition
RSSs (Recombination Signal Sequences)
Term
What is the RSS heptamer?
Definition
CACAGTG
Term
What is the RSS nonomer?
Definition
ACAAAAACC
Term
What is the 12/23 rule?
Definition
A gene segment flanked by an RSS with a 12 bp spacer, can be joined most often to an RSS with a 23 bp spacer.
Term
Which spacers flank the D region?
Definition
D regions are flanked on both sides by 12 bp spacers
Term
Which segment encodes CDR1, CDR2, CDR3?
Definition
CDR1 and CDR2 are encoded in the V segment
CDR3 created by VJ (L chain) or VDJ (H chain)
Term
How is the forward orientation of the V gene segment
Definition
The intervening V or J regions are looped out and deleted after joining V with J
Term
How is the reverse orientation of the V gene segment
Definition
During alignment, DNA is coiled - this is not deleted. This is the less common orientation.
Term
Which enzyme complex is involved in the recombination of V,D,J?
Definition
V(D)J Recombinase complex
Term
Which proteins make up the V(D)J Recombinase? What do they do?
Definition
Lymphocyte specific proteins
-RAG1 and RAG2
-TdT (nucleotide addition)
Ubiquitous DNA Modifying Enzymes
-Ku70:Ku80 (non-homologous end joining)
-Artemis (Removes nucleotides)
-DNA Ligase IV and XRCC4 (Joins DNA)
Term
What are the steps in Ig gene rearrangement (RAG-dependent recombination)?
Definition
1. RAG-1 and RAG-2 bind to RSS of the segment to be joined
2. RAG-1 and RAG-2 create a synapse of V and J RSSs
3. RSSs are cleaved and hairpin loops formed
4. Coding sequence joints, with RSSs removed, are bound by Ku70:Ku80 complex
5. Signal joints also bound by separate Ku70:Ku80 complex
Term
How is the Coding joint formed during the RAG-dependent recombination?
Definition
- Ku70:Ku80+L+J complex recruits DNA-PK
- Artemis is recruited and activated by phosphorylation; it then opens the hairpin loop by nicking the single stranded DNA
8. TdT processes DNA ends
9. DNA ligase IV:XRCC4 now ligates the DNA to form an imprecise coding joint
Term
How is the Signal Joint formed during the RAG-dependent recombination?
Definition
-DNA ligase:XRCC4 ligates the RSS sequences only for joining segments that are the same orientation and will be excised from the genome of the cell.
Term
What are the four main processes that generate the Ig repertoire diversity?
Definition
- Multiple copies of each type of gene segment
- Junctional diversity - the joining regions where CDR3 is formed
- H and L chain: variable regions that pair to form antigen binding site
- Somatic hypermutation - point mutation in the V region genes
Term
How is Junctional diversity formed?
Definition
CDR3 diversity made by the addition of P and N nucleotides
Term
What are P nucleotides?
Definition
Palindromic; Single stranded ends of the hairpin loop - were originally complementary
Term
What are N nucleotides?
Definition
Non-template encoded nucleotides, added by TdT, randomly
Term
What does the TCR alpha chain encode?
Definition
V and J segments
Term
What does the TCR beta chain encode?
Definition
V, D, and J segments
Term
Where do the T cells have to be to rearrange?
Definition
The Thymus
Term
How is gene rearrangement for TCR alpha happen?
Definition
V joins J
transcription
splicing
C joins VJ
Term
How is gene rearrangement for TCR beta happen?
Definition
D joins J
V joins DJ
Transcription
Splicing
C joins VDJ
Term
What flanks TCR V, D, and J segments?
Definition
RSSs
heptamer CACAGTG
nonomer ACAAAAACC
12/23 rule still applies
P and N nucleotides added as well
Term
Where is the majority of the diversity in TCRs?
Definition
CDR3
Term
Antibodies are first made using which two constant region segments?
Definition
C mu
C delta
Term
Which C Isotype is produced first?
Definition
IgM
Term
Which Isotypes lack hinge regions?
Definition
IgM and IgE
Term
What are the three main functions?
Definition
1. Fc portions are recognized by specialized Fc Receptors on different cells
2. Fc portions of antigen:antibody complexes bound by C1q
3. Fc portion can deliver antibodies to inaccessible places by active transport
Term
Which Igs do mature naive B cells express?
Definition
IgM and IgD
Term
Which Ig do immature B cells express?
Definition
IgM
Term
Which Igs have J chains?
Definition
IgM and IgA
This allows them to form multimers
IgA = dimer
IgM = pentamer
Term
Where does secondary diversification occur?
Definition
In activated B cells
Term
What are the three mechanisms of secondary diversification?
Definition
1. Somatic hypermutation (occurs in the V regions of L and H chains)
2. Class switching (recombination of C regions)
3. Gene conversion (Replacement of V coding regions with pseudogene regions)
Term
Which molecule initiates the 3 mechanisms of secondary diversification?
Definition
AID (Activation induced cytidine deaminase)
Term
What does AID do?
Definition
-Will not bind ds DNA
-DNA must be unwound for AID to act
-AID attacks cytidine on cytosine ring
-Removal of an amino group
-Uridine is formed in place of cytosine in DNA
-This forms a ds lesion as Uridine is foreign to normal DNA; Uridine is mismatched with guanine
-Triggers several types of DNA repair: Mismatch repair, base excision repair
Term
What is the mismatch repair pathway
Definition
1. Mismatch repair enzymes MSH2 and MSH6 detect uridine
2. They recruit nucleases that remove uridine and surrounding bases
3. Patch repair via a DNA polymerase which is imprecise in B cells
Term
What is the Base excision Repair
Definition
1. UNG removes the uracil base from uridine to create an abasic site in the DNA
2. Abasic = no purine or pyrimidine present
3. If no modification is made, then on the next round of DNA replication it is randomly filled by REV1
4. REV1 can repair the lesion
5. This creates a further mutation
Term
Which sites do mismatch repair and base excision repair mutate?
Definition
Mismatch repair mutates A:T sites
Base Excision Repair mutates C:G sites
Term
summary of Hypermutation Summary?
Definition
-AID via nucleophilic attack transforms cytosine to uridine
-Mismatch repair - MSH2/6 which repairs uridine site but mutates A:T sites
-Base excision repair - UNG transforms uridine to an abasic residue, REV1 then writes over this site creating mutations at C:G sites
Term
When does class switching occur?
Definition
Only after the B cell sees its antigen
Term
Where and what are the switch regions?
Definition
They are stretches of repetetive DNA that cuide the nonhomologous recombination in class switching
They are in the intron between J and C regions
Term
What is class switching?
Definition
It occurs when the switch region of a C region recombines with another S region of a subsequent C region.
Term
What are the steps to class switching?
Definition
1. Transcription must be active so the AID access ssDNA
2. R-loops formed in the switch region during transcription
3. R-loops give access of DNA to AID, UNG, and APE1, which nicks the DNA at C residues on both strands
4. Activates double break DNA repair proteins to repair the lesions in the S regions
5. Joining of the nicked regions
6. Loops out the intervening sequences
7. Brings the VDJ region adjacent to the new C region and the isotype is switched
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