Immunology Exam 2 – Flashcards
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| What are the four main classes of Pattern Recognition Receptors? |
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| 1. Free receptors in the serum 2. Membrane bound phagocytic receptors 3. Membrane bound signaling receptors 4. Cytoplasmic signaling receptors |
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| What are the two types of DC's (Dendritic cells) and what are their roles? |
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| 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 |
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| What are the different types of Membrane Bound Phagocytic Receptors? |
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| 1. Dectin-1 2. Mannose Receptor 3. Scavenger Receptors 4. Lipid and Complement Receptors |
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| What does Dectin-1 (membrane bound phagocytic rceptor) recognize? |
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| recognizes glucans on pathogens |
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| What does Mannose Receptor (membrane bound phagocytic receptor) recognize? |
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| recognizes mannose residues on pathogens |
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| What are the different types of scavenger receptors (membrane bound phagocytic receptors)? |
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| SR-AI SR-AII MARCO (macrophage receptor with collagenous structure) Class A and B |
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| What are the lipid and complement receptors of the membrane bound phagocytic receptors? |
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| Lipid - CD36 Complement - CR1, CR3 |
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| What are the mechanisms of destroying pathogens? |
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| - 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) |
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| What are Membrane bound signaling receptors |
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| G protein coupled receptors |
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| What does fMet-Leu-Phe receptor (fMLP)(a type of membrane bound signaling receptor) recognize? |
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| N-formylmethionine of bacteria |
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| How do neutrophils produce toxins to kill pathogens? |
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| 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 |
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| What are the 3 roles of inflammation in combating infection? |
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| 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 |
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| What are the 3 families of receptors important for cytokine and chemokine production? |
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| 1. Toll-like Receptors (TLRs) 2. NOD-like receptors 3. Rig-I-like Helicases |
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| Briefly describe Toll-like Receptors |
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| - 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 |
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| What are the types of TLRs? Location and what do they recognize? |
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| 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) |
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| What does TLR-4 recognize? |
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| LPS (lipopolysaccharides) |
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| What is the accessory protein that TLR-4 uses to bind LPS? |
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| MD-2 |
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| What is the difference between direct and indirect binding with TLR-4? |
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| Direct binding - LPS binds to TLR-4 molecule Indirect binding - LPS binds to MD-2 (which is bound to TLR-4) |
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| What are the two additional accessory proteins, besides MD-2 that TLR-4 needs to bind LPS? |
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| 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. |
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| What does the dimerization of TLR molecules induce? |
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| It allows the TIR domains to come together and allow for binding to TLR adaptor molecules. |
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| What are the four types of adaptor molecules? |
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| 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) |
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| Which TLR molecules interact with which adaptor molecules? |
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| 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 |
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| What are the two domains that MyD88 has? |
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| 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 |
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| What does the IRAK complex do? |
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| It recruits the E3 ubiquitinase TRAF6 and then the E2 ubiquitinase TRICA1. |
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| What do TRAF6/TRICA1 do? |
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| They generate polyubiquitin chains on TRAF6 and NEMO/IKK creating a scaffold. The binding to TRAF6/TRICA1 scaffold activates the serine threonine kinase TAK1. |
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| What are the two important actions of TAK1? |
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| 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 |
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| Which adapter molecule do TLR-7,8,9 signal through? What does this activate? |
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| Through MyD88 It activates Interferon Regulatory Factor (IRF) genes important for type I IFN production (this is important for rapid control of viruses). |
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| Which adapter molecule does TLR-3 signal through? |
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| TRIF |
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| What does NOD stand for in NOD like receptor? |
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| Nucleotide-binding oligimerization domain - it is a centrally located domain on this receptor. |
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| What do NOD1 and NOD2 sense? |
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| NOD1 senses y-glutamyl diaminopimelic acid (iE-DAP - breakdown product of bacterial peptidoglycan) NOD2 senses muramyl dipeptide found in most bacterial peptidoglycan |
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| What are the steps of NLR (NOD like receptor) activation and signaling? |
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| 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 |
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| What other domains, besides CARD, can NLRs use? |
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| NLRPs (pyrin domain) |
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| How do NLRPs signal? |
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| 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 |
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| What do RIG-I-like helicases detect? |
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| Cytoplasmic viral RNAs |
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| What domains do RLHs contain? |
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| An RNA helicase like domain 2 CARD domains |
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| What are the two RLHs we will discuss? |
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| RIG-1 - Retinoic acid inducible gene 1 MDA5 - Melanoma differentiate associated 5 |
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| What is the adapter protein of RIG-1 and MDA5? |
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| MAVS - mitochondrial anti-viral signaling protein |
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| What are the steps of the signaling pathway for RLHs? |
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| 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 |
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| What are the cytokine families? |
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| IL-1 family Hematopoetin family TNF (Tumor necrosis factor) family Type 1 interferons IL-12 family |
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| Describe IL-1 family of cytokines |
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| 11 family members Most cleaved signal via NFkB pathway |
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| Describe Hematopoetin family of cytokines |
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| Growth and differentiation cytokines IL-6 and GM-CSF |
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| Describe TNF family of cytokines |
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| 17 members most are transmembrane proteins limited action |
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| Describe Type 1 interferon cytokines |
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| Important in initial control of viruses Produced at high levels downstream of TLR-7 and 9 |
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| Describe IL-12 family of cytokines |
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| Cell mediated immunity |
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| Which cell produces Type 1 interferons? |
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| plasmacytoid DCs (pDC) |
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| What are the actions of Type 1 interferons? |
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| - 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 |
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| What are the two groups of chemokines? Functions? |
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| -CC Chemokines (with 2 adjacent residues) - promote monocyte migration -CXC Chemokines (seperated by an additional amino acid) - promote neutrophil migration (and T cell migration) |
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| What are the three families of Adhesion molecules? |
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| 1. Selectins 2. Integrins 3. Intercellular adhesion molecules (ICAMs) |
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| How do Adhesion molecules work in the immune response? |
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| -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 |
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| What are the two families of NK cell recpetors? |
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| 1. KIRS (killer cell immunoglobin-like receptors) 2. KLRS (killer cell lectin-like receptors) |
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| What three gene clusters encode the NK cell receptors? |
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| -extended leukocyte receptor complex -leukocyte receptor complex -NK receptor complex |
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| What are the two functions of the NK Cell receptors? |
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| -activation -inhibition |
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| What do activating NK cell receptors use to signal? |
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| Adapter molecules |
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| Do inhibiting NK cell receptors use adapter molecules to signal? |
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| No |
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| What is DAP12? |
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| An adapter molecule that activating NK cells use to signal. It contains ITAM (immuno tirosine activation motif) |
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| What is ITIM? |
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| It stands for immuno tyrosine inhibition motif, it is in the cytoplasmic tail of the inhibiting NK cell receptors. |
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| Do all activating NK cell receptors need to use adapter molecules to signal? |
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| No, some can do it directly. -NCRs (natural cytotoxicity receptors) -NKp30, 44 and 46 are immunoglobulin-like receptors -NKGD is a c-type lectin |
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| Which ligands does NKG2D bind to? |
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| -MIC-A -MIC-B -RAET1 |
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| What can RAET1 bind? |
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| cytomegalovairus proteins |
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| What are the different types of NK cells based on? |
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| -surface receptors -ability to attack self |
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| What do NK cell activating receptors detect? |
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| SIL (stress induced signals) |
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| What do NK cell inhibiting receptors detect? |
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| Recognize self MHC class 1 |
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| When there is no infection present, when will a licensed NK cell become activated? |
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| -if the target is missing self -if the target is stress induced |
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| When there is no infection present, when will an unlicensed NK cell become activated? |
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| It will not be activated |
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| When there is an infection (inflammation), when will licensed and unlicensed NK cells become activated? |
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| All cells can or are given permission to attack self |
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| what are the five classes of immunoglobins? |
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| IgM IgD IgG IgA IgE |
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| Which chains make up IgG? |
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| 2 polypeptide chanins: Heavy (L) and Light (L) Each antibody is made up of 2 H and 2 L chains |
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| How many antigen binding sites does each antibody have? |
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| 2 identical sites |
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| Avidity |
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| The combinatorial binding gives increased strength of binding |
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| Affinity |
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| The strength of interaction between 1 binding site to antigen |
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| How many immunoglobin domains do the H and L chains have? |
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| H chain - has 4 domains L chain - has 2 domains |
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| Which part of the H and L chains is the most variable? |
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| Variable or V region (the amino terminus) |
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| Which part of the Ig is felixble? |
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| The hinge region - links Fc and Fab portions of the Ig |
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| How are the V and C domains shaped? |
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| Beta sheets making a barrel shape |
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| How many beta sheets make up the V and C domains? |
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| V domain - 8 beta sheets C domain - 7 beta sheets |
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| Which part of the variable region is the most diverse? How many per V domain? |
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| Hypervariable region (HV) There are 3 per V domain |
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| Which is the most variable HV range? |
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| HV3 |
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| What is CDR? WHat is it made up of? |
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| Complementary determining region Made of 6 HV loops |
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| What are the different interactions between Ig-Antigen? |
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| electrostatic hydrogen bonds Van der Waals hydrophobic |
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| TCR is similar to which region of the Ig? |
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| The Fab region |
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| How many chains make up the TCR? |
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| Two - alpha and beta (linked by a disulfide bond) |
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| What are the minority of T cells made up of? |
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| gamma and delta chains |
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| Which region of TCRs anchors it to the membrane? |
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| The hydrophobic c-terminus |
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| How many antigens can one TCR bind? |
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| only one |
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| Do TCRs have variable and constant regions? |
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| yes |
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| What position does the TCR bind the MHC? |
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| It binds in a diagonal position |
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| Where does the TCR alpha segment bind the MHC? |
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| TCR alpha chain lies over the alpha 2 domain of MHC and the amino-terminus of the peptide. |
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| Where does the TCR beta segmant bind the MHC? |
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| TCR beta chain lies over the alpha 1 domain of the MHC and the c-terminus of the peptide. |
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| Describe the structure of MHC class 1 molecule? |
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| 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 |
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| How many peptides does the MHC class 1 bind? |
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| 8-10 amino acids |
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| Describe the structure of MHC class 2 molecule |
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| formed by and alpha and a beta chain binding cleft is folded in a more open conformation |
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| What length of peptides does MHC class 2 bind? |
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| unconstrained, but on average 13 amino acids |
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| How is the stabilization of the MHC class 1 vs class 2 differ? |
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| MHC c1 - stabilized at both ends of the peptide MHC c2 - stabilized at various distances along the peptide |
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| How many Ig-like domains make up the CD4 coreceptor? Which binds to the MHC II molecule? |
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| 4 (D1-4) D1 binds MHC II |
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| To what does the intracellular domain of CD4 interact strongly with? What does this do? |
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| Lck (tyrosine kinase) this enhances signaling |
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| Which domains make up the CD8 coreceptor? |
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| An alpha and a beta - each contains a single Ig-like domain |
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| Where does CD8 bind to the MHC I molecule? |
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| to the alpha3 domain |
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| CD8 recognizes which kind of pathogens? |
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| Peptides from intracellular pathogens |
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| CD4 recognizes which kind of pathogens? what else does it do? |
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| extracellular It also helps develop CD8 T cells and B cells |
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| Which kind of antigens do gamma and delta T cells recognize? |
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| They are not restricted by MHC I or II and can recognize free antigens Also they can recognize lipopeptide antigens presented by CD1 |
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| Where are gamma/delta T cells located mostly? |
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| they are specialized and located in mucosal sites such as GALT |
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| CD8alpha/alpha are specialized to where? |
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| gut mucosa as intra epithelial lymphocytes |
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| Which gene segments encode the L chain? |
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| 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 |
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| How is the gene rearrangement for the L chain? |
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| V and J join transcription RNA splicing C joins VJ translation |
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| Which gene segments encode the H chain? |
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| 1. V gene segment 2. J gene segment 3. D gene segment |
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| How is the gene rearrangement for the H chain? |
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| D joins J V joins DJ Transcription RNA splicing C joins VDJ Translation |
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| Which genetic sequences encode the V region? |
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| kappa, lambda, and H |
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| What flanking sequences guide gene rearrangement of the V, D, and J regions? |
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| RSSs (Recombination Signal Sequences) |
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| What is the RSS heptamer? |
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| CACAGTG |
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| What is the RSS nonomer? |
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| ACAAAAACC |
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| What is the 12/23 rule? |
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| 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. |
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| Which spacers flank the D region? |
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| D regions are flanked on both sides by 12 bp spacers |
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| Which segment encodes CDR1, CDR2, CDR3? |
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| CDR1 and CDR2 are encoded in the V segment CDR3 created by VJ (L chain) or VDJ (H chain) |
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| How is the forward orientation of the V gene segment |
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| The intervening V or J regions are looped out and deleted after joining V with J |
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| How is the reverse orientation of the V gene segment |
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| During alignment, DNA is coiled - this is not deleted. This is the less common orientation. |
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| Which enzyme complex is involved in the recombination of V,D,J? |
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| V(D)J Recombinase complex |
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| Which proteins make up the V(D)J Recombinase? What do they do? |
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| 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) |
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| What are the steps in Ig gene rearrangement (RAG-dependent recombination)? |
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| 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 |
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| How is the Coding joint formed during the RAG-dependent recombination? |
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| - 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 |
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| How is the Signal Joint formed during the RAG-dependent recombination? |
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| -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. |
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| What are the four main processes that generate the Ig repertoire diversity? |
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| - 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 |
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| How is Junctional diversity formed? |
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| CDR3 diversity made by the addition of P and N nucleotides |
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| What are P nucleotides? |
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| Palindromic; Single stranded ends of the hairpin loop - were originally complementary |
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| What are N nucleotides? |
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| Non-template encoded nucleotides, added by TdT, randomly |
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| What does the TCR alpha chain encode? |
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| V and J segments |
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| What does the TCR beta chain encode? |
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| V, D, and J segments |
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| Where do the T cells have to be to rearrange? |
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| The Thymus |
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| How is gene rearrangement for TCR alpha happen? |
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| V joins J transcription splicing C joins VJ |
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| How is gene rearrangement for TCR beta happen? |
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| D joins J V joins DJ Transcription Splicing C joins VDJ |
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| What flanks TCR V, D, and J segments? |
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| RSSs heptamer CACAGTG nonomer ACAAAAACC 12/23 rule still applies P and N nucleotides added as well |
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| Where is the majority of the diversity in TCRs? |
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| CDR3 |
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| Antibodies are first made using which two constant region segments? |
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| C mu C delta |
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| Which C Isotype is produced first? |
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| IgM |
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| Which Isotypes lack hinge regions? |
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| IgM and IgE |
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| What are the three main functions? |
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| 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 |
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| Which Igs do mature naive B cells express? |
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| IgM and IgD |
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| Which Ig do immature B cells express? |
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| IgM |
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| Which Igs have J chains? |
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| IgM and IgA This allows them to form multimers IgA = dimer IgM = pentamer |
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| Where does secondary diversification occur? |
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| In activated B cells |
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| What are the three mechanisms of secondary diversification? |
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| 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) |
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| Which molecule initiates the 3 mechanisms of secondary diversification? |
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| AID (Activation induced cytidine deaminase) |
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| What does AID do? |
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| -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 |
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| What is the mismatch repair pathway |
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| 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 |
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| What is the Base excision Repair |
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| 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 |
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| Which sites do mismatch repair and base excision repair mutate? |
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| Mismatch repair mutates A:T sites Base Excision Repair mutates C:G sites |
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| summary of Hypermutation Summary? |
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| -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 |
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| When does class switching occur? |
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| Only after the B cell sees its antigen |
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| Where and what are the switch regions? |
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| They are stretches of repetetive DNA that cuide the nonhomologous recombination in class switching They are in the intron between J and C regions |
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| What is class switching? |
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| It occurs when the switch region of a C region recombines with another S region of a subsequent C region. |
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| What are the steps to class switching? |
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| 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 |
