Immunology Study Guide c1-5

Explain the function of the C3a and C5a fragments as anaphylatoxins

C3a and C5a are anaphylatoxins (ANA) that bind to surface receptors of phagocytes, endothelial cells, and mast cells. ANA induce physiological changes: • smooth muscle contraction • mast cell/basophil degranulation • increase local blood flow • increase capillary permeability

Understand the significance of C3 cleavage leading to C3b and C3a

C3b tags bacteria C3a attracts phagocytes

Understand how complement C5 activation leads to Membrane Attack Complex (MAC) formation

C3bBb can form different convertase complexes: additional C3 conversion & opsonization OR C5 activation by alternative C5 convertase (C3b₂Bb). C5 convertase converts C5 into C5a and C5b. C5b initiates the terminal complement cascade, involving Factors C6 thru C9 to form a membrane attack complex (MAC).

Explain the function of the MAC in targeting pathogens

C5b recruits C6, allowing C7 binding. C7 inserts into lipid bilayer of target, positioning C8. C8 begins process of polymerizing multiple C9 units = MAC completed MAC creates uncontrolled H₂O and allows solute flow. as MAC multiply, pathogen loses intra/extracellular regulation and destruction swiftly follows.

Understand the role of CXCL8 in attracting neutrophils.

CXCL8 is a homing signal for neutrophil migration into tissue → stimulates chemotaxis (directed movement) of the neutrophil.

Why do most cells constitutively express MHC I but typically only "professional antigen presenter" cells (B-cells, dendritic cells, macrophages) also express MHC II?

all nucleated cells express MHC I because any cell can be infected by intracellular pathogens and would then need to killed. mostly antigen-presenting cells (macrophages, dendritic cells, B cells) express MHC II because such cells engage with extracellular pathogens and would need to be encouraged.

What are the three pathways of complement activation?

alternative pathway (first to act) pathogen surface creates local environment conducive to complement activation. lectin pathway (second to act) mannose-binding lectin binds to pathogen surface. classical pathway (third to act) C-reactive protein or antibody binds to specific antigen on pathogen surface.

Understand that opsonization and MAC happen in parallel

as part of the innate immune system's immediate response. complement protein cause rapid opsonization of pathogen via chain reaction and the formation of MAC (pore in the pathogen surface).

List the four main categories of pathogens?

bacteria, virus, fungi, parasites

What surface features of some bacteria make them hard to bind by macrophages?

bacterial outer coats are tricky to bind. gram-negative bacteria have polysaccharide coats. surface proteins are masked/hidden. constant evolution of different strains adds to challenge. highly pathogenic bacteria tend to be gram-negative strains.

What is common, what differs among the three pathways?

Three pathways of complement activation differ in how they are triggered and in a few reactions of the cascade but they all lead to C3 activation, the deposition of C3b on the pathogen's surface, and the recruitment of similar effective mechanisms for pathogen destruction. alternative pathway works at the start of infection. lectin pathway is induced by infection and requires some time before it gains strength. classical pathway is part of both innate and adaptive immune systems and requires the binding of either an antibody or innate immune system protein called C-reactive protein to the pathogen's surface.

Distinguish between roles of Type I (IFN-β and IFN-α) and Type II (IFN-γ) interferons in terms of what cells produce them, what stimulates production, and their function.

Type I (IFN-β and IFN-α) made when cell is infected by virus to • induce resistance to viral replication in all cells. • increase expression of ligands for receptors on NK cells. • activate NK cells to kill virus-infected cells. Type II (IFN-γ) made by NK cells to stimulate macrophages/inflammation. • increasing phagocytosis and secretion of inflammatory cytokines.

What is the functional definition of a pathogen?

biological entity that has the potential to invade and colonize the human body, causing disease. may be single-cell, multi-cellular, or even just a collection of biological material but must have a genome.

Compare/contrast the effector mechanisms of innate vs. adaptive immunity.

both innate and adaptive responses involve protein to cell interactions. innate uses many proteins to detect "typical" features of a group of pathogens and proteins cooperate to label targets and raise immune awareness. adaptive uses a protein of a single, specified type that matches a unique feature of the "exotic" pathogen and only cells that are familiar with the feature are activated, amplified, and attack the pathogen.

Understand why we say innate immunity is concerned with "typical" pathogen profiles

broad sensitivity against general pathogen profiles. recognizes "typical" profiles. enforcers don't have to be highly skilled. limited number of enforcers needed. pathogens in modest numbers easily dealt with. maintenance at moderate cost. pros: quick response and modest cost cons: may overlook "non-typical" invader and response plan is always the same.

Understand the role of lectins binding carbohydrates such as mannose

cell surface receptors that recognize carbohydrates. examples present on macrophages: mannose receptor and dectin-1. macrophages use lectins to bind carbohydrates on bacteria. mannose is abundant on surfaces of many pathogens. mannose receptor and dectin-1 facilitate phagocytosis. mannose-binding lectin (MBL) • consists of 6 triple-helices with 3 mannose binding sites each. • thus forms very strong binding to 18 sugars on pathogen surface.

opsonization

coating of a pathogen with a protein that facilitates phagocytosis

What are commensal bacteria, and how do we benefit from them?

commensal organisms co-exist with us in balance, relationship is beneficial to the bacteria and host. commensal bacteria keep other harmful microbes from taking up residence as well as assisting in nutrient metabolism, vitamin production, and waste processing.

Explain what the acute-phase response of the liver represents

concentration of around 30 different plasma proteins increase (examples: mannose-binding lectin and C-reactive protein).

What is "junctional diversity" in the context of V(D)J recombination, and how does non-homologous end-joining DNA repair contribute to this?

contribution of P and N nucleotides to the coding joints is called junctional diversity and increases diversity in the resulting amino acid sequences of the CDRs of immunoglobulin chains.

What is the purpose (the eventual desired outcome) of a cell presenting antigen on MHC I vs MHC II? Understand the scenarios of T-cell interaction with target cells described in Fig 5.13.

cytotoxic CD8 T-cell makes contact with MHC I of infected cell, which is killed. CD4 helper T-cell makes contact with MHC II of macrophage phagocyting bacteria and facilitates macrophage activation. CD4 helper T-cell makes contact with MHC II of B-cell bound to antigen and causes B cell to differentiate into anti-body secreting cell.

What is the role of NK cells?

destroy infected cells. increase inflammation.

Explain what is meant by the heavy vs. light chains.

differences in heavy chain C regions define five main isotypes, which have different functions in the immune response. light chain has only two isotype classes (κ and λ). · no functional differences have been found. · in humans, relative abundance of κ is 66% and λ is 33%.

What are the concepts behind adaptive response?

effector mechanism for specialized response. requires extra training to ID novel pathogen. pros: overwhelming reaction and memory of pathogen for next time. cons: takes valuable time to coordinate and expensive investment of resources.

IL-12

interluekin (inflammatory cytokines) secreted by resident macrophages at site of infection. recruits and activates NK cells that in turn secrete cytokines that strengthen the macrophages' response to infection.

CXCL8

interluekin (inflammatory cytokines) secreted by resident macrophages at site of infection. recruits neutrophils from the blood and guides them to the infected tissue by chemokine receptor on neutrophils that binds CXCL8, which then signals the cells to move up the concentration gradient of the chemokine.

What are Toll-like receptors (TLRs)?

key for innate signaling. bacterial LPS activates cytoplasmic ends of Toll-like Receptor 4 (TLR4). complementing the phagocytic receptors are signaling receptors (like TLRs) that, by recognizing the pathogen, instruct the macrophage to recruit additional cells of innate immunity to the infected tissue.

Where are NK cells found?

known to differentiate and mature in the bone marrow, lymph nodes, spleen, tonsils, and thymus, where they then enter into periphery blood circulation.

Explain why complement fixation greatly increases phagocyte efficiency

macrophage Complement Receptor 1 (CR1) binds C3b on pathogens. complement activation leads to deposition of C3b on the bacterial cell surface. CR1 macrophage binds C3b on bacterium. endocytosis of the bacterium by the macrophage. macrophage membranes fuse, creating a membrane-bounded vesicle, the phagosome. lysosomes fuse with the phagosomes forming the phagolysosome.

Explain how having a variety of cell membrane receptors helps macrophages detect pathogens

macrophage receptors for pathogen binding. over 100 different receptor types. each type of immune cell expresses a subset of types. this variability allows wide pathogen detection in the body.

Understand the phagocytotic AND cytokine signaling role of macrophages

macrophages constantly patrol tissues looking for pathogens. surface receptors recognize "typical" pathogen features. can phagocytose (engulf and degrade) many microbes. pathogen binding triggers synthesis and expression of cytokine genes, which are generally inflammatory and act as alerts.

What cell makes the CXCL8? In response to what?

macrophages make CXCL8 in response to pathogens.

Explain how/why neutrophils can typically only destroy one or two bacteria by phagocytosis, but several by Neutrophil Extracellular Traps (NETs)

mature neutrophil cannot replenish granule contents; once used up, the neutrophil dies. in netosis (neutrophil dies in process that produces NETs) the nucleus swells and bursts, and the chromatin dissolves and is extruded from the cell in a network of decondensed DNA decorated with cationic proteins derived from the neutrophil granules. thus, neutrophils trap and kill pathogens after death.

Why do we say that microbes don't have malicious intent to harm their host?

microbes are carrying out their genetic program of survival and reproduction for as long as host's resources support them. any damage is a possible consequence, a side effect.

What is meant by infection?

microbial entry into the internal body.

antigen

molecule that is recognized by an antibody to initiate an immune response. commonly proteins and carbohydrates.

Understand the distinction between "inside" and "outside" our body

physical barriers separate the body from external environment. the strong barriers of skin, hair, and nails are colored blue. the more vulnerable mucosal membranes are colored red.

Understand how the jigsaw puzzle example in lecture demonstrates the concept of "close enough" fit as the basis for immunoglobulin selection

pieces may not fit perfectly but unfamiliar antigens instead bound by several "close enough" Ig.

Compare/contrast the pros vs. cons of innate vs. adaptive immunity

preset readiness vs flexibility fast vs slow response time moderate vs expensive maintenance costs

What is the main functional distinction between "primary" versus "secondary" lymphoid (immune) tissues in the body?

primary tissues (bone marrow and thymus) are where immune cells (lymphocytes) are made. secondary tissues (tonsils, lymph nodes, spleen, gut lining, appendix) are where lymphocytes encounter antigens and activate.

What parts of the Ig locus are involved in class/isotype switching?

process of isotype switching via further somatic recombination of the expressed heavy chain gene, in which the rearranged V(D)J segment is moved next to a "new" C region. both somatic hypermutation and isotype switching depend upon activation-induced cytidine deaminase (AID), made only by B cells proliferating in response to antigen.

What is the activated B-cell trying to accomplish by expressing the antibody form of IgM? What are the benefits and limitations of doing so?

purpose is to secrete "close enough" antibodies into blood → "quick and dirty" first attempt at fighting the pathogen. · five IgM link up with a J chain protein, forming a pentameric ring with 10 antigen binding sites. · can neutralize/block antigens. · not good at recruiting other effector cells. · very effective in activating complement proteins to pathogen.

Understand that our innate response involves pathogen recognition and effector mechanisms

recognition that a pathogen is present • involves soluble proteins and cell-surface receptors. • may bind to pathogen or its products. • may bind to infected host cells that changed shape. recruitment of destructive effector mechanisms • various effector cell types engulf bacteria, kill virus-infected cells, attack protozoan parasites. • serum complement proteins mark surfaces of pathogens for quick identification by effector cells, or directly destroy pathogen themselves.

Explain how a neutrophil flowing past infected tissue is slowed/stopped at the site

selectins are expressed on the surface of endothelial cells in response to underlying tissue infection (serving as way for neutrophils to know they've arrived at destination). rolling adhesion is converted into tight binding by interactions between integrins (LFA1) and adhesion molecules on the endothelium (ICAM1). under guidance of the cytokines (CXCL8), the neutrophil squeezes between the endothelial cells and penetrates the connective tissue to migrate to the center of the infection along the CXCL8 gradient.

Be comfortable with the concepts of V(D)J recombination, including the principles of recombinase proteins such as RAG 1 and 2 using RSS sequences flanking immunoglobulin genes (the "12/23 Rule") to increase antigen-binding diversity.

sequences around V(D)J genes control recombination. · each V, D, or J gene segment is flanked by Recombination Signal Sequences (RSS) of heptomer + nanomer with 12bp or 23bp spacers · V(D)J recombinase complex brings two RSS sites together. · 12/23 rule: only sites of different RSS orientation can pair. · RAG1 and RAG2 form the RAG complex which also has endonuclease function. 1. Recombination Activating Gene (RAG) binds RSS near a J gene (9-12-7 site). 2. RAG binds complementary RSS (7-23-9 site) near V gene. 3. Other proteins in complex cut DNA, forming discarded circle of DNA. 4. Chosen V and J sites joined together by DNA repair mechanisms.

What are some features of skin and mucosa that serve as barriers to infection?

skin provides barrier that prevents invasion by microorganisms unless it is damaged (for example, by an injury, insect bite, or burn). mucous membranes are coated with secretions that fight microorganisms. example: the mucous membranes of the eyes are bathed in tears, which contain an enzyme called lysozyme that attacks bacteria and helps protect the eyes from infection.

Explain the roles of interferons as a subset of cytokines

special cytokines made by all cells in response to viral infection and activated by NK cells communicating with macrophages.

epitope

specific region of the antigen surface where matching contact occurs to the antibody's HV site.

Understand how the "switch" from immediate to induced innate response should more appropriately be thought of as a "shift" rather than "switch"?

the immediate response to infections is a quick, sharp increase that soon plateaus at a medium level; while the induced response is a slower, gradual increase and continues to grow until reaching a higher plateau. when the infection is defeated, both immediate and induced responses ramp down.

Understand why both innate and adaptive immunity are required for our health

the immune system starts with innate immune mechanisms that are fast, fixed, and effective in stopping most infections at an early stage. when the innate immunity fails, the adaptive immune mechanisms that are slow to start, eventually becomes powerful enough to terminate almost all of the infections that overcame the innate immunity.

Understand the concept of induced response slowly activating in response to cytokine signaling, and why this means a successful immediate response will "cancel" an induced response.

this prevents stimulation of more expensive and time-consuming induced response until absolutely necessary or stops stimulation if not needed.

Explain what is meant by the variable vs. constant regions.

variable region: polypeptide chains of different antibodies have varying amino acid sequences concentrated in the N terminal regions of each type of chain. · this variability is the basis for the great diversity of antigen-binding specificities that antibodies have. forming the antigen binding site is a pair of variable regions, one from the heavy chain and one from the light chain. · two identical antigen-binding sites, one at the end of each arm. constant region: remaining parts of the light chain and heavy chain have limited amino acid sequence variation between different antibodies.

Understand IFN signaling is both autocrine and paracrine - what does this accomplish?

virus infected cells produce Type I interferons (IFNβ). autocrine: IFNβ binds to interferon receptor on surface of infected cell surface to mobilize other interferon-response factors and change patterns of gene expression. paracrine: IFNβ binds to nearby uninfected cells to induce interferon response that helps those cells resist infection.

What are the 3 main functions of complement proteins?

1. making phagocytosis more efficient. 2. sending molecular signals that attract reaching macrophage. 3. directly disrupting membrane of microbe leading to lysis.

Understand why B-cells and T-cells are involved in adaptive training and specialized attack

B cells identify novel pathogens and spread the knowledge of their ID. B cells have surface immunogloblins; when Ig leave the B cell, they are called antibodies (soluble form). T cells learn the ID and mount powerful attack T cells have surface T cell receptors (no soluble form).

What is the role of interleukin 6 (IL-6)?

IL-6 alters soluble protein expression by the liver. acting on hepatocytes to induce acute-phase response.

Understand that TLRs signal through MyD88 resulting in NFκB activation and cytokine expression - a VERY important part of innate immune response. You do NOT need to memorize the other intermediate proteins in the chain.

Sensing of LPS by TLR4 on macrophages leads to activation of the transcription factor NFκB. TLR4 recognizes bacterial LPS. TLR4 and LPS complex is assembled at the macrophage surface. MyD88 binds TLR4 causing cascade within cell that leads to release of NFκB. NFκB enters the nucleus and activates transcription of genes for cytokines, which are synthesized in the cytoplasm and secreted via the ER. TLR4-mediated expression of cytokines.

Explain what is meant by Fab / Fc fragments of an Ig.

Ig molecule can be cleaved at hinge region producing two types of antibody fragments: · Fragment Antigen Binding (Fab): two arm fragments that bind antigen. · Fragment Crystallizable (Fc): stem fragment that readily crystallizes, mediates the effector functions of the antibody molecule by binding to serum proteins and cell-surface receptors.

How do MBL and C-reactive protein fit into our discussion of the three C3 complement fixation pathways (Alternative, Lectin, Classical)

MBL binds to pathogen surface and activates the Lectin Pathway. C-reactive protein binds to specific antigen on pathogen surface and activates classical pathway.

Be familiar with the signaling of mannose-binding lectin (MBL) and C-reactive protein as they relate to C4b fixation

MBL consists of 6 triple-helices with 3 mannose binding sites on each, thus forming very strong binding to 18 sugars on pathogen surface. • MASP proteases cleave C4 and generate C4b, some covalently bind to the pathogen surface. C-reactive protein binds complement component C1 complex to cleave C4. C1 binding to C reactive protein on the pathogen surface activates the classical pathway of complement fixation.

Distinguish between MHC I and MHC II class structure and function.

MHC I is composed of one membrane bound heavy chain and noncovalently bonded β₂m. · all nucleated cells express MHC I. presents peptides produced by cytosolic degradation to cytotoxic CD8, which kills infected cells. MHC II is composed of two membrane bound chains. · mostly antigen-presenting cells (macrophages, dendritic cells, B cells) express MHC II. presents peptides produced by lysosomal degradation to cytotoxic CD4 helper, which facilitate macrophage activation and B cell differentiation.

Explain the relationship between NK cells and macrophages in infected tissue

NK cells and macrophages activate each other. macrophages secrete interleukin 12 (IL12) that activates NK cells. NK cells secrete IFNγ that stimulates macrophages.

Understand the function of the NK-synapse - why is this important? What is happening back/forth in the synapse that helps the NK cell "decide" what to do?

NK cells form a synapse to induce apoptosis. receptors and ligands are exchanged directly with target, transferring enzymes and proteins through synapse. NK cell makes initial transient contacts with any tissue cell it encounters. if the cell is healthy, NK cell moves on. if the cell is infected, firmer adhesion occurs forming an immunological synapse that helps hold the cells and exchange information and material. activating and inhibitory signals from various ligand-receptor interactions are integrated by the NK cell • if inhibitory signals predominate, target cell is released. • if activating signals predominate, execution proceeds.

List the 5 types of circulating leukocytes and know their relative proportion in blood

Neutrophil (40-75%) Lymphocyte, small (20-50%) Monocyte (2-10%) Eosinophil (1-6%) Basophil (less 1%) (Never Let Monkeys Eat Bananas)

Understand the functions of the RLR receptors RIG-I and MDA5, and how they involve the MAVS proteins on mitochondria to regulate IFN gene expression

RIG-like receptors, RIG1 and MDA5, detect viral RNAs in cytoplasm. dsRNA binding to RLRs leads to binding mitochondrial antiviral signaling protein (MAVS) initiating interferon regulatory factor 3 (IRF3) expressing IFN-β and IFN-α.

Describe in general terms how C3b fixation is regulated up/down by Complement Control Proteins (CCP) such as Factor H, P, DAF, MCP

Regulatory proteins control C3b deposition. CCPs act on surface bound C3b. Factor P (Properdin) stabilizes C3bBb on pathogen surface and protects it from proteolysis. Factor H changes C3b shape, making it substrate for Factor I. Factor I cleaves C3b into inactive iC3b. Factors prevent opsonization of human cells. Decay-accelerating factor (DAF) removes Bb from from C3b. Membrane cofactor protein (MCP) increase Factor I action. Both halt addition of new C3b to human cell surface → favoring deposition of C3b on pathogen, not human cells.

Understand why/how we prevent MAC attack of our normal body cells

Soluble and membrane bound control protein CD59 (protectin) prevents recruitment of C9 to MAC, this stops formation of pore in human cells.

What is the main antigen type that TCR bind?

TCR only bind MHC presented peptide antigens.

Describe how C3 activation, Factor B and D, lead to iC3Bb creation / C3bBb creation, and C3b fixation on pathogen surfaces

environment near bacteria surface encourages iC3 formation due to presence of bacterial enzymes/hydrolytic factors, thus a spontaneous iC3 formation rate higher compared to blood. C3 reacts with H₂O to form iC3, the first step of alternative activation. iC3 binds to zymogen (inactive) form of complement Factor B, this causes shape changes in Factor B. Factor B is now susceptible to cleavage by Factor D. Factor D cleaves Factor B into Ba and Bb. Ba is released, Bb stays bound to iC3 = iC3Bb. Another C3 arrives and binds to iC3Bb. iC3Bb cleaves the new C3 into C3a and C3b. Some C3b bind to H₂O and float away in inactive soluble form. Due to proximity, many C3b bind to bacterial surface. Pathogen bound C3b can still attract Factor B and Factor D forming C3bBb. C3bBb is powerful, pathogen bound alternative C3 convertase. Location results in most new C3b attaching to pathogen surface, forming a positive feedback loop of new C3b repeating convertase activity.

MyD88

example of an adaptor protein, which brings together two signaling components.

Understand the distinction between extracellular and intracellular infection

extracellular pathogens do not invade cells, instead they proliferate in the extracellular environment. intracellular pathogens invade and infect cells.

What are some things that pathogens are seeking to find in a host?

favorable environment in which to grow and propagate: nutrients water favorable pH structural support physical protection

Explain why inflammation, pain, fatigue and fever are normal components of the induced response - why do they happen?

if the immediate response doesn't eliminate pathogen, activation of cells in the infected tissue will induce innate response. inflammation increases vascular permeability → increased fluid leakage from blood vessels. • extravasation (leakage) of complement and other plasma proteins. • migration of monocytes and neutrophils increase. • macrophage and neutrophil activities increase. pain from damage to infected tissue. fatigue due to focusing energy on fighting infection, represents tactic to avoid wasting energy on other activities fever (raised body temp) helps the immune system fight infection since most bacterial and viral pathogens grow and replicate faster at temps lower than that of the human body and adaptive immunity becomes more potent at higher temp.

Describe the function of macroglobulins

immediate bacterial inhibitors. bacteria secrete proteases to condition surrounding environment. immune system responds with protease inhibitors. α2-macroglobulin sequesters bacterial proteases.

Describe the function of defensins - where are they typically secreted and why?

immediately lyse pathogens. short 35-40 amino acid peptides with amphipathic properties. insert and disrupt membranes of bacteria, fungi, viruses. component of mucus and neutrophil granules (vesicles). mainly active in sweat, tears, gut lumen, phagosomes. found outside the body to avoid damaging human cells.

Why is innate immunity called "innate"?

immune response proteins and cell factors are pre-programmed in our individual genetic make up.

Explain the relationship between NK cells and dendritic cells - how might this determine whether the adaptive immune response is activated?

in virus infected tissue, an immature dendritic cell expressing viral antigens can activate NK cells and encourage their differentiation into effector cells. when cytotoxic NK cells are abundent and innate immunity is overcoming infection, NK cells kill dendritic cells and prevent their activation of adaptive immunity. when NK cells are scarce and innate immunity cannot control the infection, NK cells induce dendritic cells to differentiate into the form that travels to secondary lymphoid tissue to initiate the adaptive response.

Understand the role of the 4 main neutrophil /endothelium adhesion molecules: CD34, L-selectin, LFA-1, ICAM-1.

inflammatory cytokines recruit neutrophils from the blood to the infected tissue, determined by interactions between complementary pairs of adhesion molecules, one partner expressed on the leukocyte surface and the other on a tissue cell surface. contact involves transient interactions between L-selectin adhesion molecules on the endothelium and CD34 (sialyl-Lewis carbohydrate groups of glycoproteins) on the surface of neutrophils. these weak interactions slow the neutrophils down relative to the blood flow, causing them to roll along the endothelial surface. the vascular endothelium expresses ICAM1, adhesion molecule that functions as ligands for complement receptor CR3 and LFA1 on neutrophils.

Review the cell lineages of hematopoietic cells and whether they are adaptive or innate effector cells

innate effectors: NK cells, macrophage, dendritic cell, neutrophil, eosinophil, basophil, mast cell adaptive effectors: plasma cell, effector T cell

Compare/contrast immediate vs. induced innate immune response

innate response has two lines of defense, both involve ready-made factors encoded by our genes. immediate: • within 0-4 hours • involvement of complement → opsonization and MAC • macrophages detect bacteria • phagocytosis and destruction pathogen out runs immediate response if • too many microbes • microbes poorly recognized • microbial actions deter response immediate innate response can't keep up induced: • within 4 hours to 4 days • more expensive for the body • macrophages release cytokines • recruitment of monocytes & neutrophils

Understand that the innate response has two parts: immediate and induced

innate response has two lines of defense, both involve ready-made factors encoded by our genes. 1. Immediate response: macrophages detect bacteria, phagocytosis, and destruction. 2. induced response: macrophages release cytokines, inflammation results, recruitment of monocytes & neutrophils

How are NK cells activated?

interferons IFN-β and IFN-α.

IL-1β and TNF-α

interluekin (inflammatory cytokines) secreted by resident macrophages at site of infection. induce blood vessels to become more permeable, enabling effector cells and fluid containing soluble effector molecules to enter the infected tissue. induce changes to the endothelial cells of blood vessels in the infected tissue that allow fluid and cells to leave the blood by dilating (increasing diameter) blood vessels thus decreasing blood flow.

IL-6

interluekin (inflammatory cytokines) secreted by resident macrophages at site of infection. induces fat and muscle cells to metabolize, make heat and raise the temperature of the infected tissue. causes local muscle and fat cells to adjust their metabolism and generate more heat.

Understand that for each of the Ig types, the B-cell can make membrane-bound or soluble (antibody) forms. Why/when would the B-cell switch between these?

when a B cell first makes IgM and IgD, the heavy chains have a hydrophobic sequence near the C terminal by which the Ig associate with additional transmembrane proteins Igα and Igβ (intracellular signaling) for a complex on the cell membranes as a receptor on naive B cell. binding of antigen triggers cell's proliferation and differentiation and ultimately the secretion of antibodies. difference between membrane bound and secreted Ig lies at the C terminal of the heavy chain: · membrane bound Ig has hydrophobic anchor sequence that is inserted in membrane. · antibody has hydrophilic sequence. this difference is determined by differential RNA splicing and processing of RNA, no DNA rearrangement.

Explain an interleukin.

when infection has been detected in a tissue, resident macrophages become activated to recruit other cells to the infected tissue by secreting several inflammatory cytokines: IL-1β TNF-α IL-6 CXCL8 IL-12

Why is important that novel Ig is first confined to the surface of a B-cell and not immediately allowed to circulate in soluble form?

when novel Ig first encounters antigen, this stimulates the "choosen" B-cell to form antibody-secreting plasma cells.

How do the hypervariable regions (HV or CDR) of Ig peptide sequences accomplish diverse binding affinities?

· HV have extreme sequence variation, making different combinations for greater range of target recognition. · changes in HV sequences lead to different binding site shapes. · HV1 & HV2 sequences are part of the chosen V gene (germline). · HV3 sequences are random, due to DNA repair (NHEJ mechanism). · these reflect variation from recombination and junctional diversity. differences in HV loops between different antibodies create both the specificity of anitgen-binding sites and their diversity.

What is somatic hypermutation of the immunoglobulin locus? When does it happen? Why does the B-cell do this during clonal expansion?

· activated/dividing B-cells rapidly mutate the V region genes. · Activation-Induced Cytidine Deaminase (AID) enzyme results in C bases converted to any of the four dNTP. · mutant daughters may/may not have higher-affinity IgM. · "better" B-cell clones are preferentially selected.

Understand that naïve B-cells make IgM and IgD in receptor form (B-cell receptor).

· alternative mRNA splicing of heavy chain Cµ and Cδ yields isotopes. · newly formed Ig associates with Igα and Igβ (normal genes that do not involve recombination) that bring IgM to cell surface. · hydrophobic stem of IgM anchors to cell membrane. · cytoplasmic stems of Igα/Igβ are antigen signal transducers. creation of IgM and IgD based on choice of C domain. naive B cells express both IgM and IgD on their surfaces, the only isotypes that are produced simultaneously.

Understand the structural similarities vs. differences between immunoglobulin (Ig) and T-Cell Receptor (TCR)

· consists of 2 Ig domain chains that consist of a variable region and constant region = α & β vs heavy & light. · two chains combine making unique antigen-binding site = both · no soluble form of TCR. · TCR do not undergo hypermutation after antigen binding.

Understand the general structure of immunoglobulins

· five different isotypes (classes): IgG, IgM, IgD, IgA, IgE. · glycoproteins made of 4 polypeptide chains: two identical heavy chains and two identical, smaller light chains → assemble into Y shaped structure. · each arm consists of a complete light chain paired with the N terminal portion of a heavy chain, linked by a disulfide bond. · stem consists of paired C terminal portion of the two heavy chains, linked by disulfide bonds. · slight structural differences lead to different effector functions. · one end recognizes antigen (Fab), other end binds effector cells (Fc). · N terminal, variable regions · C terminal, constant regions

What are the functions of CD3 and Zeta chain proteins in helping TCR signaling?

· new α/β TCR chains associate with CD3 complex. · CD3 consists of ε, δ, γ coded by chromosome 11. · not part of CD3 is separate ζ chain coded by chromosome 1. CD3 complex and ζ chain help position TCR on surface of cell and pass the signal of antigen binding from the outside of the cell into the cytoplasm.

Why do we say TCR will only bind to "presented" antigen?

· peptides come from pathogens destroyed by other cells. · proteins broken down into short peptides. · must be brought to cell surface by other proteins (MCH) for T-cells to see. TCRs bind both the antigen and the presenting MHC.

Understand there are 5 isotypes/classes of immunogobulins. You do NOT have to memorize or draw each one, but recognize what elements are different among them that contribute to functional differences.

· produced from the same B-cell based on need. · each V region (antigen specificity) is identical. · C region (Fc) differences recruit different effector functions. · each isotype has a transmembrane form (B-cell receptor) and soluble form (antibody).

How does our immune system use the hypervariable regions of Ig to compensate for not possibly being able to predict every pathogen it encounters?

· there's no way for the body to predict every antigen it will ever encounter. · so millions of different V domains are produced at once. · "close enough" fit is sufficient to detect something novel that requires an immune response.

What are some parts of the "interferon response"?

• induce resistance to viral replication in all cells. • increase expression of ligands for receptors on NK cells. • activate NK cells to kill virus-infected cells.

List some reasons why we needed to evolve an adaptive immune system on top of our innate immune system

• live longer and thus more likely to be exposed to exotic pathogens. • multicellular organisms have more areas in need of protection. • simple organisms can more "easily" notice pathogens. • our internal body is perfect environment for many pathogens.

Understand the process by which the respiratory burst phenomenon is involved in neutrophils destroying pathogen

• neutrophil granules contain potent pro-enzymes awaiting activation. • granules fuse with phagosome containing pathogen. • respiratory burst (transient increase in oxygen consumption) leads to sudden pH increase, activating enzymes. • pathogen and neutrophil dies as a result.