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  1. 1. ImmunologyInnate Immune Protection1. What are the features of and differences between innate immunity and adaptive immunity?12. What times following exposure to a pathogen do (i) the innate immune system and (ii) the adaptive immune system, take to respond?23. Which 3 areas of the body contain the main physical/anatomical barriers to ‘external’ pathogens, and give an example of how the structure and function of these barriers prevents the entry or growth of pathogens? 34. What is the complement system?45. What are cytokines?56. What are the 3 pathways leading to the production of C3 convertase enzyme (required for the production of C3 complement protein)?67. What is a protein-associated molecular pattern (PAMP)?78. Pattern recognition receptors are the means by which the innate immune system tells the difference between host and pathogen cells, what are the three types of PRR and where are they located?81 Innate immune system is the ʻfirst line of defenceʼ it responds to pathogens in a non-specific way andincludes NK cells, complement cells, phagocytes and epithelial barriers. The Adaptive immune systemrecognizes specific pathogens and initiates processes to eliminate these pathogens, then remembers themthrough T cell receptors or ʻmemory cellsʼ. Includes antibodies, B and T lymphocytes.2 Innate immunity 0-4 hours, acquired immunity >96 hours3 Skin (dry, difficult for pathogens to grow or penetrate), respiratory system (tight junctions prevent bacteriafrom getting through epithelium, mucus production and cilia), GI tract (same as respiratory system +peristalsis, HCL and gastrin secretion).4 Part of the innate immune system which complements antibodies in the adaptive immune system. Consistsof a series of liver-synthesised proteins (proteases) which operate via cascade (production of one inducesthe next). These circulate in the blood and cleave to larger proteins triggering them to release cytokines.5 Cytokines are signaling molecules which signal immune cells to release T-cells and macrophages6 1. Classical: antibody complex, MB lectin: Mannose on pathogen, Alternative: Pathogen7 Molecules associated with groups of pathogens which are recognised automatically by ʻToll like receptorsʼin the innate immune system. This is how the innate immune system tells the difference between host cellsand pathogens. PAMPs are also essential for the survival of the pathogen.8 Collectin - serum (blood plasma) these are soluble PRRs, Toll like receptors - found on membrane (like atoll-gate), Nod like receptors - cytoplasm
  2. 2. 9. What are the two parts of a collectin and what are their separate functions?910.Which Toll-like receptors recognize the following pathogens: Flagellin, Unmethylated CpG DNA, LPS (Gram-negative), dsRNA, Peptidoglycan & Lipoproteins10?11.There are 2 types of NOD like receptors in cell cytoplasm (NOD 1 & NOD 2), which pathogen associated molecules do they detect? 1112. What are monocytes and what is their function in immune response?1213.What are macrophages and what do they do and how long do they last?1314.What are neutrophils and what do they do and how long do they last?1415. What happens during phagocytosis? (there are roughly 8 stages) 1516.Describe the killing mechanism of macrophages and neutrophils via reactive oxygen intermediaries? (mainly neutrophils)169Coll (collagen) like region interacts with the effector part of the immune system, Lectin region binds to sugarmolecules on the surface of pathogen.10Flagellin = TLR 9, Unmethylated CpG DNA =TLR 5, dsRNA = TLR 3, Peptidoglycan & Lipoproteins = TLR1,2 &6, LPS (Gram-negative) = TLR 411 NOD 1 = gamma glutamyl diaminopimelic acid, NOD 2 = muramyl dipeptide12 Monocytes are a type of white blood cell which move to sites of infection/inflammation and divide intomacrophages and dendritic cells to elicit immune response. Lifespan is 2-8 days.13Macrophages are what monocytes divide into when they reach an inflamed area. These cells arephagocytes which engulf and digest cellular debris (dead matter) and pathogens. They last about 6-16 daysand can ingest over 100 bacteria before they eventually die due to their own digestive compounds.14Neutrophils are the most abundant type of white blood cell. They are the ʻfirst respondersʼ to a site ofinflammation and travel in the blood in their active form. They are phagocytes but respond quicker thanmacrophages. Last about 5 days (short lived) and are only found in blood.15 Chemotaxis (organisms directing movement by swimming towards highest concentration of foodmolecules, receptors or away from poison) and adherence of microbe to phagocyte, ingestion of microbe,formation of a phagosome (a vesicle formed around a particle absorbed by phagocytosis), fusion of thephagosome with a lysosome (an organelle which contains enzymes to break down waste materials) to forma phagolysosome (a phagosome containing digestive enzymes), digestion of microbe and discharge ofwaste materials.16Following phagocytosis, there is an increase in O2 uptake by the cells, oxygen is reduced by NADPHoxidase to form hydroxyl radicals and hypochlorite. This causes DNA damage and alterations in bacterialmembranes.
  3. 3. 17.Describe the killing mechanism of macrophages and neutrophils via reactive nitrogen intermediaries (mainly macrophages)?1718.What are the receptors bound by cytokines to induce inflammation and fever?1819.What are the receptors bound by cytokines to induce macrophage activation?1920.What are the receptors bound by cytokines to induce CD4 T Cell differentiation? 2021.What are chemokines?2122.What are interferons?2223.What is the function of dendritic cells? 23Antibody, Lymphocytes and the Generation of Diversity1. What is a lymphocyte? 242. What are the main two types of cells of the adaptive immune system? 253. Where is a T cell’s receptor located on it?264. What are the two types of T cell and how do they differ?2717 The reaction forming L-citruline from L-arginine generated NO radicals, catalyzed by the enzyme ʻinduciblenitric oxide synthaseʼ which is induced by cytokines and bacterial components. NO free radicals cause DNAdamage.18 IL-1 (interleukin 1) and IL-6 (interleukin 6)19 TNF (alpha) (tumour necrosis factor)20 IL-1221Class of cytokines with chemoattractant properties which promote inflammation by making cells adhere tothe surface of blood vessels and migrate to infected tissue (chemotaxis).22 Produced in response to virally infected cells, includes natural killer cells.23Dendritic cells process antigen material and present it to other cells of the immune system (antigenpresenting cells)24Lymphocyte is the name for the whole group of white blood cells which includes T cells, B cells and NKcells25 B cells and T cells26 On the cell surface27Cytotoxic T cells kill other pathogens and Helper T Cells release cytokines, responsible for for B cellantibody class switching, activating cytotoxic T cells and maximising phagocytosis.
  4. 4. 5. How to B cells change when their surface receptor recognizes a whole antigen (without the need for it to be fragmented and presented)?286. What are the four main ways that antibodies (a.k.a. B cell receptors in soluble form, immunoglobulins) attack viruses and toxins? 297. What is the basic structure of an antibody and how does this relate to binding?308. What is a heterodimer and what types of immune cells can be described as these? 319. What is gene rearrangement?3210. Whereabouts in the body does the gene rearrangement happen for (i) B cells and (ii) T cells?3311. What is the process of hypermutation and which lymphocytes undergo this process? 3412.What is the process of affinity maturation? 3513. What is class switching? 3628Cell differentiates into plasma cells that secretes the receptors as antibodies. Antibody is just a word for asoluble (unattached) B cell receptor.29Blocks interaction with other cells, promotes phagocytosis and killing activity by other cells, activates thecomplement cascade, agglutinates (clumps together) particles.30All antibodies contain a variable region with two binding sites, and a constant Fc region which determinesthe single species of the antibody. The two regions are connected by a hinge region.31 A heterodimer is a molecule formed by two distinctly different macromolecules. In the case of antibodiesthis means it has two bonding sites which consist of one light chain and one heavy chain each. In the case ofT cell receptors consist of one copy each of two different chains. Forming either an alpha-beta or a gamma-delta T cell receptor. Contrast to antibodies, T cell receptors only have one binding site.32A process carried out to establish an antibody. Where one whole gene is made by combining differentsegments of genes (V regions, D regions, J regions) by Recombination activating genes (RAG)33B cells in the bone marrow and T cells in the thymus (a specialised immune organ which “educates” Tlymphocytes34 Further mutation of a B cell which has an antibody attached to it to match it further to the pathogen.35Picking the best fit out of multiple mutated Ig genes. So as the B cells mature, those with lower pathogenaffinity are weeded out36Varying of the gene which codes for antigen specificity and so changing the ʻvariable regionʼ of theantibody
  5. 5. 14.What are the four main antibody types and their shapes?3715.What is IgM and what is its characteristic functional property? 3816.How many binding sites does an IgM pentameter have?3917.What is the main function of IgG?4018.Which immunoglobulin type is associated with mucosal secretion? 4119.Which immunoglobulin type is associated with parasitic infection and mast cells? 4220.What enzyme is used both for affinity maturation and class switching?4321.Whereabouts within the B cell do affinity maturation and class switching occur?44T Cells, Effector Junctions and the Generation of the MHC1. What are the main functions of T cells?452. What are MHC molecules463. What is the RAG enzyme responsible for?474. Where do T and B cells originate from in the body?4837 IgG1 and IgE = ʻY shapedʼ, IgA (dimer) and IgM (pentameter)38 IgM is the default immunogobulin that B cells start with in development, the Fc region enables themolecules to form pentameters which is useful in forming immune complexes.39 Five immunoglobulin branches with 2 binding sites each so 10 in total40Secreted into the blood after class switching and collate pathogens so that phagocytes can recognizethem, pathogens coated in IgG become targets for NK cells. (antibody dependent cellular cytotoxicity)41 IgA42 IgE43 Activation Induced Cytidine Deaminase (AID)44 The Germinal Centre45T cells recognize bound antigen-complexes called MHCs. MHCs (Major Histocompatability Complexes)are46MHC stands for major histocompatability complex, it is a specific molecule to which degraded antigens(epitopes) bind to47 Rearranging gene segments to create functional receptors (gene rearrangement)48 Lymphoid progenitor in the bone marrow
  6. 6. 5. Regarding gene variation on alpha-beta T cell receptors, what are the 5 names for the variable chain segments?496. What is needed for a cell bound antigen to bind with a T cell receptor?507. What are the main similarities and differences between MHC I and MHC II molecules? 518. What are the three basic structural features of antigen presenting cells?529. Where do MHC II primarily draw the peptide molecules they present from? 5310. Whereabouts on the human chromosome are MHCs 1 and 2 located?5411. In terms of polymorphism in MHCs, where (structurally) do most variations occur within the molecule? 5512. What are the two main subtypes of T cell and what do these mean?5613. What step(s) other ‘signal 1’ must occur before a T cell and APC can bind and start adaptive immune response? 5714. Explain the difference between ‘step 1’ and ‘step 2’ of T cell activation?49 On both chains there are ʻvariableʼ and ʻjunctionʼ chains50T cells do not bind to antigens on their own, they must have an antigen presented to them after havingbeen partially degraded into peptide ʻepitopesʼ51Both are transmembrane proteins which contain a peptide binding groove with a central role in activatingA/B T cell receptors, MHC 1 associates with beta 2 microglobulin whereas MHC 2 is found on all nucleatedcells. MHC 1 present an example of the proteins being synthesised on the inside of the cell.52 Two alpha helixes either side of an antigenic peptide, all of this sits on top of a beta pleated sheet53In contrast to MHC 1, MHC II present peptides from exogenous (outside the cell) antigens as opposed toendogenous (inside the cell) antigens.54 Chromosome 6, the most highly polymorphic of all the human chromosome regions.55 In the beta pleated sheet beneath the peptide binding groove (diversity where it is relevant for themolecule), governs binding to varied ʻepitomesʼ.56CD8+ and CD 4+ They refer to different types of co-receptor on the T cell. In terms of function CD8 cellsare killers and CD4 are helper. CD8+ T cells preferentially bind antigen-(endogenous) peptide complexespresented by MHC 1 molecules. Their role is to detect and kill virus producing cells based on their MHC 1molecules. By contrast CD4 T cells prefer (exogenous) antigen peptide complexes presented by MHC 2.57 As well as the CD8+ or CD4+ co-receptor (step 1), you also need co-stimulatory molecules which areexpressed in low levels on the surface of antigen presenting cells and bind to another set of molecules whichare also present in low levels on the surface of the T cell. T cell is only activate when the right kind of co-stimulatory molecules are present on the surface of the corresponding APC.
  7. 7. 15. When T cells are activated, they differentiate into various kinds of T cell which are told apart by they kind of ‘cytokines’ (immune messengers) they produce. What are the four main changes cytokines signal in the immune response? 5816. What are perforins, granzymes and granulysin?5917. What are the two main types of CD4+ (T-Helper) cells and what are their functions?6018.What are regulatory type T cells responsible for?6119.What defines a T cell?20.How is a T cell receptor generated?21.Describe the mechanism(s) by which T cells & T cell receptors can generate vast diversity22. What are the different types of MHC molecule and why are they important?23.How do killer cells work differently to Th1 and Th2 cells function to mount an adaptive response?Immune Tolerance and Immune Recognition1. What are the 6 main players in the immune system (3 immune, 3 adaptive)?6258 1. Activation and polarisation of immune response (immune cells) 2. Decrease in viral replication (virusinfected cells) and increase in apoptosis in virus infected cells 3. Increase in blood vessel permeability(endothelial cells) 4. Increase in body temperature (hypothalamus)59All are proteins within the T cellʼs lysosomes, these are secreted onto molecules (APCs) which haveactivated them. Perforin = forms a pore in target membrane, Granzymes = activate apoptosis once in thecytoplasym of the target cell, Granulysin = induces apoptosis60 T-helper 1 cells act on intracellular pathogens and are responsible for the activation/function ofmacrophages, T-helper 2 cells act on extracellular pathogens and are responsible for the activation andmaturation of B cells, they are vital in causing class switching in B cells. They both produce distinct cytokines61Regulatory t cells suppress inflammation (including suppression of T cells and APCs), they are thus veryimportant for preventing autoimmune disease. Their targets of actions include supressing antibody orcytokine function, function of NK and NKT cells etc.62Adaptive: T Helper cells (CD4, TReg), T Killer cells (CD8), B cells (antigen presenters and antibodyproducers), Innate: dendritic cells (antigen presenters), Macrophages (killer cells, antigen presenters) andNeutrophils
  8. 8. 2. What is responsible for controlling the balance between autoimmunity and immunodeficiency, this is what T cells get their name from?633. What happens to thymocytes in the thymus? 644. What is the first stage of ‘testing’ in the ‘thymic education’ of T cells? 655. What happens to the thymocyte after this stage in terms of MHC binding666. What is negative selection and where does it take place?677. What are all three stages of thymic education in order?688. What causes newly released T cells in circulation to become activated?699. What is T cell anergy? 7010. What is the mechanism of regulatory T cells?7111.What are the two types of regulatory T-cells? 7263 Thymus64Thermocytes go into the thymus and come out as fully mature CD4+ (helper) or CD8+ (killer) cells. The Tcell receptors have been rearranged and cells will express CD4 OR CD8 specifically. They are tested toensure receptors are ʻsafeʼ and will not kill host cells.65 Whether alpha and beta chains can bind without cell death to create a functional T cell receptor.66Despite possessing both CD4 and CD8, the thymocyte will have a preference for MHC 1 or 2. Once thishas been established, the thymocyte will shed either CD4 or CD8 co-receptors and ʻspecializeʼ67 Negative selection takes place in thymic medullary epithelial cells or T-mecs, a range of ʻselfʼ antigens arepresented on the cell surface. The fit of the T cell is tested against self antigens, if the fit is induced toostrongly the T cell is then killed off because releasing it would be dangerous (it is an auto-reactive t cell).681/ Is it a functional TCR, 2/ Does it interact with self MHCs at all? 3/ Does it have too high an affinity forself antigens.69They have to come into contact with an antigen which they have not seen before (i.e. not in the thymus),generally something which has a foreign source.70 When a T cell remains in circulation but is unresponsive to future stimulation. Signal 2 as well as signal 1is required to activate cells. If signal 1 is detected the cell becomes anergic. It is a key mechanism ofmaintaining tolerance to proteins not expressed in the thymus.71 Stop proliferation or cytokine production of CD4/CD8 cells, reduce co-stimulation or alter cytokine produc.72nTreg - naturally occuring regulatory cells, produced in thymus and respond to self antigens. aTreg -developed in periphery (outside thymus), constant low level exposure to antigen.
  9. 9. 12. Toll-like receptors are found on the surface of interdigitating dendritic cells/ Langerhans cells, what do they recognize?7313. What is the process within dentritic cells which causes the cross-over between the innate immune system and the adaptive immune system?7414. How do dendritic cells which have interacted with pathogens cause inflammation?7515. What is the ‘third signal’ in T cell activation (other than the co-stimulators and co-receptors)?7616. What type of T-cells are produced when there antigen presenting cells prime naive T cells in the absence of any inflammation?17. What type of T cells are primed by antigen presenting cells in the case of asthma or allergy? 7718. What causes T cells to migrate into inflamed tissue from blood vessels? 7819. What kind of cells are stored in immunological memory and where are they stored? 79Spread of Infection/Control/Resistance1. How many people globally are living with HIV?8073Toll like receptors recognize Pathogen Associated Molecular Patterns (PAMPS) attached to foreignpathogens. These are unique to whole classes of microbes and are a product of bacterial metabolism.74 Dendritic cells recognize PAMPS on pathogens, pathogens are engulfed by dendritic cells, put intolysosomes within the cell, proteins from the pathogen are then expressed as MHC molecules on the surfaceof the dendritic cell. These MHCs are then picked up by T cells in the adaptive immune system.75The dendritic cells release cytokines whilst in lymph nodes which up-regulate adhesion molecules (whichmake cells stick to blood vessels), so T cells migrate into lymph node and become trapped within lymph for2-5 days.76APC secretes cytokines which affect the T cell dependent on which pattern recognition receptors havebeen activated by dendritic cells. Controls information on which type of cell the CD4 cell should become.77 T Helper 2 cells (CD4)78 Cytokines cause infected area to have more porous capillary epithelium and adhesive factors make cellsstick to edges of blood vessels. If the pathogen they are specific to is not in the area, T cells then return viaafferent lymphatic. If the MHC is present, the T cell binds to it.79CD4 and CD8 T cells, B cells, plasma cells. The cells are stored in bone marrow, lymph nodes and spleen.They are called ʻmemoryʼ rather than ʻnaiveʼ cells and exist in 10x-100x frequency (for particular pathogen) ifyou have been exposed to that particular pathogen.80 34 million
  10. 10. 2. How many new cases of TB are there per year and what % morbidity does the disease have?813. How many acute cases of malaria are there per year? 824. What are the main ‘routes of transmission’?835. List the 4 steps an infection travels from ‘reservoir’ to ‘cross infection’846. What are the characteristics of gram positive bacteria?857. What are the characteristics of gram negative bacteria? 868. What are the characteristics of viruses? 879. Give some examples of airborne transmitted infections8810. What is a zoonosis and give a few examples?8911. Explain the resistance mechanism ‘conjugation’9012. Explain the resistance mechanism ‘transformation’9113. Explain the resistance mechanism ‘transduction’9281 8.8 million new per year, 80% morbididty82 Around 300 million83 Ingestion, inhalation, inoculation (bite, needle injury, sexual intercourse), contamination of environment,mother to baby84 Reservoir --> route of transmission --> portal of entry --> colonisation or infection --> cross infection85Resist drying and thus colonize the dry environment of normal skin, produce toxins, spores, slimecapsules.86 Prefer a moist environment and so colonize the gut and some abnormal skin87 Differing heat stability, some may be enveloped and therefore resistant to heat and detergent, may betransmitted in the ʻprodromeʼ the period before the person feels ill, may be carried without symptoms.88 TB, measles, mumps, colds, flu (incl. most viruses), legionnaires disease89 An infection which is transmitted between species, e.g. salmolnella, tapeworms, bird flu90 Conjugation - bacterial plasmid DNA spread between two organisms (usually of the same species)91 Transformation - when a bacterium takes up DNA from the environment (e.g. from a dead organism)92 Transduction - when DNA is spread by bacteriophages (viruses that infect bacteria)
  11. 11. 14. Where do resistance genes come from?93What Happens When the Immune System Goes Wrong?1. What are the three main categories of immune disease?942. Which immunoglobulin mediates allergy? 953. What is atopy?964. How would anaphylaxis be treated in hospital? 975. What happens in Graves’ thyroiditis? 986. What mechanism causes some autoimmune diseases to be organ specific and others non-organ specific? 997. In what ways can diabetes melitus be characterised as autoimmune and how does its mechanism differ from that of Grave’s thyroiditis?8. Which cell is attacked by HIV?1009. What cells and molecules are involved in allergic/type 1 hypersensitivity response? 10193 From the antibiotic organisms themselves, they donʼt just arise from mutation94 Hypersensitivity, autoimmunity, immunodificiency95 IgE96An inherited tendency to make type 1 hypersensitivity responses (wheal and flare), degradation of mastcells and outflow of inflammatory mediators97Desensitization (giving the same antigen over and over again, suppresses allergic response), monoclonalantibody given to negate IgE (not first line treatment).98Autoimmune disease where anti-thyroid antibodies are produced so thyroid gets inflamed, inflammationbehind the eyes which pushes eyes forwards and damages sight99In organ specific conditions only B cell is destroyed by a specific antigen, In systemic autoimmune diseasethere are multiple antigens (non-specific)100 CD4 cells, so people with HIV become immunodeficient without treatment.101 In type 1 hypersensitivity an antigen is presented to CD4+ cells which stimulates production of IgEantibodies specific to the antigen. (only IgE are produced in type 1 response). IgE antibodies cause mastcells to release histamine, leukotrienes and prostaglandins
  12. 12. 10.What is the difference between a primary and secondary immune deficiency?10211.How do immune based therapies monoclonal antibodies and cytokines work?103102Primary = part of the bodyʼs immune system is missing or does not function properly (i.e. from birth),Secondary = where part of the immune system is missing or does not function but this has a clearlyidentifiable cause i.e. disease, drug treatment, environmental toxins.103Monoclonal antibodies are antibodies that are highly specific to a certain cell or pathogen and destroyonly these cells. Cytokines are immune messengers which can stimulate a particular immune responsee.g.elevated white blood cell count. Both can be given as drugs to stimulate a specific response.