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Types of ionizing radiation X-rays Gamma Rays Types of non-ionizing radiation UV light Between 15-400 nm Most lethal UV Absorbs DNA best at 200-290 Most lethalq When DNA absorbs UV Pyrimidine Dimer formation Pyrimidine dimers Abnormal bonding of two adjacent thymines causing a buldge in DNA Caused by UV absorption Repairing UV damage in light Photolyases remove dimer and restores DNA to original form Reparing UV damage in dark Endonuclease chews out DNA DNA polymerase replaced removed section DNA ligase seals the ends Enzymes for UV damage in dark Endonuclease DNA polymerase DNA ligase Nitrogen needed by microbes to biosynthesize Proteins Nucelotides Amino Acids DNA and RNA Sulfur needed to make Cysteine and methionine Remove lids in UV ligfht experiment UV doesn't penetrate plastic Growth only at the top of the tube Obligate aerobes Growth mainly at the top but also throughout the tube Facultative Growth only at the bottom of the tube Obligate anaerobes Even growth throughout the tube Aerotolerant anaerobes Growth in the middle of the tube Microaerophiles Obligate aerobes perform Aerobic respiration only Must have O2 as final electron acceptor Facultatives perform Aerobic, anaerobic, fermentation but grow best with Aerobic Example of Obligate aerobe Staphylococcus epidermidis Facultatives grow best with O2 as final electron acceptor because it has the highest potential and conserves the most energy Example of Facultative E. Coli Microaerophile perform perform aerobic respiration but are Inhibited by high concentrations of O2 Many microaerophiles are Capnophiles- grow best with high concentrations of CO2 Capnophiles grow best with higher carbon dioxde levels Aerotolerant anaerobes perform Preform fermentation but can tolerate O2 Example of aerotolerant aerobes Lactococcus Lactis Obligate anaerobes perform fermentation or anaerobic respiration Obligate anaerobes and oxygen Inhibited or killed by oxygen because they lack the enzymes to detoxify oxygen metabolic byproducts Example of Obligate anaerobes Clostridium Clostridium Strict fermentater Gram positive Endospore former Culturing aerboes Broth cultures with forced aeration Culturing microaerophiles Candle Jar Candle Jar Used for microaerophiles Candle uses up most of the O2 with combustion but not all O2 is used up Culturing Anaerobes Thioglycolate Broth Brewer Anaerobe Jar Glove boxes Thioglycolate broth Reducing media Thioglycolate reduces O2 to H20 Resazurin is pink in presence of O2 Brewer anaerobe Jar Gas pack releases gases to replace O2 Palladium catalyst in lid to combine H2 with O2 to form H20 Methylene blue strip turns blue in presence of O2 Toxic forms of O2 Formed as by-products biochemically by aerobic resperation and photochemically photochemical free oxygen produced by splitting of water molecules by UV Aerobic organisms and facultatives with O2 Have enzymes to eliminate toxic O2 Enzymes used to eliminate toxic oxygen Superoxide dismutase-->hydrogen peroxide(H2O2) Catalase and Peroxidase--> Peroxide to H20 some aerotolerant anaerobes and toxic oxygen MN+2 to tolerate superoxides Obligate anaerobes and toxic oxygen Superoxide reductase--> Reduce superoxides to peroxide without O2 Superoxide dismutase vs reductase Both reduce superoxide to peroxide Dismutase uses O2 and reductase without Which methods count dead cells Electronic counter Spectrophotometer Exponential growth seen in which phase Log Phase Phas most vulnerable to antibiotics and disinfectants Log phase Use the uninnoculated medium to standardize equipment set instrument to 100% transmittance to take into account the absorbance of the media Dependent variable in growth curve absorbance on Y-axis Instrument used to measure growth Spectrophotometer Log phase Fastest growing rate Generation time Time that it takes a cell to divide into two cells Short generations cause faster doubling times Growth in a population measured by innoculating growth medium and counting cells over time Measuring what for growth curve measure turbidity with spectrophotometer not a direct measure of growth but does indicate growth X and Y axis, + slope in growth curve x- Time Y- absorbance Slope- rate of growth Why not likely to get lag/death phases in our experiment ~24 hours for accurate readings Optimum temperature for human pathogens, type and where are they found 37 degrees Mesophiles Found in aquative and terrestial environments in temperature Tropical lattitudes E. Coli temperaturs Min-8 Opt-37 Max-48 Why is turbidity not an accurate measurement of viable bacteria Counts dead cells Operon a segment of DNA containing adjacent genes includes structural genes and an operator gene and a regulatory gene Promoter Region of DNA where RNA polymerase binds Operator Signals whether transcription will occur Regulator Gene binds to the operator to activate or inhibit transcription structural genes a DNA sequence that codes for a specific product inducible operon An operon that is normally off but can be activated and is normally catabolic repressible operon type of operon that is continually transcribed until deactivated by repressors. Trp operon Tryptophan binds to regulator protein, Tryptophan-protein complex acts as a repressor to inhibit more synthesis of tryptophan Operons in E.coli Nar operon encodes genes for nitrate redcutase Ara operon encodes enzymes for catabolism of arabinose Regulatory genes for nar/ara operon in E. Coli Produce a protein that binds to the operator to either inhibit transcription promote transcription of RNA polymerase Ara operon Both positively and negatively. DNA is bent when no arabinose, blocking transcription It bends the DNA when no arabinose is present to block transcription. Arabinose is present, it breaks the DNA look open so that transcription occurs. Biofilm population of different prokaryotes that grow on surfaces attached to water M/o that create biofims usually are encased in extracellular polysaccharide they synthesize As polysaccharide gets larger in biofilms... more microbes can adhere to it quorum sensing cells produce and secrete inducers other cells move towards and produce their own inducers More cells more inducers Biofilms structure and function composed of pillars and channels through which water can flow Brings in nutrients excretes wastes Biofilms and disease More resistant more difficult for immune system to destroy Wavelengths and energy Short wavelengths = more energy Protist autotrophic or heterotrophic multicellular or unicellular eukaryotes lack complex organ systems live in moist environments Protozoans animal-like protists heterotrophic no cell wall Algae protists plant like protists autotrophic cell wall Fungal-like protists Nutrients by absorption Protist movement Cilia Flagella Psueopods Non-motile Vesciles in protist Contractile vacuoles Food Vacuoles Contractile vacuoles A membranous sac that helps move excess water out of the cell. Food Vacuole phagocytosis Cell surfaces in protists Cell walls Cell membranes Cell walls in protists made up of Silica or calcium carbonate Reproduction in Protists Sexual(gametes by meiosis) Asexual(Mitosis) Most do both Fungi characteristics Multicellular molds Unicellular yeasts Strict heterotrophs Saprobes(decompposers) Fungi Cell walls Made of chitin Modified polysaccharide Nitrate reduction operon anaerobic Nitrate as final electron acceptor If O2 present catabolically reduces nitrate since O2 has greater redox potential E. coli uses Nitrate as a terminal electron acceptor when Oxygen is absent Transduction Transferring genetic material from one cell to another by a plasmid or bacteriophage Lysozyme used to lyse the bacterial cells arabinose is a ____ catabolized via Pentose via pentose phosphate pathway Flourescent colonies on which agar plate Arabinose nutrient agar Bacteria get DNA from their environment Transformation E.coli ____ Nitrate to _____ Reduces to nitrite 5M NaCl used in transformation experiment to denature proteins Stabilize DNA Bacteria get DNA from dead bacteria Transformation How were bacillus cells disrupted in the transformation of bacteria lab Resuspension buffer contained lysozyme and Rnase to disrupt cell Why can DNA be spooled out on a glass rod and a protein cant Length of DNA and strength of Hydrogen bonds between 2 strands of DNA. Proteins are too small Why are you sure Spooled product is DNA and not RNA Buffer contained rNAase which broke down RNA into New gene looking for in transformed bacteria phenylalanine Purpose of carborundum in plant viruses abrade the leaf surface to allow viral infection Viruses are in which domain not in any Molds identified by Color Morphology Hyphal organization structure and organization of spores Culture molds on what Sabarouds agar "sac" fungi Ascomycota Winogradsky enhances growth of Bacteria involved in the anaerobic sulfur cycle To infect plants, viruses need Plant to be abraded or damaged insect to carry virus from plant to plant Fungi are strict Heterotrophic Fungi get nutrients Absorbption of nutrients by extracellular enzymes Fungi Cell walls Made of modified polysaccharide chitin Reproduction in Fungi Sexual/asexual spores classification of Fungi by Sexual reproduction Significance in asexual reproduction in Fungi Identify to the genus or species level Multicellular Fungi Mold Unicellular Fungi Yeast Mold structure Mass of Hyphae Septate or aseptate Mycelium mass of hyphae Benefits of Fungi Decomposition mycorrizae fungus that grows close to root, symiotic relationship. Absorbs minerals and helps plant grow. Plant provides sugar to fungus for respiration Yeast oxygen requirment facultative anaerobe Reproduction in yeast Asexual reproduction New cell forms as protuberance Psuedohyphae a short chain of fungal cells that results from the lack of separation of daughter cells after budding Molds Multicellular filamentous fungi Thallus composed of mycelia(mass of hypha strands) Thallus plant body vegetative hypha Essential for growth of mold. Extracts nutrients. Types of Hyphae Vegetative Reproductive Coenocytic Reproductive Hyphae produce spores for reproduction Coenocytic Hyphae hyphae that contain no septa Appear as long, continuous cells with many nuclei Oomycota "water molds" Sexual spores (oospores) Asexual reproduction (zoospores) Zygomycota saprophytic molds with coenocytic hyphae Obtain Nutrients from dead organic matter Asexual spores(Conidiospores/Sporangiospores) Sexual spores( zygospores) Sporangiospores asexual spores in Zygomycota Formed in sporangium Zygospores Sexual spores in Zygomycota Formed by fusion of two cells Ascomycota "sac fungi" Molds with septate hyphae Why sacomycota called "sac" fungi Sexual spores(ascospores) are produced in the sac(Ascus) Basidiomycota "Club fungi" Form sexual spores on clublike basidia Basidiospores Sexual spores of the Basidiomycota "fleshy fungi" Basidiomycota "conjugation fungi" Zygomycota "club fungi" Basidiomycota Sexual reproduction "conjuction fungi" Zygospores Aseuxal reproductiong in "conjuction fungi" Sporangiospores Growth characteristics in zygomycota Coenocytic Hyphae Growth characteristics in Ascomycota Septate hyphae Yeast-like Septate hyphae have cross walls (septa) between individual cells "water molds' Oomycota Growth characteristics in oomycota coenocytic hyphae Coenocytic hyphae hyphae that contain no septa and appear as long, continuous cells with many nuclei Asexual reproduction in ascomycota conidiospores budding sexual reproduction in "sac" fungi ascospores Sexual reproduction in Basidiomycota Fragmentation asexual reproduction in "club fungi" Basiodiospores saprophytic living on dead or decaying organic matter Yeast Nonfilamentous single cell fungi that reproduce asexually by budding or division Psuedohyphae found in Yeasts lysozyme and RNAase Lysozyme breaks down the bacterial cell wall and the RNAase then breaks down the RNA inside so that the DNA can be spooled RNAase this enzyme digests RNA Wet mount microscope settings Condenser down Diaphragm closed Types of plant infections Localized Systematic When things die, microbes decompose them by Proteolysis ammonification Proteolysis Hydrolysis of proteins to form amino acids Ammonification decomposers convert organic waste into ammonia and release into soil Nitrifying bacteria are chemoautotrophs Many inhibited by organic matter Nitrification the oxidation of ammonium compounds in dead organic material into nitrates/nitrites by soil bacteria (making nitrogen available to plants) Denitrification process in which fixed nitrogen compounds are converted back into nitrogen gas and returned to the atmosphere Denitrifying bacteria use what respiration anaerobic respiration Nitrogen fixation process of converting nitrogen gas into nitrogen compounds that plants can absorb and use Nitrogen fixation enzyme Nitrogenase Nitrogen cycle Ammonification (decay to ammonia) Water dissolves (Ammonia to ammonium ions) Nitrification (ions --> Nitrate-->Nitrite) Denitrifcation (Nitrate-->Nitrogen gas) Nitrogen fixation( Nitrogen gas--> Ammonia) Bacteriochlorophylls Found in green/purple Photosynthetic bacteria Generate electrons for ATP synthesis Photosynthetic bacteria in sulfur cycle Use Bacteriochlorphyls to generate electrons for ATP synthesis Use sulfur, Hydrogen gas, etc for electron donors Green photosynthetic bacteria colored by bacteriochlorophylls Purple photosynthetic bacteira colored by large amounts of cartenoids also have bacteriochlorphylls sulfur cycle cyclic movement of sulfur in various Chemical forms from the environment to organisms and back to the environment Why obligate anaerobes grow in thioglycolate broth Sodium thioglycolate combines with water Agar adds increases viscosity viscosity a liquid's resistance to flow Odors of anaerobic decomposition fermentation of amino acid products how are Biofilms beneficial A multicellular network can be generated where each individual bacteria expresses different genes, depending on what it's new purpose is. This can support a higher growth potential, as well as improving efficiency of nutrients reaching desired cells via irrigation type pathways etc. What cell structures help bacteria stay attahced to biofilms Pili Slime Layers flagella capsules axial filaments Inducer for nar operon Nitrate Inducer for ara operon L-Arabinose Value of Nitrate reductase to E. Coli When there is no O2 present, nitrate can be used as a electron acceptor Winogradsky aerobes vs anaerobes Aerobes- Algae, cyanobacteria anaerobes- Green/purple bacteria, Sulfate reducers Media selective for gram negative EMB Media selective for Gram Positive Mannitol Salt Staphylococcus only Usually liquid media Enrichment UVC range biocidal 200-290nm optimal absorption for DNA UVB range 290-320nm also cause damge/mutations in DNA UVA range 320-400nm Not as readily absorbed so not as active UV radiation Non ionizing 15-400 nm Why is quorum sensing important for biofilm formation If the concentration of cells was too low energy spent creating biofilm would be wasted. More cells can synthesize biofilm polysaccharides Beneficial for nutrients and O2 use The aggregate of m/o can have distinct functions to maximize efficiency Diatoms Single cell algae Sabouraud agar Selective for fungi Simple nutrients Low Ph Lag phase A short period of time **prior to exponential growth of a bacterial population during which no, or very limited, cell division occurs. stationary phase new cells are made at the same rate of cell death Phase order Lag Phase--> Log Phase--> Stationary--> Death phase Some photosynthestic bacteria store sulfur Used as electron donor in photosynthesis Producing sulfates Production of Hyrogen sulfide Reduction of sulfates in anaerobic respiration Degradation of sulfur containing amino acids Fermentation of CHO in an anerobic environment provides CO2 for photosynthetic bacteria Favorable growing conditions for Fungi Acidic High osmotic pressure Low moisture Yeasts what type of oxygen requirements Facultative anaerobes Hyphae found in Molds Not in Yeasts Vegetative hyphae grow... in or on the surface of the media Reproductive Hyphae "aerial hyphae" Originate from vegetative Produce asexual spores Most Fungal hyphae is Septate hyphae(separated by cross walls) A few fungi have Coenocytive hyphae Lack septa continous mass of cytoplasm with nuclei EMB Differential for Lactose fermentation Selective for Gram Negative Tichomonas Purple wiggly stuff in the shape of a M/W Plasmodium Purple things inside red blood cells Trypanosoma Purple circular things with hair like extensions Conjugation Transfer of Genetic Material from bacteria through direct Cell to Cell contact Transformation Picking up DNA from outside the cell photoautotrophs Energy from light to reduce CO2 Autotrophs organisms that make their own food Examples of Photoautotrophs Green and purple sulfur bacteria Cyanobacteria Chemoautotrophs autotrophs that obtain energy from oxidation of inorganic molecules Heterotrophs Consumers Photoheterotrophs Energy from light Exampls of photoheterotrophs Purple and green non-sulfur bacteria Chemoheterotrophs Energy from organic compounds Examples of chemoheterotrophs Most bacteria all protozoans, fungi, animals Carbon requirements Make all organic compounds(cell material) CHO polymerized to polysaccharides a.a polymerized into protiens nucleic acids into DNA/RNA Nitrogen requirements proteins(made of a.a) amino acids(amino group) Nucelotides(nitrogenase bases) Phosphorous used for Nucelotides(phosphate group while polymerized) ATP(tri-phosphate) Sufur used for anabolism of Amino acids cysteine and methionine Calcium used for endospore stability