Evolution and Ecology of Microbes – Flashcards
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| Wastewater Treatment |
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| screens remove large items fine screens remove sediment microbial ecosystems decompose soluble wastes chemical applications remove everything else |
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| Faculative Intracellular Pathogens |
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| can live in host or freely |
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| Intracellular Pathogens |
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| seek refuge by invading host |
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| Pollutants that cause eutrophication |
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| nitrogen, phosphates |
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| Cold Seeps |
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| microbial communities at unheated benthic where methane and petroleum seep out |
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| Amensalism |
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| one species harms another (nonspecific) |
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| Synergism |
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| mutualism, but both species can thrive separately |
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| Syntropy |
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| feeding together of two species on something that wouldn't otherwise be digestable |
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| Metagenomics |
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| sequencing of genomes in an environmental community |
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| Pan-genome |
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| core genome and accessory genes present in isolates |
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| Core genome |
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| genes present in all sequenced genomes of species |
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| Hopanoids |
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| steroid-like molecules of bacteria membranes |
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| Pulsed-field gel electrophoresis |
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| high resolution separation of large DNA fragments |
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| Restriction Fragment Polymorphism (RFLPs) |
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| variations in number and size of DNA fragments made by using restriction endonuclease |
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| Serotyping |
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| identifying variations within subspecies of pathogen |
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| How technology spreads disease |
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| colonization of woods and rainforests transplants and transfusions modern meat-processing transportation |
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| Pandemic |
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| epidemic over large area |
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| Propagated Epidemic |
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| epidemic where infected spread disease to healthy |
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| Epidemic |
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| outbreak, high frequency over short period from one source; little transmission by infected |
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| Endemic |
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| low frequency of disease; normally present |
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| Epidemiology |
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| study of factors affecting illness and health of populations |
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| Hemolytic Uremic Syndrome (HUS) symptoms |
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| destruction of red blood cells kidney failure infection by AB toxins |
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| Pathogenic E. coli symptoms |
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| internal bleeding bloody diarrhea |
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| Tuberculosis Infection Cycle |
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| encountered in air enters lungs infects lungs and can remain latent most damage caused by immune response |
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| Survival strategies for pathogens of of cell, but still in host |
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| secretion of capsule manufacturing of proteins that bind to antibodies cause apoptosis of phagocytes alter cell surface (all to avoid detection and attachment of antibodies) |
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| Survival strategies for pathogens in cell |
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| use hemolysin to break out of phagosome secrete proteins to prevent fusion of phagosome with lysosome mature in acidic lysosome |
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| Vectors |
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| intermediates for pathogen transmission |
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| Fomites |
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| inanimate objects that relay pathogens |
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| Opportunistic pathogens |
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| cause disease in compromised host |
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| Primary pathogens |
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| cause disease in otherwise healthy host by breaching defenses |
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| Signature-tagged mutagenesis |
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| mutate pathogen and tag it inoculate host recover pathogen and determine which mutations prevented growth in host |
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| in vivo expression technology |
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| identify promotors that transcribe only when infecting a host |
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| Type IV secretion pathway |
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| similar to conjugation transports DNA and proteins |
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| Type III secretion pathway |
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| injects proteins directly into host using flagellum injection induces engulfment |
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| Type II secretion pathway |
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| uses structures similar to pili that extend/contract for motility and injection of toxins |
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| Type I secretion pathway |
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| proteins form continuous pathway through membrane of bacteria |
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| Lipopolysaccharides |
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| endotoxin that activates inflammatory response that can also cause toxic shock |
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| Anthrax toxin |
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| edema factor raises cAMP levels causing fluid secretion/swelling lethal factor cleaves protein kinases, which halts immune system |
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| Diphtheria |
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| blocks ribosome causing cell death |
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| Cholera toxin |
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| ribosylates overactivate adenylate cyclase cAMP activates ion transport, water follows causing diarrhea |
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| AB toxin |
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| 5 B subunits surround A and delivers A to host A subunit is toxic |
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| 5 types of toxin function |
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| 1. causes host cell membrane leakage 2. block protein synthesis 3. block 2nd messenger pathways 4. superantigens overactivate immune system 5. proteases cleave host proteins |
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| Pilus assembly |
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| protein secreted into periplasm secreted to site of assembly subunits strung together tips of pili bind to host |
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| Type IV pili |
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| mannose resistant dynamic; various surface arrangements |
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| Type III pili |
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| mannose resistant; bind to red blood cells |
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| Type I pili |
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| adhere to mannose residues on host cell surface |
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| Pili/Fimbriae |
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| hollow fibrils made of pilin with tips that bind to host prevents expulsion from host |
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| Pathogenicity island characteristics |
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| multiple genes associated with pathogenicity transferred as block from other organisms flanked by phage or plasmid genes different base ratio than other parts of genome |
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| Examples of virulence factors |
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| toxins, attachment proteins, capsules |
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| Lethal Dose (LD50) |
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| number of organisms to kill 50% of hosts |
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| Virulence |
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| frequency of lethal infections |
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| Infectious Dose (ID50) |
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| number of organisms to colonize 50% of host measure pathogenicity |
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| Exotoxin |
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| nonprotein; hyperactivates immune system |
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| Endotoxin |
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| toxic proteins; kills host to unlock nutrients |
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| Pathogenicity |
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| ability to cause disease |
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| Steps of Infection |
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| 1. encounter 2. entry 3. establish infection 4. cause damage |
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| Benefits of biofilms to microbes |
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| protection from: predators phages biocides antibiotics immunophagocytes antibodies |
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| Biofilms |
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| community of bacteria enclosed in ECM |
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| Quorum sensing compounds |
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| oligopeptides (gram +) n-acyl homoserine lactones (AHLs) (gram -) Al-2 INTER species communication (gram +/-) |
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| Uses of quorum sensing |
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| adapt to availability of nutrients defense avoidance of toxins coordination of virulence to escape immune response and establish infection |
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| Quorum sensing |
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| ability of bacteria to communicate and coordinate behavior via small molecules (inter and intra species) |
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| Microbial predators |
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| protists, viruses, bacterial predators |
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| Tube worms and microbes |
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| worm takes up CO2 and H2S microbes must oxidize to make organic matter |
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| Metabolism of deep sea ocean vents |
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| producers oxides H2S for energy methanogens and methanotrophs prevent CO2 buildup hydrogen oxidizers convert H2 and S --> H2S |
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| Hawaiian bobtailed squid |
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| host for bioluminescent bacteria bacteria emit light to match moonlight to eliminate shadow on ocean floor undetectable by predators |
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| Microbes and coral |
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| bacteria and algae help coral fix N2, photosynthesis, protection against pathogens |
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| Rumen and microbes |
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| break down cellulose in anaerobic environment |
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| Arbuscular mycorrhizal fungi |
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| improve acquisition of phosphate, nitrogen, water reduce incidence of root disease |
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| Rhizosphere |
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| region of soil surrounding rocks |
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| Rhizoplane |
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| root surface |
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| Mycorrhizae |
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| fungal infection in plants that increase ability to absorb nutrients |
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| Rhizobium infection cycle |
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| legumes secrete flavanoids rhizobia express nod genes and enter cortical cells remains in symbiosome Rhizobia fix nitrogen; plant provides nutrients |
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| Chloroplast homolog |
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| cyanobacteria |
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| Mitochondria homolog |
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| rickettsiae |
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| Syntrophy |
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| both organisms combine metabolic capabilities to catabolize substances they couldn't alone |
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| Winograsky column |
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| model of wetland with regions of enrichment for different microbes |
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| Cycle leading to acid rain |
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| phytoplankton produce DMSP to protect against UV other bacteria convert DMSP-->DMS (volatile, acts as nuclei for cloud formation) DMS is hydrated to sulfuric acid, which falls as acid rain |
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| Characteristics of phosphorus cycle |
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| same oxidation state no gas intermediate soluble in oceans |
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| Dissimilatory nitrate |
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| used as and e- acceptor in e- transport chain |
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| Assimilatory nitrate |
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| used as nutrient |
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| Annamox |
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| anaerobic formation of N2 from ammonia and nitrite |
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| Denitrification |
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| cascade of anaerobic respirations converting nitrate-->N2 nitrate-->nitrite-->nitric oxide-->nitrous oxide-->nitrogen gas |
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| Nitrification |
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| ammonia-->nitrite-->nitrate oxidation makes nitrogen available to plants |
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| Nitrogen fixation |
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| nitrogen gas-->ammonia nitrogenase reduces nitrogen complex cofactors make it oxygen sensitive |
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| Methylotrophs (rxn too.) |
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| oxidize methane to CO2 CH4 + SO4 --> CO2 + H2S + OH- CH4 + H2O --> CO2 + 4H2 removal of H2 drives rxn to right |
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| Methanogenic Archaea |
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| break down trapped carbon compounds in anaerobic environments to CH4 |
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| Why viruses aren't "living" |
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| no cellular integrity only a protein and nucleic acid depend on host for survival and replication |
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| Dinoflagellates |
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| alveolate 2 long flagella red algal chloroplast secrete neurotoxins via extrusome |
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| Yeast classification |
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| unicellular fungi |
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| Growth of fungi |
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| growth material is secreted at hyphal tips |
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| Fungi food absorption |
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| must absorb as individual molecules |
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| Material of fungi walls |
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| chitin |
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| Alveolates |
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| ciliated protists |
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| Protist classifications |
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| amoebas, alveolates, heterokonts, euglenozoa, excavates |
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| Archaeal genomes |
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| circular, similar to bacteria |
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| Protein chemistry for increased stability |
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| ion pairs, acidic/basic residues, disulfide bridges, hydrogen bonds, hydrophobic interactions |
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| Archaeal lipids |
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| ether-linked, making it more resistant to acid and heat |
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| 2 phyla of Archaea |
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| Crenarchaeotes Euryarchaeotes |
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| H. pylori |
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| causes stomach ulcers |
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| Gram-negative proteobacteria |
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| light-supplemented heterotrophs adaptable metabolisms |
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| Akinetes |
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| specialized pore cells survive desiccation and then germinate at better conditions |
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| Hormogonia |
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| short chains of motile cells |
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| Gas vesicles |
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| used for buoyancy to maintain position |
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| Carboxysomes |
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| carbon dioxide fixation location |
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| Thylakoids |
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| photosynthetic apparatus separate from plasma membrane |
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| Heterocysts |
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| cell part specialized in nitrogen fixing |
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| Cyanobacteria |
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| oxygenic phototrophs photolyze water to make oxygen photolyze hydrogen reduce sulfur compounds only bacteria producers |
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| Chloroflexi |
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| phototrphic, filamentous moderate thermophiles lots of membrane-bound chlorophylls |
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| Xerophile |
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| have little water activity |
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| Psychrophile |
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| live at low temperature environments |
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| Oligotroph |
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| live in low carbon environment |
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| Hyperthermophile |
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| live in high temperature environments |
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| Halophile |
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| lives in high salt environments |
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| Endolith |
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| live within rock crystals |
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| Prebiotic soup |
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| basic components from abiotic factors infused with electricity formed biomolecules |
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| Panspernia |
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| idea that life came from other planets |
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| Metabolism of early microbes |
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| sulfur-based anaerobic metabolism reduction of nitrate and sulfate |
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| Early Earth atmosphere |
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| CH4, CO2, N2, NH4+, H2S, FeS, CO, H2 |
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| Viroids |
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| infectious single strand RNA |
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| Stanely Prusiner |
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| studied prions causing scrapie |
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| Fleming |
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| discovered penicillin killed gram + bacteria |
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| Hershey and Chase |
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| demonstrated DNA is responsible for bacteriophage infection |
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| Koch's postulates |
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| microbe found in all cases, but not healthy microbe isolated and grown induce disease by introducing microbe can obtain microbe from diseased |
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| Leeuwenhoek |
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| first to observe bacteria with a lens |
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| Robert Hooke |
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| developed first compound microscope |
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| Louis Pasteur |
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| germ theory boiled broth in necked glass exposed to air to disprove spontaneous generation |
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| Lazarro Spallanzani |
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| boiled broth in evacuated chamber and sealed, no spontaneous generation thought that spontaneous generation required air |
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| John Needham |
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| boiled broth that clouded days later; thought to be spontaneous generation |
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| Francisco Reidi |
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| studied infestation of maggots on meat |
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| Edward Jenner |
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| used cowpox pustules as smallpox vaccine |
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| Microbes are: |
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| ubiquitous abundant diverse |
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| RNA World Theory |
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| RNA can: store info duplicate catalyze (ribosomes) later, DNA and proteins took over these roles |
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| Definition of Life |
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| structure and form catalytic activity self-replication membrane compartmentalization metabolism of energy |
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| Barophile |
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| live in high pressure environment |
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| Alkaliphile |
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| live in basic environments |
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| Acidophiles |
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| live in acidic environments |
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| Metabolist theory |
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| components of metabolism arose from self-sustaining abiotic rxns proteins and metabolism formed first |
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| Extremophiles |
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| species that grow in extreme environments |
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| Psychrophiles |
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| thrive at cold temperatures |
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| Paralogous proteins |
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| gene duplication and independent mutation of two protein lines |
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| Orthologous proteins |
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| proteins that diverge from one another in different species |
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| Proteobacteria resemble... |
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| mitochondria |
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| Endosymbiosis example: sea slug & chloroplasts |
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| sea slugs engulf chloroplasts chloroplasts perform photosynthesis |
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| Endosymbiosis example: aphids |
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| have symbionts that make essential amino acids for them |
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| Endosymbiosis example: amoeba and cyanobacteria |
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| cyanobacteria provides food amoeba provides protection |
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| Virulence factors |
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| help establish organism that can alter host functions to cause disease |
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| Immunopathogenesis |
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| when immune response to pathogen is contributing cause to pathology |
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| Genomic islands |
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| group of genes transferred together horizontally frequently linked to tRNA abnormal base-pair ratio flanked by genes similar to phage/plasmid |
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| Horizontal gene transfer |
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| DNA transfer via plasmids, transposons, bacteriophages with genes coding for metabolism, stress response, pathogenicity |
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| Vertical gene transfer |
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| parent-->child |
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| Reductive evolution |
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| loss or mutation of DNA encoding for unselected traits |
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| Shared ancestor (progenote) characteristics |
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| genetic code fueling pathways protein synthesis very inefficient |
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| When microbes originated |
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| 3 billion years ago |
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| Requirements for phylogenetic marker study |
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| gene must be present in organisms studied gene can't be horizontally transferred gene must have conservation must be large enough |
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| Chemiosmotic theory |
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| redox reactions of e- transport chain store energy in proton gradients in mitochondria |
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| Lithotrophs |
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| feed on only inorganic minerals |
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| Archaea |
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| can survive extreme pH and temperatures |
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| Lichens |
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| algae live in fungus algae provides food fungus provides protection |
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| Stomalites |
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| layers of earliest microorganisms |
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| Types of microbes |
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| bacteria archaea eukaryotic microbes: yeasts, protists, algae |
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| Thermophile |
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| live in hot water branched off early |
