Microbiology 101 Week 5 Lecture Notes
Microbiology 101 Week 5 Lecture Notes 101.0
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This 10 page Class Notes was uploaded by Isabel Markowski on Friday October 9, 2015. The Class Notes belongs to 101.0 at University of Wisconsin - Madison taught by a professor in Fall 2015. Since its upload, it has received 56 views. For similar materials see General Microbiology in Microbiology at University of Wisconsin - Madison.
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Date Created: 10/09/15
Microbiology Week 5 Lecture Notes 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 2 Acetylaldehyde A 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 7 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 Microbial Genetics DNA Replication Gene Expression Transcri tion Replication 390 RNA Expression 4 Translation 1 O gt 0 One of 2 DNA strands copied template strand top strand Information Transfer Gene Expression Transcription mRNA gt Gene Expression Translation Protein BacteriaArchaea Eukaryotes 0 Both in cytoplasm 0 Transcription occurs in nucleus Transcription produces SS RNA copy of 0 RNA processed and moved to DNA cytoplasm 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 Transcription o 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 1 Sigma recognIzesbInds to promoter RNA I 39 7 Sigma recognizes polymerase vi Sigma 7 InItIatIon Site rammoter and ch T factor inttiatien site 2 Transcription begIns Sigma released creates enzyme RNA chain 539 3 39 a 539 3 RNA chaIn grows untII reach termInatIon Site 3 I 7 7 I I 7 7 7 7 7 7 Promoter Genes to be transcribed and stops region light green strand 4 Polymerase and RNA released Transcription beg ns sigma released RNA chain grows 7 Sigma 539 3 3439 Termination site reached chain growth stops 5quot a Polymerase and RNA released 5 3 a 2012 Pearson Education Inc 0 Most bacteria different sigma factors 0 Ex sigma70 protein main EColi sigma factor 0 Polymerasesigma factor has most contact with two certain groups of sequences 35 box and 10 box Promoter l l l CTG TTG CATAAATCATTG CGG GAC AACGTA39ITI39AGTAAC 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 539 339 O 4 Hbonds bn complementary base pairs GCAT A Templatestrand 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 Translation mRNA contains code tRNA translates code Ribosome makes protein Codon sequence of 3 nucleotides The Genetic Code triplet codons 0 Know start AUG and stop codons UAA UAG UGA 0 Stop codons no corresponding amino acid Ribosome contains proteins and rRNA 0 Made of large subunit LSU and small subunit SSU o S unit for sizeshape I Bacteria 70 S a a 5 0 I o 0 9 0 0 Amino acids 0 a Polypeptide tRNA with amino acid attached Ribosome P site A site E site LSU SSU o 50 s o 30 S o 23 S rRNA o 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 tail 5 cap I coding sequencel 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 2ncl 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 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 Polypeptide folds Translation starts after transcription on gene sequence use different signalsclues Translation uses ATP expensive Gene Expression in Eukarvotes Main difference additional processing steps Exons coding sequences within gene lntrons noncoding sequences Primary transcript is processed to remove introns Gene Transcription RNA Processing Transport to cytoplasm Translocation Gene Expression Regulation 0 Transcriptional control beginning Translational control middle Posttranslational control end Affects speed and cost 0 Posttranslational control changes cell activity fastest but is most costly o Transcriptional control slowest but most efficient Most genes regulated at multiple layerslevels Transcription Regulation o 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 Repressors Activators Negative Control Turn genes off 0 Positive Control turn genes on 0 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