Microbiology 303 Final Exam – Flashcards
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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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| 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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| 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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| Lipopolysaccharides |
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| endotoxin that activates inflammatory response that can also cause toxic shock |
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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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| 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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| 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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| 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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| 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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| 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 |
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| Uses for Sugar |
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| carbon & energy sources, storage material, adhesives, parts of other structures, virulence factors, signaling |
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| Stabilizing forces of proteins |
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| hydrophobic interactions, hydrogen bonds, ionic interactions, disulfide bonds |
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| Lipid structure |
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| glycerol backbone with hydrophilic phosphate group and two fatty acid side chains |
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| Hopanoid |
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| planar, rigid structure within phospholipid bilayer; improves membrane stability |
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| Linkage in bacterial and eukaryotic membranes |
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| ester-linked |
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| Linkage in archaeal membranes |
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| ether-linked; more stable |
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| Membrane structure is stabilized by |
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| hydrophobic interactions, hydrogen bonds, negative charges on proteins and cations |
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| Diffusion |
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| passive transport through membrane from high to low concentration |
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| Facilitated diffusion |
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| passive transport flowing down concentration gradient via protein |
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| Symport |
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| transport of two molecules through same protein in same direction |
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| Antiport |
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| transport of two molecules through same protein in opposite direction |
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| ATP-binding cassette transporter |
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| active transporter hydrophobic channel and two proteins that bind ATP for uptake of particular molecule |
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| Group translocation |
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| active transport; intake of one molecule affects the uptake of others nearby via different proteins |
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| ATP synthase |
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| generates ATP through flowing of H+ ions |
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| periplasm location in gram+ |
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| between cytoplasm and peptidoglycan |
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| periplasm location in gram- |
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| between cytoplasm and outer membrane |
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| Functions of the periplasm |
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| has protein-folders, hydrolytic enzymes, used to adjust osmotic stress, transport, chemoreception, detoxification |
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| FtsZ function |
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| forms contractile ring for cytokinesis |
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| MreB function |
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| encircles cell; involved in cell division |
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| Cytoplasm functions |
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| involved in shaping, strength, transport, movement, chromosome separation, cell division, organization |
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| Carboxysomes |
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| CO2 concentrator that contains RubisCO that fixes CO2 |
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| Mitochondria |
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| catabolizes nutrients via TCA cycle to make ATP |
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| Chloroplast |
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| contains thylakoids (folds) where photosynthesis takes place; converts light to ATP & reducing power |
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| magnetosome |
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| bacteria that move along magnetic fields in order to maintain proper spacing in water column to live in environment with right amount of oxygen |
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| Gas vesicles |
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| filled by cell to manage level in water column |
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| Endospore |
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| cell structure that is resistant to heat, radiation, chemicals, dessication |
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| Capsule |
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| adds protection especially against phagocytes of immune system |
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| Outer membrane functions |
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| contains porins to allow passage of small molecules |
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| Peptidoglycan structure |
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| cross-linked glycopeptides; amide bonds between strings of amino acids and glucose derivatives |
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| location of peptidoglycan |
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| in bacteria; one molecule that surrounds entire cell |
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| Techoic acid |
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| stabilizes cell wall in gram+ bacteria |
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| S-layer |
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| lots of disulfide bonds, but function unknown |
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| Gram+ envelope structure |
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| polysaccharides and S-layer (protein) thick cell wall with peptidoglycan cross-links; thin periplasm; contains membrane |
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| Gram- envelope structure |
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| some have capsule of polysaccharide; outer membrane of lipopolysaccharide in outer leaflet; thin cell wall with fewer crosslinks; thick periplasm, plasma membrane |
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| Gram- outer membrane |
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| made of lipopolysaccharides contains O-polysaccharide antigen that determines virulence and can be altered endotoxin |
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| Cell wall structure |
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| made of peptidoglycan and sugar chains linked by amino acid polymer cross-links |
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| Archaeal cell wall |
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| made of peudomurien (like peptidoglycan); may have S-layer, ether linked |
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| Polar arrangement of flagella |
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| one flagellum on cell |
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| Lophotrichous arrangement of flagella |
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| many flagella on one end of cell |
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| Peritrichous arrangement of flagella |
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| multiple flagella at different places |
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| Difference between prokaryotic and eukaryotic flagella |
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| prokaryotic flagella rotate to move cell eukaryotic flagella whip to move cell |
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| Swarming Motility System |
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| movement across solid surface by hyperflagellated cells |
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| Swimming Motility System |
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| movement through liquid medium with flagella |
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| Type IV pili mechanism |
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| "cast & reel" mechanism |
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| Mechanisms of cell movement |
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| swarming, swimming, type IV pili, excretion of surface slime to slide across, rotary motors |
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| Mycoplasma |
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| cell wall-less bacteria; must live in host; tough membrane w/sterols |
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| Thermoplasma |
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| cell wall-less; low pH and high temperature environment; rigid membrane with tetra-ether lipids |
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| Gram Stain technique |
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| distinguishes gram+ and gram- bacteria add crystal violet to bacteria precipitate dye with I- extract precipitated dye this removes all dye from gram- gram positive still contains crystal violet due to the peptidoglycans that are present |
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| Macronutrients for microbes |
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| carbon, oxygen, nitrogen, hydrogen, phosphorus |
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| Sources of carbon |
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| CO2, sugar, organic acids, fatty acids, amino acids |
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| Nitrogen is needed for |
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| amino acids, nucleic acids, peptidoglycan layer |
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| Nitrogen sources |
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| amino acids, nucleic acids, nitrate, ammonia, nitrogen gas |
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| Phosphorus is needed for |
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| phospholipids, nucleic acids, ATP synthesis |
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| Phosphorus sources |
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| phosphate, degraded organics |
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| Micronutrients for microbes |
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| sulfur, potassium, magnesium, calcium, iron |
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| Sulfur needed for |
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| amino acids, vitamins |
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| Sources of sulfur |
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| sulfate, elemental sulfur, dihydrogen sulfide |
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| Potassium use |
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| acts as cell cation |
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| Magnesium use |
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| stabilizes ribosomes, cell membranes, nucleic acids required for ATP-dependent enzymes (forms complex w/ATP) |
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| Calcium use |
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| stabilizes walls and spores |
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| sodium use |
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| maintenance of osmotic balance |
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| iron use |
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| used by cell enzymes |
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| Trace elements needed by microbes |
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| transition elements |
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| Growth factors |
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| used by cell to make coenzymes |
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| Conenzyme of folic acid |
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| tetrahydrofolate |
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| Function of tetrahydrofolate |
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| synthesis of nitrogenous bases |
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| Coenzyme of biotin |
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| biotin |
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| Function of biotin |
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| CO2 fixation |
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| Coenzyme of lipoic acid |
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| lipamide |
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| Function of lipamide |
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| Decarboxylation of keto acids |
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| Coenzyme of Pantothenate |
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| coenzyme A |
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| Function of coenzyme A |
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| utilized in metabolism |
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| Coenzyme form of nicotinic acid |
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| NAD and NADP |
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| Function of nicotinic acid |
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| electron carrier |
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| Coenzyme form of pyridoxine |
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| pyridoxal phosphate |
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| Function of pyridoxine |
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| amino acid metabolism |
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| Coenzyme of Riboflavin |
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| FAD |
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| Function of FAD |
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| electron carrier |
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| Thiamine coenzyme |
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| TPP |
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| Function of TPP |
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| C2 unit carrier |
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| Cobalamin coenzyme |
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| adenosylcobalamin |
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| Function of adenosylcobalamin |
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| transfers methyl groups |
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| Photolithoautotrophs |
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| energy source: light carbon source: CO2 reducing power source: inorganics |
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| Photoheterotrophs |
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| energy source: light carbon source: organics reducing power source: organics |
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| Chemolithoautotrophs |
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| energy source: chemicals carbon source: CO2 reducing power source: inorganics |
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| Chemoheterotrophs |
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| energy source: organics carbon source: organics reducing power source: organics |
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| Chemo- |
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| gets energy from chemicals and organic compounds |
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| Process of division in spherical bacteria |
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| septation |
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| Division in Gram- rod-shaped bacteria |
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| Z ring forms when both nucleoids are present pulls membranes inward synthesizes new peptidoglycan |
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| Division in Gram+ rod-shaped bacteria |
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| Z-ring forms at middle peptidoglycan forms down middle |
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| Min protein function |
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| determines location of Z ring MinE depolymerizes MinCD, causing both proteins to oscilate back and forth when MinE runs out, MinCD complex reforms and causes Z-ring to form |
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| Influences on growth rate |
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| rate of catalysis, metabolism speed, nutrient availability, temperature, pH, gases available |
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| Growth rate constant |
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| rate of exponential growth |
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| Growth rate equation |
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| final # cells= initial # cells * 2^(# generations) |
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| Psychorphile |
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| lives in -5-10 degrees Celsius |
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| Mesophile |
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| lives in 10-45 degrees Celsius |
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| What temperature classification of bacteria infect humans? |
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| mesophiles |
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| Thermophile |
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| lives in 40-80 degrees Celsius |
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| Hyperthermophile |
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| lives in 80+ degrees Celsius |
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| How do cells adjust to cold temperatures? |
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| incorporate unsaturated fatty acids to increase membrane fluidity; express enzymes that are effective at low temperatures |
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| How do cells adjust to hot temperatures? |
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| incorporate saturated fatty acids, more sterols and hopanoids to decrease membrane fluidity; express enzymes resistant to denaturation; use chaperones to stabilize proteins |
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| Strict aerobes |
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| require oxygen |
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| Strict anaerobes |
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| don't use oxygen and are killed by it |
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| Facultative anaerobes |
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| can use oxygen, but can grow without it |
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| Aerotolerant anaerobes |
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| can survive in oxygen, but don't use it |
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| Microaerophiles |
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| require oxygen, but can't survive in atmospheric conditions |
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| How do cells adjust to acidic conditions? |
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| seal off membrane to prevent H+ ions from entering |
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| How do cells adjust to basic conditions? |
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| utilize other monovalent ions for cell processes; use antiport to expel ion and take up H+ ions |
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| Membrane-permeant organic acids |
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| weak acids that can enter cell membrane in uncharged form and then dissociate to cause decrease in pH |
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| Neutralophiles |
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| grow best in pH 5-8 |
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| What pH classification of microbes are pathogens? |
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| neutralophiles |
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| Acidophiles |
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| grow best in pH 0-5 tetraether lipids in membrane decrease H+ permeability |
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| Alkaliphiles |
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| grow best 9-11 diether lipids that prevent proton linkage expel Na+ ions to take up H+ |
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| How do cells prevent water loss? |
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| synthesize compatible solutes |
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| How do cells prevent water gain? |
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| release solutes |
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| Sterilization |
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| process where living cells, spores, viruses, are destroyed on an object |
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| Disinfection |
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| killing or removal of disease-producing organisms from inanimate surfaces |
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| Antisepsis |
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| removal of pathogens from surface of living tissues |
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| Sanitation |
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| reducing microbial population to safe levels |
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| Bactericidal |
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| antibacterial agents |
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| Germicidal |
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| chemical substances that kill microbes and pathogens |
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| Pasteurization |
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| heating food to temperature long enough to kill most heat resistant nonspore pathogens |
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| Decimal reduction time |
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| length of time it takes agent to kill 90% of population |
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| Decimal reduction time is affected by |
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| population size, population composition, agent concentration, duration of exposure |
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| targets of antiobiotics |
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| cross-link assembly in membrane, protein synthesis, nutrient synthesis, gene expression, DNA replication |
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| How microbes resist drugs |
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| add group to antibiotic to inactivate it, pump out antibiotic, lack molecular target of antibiotic, modify receptors so it is unrecognizable |
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| Bioremediation |
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| treatment of radioactive waste using genetically engineered bacteria |
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| Fe/Mn oxidation |
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| oxidize iron, making it insoluble (Fe2+-->Fe3+) gets carbon from CO2 |
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| Methanogenic archaea |
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| reduce CO2-->CH4 |
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| How to drive a reaction by altering concentrations |
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| increase reactants; decrease products |
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| Oxidant |
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| accepts electrons |
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| Reductant |
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| donates electrons |
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| Sign of redox potential that means oxidized form is more stable |
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| negative |
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| Sign of redox potential that means reduced form is more stable |
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| positive |
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| NAD+ |
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| accepts 2e- at once and 2H+ |
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| FAD |
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| accepts 1e- or 2e-, can also accept H+ |
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| one-electron carriers |
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| transition metal complexes that cannot accept protons |
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| Characteristics of energy carriers |
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| phosphorylated compounds or compounds with high energy bonds |
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| Types of high energy bonds |
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| anhydride bond, thioester bond, ester bond |
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| Holoenzyme |
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| complete enzyme |
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| What does catabolism achieve? |
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| chemical energy, reducing power, building blocks for biosynthesis |
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| oxidative phosphorylation |
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| synthesis of ATP by ion-driven ATPase; respiration substrate is passed from carrier to carrier to be reduced and eventually combines O2 and H+ to make water; generates proton motive force |
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| substrate level phosphorylation |
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| synthesis of ATP from ADP coupled with breakdown of bonds; fermentation |
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| NAD+/NADH |
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| energy carrier that donates and accepts 2-3 times more energy than ATP |
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| structure of NADH |
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| ADP attached to stable ring; ring has N base and sugar phosphate |
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| How NADH holds electrons |
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| aromatic ring is disrupted by addition of 2 electrons and H+; must transfer electrons to another carrier or substrate to reduce it |
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| FAD |
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| accepts 2e- and 2H+ to form FADH2 |
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| cytochrome |
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| extracts energy from electron by pushing protons out of cell; must tolerate/avoid oxygen |
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| ETS in steps |
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| 1. protons & electrons brought to flavoprotein 2. electrons passed to Fe/S 3. Proton extruded to make PMF 4. electrons from Fe/S enter quinine pool 5. protons picked up from cytosol 6. electrons are brought to heme and Fe/S clusters of cytochromes 7. electrons from Fe/S centers are brought to heme 8. cytochrome oxidase transfers electrons to final acceptor and consumes protons from cytoplasm |
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| F0 mechanism of ATP synthase |
answer
| a-subunit port of entry for protons interacts with c unit to deprotonate amino acid residue neutralized c subunit can rotate and bring neutral c to exit where proton is lost, and then reprotonated |
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| F1 mechanism of ATP synthase |
answer
| active site on beta unit where ADP and phosphate loosely bind rotation of F0 drives this rotation rotation switches binding to tight state forming ATP Another rotation brings to open state to release ATP |
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| Proton motive force-driven ATP synthesis |
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| splits hydrogen to create protons and provide energy to make NADH and ATP |
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| Sulfur oxidizers |
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| oxidize sulfur to pump out H+ and drive production of ATP and NADH |
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| Iron oxidizers |
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| oxidize iron to pump out H+ and drive production of ATP |
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| Anaerobic respiration |
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| less efficient than aerobic respiration; still involves ETS, but O2 is not terminal acceptor |
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| Nitrate reducers |
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| nitrate-->nitrite, nirate-->nitrogen gas ineffective, toxic only used when oxygen is scarce |
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| hydrogenotrophic methanogenesis |
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| CO2-->CH4 CO2 is activated and then reduced by methanofuran Methanopterin reduces it twice more then forms CH4 |
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| Homoacetogenesis |
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| CO2-->acetate |
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| light-drive energy generation |
answer
| use light to make ATP & reducing power |
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| Light-driven proton motive force |
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| light hits compound to bring electron up an energy level electron flows down transport system to make NADPH or NADH enters a second photosystem to repeat and recycle electrons |
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| Capture of light in archaea |
answer
| involves retinal |
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| sensory rhodopsins |
answer
| drive archaeal cell away from damaging light and towards optimal absorbing light |
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| CO2 fixation |
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| gets reducing power from sulfur containing compounds (anaerobic) or water (aerobic) |
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| organotrophy |
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| organic compounds donate electrons |
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| organic respiration |
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| catabolism with inorganic or small organic electron acceptor using glycolysis, TCA cycle, ETS |
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| Lithotrophy |
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| inorganic compounds donate electrons |
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| methanogenesis |
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| anaerobic with inorganic donor and CO2 acceptor |
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| Photoautotrophy |
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| photolysis of water (aerobic) or others (anaerobic) using photosystems |
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| photoheterotrophy |
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| catabolism with light absorption supplements |
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| What do obligate fermenters lack? |
answer
| ETS |
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| Fermentation steps |
answer
| 1. activate substrate 2. rearrange C skeleton 3. oxidize activated substrate 4. couple reaction to synthesize ATP 5. balance oxidation with reduction 6. excretion of products |
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| What glucose breakdown yields |
answer
| two 3-carbon sugars + 4H+ on NADH |
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| Glycolysis |
answer
| glucose 6-phosphate-->fructose 6-phosphate-(phosphorylation)->2 pyruvates, 2 net ATP, 2 net NADH |
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| Entner-Duodoroff (ED) pathway |
answer
| glucose 6-phosphate-(oxidation)->6-phosphogluconate-->1 pyruvate + 1 G3P-->G3P enters glycolysis , 1 net ATP, 1 net NADH, 1 net NADPH |
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| Pentose-phosphate shunt (PPS) |
answer
| glucose 6-phosphate-(oxidation)->6-phosphogluconate-(decarboxylation)->ribulose 5-phosphate (used for biosynthesis, or converted to pyruvate) makes 1 ATP and 2NADPH |
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| Amphibolic pathway |
answer
| can participate in both catabolism and anabolism, simply by reversing process |
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| Steps that regulate glycolysis |
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| involves steps that are not reversible |
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| How fermentation completes catabolism |
answer
| recycles e- carriers by transferring H's back to pyruvate products |
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| Mixed acid fermentation |
answer
| forms various products depending on pH |
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| Acetyl-CoA |
answer
| esterified coenzyme A to acetyl group |
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| Catabolism of fats |
answer
| uses lipases to generate acetyl-CoA that feeds into TCA cycle by dehydrating, then adding water and oxidizing to ketone |
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| Catabolism of aliphatic hydrocarbons |
answer
| addition of oxygen, then two oxidations |
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| Catabolism of aromatics |
answer
| attach CoA, removal of aromaticity, break ring, then oxidize |
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| Catabolism of proteins |
answer
| broken down to peptides then amino acids to feed into TCA cycle |
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| Cycles involved in CO2 fixation |
answer
| Calvin cycle, reductive TCA cycle, reductive acetyl-CoA pathway, methylotrophic strategy |
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| Calvin cycle steps |
answer
| 1. 3CO2-->G3P 2. 1CO2-->rubisco-diphosphate -->6-carbon product-->2 G3Ps each cycle yields 1 G3P and spends 9ATP |
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| Reductive TCA cycle |
answer
| TCA cycle in reverse, but some enzymes are replaced because they can't run in reverse |
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| Methylotrophic strategy |
answer
| pick up CO2 to detoxify formaldehyde |
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| Biosynthesis of fatty acids |
answer
| CO2+acetyl-CoA-->malonyl CoA that then progresses to form fatty acid and kick off CO2 |
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| Rubisco |
answer
| fixes CO2, housed in carboxysome |
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| Where does nitrogen fixation occur? |
answer
| in cells that have differentiated into heterocysts so that O2 isn't there because nitrogen fixation is toxic in presence of oxygen |
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| Rhizobia |
answer
| fix nitrogen in symbiosis with legumes make leghemoglobin that binds to oxygen and prevent it from reacting with nitrogen fixation; also don't let ammonia freely float around |
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| Why do ensymes require metal cofactors? |
answer
| bind to active sites of enzymes; play structural roles |
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| Siderophores |
answer
| take up iron for bacterial cells; used by pathogens to survive and cause disease |
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| What's the difference between cofactors and coenzymes? |
answer
| coenzymes: organic, required by some enzymes for catalysis cofactors: inorganic, required for or increase rate of catalysis |
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| Nucleoside |
answer
| base + sugar |
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| Nucleotide |
answer
| base, sugar, phosphate |
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| Purines |
answer
| adenine and guanine; double-ring |
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| pyrimidines |
answer
| thymine, cytosine, uracil; single-ring |
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| Difference between RNA and DNA sugar |
answer
| ribose has 2' -OH group, so it's more easily cleaved |
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| What does double-stranding of DNA accomplish? |
answer
| protection from chemical attack; information redundancy; repair mechanisms |
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| Ribozymes |
answer
| RNA that catalyzes reactions |
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| Riboswitch |
answer
| mRNA with a UTR that binds to metabolite in order to hide a ribosome binding site, creating a terminator |
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| Helicase |
answer
| unwinds DNA |
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| Primase |
answer
| adds RNA priming strand |
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| DNA Polymerase III |
answer
| adds nucleotides during replication |
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| Sigma subunit of RNA polymerase recognizes what? |
answer
| -35 and -10 regions and binds to promoter |
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| Rho-independent termination |
answer
| G-C rich stem-loop forms, followed by a series of A's, causing the polymerase to fall off |
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| Rho-dependent termination |
answer
| polymerase stalls and Rho protein cleaves it off |
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| Wobble rule |
answer
| 3rd nucleotide of a codon can bind to something else; G can bind to U or C; U can bind to A or G |
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| Polar mutations |
answer
| block translation, causing a stoppage in downstream transcription, since both occur at the same time |
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| Transition mutation |
answer
| conversion of a purine to another purine or pyrimidine to another pyrimidine |
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| Transversion mutation |
answer
| conversion of purine to pyrimidine or vice versa |
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| Effect of UV rays |
answer
| cause pyrimidine dimers to form |
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| Effects of X-rays and Gamma rays |
answer
| double-stranded breaks in DNA |
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| Effects of oxidation on DNA |
answer
| deamination, depurination, methylation |
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| Mismatch repair mechansim |
answer
| repairs base substitutions substitution is recognized by MutS; Excision is performed by MutL and MutH; repair is performed by Pol I |
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| Base excision repair |
answer
| removal of damaged bases, and then a separation of that gap |
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| Addiction System |
answer
| plasmid has a long-lived poison and a short-lived antidote; daughter cells that inherit the plasmid will survive because they have the antidote code, but ones that don't will die because the poison lingers from the parental cells |
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| Uncoating of Eukaryotic viruses |
answer
| can be uncoated upon attaching to membrane; can be uncoated once inside cell into an endosome (derived from cell membrane); can be uncoated upon attaching to nuclear membrane |
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| RNA-RNA polymerase |
answer
| involved in replication of RNA of viruses; doesn't proofread |
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| +RNA virus |
answer
| has ribosome that makes RNA-RNA polymerase |
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| -RNA virus |
answer
| needs to bring an RNA-RNA polymerase with it because it doesn't have a ribosome to transcribe RNA-RNA polymerase |
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| Viroids |
answer
| naked nucleic acid molecules that act as plant pathogens |
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| Prions |
answer
| single protein molecules that infect |
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| Histidine protein kinase |
answer
| senses stimulus; phosphorylates itself and transfers phosphate to response regulator |
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| phosphatase |
answer
| removes phosphate from response regulator |
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| What does membrane curvature control? |
answer
| where lipids are positioned and localization of some proteins |
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| What shapes membrane curvature? |
answer
| peptidoglycans |
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| Cardiolipin (CL) structure |
answer
| 2 phosphate groups with side chains on each |
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| Where is cardiolipin found? |
answer
| found in bacteria and membranes related to mitochondria and chloroplasts at poles of septum |
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| What does cardiolipin do? |
answer
| destabilizes planar lipid bilayers |
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| How to bend bacteria |
answer
| use lysozyme to turn it into a sphere then confine them to microchambers; sphere membranes will then conform to curvature of the chambers |
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| MinD |
answer
| protein that inhibits division plane formation |
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