MIC 320 Exam 2 Study Guide
MIC 320 Exam 2 Study Guide MIC 320
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This 17 page Study Guide was uploaded by Serena Buckley on Friday March 6, 2015. The Study Guide belongs to MIC 320 at University of Miami taught by Roger Williams in Fall2012. Since its upload, it has received 67 views.
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Date Created: 03/06/15
Exam 2 Review Lecture 8 Classi cationThe ordering of things into groups TaxonomyThe science of identi cation classi cation and nomenclature PhylogenyThe classi cation of species based on evolutionary or natural relationships Early idea of Phylogeny 2 ideas pre Koch 1 Some thought that the different forms of bacteria were in fact different stages of one species pleomorphic 2 Others thought that these different forms of bacteria represented separate species Modern ideas on bacterial phylogeny postKoch 2 ideas post Koch 1 Forms bred true rod 2 Nutritionally requirements andor biochemical properties also bred true Convergent Evolution Functionally similar but evolutionarily unrelated 2 or more bacteria s that are evolutionarily unrelated but have similar traits ie Birds vs Bats Divergent Evolution Functionally dissimilar but evolutionarily related 1 ancestry evolutionarily related but have different traits Limitations of the quottraditionalquot approach 1 False phylogenies due to convergent evolution 2 Usually requires culturing the microbe Chronometer keeps track of time Determines true39 phylogenies Does DNA sequence and analysis and calculates evolutionary distance by sequence differences 16S rRNA advantages 1 All organisms have it all living organisms have 165 rRNA 2 Very similar overall structure well conserved 3 Can determine sequence without culturing ie growing the bacteria Why is there such metabolic diversity among the bacteria Bacteria can make a living in diverse ways Microbial Metabolism derive energy Phototrophs plants amp microbes get their energy from the sun light ATP Chemoorganotrophs humans animals fungi amp microbes get their energy from organic compounds ie glucose acetate etc organic compound redox rx D ATP Chemolithotrophs microbes ONLY get their energy from inorganic compounds ie Hydrogen Hydrogen Sulfur Iron etc inorganic compound redox rx D ATP Energy Sources High Energy e require light or e source Low Energy e require a good e receptor BOTH need PROTON motive force ATP Redox Reactions Example H2 l 2e39 2 H E39 source Electrondonating half reaction 1st half donating reaction 12022e39 DO E39 acceptor Electronaccepting half reaction 2 I half acceptor 2H 0239 l H20 Formation of water Final output from 1st and second half D donor acceptor reaction 2 things determine how much energy is released 1 Energy level of the electrons provided by the donor 2 How easily the electron acceptor accepts the electron The Electron tower ranking of electron accepting half reactions based on how easily they occur Animals require glucose for electron donors and oxygen as the terminal electron acceptor Ultimate goal of the e is to produce a proton motive force which is ATP The more negative the more energy released Proton Motive Forceenergy from redox reactions used to generate a proton gradient across the membrane Gain e REDUCE Loose e OXIDIZE When ATP is hydrolyzed to ADP Pi energy becomes available to the cell The phosphorilization of ADP to AATP requires energy from the cell ATPase 1 NADH proton carrier REDUCED 2 e get passed through an iron sulfur protein channel Fe3 D Fe2 they can accept the e but not the proton 3 For every 3 protons the whole F1 portion turns When it snaps back ADP Pi 1 ATP molecule 4 F1 turns and is in the cytoplasm F0 stable Energy from redox reactions used to generate a proton gradient across the membrane Lecture 9 Nitri cation recovers ammonia NH3 2step process nitrite gtnitrate 1 Oxidation losing e of Nitrite 2 Oxidation losing e of Nitrate I Nitrogen compounds serving as electrons donors The quotNitrifying Bacteria Two groups of Marine and soil inhabiting bacteria 1 Ammoniaoxidizing aka the nitrosifyers 2 Nitriteoxidizing aka the quottruequot nitrosifyers 3 End product of nitriteoxidizing is NITRATE 4 SUM of the 2step process is AMMONIA OXYGEN water N02 Since nitrogen and ammonia are in the middle of the e tower it can either be used as good donorreceptor No single microbe can convert AMMONIA NH3to NITRATE NO3 the nitrosifyers is what convert ammonia to nitrite and then nitrite is the one that oxidizes NHZOH which ends with NITRATE NO3 This process is aerobic respiration needs oxygen Chemoorganotrophs Chemolithotrophs and Phototrops Nitrifying bacteria use C02 as a carbon source of biosynthesis The Nitrifying Bacteria In phylogenic Tree most of these bacteria s are found in the sub division of proteobacteria which entails different divisions and is a catch all phylum for all different shape ie rods spiral etc Characteristics of the Nitrifying bacteria 1 Nitroso Oxidize Ammonia 2 Nitro Oxidize Nitrite Critical enzymes and their topology in the Nitrosifyers more energy from this rx 1 Ammonia monooxygenase AMO 2 Hydroxylamine oxidoreductase HAO Nitrogen compounds serving as electrons donors Hydroxylamine is generated ammonia is oxidized loosing e its accomplished by the enzyme AMO in the membrane which add 1 oxygen to ammonia 1NH3022e72H gthwt0Hkto 2 NHZOH H20 02 gt No 2 H20 Hi Sum NH3 1 02 N0 HZO AGD 27 5 kJreaction Sum Ammonia 15 water Nitrite H20 water Which consuming 2 protons Send the 2 e up the AMO HAO oxidizes the NHZOH which is the hydroxalamine A proton a gradient was created by the hydroxalamine which passes through membrane and ends in the periplasm Because of the proton gradient electrons were created and then the HAO enzyme takes them in 7 Then the HAO enzyme releases 4 e 2 e to CYTOCHROMEC and 2 e to Q 8 The 2 e that go through CYTOCHROMEC then transfer to CYTOCHROMEaa3 reduction of oxygen 9 The 2 e that go to Q go back to AMO 10 ATPase happens 9 P PPP TRUE39 Nitrifyers less energy from this rx Oxidation of nitrite happens because of the NOR enzyme Looses e and combine w water H20 to get 2 protons The e that get liberate pass through CYTC Which then go through CYT aa3 ATPase happens meNr Because Nitrite and Ammonia on the ETC tower is closely related to the CYTOCHROMEC e can only go down the reduction potential and cannot go up Nitrogen compounds serving as electron acceptors Oxidation of ammonia in the absence of oxygen quotANAMMOX RXquot generate very little energy What produces the nitrite Supplied by the NITROSIFYERS End product Produces nitrogen gas Anammox Brocadia Anammoxidans They almost have organelles special membranes don39t have fatty acids Hydrosine molecule is toxic oxidizing agents 1 Ammonia NH3 Hydroxalamine enters the hydrosine molecule 2 Because it s a modi ed ETC takes the e that is liberated and passes them nitrite 3 Nitrite is accepting those nal electrons its not that ef cient but it still releases some type of energy Nitrite can serve either as an electron donor or as an electron acceptor Anaerobic Respirationusing terminal electron acceptors other than oxygen can be inorganic or organic Common among prokaryotes uncommon among eukaryotes 1 Obligate Aerobes require oxygen no other terminal electron acceptors 2 Obligate Anaerobes oxygen is toxic 3 Facultative Anaerobes can go both ways require Oxygen if available and can be Oxygen toxic Example of Facultative Anaerobes Ecoli 02 Aerobic respiration 02 Nitrate Redution also there is a Nitrate Reductase Enzyme at the end of the cycle which 02 doesn t have Gene expressing nitrate reductase is not expressed when 02 is present Nitrate reductase nitrate is used to make nitrite Denitri cation Successive reduction of nitrate to gaseous nitrogen compounds Start w Nitrate oxidized by nitrate reductase Then it becomes nitrite which is oxidized by nitrite reductase Which then it becomes Nitric Oxide that is oxidized by nitric oxide reductase Then it becomes Nitrous oxide that is oxidized by nitrous oxide reductase 5 Which then nalizes with Dinitrogen gas 5 WNH 35 is released into the atmosphere of the cell 0 Energy generating reactions Dissimilative Metabolism reduction Energyrelated processes as opposed to nutritionalrelated processes All life requires reduced nitrogen compounds l DNA Protein Assimilative Metabolism Reclaiming nitrogen from the environment Dinitrogen is very stable therefore to reduce it requires a lot of energy This whole process requires not only energy but a special enzyme Nitrogenase Oxygen is toxic to this speci c enzyme 0 Important Points A wide variety of Bacteria and Archaea x nitrogen but not euka ryotes l A very special enzyme that can39t function in the presence of 02 Bacteria have evolved several different ways to keep 02 away from nitrogenase Example l 02 very loose and permeable to its surroundings 02 excretes slime makes it impermeable and keeps it safe Bacteria xing nitrogen for plants A mutualistic relationship Plant food amp shelter Bacterium Nitrogen Fixing 0 Not all plants do this How is this infection39 regulated Plant Legume 1 Flavonoids released by the hair of the roots Bacterium Rhizobiuml 2 Induce the expression of Nod factors that are then released by the bacterium 3 Nod factors released by BACTERIA acts on the plant in such a way that it quotallowsquot infection to proceed Very tightly regulated o Flavonoids and Nod Factors insure speci city o Mutant Rhizobium that are unable to x nitrogen are treated by the plant as a pathogen Nod factor signals to the plant for a nod factor sugar based either its good or bad for the plant so it will signal to the plant to either go or stop in the creation of the nodules Summary 1 Nitrogen compounds can serve as electron donors or acceptors 2 Nitrogen and 02 availability to a large extent determine the local bacterial community structure 3 Nitrogen xing is a strictly bacterially mediated process although plants have been able to take advantage of it Lecture 10 Eating quotrecalcitrantquot Organic Compounds not very reactive I 1 Microbes are able to quotsurvive on dif cult to metabolize carbon sources 2 Aerobic reactions where 02 is combined with organic compounds by a special class of enzymes 3 Oxygen is a direct reactant and require a special enzyme called Oxygenases Methane is stable because it lacks any carboncarbon bonds to donate electrons from 1 02 methane and 2 protons 2H are combined with methane to produce methanol CH3OH by methane monooxygenase 2 Methanol regenerates protons 2H to form formaldehyde CHzO Formaldehyde can be used as a carbon source for the cell or it can be further oxidized in two steps to carbon dioxide C02 These steps generate electrons in the form of NADH 3 This NADH can then feed into the electron transport chain resulting in ATP production by oxidative fermentation 4 Notice that 02 is both a reactant and a nal electron acceptor here Eating Recalcitrant39 Organic Compounds ll aerobic respiration 1 Benzene one single oxygen 2 Catechol 2 oxygen atoms 3 Toluene requires sequential dioxygenase separate requires which modi es through the process Eating Recalcitrant39 Organic Compounds in the absence of oxygen anoxic 1 Add acetylCoA 2 Betaoxidation not energy producing breaks down greasy molecules 3 Microbes can make a living in nastystuff 4 Gulf oil spill study39s surprising nd Bacteria ate methane in three months The study39s leaders say rates of methane decomposition after the Gulf oil spill 39were faster than had ever been recorded in any other place on the planet39 5 Gulf oil spill was abated by bacteria that feed on hydrocarbons Wastewater treatment microbes can help to clean up the water Point To mineralize39 the organic material as well as degrade other compounds eg NH3 H2 etc Measuring microbial growth 2steps DIRECT amp INDIRECT 1 DIRECT Coliform bacteria lter original water onto pitridish and see how much bacteria growth happen 2 INDIRECT quotBODquot biochemical oxygen demand If you measure the oxygen that is being produce overtime if oxygen goes down that is proof that there is microbial metabolism going on INDIRECT process Primary Screen which allow bulkystuff to settle then divides in 12 Soluble amp Sludge By this time it reduces the BOD by 13 Secondary Put the soluble water by oxidation 1 Activate Sludge 2 Trickling Filter a Bio lms for on the surface of crushed rocks b Complete oxidation of organic and inorganic c Released treated water should not be able to support microbial growth 3 Aeration 4 Reduces the BOD by 20 Tertiary Disinfection BOD about 3mg SLUDGE division anoxic digestion has complex polymers monomers sugars fatty acid etc and 2 different types of fermentation Respiration vs Fermentation Respiration e are exogenously supplied 1 The process of Respiration uses the electron transport chain and either 02 or inorganic compounds as nal electron acceptors 2 The electron transport chain is sometimes referred to as the respiratory chain 3 ATP synthesis is accomplished by Oxidative Phosphorylation where energized membranes are depolarized to a less energized state Proton movement allows ATPase to make ATP 4 In respiration electrons are generated from oxidation of an organic compound and end up with the nal electron acceptor such as 02 Fermentation no exogenous e acceptors e transfers are internally balanced 1 The process of Fermentation occurs when the products accept electrons generated during initial oxidation of primary substrate Reactions are balanced all generated electrons must be accepted 2 The electron transport chain is not involved 3 ATP synthesis is accomplished by Substrate Level Phosphorvlation couple to ezymotic rx39s where ATP is made from an energy rich intermediate EnergyRich39 Compounds high energy e Anhydride bondsare high energy while Ester bonds are low energy Highenergy intermediates must have higher energy ATP to be able to serve as electron donors to form ATP Examples are phosphoenolpyruvate 516 kl 13 Bisphosphoglycerate 52 kj and acetyl acetate 448 kj All of these are higher in energy than ATP 318 kj Low energy compounds such as AMP 142 kj or Glucose 6 phosphate 138 kj could not be used directly to make ATP The EmbdinMeyerhof Pathway Glycolysis Glycolysis is an example of a fermentation 1 Electrons are transferred in the form of NADH which is the reduced form of NAD 2 NAD becomes reduced to NADH with electrons in STAGE ll during the production of Pyruvate 3 NADH returns those electrons to form products Lactate or Ethanol in STAGE Ill when it is oxidized back to NAD 4 Hence electrons are balanced Autotrophs amp Autotrophy an organism that can use C02 as sole carbon source 0 Requires reducing power energy Sources of Reducing Power amp Energy in Autotrophic bacteria 2 Alternatives 1 Light 2 Light inorganic compounds 3 Inorganic compounds ALL 3 alternatives reducing powerenergy light rx39s C02 xing dark rx39s Two Types of Photosynthesis 0xygenic Photosynthesis Autotrophs Chloroplast Cyanobacteria and algae A D On the electron tower PSII P680 photon of light it becomes a better electron donor Electrons get donated to the P680 those electrons get through by water splitting Cyanobacteria zscheme microbes can only use inorganic compounds to generate the reducing power PHOTOTROPHS Electrons can be passed down to another compound PSII P700 accepts another quantum of light becoming a better donor it is then passed down to other moleculesproteins but the point is that you have an end product of NADPH Reducing power Also feed e back based on their production potential the e go down the scale and gets a cyclic e ow PSI P700 amp P680 are chlorophyll There are lots of different versions of chlorophyll ie Chlorophylla and Bacteriochlorophylla Chlorophyll a light sensitive Mgcontaining porphyrin if phototrophic organism that initiate the process of photophosphorylation 1 Note if you boil up these chlorophylls for too long then the Mg dry up and become grey 2 The goal of these substitutions is to change the absorption pro lespectra wavelengths of the chlorophyll The reason is that these dynamic range of life forms can have a variety of spectrum of light source Anoxygenic Photosynthesis Autotrophs Purple green sulfur and heliobacterium The purple bacteria cvclic photophosphorvlation39 A D To make ATP P870 photon source of light makes it a better e donor which donate the e s to the quinone e pool which then go to the FeS center consume protons in the cytoplasm and get them across the membrane creating a PMF and then depolarize by ATP synthase to create ATP Essentially generates through the cyclic transfer of e s and ends up creating PMF amp generating ATP Where does the reducing power come from When there39s plenty of ATP it runs the system in reverse to generate NADPH reducing power when that happens you need external e donors ie sulfur iron inorganic compounds and the e s get passed up the chain and used to produce NADP a NADPH Its burning ATP to accomplish this but its able to generate power by e transfer ow NOTE Anytime e go up against e potential requires energy Another way is through sulfur bacteria or heliobacteria the only difference is that it39s absorbed in their different wavelengths The C02 Fixing Reactions the dark reactions The Calvin cvcle plants chlor0plast algae and cvanobacteria A B C D Taking larger organic compounds and incorporating C02 in the process This is occurs during the calvin cycle Each time around the circle its consuming a lot of ATP also reducing potentials Start w phosphglycerate carbon dioxide and then the rearrangements of the calvin cycle continues Feeding the C02 and splitting fructose and using a lot of your energy and producing carbon in the process Inorganic Compounds autotrophs Hydrogen Sulfur and Iron oxidizing bacteria Hydrogen Oxidizers A Requires a specialize enzymes cytoplasmic hydrogenase and a membraneintegrated hydrogenase B These hydrogenase39s split the hydrogen to give protons and e e can be transferred by the cytoplasmic hydrogenase to make reducing potential C The e can also be passed by the membrane integrated hydrogenase to respiratory chain to make ATP These are chemolithotrophs that are also autotrophs they39re just like phototrophs that they take the C02 and go up the compounds but instead of using light to generate reducing potential they39re using hydrogen Oxidizing Reduced Sulfur These oxidize reduced sulfur compounds so the e donate in the cytochromec and can either go to 2 directions A Generates GMF which then makes ATP when you have enough ATP you can run in reverse to generate producing potential Not the most optimal condition but it allows being consistent in its environment where other things cant Ironoxidizing bacteria A Using different proteins they39re in the membrane B You have to invest some of that ATP to do the reverse e ow It generating producing potential and then it can develop reaction and x the pH Lecture 11 Mixed Populations A Pure cultures Pasteur Koch needed for Germ Theory Metabolism i Microscopic orgs exert macroscopic effects on INDIVIDUAL scale B Mixed pops Winogradsky aka father of environmental microbiology discover chemolithotrophy inorganic compounds as nal e acceptor and chemotrophy quot and C02 as sole carbon source i Microscopic orgs exert macroscopic effects on GLOBAL scale ii Hypothermal vents and hydrogen sul de H25 gas 1 Bacteria starved of H25 don t produce Sulfur granules 2 H25 oxidized Sulfur 209 kj 3 Sulfur oxidized Sulfate 798 kj Winogradsky39s column He was able to nd evidence of different bacteria39s 1 Photoautotrophs using sunlight for energy C02 is the soul carbon source for synthetic rx 2 Photoheterotrophs ie purple bacteria using light and using inorganic compounds as e donors reverse e transfer chain 3 Chemoautotrophs using carbon dioxide as a carbon source using inorganic compounds to donate e s to glucose 4 Chemolithotrophs metabolizing the glucose and using inorganic compounds as the nal e receptors very anaerobic no oxygen to act as the nale receptor 5 Fermentating bacteria The isolation of Azotobacter Take a ask and make a minimal protein mineral salts etc will support growth but there39s no nitrogen source important because nitrogen is an important component of proteins etc 1 Added infused w nitrogen gas the only thing that can grow was bacteria that were able to x that nitrogen and make it useable 2 Used ammonia instead things would grow up in this liquid medium replate them in a solid medium that either lacked ammonia or had ammonia a Everything that grew in the NH4 medium required ammonia as a nitrogen source No growth b In the NH4 medium any bacteria that used ammonia would grow c Species of pseudonomes Point By using different inorganic compoundsresources you39re able to enrich microbial populations Impact of Winogradski39s work 1 On a small scale Chemlithotroph y and Chemoautotrophy 2 On a global scale bacteria can be important biogeochemical agents Normal Flora of the Gut A Top half break down for absorption B Large intestine synthesize vitamins we can39t make on our own C 395 unique phylotypes 80 not cultivated all unique D Gut Microbes and the Phylogenetic Tree Both fermenters 1 Phylum bacteroidetes less than 14 a Obligate anaerobes diverse fermenters b More in meat eaters i Vegetarian lots of lactobacillus 2 Phylum Firmicutes 75 a Class Clostridia b Lack respire chain ATP via substratelevel phosphorylation diverse fermenters Commensal microbes Aid is breakdown of compounds digestion Produce important biomolecules Provide a barrier against pathogenic microbes Essential for development of immunity DWNH The Normal Flora and Developmental Processes in the Gut Communicationinterdependency between gut microbes and intestine Enterocytes line intestine secrete carbs 20 days after birth Normal ora secretion continues 1 Germfree ABNORMAL secretion starts but STOPS a Bacteroides thetaiotaomicron normal ora metabolizes secreted carbs introduced enterocytes secrete carbs agaIn b MUTANT Bacteroides thetaiotaomicron introduced UNABLE TO METABOLIZE CARBS enterocytes do NOT restart secreting carbs 2 Diseases a In ammatory bowl Crohn s b Infectious HIV AIDS Marine Biology A Sampling genetic composition of microbial community Sargasso Sea nutrient impoverished Extract 1500 liters of surface water Determine sequences of all quot DNA Culture Independent sampling 2 cut up DNA into pieces determine sequence of all pieces 2 million DNA fragments 1 billion BPs sequences use elongation factor T i 12 million new39 genes ii Diversity iii Even impoverished habitatD diverse ora 9959 E Deepsea Microbiology A Hydrothermal vents a Not culturable can detect by 16srrna sequencing b Tubeworms i Worms concentrate SULFUR in trophosomes where bacteria is densely packed 1 Large DeltaG thru conversion of sulfur 2 Bacteria xes C02 for worm use Beer amp Vinegar Pasteur 1860 alcoholic fermentation RESULTS from yeast growth Sugara yeast cells alcohol C02 Germ Theory of Fermentation Fermentation i Use of an organic substrate as a reductant electron donor and of the same partially degraded organic substrate as an oxidant electron acceptor ii Growth dependent on substratelevel phosphorylation iii Food spoilage iv Biological process that happens anoxically v Mass culture of microorganisms either anaerobic or aerobic vi Production of alcoholic drinks on gt Brewing Beer A Making malted barley germinated barley seeds a Soak barley seeds and add heat then dry b Purpose get the starchdegrading enzymes to be expressed B Makin39 the mash Crush malted barley to break kernels Remove husks Move crushed barley to mashlautertun39 Heat for 1 hour Add heated water then remove Extract wort is sweetsticky Purpose break down starch into fermentable sugars C Fermentation a Cool wort put into fermentation chamber with yeast and hop avor antibacterial activity b Seal chamber constant temp for 2 weeks c Purpose break down fermentable sugars into ethanol and C02 D Bottling a Industrial remove beer from chamber lter carbonate bottle b Home remove beer from chamber mix with sugar bottle wait a week c Purpose produce carbonated drink 2999959 Vinegaracetic acid CH3C00H r pmwupp Vin aigre sour wine Used as preservative Pasteur 186039s wine to vinegar via bacteria Acetic acid bac acetobacter and gluconobacter Can start with any substance with ethanol Aerobic requires suf cient aeration Don39t oxidize ethanol to C02 and water completely produces acetic acid Acid tolerant bac DOES generate proton motor force and ATP Emwhg Beer x H H HM Wines 1ar 1 lee sf an arganis substrate as a redaetaat eleatren dunner and ef the same partially degraded erganis substrate as an ssidalnt eleetren aesepter j dependent an sabstratelevel phespheryllatiea biellegieal presses that assure in the altsense ef Di Feed speillage preeess invelaing the mass sulture df misreerganisms eitJlquotIer aerebis er aaaerelhie The predustien sf alleehelis beverages I I sass
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