Microbiology 101 Exam 2 Study Guide
Microbiology 101 Exam 2 Study Guide 101.0
Popular in General Microbiology
verified elite notetaker
Popular in Microbiology
This 22 page Study Guide was uploaded by Isabel Markowski on Saturday October 17, 2015. The Study Guide belongs to 101.0 at University of Wisconsin - Madison taught by a professor in Fall 2015. Since its upload, it has received 237 views. For similar materials see General Microbiology in Microbiology at University of Wisconsin - Madison.
Reviews for Microbiology 101 Exam 2 Study Guide
Report this Material
What is Karma?
Karma is the currency of StudySoup.
You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!
Date Created: 10/17/15
Microbiology 101 Study Guide Study Guide Exam 2 Objectives 1 Cellular Metabolism Phototrophs 2 Applied Microbial Metabolism a Impact b The Ncycle c The Sulfur Cycle d Microbes and Food Production e Wastewater Treatment 3 Microbial Genetics Part I a Genes b Transcription c Translation d Differences in Eukaryotes e Transcription Regulation 4 Microbial Genetics Part II a DNA Replication b Innate Immunity RestrictionModification Systems c Microbial Genomics 5 Applied Genetics a PCR Polymerase Chain Reaction PHOTOTROPHS Continuation of Cellular Metabolism o Organisms convert light energy to chemical energy 0 Use photosystems o Photosystems a reaction center rxn center and electron transport chain ETC Photosystem Rxn Center amp Light Harvesting Center o Rxn Center site of electron excitation 0 Contains multiple proteins and lightreactive pigments chlorophylls o LightHarvesting Center LHC assist rxn center 0 Absorb at different wavelengths than Rxn Center 0 Capture photons and transfer energy to Rxn Center 0 Contains additional pigments and proteins slightly different than Rxn Center 0 Conversion of light to chemical energy 0 Rxn center contains chlorophylls 0 Light proton hits rxn center and chlorophylls I Energy transferred to electrons making them have higher potential energy making good electron donors LHC Rxn Center A ETC 3 o I f 4 o I O Donor DonoroXidized NADP NADPH T Acceptor Replenishes Electrons Photoheterotrophv Photoautotrophv 0 Organic compounds as carbon source 0 C02 as carbon source 0 Use light to make ATP 0 Use light to make NADPH cterial Phototrophs 0 Mostly bacteria phototrophs 0 Classes of Phototrophs o Anoxygenic Phototrophs Use one photosystem only and don t produce 02 I Green Bacteria Use photosystem I 0 Green Sulfur sulfur as electron donor 0 Green NonSulfur I Purple Bacteria Use photosystem II o Proteobacteria o Often ablegrow w aerobic or anaerobic metabolism or fermentation diversity 0 Extra membranes where phototrophic apparatus is More surface area 0 Oxygenic Phototrophs plants Use 2 photosystems together and produce 02 I Cyanobacteria o Bluegreen algae originated 02 photosynthesis 0 Combine PSI and PSII photons gt PSII Rxn Center gt quinones gt PSI more light excites gt NADPH 0 Water 02 waste product I Eukaryotes o Eukaryotic chloroplasts evolved from ancient cyanobacteria APPLIED MICROBIAL METABOLISM A Impact on Earth 0 Microbes global element cycling 0 Carbon nitrogen sulfur phosphorus iron etc 0 Impact growth animalsplants o Metabolism affects manmade environment B The NitrogenCycle N2 Q o x 0 A Nitrification N0339 NH3 Nitrate Reduction Cellular N amino acids nucleotides etc 0 Almost all Ncycle bacteria and archaea 0 Important 0 Fixed N limiting for plantanimal growth 0 Humans altered natural N cycle synthetic N o Intermediates in N cycle may affect eutrophication be toxic increase global warming destructive to ozone layer be carcinogens decrease air quality 0 Processes o NFixation Reducing N2 to NH3 biological I HaberBosch Process chemicalsynthetic o Nitrification Use reduced N NH3 or NOg39 as electron donor I Ammonia Oxidation convert NH3 to N03 0 Lithotrophic aerobic respiration o NH3 donor Nitrite produced then Nitrate 02 Electron acceptor I Nitrite Oxidation convert Nitrite to N03 0 Lithotrophic aerobic respiration o Nitrite electron donor Nitrate produced 02 acceptor 0 Next step after NH3 oxidation 0 Denitrification Nitrate as electron donor I Anaerobic respiration I Most facultative anaerobes grow better in 02 but can grow in non02 environment I Not much different than other respiration I Nitrate gt N2 Nitrate Nitrite Nitrr Oxide Nitrous Oxide Nitrogen Impacts of NitrificationDenitrification o Nitrification o Produces acids building destruction 0 Removal of NH3 beneficial in aquatic systems fish tanks but detrimental for crop production products more soluble in water and leech away 0 Historical development of explosives quotnight soil human poop o Denitrification o Removes fixed N from ecosystem Nitrogen Cycle in Humans 0 Most Nitrate from diet then metabolized by microbes 0 Most secreted in urine up to 25 through saliva o Microbes in oral cavity reduce nitrite o Nitrite reacts form more reactive N metabolites o Newly discovered archaea C Sulfur Cycle Sulfur dioxide Sulfur Oxides in atmosphere from combustion Sulfursulfates in soilsedimentswater 0 Major Sulfur forms 0 H25 Hydrogen Sulfide I Toxic to animalsplants I Corrosive I Reacts rapidly with O at neutral pH 0 Elemental Sulfur 5 o Sulfate 504239 I Abundant ion in the oceans I Part of sulfuric acid 0 Sulfur Oxidizers Bacteria and archaea that use reduced sulfur compounds as electron donor for aerobicanaerobic respiration 0 Bacterial examples I Thioplaca spp secrete slime that forms sheath for bacterial commuting I Thiomarogarita namibiensis nonmotilesediment disturbances releases them into water column I Help plantsanimals growth ex seagrass beds deep mudded roots clams contain this bacteria to provide nutrients to soilremoving sulfide o Sulfur Reducers use sulfate as electron acceptor for anaerobic respiration o Tend to be proteobacteriasome firmicutes I Multiple electron donors are possible I Cause metalconcrete corrosion Sulfur Metabolism in Humans o Sulfurreducing bacteria in colon 0 Dietary sulfur compounds gt Sulfide 0 Large amounts sulfide toxic 0 Small amounts signaling molecule D Microbes and Food Production 0 Fermentation method to alter raw food through microbial processes 0 Cheapefficient way to preserve food 0 Acidsalcohols inhibit spoilage o Lactic acid bacteria I Grampositive I Generally firmicutes I Often aerotolerant I Produce of fermentation I Found in plantsanimals I Pathway hemolactic fermentation Net 2 ATP produced Glucose gt pyruvate 2 lactate I Reflects need to reoxidize NADH to NADH Yeasts and Ethanol Fermentation o Yeasts eukaryotes but some bacteria use ethanol fermentation too 0 Ethanol Fermentation glucose gt ethanol and C02 0 C02 gt bread 0 Ethanol gt alcoholic products 0 Typically saccharomyces species 2 ADP 2 ATP Glucose gt 2 Pyruvate 2 NAD NADH 2 Ethanol U A 2 Acetylaldehyde 2 C02 0 Beer Fermentation 0 Yeast hops water barley o Barley undergoes malting I Grains soaked and briefly germinated I Conversion of starches to simples sugars I Nutrients have to be accessible to the microbes 0 Sugars allow yeast to now grow I Then can continue regular respiration I Product Ethanol o Grapes more initial sugars so don t need malting process 0 Different strands of yeast different flavors Acetic Acid Bacteria AAB o Proteobacteria 0 Product acetic acid 0 Generally aerobic respiration obligate o Usedmake vinegar acetic acid aerobes o Usedmake kombucha as part of SCOBY o Ethanol electron donor symbiotic culture of bacteria and 0 Oxygen electron acceptor yeast Oxidized Oxidized Alcohol gt Aldehyde gt Acid o Electrons travel through quinones end up in cytochromes o ETC PMF gt ATP typical respiration o Vinegar Production Starting Material Added to physical substrate for bacteria to grow on beechwood shavings Oxidation Coohng Product Removal Chocolate 0 Complex Fermentation 0 Cocoa seedsbeanscoated in pulp mucilage complex carbohydrates 0 Must ferment beans before roastingmaking chocolate 0 Naturallyoccurring microbes ferment mucilage for 210 days 0 Changes in pH oxygenlevel and temperature affect enzymology and chemistry of beans Pulp l Yeasts LAB Primary Fermentation Products lactic acid C02 ethanol 1 AAB Secondary Fermentation Products acetic acid Wastewater Treatment 0 Uses community of microbesdegrade waste and convert to inoculous materials 0 Bulk of treatment in treatment plants secondary treatment digestion 0 Goals Soluble Wastes carbohydrates fats NH3 etc Microbial Activity Microbial Biomass Useful Microbial Products fuels fertilizers etc Nontoxic Products Impact of untreated waste Nitrogen and Impact of untreated waste Carbon Phosphorus Release untreated waste to environment Excess carbon in waste Release untreated waste to environment 1 Excess N and P 1 Normally N amp Plimited microbial autotrophs can flourish produce carbon Microbial aerobic respiration consumes carbon and oxygen Local oxygen deficit hypoxia in location of carbon release can kill organisms Microbial aerobic respiration consumes carbon and oxygen 0 Large hypoxia site at base of Mississippi River 0 Excess 0f Utrients draining Local oxygen deficit in location of N amp P 0 uses up 3 ava39lable oxygen release can kill organisms 0 Goal Reduce levels of 0 Organic carbon treatment plant organotrophic o Nitrogen Organic N gt Ammonia NH3 Nitrification Nitrate NOg39 Nitrogen Gas N2 Denitrification 0 Phosphorus I Microbes convert phosphate to polyphosphate store inside cell storage granules I Converts soluble molecule to insoluble intracellular polymer I EBPR enhanced biological phosphate removal 0 Waste can be treated by anaerobic treatment Fermentation and methanogenesis Dominate over aerobic respiration Degrade polysaccharides but different products fermentation products Methanogens then use these products as donorproduce methane useful fuel Methanogenesis I Industrial application as biogas I C02 electron acceptor OOOOO Objectives 6 Cellular Metabolism Phototrophs a Bacterial Phototrophs 7 Applied Microbial Metabolism a Impact b The N cycle c Yeasts and Ehtanol Fermentation d Acetic Acid Bacteria e Chocolate f Wastewater Treatment 8 Microbial Genetics Part I a Genes b Transcription c Translation d Differences in Eukaryotes e Transcription Regulation 9 Microbial Genetics Part II a DNA Replication b Innate Immunity RestrictionModification Systems c Microbial Genomics 10 Applied Genetics a PCR Polymerase Chain Reaction MICROBIAL GENETICS PART I Replication A Genes Information Transfer Gene Expression DNA Replication Gene Expression Transcription RNA Expression Translation 1 0 0 0 One of 2 DNA strands copied template strand top strand Transcription mRNA Translation Protein gt Gene Expression BacteriaArchaea Eukaryotes 0 Both in cytoplasm o Transcription occurs in nucleus 0 Transcription produces SS RNA copy of 0 RNA processed and moved to DNA cytoplasm 0 Translation produces polypeptide from 0 Translation in cytoplasm mRNA sequence 0 Additional step of RNA Processing 0 Transcription amp Translation are coupled o Compartmentalization slower together Gene Structure 0 Gene segment of DNA transcribed to RNA unit of hereditary info 0 Operon multiple genes controlled by one promoter 0 Promoter sequence of RNA bonded to DNA promotes transcription 0 Gene control region promoter 0 Directionality of DNA RNA important 0 Strands are antiparallel upstream 5 gt 3 downstream Coding Strand top 5 3 Template Strand 3 I 5 bottom B Transcription Transcription in eukaryaarchaea more alike 0 Bacteria outlier 0 Core RNA Polymerase can t bind by itself like Archaea 0 Needs sigma factors proteins carrydirect polymerase to promoter region to bind 0 Template strand needs to be in 3 to 5 direction New strand 5 to 3 Sigma recognizesbinds to promoter initiation site Transcription begins sigma released creates RNA chain RNA chain grows until reach termination site and stops Polymerase and RNA released P9P Most bacteria different sigma factors 0 Ex sigma7O protein main EColi sigma factor Polymerasesigma factor has most contact with two certain groups of sequences 35 box and 10 box Promoter l l l CTG ATTG CATAAATCATTG CGG GAC AACGTATTTAGTAAC GCC o Represents optimal sequencing consensus sequence 0 Closer to the consensus the better stronger promoter 0 Best binding site for sigma factor New nucleotides add to 3 end RNA 5 3 O 4 Hbonds bn complementary base pairs GCAT A Template strand 5 DNA RNA sequence complementary and antiparallel to DNA Types of RNA made 0 Messenger RNA mRNA I Template for translation 0 Ribosomal RNA rRNA I Part of ribosome 0 Transfer RNA tRNA I Translation 0 Other types often regulatory o If given gene think I What organism is it from bacteria sigma factors so have promoter sequences look for TTGAGA and TATAGT this coding strand I Where transcription starts C Translation 0 mRNA contains code tRNA translates code Ribosome makes protein 0 Codon sequence of 3 nucleotides 0 The Genetic Code triplet codons 0 Know start AUG and stop codons UAA UAG UGA 0 Stop codons no corresponding amino acid 0 Ribosome contains proteins and rRNA Made of large subunit LSU and small subunit SSU o S unit for sizeshape I Bacteria 70 S O a o a 0 I o 0 2 o a 0 Amino acids 0 a Polypeptide tRNA with amino acid attached Ribosome 5 r 3 quotIRMA E site P site A site LSU SSU o 50 s o 30 S 0 23 S rRNA 0 16 S rRNA o 5 S rRNA o Positioning o Enzymaticcatalytic o BacteriaArchaea Ribosomebinding site 5 coding sequence I3 4 Ribosomebinding site start codon AUG stop codon o Eukarya don t have ribosomebinding site have cap and polyA tai 5 cap I coding sequence I polyA 3 0 Start codon AUG so 1St amino acid Methionine 1 Initiation 0 mRNA binds to ribosomal SSU small subunit Aligns properly because of ribosome binding site 1 I start codon is in P site 0 tRNA binds recognizes codons and is charged with amino acid I Anticodon complementary to codon in mRNA 1 I AminoacyltRNA Synthetase enzymes charge each tRNA with right amino acid accuracy critical 0 Add LSU E site P site A site 2 Elongation 0 Cycle Initiation codon incoming tRNA 2quot 1l tRNA Growing peptide tRNA binds to Asite Entire ribosome moves down to next peptide bond forms 3 codons shift to Psite Amino acid of Psite binds to Asite acid 1St tRNA leaves 4 3 Termination o Polypeptide grows until reaches stop codon stop codons no tRNA matches I Release factors bind and complex falls apart Translation Summary Initiation RBS signals appropriate start site and reading frame 0 Start site AUG 1St amino acid methionine Elongation cycle Termination Ribosome reaches stop codon No matching tRNA Release factor proteins bind release Polypeptide folds Translation starts after transcription on gene sequence use different signalsclues Translation uses ATP expensive D Differences in Eukaryotes Gene Expression in Eukarvotes 0 Main difference additional processing steps 0 Exons coding sequences within gene lntrons noncoding sequences 0 Primary transcript is processed to remove introns Gene Transcription RNA Processing Transport to cytoplasm Translocation Gene Expression Regulation 0 Transcriptional control beginning 0 Translational control middle 0 Posttranslational control end o Affects speed and cost 0 Posttranslational control changes cell activity fastest but is most costly o Transcriptional control slowest but most efficient 0 Most genes regulated at multiple layerslevels E Transcription Regulation 0 Initiation most common point of regulation fix before waste energy on it 0 Regulatory proteins preventsenhances RNA polymerase action at promoter turn onoff genes 0 2 kinds Represso rs Activators 0 Negative Control Turn genes off 0 Positive Control turn genes on o No transcription 0 Triggers transcription 0 If specific DNA sequence operator 0 Ex maltose utilization genes that repressor binds to overlaps with promoter repressor shuts off by blocking RNA polymerase s path 0 Ex arginine biosynthesis gene 0 Turns off gene when excess arginine essential amino acid to save energy MICROBIAL GENETICS PART 2 Basics Genome Structure 0 Genome All genetic material chromosomes and accessory DNA pieces 0 Typically have one chromosome and one plasmid o Chromosome 100012000 kb carry essential genes Kb kilobase 1000 base pairs 0 Plasmid 3500 kb I Completely different DNA than chromosomes I Much smaller I Nonessential genes but beneficial ex antibiotic resistance nutrient degradation virulence functions I DIPSENSABLE I 1000 s different plasmids I Have ori origin for replication A DNA Replication o Held together by Hbonds Errors Separation of DNA strands to daughter DNA molecules each one one parental strand and one new Sequence determined by base complementarity DNA opened unwound and primed help polymerase in step 2 o Helicase unwindsopens strands o SSBP SingleStrand DNAbinding proteins stabilize single strands o Primase makes RNA primer 0 Topoisomerase relieves twisting forces unwinds tension Synthesis of leading strand begins 0 DNA Polymerase makes new DNA I Needs primer to start and adds new nucleotide to 3 end only 5 to 3 direction Both strands being worked on at same timerate 0 Leading strand and lagging strand 0 Replisome set of proteins Both RNA transcription and DNA replication polymerases synthesize nucleic acid in 5 to 3 direction 0 But DNA polymerase requires primer to begin DNA Replication is NOT perfect Bacteria Pmtems o DnaA binds to oriC and recruits other proteins 1st step in replication 0 Circular chromosomes 0 Replication bidirectional Error Rate characteristic for organism o Determined by I DNA Polymerase accuracy during synthesis I Proofreading many DNA Polymerases correct their mistakes during replication DNA polymerase III noticescorrects if adds mismatched base pair Errors gt Mutations o Heritable change in nucleotide sequence of genome 0 Errors during DNA Replication about 1 nucleotide in 108 incorrect o Caused by I Spontaneous chemical changes in bases I Mutagens agents that damage DNA chemicals UV radiation etc o Impacts I Change in genotype nucleotide sequence of genome I Does it change phenotype observable properties of organismphysical I Impact can be neutral detrimental or beneficial depends on what s encoded 0 Loss of function quotknockoutquot 0 Altered function 0 Gain of function ex antibiotics Point Mutation Missense Point Mutation 0 Change amino acid sequence Nonsense Point Mutation Puts in stop codon Insertionsdeletions Insertion frameshift 0 Insert extra 0 Scrambles message Knockout effect 0 Bi im act translation sto s Deletion frameshift g p p o Knockout effect a Deletes 0 Changes reading frame Knockout effect Silent Mutation undilglng single point in sequence 0 Nucleotidepair substitution silent 0 Will only affect genotype 0 Uncorrected errors genetic change in daughter cells quotWild Type mother cell base pair mismatch Mutant Daughter Cell changed base pair Daughter Cell like original DNA 0 DNA Repair systems 0 Set of enzymesremove errors and insert correct sequence 0 Ex Nucleotide Excision Repair scan for problems cut nucleotide replace it repair linkage bonds 0 Horizontal Gene Transfer 0 Three types Transformation Transduction Uptake of free DNA and incorporates into own 0 Bacterial virus moves DNA cell to cell 0 Natural Transformation some microbes naturally able to o Generalized transduction random take up foreign DNA streptococcus heisseria spp bacillus packaging of host chromosomal subtilis fragments 0 Artificial Transformation lab can induce many species 0 Viral DNA injected and genes copied o Called quotcompetencequot when replication Iytic cycle 0 Historical importance streptococcus pneumoniae o Transduction transducing particle and the transforming principle contains donor cell DNA 0 Lead to evidence that genes made of DNA 0 Homologous recombination o S smooth produces capsule virulent disease 0 Chromosomal not viral DNA causing injected no virusescell o R rough no capsule nonvirulentdoesn t cause death disease 0 Heatkilled dead S cells can still kill animals in combination with R cells because of transformation when S cells killed DNA liberated by heat and can be taken up by R cells 0 Capsules important Conjugation o Involves celltocell contact 0 Some plasmids encode transfer machinery for their transfer to another cell 0 Requires DNA export system and pili attaches to other cell and reels in o Requires two live cells 0 Can transfer DNA bn widely different species less specific 0 Microbial genomes can change by mobile DNA dynamic I All species have core genome some have pan genome variable even within species I 2 strands same species can vary greatly 0 Very commonBacteriaArchaea less in Eukaryotes 0 Can transfer across laterally to other living cells vs down through reproduction B Innate Immunity RestrictionModification Systems 0 Quality check 0 REase restriction endonuclease degrades o MTase DFNA methyltransferase marks cell self 0 Occurs during all three types of gene transfer 0 Cell produces enzymes restriction modification complex chemically modify DNA Recognition Site foreign nonself Methylated recognition site marked as self REase MTase Hundreds of restriction enzymes Viral response types to restrictionmodification system how to overcomedefeat systems to infectsurvive 0 Use of unusual nucleotides modify geneshide 0 Use of DNA binding proteins protectionshield o Stimulation of methylation try to beat out speed of restriction enzymes 0 Degradation of restriction enzymes C Microbial Genomics Look at all of genes together and interpret Use computer programs 0 Find coding sequences ORF s open reading frame 0 ORF s potential protein to be made 0 Computers look for ORF s for potential to make protein on both DNA strands Find similar protein sequenceshelp suggest function Bacterial and archaeal genomes efficient infodense 0 Almost all of DNA codes for proteins 0 Vs eukaryotes full of noncoding DNA Microbial genomes vary even win species diversity APPLIED GENETICS A PCR Amplification of DNA PCR polymerase chain reaction procedure to selectively amplify piece of DNA Involves quotin vitro DNA synthesis make copies of specific DNA section Can amplify from tiny amounts of template DNA very sensitive Components DNA template strand primers DNA polymerase dNTP s deoxynucleotide triphosphates Process PCR mix in a PCR machine thermocycler Denaturation 0 Heat 9495 C for 30 seconds 0 Strands separate helicase unwinds DNA 0 PCR primers must bind to sequences on either side of target sequence on opposite strands Primer 5 I 3 39 3915 Primer Annealing 0 Cool 55 C for 30 seconds 0 When target DNA is singlestranded primers bind anneal and allow DNA polymerase to work S39 y Prlmer 3 5 Primer 539 339 5 3i 0 Extension 0 72 C for 60 seconds per kb of target 0 Repeat 0 Usually 30 cyclesto get many copies 0 Because polymerases would be destroyed by heat in denaturation step and you d have to keep putting polymerases back in after each cycle found different thermostable polymerases from microbes o Taq polymerase I Thermos aquaticus thermophilic bacterium from hot springyellowstone I Grows at temperatures of up to 90 C I Can use in PCR process I Lacks proofreading ability 0 Vent polymerases I Thermococcus litoralis hyperthermophilic archaeon isolated from submarine thermal vent I Proofreading ability higher fidelity and stability 0 Deep vent polymerase I Pyrococcus sp Strain GBD hyperthermophilic archaeon isolated from submarine thermal vent I Able to grow at temperatures 104 C I Proofreading higher fidelity and stability
Are you sure you want to buy this material for
You're already Subscribed!
Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'