Microbiology Exam 3 Review update
Microbiology Exam 3 Review update 4100
Popular in Microbiology
Popular in Microbiology
Cleta Shields V
verified elite notetaker
This 64 page Study Guide was uploaded by Carlos Suarez on Monday February 9, 2015. The Study Guide belongs to 4100 at Ohio State University taught by Charles Daniels in Fall. Since its upload, it has received 97 views. For similar materials see Microbiology in Microbiology at Ohio State University.
Reviews for Microbiology Exam 3 Review update
You can bet I'll be grabbing Carlos studyguide for finals. Couldn't have made it this week without your help!
-Ms. Joaquin Predovic
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: 02/09/15
Microbiology Exam 3 Review 10252014 Lec 12 Viruses What is a virus 0 Virus 0 Noncellular particle Must infect a host cell where it will reproduce a Viruses typically subvert the cells machinery Replication transcription and translation and directs these to produce viral particles What types of nucleic acid are found in viruses 0 Virion o Consists of a single nucleic acid ssdsDNA Contained within a protective protein capsid What are the two main types of virus structure What are the two types of symmetrical virus particle The packaged structure of the virus provides two important funcUons o Capsid protects the viral genome from degradation and provides a quotsafequot means for the viral DNA to be transmitted from the host to another cell 0 The structure also provides a means for the virus to interact with a new host and deliver its DNA inside the cell 0 Different Viruses make different capsid forms 0 Symmetrical Virus particles have capsids that are either icosahedral 20 sided or lamentous helical symmetry 0 Asymmetrical Virus particles have complex multipart structures and often have accessory proteins Some have complex delivery devices others have an envelope and a second outer membrane a Poxviruses have DNA in a core envelope with proteins surrounded by an outer membrane What are the three classi cation schemes for viruses 0 The International Committee on Taxonomy of Viruses Genome composition Capsid symmetry Envelope Size of the virion Host Range 0 The Baltimore Virus Classi cation 0 Genome Composition 0 The route used to express RNA Means of mRNA production 0 Emphasizes the form of the genome DNA vs RNA ssds and the route to generate mRNA 0 Molecular evolution of viruses 0 Relatedness of viruses by comparing genome sequences Organization coding and noncoding sequences 0 Relatedness of viruses by comparing the proteome of the viruses 00000 What characteristics of the viruses are used in the Baltimore classi cation scheme 0 What route is used to produce mRNA 0 Group I dsDNA n Uses its own or host DNA Pol for replication 0 Group II ssDNA n Requires DNA Pol to generate a complementary strand 0 Group III dsRNA n Requires RNADependant RNA polymerase to make mRNA and genomic RNA 0 Group IV ssRNA n Requires RNADependant RNA Pol to make a template for mRNA and genome replication 0 Group V ssRNA H n Requires RNADependant RNA Pol to make mRNA and replicate its genome 0 Group VI Retroviruses n Packages its own reverse transcriptase to make dsDNA 0 Group VII dsDNA pararetrovirus n Requires a plant hosts reverse transcriptase to make dsDNA Virus Life Cycle Characteristics 0 All viruses require a host for reproduction and all follow the same general life cycle 0 Host recognition 0 Genome entry 0 Assembly of virions 0 Exit and transmission What are lytic and lysogenic life cycles of bacteriophage What triggers the conversion of a lysogenic to a lytic life cycle Lytic Cycle 0 Bacteriophages quickly replicate Kills host cell Lysogenic Cycle 0 Bacteriophage is quiescent o Integrates into cell chromosome as a prophage 0 Can reactive to become lytic 0 These phages are referred to as temperate phages The quotdecisionquot between the two cycles is dictated by environmental cues o Lysogenic Phage DNA integrates into host genome to form prophage Integrated phage DNA reproduces with host genome Stress induces excision of phage DNA Phage recombines by rejoining the ends of its phosphodiester chain and enters the lytic cycle What DNA is present in the slow release phage M13 0 M13 Slow Release Bacteriophage o Filamentous phages can extrude individual progeny through the cell envelope 0 Host cells grow slowly but do not die 0 Group II ssDNA Genome n Phage inserts ssDNA Phage DNA forms a double stranded circle U dsDNA Cell replicates circular ssDNA H mRNA Phage assembles and exits without lysis n Proteins While the phages reproduce and exit the cell the cell reproduces slowly What form of DNA acts as the template for mRNA production and in the production of DNA for packaging into the virus particle o Phage inserts ssDNA and forms dsDNA circle 0 Replicates circular ssDNA o Phages assemble and exit without lysis When animal viruses enter as intact viruses in which subcellular locations are the viruses uncoated Uncoating within endosomes o Lysosome fuses with and acidi es endosomes 0 Viral envelope fuses with endosome membrane 0 Uncoating of RNA genome Uncoating at the cell membrane Uncoating at the nuclear membrane 0 Endosome docks onto nuclear membrane Uncoating of dsDNA genome What classes of virus Baltimore classi cation utilize the enzyme RNAdependent RNA polymerase What role does this enzyme play in the life cycle of the virus Group IIIIVV o RNADependant RNA Pol o Helps make mRNA and genomic RNA Takes ssRNA and transcribes from this to give ssRNA genome n Enzyme that catalyzes the replication of RNA from an RNA template What class of virus Baltimore classi cation utilize the enzyme reverse transcriptase What role does this enzyme play in the life cycle of the virus 0 Group WWquot 0 Retroviruses Replicates with DNA intermediate 0 Reverse Transcriptase 0 Makes ssRNA genome by transcription of dsDNA H ssRNA to ssDNA to dsDNA 0 Use RT to copy their genomic sequence into DNA for insertion into the host chromosome Terms Virion o The virus particle o Consists of a single nucleic acid ssdsDNA o Contained within a protective protein capsid Symmetrical virus particle Virus particles that have capsids that are either icosahedral or lamentous Icosahedral 20sided Filamentous Helical symmetry The International Committee on Taxonomy of Viruses Genome composition Capsid symmetry Envelope 0 Size of the virion Host Range Baltimore classi cation Genome Composition 0 The route used to express RNA 0 Means of mRNA production Lytic Bacteriophage quickly replicates and kills host cell Lysogenic Bacteriophage is quiescent Integrates into cell chromosome as a prophage Can reactive to become lytic These phages are referred to as temperate phages Temperate Viruses under the Iysogenic cycle Slow release 0 Some bacteriophages use the host machinery to make progeny that bud from the cell slowly o Slowing the growth of the host without lysis Bacteriophage o A virus that infects and replicates within a bacterium o Composed of proteins that encapsulate their DNARNA genome Tropism 0 Animal viruses bind speci c receptor proteins on their host cell 0 Receptors determine the viral tropism The cells and tissues of a host which support growth of a particular virus or bacteria RNAdependent RNA polymerase 0 An enzyme that catalyzes the replication of RNA from an RNA template 0 Used by Group III IV V Reverse transcriptase 0 Enzyme used to generate cDNA from an RNA template Questions What environmental and chemical conditions were required for the evolution of cellular life on Earth 0 Essential Elements 0 CNPOS Compose organic molecules Continual source of energy 0 Mainly nuclear fusion reactions within the sun 0 Temperature range permitting liquid water 0 Otherwise metabolic reactions would cease What types of evidence is in use as geological evidence for early life Stromatolites o Layers of phototrophic microbial communities grew and died their form lled in by calcium carbonate or silica Microfossils 0 Early microbial cells decayed and their form lled in by calcium carbonatesilica Size and shape of microfossils resemble those of modern cells 0 Isotope rations o Microbes x 12C02 more readily than 13C02 Thus limestone depleted of 13C must have come from living cells Similarly sulfate reduced by sulfaterespiring bacteria shows depletion of 345 compared with 325 o Biosignatures 0 Certain organic molecules found in sedimentary rock are known to be formed only by certain microbes These molecules are used as biosignatures o Oxidation state 0 The oxidation state of metals such as iron and uranium indicates the level of 02 available when the rock formed Banded iron formation BlFs suggest oxidation by microbial phototrophs that intermittently produced oxygen What types of metabolism are thought to be representative of early metabolism Anaerobic redox reactions 0 Oxidized forms of N S and Fe were generated by reactions driven by UV light LightDriven lon Pumps 0 Bacteriorhodopsin of haloarchaea Could have conducted the rst kind of autotrophy using the available energy from sunlight U 500600nm Methanogenesis o Methanogenic archaea combine H2 and C02 producing CH4 and H20 Oxygenic phototrophs cyanobacteria 0 Split water to form 02 Evolved later Why are lightdriven ion pumps such as the bacteriorhodopsin of haloarchaea proposed to be examples of the rst kind of autotrophy They could conduct autotrophy using available sunlight wavelength 0 Chlorophyll absorbance photosynthesis is inversely proportional to sunlight wave light where as bacteriorhodopsins are in optimal absorbance Between 500600nm What are models for the development of early life Prebiotic Soup 0 Small organic molecules arise abiotically from simple reduced chemicals sparked by lightning These produced complex macromolecules that eventually acquired the apparatus for selfreplication and membrane compartmentalization Metabolist Model 0 Selfsustaining abiotic chemical reactions could have formed the basis of cellular metabolism 0 The genetic code may have originated from synthesis of an amino acid complex to a dinucleotide o The RNA World 0 RNA is a better candidate than DNA for the earliest information molecule Used as genomes by some viruses Uracil is a precursor for thymine Possesses catalytic properties as ribozyme What processes or features of modern day organisms are consistent with the RNA world model for the development of early life 0 RNA is a better candidate than DNA for the earliest information molecule 0 Used as genomes by some viruses 0 Uracil is a precursor for thymine o Possesses catalytic properties as ribozyme What processes lead to divergence in DNA 0 Random mutation 0 DNA sequence changes that occur by mistake Most occur in replication a Most neutral 0 Natural Selection 0 Genes unoler selective pressure show a higher rate in mutation frequencies Favored in organisms with greater offspring potential I Genes from here cannot serve as molecular clocks Reductive evolution degenerative evolution 0 Loss or mutation of DNA encoding unselective traits Mutationsloss does not affect reproductive success What is a molecular clock 0 The temporal information contained in a macromolecular sequence of proteins or nucleic acids 0 Based on Acquisition of new random mutations in each round of DNA replication n Assumed that offspring acquire a speci c number of mutations from parents and therefore the number of sequence differences between two species is proportional to their divergence What are the criteria for molecular clocks What molecule was used in the development of the three domain model for life 0 Gene sequence has to have the same function across all species compared 0 The generation time for all species being compared should be similar for each species compared 0 Faster doubling times can lead to an over estimate of the divergence time as result of increased opportunity for mutations The average mutation rate remains constant among species and across generations 0 The gene should have conserved sequences that allow for the accurate alignment of the molecules and variable regions that change with similar rates among all species The most widely used molecular clock is the gene encoding the small subunit rRNA SSU rRNA o rRNA sequencing determined the three domains of life 0 165 rRNA Bacteria Advantageous because it is present is all bacteria and has a universally conserved sequence useful for PCR n HGT is rare 0 185 rRNA Eukaryotes How do Maximum likelihood and Maximum parsimony differ as approaches for constructing phylogenetic trees Maximum Parsimony o The quotbest fitquot tree is de ned as the one requiring the fewest mutations to t the data Maximum Likelihood o The probability that a tree would have produced the observed DNAProtein sequences What are unrooted and rooted trees Rooted trees 0 Indicate position of the common ancestor Unrooted trees 0 Do not indicate position of the common ancestor Who proposed the three domain model Carl Woese 0 Used SSU rRNA phylogeny to reveal Archaea What characteristics are shared between archaea and eukarya that are generally not present in bacteria Similar intron splicing tRNA no mRNA splicing Similar RNA polymerase Similar transcription factors Similar ribosome sensitivities to antibiotics resistant to chloramphenicol kanamycin streptomycin Methionine translation start Simple cell wall structural components How does horizontal gene transfer alter our view of the rRNA monophyletic tree of life 0 The traditional view of phylogeny holds that the vast majority of gene transfer is vertical and that most lineages are monophyletic 0 An alternative view argues that horizontal gene transfer is so prevalent among microbes that it obscures monophyletic distinctions 0 Among prokaryotes DNA is transferred horizontally by plasmids conjugation transposable elements naked DNA transformation and bacteriophages transduction What are the parts of the taxonomic description of organisms Classi cation 0 Organisms are classi ed by different schemes and are grouped into taxa Taxon based on similarity Nomenclature 0 Assignment of names Iden ca on 0 Most practical side of the taxonomy Assignment of an organism to a particular taxon What is polyphasic taxonomy and what criteria are used in this analysis 0 Use of a wide variety of measures to establish similarities and features that allow for the comparison of organisms based on evolutionary relationships 0 Phenetic system Mutual or shared phenotypic characteristics 0 Phylogenetic classi cation Classi cation basis of evolutionary relatedness o Genotypic Classi cation Compares the genetic similarities genes or whole genomes between organisms What are the taxonomic Ranks 0 Microbes are placed in hierarchical taxonomic levels with each level or rank sharing a common set of speci c features Highest rank is Domain n Bacteria and Archaea Microbes only a Eukarya Microbes and macroorganisms Within domains are the ranks n Kingdom n Phylum a Class D Order a Family a Genus n Species epithet I Some microbes have subspecies o Mnemonic o Dandy Kings Play Chess On Fancy Glass Seats Dumb Kids Playing Chicken On Freeways Get Squished What are the differences between species strain and type strain 0 Species 0 Collection of strains that share many stable properties and differ signi cantly from other groups of strains 0 Collection of organisms that share the same sequences in their core housekeeping genes 70 Identity SSU rRNA 97 Average nucleotide identity of orthologs gt95 0 Strains o Descended from a single pure microbial culture Share many stable properties and differ signi cantly from other groups of strains TypeStrain 0 One of the rst strains of a species studied often most fully characterized How are differences within strains described 0 Strains within a species vary from each other in many ways 0 Biovars Differ biochemically and physiologically o Morphovars Differ morphologically o Sevorvars Differ in antigenic properties How is of a dichotomous key used for identifying organisms What level of classi cation can typically be achieved using this method 0 A common strategy of practical identi cation 0 Series of yesno decisions successively narrows down the possible categories of species 0 The key identi es some organisms down to the genus level and others only to numbered samples Terms Biosphere o Portion of the earth the supports life Stromatolites o Layers of phototrophic microbial communities that grew and died their form lled in by calcium carbonate or silica Microfossils Early microbial cells decayed and their form was lled in by calcium carbonate or silica 0 Size and shape of microfossils resemble those of modern cells Isotope ratios 0 Microbes x 12C02 more readly than 13C02 Thus limestone depleted of 13 C must have come from living cells 0 Similarly sulfate reduced by sulfate respiring bacteria shows depletion of 34S compared to 32 S Biosignatures Certain organic molecules found in sedimentary rock are known to be formed only by certain microbes Oxidation states 0 The oxidation state of metals such as iron and uranium indicates the level of 02 available when the rock formed Bacteriorhodopsin Haloarcheae 0 Used lightdriven ion pumps 0 Could have conducted the rst kind of autotrophy The prebiotic soup 0 Small organic molecules arise abiotically from simple reduced chemicals sparked by lightning These produced complex macromolecules that eventually acquired the apparatus for selfreplication and membrane compartmentalization Metabolist models Selfsustaining abiotic chemical reactions could have formed the basis of cellular metabolism 0 The genetic code may have originated from synthesis of an amino acid complex to a dinucleotide The RNA world 0 RNA is a better candidate than DNA for the earliest information molecule 0 Used as genomes by some viruses 0 Uracil is a precursor for thymine o Possesses catalytic properties as ribozyme o Phylogeny The study of evolutionary relatedness among various groups of organisms 0 Presented as trees representing evolutionary relatedness and divergence Clade A series of branching groups of related organisms Species Collection of strains that share many stable properties and differ signi cantly from other groups of strains 0 Collection of organisms that share the same sequences in their core housekeeping genes 70 Identity SSU rRNA 97 Average nucleotide identity of orthologs gt95 Molecular clock 0 The temporal information contained in a macromolecular sequence of proteins or nucleic acids 0 Based on Acquisition of new random mutations in each round of DNA replication n Assumed that offspring acquire a speci c number of mutations from parents and therefore the number of sequence differences between two species is proportional to their divergence Maximum parsimony 0 Maximum Parsimony o The quotbest tquot tree is de ned as the one requiring the fewest mutations to t the data 0 Maximum likelihood 0 Maximum Likelihood o The probability that a tree would have produced the observed DNAProtein sequences 0 Rootedunrooted trees Rooted trees 0 Indicate position of the common ancestor Unrooted trees 0 Do not indicate position of the common ancestor 0 Three domains Bacteria Archaea Eukarya Horizontalvertical gene transfer 0 Horizontal Acquisition of a piece of DNA from another cell 0 Vertical Transmission of an entire genome from parent to offspring Taxonomy 0 Classi cation 0 Organisms are classi ed by different schemes and are grouped into taxa Taxon based on similarity Nomenclature 0 Assignment of names ldenU cann 0 Most practical side of the taxonomy Assignment of an organism to a particular taxon Polyphasic taxonomy Use of a wide variety of measures to establish similarities and features that allow for the comparison of organisms based on evolutionary relationships 0 Phenetic system Phenetic system 0 Mutual or shared phenotypic characteristics 0 Taxonomic Ranks Microbes are placed in hierarchical taxonomic levels with each level or rank sharing a common set of speci c features 0 Highest rank is Domain Bacteria and Archaea n Microbes only Eukarya n Microbes and macroorganisms 0 Within domains are the ranks Phylum Class Order Family Genus Species epithet Some microbes have subspecies n Mnemonic n Dandy Kings Play Chess On Fancy Glass Seats Dumb Kids Playing Chicken On Freeways Get Squished Species strain and type 0 Species 0 Collection of strains that share many stable properties and differ signi cantly from other groups of strains 0 Collection of organisms that share the same sequences in their core housekeeping genes 70 Identity SSU rRNA 97 Average nucleotide identity of orthoogs gt95 0 Strains o Descended from a single pure microbial culture Share many stable properties and differ signi cantly from other groups of strains TypeStrain 0 One of the rst strains of a species studied often most fully characterized Dichotomous Key 0 A common strategy of practical identi cation 0 Series of yesno decisions successively narrows down the possible categories of species 0 The key identi es some organisms down to the genus level and others only to numbered samples Questions What are the two general types of metabolic processes and what types of processes are associated with each Catabolism o Fueling reactions 0 Energyconserving reactions 0 Providing ready source or reducing power Electrons 0 Generate precursors for biosynthesis o Anabolism o The synthesis of complex organic molecules from simpler ones 0 Requires energy from fueling reactions ATP 0 Requires a source of electrons stored in the form of reducing power What are redox reactions and which molecule reducedoxidized donate electrons and which receive them ReductionOxidation reactions 0 Reduction Gain of electrons o Oxidation Loss of electrons What are the energy sources electron sources used by organotrophs lithotrophs and phototrophs Organotrophs 0 Organic molecules donate electrons Lithotrophs 0 Inorganic molecules donate electrons Phototrophs 0 Light absorption excites electrons to a high energy state What are examples of work energy requiring processes that are typically required by microbial cells What is the common energy molecule in the cell Cells obtain energy from a source in their environment and convert into a form that is useful to the cell 0 ATP 0 Chemical Work Synthesis of complex molecules 0 Transport Work Take up nutrients elimination of wastes and maintenance of ion balances 0 Mechanical Work Cell motility and movement of structures within cells What is the GibbsHelmholtz equation and what does the free energy component AG of a reaction or a series of reactions indicate 0 AG AH TAS 0 Indicates the change in free energy in joulesmol Expresses the change in energy that can occur in chemical reactions and other processes a Amount of energy available to do work Used to indicate if a reaction will proceed spontaneously without added external energy Negative n Either heat is released andor the order is decreased In The reaction is spontaneous and goes forward Positive n Heat is consumed and order is increased a Reaction is not spontaneous n The reaction or process goes in reverse What is AGo39 Change in the standard free energy in kJmol o 298 K o 1 ATM o All concentrations of substrates and products are 1M How is the AG related to the concentration of the reactants and products of a reaction Concentration of reactants may determine the direction of a reaction Reactant excess AG is more negative favors forward reactions 0 Product excess AG is more positive favors the reverse reaction How might an unfavorable reaction or reactions be affected by changes in the concentration of the reactants and products 0 Higher concentration of reactants drives the reaction forward 0 Higher concentrations of products drives it in reverse What are examples of energy carriers in the cell Which are also electron carriers 0 Energy carriers 0 Molecules that gain or release small amounts of energy in reversible reactions NAD and ATP 0 Electron carriers 0 Energy is conserved in a redox reaction and not lost as heat NAD NADP FAD What is the approximate AGo39 value with units for the phosphate hydrolysis of ATP 0 305 kJmol Which two intermediates of the EMP pathway have phosphate hydrolysis energy suf ciently large to donate a phosphate to ADP Phosphoenolpyruvate PEP 13 bisphosphoglycerate Pyrophosphate How does coupling the hydrolysis of ATP to the hexokinase reaction of the EMP pathway allow this reaction to proceed to the formation of Glucose 6P o Hexokinase couples glycolysis to ATP hydrolysis or phosphorylation to make the reaction more favorable o The enzyme s active site excludes H20 favoring the coupled reaction 0 Adds a phosphate to Glucose 6 to make it Glucose 6p What is the standard reduction potential and what does the E0 value indicate about the tendency of compound to to donate electrons E is the standard e potential for a reduction reaction 0 Indicates the tendency for a compound to lose e What is Eo39 What are the units of E039 o E o The standard electron potential for a reduction reaction the tendency for a compound to lose electrons Reaction of H20 H2 is donating e acting as a reductant H2 loses e and becomes oxidized and less energy rich 02 is the e acceptor becomes reduced and consequently more energy rich What is the equation that relates the change in the electron potential AEon of a redox reaction to the change in free energy AGO39L o AG nFAE The Nernst Equation 0 AG is the change in standard free energy in kJmol o AE is the change in the standard reduction potential for the redox couple 0 F is the Faraday constant 96480 jmol volt o n is the number of e transferred in the reaction Under what conditions will a redox reactions have a favorable free energy Redox pairs with more negative reduction potential will spontaneously donate electrons to couples with more positive reduction potentials 0 Different in reduction potentials of the electron carriers NADH and 02 is large Results in the release of energy Terms Catabolism Fueling reactions 0 Energy conserving reactions Provide ready source or reducing power electrons Generate precursors for biosynthesis Anabolism the synthesis of complex organic molecules from simpler ones 0 requires energy from fueling reactions usually as ATP 0 requires a source of electrons stored in the form of reducing power Redox reaction 0 Reactions central to energy production in biological systems Oxidizedreduced o LEO 0 Loss of electron Oxidized GER o Gain of electron Reduced Organotrophs Organic molecules donate electrons Lithotrophs Inorganic molecules donate electrons Phototrophs Light absorption excites electrons to a high energy state Gibbs free energy AG 0 Energy associated with a chemical reaction that can be used to do work AGO39 Change in the standard free energy in kJmol o 298 K o 1 ATM o All concentrations of substrates and products are 1M Equilibrium constant Keq 39 KeQ Cdab o Productsreactants NAD 0 Energy carrier 0 Gain or release small amounts of energy in reversible reactions NADPFAD Redox reaction 0 Energy carrier that transfers electron Energy is conserved in redox reaction and not lost as heat Phosphoenolpyruvate PEP Has the highest energy phosphate bond found 0 619 kJmol Involved in glycolysis 13 Bisphosphoglycerate 3 carbon organic molecule present in most living organisms o primarly exists as a metabolic intermediate in both glycolysis and the calvin cycle photosynthesis Hexokinase Hexokinase couples glycolysis to ATP hydrolysis or phosphorylation to make the reaction more favorable The enzyme s active site excludes H20 favoring the coupled reaction Electron potential 0 Measure of tendency of a chemical species to acquiregive electrons E039 and AEO39 E0 0 Standard electron potential for a reduction reaction The tendency for a compound to lose electrons AEO39 0 Change in the standard reduction potential for the redox couple Nernst Equation 0 AG nF AE Questions What are the three main pathways processes for catabolism Fermentation 0 Partial breakdown of organic food without net electron transfer to an inorganic terminal electron acceptor Respiration 0 Complete breakdown of organic molecules with electron transfer to a terminal electron acceptor such as 02 o Photoheterotrophy o Catabolism is conducted where light absorbed by pigments such as chlorophyll aids in catabolic reactions What are the three pathways for the catabolism of glucose Glycolysis EMP pathway 0 Glucose 6phosphate isomerizes into fructose 6phosphate and is ultimately converted to two pyruvate EMP generates a 2 pyruvates n 2 ATP n 2 NADH o Entner Doudoroff ED pathway 0 Glucose 6phosphate is oxidized into 6phosphogluconate and ultimately into two pyruvate ED Pathway generates U 1 ATP U 1 NADH U 1 NADPH ED is used by enterics bacteria that colonize the gut Essentially replaces the rst phase of the EMP pathway Pentose Phosphate Shunt PPS o Glucose 6phosphate is oxidized into 6phosphogluconate and then decarboxylated to the 5 carbon sugar ribulose 5 phosphate PPS produces a 37 Carbon sugars 0 Some of which serve as precursors for aromatic amino acids and purine biosynthesis n 3 carbon sugar Pyruvate o Enters into the EMP or ED pathways PPS Generates a 2 NADPH n ATP may also be generated if fructose 6 phosphate reenters the EMP What are the two stages of the EMP pathway How is glucose activated in the rst stage and what is the energy cost 0 Activation Stage 0 Glucose is activated by two ATP requiring phosphorylation reactions Free energy required No Redox steps no NADH formed 0 Energy yielding stage 0 Two gyceradehyde 3phosphate molecules are oxidized by NAD leading to the production of two pyruvate and two NADH Four ATP are formed by substrate level phosphorylation In the second stage of the EMP pathway which intermediates are involved in substrate phosphorylation reactions NAD ADP What is the yield of ATP and NADH in the conversion of glucose to pyruvate in the EMP pathway 0 2 Pyruvate o 2 NADH How does the phosphofructokinase reaction participate in the regulation of the EMP pathway Glycolysis is amphibolic o Participates in catabolism Breakdown 0 Participates in anabolism Biosynthesis o Phosphofructokinase has a role in the direction of the pathway 0 In glycolysis the ATP phosphorylation of fructose 6 phosphate is catalyzed by phosphofructokinase Activated by ADP n A signal of energy need where as the biosynthetic enzyme is inhibited by such signals 0 In biosynethisis this step is reversed by a different enzyme 0 Instead of regenerating ATP it removes the second phosphoryl group A step yielding energy and thus driving the pathway in reverse How is glucose activated in the ED pathway What is the fate of the activated molecule and what reduced electron carrier is produced Glucose is activated by one phosphorylation reaction 0 Then dehydrogenated to 6phosphogluconate o Dehydrated and cleaved to pyruvate and glyceraldehyde3P which then enters EMP pathway to form a 2nCI pyruvate What is the yield of ATP and NADH in the conversion of glucose to pyruvate in the ED pathway 0 1 ATP 0 1 NADH 0 1 NADPH How are the reactions of the ED pathway related to those of the EMP and PPS pathways 0 All use glucose 6phosphate to generate ATP and NADPNADPH 0 ED replaces 1st phase of EMP then will enter into EMP to form 2nCI pyruvate o PPS can operate at the same time as EMP or ED What is the electron carrier in the oxidative section of the PPS pathway and what is the fate of this molecule 0 NADPH is the electron carrier 0 Glucose 6phosphate gives up two electrons to form NADPH and is oxidized to form 6phosphogluconate What two enzymes play key roles in the interconversions of sugars in the nonoxidative branch of the PPS pathway Transketolase Transaldolase What intermediates of this branch of the PPS pathway are used in the biosynthesis of aromatic amino acids and purines Ribose 5phosphate o Purine synthesis Erythrose 4phosphate o Aromatic amino acids How do cells undergoing fermentation generate energy What is the fate of NADHH generated in the rst stage of fermentation Substrate level phosphorylation o Microbes compensate for the low efficiency of fermentation by consuming large quantities of substrate and excreting large quantities of products 0 The electrons and hydrogen s from NADHH are transferred back onto the products of pyruvate o Forming partly oxidized fermentation products 0 Does not deliver its electrons to an electron transport chain During fermentation what pathway intermediate serves as a branch point leading to the production of the end products Pyruvate o Fermentation uses an endogenous electron acceptor usually an intermediate of the pathway to oxidize the organic energy source How are fermentation pathways classi ed Homolactic Fermentation o Produces two molecules of lactic acid 0 Ethanolic Fermentation o Produces two molecules of ethanol and two C02 Heterolactic Fermentation o Produces one molecule of lactic acid one ethanol and one C02 0 MixedAcid Fermentation o Produces acetate formate lactate succinate 0 Plus Ethanol H2 and C02 What are the two general functions of the tricarboxylic acid TCA cycle Oxidation of pyruvate to C02 with the production of high energy phosphate compounds and reducing equivalents TCA intermediates are also an important source of carbon skeletons for use in biosynthesis What role does the pyruvate dehydrogenase complex PDC play in the routing intermediates into the TCA cycle 0 PDC activity is a key control point of metabolism 0 The rst molecular player to direct sugar catabolism into respiration o Induced when carbon sources are plentiful and repressed under carbon starvation Removes C02 from pyruvate generating acetylCoA 0 Two electrons are transferred to NAD forming NADHH Substrate by product Acetylphosphate is a signal that leads to certain intermediates going into the TCA cycle or ETC Connects glycolysis to TCA What are the reaction products of the reaction 0 AcetylCoA C02 NADHH What is the overall reaction for the passage of one pyruvate through the TCA cycle Stoichiometry for pyruvate includes the intermediate step 0 Pyruvate 4 NAD FAD GDP Pi 2 H20 0 l 4NADH 4H FADH2 GTP 3C02 What is the overall reaction for the conversion of glucose to C02 via the EMP and TCA pathways Glucose 602 6C02 l 6H20 38ATP What is the overall energy yield for these reactions if the oxygenic electron transport chain and ATP synthase of E coli are used 0 20 Under what growth conditions is the glyoxylate bypass used 0 When glucose is absent cells can catabolize acetate or fatty acids using glyoxylate bypass When cells grow on fatty acids acetate or other substrates that do not enter the EMPED pathways they use a modi ed form of TCA called glyoxylate bypass o Requires two enzymes lsocitrate lyase and malate synthase No carbons lost as C02 How are the reactions of the glyoxylate bypass related to the TCA cycle Glycoxylate bypass regenerates TCA cycle intermediates and provides substrates to build glucose and carbohydrates What reactions are unique to the pathway 0 Using acetatefatty acids as energy source 0 Diversion of isocitrate to glyoxylate Incorporation of a second acetylCoA to form malate Glycoxylate bypass cuts out all loss of C02 and generation of ATP FADH2 and NADH 0 Exception of one NADH from malate to oxaloacetate What are examples of intermediates of the TCA cycle that are removed for anabolic reactions Oxaloacetate citrate aketoglutarate and succinylCoA Terms Amphibolic o EMP ED PPS TCA Fermentation 0 Partial breakdown of organic food without net electron transfer to an inorganic terminal electron acceptor Respiration Complete breakdown of organic molecules with electron transfer to a terminal electron acceptor such as 02 Photoheterotrophy Catabolism is conducted where light absorbed by pigments such as chlorophyll aids in catabolic reactions EmbenMeyerhoffParnas EMP pathway Glycolysis o Glucose 6phosphate isomerizes into fructose 6phosphate and is ultimately converted to two pyruvate EMP generates a 2 pyruvates n 2 ATP n 2 NADH Entner Doudoroff ED Pathway Series of reactions that catabolize glucose into pyruvate using a set of enzymes different from glycosis or PPS o Glucose 6phosphate is oxidized into 6phosphogluconate and ultimately into two pyruvate ED Pathway generates U 1 ATP U 1 NADH U 1 NADPH Pentose phosphate shunt PPS Parallel pathway to glycolysis that generates NADPH and 5carbon sugars o Primarily anabolic 2 phases a Oxidative phase NADPH generated a Nonoxidative phase 0 Synthesis of 5carbon sugars Glucose 6phosphate is oxidized into 6phosphogluconate and then decarboxylated to the 5 carbon sugar ribulose 5phosphate o PPS produces 37 Carbon sugars I Some of which serve as precursors for aromatic amino acids and purine biosynthesis 3 carbon sugar Pyruvate n Enters into the EMP or ED pathways 0 PPS Generates 2 NADPH ATP may also be generated if fructose 6phosphate reenters the EMP Substrate phosphorylation Metabolic reaction that results in the formation of ATP or GTP by direct transfer and donation of a phosphyorl group to an ADP or GDP from a phosphorylated reactive intermediate Phosphofructokinase Enzyme that phosphorylates fructose 6phosphate in gycoysis 6phosphogluconate 0 Intermediate in the PPS and ED pathway 0 Produces ribulose 5phosphate Purine synthesis Erythrose 4phosphate 0 Intermediate of the PPS pathway o Aromatic amino acids Ribose 5phosphate Purine synthesis Transketolase 0 Enzyme used in the PPS o Catalyzes two important reactions Nonoxidative pentose phosphate pathway Transaldolase 0 Enzyme of the nonoxidative phase of PPS Homolactic ethanolic heterolactic and mixed acid Homolactic Fermentation o Produces two molecules of lactic acid Ethanolic Fermentation o Produces two molecules of ethanol and two C02 Heterolactiv Fermentation o Produces one molecule of lactic acid one ethanol and one C02 MixedAcid Fermentation o Produces acetate formate lactate succinate Plus Ethanol H2 and C02 Fermentations 0 Metabolic process converting sugar to acids gases and or alcohol Pyruvate dehydrogenase complex PDC 0 PDC activity is a key control point of metabolism 0 The rst molecular player to direct sugar catabolism into respiration o lnduced when carbon sources are plentiful and repressed under carbon starvation Removes C02 from pyruvate generating acetylCoA 0 Two electrons are transferred to NAD forming NADHH Substrate by product Acetylphosphate is a signal that leads to certain intermediates going into the TCA cycle orETC Connects glycolysis to TCA Glyoxylate Bypass 0 Variation of TCA o Anabolic Centers on the conversion of acytlCoA to succinate for the synthesis of carbohydrates lsocitrate lyase Together with malate synthase it bypasses the two decarboxylation steps of the TCA cycle 0 Used by bacteria fungi plants Malate synthase What are the three major classes of electron transport systems What are examples of electron donors for these systems Respiration o lnvolves organic electron donors such as sugars lipids or amino acids that are converted to C02 and water The electrons are passed to inorganic or organic terminal electron acceptors o Lithotrophychemolitotrophy o Involves inorganic organic electron donors Fe2 or H2 0 AND inorganicorganic terminal acceptors 0 Many of these organisms are also autotrophs Fixing C02 as the carbon source 0 Phototrophy o lnvolves light capture by chlorophyll usually coupled to splitting of H25 or H20 or organic molecules What is the equation de ning the relationship between the differences in reduction potential of a redox couple and the free energy change AGo39 o In redox reactions AG is a function of the reduction potential E between the oxidized and the reduced forms of a molecule AG nF AE Nernst equation a AG is the change in the standard free energy in kJmol n AE is the change in the standard reduction potential for the redox couple a F is the Faraday constant 96480 joulesmol volt n n is the number of e transferred in the reaction Recall E is value of E with all components at 1M pH 7 and 298 K in units of mV Under what conditions will a redox reaction yield a negative free energy 0 A reaction is favored by E values which yield AG values What does the quotelectron towerquot tell us about the ability of a molecule to act as an electron donor or acceptor Justify why the transfer of electrons from NADHH to 02 is a favorable redox reaction 0 Electron tower o A comparison of E allows the prediction of the electron ow direction among various redox pairs in a given ETS The difference in reduction potentials of the electron carriers NADH and 02 is large 0 Results in the release of a lot of energy How does Gallionella thrive in iron mine drainage streams by oxidizing Fe2 and using 02 as its terminal electron acceptor when the Eo for this redox couple is only 005 V o E values in a cell vary with the concentration of the reactants so the reaction is moved forward by a high concentration of Fe2 in the environment What roles do oxidoreductases and ubiquinone play in an electron transport system Oxidoreductases o Oxidize one substrate removing electrons and reduce another donating electrons They couple different halfreactions of the electron tower o Consist of multipleprotein complexes that include cytochromes as well Ubiquinone o Serves as an electron carrier in the ETC What are the two components of the proton motive force How are they generated by an electron transport system 0 PMF or Ap when ETS pumps H establishing a ApH and a charge difference 0 Includes change in charge amp change in ApH across the membrane respectively How does the activity of an electron transport chain ETC lead to the synthesis of ATP 0 Transport of protons H back into the cytoplasm leads to ATP synthesis by the enzyme ATP synthase F1F0 ATPase type 0 Uses the PMF to catalyze ATP synthesis Which enzyme is responsible for ATP synthesis in response to the activity of the ETC 0 ATP synthase What is the general structure of this enzyme What are the approximate requirements for the synthesis of one ATP 0 F0 is the proton channel C rings acts as a rotor rotating the shaft E and v subunits act as shaftstalk connecting F0 and Fi Active sites are on the B subunit of F1 0 As protons enter v subunits rotate and cause a conformational change in the B subunits leading to ATP formation What are the different forms of the PMF what molecules are present on externalinternal sides of the membrane 0 Charge gradient and pH gradient Ap ALp 60ApH Charge gradient no pH gradient Ap ALIJ ApH 0 0 pH gradient no charge gradient Ap 60ApH ALIJ 0 What processes utilized the energy stored by the PMF ATP synthesis Rotation of agella Uptake of nutrients Ef ux of toxic drugs What are the three components of a respiratory electron transport chain 0 An initial substrate oxidoreductase or dehydrogenase o Receives a pair of electrons from an organicinorganic substrate 0 A mobile electron carrier 0 Quinones Picks up 2H from the cytoplasm and is reduced into quinol A terminal oxidase complex 0 Transfers the electrons to a terminal electron acceptor 02 0 Typically includes a cytochrom receiving two electrons from quinol What determines the direction of electron ow in an ETC 0 Substrate dehydrogenase receives a pair of e from an organic substrate such as NADH or an inorganic substrate such as H2 t donates the e ultimately to a mobile e carrier such as quinone Quinone picks up 2H from the cytoplasm and is thus reduced to quinol 0 There are many quinones w different side chains collectively referred to as Q and QH2 o A terminal oxidase complex which typically includes a cytochrome receives 2 e from quinol QH2 The 2H are translocated outside the membrane In addition the transfer of the 2 e through the terminal oxidase complex is coupled to the pumping of 2H 0 The terminal oxidase complex transfers the e to a terminal e acceptor such as 02 0 Each 0 atom receives 2 e and combines with 2 protons from the cytoplasm to form 1 molecule of H20 0 12 02 2H l H20 Thus the E coli ETS can pump up to 8H for each NADH molecule and up to 6H for each FADH2 molecule In the case of the E coli respiratory ETC where 02 is the terminal electron acceptorhow many protons are pumped out for each NADHH and each FADH2 Up to 8H for each NADH molecule and up to 6H for each FADH2 molecule What components of the E coli ETC change when cells switch from aerobic to anaerobic growth 0 E coli can use alternative types of terminal e acceptors in anaerobic respiration 0 Donors and acceptors usually induce expression of genes coding for their redox enzymes and repress the expression of others 0 Terminal 9 acceptors can be organic or inorganic What is the role of an oxidized form of nitrogen eg nitrate NO3 during dissimilatory denitri cation How does this differ in an assimilatory process 0 What forms of oxidized sulfur serve as electron acceptors 0 04 2 0 03 2 0 S203 2 0 S 0 H25 What does the structure of a lake sediment microbial community tell us about the utilization of electron donorsacceptors 0 N S and metal series are consumed in order of their strength as e acceptors 0 As each successive terminal e acceptor is used up its reduced form appears the next best e acceptor is then used generally by a different microbe species 0 Microbial mineral reduction is important in geochemical cycHng Aerobes denitri ers manganese reducers iron reducers sulfate reducers methanogens What is the nature of the electron donor during lithotrophy o Energyyielding form of metabolism in which reduced minerals can serve as electrons for an ETS 0 Inorganic substrates other than H2 are poor e donors the terminal e acceptor is usually a strong oxidant 02 N03 Fe3 o Obligate lithotrophs consume no organic C source build biomass by xing C02 autotrophs What are examples of nitrogen and sulfur compounds that serve as electron donors during lithotrophy Nitrogen o Ammonium NH4 o Hydroxylamine NHZOH o NH3N02 Poor electron donors Sulfur 0 Hydrogen sul de H25 0 Elemental sulfur How does molecular hydrogen compare as an electron donor Hydrogenotrophy is the use of H2 as an e doner 0 H2 has suf cient reducing potential to donate e to nearly all biological acceptors What is an example of how H2 as an electron donor participates in a bioremediation process 0 Dehalorespiration o Halogenated hydrocarbons are reduced by H2 PCE to DCE and then to ethane through various microbes What role does H2 play in the conversion of C02 to CH4 by methanogens Methanogenesis is the reduction of C02 and other singlecarbon compounds to methane o Performed only by archaea called methanogens o Simplest form involves H reduction of C02 0 C02 4H2 CH4 2H20 What group of organisms utilize methane as a carbon source Methanogenesis 0 Reduction of C02 and other single carbon compounds to methane Performed only by archaeas How does phototrophy differ from other forms of respiration o Phototrophy o Harnessing of photoexcited electrons to power cell growth Brought about by using the photoexcited electron to pump H What are the three major type of phototrophy Bacteriorhodopsinproteorhodopson 0 Single protein light driven proton pump found in haloarchaea and some marine microbes Single cycle photosystems l and II 0 PS I Separates e from HZS organic donors or reduced iron Fe 2 leading to the formation of NADPH and PMF leading to ATP synthesis 0 PS ll Obtains an e from bacteriochropyll Generates a PMP leading to ATP synthesis and does not produce NADPH Double cycle or ZPathway o Oxygenic photosynthesis Combines features of both PS and PS II and produces 02 PMF leading to ATP synthesis and NADPH How does bacteriorhodopsin function in as a phototrophic system for energy generation Bacteriorhodopsin is a a membraneembedded protein light driven Hpump that supplements metabolism 0 Contains seven alpha helices The helices of the protein surround a cofactor molecule of retinal n Covalently linked to a lysine residue of the protein 0 A photon is absorbed by retinal which shifts its con guration from trans to cis The cycle of excitation and relaxation back to the trans form is coupled to pumping of 1H from the cytoplasm across the membrane Which organisms utilize this system Organisms from all three domains carryout photosynthesis archaea have bacteriorhodopsin not PS or II What features are common to photolytic electron transport systems 0 Antenna system 0 A complex of chlorophylls and accessory pigments in the photosynthetic membrane that funnels e to the reaction center Each type of chlorophyll contains a characteristic chromophore ight absorbing electron carrier 0 Reaction center RC 0 The location in which energy from chlorophyll photoexcitation is used to separate an e from a small molecule or from bacteriochlorophyll itself 0 Electron transport chain ETC 0 The excited e from the RC enters a membrane embedded chain of oxidoreductases and QQH2 as in respiration and lithotrophy 0 Energy carriers 0 In photosystem PSI NADPH is produced and e transfer yields energy to pump protons and synthesize ATP in PS II protons are pumped to synthesize ATP but NADPH is not formed What types of molecules act as lightabsorbing electron carriers in the antenna systems Chromophores o Lightabsorbing electron carriers Chlorophylls a and b Bacteriochlorophyll What physical properties do they have that are bene cial to the cell 0 Their absorption spectra differ which allows for more light to be absorbed by the cell for more energy production 0 Environmentally based What roles do accessory pigments play in the antenna systems Absorb light in a range not absorbed by the chlorophylls 0 Transfer energy to the chlorophylls 0 Increasing the ef ciency of photosynthesis by extending the range light absorbed carotenoids and phycocyanobiin They can be protective preventing damage to the chlorophyll How are antenna systems organized Antenna Complexes 0 Arranged like a satellite dish within the plane of the membrane in an elaborate cluster around accessory protein 0 Clusters then associate in a ring around the RC In an anaerobic PS I system what types of molecules serve as electron donors What soluble reduced electron carrier is produced and what is its function in the cell 0 Electron donors 0 e associated with hydrogens from H25 0 organic e donors eg succinate 0 reduced iron Fe2 0 Electron carrier Reduced electron carrier 0 NAD or NADP They participate in C02 xation or biosynthesis How does this system lead to the synthesis of ATP Proton motive forces 0 The accumulation of H within the system creates a gradient which is then used in the ATP synthase to produce a molecule of ATP In an anaerobic PS II system what is the source of the electron during photoexcitation What is the fate of these electrons 0 Source of electron bacteriochlorophyll 0 Electron is used in the ETC 0 Ultimately an electron is returned back to the bacteriochlorophyll however a H potential is generated 0 N0 gradient is formed in P5 II no extra H are pumped into system How is ATP synthesized in this system and is an reduced electron carrier produced H is released and a net proton motive force is generated to generate ATP What is the general composition of the oxygenic Z pathway How is 02 produced by this pathway 0 General composition eight photons are absorbed and two electron pairs are removed from 2H20 ultimately producing 02 o Combines key features of PS I and II yielding more energy than anaerobic PS and PS alone Includes homologs of photosystems and II What is the yield of ATP and NADPH during oxygenic photosynthesis following the absorption of eight photons and the removal of electrons from two water molecules 0 3 ATP 2 NADPH per 2 H20 photolyzed and 02 produced What role does plastocyanin play in the oxygenic Zpathway o It transfers e from photosystem II to photosystem I Respiration The oxidation of a reduced organic or inorganic electron donor through a series of membrane associated electron carriers to a terminal electron acceptor Lithotrophy chemolithotrophy The acquisition of energy by oxidation of inorganic electron donors Phototrophy The harnessing of photoexcited electrons to power cell growth Nernst Equation An equation that relates the reduction potential of a halfcell electromotive force at any point in time to the standard electrode potential temperature activity and reaction quotient of the underlying reactions and species used AEO39IAE The change in the standard reduction potential for the redox couple quotElectron towerquot A comparison of E 39 which allows the prediction of the electron ow direction among various redox pairs in a given ETS Oxidoreductases A class of enzymes that facilitates catalyzes the transfer of electrons from reductants electron donors to oxidants electron acceptors Ubiquinone Any of a class of compounds that occur in all living cells and that act as electrontransfer agents in cell respiration Proton motive force PMF Energy that is generated by the transfer of protons or electrons across and energytransducing membrane and that can be used for chemical osmotic or mechanical work ATP synthase An important enzyme that provides energy for the cell to use through the synthesis of adenosine triphosphate ATP Electron transport chain ETC A series of compounds that transfer electrons from electron donors to electron acceptors via redox reactions and couples this electron transfer with the transfer of protons H across a membrane Dissimilatory denitri cation The reduction of nitrogen compounds mainly nitrate into oxidized forms of nitrogen which is used for repiration Assimilatory processes The breakdown of ammonia into biomass Hydrogenotrophy The use of molecular hydrogen H2 as an electron donor Methanogenesis The reduction of C02 and other singlecarbon compounds to methane Methanotrophs Prokaryotes that are able to metabolize methane as their only source of carbon and energy Phototrophy The harnessing of photoexcited electrons to power cell growth Bacteriorhodopsin Proteorhodopsin Single protein light driven proton pump found in haloarchaea and some marine microbes Photosystem I Separates e from H25 organic donors or reduced iron leading to the formation of NADPH and PMF which leads to ATP synthesis Photosystem ll Obtains an e from bacteriochrophyll Generates a PMF leading to ATP synthesis and does not produce NADPH Zpathway Combines features of both PS and PS II and produces 02 PMF leading to ATP synthesis and NADPH Retinal Allows certain microorganisms to convert light into metabolic energy Photoexcitation The process of exciting the atoms or molecules of a substance by the absorption of radiant energy Photolysis The lightdriven separation of an electron from a donor molecule such as H20 or H25 Antenna system Membrane associate complexes of chlorophylls and accessory pigments Thylakoids Each of a number of attened sacs inside a chloroplast bounded by pigmented membranes on which the light reactions ofphotosynthesis take place Reaction center RC A complex of several proteins pigments and other cofactors assembled together to execute the primary energy conversion reactions of photosynthesis Energy carriers A substance that contains energy which can be later converted to other forms such as mechanical work or heat or to operate chemical or physical processes Chromophore An atom or group whose presence is responsible for the color of a compound Chlorophylls Responsible for the absorption of light to provide energy for photosynthesis Carotenoid Any of various usually yellow to red pigments found widely in plants and animals and characterized chemically by a long aliphatic polyene chain composed of eight isoprene units Phycocyanobilin Terminal acceptor of energy in photosynthetic plants Bacteriochlorophyll A pyrrole derivative in photosynthetic bacteria related to the chlorophyll of higher plants Terminal acceptor of energy Cyclic photophosphorylation The synthesis of ATP during photosynthesis coupled to the cyclic passage of electrons to and from P700 the specialized form of chlorophyll a which is involved in photosystem I using a series of carrier molecules Oxygenic Zpathway Includes homologs of photosystems l and II Eight photons are absorbed and two electron pairs are removed from 2 H20 ultimately producing 02 Plastocyanin A coppercontaining protein that acts as an intermediary in photosynthetic electron transport What is anabolism and what are the three general requirements for these processes Anabolism is the opposite of catabolism o It encompasses the processes and reactions needed to build biomolecules The three general requirements for these processes are 1 Essential elements C H O N and other essential elements macromicro nutrients 2 Reduction Many biosynthetic reactions occur through reduction of precursors using molecules such as NADPH 3 Energy Energy is required for many biosynthetic reactions This occurs through coupling reactions to ATP hydrolysis NADPH oxidation or ion ow down a transmembrane concentration gradient Why are the EMP ED PPS and TCA cycle metabolic pathways referred to as amphibolic All follow the three general requirements encompassed in anabolism All can use catabolism and anabolism M ED pathway the net ATP gain is one ATP and one NADH and one NADPH The ED pathway catabolizes sugars and sugar acids 5 The overall net gain is one ATP and two NADPH The PPS generates more complex intermediates than either the EMP or ED pathways m also referred to as the citric acid cycle or the Krebs cycle at least ten known variations of TCA cycle electron transport system The entire process can yield up to 38 ATP but it depends on the carbon source and oxygen availability What are examples of pathways or reaction schemes that are used by microbes to x C02 for assimilation into cellular material Calvin cycle 0 PPS Reductive TCA cycle Reductive acetylCoA pathway What are the three phases of the Calvin cycle 1 CarboxylationFixation Phase 2 Reduction phase 3 Regeneration phase What types of processes take place in each phase of the Calvin cycle and what key intermediates are made 0 1 Carboxylation Phase 0 Ribulose 15 bisphosphate carboxylase oxygenase RuBisCO catalyzes the addition of C02 to the C5 molecule ribulose 15 bisphosphate RuBP forming a six carbon intermediate that rapidly and spontaneously splits into two molecules of 3 phosphoglycerate PGA 2 Reduction phase 0 PGA is converted to 13bis phosphoglycerate and then reduced to glyceraldehyde 3 phosphate G3P by a NADPH requiring dehydrogenase enzyme 0 3 Regeneration phase 0 In the regeneration phase RuBP is reformed so that the cycle can repeat This portion of the cycle is similar to the PPS pathway and involves the transketolase and transaldolase reactions A number of other precursor metabolites are produced during this phase Which steps of the Calvin cycle require ATP What form of reductant is used The reduction phase uses the phosphoglycerate kinase to break down ATP and the regeneration phase uses phosphoribulokinase to break down ATP What is the role of the Ribulose 15 bisphosphate carboxylase oxygenase enzyme 0 Organic substance that is involved in photosynthesis reacts with carbon dioxide to form 3PGA What roles do the transketolase and transaldolase enzymes play in this pathway What important intermediates do they produce that are used in the biosynthesis of aromatic amino acids and purines Interconversion of sugars o Ribose 5phosphate Purine synthesis 0 Erythrose 4phosphate Aromatic amino acids For each three C02 entering the Calvin cycle what three carbon 3C intermediate is produced that can participate in anabolic reactions Glyceraldehyde 3phosphate G3P What are carboxysomes and how do they function in C02 xation What enzyme is found in these structures Carboxysomes o Proteinaceous structures that contain the enzymes of carbon dioxide xation in organisms The carboxysome takes up bicarbonate HCO3 which is then immediately converted to C02 by carbonic anhydrase which catalyzes the rapid interconversion of carbon dioxide and water to bicarbonate and protons Why are alternative enzymes are needed to quotrunquot the TCA cycle in reverse during C02 assimilation It allows the reduction of C02 to regenerate acetylCoA and build sugars What are these enzymes ATPcitrate lyase 2oxoglutarateferredoxin oxidoreductase Fumarate reductase What is the product formed by the incorporation of four C02 by the reverse TCA cycle Oxaloacetate What three additional nonTCA enzymes are needed to convert acetylCoA to oxaloacetate Ferredoxin dependent Pyruvate synthase acetylCoA to pyruvate o PEP synthetase M 10 pyruvate to PEP PEP carboxylase PEP to oxaloacetate What are the two intermediates formed during the reduction of C02 in the reductive acetylCoA pathway What is the nal product of these reactions Intermediates o Formic acid and Carbon Monoxide 0 Final product acetylCoA What two metabolic reactions in the EMP pathway glycolysis are not reversible and how are the reverse metabolic interconversions carried out during gluconeogenesis 1 The conversion of Fructose 16 bisphosphate to Fructose 6 phosphate 0 The gluconeogenic reaction uses fructose 16bisphosphatase o 2 The conversion of pyruvate to PEP o This process requires two enzymes 0 Pyruvate carboxylase o o Phosphoenolpyruvate carboxykinase What are anaplerotic reactions What two reactions can replenish oxaloacetate that may have been removed from the TCA cycle for use in biosynthesis Anaplerotic reactions 0 Replace intermediates of the central metabolic pathway lost to biosynthetic reactions 0 Malic enzyme PEP carboxykinase 0 Important for the generation of pyruvate and PEP in cells growing on succinate Pyruvate ca rboxylasePEP ca rboxylase 0 Important for replenishing oxaloacetate in cells growing on glucose What is the unit of growth of a fatty acid during its biosynthesis 0 Fatty acids are built from repeating units The repetitive nature of the fatty acid structure allows their synthesis with fewer enzymes working in a cyclic manner What is the building block that condenses with the growing chain 0 MalonylACP condenses with the growing chain with the loss of C02 What are the energy ATP and reductant requirements for the addition of one unit to a growing fatty acid molecule At what stage in the biosynthesis process are unsaturations introduced into fatty acids and at what positions Unsaturation can be generated during a cycle of elongation at the C10 stage What amino acids are derived from the TCA cycle intermediates 2oxoglutarate and oxaloacetate o 2oxoglutarate 0 Glutamate produces proine arginine and glutamine Oxaloacetate 0 Aspartate produces asparagine and pyrimidines 0 With the assistance of the succinylcoA it also produces threonine isoeucine methionine diaminopimeate and lysine Terms Anabolism The opposite of catabolism Encompasses the processes and reactions needed to build biomolecules cellular constituents Amphibolic Used to describe a biochemical pathway that involves both catabolism and anabolism Calvin Cycle The set of chemical reactions that take place in chloroplasts during photosynthesis The cycle is lightindependent because it takes place after the energy has been captured from sunlight Reductive TCA cycle Uses 4 5 ATPs to x four molecules of C02 and generate one oxaloacetate Reductive acetylCoA pathway alt def below Used by anaerobic soil bacteria autotrophic sulfate reducers and methanogens Two C02 molecules are condensed through converging pathways to form the acetyl group of acetylCoA Carbon monoxide is an intermediate Reducing agent is H2 instead of NADPH Ribulose 15 bisphosphate An organic substance that is involved in photosynthesis The anion is a double phosphate ester of the ketose called ribulose carboxylase oxygenase Carb an enzyme that catalyzes the addition of a carboxyl group to a speci ed substrate Oxy an enzyme that catalyzes the reaction of an organic compound with molecular oxygen Transketolase and an enzyme that catalyzes the transfer of an alcohol group between sugar molecules Transaldolase an enzyme of the nonoxidative phase of the pentose phosphate path way Glyceraldehyde 3phosphate G3P A chemical compound that serves as an intermediate in several central metabolic pathways in all organisms cycle Erythrose 4phosphate A phosphate of the simple sugar erythrose An intermediate in the pentose phosphate pathway and the Calvin Ribose 5phosphate Both a product and an intermediate of the pentose phosphate pathway Produced in the last step of the oxidative reactions Carboxysomes Intracellular structures found in many autotrophic bacteria Contain the enzymes of carbon dioxide xation in these organisms Carbonic anhydrase An enzyme that catalyzes the interconversion of dissolved bicarbonates and carbon dioxide ATPcitrate lyase The primary enzyme responsible for the synthesis of cytosolic acetyl CoA in many tissues AcetylCoA serves several important biosynthetic pathways Fumarate reductase The enzyme that converts fumarate to succinate and is important in microbial metabolism as a part of anaerobic respiration Succinate acceptor ltgt fumarate reduced acceptor 2Oxogluta rateferredoxin Metabolic intermediate Oxidoreductase An enzyme that catalyzes the transfer of electrons from one molecule the electron donor to another the electron acceptor CoA Utilizes NADP or NAD as cofactors Pyruvate synthase An enzyme that catalyzes the interconversion of pyruvate and acetyl PEP synthetase An enzyme that catalyzes pyruvate to PEP PEP carboxylase An enzyme that catalyzes PEP to oxaloacetate Reductive acetylCoA pathway Enables certain organisms to use hydrogen as an electron donor and carbon dioxide as an electron acceptor as well as a building block for biosynthesis Gluconeogenesis A metabolic pathway that results in the generation of glucose from noncarbohydrate carbon substrates Substrate examples pyruvate lactate glycerol and glucogenic amino acids Pyruvate ca rboxylase An enzyme that catalyzes the depending on the species irreversible carboxylation of pyruvate to form oxaloacetate 0AA Pyruvic acid Oxaloacetic acid Anaplerotic reactions Those that form intermediates of a metabolic pathway Ex Tricarboxylic acid TCA Cycle MalonylCoA MalonylACP Both play a key role in chain elongation in fatty acid biosynthesis and polyketide biosynthesis
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'