Immunology Notes PDF

- Produces 10-100 times more antibodies, mostly IgG Antigen binding by immunoglobulin - Binding depends on shape of pocket - Binding is a function of the folding pattern of the heavy and light polypeptide chain - Variable domains of different antibodies are different from one another, especially i...

- Produces 10-100 times more antibodies, mostly IgG Antigen binding by immunoglobulin - Binding depends on shape of pocket - Binding is a function of the folding pattern of the heavy and light polypeptide chain - Variable domains of different antibodies are different from one another, especially in complementarity-determining regions (CDRs) - The three CRDs provide most of the molecular contacts with antigen (see slide) - The antigen-binding site of an antibody is large enough to accommodate the binding of an epitope with both the heavy and light chain variable regions - Different antibodies bind their epitopes with different strengths, called binding affinities Generating antibody diversity Multiple unusual mechanisms at play: - Somatic recombination - The gene encoding each immunoglobulin is constructed from several immunoglobulin gene segment - As each B cell matures, immunoglobulin gene segments undergo random rearrangements by recombination and deletion of intervening segments - Once one antibody rearrangement is successful, the process stops - Allelic exclusion: only the rearranged allele is expressed so that each B cell produces only one antibody - The C are for the dif Ig# The recombination of the gene segments between V-D and D-J is imprecise - Can vary by several nucleotides and change the amino acid sequence thus generating diversity - Random heavy and light chain reassortment - Two different light chains: kappa and lambda - The five heavy chains (five classes of immunoglobulins) can join with either the kappa or lambda light chain to form antibody - From number of gene segments, gene rearrangement and reassortment can generate >3.3 million possible antibodies - Coding for joint diversity - Somatic Hypermutation: mutation rate of B cell immunoglobulin genes is higher than other genes - Occurs only in the V regions of heavy and light chains, creating slightly altered Ig cell surface receptors with changing binding affinities for the antigen - Affinity maturation: B cells with receptors displaying higher affinity for the antigen are selected (those who bind tighter r maintained, highly specific) - The strengthening of antibody binding is responsible for the dramatically stronger secondary immune response MHC Class I proteins: found on surface of all nucleated cells - Present internal antigens to T-cytotoxic cells - Internal (cytoplasmic) antigens can originate from viral proteins or cancer proteins - If the peptide presented by MHC Class I is recognized by the T cell receptor of a T-cytotoxic cell, the antigen-containing cell is destroyed - MHC Class I proteins are the major antigen barriers for tissue transplant MHC Class II proteins: found only on the surface of antigen-presenting cells (B lymphocytes, macrophages, and dendritic cells) - Present antigens to T-helper cells - Stimulate cytokine production and lead to antibody-mediated immunity or inflammatory responses Based on the peptides (self or foreign) presented by MHC proteins, the immune system distinguishes cells with foreign antigens from cells with self antigens Antigen presentation by MHC I proteins - - Protein antigens degraded by the proteasome in the cytoplasm = fragments Peptide fragments are transported into the endoplasmic reticulum through a pore formed by the TAP (transporter associated with antigen processing) proteins) MHC I proteins in the endoplasmic reticulum are stabilized by chaperonins until peptide fragments are bound peptide fragments are bound by MHC I, the complex is transported to the cell surface The MHC I-peptide complex interacts with T cell receptors (CD8) on the surface of T-cytotoxic cells The T-cytotoxic cell is activated by the binding events, causing it to release cytokines and cytolytic toxins and kill the target cell T cell-mediated immunity : depend on MHC 1 OR 2 - Antigen-presenting cells, such as the phagocytes in innate immunity, ingest, degrade, and process antigens - then present antigens to T cells that secrete protein cytokines that activate the adaptive immune response - T-helper cells produce and release cytokine that induce inflammation - T-cytotoxic cells produce and release perforin and granzyme for target cell lysis - T cell receptors of a given T cell bind only to MHC molecules having foreign antigens embedded in the MHC protein Diversity of T cell receptors is generated by some of the same mechanisms involved in producing diversity of antibodies - Somatic recombination, Random chain reassortment, Coding for joint diversity Immunoglobulin gene superfamily: immunoglobulins, T cell receptors and MHC proteins - Consists of two nonidentical polypeptide chains - Constant and variable regions - Share protein domains - Similar mechanisms of generating diversity for immunoglobulins and T cell receptors T-cytotoxic cells - Directly kill cells that display surface foreign antigens - Contact between T-cytotoxic cell and target cell is required for cell death - On contact, granules in T cytotoxic cell migrate to contact site - Degranulation releases granzymes (causing apoptosis) and perforin (causing pores formation in target cell) T-helper cells - T-helper -1 subset activates macrophages - T-helper-2 subset plays a crucial role in B lymphocyte activation and antibody production Lecture 20 Disorders of the immune system: - Hypersensitivity: - Allergies/Immediate hypersensitivity/Type I - Cytotoxic/Type II - immune complex/Type III - Delayed-type hypersensitivity/Type IV - Autoimmunity: Condition when immune system attack self-antigens. - Autoantibodies or Cell-mediated autoimmune disorders Superantigens - Superantigens bring together APCs and T-cells, but bypass the antigen-TCR complementarity. - They do this by targeting conserved regions outside the antigen-binding sites. - This activates a large fraction of T cells in the body: up to 25%. Causes superantigen shock. Vaccines: disease prevention - Inoculate person with an inactivated pathogen or pathogenic epitope. - Injected, memory cells deployed - This causes the production of memory cells which can mount a swift and strong response if actually infected - mRNA: Antigen produced inside body instead of getting it - Protein - Inactivated: Heat/chemical treated pathogens (e.g. Vibrio cholerae, Influenza) - Attenuated: avirulent strains of a pathogen (e.g. Tuberculosis, measles, Rubella) - Subunit: component of pathogens like toxoids, isolated virulence antigens (e.g. Tetanus toxoid, meningitis caused by Neisseria meningitidis) - Conjugate: genetically engineered antigens (often polysaccharides) coupled with large harmless proteins that elicits an effective immune response (pneumococcal vaccines, meningitis caused by Haemophilus influenzae) - Nucleic acid vaccines: - DNA vaccines: antigens delivered to cells directly in plasmids. Host cells transcribe and translate the antigen to produce the antigen (e.g. Hepatitis A, B) - mRNA vaccines: antigens delivered as pre-processed mRNA for translation in the host cells (e.g. Pfizer’s COVID-19 vaccine). - Advantages: virtually zero risk of infection from the vaccine itself. mRNA vaccines also have a short half life, difficult to transport for temperature requirements. - Disadvantages: vaccine delivery and host cell update; mRNA vaccines can be unstable - Plant Based: Antigen delivered into plants using Agrobacterium tumefaciens. - extracted from plant cells in the form of virus-like particles (VLP): - VLP: antigens embedded in phospholipid vesicles. - Elicits a strong immune response, but lacks pathogen DNA, hence cannot cause disease. - Large farm for vaccines: sustainable, instead of factors - No vaccines exist Immunotherapy - Anticancer vaccines - Prophylactic: preventive; targets oncogenic pathogens - EX. HPV leads to cervical cancers, so we use vaccine to lower HPV which lowers our chances - Therapeutic: Immune cells can be sensitized to tumor antigens to mount a response against cancer cells. - Anticancer therapies: Checkpoint inhibitors - cancer cells overexpress immune-suppressing checkpoint proteins - PD1: programmed cell death protein 1 - Checkpoint inhibitors block the activity of these proteins to prevent neutralization of cytotoxic T cells - pembrolizumab; binds to PD-1 receptors of T-cells - We can block checkpoints to stop immune system from recognizing - Adoptive T-cell transfer - Tumor infiltrating T cells (TILs): - Extract T-cells that have natural anticancer ability from within tumors. - Propagate in the lab. - infuse back into the patient. - In use to treat melanoma. - Chimeric antigen receptor (CAR) T cells: (more advanced version) - T cells with engineered receptors that can recognize tumor antigens even without their presentation on MHC complexes. - T cells extracted from patients. - Engineered using viral vectors to give cells enhanced receptors. - Infuse back into patients. - In use to treat melanoma. - T cells even more sensitive than natural cancer T cells - Challenges: Overcoming immunosuppressive tumor microenvironments. Checkpoint inhibitors often used in combination to improve this. - Side effects: - Neurologic toxicity - inflammation (MORE t cells = higher chance inflammation) - Variation in treatment outcome from person to person. Gut microbiome - People who respond to PD1 more have dif gut microbiome than those who don't - Patients that seem to respond better to anticancer treatments show higher amounts of Bifidobacterium in their feces. - Beneficial gut bacteria like Bifidobacterium are thought to induce release of immune-stimulating cytokines - enhance tumor clearance in mice - Why feces transplant instead of purified bacteria? We don't know exact composition of bacteria in microbiome, don't know exactly what heals. Antibacterial drugs - Target: Cell wall synthesis - Β-lactams: inhibits transpeptidation reaction (catalyzed by penicillin binding proteins (ex.transpeptidase)) during cross-linking of peptidoglycan - Most widely used - B-lactam ring stays consistent, other parts change for effectivity - Bc we don't have cell walls - More in + bacteria - Isoniazid: analog of nicotinamide, a vitamin required for mycolic acid essential for mycobacterium cell wall synthesis. - Used to treat tuberculosis. - Vancomycin: akin to β-lactams, but binds to the two D-ala residues on the end of the peptide chains, preventing cross-linking of peptidoglycan. - Only effective in Gram positive bacteria (bc outer membrane) - Does Not inhibit enzyme, binds to peptides so cross linking cant attach - Protein synthesis - Inhibits 70S prokaryotic ribosomes (50S+30S). (not our ribsomes - Aminoglycosides: Inhibits the 30S subunit. Broad spectrum. - Side effects like nephrotoxicity limit their use. - Example: gentamicin. - Tetracyclines: Inhibits the 30S subunit. Broad spectrum. - Both aminoglycosides and tetracyclines are produced by several species of streptomyces - Example: tigecycline. - Macrolides: Inhibits the 50S subunit. - Example: azithromycin. - For humans, same effect bacteria cant produce proteins - Nucleic acid synthesis: - Quinolones: Inhibits DNA gyrase, preventing DNA packaging and unpacking in bacteria. - Broad spectrum - Fluoroquinolones are the most predominantly used. - Rifamycin: Inhibits RNA polymerase. - Can fuck us up too a lil - Actinomycin: Blocks RNA elongation by binding to DNA. - Folic acid synthesis inhibitors: - Sulfonamides (sulfa drugs): growth factor analogs - Sulfanilamide, for example, mimics p-aminobenzoic acid (PABA) required to produce folic acid - Folic acid is essential in nucleic acid synthesis. - Commonly used with trimethoprim, which inhibits another step of folic acid synthesis. - Membrane disruptors: - Daptomycin: binds to cytoplasmic membrane of bacteria and forms pores - Polymyxins: disrupts the outer membrane and forms pores in the cytoplasmic membrane of bacteria. - Generally not used, can dissolve our cell membrane but some selectivity bc of LPS - Lipid biosynthesis - Platensimycin: inhibits fatty acid synthesis. - We dont do fatty acid synthesis Antiviral drugs - Reverse transcriptase inhibitors (RTIs): blocks reverse transcription that converts viral RNA genomes to DNA in retroviruses (e.g. HIV). - Virus use our machinery so targeting them targets us - Nucleoside RTIs (NRTIs): dideoxy analogs of nucleosides for chain termination I THINK - Sanger sequencing methods - Has toxic side-effects. Example: Zidovudine. - Non-nucleoside RTIs (NNRTIs): non-competitive inhibitor of reverse transcriptase. (we dont have this so its chill on us) - Protease inhibitors: inhibits viral protease required for viral protein processing - Fusion inhibitors: binds to viral membrane proteins required for docking and host-cell entry. Neuraminidase inhibitors: blocks release influenza particles from host cell surface. Interferons: IFNs, produced by host cells against viruses Antifungal Anti-protozoan drugs - Quinine and derivatives: blocks hemoglobin metabolism in species of Plasmodium which cause malaria - Artemisinin: antimalarial drug derived from Artemisia plants. - Unclear mechanism of action, but possibly produces free-radicals upon haem metabolism. - Metronidazole: blocks nucleic acid synthesis in anaerobic organisms. - Used to treat infections caused by Giardia intestinalis, Trichomonas vaginalis, Entamoeba histolytica - Mebendazole: inhibits synthesis of microtubules. Popularly used to treat helminth infections. Antibiotic resistance: antibiotic-resistant pathogens. - Widespread (mis)use of antibiotics. - Unnecessary prescriptions - Self-prescriptions, often in LMICs. - Patients not completing treatment regimens. - Use in animals in agriculture. - Proper use of antibiotics - Limiting use in agriculture - incentives to discover and commercialize new antibiotics - Antibiotics that inhibit novel targets: platensimycin inhibits lipid biosynthesis, a target largely not targeted in bacteria. - Antibiotics that inhibit hard-to-evolve targets: teixobactin inhibits a small lipid molecule involved in bacterial cell wall synthesis, and is difficult to evolve resistance against. - Enzyme inhibitors: β-lactamase inhibitors e.g. clavulanic acid - Drug combinations