BAS BIOL MICROORGAN
BAS BIOL MICROORGAN MCB 3020
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This 34 page Class Notes was uploaded by Ms. Carol Kautzer on Friday September 18, 2015. The Class Notes belongs to MCB 3020 at University of Florida taught by Staff in Fall. Since its upload, it has received 15 views. For similar materials see /class/206657/mcb-3020-university-of-florida in Microbiology at University of Florida.
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Date Created: 09/18/15
Lecture overview 0 Translation components initiation elongation termination 0 Post translational modification and protein folding 0 Protein transport 0 Making cell structures envelope appendages Prokaryotic Ribosome components Large subunit has 2 250A ggggofggge RNAs 34 prots Small subunit has 1 M92N Mgz RNA 21 prots SOSSubumt SOSsubunit 145 X 106 085 X 106 Overall prokaryotic ribosome is 70S wrea 53 RNA 23 RNA 4x 104 10x 106 g biology kenyon edu cour e biol63ribo Fig03 I I LLLZTTTiLM 31327351 321 2 Initiation of translation a 0 Starts With formation of initiation complex at start site AUG of mRNA 0 Inactive 70S ribosome must dissociate need IFl amp IF3 binding to 30 subunit 0 A complex of IF2 GTP and g fMET tRNA binds to3OS 9 subunit 7 0 This complex binds 50S subunit iiiuer L GTP then hydrolyzed and GDP 1 and IF2 leave E department oxyedu Initiation of translation Start sequences in mRNA 10 lll AUG r nRNA Basepairs with ribosomal RNA A Proka ryotic start signal fMet A xvV e W 39 rquot r P rot e i 11 Sequence at 10 is Shine Dalgarno SD sequence complementary to 16S RNA in 30S ribosome Presence of SD sequence determines start of translation fMET only used by bacteria 0 tRNAs key to translation Genetic code Fig 8 14 amp 813 j Ar39aLiL39udur l quot riplet quot72 Base32 llTl ELl J l lll Y Inudi l ieLl If 1 Either base5 l Ill Extra loom Eniusil l wilfrr U C A G ULILI Fl IL Him 5 LALI T39r Gl 39Zys U lll39 Plquot ULII quot91 Hit yr lite 39w I2 u ULIA Leu U233 Eer UAR Stop UEA Em A LIIIIQ m will 5m UM Stop llt39rln 1 1quot 395 CLJ Leu CCU 3n IDSLl ii IIGU Aquot U flu en LIE PM FIE F1 1112 uit C c LA LE39U I335 Pac Cr b l Glr IDEA rg A LG Pu IE1 l I39J ICE jll 3312 m E lent a x 39 lpneI AL J m pCLI Thr MU Am AEU Sui U I39Jx3939 Ilaquot fIiif ll n Mil Ivan MI 3quot C A ALL Ila REA 1r AM L502 EM Ar 1 I ILafj Mu tij quotIr fns vt Ln Mil fun G GLILl 39Ii39ul I will Ala GAL lam I EGJ Gig U out 39I El Gilli ua GAE ap EEK Ely i G GLIA his age Ala ISA394 Elu El n IS F1 Gilli 39a39 1l L39JIZII Ala 11 391 it Cyly G 0 Each tRNA has anticodon loop opposite to Where specific AA is attached at CCA end 0 Proofreading at level of charging tRNA 5 39H fMet Phev r l l E UACAAA 5 AUGUUUACGGCACAAGCUGGG Polypeptide chain elongation Bauman Fig 716 i E l l AKAUGC 3 Thr fMet Phe lquot s 5V l l y l E l l 39 u39ACAAA gtuA39c E 7 EC AAA l AUGUUUACGGUA 3 AUGUUUACGGCAAAGCUGGG P A 5 l P A Peptidebond 1 l I 7 We Phe Thr lMetVPheV 3 i l gt Movement of ribosome AUGUUUACGGCACAAGCUGGG 3 P fMet Fhe UACAAA AUfGUUUACGGCACAAGCUGGG 3 1 E Jl l39 ll lTwo more cycles Ala l i P A A e 39 W 1 fMet Phe Thr Ala Growing r Gm polypeptide 9 gt Movement of ribosome 5 PA Copyright 2006 Pearson Education Ino publishing as Benjamin Cummings PA l K 1 l l GA on E W GUU AUGUUUACGGCACAAGCUGGG 3 a 3 sites on ribosome E P A are Where anti codon of tRNAs bind fMET occupies P site and the next charged tRNA binds at A After a peptide bond is formed by 23S RNA all tRNAs are translocated one position as ribosome moves down mRNA Polypeptide Elongation accessory factors Fig 816 0 A site binding 7 requires EF Ts EF I V gll Tu amp r 1 Peptide bond 2 catalyzed by 23S Mliii39imN Translocation requires EF G amp H b i Ia 7 i if 0 Translation rate transcription rate 3 45 nucssec 7 Termination of translation 0 Termination occurs When ribosome tries to translate a stop codon no cognate anti codon on tRNA 0 Stops are UAA UGA UAG 0 Exception is tRNA for selenocysteine inserted at some UAGs 0 Release factors RF l or RF 2 and RF 3 needed for translation termination Post translational modification in prokaryotes Table 82 Examples of bacterial protein modifications Modification type Proteina Chiefly assembly reactions Signal peptide cleavage Formation of 55 bonds Addition of lipid moiety Addition of sugar moiety Attachment of prosthetic group Chiefly modulation reactions Phosphorylation Methylation Acetylation Adenylylation Secreted proteins Many proteins Murein lipoprotein Membrane glycoproteins Many enzymes Ribosomal protein 56 isocitric dehydrogenase many proteins with regulatory functions Chemotactic signal transducers Ribosomal protein L7 Giutamine synthetase Examples are drawn from Escherichia coli 0 f MET always removed 0 diS bonds only occur in periplasm of most bacteria 9 Trigger factor Polypeptide protein 9 egg Ribosome W O DnaK Protease Protein folding Fig 817 Remodeling V V Degraded protein Chaperones aid folding Mature protein 10 sequence alone does not yield properly folded Trigger factor has PRO isomerase DnaK GroEL and GroES all aid in proper folding Translocation of proteins signal peptides Precursor of Local Amino acid sequence ization Lipoprotein OM Met Lys Ala Thr Lys Leu Val Leu Gly Ala Val Ile Leu Gly Ser Thr Leu Leu Ala Cys lreceptor OM MetMet lle Thr Leu Arg Lys Leu Pro Leu Ala Val Ala Val Ala Ala Gly Val Met Ser Ala Gln Ala Met Ala Val Maltosebinding PS Met Lys lle Lys Thr Gly Ala Arg Ile Leu Ala Leu Ser Ala Leu Thr Thr Met Met Phe Ser Ala Ser Ala Leu Lys protein BLactamase Arabinosebinding protein fd phage major coat protein fd phage minor coat protein l PS Met Ser e Gln His Phe Arg Val Ala Leu Ile Pro Phe Phe Ala Ala Phe Cys Leu Pro Val Phe His PS Met Lys Thr Lys Leu Cal Leu Gly Ala Cal Ile Leu Thr Ala Gly Leu Ser Gly Ala Glu CM Met Lys Lys Ser Leu Val Leu Lys Ala Ser Val Ala Val Ala Thr Leu Val Pro Met Leu Ser Phe Ala Ala CM Met Lys Lys Leu Leu Phe Ala lle Pro Leu Val Val Pro Phe Tyr Ser His Ala Hydrophilic basic region Hydrophobic region 0 Proteins that function outside cytoplasm have signal sequences to aid translocation SecA binds to signal 0 2 translocation pathways use Sec proteins all use ATP SecA used for secreted proteins SRPs used for inserted proteins Translocation Z pathways Fig 819 r55F 39i39u rmtiz s g LcE39G 39 Protein to t a if Eggclefquot Sigl iall seguerice be exported 71 3939 ul quot391 l b L yIr I map I 3 Qpr i iflj39 quot nal segueVICE ganglia i 5 l patina llllllllil c v l l l initial i e V 39 WDSDI 39 39 i ll nif 2v vii quot y 49v 3 r 2quot 39rT j39irrw thanalll l jlllallilililllill illllllillllilliilllili lllllllill itllilllilllll Other secretory systems Table 83 and Fig 820 Type I ABC exporter x or e r em Type IV Conjugal transfer system See type III for diagram Type V Autotransport ABC system works With proteins lacking signals TYPE 11 second step moves prots across OM TYPE III moves protein into a host cell pathogenic TYPE V uses only Sec in rst step secretion across OM not dependent on other proteins Assembly of cell envelope 0 Not much known about assembly of inner and outer membranes except LPS 0 Cell wall see next slide 0 Appendages agella pili O Capsules assembled are sometimes formed outside cell by extracellular enzymes or polymers secreted already polymerized Assembling the cell wall Fig 822 amp 24 HITIP ur39n Lu quot39 uquotquot39 quotI Ilrixli rlrI39unvlrzvhnsFI39I 39ni Iran Ir39y39y39lp39ihi i m F39Ii WL 1I391J i PJ J39 I I 39I q El 39 uriI rgtv 2 39 39quot quot39 b inquot innnlg39l Ha p39ihrnivmh 1riw lp l n nh i quotr 39I i l39gtJJ1 I it1 b II I I H II quot 39 i z t smalliwmalzlin IHIwillllllzlglgllgltli II I lll glIIII ig39glulg EII h 1 x LILi II III 1 jgj H in ILsllI quotiji l39i ill I mt m SJ Iii V J 9 a i t a39u39lnr ri q iiiiij ti u i ritzim1151 i at i IIErr39il Gram positive GcNAc MurNAc n L llila DIGIU LLys Gly5 D Ala Da L Llys D lu LAla GcNAc MurNAc n Il39l llL A r quotquot w ill u39 iquot Hl l139IEFI39I 1l 1 f li u i f r v M rt vquot 1 Gram negative GcNAc MurNAc l n LAla Dlilu DiIAP DAla DlAIa DiAP D lu Llila l N11 JJJJJJ n zvilliMarjilgli Muni I GcNAc MurNAc n Murein precursors NAG NAM pentapeptide from cytoplasm shuttle through CM linked to C55 undecaprenylP glycan polymerizes in periplasm Transpeptidation makes x links Synthesis of LPS Fig 823 amp 29 u7 up 0 antigen is synthesized on undecaprenylP carrier Core is assembled on lipidA lipidA serves as carrier across CM LPSis put together once precursors cross CM Overview of transcription Process of making an RNA copy from DNA In prokaryotes only one enzyme involved for all types of RNA mRNA tRNA and rRNA from genesgtRNA polymerase RNAP Primers used during replication is different enzyme 3 stages initiation elongation and termination Termination WWWgeneticengineeringcom Structure of RNAP E coli Structure of core enzyme dz uo Core binds to DNA in nonactive mode core RNAP 0 subunit yields active holoenzyme OMyRNAP holoenzyme initiates gene transcription at promoters RNA 3 y lf1 Pause hairpin r Overview of transcription Fig 89 Core RNA polymerase Sigma factor Core RNA polymerase Initiation of transcription 0 Regulation of transcription at initiation step RNAP subunits on and o bind to promoters to form closed complex 0 DNA 12 bp melts to form open complex Transcription bubble extends to 18 bp and can now begin elongation Anatomy of a promoter Fig 810 T T G A C A 17basepairspacer T A T A A T 69 79 61 56 54 54 43 77 76 6O 61 56 82 35 region 10region It A x X 39 47 DNA y l 60 35 10 1 20 J Core promoter Transcript 0 35 region often has sequence related to TTGACA 0 10 region often has sequence related to TATAAT Pribnow box sigma subunit makes contact With these 2 reg1ons Transcription in Archaea and Eukarya 0 Eukaryotes have 3 RNAPs With different specificities 0 polyA added post transcriptionally 0 More factors needed to initiate transcription 0 Archaea have 1 RNAP similar to Eukaryotic RNAP II mRNA use accessory factors and promoters resembling eukaryotic promoters Termination of gene transcription 0 2 types of transcription termination rho dependent and rho independent 0 Premature termination of transcription attenuation is regulatory Rho independent termination of transcription mo TERMINATION OFTRAMSCFIIPTION forms inverted repeats high GC content 0 Hairpin followed by polyA sequence 0 RNAP can terminate with these two elements wwwscience siu edumicrobiology micr302 Rho dependent transcription termination 0 rho binds at sites after stop codons no ribs 0 rho wraps around RNA and pulls it off RNAP Rho binding is ATP dependent cwxprenhallc mh It nmedialibmediaip r tf 1i teXtimage Stability of RNA Ribosomal RNA tRNA very stable under most conditions mRNAs have half life t1 2 lt 1min Prokaryotes use this for quick response to changing environmental conditions Organization of prokaryotic THE LAC OPERON I hwcnmmwmm E Regulaturyregimls mmregmwmmm 1 165 tRNA 235 55 l Paymemse ER Meth Iation HE y oooooooooo 6mg r Cleavage ICAPI I o P lLacZ ILachLacAl 39 1 175 llltRNAl 235 II t W i Nuclease l Nuclease I 6i ribosomes l I l nnnnnn 235 allow glucose P w w w 0 in prokaryotes genes are poly cistronic ie 1 RNA gives rise to gt1 polypeptide multiple genes 0 Stop codons terminate translation between genes 0 wellesleyedu left and Fig 8 11 right Stable RNA 165 tRNA 23s 55 Methylation l Cleavage 175 tRNA 235 55 l Nuclease l Nuclease 165 J 235 0 Long half life 0 genes are ribosomal SS 168 238 amp t RNA 0 During rapid growth gt 50 of transcripts are rm amp 98 of RNA in cells are from rm genes 0 Both gene copy number and strong promoters contribute Stable RNA processing l 165 tRNAl 235 55l Methylation j Cleavage I vs llltRNAlll 23s ll Nuclease l Nuclease l 235 l Large group of RNAses work on primary transcript cutting it into pieces and modifying it 3 10 enzymes modify l6S rRNA and 313 work on 238 Post transcriptional modification eg methylation results in odd bases pseudouracil inosine etc especially in tRNA Degradation of RNA species in prokaryotes cisacting elements involved e g eXposed AU rich regions with no 20 structure readily cleaved RNAse E a major endonuclease for SS RNA RNAse III endonuclease cleaves DSRNA 3 major 3 5 exonucleases PNPase RNase II and Rnase R degrade RNA fragments completely Degradation of RNA species in prokaryotes cont RNA is vulnerable if it is not coated in protein Endoribonucleases work first then exoribonucleases sometimes combined with helicase in degradosome rRNA cleaved when it becomes uncoated during starvation RNAse I periplasmic degrades rRNA when Mg2 is lost from cell membrane injury Endoribonucleases also work in rRNA processing Coupled transcription amp translation in prokaryotes o Ribosomes attach to message and begin to make protein While message is transcribed Process streamlined compared to eukaryotic l 025 pill BMW Regulation of one process 4 u r DNA 5 y mease affects the other more later 39 WWW muncabiologyscarr 13883 1pol yribosomesjpg i Rlbosome F I H mRNA We a systems Biotechnology Part2 Expressing cloned genes Cloning genes vectors Making and screening libraries Expressing genes in different hostvector Getting DNA into cells Agrobacteria and agricultural applications Cloning genes Brock Fig 1035 Foreign DNA4 I enzyme Add vector cut with same Sticky lt ends quot Vector restriction enzyme Add DNA ligase to f rrrrrr ombinant Cloned DNA Introduction of recombinant vector into a host 39croorganisms 11e F Mat 6 2006 Pearson Prenli lllllllll c Proten n in rich rig glutathi one Serraretainam Multiple Clonin Eilill be 11ml lac repres Cut with restriction Genes are ligated into vectors Vectors may be plasmids or phage All vectors contain genetic elements including MCS s ori s selectable markers Many other features including expression elements for microbial and nonmicrobial hosts Libraries of random gene sequences can be made and screened Finding new genes can be done by screening for sequences homologies with labeled NAs using Abs or bioactivity Making and screening libraries Bauman Fig 85 Genome ocells Ax a J39 is v v 2 2 gt 3 L f f i quot L 6 WWW AW WW Isolate gen me JVW ML FAVn 7 7 l o rganism g g Z 5 Wow3 have x vr 6 L Vk ML 5 7 7g 8 s 9 Lib quotJ l wfzu I G eeeee te fragments using rrrr rictio l76 ME 1 enzymes gr 3 10 g g 3 5 mog DRAWJ 10 1 Cultur re mb II I eeeeee ach fragment vector L5 77 3975 lV8 73943 5111 I 39 I 39 I y 39V y l 1 2 3 4 5 6 7 8 9 10 11 CCCC right 2006 Pearson Education Inc publishing as Benjamin Cummings DNA from organism is cut up into random pieces and each piece is cloned into a plasmid or phage 0 Individual bacteria containing a plasmid or individual plaques from phage are screened using labeled probes or via antibodies 0 Activities of cloned gene products can also be screened Getting DNA into cells Transfor1nation of bacteria Bauman Fig 8 10 Pores in wall and membrane 0 Cells are made Ch 7 39 quot e x e e n competent v1a 3 WEI M W i 3 i Enigma 7 u I electroporatl on or v1a le 392 39 applied mete cequot DNAQ Remmbmt CEquot pre tre atm ent W ith a Electroporation Copyrlgm 2006 Pearson Educauon 100 publlshlng as Eenlamm Cummings d 0 DNA plasmid i s added r x f and eel l s that have taken g 0 II CK S k 0 NWl 7 7 quot 5quot51l k gt I 7 o x up the plasmld are Enzymes P yethylene l 6 I V 7 identified by plating on selective Inedia 2 remove QIYCOI i cell iL Q rir j V Jig Recombinan xx 7 fl walls Lquot 7 cequot Protoplasts Fused protoplasts New wall b Protoplast fusion Copyright 2006 Pearson Educatlon nc pubhshing as Benjamln Cummings Expression of recombinant proteins in Bacteria Di sadvantages 0 Bacteria cannot splice introns 0 Reduced intracellular environment 0 No eukaryotic type of post translational modification Advantages 0 Inexpensive to scale 0 From clone 9 scaled up expression in 2 Wks 0 10 30 gl hINS bGH many proteins used to generate vaccines 5 Expression of recombinant proteins in Baculovirus and yeast Baculovirus very popular but glycosylation not correct From clone 9 scaled up expression in 4 Wks Serum free growth at 270C no C02 0 1 10 gl Yeast Can splice some introns glycosylation not correct Doesn t fold many proteins correctly Multi diS containing proteins a real problem From clone 9 scaled up expression in 2 3 Wks 001 10 gl Expression of recombinant proteins in Mammalian cells in culture or in Bioreactors Tissue culture Tissue culture expensive and low yield From clone scaled up expression in 4 months Correct post translational modifications 10 20 mglit hybridomas making Abs 40 80 mglit Bioreactors 39 Environmental concerns 39 From clone scaled up expression in 2 years for mammals 39 Plants proteins not properly glycosylated and very immunogenic protein difficult to purify Up to 10 gl in milk Getting DNA into cellsTransfection of eukaryotic cells Bauman Fig 810 areas message 0 Can be done using CaCIZ electroporation special chemicals micro injection a 39 To make transgenic animals either mien injection of fertilized eggs or gene gun is used 39 Plants are made transgenic using Agrobacteria or via gene gun Use of Agrobacteria CullLIrEd I 3 FlaInlet hr Transgenic Bella Ecbacuc mam 0 Agrobacterium tumefaciens contains a special Ti plasmid tumor inducing that can be genetically engineered in E coli then transferred back to the Agrobacteria via conjugation 0 T DNA transfer DNA then transferred to plants via conjugationnormal wounding response or via particle gun 9 Agricultural Applications of Biotechnology Delayed ripening fruit Pest resistance Freeze resistance Drought resistance and salt tolerance Herbicide resistance Vaccines made in transgenic plants Growth hormone to increase milk production Neutraceuticals Overview of microbial ecology 0 There are currently 1030 prokaryotes on earth 0 Microbes are metabolically active and change the environment they live in 0 Microbes responsible for levels of 02 CO2 and N2 in atmosphere Where microbes live Fig 181 Organic compounds oxidized to C02 or fermented to various acidic or neutral products Soil Lake or Pond Acetate 8Fe3 4HZO gt mm 8Fe2 9H Sediment Shallow groundwater gt Benzene 6NO3 6H r gt 6COZ 3N2 6H20 H FeSZ 14Fe3 8H20 gt 15 Fe2 25042 16H Mines Ancient sandstone or shale gt Organic compounds 5042 gt HCO3 H5 1 6 km Hydrothermal fluids gt H2 C02 gt CH4 2H20 Studying microbes in the lab 0 Most microbes from environment cannot be cultivated ltlt1 0 Enrichment cultures can help in some cases 0 Culturing often changes phenotype 0 Many microbes only grow in communities Enrichment cultures Table 181 Some examples of enrichment culture Microbial class Critical cultural condition Rationale Thermophiles Endospore formers Nitrogen fixing cyanobacteria Sulfate reducing bacteria Microbes able to degrade a particular pesticide Incubate at a temperature in the thermophilic range eg 55 C Boil soil inoculum before adding to culture medium Incubate aerobically in the light in a mineral salts medium lacking fixed nitrogen Incubate in the dark anaerobically with a nonfermentable carbon source and sulfate ion Incubate aerobically in the dark in a mineral salts medium with the pesticide as the only source of carbon and energy Only thermophiles can grow at such temperatures Very few vegetative microbial cells can withstand being boiled endospores can Only certain cyanobacteria can grow aerobically and phototrophically and fix nitrogen Under such conditions sulfate reducing bacteria can derive energy by anaerobic respiration photosynthesis aerobic respiration and fermentation are not possible Under such conditions capability to degrade the pesticide is essential for growth Modern approaches to the study of microbial 0 FISH ecology Immuno uorescence microscopy 0 FACS 0 PCR 0 Micro autoradiography 0 Carbon 0 Oxygen 0 Nitrogen Sulfur Bio geochemical cycles 0 Phosphorus 0 All cycles made up of RedOX reactions Carbon cycle I Sinlug tn EH Hm In EHsz 0 httpearthobservatorynasa govLibraryCarbonCycle E iiifilf jig quot37 Ski04015131l u Atmosphere 3 30 an per year Ari 3 E wine mu Binlogiml a w h 39 w lhE S swirls Respiration Defu39 imlim Fossil Fuel Biolag39isu39 DHQITIPG SIIIHII 5 Protessas Ehemlml W 39 7 9391 Prom555 l 1 s l uquot haquot H is t e e u 3 g i was an e a s wre use r s Soil lle lail nrem assoc10000 1 man 33e ulwr rm 0 CO2 H20 CHZO 02 0 Fixed carbon degraded to CO2 and CH4 methanogens 0 CH4 oxidized to CO2 by methanotrophs 0 More C in humus than in living orgs 0 httpwwwbom gov auinfo climate Carbon reservoirs Brock Table 193 Table 193 Major carbon reservoirs on Earth Carbon Percent of total Reservoir gigatons carbon on Earth Oceans 38 x 103 gt95 005 is inorganic C Rocks and sediments 75 x 106 gt80 gt995b is inorganic C Terrestrial biosphere 2 X 103 0003 Aquatic biosphere 1 2 0000002 Fossil fuels 42 x 103 0006 Methane hydrates 104 0014 a One gigaton is 109 tons Data adapted from Science 290291 295 2000 b Much of the organic carbon is in prokaryotic cells ogy of Microorganisms 1 We 0 Most carbon on earth is stored in rock 0 Over 2X amount of methane hydrates as fossil fuel stored in artic and deep sea sediments gt 99 of this is from microbial degradation of organic material Methane Estimates 0 CH released Into the Table 195 atmosphere Source CH4 emission 10lz gyear Biogenic Ruminants 807100 Termites 25 150quot Paddy fields 70 120 Natural wetlands 120 200 Landfills 5 70 Oceans and lakes 1720 Tundra 1 5 Abiogenic Coal mining 10a35 Natural gas flaring and venting 10 30 Industrial and pipeline losses 15 45 Biomass burning 10 40 Methane hydrates 2 4 Volcanoes 05 Automobiles 05 Total 350 820 Total biogenic 3027665 81a86 of total Total abiogenic 484155 13 19 of total quot Data adapted from estimates in Tyler 5 C 1991 The global methane budget pp 7 58 in E I eds Mirrobinl Production an Cnnstuupfiuu iy Cn mhmm39 Cases Multmm Nitrogen Oxides and I39lulumeftmm s American Society for Microbiology Washington DC 139 More recent estimates indicate that the lower value is probably the more accurate Table 195 Brock Biology of Microorganisms 1 We 9 2006 Pearson Prentice Hall Inc 0 Note only small amounts of CH4 from fossil fuels 0 CHA 10x better a greenhouse gas than CO2 Oxygen cycle hv 413 4 Man 0 ozoneshieldrabsnrplion v at utlraviulel radiatinn v 0 Inn 03M Imm 220 nm to an In 02 mam J 200 20 f 0 3912 02 co oxygen consumed 02 hyreducmggasas 7 a volcamcurgm 39 39tcumo cuzuu trespimion by animals 2an at reduced In arals Oxycycle The Partitioning of Oxygen figure 109 The Atmosphere 1100000 Gt O 1 an GTonOM 013 Gt Oyr Ne t uptake by weathering burial of organic carbon 039 fOSSIIIZGG carbon um Grenom 7500 310 Assimilated 0 05 GtCyr lt7 photosynthesis Mott ttds at 013 GtO r 51 i a g e D 6 The Biosphere i F 2800 GtC Organic carbon 005 Gt Cyr organic carbon burial fossil carbon upli ing Sediments buried organic carbon f 10000000 Gt C 0 Oxygen uxes are balanced and stable Nitrogen cycle Brock Fig 1928 Key Processes and Prokaryotes in the Nitrogen Cycle Example organisms Processes Nitrification NH4 gt N03 Nitrification N02quot NH2 groups 455 NH 4 gt N02quot Nitrosomonas f r te t 0 P 0 In I ro en No2 No3 Nitrobacter m v fixu39an Denitrificution NO339 gt N2 Bacillus Paracoccus No3 43 Pseudomonas l o I39 39 N2 Fixation N2 8H gt NH3 H2 fqh0n NH3 0x FreeIIVIng t n Anoxk Aerobic Azotobacter Li a t Cyanobacteria fHngiL ps v99 Anaerobic Clostridium purple and N02 p 1 green bacteria Ammo Nitrogen symbiotic Rhizobium fixation Bradyrhizobium Frankia a N2 Ammonification organicN gt NH4 Many organisms can do this Anammox NOf NH3 gt 2N2 Brocadia Denifri u on Figure 1928 part2 Brock Biology of Microorganisms 1 We Figure 1928 part 1 BrockBiology of Microorganisms le 2006 Pearson Prentice Hall Inc 2005 Pearson Prentice Hall Inc Sulfur cycle B rock F1 g 1 929 Key Processes and Prokaryotes In the Sulfur Cycle C emovnhotrzlsluc esudc Process Organisms S II Sulfide sulfur oxidation H25 gt 50 504239 Aerobic Sulfur chemolithotrophs a o SH groups Des Thiobacillus Beggiatoa many others of proteins 06 Anaerobic Purple and green phototrophic bacteria some chemolithotrophs 2 90 0xrc Sulfate reductlon anaerobic 04 gt H25 DMSO D M S A quotD Ifb t F noxu Desulfovrbrro esu 0 ac er so 2 sulfate redu on H S 4 2 Sulfur reduction anaerobic 50 H25 Desulfuromonas many hyperthermophilic Archaea Sulfur disproportionation 2032 gt H25 042 Desulfovibrio and others Organic sulfur compound oxidation or reduction CH3SHgtC02 H25 DMSO gtDMS Many organisms can do this Desulfurylation organic S gtHZS Many organisms can do this Figure 19 19 part 1 Brock Biology of Microorganisms 1 the 2006 Pearson Prentice Hall Inc Figure 1 929 part 2 Brock Biology of Microorganisms 1 We 2006 Pearson Prentice Hall Inc Phosphorus cycle Fig 189 Birds 1 Inorganic MOStorganlsmS Organic phosphate phosphate l V Microbes Most organisms Organic 4 Inorganic phosphate gt phosphate Microbes Geological uplift Phosphite deposits Main groups of eukaryotic microbes Tabe161 Main groups of euloryotic microbes Group Examplesoltypes Characteristiccellenvelopeand constituents Fungi leastmolds Cellwalcontainingglytoproteinsegmannoprotelns polysaccharides egchitingucanslother Protozoa Poromeciomamoebas6iordioPlosmodium Peiteinteriortoplasmamembraneaonsisttolintetronneoed agents of malarialletrolymeoo protein moleculesgites shape to the cell Algae EugleooChlorelodiatomsdinollagellates lhrorophylltellwallcontainingcellulosesilitainsometacium In some Notallaremicroscopitegmushroomsllungiorseaweedalgae Properties of fungi Comprised of yeasts molds and mushrooms 0 From microscopic to macroscopic mushrooms 0 All nonphotosynthetic and nonphagocytotic 0 Cell walls of chitin NAG polymer 0 Can grow as filaments hyphae without sexual cycle 0 Propensity to live in other organisms either symbiotically or parasitically Decomposers saprobes Nonreproductive forms of fungi Nonreproductive body of fungus is thallus Thalli of yeasts are unicellularthalli of molds are composed of multicellular branched tubes called hyphae septate or aseptate Dimorphic forms include Histoplasma capsulatum and Coccidiodis immites Asexual reproduction in filamentous fungi Spjfngin Straw J 39 5quot Sporangiospores form V b on stocks called sporangiophores Chlamydospores form within thickened cell walls in hyphae Conidiospores are produced at the tips of hyphae i quot i i C W 15pm Copyright 2006 Pearson Education Inc publishing as Benjamin Cummings Sexual reproduction in fungi 0 HaplOIdt spores of 2 a ma mg ypes grow as 373x mf t J 0 Hyphae of 2 different I mating types can fuse to make dikaryon that I differentiates into fruiting body 0 Haploid spores are produced after fusion of 2 nuclei and meiosis g Haploiducleus Haploid nucleus TTiTTTTWquot 39 a Copyright 2006 Pearson Education Inc publishing as Benjamin Cummings Yeast as eukaryotic model Fig161 amp 163 Bud Bud scars 0 Yeast are transformable and can make some recombinant proteins 0 Yeast have some regulation similar to that of higher multi cellular eukaryotes and 16 chromosomes 0 Can grow in both haploid and diploid states can look at lethal mutations Mating types in yeast Fig 165 Silent a gene Promoter MAT cassette site Silent 0t gene 1 Gene or is expressed 0 2 mating types a and or alpha and both are initially silent Mating type develops by copying either a or or and inserting it into the mat site Life cycle of a mushroom Cross section of gillN 1 showing hyphae 7 Pair of haploid 39 nuclei fuse 2n Meiosis produces four haploid nuclei 1 spores 1 n devalop Basrdiospo res Zlig Basidium limb form Basidiospore 7 V released m do Button 7 Basidiospores germinate to produce mycelia r l 3935 it Dikaryon mycelium leal yom produces basidiocarp THn mushroom r Hypha of opposite mating types fuse below ground to produce dikaryotic mycelium Copyright 2006 Pearson Education Inc publishing as Beniamin Cummings 0 Amanita muscariatypical mushroom Protists protozoa plus algae Table 162 Some of the major groups of protists Means of Main mode Group Examples locomotion of nutrition Flagellates Trypanosoma African Flagella Absorption uptake of sleeping sickness soluble food American Chagas disease Giardia hiker s diarrhea Trichomonas sexually transmitted infection Amoeboids Entamoeba histolytica Pseudopodia Phagocytosis uptake of dysentery abscesses particulate food Naegleria fowleri encephalitis Ciliates Paramecium Balantidium Cilia Ingestion of particulate human intestinal food via a mouthlike infection organ Apicomplexa Plasmodium malaria Nonmotile except for Absorption uptake of so called Toxoplasma some stages in the life soluble food because they toxoplasmosis cycle produce a structure called an apicoplast 9 Protozoa basics Most live in ponds streams lakes ocean and make up an important part of plankton some in damp soil Show great variety in number and type of mitochondria All free living protozoa eXist as motile feeding trophozoite and many have a cyst hardy resting stage Most are chemoheterotrophs 10 Flagellates V f es s i ii r 1 395 w K x f f 4quotquot 39 quot4 v J f I f i L I I A Iquot W Copyright 2006 Pearson Education Inc publishing as Benjamin Cummings 0 Many pathogens including Trypanosoma brucei African sleeping sickness above 0 Leismania grow inside macrophages Giardia intestinalis GI disease 11 Some amoebae 0 left Entamoeba histolytica causes amebic dysentery 0 Acanthamoeba and Naegleria cause encephalitis 39 50 um I I asBenjaminCummings 12 Ciliates Copyright 2006 Pearson Education Inc publishing as Benjamin Cummings Didinium eating a Paramecium Balantdium is a human pathogen causing dysentery 13 Paramecium Fig 167 Contractile vacuole Micronucleus Macronucleus Cilia g gag5 i39WPellicle 2 Food vacuole Contractile vacuole Anal pore Macronucleus not true nucleus micronucleus is 0 Macronucleus contains 401000 copies of genes needed for rapid growth 0 httpfacultyplattsburghedujosedeondarzaresearch 14 Algae groups 39 Classification based on pigments 39 Diatoms and coccolithophores 0 Dinoflagellates actually more related to ciliates Via 16S rRNA analysis 39 Can be unicellular or colonial 0 Large marine algae are seaweeds Table 124 Characteristics of Various Algae Group Storage Cell Wall Representative Common Name Kingdom Pigments Product 5 Components Habitat Genera Chlorophyta Plantae Chlorophylls a Sugar starch Cellulose or protein Fresh brackish Spirogyra green algae and b carotene absent in some and salt water Prototheca xantliophylls terrestrial Codium Trebouxia Rhodophyta Rhodophyta Chlorophyll a Glycogen Agar or carrageenan Mostly salt water Chondrus red algae phycoetythrin oridean starch some with calcium Gelidium phycocyanin carbonate Antithamnron xanthophylls Chrysophyta Stramenopila Chlorophylls a Chrysolarninarin Cellulose silica Fresh brackish Stephanodiscus golden algae c and c carotene calcium carbonate and salt water yellowgreen xanthophylis terrestrial ice algae diatoms Phaeophyta Stramenopila Chlorophylls a and Laminarin oils Cellulose and Brackish and Macrocystis brown algae c xanthophylls alginic acrd salt water Pyrrhophyta Alyeolata Chlorophylls a c Starch oils Cellulose Fresh brackish Gymnodinium dinoilagellates and c1 carotene and salt water Gonyaulax P esteria Euglenophyta Euglenozoa Chlorophylls a Paramylon OtlS Absent Fresh brackish Euglena euglenids and b carotene sugar and salt water terrestrial Copyright 2006 Pearson Education Inc publishing as Benjamin Cummings 16 Algae pictures 0 Gonyaulax is dino agellate that makes neurotoxin shellfish 0 Red tide a product of dino agellate bloom httpWWWmicroscopV ukorguk 17 httpimagesusatodaycorntech Diatoms and coccolithophores Fig 16 l l Diatoms right are single cells algae With protective coats made of Si02 coccolithophores cell wall of CaCO3 0 50000 species known 0 Major part of plankton H Myxamebae germinake mm Comyaxible myxamehae fuse Hanlaid spams 39 Sncvangium released g Slime molds coauocyxi plasmndium 2n Spurangia gmw lmm plasmo ial masses ares 5n released r Nucleus Kff y l s or Sgorangium 3 ll l rmning hudy with f symangium l 025 m 39 7 lt quot Myxamebaa ongregale to 1am pseudoplasmodium slug mu 1hey main Ei individuality development and cell signaling Copyright 2006 Pearson Educatlon nc publlshmg as Benjamin Cummings Dietyostelinm diseoidenm a model for Prokaryotic cytoplasmic structures Nucleoid and cytoplasmic DNAs Gas vesicles Cell inclusions Endospores Nucleoid Fig 31 32 0 Bacteria and Archaea typically have a single chromosome that is condensed by scaffolding and DNA binding proteins 0 Proks are haploid 0 DNA has neg SCs gyrase 0 Typically no nuclear membrane 0 Transcription and translation occur at same time in 512 quotV 2 Fig 33 Sizes of genomes of prokaryotes Archaea Methanosarcina acetivorans Halobacterium salinarium Sulfolobus solfataricus Pyrococcus furiosus Methanococcusjannaschii Thermoplasma acidophilum Nanoarchaeum equitans Bacteria Nos toc punctiforme Streptomyces coelicolor Mesorhizobium loti Pseudomonas aeruginosa Escherichia coli 0157H7 Agrobacterium tumefaciens Salmonella enterica serovarTyphimurium Escherichia coli K 1 2 Mycobacterium tuberculosis Bacillus subtilis Caulobacter crescen tus Vibrio cholerae Deinococcus radiodurans Haemophius influenzae Rickettsia rowazekii Geobacter sul urreducens Mycoplasma pneumoniae Mycopasma genitalium O 1 2 3 4 5 6 7 8 9 10 Genome size millions of base pairs 20 fold range of genome sizes 2 strains of E coli vary by 20 gtmillion basepains Cytoplasmic DNAs 0 Plasmids are extra chromosomal circular DNAs that replicate autonomously 0 Size varies from 1 kb kilobasepairs to over 1000 kb 0 Copy number average number of plasmids in a single cell varies from 1 to gt 1000 0 Plasmids have auXiliary functions ie non essential The prokaryotic cytoplasm 0 Large conc of ribosomes 2 X 104 2 X 105 in each cell 0 Very viscous diffusion rates 4X less than in eukaryotic cells 0 Many different vesicles and inclusions some have protein membranes some lipid 0 Some species make endospores Gas vesicles in Cyanobacteria Brock 445 39 0 Gas vesicles found in both f 39 v Q I Bacteria and Archaea quot39Ljf ffg 4 0 Purpose is to confer quot buo anc not stora e jgbx us 0 Usually found in photosynthetic organisms 0 Vary in number from several to several hundred Vary in size S Pellegrini and M lT ariwlli Cainla O Structure of gas vesicles Brock 444 446 0 Made of waterproof Proteins GVpA and GVpC 0 GVp A is rigid sheet 0 GVpC is X linking oc helical structure 0 Membrane is permeable to air but not to water 339 No gas selectivity 2006 Pearson Prenti lllllllll c 7 Cell inclusions 0 Storage granules 0 Inclusion bodies 0 Carboxysomes 0 Magnetosomes 8 PHA storage Brock 440 B cH3 IZH3 CH3 PHApolyhydroxyalk COCHCH2C CH c CH anoates PHB most common storage for excess carbon Figure 44021 Brock Biology of Microorganisms 11e 2006 Pearson Prentice Hall inc Glycogen inclusions also occur membrane is non unit not bilayer Pa y iEi hydr39uxybutrate 5 r W i 4quot F FLTurntr and M T Madman u lmal hungrm wmpmm 39a I r ri u i r Magnetosomes Brock Fig 442 H ail37 I df f dquot w Pi J s jg 0 Part1cles conta1n1ng quot h quot e f f gig 0 Work as magnet and I 9 33 allow cells to ali n i a g I along Earth S pole 0 Non unit membrane DennisBazylinski lO Other storage granules Brock 441 g g 9 5 1 ray 393 IE nrl39 Pfennig Harb Above Oxidation of H28 leads to accumulation of elemental S that is stored in granules 0 Phosphate stored as polyphosphate in granules 0 Recombinant proteins stored in inclusion bodies probably protein as membrane 11 Other somes Fig 36 0 A Carboxysomes in Cyanobacteria contain protein membrane surrounding RuBisCo B carboxysomes in a sulfide reducer 0 C Enterosomes contain proteins used in propanediol or other metabolism 12 Endospores Brock 447 2 H Hippe I t b Figure 447 Brock Biology of Microorganisms 11e 2006 Pearson Prentice Hall Inc 0 Location terminal A lo a o quot 1 s39 V a t p quot X v939g39ol va lt lt7 a IQ QE mlt s ll39 4quot f w i C subterminal or central characteristic of species 0 Sporulation occurs When times get tough and cell cannot survive cell does not survive sporulation Spores resistant to desiccation heat may survive for centuries 13 Cell wall quotquot9quot Vquot Cytoplasmic Ex 5P rium 5 membrane Lysis of cell and Core quot V 39 DNA release of free DNA becomes equotd 5P 39e more dense Stage VI Maturation development of resistance to heat and chemicals 39 Cortical layers 25223ng Ca2 incorporation use v further dehydration k 7 production of SASPs v and dipicolinic acid Endospore coat layers are formed septum grows 1 Stage III around protoplast out Cm Stage IV enguument Dehydration E E Fores ore V formalinquot Inner spore EXPSP quot m aPPe rsi Exosporium membrane prlmordlal cortex Is Primordial formed between the two cortex Figure 4 51 Brock Biology of Microorganisms 1 We 2006 Pearson Prentice Hall Inc membranes Table 43 JW I is Characteristic Vegetative cell Endospore Structure Microscopic appearance Calcium contonl Dipicol39uu39c acid Enzymalic activity Metabolism 02 uptake Macromolecular synthesis m RN A Heat resistance Radiation resistance Resistance to chemicals for example H202 and acids Stainability by dyes Action of lysozymc Water content Small acid soluble proteins product of 55 genes Cytoplasmic pH Table 4 3 Brock Biology of Microorganisms 1 We 2006 Pearson Prentice Hall Inc Typical gram posilive cell a few grammegative cells Thick spore cortex Spore coat Exosporium Nonretractile Refractile Low High Absent Present High Low High Low or absent Present Absent Present Low or absent Low High l ow High Low High Stainable Stainable only with special methods Sensitive Resistant High 8079094 Low 10 25 in core Abscnl Present About pH 7 About pH 55 60 in core Endospore diversity Endospore forrners all related phylogenetically All are grarn positive a few exceptions 0 Many species belong to genera Bacillus or Clastri ium Sporulation related to pathogenicity
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