Microbiology- Final Exam Study Guide!
Microbiology- Final Exam Study Guide! BIOS 111
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This 11 page Study Guide was uploaded by Sierra Mongeon on Wednesday April 27, 2016. The Study Guide belongs to BIOS 111 at University of Nebraska Lincoln taught by Dr. Kenneth Nickerson in Spring 2016. Since its upload, it has received 165 views. For similar materials see Microbiology in Biology at University of Nebraska Lincoln.
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Date Created: 04/27/16
BIOS 111 Final Exam study guide!! Antibiotic Resistance • Plasmids = R factors • Antibiotics in animal feeds; leads to more resistance + more human disease o 50% of all Abx used in animal foods o Ex: Salmonella in turkeys, used to be non-pathogen. E.coli passed R factor to it, now it’s resistant • R factors passed on by conjugation (transferred to other bacteria) • R factors à Resistance using one of four ways. Bacteria can: o pump out Abx o destroy Abx o change their target o prevent entry Microbial Genetics • divide and produce 2 identical daughter cells (vertical gene transfer; no recombination) = binary fission o can also acquire DNA from outside sources! (horizontal transfer) • Nucleic acids o 4 base pairs = ATCG o structure of DNA is base pairing (AàT, CàG) § it’s the sequence of bases that’s important! § change in sequence = mutation • Prokaryotic DNA replication o Bacteria = one supercoiled circular chromosome o DNA gyrase à coils DNA so it fits inside cell § target of quinolones o Replication forks • Bacterial Sex; partial DNA transfer o Transformation § naked DNA released from donor, taken into recipient cell § competent = able to take in new DNA § some bact. use viruses to transfer DNA o Conjugation § use of sex pilus : hollow protein tube, DNA “injected” into recipient cell § F plasmid = fertility plasmid (able to make pilus) § Most common in Gram – § Genetic map: how fast + what sequence genes are transferred during conjugation § only occurs at 37°C • RNA synthesis: o RNA polymerase attaches to DNA,”unzips” the two strands, and synthesizes RNA from one of the strands using base pairing § single stranded RNA (mRNA, rRNA, tRNA) § promoter/ terminator = start/stop making RNA § ribosomes attach to mRNA before it’s even complete (only in bacteria) • Transcription (making new RNA) and translation (“reading” the RNA and making proteins) occur in the same place. In eukaryotes, transcription in nucleus, then mRNA goes out to ribosome in cytoplasm § Eukaryotes also have introns and exons; introns separate genes, exons are the genes • bacteria = no introns, doesn’t know what to do with them. Must be taken out for bacteria to use euk. DNA • Ribosome function o review notes on protein synthesis and how it works (already posted on studysoup) § 3 types of RNA § codons; start and stop § know names of amino acids (at least recognize them) § peptide bond made by ribozyme (ribosomal enzyme) • The genetic code o 4 bases à 20 amino acids because we use triplet system § triplet: set of 3 base pairs codes for one amino acid § set of 3 base pairs = codon § some aa (amino acids) coded for by multiple codons o triplet system same throughout all life forms (universal) § why viruses can work; bacteria will read viral DNA because it’s the same for all life forms o also degenerate (64 possibilities, but only 20 amino acids) o “cracking the code”: Marshall Nirenberg – protein synth in a test tube § UUU and AAA artificial mRNA § helped us figure out the genetic code! • genetic engineering o human gene (introns removed) injected into B (bacteria)à B now makes human proteins § we can use B as protein synthesis factories for medicine (such as insulin), make prices go down • example: botulism vaccine made from genes put into yeast § called recombinant DNA § removed introns to make cDNA (copy DNA) • reverse transcriptase = cDNA is made from mRNA (transcription backwards) • Mutations o wild type = before mutations o mutation = change in DNA, is inheritable (can occur spontaneously, but very low frequency) o mutagen = something that makes mutation more likely/frequent o clone = identical cells descended from a single cell o auxotrophic = now needs another growth factor that wild type doesn’t need (can’t make on its own) § defective biosynthetic pathway o isolating mutants § bathe culture in mutagen, plate and observe visible differences in colonies § use selective media (only mutant can grow, wild type can’t) § isolating auxotrophs is harder • Replica plate method; use velvet, make a “stamp”, observe where colonies are missing on the new plate o Types of mutations 1. nitrous acidà alters DNA bases and which ones they pair with 2. thymine dimers -covalent change bonds adjacent thymine bases, causes randomization+ probs with replication 3. missense mutation- wrong amino acid in sequence 4. nonsense mutation-premature stop codon = incomplete nonfunctional protein 5. frameshift mutation-deleting a base, screws everything up! o 90% carcinogens are mutagens (and vice versa) o Ames test – way to screen many chemicals to see if they’re mutagens 1. histidine auxotrophs – positive selection; if more colonies on mutagen (His -) plate, then chem. is mutagen 2. rat liver (liver enzymes-detoxify or can create toxin, use to see what would happen in human) Virulence- How we get infections • able to get into body-portals of entry o mucous membranes! (GI, GU, respiratory,eye) • # of invading microbes • adherence (capsules, other attachment mech.) • evading host defenses (macrophages) o able to resist oxidative stress • Causes damage to host o toxins, lysogenic, physical growth blocking things • portals of exit- how it gets out and can infect other cells/people o often same as portals of entry Iron and Virulence • bacteria need iron!= more virulent o LD50 = dose needed to kill 50% of population (mice) decreases with more iron o high iron diets/damage to cells = more likelihood of infection • breast milk and egg whites- contain iron • binding proteins, good! • body’s defense mechanism = keep iron away from pathogen (hide it in liver) o hemolysis of RBC by pathogen releases iron; adaptive function § hemolysin o alcoholismà liver damage = iron release • Transferrin – carries iron through blood to liver o iron binds, is inaccessible to pathogens Epidemiology= study of how diseases are spread • air, water, fomites, animal vectors, sexual or direct contact Virology • virus particle = virion • not alive (not a cell) o protein particle with genetic info. inside o can either be DNA or RNA, but not both! § ds DNA, ds or ss RNA § ss RNA can be the + or – strand • + strand = sense strand, the one you make proteins out of • - strand= nonsense strand, have to first make the + strand from this one, then use + to make proteins • obligate intracellular parasite!! = can’t reproduce without host! • viruses: no cell membrane, no binary fission or ribosomes, not susceptible to antibacterial antibiotics but sensitive to interferon • very small- go through filters • retroviruses = reverse transcriptase, RNAàDNA • Structure of viruses: o Protein capsid – surrounds DNA/RNA o can be enveloped or not § envelope is part of host cell membrane that pinched off • Stages of viral infection (Lytic cycle) 1. attachment a. in mammal, pinocytosis (just sucks virus in) 2. penetration (it gets in – in human cells it’s sucked in but in bacteria it injects DNA through cell wall) 3. biosynthesis – producing new viral parts in host cell, replicates DNA/RNA a. early/late translation 4. maturation – assembly of viral parts 5. release from host cell (either lyses cell or buds off, creating envelope) • specificity in which type of cell they infect d/t surface proteins (where they attach) • Quantifying # of viruses: plaque assay o counting PFU (plaque forming units) instead of CFU – serial dilution § plaque = holes in bacterial lawn, dead or infected host cells • 1 step Growth curve o penetration à latent period (when viruses are being made)à burst (phages released) § burst size varies (30-300) • Plant and animal viruses = very simple o icosahedron (20 sides, looks like sphere under microscope) o capsomeres- proteins forming capsid • Bacteriophage o complex structure to get through cell wall (human viruses very simple – we have no CW) o Hershey-Chase experiment – showed DNA was passed on to offspring. proved that it was component of genetic inheritance, used viruses o long stalk that compresses to inject DNA • Tobacco Mosaic Virus o first virus discovered § crystallization – proved viruses not living-Wendell Stanley • adenoviruses = correlation with obesity • Taxonomy of viruses (classifying them) o type of nucleic acid o shape o envelope or not o size o where they replicate § most DNA viruses = nucleus, RNA viruses in cytoplasm (where ribosomes are) • Retroviruses o RNAà DNAàinto host chromosome § called pro-virus § uses reverse transcriptase o come cause cancer à oncovirus § normal cell DNA changeàcancer cell o lysogenic cycle § Viral DNA à host chromosome § able to replicate with normal host DNA, passed on § can “turn on” viral DNAà lytic cycle • viral protease: cleaves polyproteins produced by viral genes into their separate components o Viral DNA responsible for many protein toxins o target of drugs = reverse transcriptase and viral protease (unique to viruses) Prions • infectious protein particles o no nucleic acids!! o affect nerve cells only; conformational change in protein makes nerve cells non-functional o long incubation (long time between exposure and showing symptoms) o can survive autoclaving o does not trigger immune response!! (seen as one of body’s own proteins) o no treatment o no way to diagnose- detect with autopsy, “sponge- like” brain • Diseases caused by prions: mad cow disease, kuru, Creutzfeld-Jakob disease (CJD) • Spread: altered conformation of normal protein = loss of normal function, consumption of prion • British cattle quarantine: o cattle fed sheep parts; sheep had scrapie; parts were rendered (heated) but prions survived o infected cowsàbeef (especially ground-had brain mixed in)àhumansà increased CJD incidences Immune System • can distinguish self from non-self antigens (Ag) • non-specific- general defenses o intact skin, § low pH, dry, UV radiation o stomach acid, normal gut flora, lysozyme in eyes, interferons o macrophages = phagocytosis § take in pathogen, bombard with ROS and nitrogen species, “digest” it • Specific/acquired immunity- recognizes specific pathogen and targets/kill it o can be naturally or artificially acquired; then active or passive (active: you make the Ab, passive: Ab made for you) § Naturally: • active: Ag enter body, body produces Ab • passive: Ab passed from mother to fetus § Artificial • active: vaccines • passive: inject pre-formed Ab into body in emergency o Antibodies (Ab) = immunoglobulins (Ig) § Y shape, 2 Ag binding sites, 4 protein chains • C chain = constant, defines basic shape • V chain = variableàspecificity of Ab to pathogens • heavy (long) and light (short) chains § epitopes recognized by Ab • polyclonal = mixture of Ab, can recognize multiple epitopes (like in blood) • monoclonal= one specific type of Ab reacts with one epitope (ideal in lab) § Types of Ab: • IgG = “standard” Ab, 80%, “monomer” • IgE= allergic rxns • IgM=pentamer (10 binding sites, polyvalent), first Ab produced in initial infection • IgA=dimer, mucous membranes-first line of defense, has secretory component (sends them where they need to go) • IgD = surface of B cells (memory cells), initiation of immune response o Primary and Secondary responses § primary = low Ab conc., body needs more time to recognize, make Ab to and fight infection § secondary= 2 and subsequent exposures, body already recognizes and has Ab, can fight quickly • basis behind vaccinations o Immune cell types: B and T cells § B cells make Ab, kill pathogens in blood (humoral immunity) § T cells kill non-blood related pathogens (cellular immunity) • bind to Ag on infected cell surface, release cytokinesàstimulate other parts of immune system • Weakened defenses: o wound/puncture o broad spectrum Abx (kill good bacteria in gut) o immunosuppressive drugs (as with organ transplant) o primary infection (often leads to secondary infection) § observe gnotobiotic (germ free) animals – they have no immune system Vaccinations • increase life expectancy (kids not dying of infections) • attenuated (weakened) or killed bacteria/virus • “Growing” viruses for vaccines/diagnostics; how? o tissue culture § Nobel peace prize for people who discovered how to do this § human tissue sterilized with Abx § normal + transformed (infected) cells separated, virus purified from trans cells o egg § why you can’t get flu shot if allergic to eggs § How they’re grown in eggs-injected into various parts Diseases of the Day Toxic Shock Syndrome (TSS) • S. aureus • Low Mg environment = produces TSST (TSS toxin) o Associated with tampons; made with material that binds to Mg and takes it out of environment • Most TSS cases following nasal surgery (remember S. aureus in nose) or childbirth • TSST: protein toxin, produced by bacteria outside body but goes into body o Superantigen à excess immune response o Cytokines released by T cells à loss of fluids/electrolytes from bloodà very low blood pressure Typhoid fever**different than typhus! (remember sound-alikes) • Salmonella typhimurium or typhi • Caused by dirty water o Decline in cases after water purification implemented § Purify water with filtration, ozone, chlorine • Carriers: have no symptoms, but carry disease o Typhoid Mary Salmonellosis (Food Poisoning) • caused by salmonella other than the ones that cause typhoid fever • #1 food bourne illness • animalsà humans (zoonosis) o often from reptiles/amphibians; bact. is cold adapted (because reptiles cold blooded) and can survive in fridge o Komodo Dragons – bite prey, inject salmonella, prey infected and dies Rabies • Caused by bullet shaped virus (rhabdovirus) o ss RNA, - strand • zoonosis (get it from animals) o from animal bite o usually raccoon, skunk, fox o virus in saliva • virus replicates in muscle à nervous system à CNS (brain) and also other organs o from time of bite until time virus enters nervous system, you have 4 weeks to years!! § can inject immunoglobulins, only case where you can vaccinate after already being infected!! § HDCV (human diploid cell vaccine) uses killed viruses; only vaccinate if bitten § once it gets into nervous system, its hidden from immune system (BBB) • mandatory vaccination for domestic animals Smallpox • Europe in Middle ages, highly contagious variola virus o 30-40% mortality, survivors had scars/blindness • Spread through air, fomite; resists drying • Reason Europeans were able to conquer the Americas – 90% Native American population, Aztec population killed by smallpox • Symptoms: o lesions all over body, sometimes run together • airàlungsàbloodàskin • Significance in vaccine development: o cowpox protects against smallpox o Edward Jenner o “buying the pox” – getting weakened versions of virus • WHO eradicated disease in 1977 o no animal reservoirs (only human disease) o lyophilized vaccines to tropical countries (more stable) o bifurcated needles = no syringe needed for vax delivery Polio • picorna virus- ssRNA, very stable (survive long time) • usually infected children- from swimming pools (d/t fecal-oral contamination) • ingestàmultiply in throat/intestineàlymph nodesà blood (viremia) o only 10% infected people have symptoms – usually fever, headache, sore throat o removal of tonsils (lymph nodes) o for 1% cases, bloodàCNSàparalysis § iron lung- can’t breathe on own, machine helps § march of dimes § president FDR o Recoveryà 30-40 yrs later post-polio syndrome (deteriorating muscles) o Vaccines § Salk 1954-injection, inactivated (“killed” with formaldehyde) virus § Sabin 1963 - OPV= oral polio vaccine, used weakened virus, protects against 3 types • actually gave some people polio o CDC attempts to eradicate polio, but religious and political conflict= people refuse vax (India/ Middle East) SARS-severe acute respiratory syndrome • epidemic in Toronto; able to be treated quickly + successfully d/t previous knowledge of polio o discovered 2003 à recognized as viral à grow in cultureàin 6 days had entire genome sequenced o 1 wk later = diagnostic kit, Koch’s postulates with monkeys Common cold • Caused by at least 200 different agents o 50% rhinoviruses, 20% coronavirus, other cases unidentified o no vaccine d/t variety of causes • in day care- exposed to 10-15 new viruses per day Influenza • 1918 Spanish flu pandemic (worldwide infection-killed millions) o killed people age 15-45 (supposedly healthy, “in their prime” • spread through air (coughing, sneezing) • modern times: people die from secondary bacterial infection, pneumonia • enveloped, ss RNA (- strand) segmented into 8 genes o proteins in envelope = spikes, N and H (help in naming strain of virus, example is H1N1) § H = hemaglutin, clumps RBCs together § N=neuraminidase, helps viruses get out of host cell • inhibited by Tamiflu (effective antiviral Abx) § Flu shot- protects against 3 known strains, prediction game (which one will be big this year?) • virsues grown in eggs o Flu mist if allergic to eggs • inactivated with formaldehyde • Why does flu change so much? (why we need yearly vax) o The H and N antigens change very easily, genetic recombination o antigenic drift- small change o antigenic shift- large change in genes, d/t crossing species barrier (remember bird and pig example) Yellow Fever • mosquito-bourne virus; arbovirus o type of mosquito = Aedes aegypti § same one that transmits zika, other diseases § only female bites • mosquito bites infected monkey (reservoir)àmosquito bites infected human o biteàskinàlymph nodesàspleen, kidney, liver (damage to liver causes jaundice) o recovery = immunity, 10-20% mortality • Historical importance o Panama Canal- first attempt 50% workers died from yellow fever § 2 attempt- drain standing water, spray water with kerosene, success of canal d/t controlling mosquitoes o Louisiana Purchase – why it was so cheap! o French conquest of Haiti o now, vaccination, killing of mosquito larvae West Nile Virus • mosquito bourne flavivirus o ss + strand RNA, envelope o Culex mosquito (in NE!) • infects more animals (horses, birds) than people o only killed about 5 elderly people o horses vaccinated, decrease in bird (owls, blue jay) population HIV (Human immunodeficiency virus) § leads to AIDS (acquired immunodeficiency syndrome) § Came from SIV (in chimpanzees) § slow progession - 10 years from infection time to symptoms § Infects T cells of immune system o attaches to CD4 receptors on surfaceàdrawn inà makes DNA and incorporates into chromosome o gp120 spikes = how it attaches to CD4 § puts these spikes on surface of T cellà T cells clump together (attach to other CD4) and are non-functional § decline in immune function o die from opportunistic pathogen – mainly TB and C. albicans o also, rare cancers (Ex. Karposi’s sarcoma) § prevalent in Sub-Saharan Africa § Spread via blood, semen, infected needles o NOT through kissing, air, fomites, toilet seats o prevention: safe sex, clean needles, thorough screening of blood to be transfused o male circumcision = 65% less likely to get infected § Treatment = many drugs, very expensive
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