Class Note for ECOL 182R with Professor Bonine at UA
Class Note for ECOL 182R with Professor Bonine at UA
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Date Created: 02/06/15
Prokaryofes Profis rs Pho rosyn rhesis Endosymbiosis Ch 286129 l 26 February 230 9 ECOL 182R UofA K E Bonine Why can39f we figure i r ou139 perfec rly More disfanf hisfory is obscured by more changes Among oldesf lineages of Bacferia and Archaea in parficular lo139s of la139eral gene Transfer quot Makes if difficulf To infer relafionships from phylogeny of single genes Diversify of Prokar yo res Bac ieria amp Archaea Reconsfrucfing The evolufion of living Things Systemafisfs sfudy evolufionary relafionships Look for shared dzrivzddifferenf from ancesfor fraifsfo group organisms Evidence used morphology developmenf and molecular dafa especially DNA sequences uLAqu Q 6 Protisls in orange ode What are microbes Only a minority make us sick Robert Koch Germ Theory of Disease In ordinary English might be anything small bacteria yeast protists viruses In science classify by evolutionary relationships Eukarya Eukarya 06 we e 2 quot oh 396 a a o are Prokaryotes monophyletic paraphyletic polyphyletic Shared by all 3 domains Glycolysis use glucose to get ATP Semiconservative DNA replication 2 strands in double helix during replication eacli daugliter cell gets one strand from parent other is new DNA encodes polypeptides Polypeptides produced by transcription and translation according to genetic code Plasma membranes and ribosomes Life can be divided into 3 domains Vow ancient pmkarvok s BACTERIA Orlgi 0 ll f Ema limo Prokaryotes bacteria archaea Prokaryote was ancestral and only form for billions of years Scheme has been revised before Haeckel 13937 Ihree iiixdionu Whittaker 09597 Woeie 19777 Woeie 19907 rive kingdoms sixkingoonu Ihxee damn Marian pxnkazymes modified from Wikipedi io Unique to Prokaryotes Circular chromosome Genes organized into operons NO nucleus translation of mRNA into protein begins before transcription of DNA into mRNA is complete organelle cytoskeleton meiosis Genes can still get moved around in otner ways botn Witnin and between species The latter is horlzonial gene transfer Antibiotic resistance can spread in tnis way ie Divide by fission ml 1 l Ilulur m 2502 Salmonella en fenquot ridquots 360x real speed replicaTe in 30 min mm Weaewi sinauev cadeeasVideaQErU mpg 14 WhaT do They look like Predominanle unicellular m immmu mi I lnhm n p m man1 u Mn 1 um I in rods bacillusbacilli l curvedspiral spheres coccuscocci may be found singly or in 2D3D chainsplaTesblocks z mulTicellular each cell is viable independenle 15 Bioluminescence Some bacTeria make lighT Useful for geTTing inTo a new fish guT mmquot Pumuauu 17 ProkaryoTes are everywhere All around us and in us Too Way more bacTeria archaea on your skin amp in your inTesTinal TracT Than quotyouquot cells WE ARE HABITAT gt 32x1028 in ocean vsvisblesTurs nuniverse Some survive exTreme heaT alkaliniTy salTiness BoTTom of The sea Rocks more Than 2km inTo EarTh39s solid crusT 14 Biofilms Many prokaryoTes and some oTher microbes lay down a gellike subsTance on a surfaceThis maTriX Traps oThers forming a biofilm Biofilms can make bacTeria difficulT To kill PaThogenic bacTeria may form a film ThaT is impermeable To anTibioTics for example DenTal plaque is a biofilm 15 MosT common bacTerial moTion is via flaella Fibril of flagellin roTein lus a 00k an basal body RoTaTes abouT iTs base DifferenT from eukar oTic flagel um 4 77 which beaTs 15 mm rumnu Cell wall differences seen by Gram sTain W i 39 jwlfi lg um 39o w 5 17m GramnegaTive bacieria hin pepiiaogiycan layer behind ouTer membrane w Morphology gives only limiTed view of bacTerial diversiTy Huge diversiTy in meTubolic paThways oxygen Tolerance energy source carbon source niTrogen and sulfur meTabolism 6 nuTriTional caTegorieSiemrgy i rlium 1 PhoTouuToTrophs energy from Mi carbon from PhoToheTeroTrophs energy from Mi 5 from oiner organisms N A ChemoliThoTrophs energy from oxidizing inorganic subslances carbon from co2 some bacleria many arcnaea 4 ChemoliThoTrophic heTeroTrophs energy from oxidizing inorganic subslances carbon from oiner organisms ExploiTing unique bacTerial feaTures Pepfidoglycan cell walls unique To bacTeria noT found in eukaryoTes or archaea Many anTibioTics disrupT cellwall synThesis This affecTs only bacTeria and has liTTle or no effecT on eukaryoTic cells BioremediaTion Hydrogen Prod ucTion Clean up oil spills Toxins Produce chemicals we find useful EnrichmenT CulTures grow microbes under variable condiTions and see which Thrive 6 nuTriTional caTegoriesieneiigy rai boiil 5 ChemoorganoauToTrophs energy from oTher organisms carbon from coz 6 ChemoorganoheTeroTrophs energy and carbon from other organisms mosT known prokaryoTes all animals fungi many proTisTs 3 ways To geT energy x 2 ways To geT carbon e nuiriiionai meiaboiic cuTegories Prokaryo i39ic Mefabolic Varie i y cm on 5 Memhnlic Categories Energy Smlrce SnlIrEE Emmawhom hghi coi mmmmh hghi mm orgasms Ckmhdwmyhs Wm mmgzm 5mm coi Chammhmuyhc Mme Wm mm 5mm mm orgasms Clummgzmmmhuyhs charms coi Ckmuxgmlemuyhs Mummy mm orgasms Oxygen Early earfh had le free oxygen 02 25 bya prokaryofes evolved abilify To splif ZHZO gt 4H 02 4e39 Elecfrons used To reduce 602 and make organic compounds 39 O was a wasfe product Evolu rion of Pho rosyn rhesis in Cyanobacferia Homequot mm m swimw Q mm 7 w mm m 0 Ammapn no iCMin OXYGEN None in aTmosphere for firsT 23 billion years Cyanobac ieria evolved pho iosyn ihesis oxygenic ATP water oxygen Aerobic more efficienf Than anaerobic 2x Stadmgelzchuns ume hghi energy ymvhncmg l ll l39lenAYSY ComW nds an mm w Then mm glucose and OYHZV sugars Oxygengenerating cyunobucteriu form rocklike structures called stromutolites ll n Glucose Glucose Glucose k a Eluumn donor m cellular iesplmllon El as Fumarate wnm uxygnn is used ls he nnal elaclmn acceptor the change in res cmgy 5 Equal lo anon 2w kJmal la Nitrate u 1 Oxygen Change in me energy mm 9 glucose kJmnl 3 z a mm annun mumquot nKluBV39 my Q quml Base of Global Ecosystem L W Ilrmrlwl lvmpmlhds 32 Oxygen Oxygen was poison when if firsf appeared Organisms evolved nofjusf To foler afe oxygen buf To le39ive Aerobic mefabolism fasfer39 and more efficienf Increasing oxygen in afmospher39e 11011110 lam mm m in Mllllllnsulylthgu 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 Prokaryotes are important in element cycling Plants depend on prokaryotic nitrogenfixers Denitrifiers prevent accumulation of toxic levels of nitrogen in lakes and oceans Nitrogen fixers Convert atmospheric N2 gas into ammonia by means of the following reaction N2 6 H 9 2 NH3 All organisms require fixed nitrogen not N2 for their proteins nucleic acids and other nitrogencontaining compounds Only archaea and bacteria including some cyanobacteria can fix nitrogen Nitrogen and sulfur metabolism Some bacteria use oxidized inorganic ions such as nitrate nitrite or sulfate Denitrifiers Nitrogen fixers Nitrifiers Sulfurbased metabolism imim39 mm Plants can39t F b use elemental 5533 hammnimnmmu Miragequot N2 in malian aim compound W mini mm was Dunmvw nn w human mm lanai um Docemposillun immsnii mm mm ii 4 mini quotm Mimi Union Iquot 5 nicammiiim iiiiniiminm V Nh llmllun mm x amnim uni 2m 4 i iii i 5mmummy WWW quotnummiiiii We use sugars as electron donor and oxygen as electron acceptor when making energy Cellular Respiration Prokaryotes Variable 42 Sulfurbased me rabolism Some pllofoaui39oi39ropllic baci39eria and chemoliflloi39ropllic arcllaea use H25 as an eleci39ron donor insfead of H20 4 Prokaryo i39es live on and in other organisms Mitochondria and chloroplasts are descendenfs of free living bacferia Plani s and baci39eria form cooperai39ive nifrogenfixing nodules on plani roofs Ruminani s depend on prokaryofes To digesf cellulose Humans use vifamins produced by our infesi inal baci39eria 45 Diversify of prokar39yofes auctenn MENea Emydrgmeom c 3 o e a of ca 3 s o o Nona a y s N go o 0 gag 33 a fty a at of saw of f lt9 rm a 47 Archaea sfave off global warming 10 frillion Tons of mefllane lying deep under The ocean floor Archaea af Hie boH om of The seas mefabolize Hlis mefllane as if rises Ofllerwise global warming would be extreme A very few bacteria are pa i hogens Endoi39oxins eg SalnaneIa and Escherichia released when bacteria die or lyse burst lipopolysaccharides from the outer membrane of Gramnegative bacteria usually cause fever vomiting diarrhea Exoi oxins eg tetanus botulism cholera plague anthrax released by living multiplying bacteria can be highly toxic even fatal vvithout fever Diversify of prokar39yofes We will discuss 6 clades of baci39eria and 2 of arcllaea More are known More sfill are uncllaracferized can be hard To culi39ure in lab PCR allows sequencing of unculi39urable organisms Phylogeny based primarily on DNA sequence oHler fraifs can evolve rapidly 43 1 Profeobac rer39ia i purple r bacteriaquot ancestor of 3 W mitochondria emuum Some fix nitrogen Rhizubium E cod Some cycie nitrogen and sulfur amninmph amp 2 Gramnegafive mol39ile chemoliefer39ofr39ophic 39 some are human par39asil39es cause syphilis and Lyme disease mini inn niiiniinn 4 Chlamydias extremely small 0215 pm diamefer Gramnegafive cocci can only live as par39asil39es cause sexually transmitted disease eye infections especially trachoma some forms pneumonia 2 Cyanobacfer39ia bluegreenquot bacfer39ia phofoaufofr ophs Transformed Ear39fli wifh 02 many fix nifr ogen ancesfor of chloroplasfs Spirochefes intoma tihiih Crii wall Outcr nnwiape Axial filamenfs produce corkscrewlike mofion 5 Fir micufes mosfly Gram posil ive some produce dormanf endospor es To waif ouf bad fimes eg heal cold droughf replicate DNA and encapsulate one copy in a tough cell wall parent cell breaks down reieasing endospore some endospores can be reactivated after more than a thousand years of dormancy Firmicutes Endmpnm L minim A mm m Mycoplasmas are firmicutes no cell walls smallest known cellular organisms very little DNA mu m g u z w Archaea We don39t know much None are human pathogens Most live in extreme environments temperature so init oxygen concentration or p Have distinctive lipids in their membranes Look at 2 groups Crenurchueotu Euryurchueotu 29 Sfrzpfumyces 5fap7yococcusis a firmicute mpimim i in mm39m in 6 Actinobacteria often w branching filaments Mycubacferium fubercuusisis an uctinomycete Most of our antibiotics come from uctinomycetes 1 Crenarchaeota Most are thermophilic and acidophilic Sufoobus live in hot sulfur springs die of cold at 131 F 10 l 0 7 5W 41 7 k ii v0J sg um e 70 X JV d EJLJQO 442 EqivalJf J yW WM mMcmi Ax 7 4 m5 gal r4 WV AAW7 W 4269M quot13 33L 5 KM f 0 h ILutk39 4 MW WoUC i ltvf fie 557ed I i ivyw 56 I zvajj x W 9 39r e 144 we 54 39 2 9 W467 Wee0W7 7 639m 2 5575de 39 I Walk J u wig 4 Iltltj 39 0 5 f mm A m f 1 39w r 39139 focol M bi V 239 4 plane 41 I r V Awr 7 K S 7 f J w 4 rt 4214 I 2 39 152 Z ifA quotquot3315 ifquot i Photographic plate 3 5xby Hp Reference source L f f I Fm 822 An arrangement for rorming a Fourier transform hologram Note The lens is not drawn to scale 6 l l I rqurror Honslorm hologram I 139 Iconjugoie gt I Image gt1 Zero order Qriginol I Image 1 I r quot 4 f quot I I Vx I m 821 icnclzlliun of hm rcl inmgu mm l ouricr transform hologram 287 ALAr0 2 rite W yVZL 43 Aim4 M MM am 7644 E77 412 V3 I W E4Mampr uc wafx Wary c9 Fig 28 Twin image rcconstruclcd h u FmIricr hologram Fm 824 Photograph of he irmgc plane of a Fourier lransform hologram meg z ADQW g Mch LL 2 WI af euz 7 9 LL quot5 Haw2r wryForm 97 UIl y ivceJ 47 V H 06 393 39739 U3 R 1 Wham 1441 j73ltn6Xn A Z drum 2 avz Mm 4 DZXIV 4 00 gt 539 5095 70 xgl r e ufEe 141 1 4 J fitwfifq 444 A Qu neJ by M 5215th 5V M WLVZ 577 L 74 74 mquot9v 47200 wltl Mal M f om Le in qu v4 M4 W lquot J c Qa4 D Hm IMAQQJ Ave g v e h I H mlajV 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V rv Jetb aWzlJvom M I M43 Tekh i Jult c wm Flav1 fiyr nc Mm Ml r t co i 4 ALecf ef A 42 quotFoef a 744 57 FAQe LL FVDVL f M4 b A lt Mia 4quot 4 64 figv Jo 7 W rag ya V Xf7f7477 5 LMVJupLMJt Q szfnrA x 7 543 W amp Ae13 39b wr nm z 2 Fixwaftng i L f Jlg fLAnc e Elam F La mmmm mm mmmm II 33333 wwww mm mmmm mm IsiNationsl smnd l 6amp0 QIAPh f Y 773 paw4 W mwj wmi exX 1 g L 0 V N ijac 78 m 3 b 3 6 1amp1 N K 3 bx 39 1 U Q LvJ 223 2 2 m xi 4 F E E Equot E 2 E 5 m vi 1414 71 J V xw T avc 7 4Vamp 5 Frm W177 f eJoreJ He w m cmmx 5 74 64quot Flowef a 5 74 749 lt4 me ee viOX 8 53 g 72 J 5quot W M We d quotWCJZ9 2 Z a wz39 fA ce A 4 UC fu Jy q h A mm W WWW T Hecfpz clog M szi quot39 V1 AC1 476 JLAz 742 4 Qaue VC y UIQI M A Sb mo M1UQ4 an A VIIam I gtx f m igkoxm 4 X7 j 2 aN 7139 0 00 v 6 g 62 1 s fAJ W A5 a 2 W v rwhAl W away Wf kk 4174 at Me a 54 x 7 0 ft Vb m 2 2 f P 2241 SO SHEETS a 22142 100 SHEETS C AMPAD E g quotD 22144 200 SHEETS Hg mwg ms P 3 03 Psmm NV sumam ni 0 F C i D V CF 5 1 E 7 Pk 3 lt4 gt u C 3 lt 2 EL Y i D a L S Eu II NASIAMPQ If NAN k iN uw m bf Fxxtaw k N magSp gt gt mmm I amp mxwxuxev W 1m H 0 VJ w ism WEEK E E tg Kw 01 m N F14 m X hf u 58 4536qu Fqlt w 91 H x 3Q N gt Time Vz ma N LTRSJMVE has Swan xNN 991331 he M l Km SA mxwio 2 2x 13120 ur Qjquot a391 quotf KkF H F3311 2134 011212415 CogD65 um bw fA L 2 2 fps 2 407 922 1 r M1 m7 E 52 13 b aGmNj 4 Wm Fruwa E k A m 9 I Z gtltJ 41 X 0 I 1 quot 395 CZZVAIAJ3 y Fomdaom nfrr Z DZo F EFT jy zx J JAe Z Cubltgtlt 7 7 x CDWFONewj m4 MP W i V o 9 dirk 12 Algae4M y 2 Z Z Z I 2 b d l wax 6 V vlrcx vlnxll 7PM m Way 517L767 f d 39ff v nvtLe fie macaw mvj 4f Mmquot ablym2 vimWar 4 74 ma acw 5 LWJ46 W WW aim W7quot 3 I WM 7 W 399 41W 7 397 2d 399 23 w W7 J W J Msz 72 awv ViewWW aw W ag 91W aw 03 54an9 I a 6 w ahayr w 774 W 7 iiV yW 343 971 7 h K 0 3 2 f 7 W 0L4 L4 lv L4L 27 637 I O 0 nix H cafvaFr a W Aw M 07 A W on rm 0 W 39l wrygt9 Q W 9 WW quot4 A quot71 A a b a A 4 mmmm mm WA 5305 g c 10 33m 0 mm 0000 mm 66mmm F F m m nm nitMarion smnd mm q mmm DUltltltM J errJ aAQgV 3gt7 L my fat V67 EEEEEE mmmm wrn mmmm own wwww ww 0000 OD J aCIf 4 V JvqKVI fw5 91 340 H 39Wefaoov e iiiii nv Kin12594 XVJ 4 am7 a ung fMHU ZZ 212 Wgw 5 M d PalVAN faced sagV V fatWIMP 7amp nuyzl 557 W V W TnlS program traces rays to a transmission hologram surface located at z 0 Output plotted coordinates to file quotziquot Input xoyozo object point coordinates Xcyczc construction source point coordinates xhyhzh hologram coordinates under evaluation xryrzr reconstruction source point coordinates First the direction cosines are calculated from object and reference point coordinates The grating equation is used with the ml order since reconstruction is with the same beam as in construction zi is the image evaluation plane The direction cosines are translated to this plane and the Xy coordinates computedA plot is made of the ray intersections on this plane WWWWWWWWWWGPWWWWWGPWWQ xmaxiz lOOOOOO xmini1000000 ymaxilOOOOOO yminileOOOOO load rt2dm I xort2d1 yort2d2 zort2d3 xcrt2d4 ycrt2d5 zcrt2d6 xrrt2d7 yrrt2d8 zrrt2d9 wllrt2d10 w12rt2dll rmaxrt2d12 dincrt2d13 zi rt2d14 ny 2rmaxdinc1 c rmax is the maximum aperture radius c Hologram coordinate calculations 170 Loop for ilny yhi rmax i ldinc xmax sqrtrmaxrmax yhi 2 nx2xmaXdinc 1 160 Loop for jlznx Xhji xmaXj ldinc jYja yhXJ1 yhl End Statement before y Loop Direction cosine calculations oxo Xhji 2 yo yhxjyi 2 zozo osqrto lo xo Xhjio m0 YO yhXle1O no 200 nxc Xhji 2 ycyhxjyi 2 zczc nsqrtn lc xhji xcn mc yhXjyiycn nc zcn rxr xhji 2 yr yhxjyi 2 zrzr rsqrtr lr XhjiXrr mr yhxjyiyrr nr zrr plo lc 2 mo mc 2 no nc 2 psqrtp Diffraction calculations 1 diffraction order 101 lo lcw12w11 lr mol mo mcw12wll mr nol noncw12wll nr ri zinol Xijirilolxhji yijirimolyhxjyi if Xijigtxmaxi xmaxiXiji else end if Xijiltxmini xminiXiji else end if yijigtymaxi ymaxiyiji else end if yijiltymini yminiyiji else end Xifji lOOOOXiji Xo yifji 10000YijiYO Z l60 continue end End of xmax Loop l70 continue end Distances in microns xccxmaxixmini100002 yccymaxiymini100002 dfxxmaxi xmini10000 dfyymaxiymini10000 XiftXi f yiftyif save xid Xift ascii save yid yift ascii End of program V 2020 2020 axisv axis39square39 plotxiftyift3939 endo Analysis of Holographic Images Several different methods can be used to evaluate images formed by holograms and holographic optical elements The techniques that we will evaluate include Exact Ray Tracing this technique is based on repeated use of the grating equation Paraxial Ray Tracing approximate method for analyzing image formation Analysis of Aberration Coef cients extends the rst order results from paraxial imaging K Vector Closure Useful for highly selective Bragg gratings PWN In general an object can be considered as a collection of source points Each of these points forms a hologram with a reference eld Therefore analysis of point source holograms will provide essential information on the holographic imaging process Holographic Imaging Relations Consider a general geometry for recording a hologram of a point y Recording f Plane 391 Reference Source M i point xr yr zr X X 0 1 g r Object Source point x0 yo zo y i r I 1 Reconstruction Source 1 P01ntxpyp zp z quotquotquotquotquotquotquotquotquot quot x quotquotquotquot quot K gt Z gt gt a Hologram A An object x0 yo 2 and a reference source point illuminate the recording material The phase of the wavefront from a point source is CXPUkrm The length r01 can be expressed as 2 2 1 2 1 2 yy 2 r01221 1 xx 2 11 21 2 z1 2 z1 Biochemistry 460 Dr Tischler LIPOLYSIS BETAOXIDATION KETONES LIPOGENESIS Related Reading Chapter 22 619644 in Stryer 639h edition OBJECTIVES 1 For the lipolytic pathway lipolysis describe the pathway identify where it occurs name the principal enzyme involved and explain the role of albumin and fatty acid binding protein in the transport and metabolism of free fatty acids liberated by lipolysis 2 For the degradation of fatty acyl CoAs describe the roles of acyl CoA synthetase carnitine palmitoyl transferases CPTI and CPTII and carnitine acylcarnitine translocase CAT and discuss the relationship of the products of the Boxidation pathway to energy production 3 For ketone body metabolism identify where and when ketone body formation ketogenesis occurs state the role of ketogenesis identify where ketone oxidation occurs and explain why normally individuals do not develop ketoacidosis even when producing ketone bodies 4 Describe the reactions catalyzed by malic enzyme and acetyl CoA carboxylase 5 For the fatty acid synthase reaction list the substrates and key products identify the sources of NADPH for the reaction and describe its general mechanism 6 Describe how fatty acids are stored as a source of fuel during starvation or stress PHYSIOLOGICAL PREMISE Would you believe that diabetics having a ketotic crisis have actually been arrested for DUIs even though they have consumed no alcohol Indeed a blood analysis would show no alcohol Why would this occur During a ketotic crisis a byproduct of the excess ketone production is acetone Having nowhere else to go it is expired through the lungs It is the acetone that arresting officers have smelled on the breath of these individuals and despite their protestations have innocently believed them to be consuming alcohol LIPOLY SIS Lipolysis is a simple process whereby the fatty acids attached to glycerol in triacylglycerols are hydrolytically removed yielding free fatty acids plus glycerol Lipolysis largely occurs in adipose tissue for the mobilization of fatty acids to serve as a fuel in the body as well as a precursor for the synthesis of ketone bodies Additionally lipolysis may also occur in muscle or liver where smaller amounts of fatty acids are stored to produce energy for the use of the cell in which they are stored Hormone sensitive cyclic AMP regulated lipase initiates lipolysis by cleaving off the rst fatty acid Then this lipase and other lipases remove the remaining two fatty acids from the glycerol backbone The fatty acids and glycerol are then released from the adipose tissue into the blood Glycerol is watersoluble and therefore can freely travel through the blood However fatty acids are very hydrophobic because of their long hydrocarbon tails Consequently they must bind to albumin a protein released from liver to be carried through the blood Lipolysis Beta Oxidation Ketones amp Lipogenesisl
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