Class Note for ECOL 182R with Professor Bonine at UA 2
Class Note for ECOL 182R with Professor Bonine at UA 2
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Date Created: 02/06/15
Prokaryo res Pro ris rs PhoTosynThesis Endosymbiougjs eeeeee m n FFFF m mmmmm n 26 FebruZ quot 53 ECOL 182R UofA Recons rruc ring The evoluTion of living Things Sysfema sfs s rudy evolu rionor39y r39elo rionships Look for39 shared derived differ39en r from onces ror39 fro7 s ro gr39oup organisms Evidence used morphology developmen r and molecular do ro especially DNA sequences Why can39T we figure iT ouT perfechy More dis ran r his rory is obscured by more changes Among oldes r lineages of Bac reria and Archaea in par ricular lo rs of la reral gene Transferquot Makes i r difficul r To infer rela rionships from phylogeny of single genes PLAGUE TEETH WITH PLAGUE wry g Ix Diversify of ProkaryoTes Bacteria lt3 Archaea Early prokaryo re fossil nu WhaT are microbes Only a minority make us sick Rober r Koch Germ Theory of Disease In ordinary English migh r be any rhing small bacTer39ia yeas r pr39oTisTs vir39uses In science classify by evolu rionar39y r39ela rionships Life can be divided info 3 domains Very ancient prokaryotes g A 7 a i A EUKARYA Ancient y Present Time Pr39okar39yo res bac rer39ia archaea Pr39okar39yo re was ancestral and only form for39 billions of years 8 Eu kar39ya Eukarya 39 9 6 a a do a 9 o ec tb e90 99 60 62gt y Protlsts In orange 0 Q0 V0 are Pr39okar39yo res monophyle ric pamphyle c polyphyle ric Scheme has been revised before Haeckel 1894 Whittaker 1959 Woese 1977 Woese 1990 Three kingdoms Five kingdoms Six kingdoms Three domains E bacte ria Bacteria Monem pickatytes modified from Wikipedia 1o Shared by all 3 domains Glycolysis use glucose To ge r ATP Semiconserva rive DNA replica rion 2 s rrands in double helix during replica rion each daugh rer cell ge rs one s rrand from paren r o rher is new DNA encodes polypep rides Polypep rides produced by Transcription and Transla rion according To gene ric code Plasma membranes and ribosomes 11 Unique To ProkaryoTes Circular chromosome Genes organized inTo operons NO nucleus TransIaTion of mRNA inTo proTein begins before TranscripTion of DNA inTo mRNA is compIeTe organelles cyToskeleTon meiosis Genes can sTill geT moved around in oTher ways boTh wiThi n and beTween species The laTTer is horizonTal gene Transfer AnTibioTic resisTance can spread in This way 12 Divide by fission a Extracellular l7 matrix Plasma membrane 2602 l Chromosome Salmonella en fer39fl39a l39s 360x r39eal speed replicate in 30 min httpIifeBeimlsinauercomNideosVideo26O2mpg LIFE THE SCIENCE OF BIDLDGY Seunm Edition Figure 92 Pmkaryoiic Cequot Division 1 3 a 2mm Sinauer Assnciales inc and w H Freeman 5 Cu ProkaryoTes are everywhere All around us and in us Too Way more bac reria archaea on your skin amp in your in res rinal Trac r Than you cells WE ARE HABITAT 39 gt 3X1028 in ocean vs visible sTars in universe Some survive ex rreme hea r alkalini ry sal riness Bo r rom of The sea Rocks more Than 2km in ro Ear rh39s solid crus r 14 Wha r do They look like Predominan l39ly unicellular a Enterococcus sp 1 Escherichia coli c Leptospim interrogans spheres curvedspiral1m coccuscocci rods bacillusbacilli may be found singly or39 in 2D3D chainspla resblocks z mul ricellular39 each cell is viable independenle 15 Biofilms Many pr39okar39yo res and some o rher39 microbes lay down a gellike subs rance on a surfaceThis ma rr39ix rr39aps o rher39s forming a biofilm Biofilms can make bac rer39ia difficul r To kill Pa rhogenic bac rer39ia may form a film Tha r is impermeable ro an ribio rics for39 example Den ral plaque is a biofilm 16 Bioluminescence Some bacTer39ia make lighT Useful for39 geTTing info a new fish guT r Vquot 39gt 1 Arabian Peninsula Africa LIFE Be Figure 268 ms ms SCIENCE or smLon Elgmll E mun 2007 sinauermumaies Inc and w H Freeman 1 Cu 17 Mos r common bac rer39ial mo rion is via Fibr39il of flagellin pr o rein plus a hook and basal body Ro ra res abou r i rs base Different from eukaryo ric flagellum which bea rs 1s Flagella 075 pm Cell wall differences seen by Gram s rain space membm of cell wall 1 P 1 Pep doglycan 2553 asmlc layer Plasma membrane Gramnegative bac rer39ia Thin pep ridoglycan layer39 behind ou rer39 membrane 19 Exploiting unique boc reriol features Pep ridoglycon cell walls unique To boc rer39io no r found in eukaryo res or39 archaea Many on ribio rics disr39up r cellwall syn rhesis This affec rs only boc rer39io and has li r rle or39 no effec r on eukaryo ric cells 20 Morphology gives only limi red view of bac rerial diversi ry Huge diversi ry in me rabolic pa rhways oxygen Tolerance energy source carbon source ni rrogen and sulfur me rabolism 21 BioremedioTion Hydrogen ProducTion Cleon up oil Spills Toxins Produce chemicals we find useful Enrichmen r Cul rures grow microbes under variable condi rions and see which Thrive 22 6 nuTriTional caTegories energy carbon 1 Pho roau ro rrophs energy from light carbon from 602 2 Pho rohe rero rrophs energy from light C from o rher organisms 3 Chemoli rho rrophs energy from oxidizing inorganic subs rances carbon from 602 some bac reria many archaea 4 Chemoli rho rrophic he rero rrophs energy from oxidizing inorganic subs rances carbon from o rher organisms 23 6 nuTr39iTional caTegor39ies ener39gy carbon 5 Chemoor39ganoau ro rr39ophs energy from o rher39 organisms carbon from CO2 6 Chemoor39ganohe rer39o rr39ophs energy and carbon from o rher39 organisms mos r known pr39okar39yo res all animals fungi many pr39o ris rs 3 ways To ge r ener39gy x 2 ways To ge r car39bon 6 nu rr39i rional me rabolic ca regor39ies Prokaryo ric Metabolic Variety Carbon 6 Metabolic Categories Energy Source Source Photoautotrophs light CO2 Photoheterotrophs light other organisms Chemolithotrophs oxidizing inorganic substances CO2 Chemolithotrophic heterotrophs oxidizing inorganic substances other organisms Chemoorganoautotrophs other organisms CO2 Chemoorganoheterotrophs other organisms other organisms 25 7 LIFE THE SCIENCE OF BVDLDGY Seventh Edition Figure 2711 Cyanohacleria Pan 2 warm Smauer Assuming m andw H Freemana Co OXYGEN None in a rmOSpher39e for39 firs r 23 billion years Cyanobac rer39ia evolved pho rosyn rhesis oxygenic ATP wa rer39 oxygen Aer39obic mor39e efficien r Than anaer39obic 28 Oxygen Ear39ly ear rh had le free oxygen 02 25 bya pr39okar39yo res evolved abili ry To spli r ZHZO gt 4H 02 4e39 Elec rr39ons used To reduce CO2 and make organic compounds 02 was a was re pr39oduc r 29 W axcm 2 cm y E m u m gt m c u o c 39Fhu t oEQStsEn39n 39 Lstneme diagram MWMIM lenmlhhumm Mm E Lower ENERGY mating Stealing electrons capturing light energy producing high energy compounds 30 STR ROMA low H J 39 Fsis w 39quot quotwere v f quotl Cytochrpme OJ 39 quot M c f z x 1 I i n f J 4 MIN 1 J 1 W F39s 9c 39r Plastbcy39anin Ogidafion of water LUHMEN hig h H Then make glucose and oTher39 sugars 31 CALVIN BENSON CYCLE 6 co2 o 6 RuBP G 6 Carbon 12 3313 xation 12 6 12 quot 6 RUMP Regeneration Reduction Of Rumquot and sugar production 12 12 GB 12 NADP 10 3313 12 G3P 12 P1 Base of Global EcosysTem Other carbon compounds LIFE THE SCIENCE OF BIOLOGY Savant Edition gure 513 The CalvinBensnn Cycle 32 a 2004 Smauev Assumes 1m and w H Freeman 1 Cu Oxygengenerating cyanobac rer ia for39m r ocklike structures called s rr39oma roli res a 39 39 33 Oxygen Oxygen was poison when if fir39s r appeared Organisms evolved no r jus r To roler39o re oxygen bu r To Thrive Aer39obic me robolism fos rer39 and more efficien r 34 c 0 O E 3 D in O O 2 D e O 1 ae Fumarate 2 E E gt 9 2 e 3 163 Nitrate 9 E 0 039 C I C o 237 Canyngmo 2005 Pearson aemamm Cummmgs All rlgms reserved Glucose Glucose Glucose t Electron donor in cellular respiration When oxygen is used as the final electron acceptor the change in free energy is equal to about 237 kJmol all Oxygen 35 73100 E80 50 33030 gt X 0 cugt10 quot5 E5 3 3 2 5 1 E 8 5 at O Increasing oxygen in atmosphere Present First owering plants H Invasion of land First chordates Exoskeletons First eukaryotes Multicellular organisms First aerobic bacteria Rocks absorb F h h b oxygen 1rst p otosynt etlc acteria f Flrst Me t t I t 4000 3000 2000 1000 500 Millions of years ago 250 100 Aerobic vs anaerobic metabolism 1 Oxygen is toxic to obligate anaerobes 2 Facultative anaerobes can shift between anaerobic metabolism such as fermentation and the aerobic mode cellular respiration 3 Aerotolerant anaerobes don39t use oxygen but aren39t damaged by it 4 Obligate aerobes cannot survive without oxygen 37 Ni rrogen and sulfur meTabolism Some bac rer39ia use oxidized inorganic ions such as ni rr39a re ni rr39i re or39 sulfa re Deni rr39ifier39s Ni rr39ogen fixer39s Ni rr39ifier39s Sulfurbased metabolism 38 Pr39okaryo res are impor ran r in elemenT cycling Plan rs depend on pr39okar39yo ric ni rrogen fixers Deni rr39ifier39s pr39even r accumula rion of Toxic levels of ni rr39ogen in lakes and oceans 39 N2 139 in atmosphere use elemental J L E2323 23nd archaea Denitrification by bacteria and archaea Organic compounds Decom osition with amino NH2 p by bacteria groups archaea fungi Uptake Decomposition from soil Uptake 1 Varquot Xn from soil i N03quot Igt Plants lt2 quotquot3 nitrate gt ammonia Uptake K V 39 1 from so Decomposutlon Jj Nitrification by bacteria Nitrification by bacteria Convngm 2m Pearson Eenzmm Cummings Ali quotgm reserved 2 8 1 6 Ni rrogen fixers Conver39f a rmospher39ic N2 gas in ro ammonia by means of The following r39eac rion m6Hesz All organisms require fixed ni rr39ogen no r N2 for39 Their pr39o reins nucleic acids and o rher39 ni rr39ogen con raining compounds Only ar39chaea and bac rer39ia including some cyanobac rer39ia can fix ni rr39ogen 41 TABLE 285 Some Electron Donors and Acceptors Used by Bacteria and Archaea ByProducts Electron Donor Electron Acceptor From Electron Donor From Electron Acceptor Category Sugars 01 CO1 H10 Organotrophs H2 or organic compounds 5041 H20 or CO HIS Sulfate reducers H2 CO2 H20 CH4 Methanogens CH4 01 C01 H10 Methanotrophs 52 or HZS OZ 5042 H10 Sulfur bacteria Organic compounds Fei C02 Fe ran reducers NH3 02 No H20 Nitrifiers Organic compounds NO C01 N20 NO or N Denitrifiers or nitrate reducers N02 02 NO H20 Nitrosifiers The name biologisls use to identify species that use a particular metabolic strategy Caowigm is 2mm Pearson Eenlzmm Cummings All ughzs reserved We use sugars as elec rron donor and oxygen as elec rron accep ror when making energy Cellular Respiration Prokaryo res Variable 42 Sulfur based meTabolism Some pho roau ro rr39ophic bac rer39ia and chemoli rho rr39ophic archaea use H25 as an elec rr39on donor39 instead of H20 43 Archaea sTave off global warming 10 Trillion Tons of meThane lying deep under39 The ocean floor39 Ar39chaea aT The boTTom of The seas meTabolize This meThane as iT r39ises OTher39wise global warming would be exTr39eme 44 Prokaryotes live on and in other organisms Mitochondria and chloroplasts are descendents of freeliving bacteria Plants and bacteria form cooperative nitrogen fixing nodules on plant roots Ruminants depend on prokaryotes to digest cellulose Humans use vitamins produced by our intestinal bacteria 45 A very few bac reria are pa rhogens Endo roxins eg Salmonella and Escherichia released when bac reria die or lyse burs r lipopolysaccharides from The ou rer membrane of Gramnega rive bac reria usually cause fever vomi ring diarrhea Exo roxins eg Te ranus bo rulism cholera plague an rhrax released by living mul riplying bac reria can be highly Toxic even fa ral wi rhou r fever A Diversify of pr39okar39yo res Bacteria Archaea r Proteobameria rCrenarchaenta Euryarchaeota1 quotb quotb quotb a a 9 lt0 amp 6 395 0090009 a 0 0 0 9 0 9 me be 25 8 3925 6 06 6 6 6 v09 0 6 009 0 00 2 0 0 9 6 0quot 0 amp amp 6 5 o 9 lt 0 b 0 06 0 amp p 9 420 QJ 2 g g 9k 0 60 09 60 0x 0 Q 9V00 9 6A V39KVQ lt9 6 meme Cummmgs AU quotgm reserved 47 Diversify of prokaryoTes We will discuss 6 clades of bac reria and 2 of archaea More are known More s rill are uncharacterized can be hard To cul rure in lab PCR allows sequencing of uncul rurable organisms Phylogeny based primarily on DNA sequence o rher rrai rs can evolve rapidly 48 1 Pr39o reobac rer39ia Group 1 3225 Ph t t t h ancestor of anfes 350p 1C gtGmup3 Tochondria proteobacteria Some fix ni rr ogen RhZobl39um gtGroup4 E caI39 Some cycle niTr39Ogen and gt GroupS Sulfur Chemolithotrophs Chemoheterotrophs Photoautotrophs 2 Cyanobac reria blue greenquot bac rer39ia pho roau ro rr39ophs Transformed Ear rh wi rh O2 many fix ni rr39ogen ances ror39 of chloroplas rs 50 3 Spir39oche res Gramnegative mo rile chemohe rer39o rr39ophic some are human parasi res cause syphilis and Lyme disease 51 Spir39oche res Internal fibrils Cell wall 011th 7quot k envelope l 39 l Axial filamen rs produce corkscrewlike mo rion 4 Chlamydias ex rr39emely small 02 15 pm diame rer39 Gramnegative cocci can only live as par39asi res 39 COUSB sexually Transmi r red disease eye infec rions especially Tr39achoma some forms pneumonia 53 5 FirmicuTes mosle GramposiTive some produce dor39manT endospor39es To waiT ouT bad Times eg heaT cold dr39oughT r39eplicaTe DNA and encapsulaTe one copy in a Tough cell wall par39enT cell breaks down releasing endospor39e some endospor39es can be r39eacTivaTed afTer39 more Than a Thousand years of dormancy 54 Clostridium tetzmi F i r39micu res Sfapvyococcus is a fir39micu re I Sta lulococcus auras 39 56 P J 1 m Mycoplosmos are firmicu res V 39 39 i39 no cell walls smolles r known cellular v organisms l J ver39y li r rle a DNA m Mycoplasma gallisepticumr 6 Ac rinobac rer39ia of ren w branching filamen rs Mycobac ferum fubercuoss is an ac ri no myce re Archaea We don39t know much None are human pathogens Most live in extreme environments temperature salinity oxygen concentration or pH Have distinctive lipids in their membranes Look at 2 groups Crenarchaeota Euryarchaeota 59 1Crenarchaeofa Mos r are and Sulfaobus live in ho r sulfur springs die of cold a r 131 F 2 Eur39yorchoeo ro Some are me rhonogens producing CH4 from 02 Responsible for39 80 90 o rmospher39ic me rhone of ren from belching cows CH4 is po ren r greenhouse gas 61 Some Eur39yor39choeo ro are holophiles ver39y sol ry envir39onmen rs mos r organisms dr y To deo rh con roin pink cor39o renoids live in commercial evopor o ring ponds