Study guide chapters 3 and 4, Study notes of Immunology

Download Study guide chapters 3 and 4 and more Study notes Immunology in PDF only on Docsity! PCB 3233 Exam 2 Study Guide Chpt. 3 and 4 Chapter 3 1)When the folowing receptors are engaged what mechanism is initiated in a phagocyte? Mannose receptor, CR3 and CR4, or Scavenger receptor. These receptors are macrophage phagocytic receptors. When engaged, they induce phagocytosis by means of opsonization. Mannose Receptor – Phagocytic PRR, targets bacteria. Ligands: LPS on Gram(-) bacteria CR3 & CR4 – Bind to iC3b fragments as wel as LPS Scavenger Receptor – Preference for negatively charged molecules 2)When the folowing receptors are engaged what mechanism is initiated in a macrophage? TLR’s. TLR (Tol Like Receptor) – cytokine signaling receptors, NOT phagocytic. They engage in production and secretion of cytokines. 3)What do TLR 3, 4, 5 and 7 bind to? Location Cel Ligand Organism Recognized TLR 3 Endosome NK Cels Double strand RNA RNA Virus TLR 4 Plasma Membrane Macrophage, Mast Cel, Dendritic Cel, Eosinophil LPS Gram(-) Bacteria TLR 5 Plasma Membrane Intestinal Epithelium Flagelin Bacteria TLR 7 Endosome Dendritic cels, B- Cels, Basophiles, Eosinphil Single strand RNA RNA Virus 4)Know the TLR4 signaling mechanism. Al of the extracelular including LBP and intracelular, MyD88-TIR domain and IKK-NFkB-signaling. Bacterial LPS from Gram(-) Bacteria is brought by LBP (LPS Binding Protein) to the complex of TLR4, MD2, and CD14 on the surface of the macrophage MyD88 adaptor protein binds to TIR domain, the TLR4 component inside the plasma membrane This sets of a chain reaction. Binds to protein kinase IRAK4 which phosphorylates, then phosphorylates TRAF6 adapter protein. This leads to phosphorylation and activation of kinase complex caled IKK, which activates transcription factor NFkB. Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822 NFkB is held in cytoplasm with inhibitor IkB in inactive form. IKK phosphorylates IkB, releasing NFkB, which travels to the nucleus and begins transcription of cytokines. These are secreted via Endoplasmic Reticulum 5)In the previous question, what 5 genes (that you learned about) are transcribed because of the TLR-4 recognition? IL-1 and TNF-a – vasodilation and vascular permeability IL-6 – metabolizes fat + muscle cels to raise temperature CXCL8 – recruits neutrophils (chemokine) IL-12 – recruits NK cels (chemokine) 6)What is the general term given to these 5 gene products? (Hint; 2 part name including what they result in along with what type of molecule they are) Inflammatory Cytokines, responsible for inflammation 7)Know what neutrophils do and what lineage they come from during hematopoiesis. Neutrophils are  Granulocytes (granules in cytoplasm)  Pyogenic – form pus  Leukocytes – white blood cels  Polymorphonuclear – multi-lobed nucleus Primary phagocytic cels of the innate immune system. Most common in circulation. Lineage: Hematopoietic stem cel in bone marrow  myeloid precursor  granulocytes neutrophil 8)What is another name for neutrophils. Polymorphonuclear granulocytes 9)Know the 4 classes of adhesion molecules and which adhesion molecule they bind to. Ex; LFA-1 binds to ICAM-1 and vascular addressin (CD-34 binds to L-selectin) 4 Classes of leukocyte adhesion molecules – determine movement of leukocytes from blood to tissue Selectins (L Selectin) bind to addressins (CD34) Vascular addressins (CD34) bind to selectins (L Selectin) Integrin (LFA-1) binds to Ig superfamily proteins (ICAM) Ig Superfamily (ICAM-1) binds to integrins (LFA-1) 10)Know the 4 steps of extravasation. Extravasation – neutrophils leave blood into tissue by squeezing through gaps in epithelial cels Step 1: Roling Adhesion Cytokines/inflammatory mediators induce selectin expression on vascular endothelium to bind neutrophils Roling adhesions slow neutrophils down Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822  Gamma 18)What cels can produce Type I interferons? Al nucleated cels 19)What is the main innate immune cel activated by Type I interferons? Type I interferons activate NK cels 20)Know the 2 e!ector functions of NK cels. Hint; one is cytotoxic Cytotoxic function – kiling infected cels via apoptosis. Part of innate immunity Produce Type I interferons 21)What type of infection do NK cels typicaly fight against? Viral infections 22)What type of response is created in a cel that an NK cel has targeted (viraly infected)? Apoptosis 23)What cytokine does an NK cel secrete to activate macrophages? Type I interferon 24)What happens to viraly infected dendritic cels when NK cels outnumber them? What happens to viraly infected dendritic cels when they outnumber NK cels?  When there are more NK cels than infected dendritic cels the NK cels are cytotoxic to the dendritic cels  When there are more infected dendritic cels than NK cels the NK cels signal the dendritic cels to migrate to the nearest secondary lymphoid tissue to activate the adaptive immune system Chapter 4 1)What does the germline configuration of the Ig variable region genes look like in al cels except mature B-cels? What does the germline configuration of the TCR variable region genes look like in al cels except mature T-cels? Has not gone through somatic recombination. L, V, D, and J gene segments. Uncut. Contains DNA exons. 2)What gene segments need to come together to make a functional gene (for the variable region) in B-cels for heavy and light chains? Heavy chain: V, J, and D gene segments Light Chain: V and J gene segments 3)What are the di!erent isotypes of heavy chains and light chains? Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822 Heavy Chain: IgG (1, 2, 3, and 4) IgA, (1,2), IgM, IgE, IgD Can be remembered as GAMED Light Chain: Kappa and lambda 4)Which chain (heavy or light) confers the antibody’s isotype, heavy or light? Heavy chain confers isotype (type of Ig, GAMED) 5)Know the major points for the di!erent antibodies. IgG  3 constant regions, has hinge  4 di"erent subclasses (1,2,3, and 4) ordered by concentration in blood  Found in vascular and extravascular spaces and secretions  Most abundant Ig in blood, provides bulk of immunity for blood borne pathogens.  Smal  Only Ig that can cross placenta  Can initiate classical pathway of complement  Secreted as monomer IgA  3 constant regions, has hinge  2 di"erent subclasses (1,2)  Most common Ig  abundant in external secretions ex. Saliva, milk  Bivalent. Held together by J-Chain.  First line of defense against microbes entering mucosal surfaces ex. Respiratory tract, urinary tract  Monomeric IgA found in circulation on surface of B-Cel.  Dimeric IgA is secreted into lumen and gut IgM  4 constant regions, no hinge  First antibody produced by B-cels. Produced by immature B-cels, stil developing in bone marrow.  Monomeric IgM on surface of B-cel as antigen receptor.  Pentameric IgM secreted as antibody  Low a!nity, high avidity  Can initiate classical pathway of complement IgE  4 constant regions, no hinge  Plays role in inflammation and alergic reactions  Binds to mast cels to trigger release of histamines  Secreted as monomer IgD  3 constant regions, has hinge  Same antigen binding site as IgM  Performs as an antigen receptor on surface of B-cel  IgM and IgD as surface BCR’s interact with antigen to trigger B cels to proliferate and di"erentiate (activation of B-cels) Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822  Secreted as monomer 6)What do the constant domains do for the Ig’s? Do they bind to the antigen, confer e!ector function or have no function at al? Constant domains determine e"ector function. 7)What does CDR stand for and why are these important? What does HV stand for? Where specificaly are these in the BCR/Ab? CDR stands for Complementarity Determining Region. HV stands for Hypervariable Region. These mean the same thing. These are located at the very tip of the variable regions in the Fab portion of the antibody, on the heavy and light chains (the antigen binding site). There are 3 HV/CDRs on each region, for a total of 6 per antibody. These are important for determining the specificity and diversity of antigen binding sites. 8)Which gene segments provide diversity to CDR1 and 2? Where does the diversity for CDR 3 come from (which gene segment)? Diversity comes from… Heavy Chain Light Chain CDR1 V segments V gene segments CDR2 V segments V gene segments CDR3 D gene segments V/D Junction D/J Junction V/J junction 9)Know the major characteristics of the di!erent antibodies (Ab’s). Ex. bivalent, highest concentration Ab in blood, alows for phagocytosis, can cross the placenta, smal (good in extravascular areas) Refer to #5 for detailed list. Ex. Bivalent – IgA Highest concentration in blood – IgG Alows for phagocytosis – IgG Cross placenta – IgG Smal - IgG 10)What are the ways we can get diversity in the antigen binding sites. (combinatorial, multiple V, J and D segments can be used and N and P nucleotide additions (junctional diversity) Ways to get diversity in antigen binding sites:  Somatic recombination  Somatic hypermutation  Junctional diversity (inclusion of P and N nucleotides) Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822 16)An Ab is made up of 4 chains (2 heavy and 2 light) what holds them together? Disulfide bonds 17)In a given Ab, are the 2 heavy chains exactly the same and are the 2 light chains exactly the same? Yes 18)What is alelic exclusion and how does it a!ect your adaptive immune cel receptors? Alelic exclusion means that only one heavy chain and only one light chain are produced and expressed in a single B-cel. This ensures that IgM and IgD have a single specificity. 19)From IgG to IgG where do you expect to find the greatest amino acid di!erences? Constant regions or variable regions and if the answer is the variable regions, which specific regions of the variable regions? You would find the greatest amino acid di"erences concentrated in the hypervariable(HV)/CDR region of the variable region of the antibody. 20)Do light chains have isotypes? If so, how many di!erent isotypes are there and what are they? Can one Ab have multiple light chain isotypes? Light chains have two isotypes: Kappa and lambda. Only can be present on a particular B-cel. 21)What happens during somatic recombination and what happens during somatic hypermutation? Where and when do each happen? Somatic recombination – during the development of the immature B-cel in the bone marrow (primary lymphoid tissue), the arrays of VDJ gene segments are cut and resliced by DNA recombination. This brings together a single gene segment of each type to form a DNA sequence encoding the variable region of the Ig, determining its specificity. Somatic hypermutation – introduces point mutations throughout rearranged variable regions using AID enzyme. This a"ects the hypervariable/CDR region on the antibody. This occurs on mature B-cels that have been activated by antigen presentation, located in secondary lymphoid tissues such as lymph nodes, but does not a"ect plasma cels. This results in a!nity maturation 22)What enzyme is involved in both somatic hypermutation and isotype switching? AID enzyme 23)Look at the di!erent epitopes. (ex. linear vs. discontinuous) Epitopes are the region on an antigen that BCR can bind to. In discontinuous epitopes, di"erent parts of the epitope are folded together. 24)What does a B-cel do to change a membrane BCR into a secreted antibody? Al membrane bound BCRs can be secreted as antibodies by plasma cels, which are mature, activated B cels that have di"erentiated. Alternative splicing of RNA can remove the membrane binding domain. Di"erences in membrane and secreted antibodies are in the carboxy terminus of H-chains. The secreted antibody has a hydrophilic sequence, which alows it to be soluble. Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822 25)IgD and IgM membrane immunoglubulins. Are the antigen binding sites the same? What is di!erent between the two immunoglobulins? How are they both on the surface at the same time? If they cut the DNA to change isotype, could they both be expressed at the same time? Circulating B-cels that have not been activated yet are caled Naïve B Cels. They express both IgM and IgD on their surfaces. This is the only scenario where two Ig’s can be expressed concurrently on the same B cel. This occurs because of di"erential splicing of same primary RNA transcript, which does not involve rearrangement of DNA. They have identical binding sites. IgM is the first antibody created by a B cel. If they altered their DNA to switch isotypes, they could not be expressed at the same time. 26)Look at fig. 4.21 and 4.28. Have an idea of the linearity of constant region genes and know which constant region genes have switch regions in front of them and which constant region genes don’t have a switch region. Why doesn’t C delta need a switch region in front of it? If you switched from IgM to IgG1 could you ever go back to IgG3 or IgD? The linearity of this heavy chain begins with the L-gene, folowed by the completed VDJ gene, folowed by the constant C genes. Delta (D) constant regions are the only ones that do not need a switch region in front, because they are highly repetitive sequences that mediate recombination. Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822 If you switch from IgM to IgG, you cannot reverse this process, because DNA components were sliced and removed. You cannot switch to or from an IgD because it lacks switch regions. 27)How many subclasses of IgG and IgA are there? Fig. 4.33 IgG has 4 sub-classes. IgG1, IgG2, IgG3, IgG4 IgA has 2 sub-classes. IgA1, IgA2, Downloaded by rachel rosario (rxchellr@gmail.com) lOMoARcPSD|18034822