Exam 2

StudyBlue printing of Exam 2 html, body, div, span, applet, object, iframe, h1, h2, h3, h4, h5, h6, p, blockquote, pre, a, abbr, acronym, address, big, cite, code, del, dfn, em, font, img, ins, kbd, q, s, samp, small, strike, strong, sub, sup, tt, var, b, u, i, center, fieldset, form, label, legend, table, caption, tbody, tfoot, thead, tr, th, td { margin: 0; padding: 0; border: 0; outline: 0; font-size: 100%; background: transparent; } body { line-height: 1; } blockquote, q { quotes: none; } blockquote:before, blockquote:after, q:before, q:after { content: ''; content: none; } /* remember to define focus styles! */ :focus { outline: 0; } /* remember to highlight inserts somehow! */ ins { text-decoration: none; } del { text-decoration: line-through; } /* tables still need 'cellspacing="0"' in the markup */ table { border-collapse: collapse; border-spacing: 0; } /* end RESET */ .header { min-width:800px; } .logo { padding:6px 20px 2px 20px; margin:0; font-size:25px; font-weight:bold; color:#808285; position:relative; border-bottom: 1px solid #c5c5c5; } .logo-blue { color:#70adc4; } .logo-desc { font-weight:normal; font-size:19px; color:#cccccc; margin-top:50px; position:absolute; display: none; } .back-button { position:absolute; top:20px; right:20px; font-size:13px; line-height:25px; color:rgb(0,175,225); font-weight:normal; } .back-button a { color:rgb(0,175,225); } .instructions { padding:0; margin:0; width:100%; position:relative; color:rgb(100,100,100); } .step-holder { border-left:1px solid #ededed; margin-left:20px; } .steps { padding:15px 0; float:left; width:24%; border-right:1px solid #ededed; text-align:center; } .steps-01 { } .steps-02 { } .steps-03 { } .steps-04 { } .label { padding:5px 10px; } .print-button { } .print-button a { background-color:rgb(0,175,225); color:white; line-height: 19px; padding:9px 8px 5px 30px; font-size:14px; text-decoration:none; background-image: url(images/printer.png); background-repeat: no-repeat; background-position: 7px 50%; -moz-border-radius: 5px; -webkit-border-radius: 5px; } .print-button a:hover { background-color:black; } .theNote .content { width: 8.0in !important; margin: 5px auto; padding:20px; background-color:white; } .theNote .header { border-bottom: 1px dashed #C8C8C8; font-size: 17px; padding: 0 0 10px; line-height: 19px; color: #00ADE1; min-width:500px; } .theNote .body { font-size: 14px; line-height: 19px; padding: 10px 0; } .theNote{ padding:6px 0; clear:both; background-color: rgb(200,200,200); } .theNote h3{ color: rgb(100,100,100); } .theNote h1, .theNote h3{ background-color:white; padding:2px 20px; width:8.0in !important; margin: 0 auto; font-size: 15px; } .theNote h1{ padding-top: 10px; font-size: 15px; } .theNote h1:first-child{ font-size: 20px; } .theNote h3 { font-size: 14px; font-weight: normal; } #options { border: 3px double #ccc; padding: 5px 12px; margin: 10px 50px 10px 20px; float: left; } #info { border-top: 1px solid #ccc; padding-top: 5px; font-style: italic; } li { margin: 5px 10px 5px 25px; } ul li { list-style: disc; } ol li { list-style: decimal; } img { border: 0; } table { clear: both; width: 100%; border: 1px solid #c5c5c5; border-width: 1px 0; margin: 0; page-break-after: always; } table#page { page-break-after: auto; } td { text-align: center; font-size: 12px; border-bottom: 1px dashed #c5c5c5; height: 1.75in; width: 50%; padding-left: 15px; } .leftside { border-right: 1px solid #cccccc; padding: 0 15px 0 0; } .bottom td { border-bottom: none; } .clearfix { clear:both; line-height:1px; height:1px; } img { max-width:80%; max-height:150px; margin:20px; } @media print {.header { display: none; } .content .header{ display:inherit; } table { border: 1px dashed #bbb; border-width: 1px 0; } .theNote{ background-color:white; } } Chapter 8: Microbial Genetics Transcription: DNA ---> RNA Translation: RNA ---> protein Reverse Transcriptase: RNA ---> DNA Mutation : a change in DNA sequence p. 228 Base substitutions: a single base at one point in the DNA sequence is replaced with a different base Missense: change in the coding of DNA (A to T or CG to GC) causing amino acid sequence to change Nonsense: change in a STOP codon causing the protein to be shorter or longer than it was originally supposed to be Silent Mutation: no change in amino acid Frameshift Mutation potentially more damaging or beneficial to the change of the cell removal or insertion of base(s) it can cause the protein to be expressed differently source of antibiotic resistance Warp mutations can occur errors in DNA replication = spontaneous mutations Mutagens : agents in the environment that directly or indirectly bring about mutation\ Ex. Nitrous acid --- chemical mutagen --- causes mis-pairing of DNA Radiation X-rays, gamma rays: cause DNA breaks nonionizing radiation: UV light thymine dimers: cause frameshift by covalent bonds forming between bases Genetic Recombination exchange of genes between two DNA molecules to form new combinations of genes on a chromosome within an organism, cause changes in amino acids of a protein Ex. Salmonella Flagella: results in changes in antigenicity allowing the Salmonella to better avoid the defenses of the host 3 Ways Bacteria can get New DNA Transformation: uptake/import of new DNA from environment Conjugation/mating: transferring DNA between cells; F. Factor Transduction: bacteriaphage carry DNA to reciprient cell from donor cell Ex. claustridium bitulinum, V. cholera What the "new" DNA could be 1. Genomic DNA: from the same species or a different species 2. Plasmid DNA "mini chromosomes" artificial or naturally occurring Naturally Occurring Plasmids A. F. factor fertility: may get integrated into chromosome yeilding af Hfr cell Hfr (high frequency of recombination) cell: transfer genomic DNA as well as F. Factor allowing exchange of useful genes B. Resistance plasmid: contain antibiotic resistance gene C. Virulence plasmids: carry genes encodoing virulence factors Ex. E. coli enterotoxin Chapter 10: Taxonomy and Survey of Microbes Taxonomy : Science of classification 3 Domains of Life: archaea: methanogens, extreme halophiles, hyperthermophiles bacteria: gram neg. and pos., mitohondria, cyanobacteria, chloroplasts eukaryotes: plants, animals, fungi Endosymbiotic Theory : mitochondrial and chloroplasts evolved from prokaryotes that were engulfed by another cell Taxonomic Ranks below species Strains: population within a species that has distinguishable traits Ex. E. coli k12 vs. E. coli 0157:H7 Type Strain: the strain of a species that defines the species Biovars: strains with biochemical or physiological differences Morphovars: morphological differences (size, shape, endospore position) Serovars: differences in antigenic properties Classification Morphological Characteristics: cell shape, size, etc. Differential Staining: gram staining Biochemical Tests: O 2 relationships, fermentation products/substrates Dichotomous Key: used for identification Figure 10.8 pg. 285 4. Sequence of ribosomal RNA genes: 16srRNA molecular chronometer: measures the passage of time *all organisms have ribosomal RNA *critical for function sequence of RNA is structural and functional *mutations accumulate slowly 16 srRNA gene sequence 1. identify organisms present in a complex population without growing the organisms 2. use sequence data to make probles to detect an organism of interest probe: short piece of DNA of known sequence Ex. detectable by using a fluorescent tag FISH: fluorescent in situ hybridization Important Bacterial Phyla 1. Proteobacteria: largest (includes most species) group enterics: E. coli, Salmonella spp, Shigella spp. pseudomonas aeruginosa: causes swimmers ear, some respiratory infections helicobactor pylori mitchondria 2. Firmicutes: gram positive bacillus spp. clostidium spp. streptococcus spp. 3. Cyanobacteria: "blue green algae", generates O 2 by photosynthesis 4. Spirochetes treponema pallidum borrelia burgdorferi: causes lime disease Chapter 27: Environmental Microbiology Carbon Cycle Photosynthesis photoautotrophs such as cyanobacteria, green plants, algae, and green and purple sulfur bacteria incorporate carbon dioxide into organic matter using energy from sunlight Chemohetertrophs (animals and protozoa) eat autotrophs and then may be eaten by other animals organic compounds of the autotrophs are digested and resynthesized, the carbon atoms of carbon dioxide are transferred up the food chain Chemohetertrophs use organic molecules for energy, therefore when this energy is released through respiration, carbon dioxide becomes available to restart the cycle Most carbon remains with organisms until excreted or they die waste is decomposed by fungi and bacteria oxidizing which returns carbon dioxide back into environment Carbon dioxide is also released into the atmosphere by the burning of fossil fuels from coal and petroleum Nitrogen Cycle Ammonification: release of NH 3 (ammonia); agriculturally important Nitrification: oxidation of nitrogen in the ammonium ion to produce nitrate First: NH 4 --------> NO - 2 (nitrite) Second: NO - 2 ----------> NO - 3 (nitrate) Denitrification: leads to a loss of nitrogen to the atmosphere, especially nitrogen gas NO - 3 ---> NO - 2 ---> N 2 O ---> N 2 (nitrate--->nitrite--->nitrous oxide---> nitrogen gas) nitrate is used as a terminal electron accepter instead of oxygen causing denitrifying bacteria substitutes the nitrates of agriculteral fertilizer --- agricultural problem --- loss of fertility in soil Nitrogen Fixation: process by which bacteria convert nitrogen gas to ammonia Nitrogenase (enzyme) causes N 2 ---> NH 3 agriculturally important Degredation of Synthetic Chemicals Xenobiotic: chemicals that do not occur naturally ex. pesticides, insecticides: highly resistant to degradation Bioremediation: use of microbes to degrade pollutants Water Microbes 1. Microbes as pollutants ex. sewage contaminated water Fecal coliform(E. coli like) bacteria: indicates of fecally contaminated water coliforms: gram neg, rods, aerobes/fac. anaerobes, non-spore forming, ferment lactose 2. Activity of microbes on chemical pollutants eutrophication: addition of organic material and nutrients and subsequent loss of oxygen from a body of water BOD (biochemical oxygen demand): measure of degradable organic material; assumes degradation using aerobic respiration when drinking well water, if large amounts are consumed, the nitrate in the water will react with the hemoglobin causing methemoglobin to present Fe 3+ rather than Fe 2+ Fe 3+ can't carry oxygen properly so you end up with low oxygen to your body can cause blue baby syndrome: lack of oxygen in hemoglobin Waste Water Treatment Systems 1. Primary Treatment nonbiological -- settling and screening particulate (20-25% BOD) goes to anaerobic sludge digestor: where oxygen is almost completely excluded liquid goes to secondary treatment 2. Secondary Treatment biological process goal: to remove remaining BOD (requires oxygen) activated sludge system is the first step trickling filter system is another way Protozoans (aerobic) and aerobic bacteria degrade organic material Coliform bacteria are eaten protozoans 3. Disinfection and release of efferent-chlorine added to kill infections bacteria before being discharged into rivers/oceans 4. Anaerobic sludge digestor methanogens consume remaining carbon methanogens: fermentive bacteria; fed by fermenation products (organic acids) of other bacteria Chapter 14: Principles of Disease and Epidemiology Pathology : the study of disease 1. etiology: cause of the disease; which organism causes it? 2. pathogens: start of disease; how does the disease progress? 3. changes causes by the disease: structural and functional changes Normal microbiota/normal flora skin: salty, dry large intestine: acidic, nutrient rich Sterile urinary tract lungs: macrophages deep in lungs to engulf microbes brain and CF blood Normal flora: Roles 1. compete with potential pathogens for nutrients and space 2. active defense against pathogens ex. bacteriocins: antimicrobial peptides----- E. coli made bacteriocins against enteric pathogens 3. participate in nutrient of host: vitamin K 4. development Symbiosis: relationship between the normal microbiota and the host 1. commensalism: one organism benefits and the other is uneffected 2. mutualism: both organisms benefit from relationship 3. parasitism: one benefits, other is harmed Koch Koch postulates: to determine the etiology of disease Types of infectious disease 1. communicable disease: can spread from person to person 2. contagious disease: easily spread 3. non-communicable disease: ex. tetanus and botulism, bacteria that come from soil endemic: a disease constantly present in a population ex. bronchitis, skin, commom cold epidemic: defined by time period; baseline in short time; defined by place ex. influenza-- H1N1 pandemic: world wide epidemic Development of infectious disease spread of infection: reservoir of infection: place where microorganism survives (lives) before it gets to the host 1. human reservoirs: could not have signs or symptoms but could be spreading it carriers: people who have the disease without signs/symptoms ex. HIV 2. animals zoonoses: diseases that can be spread from animalsto humans 3. nonliving reservoirs: soil and water Opportunistic pathogens organisms that do not usually cause disease, but may cause disease under certain conditions condition of host location of microbe Transmission: mechanism by which pathogen gets from reservoir to host 1. contact transmission A. direct: aka person to person B. indirect: fomite: non-living object involved with spread of disease ex. door handle, railings, utensils C. droplet transmission: somebody coughing or sneezing short distances < 1m 2. vehicle transmission: transmission of inaminate reservoir ex. microbesin large food supply or water 3. vectors: animals that carry pathogens mechanical: flies --- from a fly's feet touching something for ex. biological: involves pathogens life cycle occuring with vector --- animal bite ex. malaria in a mosquito Nosocomical infections: hospital incquired infection 1. microbes in the hospital pathogens normal flora (opportunistic pathogens) antibiotic resistant microbes 2. compromised hosts people who are already ill, or at surgical sites cathetorized patients burns: easily infected by pseudomonas for ex. 3. chain of transmission A. main route of transfer is staff to patients B. fomite transmission: ex. catheters, equipment etc. Control 1. proper use/disposal of equipment 2. disinfection 3. **hand washing 4. infection control teams in clinics and hospitals Emerging infectious disease "new" or changing diseases or becoming more prevalent ex. mutation: different antigenic forms weather patterns ex. mice overpopulation carrying diseases due to weather that provided them more food change in proximity of humans and animal reservoirs ex. lime disease: carried by deer tick people and animals are living closer together causing more risks of disease