Micro 220 – Microbiology – Flashcards
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| What methods are there for quantifying viruses? |
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| Titer: a measurement of the number of infectious units per volume Plaque Assay: analogous to the bacterial colony; one way to measure virus infectivity. **Plaques: clear zones that develop on lawns of host cells. - lawns can be bacterial or tissue culture - each plaque results from an infection from a single virus particle |
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| Intact animal methods for virus quantification. |
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| Procedure: 1)serial dilution of virus sample (generally at 10 fold dilutions) 2) inject samples into several sensitive animals 3) after incubation period: fraction of dead and live animals at each dilution is tabulated. End tabulations are rated in the form of LD_% (lethal dose...% subjects deceased) |
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| Phases of viral replication. |
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| - Attachment (absorption) of virus to a suitable cell - entry (penetration) of the virion or its nucleic acid - Synthesis of virus nucleic acid and protein by cell metabolism as redirected by virus - (maturation) -> Assembly of capsids and packaging of viral genomes into new virions - release of mature virions from host cell |
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| What type of growth curve is characterized for virus replication? |
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| A one step growth curve |
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| What are the steps in the virus replication growth curve? What occurs in each step |
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| Latent period: Eclipse - Early enzymes --> Nucleic acids --> Protein coats and then maturation - assembly and release. |
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| Explain the features of viral attachment to cells. |
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| - attachment of virion to host cell is highly specific...Requires complementary receptors on the surface of a susceptible host - Receptors on host cell carry out normal functions for cell (ie uptake proteins, cell to cell interactions) - attachment results in changes to both virus and cell surface to facilitate penetration |
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| What is a permissive cell? |
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| a host cell that allows the complete replication cycle of a virus to occur |
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| Explain the viral attachment and penetration of Bacteriophage T4. |
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| Bacteriophage T4: Virus of E. Coli bacteria - attach to cells via tail fibers that interact with polysaccharides on E. coli cell envelope - Tail fibers retract and tail core makes contact with E. coli cell wall - Lysozyme-like enzymes forms small pore in peptidoglycan - tail sheath contracts and viral DNA passes into cytoplasm |
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| What DNA destruction system is only effective against double-stranded DNA viruses? |
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| Bacterial Restriction-modification systems |
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| What are restriction enzymes? |
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| Restriction endonucleases - cleaves DNA at specific sequences. |
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| What is the restriction-modification system? |
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| it is a bacterial defense system against virus penetration. DNA destruction system that is only effective against double-stranded DNA viruses |
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| What are the viral methods of evading bacterial restriction systems? (like the restriction-modification system) |
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| - Glycosylation or methylation (IE chemical modification of viral DNA) - Production of proteins that inhibit host cell restriction enzymes |
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| Explain the baltimore classification scheme. (Class I to class VII) |
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| Class I - Double Stranded (ds) DNA viruses Class II - Single Stranded (ss) DNA viruses Class III - dsRNA Class IV and V - ssRNA (+ or -) Class VI are retroviruses Class VII are dsDNA viruses that replicate thru RNA intermediates |
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| What are the steps in the production of viral nucleic acid and protein. |
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| - Generation of mRNA occurs first - Viral genome serves as template for viral mRNA - in some RNA viruses, viral RNA itself is the mRNA **in some cases essential transcriptional enzymes are contained in the virion |
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| What is a positive strand RNA virus? |
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| Single-stranded RNA genome with same orientation as its mRNA |
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| Negative strand RNA Virus: |
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| single-stranded RNA genome with orientation complementary to its mRNA |
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| What are early proteins and late proteins? What are their functions? |
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| Early proteins and late proteins are proteins formed during a viral life cycle, after the synthesis of viral mRNA Early proteins: -Synthesized soon after infection -necessary for replication of virus nucleic acid -typically catalytic functions -**synthesized in smaller amounts Late proteins: - typically structural components, including virus protein coat - synthesized in larger amounts |
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| Most bacteriophages consist of what type of genome (ss or ds) (RNA or DNA) |
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| dsDNA genomes. |
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| Are most bacteriophages naked, or do they possess lipid envelopes? |
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| Most are naked but some do possess lipid envelopes. |
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| What are the different viral life cycles? |
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| temperate and virulent. Virulent: viruses lyse host cells after infection. Temperate: Virus replicates their genome in tandem with host genome and without killing host. IE can undergo a stable genetic relationship within the host --> but can also kill cells during lytic cycle. |
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| What is T4? What is its genome structure? |
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| T4 is a virulent bacteriophage that is also related to T6 and T2 - Genome is dsDNA that is circularly permuted and terminally redundant |
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| What does the fact that T4's genome is circularly permuted and terminally redundant effect? |
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| Both factors effect genome packaging. |
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| What is a concatemer? |
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| A concatemer is a long continuous DNA molecule that contains multiple copies of the same DNA sequences linked in series. |
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| What is the modified DNA base that T4 contains? What is this the site for? |
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| 5-hydroxymethylcytosine (HOH2C) **this DNA is resistent to virtually all known restriction enzymes It is the site for glucosylation (on the hyroxyl group) |
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| The T4 genome can be divided into what parts? |
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| Early, middle and late proteins. Early and middle proteins: enzymes needed for DNA replications and transcription Late proteins: head and tail proteins. Enzymes required to liberate mature phage particles. |
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| Why are the T-. bacteriophages labeled T-? |
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| because they have tails |
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| Lysogeny |
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| State where most virus genes are not expressed and virus genome (prophage) is replicated in synchrony with host chromosome |
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| Prophage state |
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| State when bacteriophage genome is integrated into the host genome and sits there passively. |
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| How can a bacteriophage enter into the prophage state? What keeps their genes from being expressed? |
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| Integrated through site recombination. Genetic regulation makes it possible. It is repressed by negative regulation. |
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| Lysogen |
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| a bacteria containing a prophage. |
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| Lysogenic virus |
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| A virus with a lytic pathway and a prophage state --> Ie a virus that is able to be integrated into the host chromosome and who's genome will be regulated thru negative regulation. |
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| Describe bacteriophage lambda and its infection methods. |
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| - Linear, dsDNA genome - Has complementary, single-stranded regions 12 nucleotides long at the 5' terminus of each strand - Upon penetration, DNA ends-base pair, forming the (cos) site and the DNA ligates and forms double stranded circle - when lambda is lysogenic, its DNA integrates into E. coli chromosome at the lambda attachment site (att(lambda)) - when it enters lytic pathway, lambda synthesizes long, linear concatemers of DNA by rolling circle replication |
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| How is the regulation of lytic vs. lysogenic events occur in lambda? What are the key repressor proteins? |
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| Through complex genetic switch cl protein: (the lambda repressor) causes repression of lambda lytic events Cro repressor: controls activation of lytic events |
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| What are the consequences of virus infection in animal cells? |
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| Persistent infections: release of virions from host cell does not result in cell lysis (infected cell remains alive and continues replicating virus) Latent infections: delay between infection by virus and lytic events Transformation: conversion of normal cell into TUMOR cell... (loss of control over cell growth) Cell fusion: two or more cells become one with many nuclei |
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| What are retroviruses? What is unique about their genome? |
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| Retroviruses are viruses that replicate through a DNA intermediate - contain reverse transcriptaste (copies information from its RNA genome into DNA) - virion contains specific tRNA molecules UNIQUE GENOME: two identical ssRNA molecules of the + orientation *contains specific genomes: gag: encodes structural proteins pol: encodes reverse transcriptase env: encode envelope proteins |
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| what is a retroviruses process of replication? |
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| 1) entrance into the cell 2) removal of virion envelope @ membrane 3) Reverse transcriptase of one of the two RNA genomes 4) integration of retroviral DNA into host genome 5) transcription of retroviral DNA 6) assembly and packaging of genomic RNA 7) Budding of enveloped virions; release from cell |
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| What are the methods of physical antimicrobial control? |
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| heat sterilization radiation sterilization filter sterilization *stops acute food poisoning *reduces damage done to materials in the industrial world |
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| Clostridium |
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| A gram + bacteria that causes botulism *only infects host if consumed in infected food (otherwise it pasts right through us) |
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| What are sulphate reducing bacteria? |
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| Anaerobic bacteria who use sulphate as terminal electrons. **in cream separater plants creates dipoles across the colony and corrodes the metal in those high-pressure pipes |
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| What are the different forms of heat sterilization? |
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| Sterilization : killing all viable organisms within a growth medium Inhibition : effectively limiting microbial growth Decontamination : the treatment of an object to make it safe to handle Disinfection : Directly targets the removal of all pathogens, not necessarily all microorganisms |
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| What is the most widely used form of sterilization? Describe it |
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| heat sterilization - High temperatures denature molecules - Amount of time required to reduce viability 10-fold is called decimal reduction time - ** spore-forming bacteria can survive heat that would rapidly kill vegetative cells |
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| Thermal death time |
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| the time at which the temperature kills all of the sample organisms. **depends on what the initial concentration of the organism is |
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| Autoclave |
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| An autoclave is a sealed device that uses steam under pressure for heat pasteurization. - allows temps to exceed 100 C |
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| Pasteurization |
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| Pasteurization is the process of using precisely controlled heat to reduce the microbial load in heat-sensitive liquids... doesn't kill all organisms though! |
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| Radiation Sterilization |
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| Microwaves, UV, Xrays, Gamma rays can reduce microbial growth **UV is NON-PENETRATING!!! |
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| Ionizing radiation sterilization |
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| - electromagnetic radiation that produce ions and other reactive molecules - generates electrons, hydroxyl radicals, and hydride radicals **Amount of energy required to reduce viability tenfold is analogous to D value |
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| Filter sterilization: What types are there. |
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| Pores of filter are too small for organisms to pass through Pores allow liquid or gas to pass through - DEPTH FILTERS --> Thick HEPA filters - MEMBRANE FILTERS -->Very thin: functions more like a sieve --> filtration by syringe, pump or vacuum |
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| How can antimicrobial agents be classified? |
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| Antimicrobial agents can be classified as either: Bacteriostatic (stop growths), bacteriocidal(kills viability of cells) or bacteriolytic (bursts cells) |
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| What is MIC (minimum inhibitory concentration) |
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| The smallest amount of agent needed to inhibit growth of a microorganism --> varies with the organism used, inoculum size, temp, pH, etc. *the way to do this procedure is by taking many vials and adding different concentrations (2 fold dilutions) of agent in each vial. The one that results in no growth is the MIC. **gold standard! |
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| What is disk diffusion assay? |
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| A method of testing chemical growth assay. - antimicrobial agent added to filter paper disc - MIC is reached at some distance --> zone of inhibition = area of no growth around disk |
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| What are the types of chemical antimicrobial agents for external use? |
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| -Industrialized applications -Products design to reduce human pathogens --> sterilants (kills everything, whatever it contacts) --> disinfectants = sanitizers (reducing pathogenic bacteria to a level below which they wont cause disease through contact) --> antiseptics (inhibit growth of bacteria) |
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| What are the beta-lactam antibiotics? |
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| Penicillins and Cephalosporins are examples |
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| What are antibiotic drugs classified on the basis of? |
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| Molecular structure Mechanism of action Spectrum of antimicrobial activity |
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| What is selective toxicity? |
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| -selective toxicity is the ability to inhibit or kill a pathogen without affecting the host. **Growth factor analogs --> structurally similar to growth factors but do not function in the cell |
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| What are growth factor analogs? |
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| Structurally similar to growth factors but do not function in the cell. Play a part in selective toxicity |
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| What are the types of synthetic antimicrobial drugs? |
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| Sulfa drugs - inhibit growth of bact. Isaniazid - growth analog effective only in Mycobacterium (interferes with synth. of mycolic acid) Nucleic acid base analogs - formed by the addition of bromine or fluorine Quinolones - antibacterial compounds that interfere with DNA gyrase |
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| What are antibiotics? |
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| naturally produced antimicrobial agents |
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| What was the first antibiotic covered? describe it? |
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| Penicillin - primarily effective against gram + bact. - some synth. are effective against gram - targets cell wall synthesis |
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| What types of antibiotics are produced by bacteria? |
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| Aminoglycosides - antibiotics containing amino sugars bonded by glycosidic linkage (considered the last-resort antibio) Macrolides - broad spec. that targets 50S subunit of ribosome Tetracyclines (contain four rings) - inhibition of protein synth... inhibits functioning of 30S ribosomal subunit ... *can make u sensitive to sun burn |
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| why may microorganisms be resistent to certain antibiotics? |
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| - organisms lack structure the antibiotic inhibits - organism is impermeable to a.b. - organism can inactivate a.b. - organism may modify the target of the a.b. - organism may develop a resistent biochem pathway - organism may be able to pump out the a.b. |
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| What is efflux? |
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| efflux pump. Proton motor force dependent ABC cassette. Establishes a high gradient outside the cell. Pumps are not very specific : can act on several antibiotics at once |
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| how long does it usually take the immune system to build up a response? |
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| Three weeks |
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| How long does it take for innate defense to kick in? |
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| immediately |
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| What are three characteristics of the immune system ? |
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| 1) specificity 2) universality 3) inducibility (immune response takes time to develop) |
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| what are three characterstics of innate defense? |
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| 1. less specific than ISR 2. Less universal than ISR 3. Is "constitutive": acts immediately, or very shortly, after inflammation. E.g. accute inflammation |
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| What are the bodies three levels of defense? |
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| 1) The surface of the body 2) innate defense (accute inflammation) 3) Immune system |
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| what are the major innate defense mechanisms? |
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| i. accute inflammation ii. phagocytosis iii. complement iv. Interferons |
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| Explain the mechanism of Innate Defence |
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| When a Mast cell gets a signal from an antibody on its surface, small granules that it contains will fuse with the membrane and the cells contents will spill out into the vicinity of the cell. One of those is histimine which will trigger a whole series of reactions tht result in acute inflammation. |
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| what does histimine do? |
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| it causes acute inflammation when it is released from mast cells. |
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| Pathogenicity |
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| Pathogenicity = the ability of a parasite to inflict damage on the host |
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| Virulence |
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| Virulence = measure of pathogenicity |
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| Opportunistic Pathogen |
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| Opportunistic pathogen: causes disease only in the absence of normal host resistance |
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| Infection |
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| Situation in which microorganism is established and growing in a host, whether or not the host is harmed |
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| Disease |
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| Damage or injury to the host impairs host function |
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| what is cystic fibrosis? |
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| Genetic disease where there's a permease that takes things into the cell. A specific permease has a mutation and does not function properly. It changes environment outside the cells all over the body. |
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| How do normal oral microflora colonize? |
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| by first attaching to acidic glycoproteins deposited there by saliva |
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| How many microbial cells are found in GI tract? |
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| 10^13 or 10^14 microbial cells |
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| Which part of the respiratory tract has microflora? |
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| A restricted group of microflora colonizes the upper respiratory tract |
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| Lactobacillus acidophilus |
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| A resident organism in the vagina, ferments the glycogen, producing lactic acid |
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| How does one measure virulence? |
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| Estimated from experimental studies of the LD_50 (lethal dose50) **the amount of an agent that kills 50% of animals in test grop |
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| Attenuation |
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| The decrease or loss of virulence |
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| toxicity |
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| Organism causes disease by means of a toxin that inhabits host cell function or kills host cells |
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| Invasiveness |
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| Ability of a pathogen to grow in host tissue at densities that inhibit host function |
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| What is bacterial adherence facilitated by? |
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| Bacterial adherence is facilitated by extracellular macromolecules that are not covalently attached to the bacterial cell surface (ie slime layer, bio film) - fimbriae and pili |
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| What are the types of exotoxins? What do they do? |
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| Cytolytic toxins : Work by degrading cytoplasmic membrane integrity, causing cell lysis and death AB toxins : consists of two subunits; A and B works by binding to host cell receptor (B unit) and transferring damaging agent (A subunit) across cell membrane. |
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| Describe Botulinum toxin |
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| an AB exotoxin. Consists of several related AB toxins tht are the most potent biological toxins known |
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| Endotoxins |
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| Endotoxin: liposaccharide portion of cell envelope of certain gram - bact. which is a toxin when solubilized --> generally less toxic than exotoxins --> presence detected by LAL assay |
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| Morbidity |
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| Morbidity of a disease refers to the incidence of disease including fatal and nonfatal disease |
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| innase resistance |
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| Collection of non-immune defense mechanisms. *Constitutive rather than inducible |
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| What are the steps in phagocytosis? |
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| 1) binding of bacterium to the surface of phagocytic cell. 2) the envelopment of the bacterium by the membrane of the phagocyte 3) the formation of a phagosome --> phagosome usually fuses with lysosome to form phagolysosome (leading to digestion) |
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| Complement |
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| Mechanism of Innate defense: Series of interacting proteins that initiate one another (one protein comp. will activate another "down stream ... Complement Cascade) |
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| what are complement components involved as? |
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| As inflammatory mediators generated during the inflammatory process. |
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| What is C3b? What is its function? |
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| C3B is an activated component of the third component of complement C3. Binds to surface of many bact. - aids process of phagocytosis --> binding of C3b to the surface leads to the formation of the membrane attack complex ... Results in the formation of holes in membranes |
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| What are the different kinds of interferons? |
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| Alpha, Beta, gamma. Occurs in cells infected by viruses. |
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| What type of interferon does lymphocytes infected by viruses produce? |
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| Alpha-IFN |
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| What type of interferon does virally infected fibroblasts produce? |
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| Beta-IFN |
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| what methods can you use to attenuate a virus? |
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| - passage through other animal species could lower the virulence - application of heat over time |
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| What is passive transfer of immunity? |
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| It is when the cell-free yellow liquid called "serum" is administered to normal, unimmunized animals. It confers protection against the toxins defended against in the serum. **discovery of this led to the discovery of antibodies! |
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| what does immune serum do to bacteria? Why does this happen? |
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| It aggutinates it (causes them to clump together). Bacteria produces soluble, filterable molecules and immune serum contains antibodies specific for these soluble antigens. **precipitin reaction!! |
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| What are the antibodies that facilitate phagocytosis called? |
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| Opsinins |
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| What kind of antibodies are bound to mast cells? |
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| cytophilic antibodies leads to discharge by mast cells |
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| What is humoral immunit? |
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| Humoral immunity are an expression by soluble antibodies. Its effects can be transferred to unimmunised animals by transfer of serum. |
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| What are the major classes of antibodies? |
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| IgM, IgG, IgA, IgE |
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| which class of antibodies causes allergic reactions? |
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| IgE |
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| Describe a unit of antibody |
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| Unit consists of: - two identical light chains (220 amino acids, first region = variable region first 110 aa vary between chains, 2nd half = constant region) 2 identical heavy chain ... first domain is highly variable and nature of other domain determines the class to which the anitbody molecule belongs (IgM, IgG, IgE, IgM) |
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| antibody selection theory |
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| Postulates that antigen selects good fitting antibodies from the vast array that are premade and waiting to be selected |
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| What are the basic elements of clonal selection theory? |
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| Selection Cells able to respond to antigen are clonal (from precursor cell) |
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| What are MHC molecules? What are the different types and their functions? |
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| Major Histocompatibility Complex (MHC) molecules *perform central role in recognition of antigens two kinds: 1) Class I MHC molecules - found on the surface of all cells of the body *hels in self-nonself differentiation 2) Class II MHC molecules are found mainly on phagocytic cells. |
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| T-cells bearing CD4 antigen (CD4+) bind peptides to what ? |
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| T-cells bearing CD4 antigen bind peptides to MHC Class II molecules |
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| T-cells bearing CD8 antigens bind to peptides bound to what ? |
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| MHC class I molecules |
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| What generates T-cells? |
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| the thymus |
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| What is a substance that can induce antibody called? |
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| immunogenic |
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| What is a hapten? |
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| A small immunogenic molecule that can bind (chemically conjugate) to non-immunogenic molecules and induce antibody. |
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| Does removing the thymus prevent an immune response? |
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| Yes. it does remove the immune response |
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| What is immunoincompetent and what causes it? |
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| What causes it?: malfunction of thymus or malfunction of bone marrow cells immunoincompetent is an individual who is unable to emit an immune response |
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| Bone marrow cells and Thymus cells |
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| Both are required in order to create an immune response |
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| Out of bone marrow cells and thymocytes, which is the precurser cell? Why? |
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| Bone marrow cells have antibody receptors on their surface (thymocytes dont) Consistent with the possiblity they are the precursor cells **thermocytes bear on their surface an antigen referred to ask Thy1 |
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| where are the cells corresponding to bone marrow and thymus cells found ? |
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| They are found in the spleen. |
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| What is the function of the thymus cells present in the thymus? where are these same types of cells found? |
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| found in the thymus and lymphoid organs. Needed to allow antigen to induce bone marrow prescusor cells to produce progeny that secrete antibody. They are called helper or inducer T cells. |
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| Helper t-cells exist only for what? |
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| only for foreign antigens |
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| Antigen-bridge model |
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| Hypothesis for the nature of the interaction between B and helper T cells required to induce antibody formation. A B cell can be induced by antigen if a second cell, the helper/inducer T cell, also binds to the antigen. |
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| B-cells express what type of antigens on their surface |
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| B cells express class II MHC antigens on their surface. |
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| What is recognized by helper T-cells ? |
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| peptide MHC complexes |
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| What is the MHC-restricted B cell/T helper cell interaction model? |
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| This model states that -MHC Class II molecules on surface of B cell binds to peptide produced by antigen molecule. -helper T-cells will recognize and bind to peptide-MHC complex. |
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| What happens when a self-antigen interacts with the receptors of a B cell in the absence of helper T cells. |
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| It results in the death of the B cell. This ensures that anti-self B cells are eliminated by a process called antigen-specific inactivation |
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| What is the concept of cross reactivity? |
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| Some antigens have very similar or identical epitopes. If two antigens initiate an antibody (precipitate reaction) than they are said to cross react |
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| What is an epitope? |
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| The area on an antigen molecule complementary to an antibody molecule |
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| what is autoimmunity |
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| immunity to self antigens. Caused by a cross-reaction of an antigenic molecules and non-antigenic molecules |
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| What type of response results in a limited disease? |
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| The induction of an exclusive cell-mediated response results in limited disease |
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| What type of response results in a chronic and/or fatal disease course? |
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| A humoral or mixed cell-mediated/humoral response results in a chronic and/or fatal course |
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| What prompts the cloning of all T cells? |
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| the presence of a particular growth hormone - IL2 - is a growth factor for all T-cells When one T-cell, stimulated with antigen in the presence of IL2, will give rise to upwards of a million identical cells. |
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| Cytokines |
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| Any of a number of substances, such as interferon, secreted by certain cells of the immune system and having an effect on other cells. |
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| What are the two major types of CD4+ T cells? What do they produce? |
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| Th1 CD4+ T cells produce IL2 and IFNg (among other cytokines) Th2 CD4+ T cells produce IL4 and IL10 (among other cytokines) |
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| What does IFNg do? |
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| Can prevent viral multiplication and its delivery to infected macrophages by pathogen-specific CD4 T cells can result in macrophage activation |
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| Macrophage activation |
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| An increase in metabolic pathways that are toxic for most pathogens inside the cell |
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| What does the administration of IL4 do? Which other growth factor does the same? |
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| It increases IgG and IgE responses. IL10 does the same. The presence of IL4 or IL10 favors the induction of humoral, Th2 responses |
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| What does the presence of IFNg cytokines do? |
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| favors the development of Th1 responses. |
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| Which antibody class has subclasses? Why is this? |
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| IgG antibody class has four subclasses, IgG1-IgG4. They are produced under different circumstances |
