Microbial Metabolism Principles of Metabolism. Harvesting Energy. All cells need to accomplish two fundamental tasks Synthesize new parts

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Microbial Metabolism All cells need to accomplish two fundamental tasks Synthesize new parts Cell walls, membranes, ribosomes, nucleic acids arvest energy to reactions Sum total of these is called

1 Microbial Metabolism All cells need to accomplish two fundamental tasks Synthesize new parts Cell walls, membranes, ribosomes, nucleic acids arvest energy to reactions Sum total of these is called metabolism uman implications Used to make biofuels Used to produce food Important in laboratory Invaluable models for study Unique s potential drug targets 6.. rinciples of Metabolism Can separate metabolism into two parts Catabolism rocesses that degrade compounds to release energy Cells capture to make Anabolism Biosynthetic processes Assemble subunits of macromolecules Use to drive reactions rocesses intimately linked CATABLISM Energy source (glucose) Waste products (acids, carbon dioxide) Catabolic processes harvest the energy released during the breakdown of compounds and use it to make. The processes also produce precursor metabolites used in biosynthesis. Cell structures (cell wall, membrane, ribosomes, surface structures) Energy Macromolecules (proteins, nucleic acids, polysaccharides, lipids) Energy Subunits (amino acids, nucleotides, sugars, fatty acids) Energy recursor metabolites Nutrients ANABLISM (source of nitrogen, sulfur, etc.) Anabolic processes (biosynthesis) synthesize and assemble subunits of macromolecules that make up the cell structures. The processes use the and precursor metabolites produced in catabolism. arvesting Energy Free energy is energy available to do work E.g., energy released when chemical bond is broken Compare free energy of reactants, products Exergonic reactions: reactants have more free energy Energy is released in reaction Endergonic reactions: products have more free energy Reaction requires input of energy Change in free energy is same regardless of number of steps involved (e.g., converting glucose to ) Cells use multiple steps when degrading compounds Energy released from exergonic reactions s endergonic reactions

product End product Starting compound Intermediate d End product Intermediate a Intermediate c (c) Cyclical metabolic Intermediate b Fig. 6.

7 Terminal Energy electron sources acceptors Energy released rganic carbon compounds S S 0 Fe N Mn rganic carbon compounds S Fe N ( to form N ) N 3 ( to form N ) Mn N 3 ( to

2 S Fig. 6. Starting compound Intermediate a Intermediate b End product (a) Linear metabolic Starting compound (b) Branched metabolic Intermediate a Intermediate b Intermediate b End product End product Starting compound Intermediate d End product Intermediate a Intermediate c (c) Cyclical metabolic Intermediate b Fig. 6.9 Glucose molecules To: Lipid synthesis To: Amino acid synthesis To: Carbohydrate synthesis To: Nucleic acid synthesis molecules energy Fig. 6.7 Terminal Energy electron sources acceptors Energy released rganic carbon compounds S S 0 Fe N Mn rganic carbon compounds S Fe N ( to form N ) N 3 ( to form N ) Mn N 3 ( to form N ) (a) Energy is released when electrons are moved from an energy source with a low affinity for electrons to a terminal electron acceptor with a higher affinity. Glucose Terminal as an electron energy source acceptors Inorganic energy sources Terminal electron acceptors Glucose N 3 (to form N ) Fe (b) Three examples of chemoorganotrophic metabolism (c) Three examples of chemolithotrophic metabolism

3 Components of Metabolic athways Role of the Chemical Energy Source and the Terminal Electron Acceptor Some atoms, molecules more electronegative than others Terminal Energy electron sources acceptors Greater affinity for electrons Energy release Energy released when rganic rganic carbon carbon compounds compounds C electrons move from low S S affinity molecule to high 0 S Fe Fe affinity molecule (E.g., glucose to ) N Mn N ( to form N ) N 3 ( to form N ) Mn N 3 ( to form N ) (a) Energy is released when electrons are moved from an energy source with a low affinity for electrons to a terminal electron acceptor with a higher affinity. Components of Metabolic athways Role of the Chemical Energy Source and the Terminal Electron Acceptor (continued ) More energy released when difference in electronegativity Glucose Terminal as an electron energy energy source acceptors is greater Electron donor: Glucose Energy source S Acceptor: Fe Terminal electron acceptor N 3 (to form N ) Inorganic sources Terminal electron acceptors (b) Three examples of chemoorganotrophic metabolism (c) Three examples of chemolithotrophic metabolism Components of Metabolic athways Role of Electron Carriers Energy harvested in stepwise process Electrons transferred to electron carriers, which represent reducing (easily transfer electrons to molecules) Raise energy level of recipient molecule NAD /NAD, NAD /NAD, and FAD/FAD 3

Components of Metabolic athways Role of Adenosine triphospate () is energy currency Composed of ribose, adenine, three phosphate groups Adenosine diphospate (AD) acceptor

Exergonic reaction s xidative roton motive force drives hoto Sunlight used to create proton motive force to drive i i Energy used The energy comes from catabolic reactions.

The Central Metabolic athways : NAD, FAD, NAD recursor metabolites Glucose molecules can have different fates Can be completely oxidized to C for maximum Can be siphoned

4 Components of Metabolic athways Role of Adenosine triphospate () is energy currency Composed of ribose, adenine, three phosphate groups Adenosine diphospate (AD) acceptor of free energy Cells produce by adding i to AD using energy Release energy from to yield AD and i Three processes to generate Substrate-level Unstable (high-energy) bonds Exergonic reaction s xidative roton motive force drives hoto Sunlight used to create proton motive force to drive i i Energy used The energy comes from catabolic reactions. Energy released The energy drives anabolic reactions. AD 6.3. The Central Metabolic athways : NAD, FAD, NAD recursor metabolites Glucose molecules can have different fates Can be completely oxidized to C for maximum Can be siphoned off as precursor metabolite for use in biosynthesis recursor Metabolites recursor metabolites are intermediates of catabolism that can be used in anabolism Serve as carbon skeletons for building macromolecules E.g., pyruvate can be converted into amino acids alanine, leucine, or valine

entose phosphate 3a Transition step 3b xidizes glucose to pyruvate X (s twice) to proton motive force Components of Metabolic athways rokaryotes remarkably diverse in using energy sources and

redox reactions Substance that loses electrons is oxidized Substance that gains electrons is reduced Electron-proton pair, or Transfer of electrons hydrogen, actually moves e e Dehydrogenation =

5 entose phosphate 3a Transition step 3b xidizes glucose to pyruvate X (s twice) to proton motive force Components of Metabolic athways rokaryotes remarkably diverse in using energy sources and terminal electron acceptors rganic, inorganic compounds used as energy source, other molecules used as terminal electron acceptor Electrons removed through series of oxidation-reduction reactions or redox reactions Substance that loses electrons is oxidized Substance that gains electrons is reduced Electron-proton pair, or Transfer of electrons hydrogen, actually moves e e Dehydrogenation = oxidation Compound Compound Compound X X Y (oxidized) (reduced) ydrogenation = reduction X loses electron(s). Y gains electron(s). X is the reducing agent. Y is the oxidizing agent. Compound Y X is oxidized by the reaction. Y is reduced by the reaction. verview of Catabolism Three central metabolic s xidize glucose to Catabolic, but precursor metabolites and reducing can be diverted for use in biosynthesis Termed amphibolic to reflect dual role Splits glucose (6C) to two pyruvates (3C) Generates modest, reducing, precursors entose phosphate rimary role is production precursor metabolites, NAD Tricarboxylic acid cycle xidizes pyruvates from glycolysis Generates reducing, precursor metabolites, verview of Catabolism Central metabolic s entose phosphate Tricarboxylic acid cycle Key outcomes recursor metabolites group and releases

3a 3b entose phosphate Glucose 6-phosphate

valine) Lipids (fatty acids) Amino acids

-phosphate Also generates reducing : NAD

6 3a 3b entose phosphate Glucose 6-phosphate Ribose -phosphate Fructose 6-phosphate Lipopolysaccharide (polysaccharide) Erythrose -phosphate Nucleotides amino acids (histidine) Dihydroxyacetone phosphate eptidoglycan Amino acids (phenylalanine, Lipids (glycerol tryptophan, tyrosine) component) 3-phosphoglycerate Amino acids (cysteine, glycine, serine) hosphoenolpyruvate Anabolic athways Synthesizing Subunits from recursor Molecules Amino acids (phenylalanine, tryptophan, tyrosine) Amino acids (aspartate, asparagine, isoleucine, lysine, methionine, threonine) xaloacetate X α- ketoglutarate Amino acids (alanine, leucine, valine) Lipids (fatty acids) Amino acids (arginine, glutamate, glutamine, proline) 6.3. The Central Metabolic athways entose hosphate athway Also breaks down glucose Important in biosynthesis of precursor metabolites Ribose -phosphate, erythrose -phosphate Also generates reducing : NAD vary depending upon alternative taken entose phosphate xidizes glucose to pyruvate Transition step X group and releases (s twice) to proton motive force 6

entose phosphate 3a Transition step entose phosphate 3a Transition step 3b 3b entose phosphate xidizes glucose to pyruvate x group and releases (s twice) xidizes glucose to pyruvate x group and

force,3-bisphosphoglycerate AD Glucose 6-phosphate Fructose 6-phosphate Dihydroxyacetone phosphate 3-phosphoglycerate hosphoenolpyruvate AD Glucose Fructose,6-bisphosphate Glyceraldehyde 3-phosphate

7 entose phosphate 3a Transition step entose phosphate 3a Transition step 3b 3b entose phosphate xidizes glucose to pyruvate x group and releases (s twice) xidizes glucose to pyruvate x group and releases (s twice) 3a Transition step xidizes glucose to pyruvate x 3b group and releases C (s twice) to proton motive force to proton motive force Chain to convert reducing to proton motive force,3-bisphosphoglycerate AD Glucose 6-phosphate Fructose 6-phosphate Dihydroxyacetone phosphate 3-phosphoglycerate hosphoenolpyruvate AD Glucose Fructose,6-bisphosphate Glyceraldehyde 3-phosphate -phosphoglycerate AD AD NAD NAD 3 is expended to add a phosphate group. 8 A chemical rearrangement occurs. is expended to add a phosphate group. The 6-carbon molecule is split into two 3-carbon molecules. NAD A chemical rearrangement of one of the molecules occurs. NAD 6 9 The addition of a phosphate group is coupled to a redox reaction, generating NAD and a high-energy phosphate bond. 7 is produced by substrate-level. A chemical rearrangement occurs. Water is removed, causing the phosphate bond to become high-energy. 0 is produced by substrate-level The Central Metabolic athways Converts glucose to pyruvates; yields net, NAD Investment phase: phosphate groups added Glucose split to two 3-carbon molecules ay-off phase: 3-carbon molecules converted to pyruvate Generates, NAD total 6.3. The Central Metabolic athways Transition Step is removed from pyruvate Electrons reduce NAD to NAD -carbon acetyl group joined to 8 coenzyme A to form acetyl- Takes place in 7 mitochondria in eukaryotes A redox reaction generates NAD. Water is added. NAD NAD Malate Fumarate xaloacetate NAD NAD Transition step: is removed, a redox reaction generates NAD, and coenzyme A is added. Citrate The acetyl group is transferred to oxaloacetate to start a new round of the cycle. Isocitrate A chemical rearrangement occurs. α-ketoglutarate NAD 3 NAD A redox reaction generates NAD and is removed. A redox reaction FAD 6 generates FAD - FAD Succinate Succinyl- NAD A redox reaction generates NAD, is removed, and coenzyme A is added. NAD The energy released during removal is harvested to produce. i AD 6.3. The Central Metabolic athways Tricarboxylic Acid (TCA) Cycle Completes oxidation of glucose roduces 6 NAD FAD recursor metabolites A redox reaction generates NAD. Water is added. A redox reaction generates FAD - NAD NAD Malate Fumarate FAD The energy released during removal is harvested to produce. xaloacetate NAD NAD FAD Succinate Succinyl- i AD Transition step: is removed, a redox reaction generates NAD, and coenzyme A is added. Citrate The acetyl group is transferred to oxaloacetate to start a new round of the cycle. Isocitrate A chemical rearrangement occurs. α-ketoglutarate NAD NAD NAD 3 NAD A redox reaction generates NAD and is removed. A redox reaction generates NAD, is removed, and coenzyme A is added. 7

3a 3b N Aspartate α-ketoglutarate N 3 (ammonia)

glutamate can be transferred to other carbon

30 From glycolysis henylalanine 3-C Compound a Branch

Compound b Tryptophan From pentose phosphate entose

8 3a 3b N Aspartate α-ketoglutarate N 3 (ammonia) Glutamate is synthesized by adding ammonia to the precursor metabolite α-ketoglutarate. xaloacetate N Glutamate The amino group (N ) of glutamate can be transferred to other carbon compounds to produce other amino acids. Fig From glycolysis henylalanine 3-C Compound a Branch point II 7-C compound Branch point I Tyrosine -C Compound b Tryptophan From pentose phosphate entose phosphate xidizes glucose to pyruvate Transition step X group and releases (s twice) to proton motive force 8

9 Table 6. verview of Catabolism transfers electrons from glucose to electron transport chain Electron transport chain generates proton motive force arvested to make via oxidative Aerobic respiration is terminal electron acceptor Anaerobic respiration Molecule other than as terminal electron acceptor Also use modified version of 6.. Uses reducing (NAD, FAD ) generated by glycolysis, transition step, and to synthesize Electron transport chain generates proton motive force Drives synthesis of by synthase rocess proposed by British scientist eter Mitchell in 96 Initially widely dismissed Mitchell conducted years of self-funded research Received a Nobel rize in 978 Now called chemiosmotic theory 9

membrane Eukaryotes: in inner mitochondrial membrane Energy gradually released Electrons from the energy source e Release coupled to ejection of protons igh energy Creates electrochemical gradient

10 Table 6.3 The Electron Transport Chain Generating roton Electron transport chain is membrane-embedded electron carriers ass electrons sequentially, eject protons in process rokaryotes: in cytoplasmic membrane Eukaryotes: in inner mitochondrial membrane Energy gradually released Electrons from the energy source e Release coupled to ejection of protons igh energy Creates electrochemical gradient Used to synthesize Low energy rokaryotes can also transporters, flagella / Energy released is used to generate a proton motive force. Electrons donated to the terminal electron acceptor. The Electron Transport Chain Generating roton Components of an Electron Transport Chain Most carriers grouped into large protein complexes Serve as proton pumps Three general groups are notable Quinones Lipid-soluble molecules Move freely, can transfer electrons between complexes Cytochromes Contain heme, molecule with iron atom at center Several types Flavoproteins roteins to which a flavin is attached FAD, other flavins synthesized from riboflavin 0

The Electron Transport Chain of Mitochondria entose phosphate xidizes glucose to pyruvate Eukaryotic cell 3a Transition step C C Acetyl Acetyl x C C 3b group and releases C Inner mitochondrial

II synthase ( synthesis) Cytochrome c ath of electrons NAD roton motive force is used to drive: Complex IV 3 3 i 3 AD Fig. 6.

11 The Electron Transport Chain of Mitochondria entose phosphate xidizes glucose to pyruvate Eukaryotic cell 3a Transition step C C Acetyl Acetyl x C C 3b group and releases C Inner mitochondrial membrane (s twice) to proton motive force Use of roton Electron Transport Chain Complex III Complex I Ubiquinone 0 / Intermembrane space Mitochondrial matrix Terminal electron acceptor NAD e Complex II synthase ( synthesis) Cytochrome c ath of electrons NAD roton motive force is used to drive: Complex IV 3 3 i 3 AD Fig. 6.0 rokaryotic cell Cytoplasmic membrane Electron Transport Chain NAD dehydrogenase Uses of roton Ubiquinol veoxidase force rive: (0 or ) synthase ( synthesis) ( or ) Ubiquinone ath of electrons 0 Active transport (one mechanism) Rotation of a flagella roton motive force is used to drive: Transported molecule utside of cytoplasmic membrane e Cytoplasm Succinate dehydrogenase NAD NAD / Terminal electron acceptor 3 3 i 3 AD The Electron Transport Chain Generating roton General Mechanisms of roton Ejection Some carriers accept only hydrogen atoms (protonelectron pairs), others only electrons Spatial arrangement in membrane shuttles protons to outside of membrane When hydrogen carrier accepts electron from electron carrier, it picks up proton from inside cell or mitochondrial matrix When hydrogen carrier passes electrons to electron carrier, protons released to outside of cell or intermembrane space of mitochondria Net effect is movement of protons across membrane Establishes concentration gradient Driven by energy released during electron transfer

12 The Electron Transport Chain Generating roton Electron Transport Chain of Mitochondria Complex I (NAD dehydrogenase complex) Accepts electrons from NAD, transfers to ubiquinone umps protons Complex II (succinate dehydrogenase complex) Accepts electrons from via FAD, downstream of those carried by NAD Transfers electrons to ubiquinone Complex III (cytochrome bc complex) Accepts electrons from ubiquinone from Complex I or II protons pumped; electrons transferred to cytochrome c Complex IV (cytochrome c oxidase complex) Accepts electrons from cytochrome c, pumps protons Terminal oxidoreductase, meaning transfers electrons to terminal electron acceptor ( ) The Electron Transport Chain Generating roton Electron Transport Chain of rokaryotes Tremendous variation: even single species can have several alternate carriers E. coli serves as example of versatility of prokaryotes Aerobic respiration in E. coli Can use different NAD dehydrogenases roton pump equivalent to complex I of mitochondria Succinate dehydrogenase equivalent to complex II of mitochondria Can produce several alternatives to optimally use different energy sources, including Lack equivalents of complex III or cytochrome c Quinones shuttle electrons directly to ubiquinol oxidase, a terminal oxidoreductase Two versions for high or low concentrations The Electron Transport Chain Generating roton Electron Transport Chain of rokaryotes (cont ) Anaerobic respiration in E. coli arvests less energy than aerobic respiration Lower electron affinities of terminal electron acceptors Some components different Can synthesize terminal oxidoreductase that uses nitrate as terminal electron acceptor roduces nitrite E. coli converts to less toxic ammonia Sulfate-reducers use sulfate (S ) as terminal electron acceptor roduce hydrogen sulfide as end product

entose phosphate xidizes glucose to pyruvate 3a Transition step Yield 3b group and releases (s twice) x to proton motive force The Electron Transport Chain Generating roton Synthase

manner Uses energy to add phosphate group to AD formed from entry of 3 protons Calculating yields Based on experiments on rat mitochondria:. made per electron pair from NAD.

Substrate-level 8 The Electron Transport Chain Generating roton Calculating theoretical maximum yields In prokaryotes: : NADà 6 Transition step: NAD à 6 TCA Cycle: 6 NAD à 8 ; FAD à

13 entose phosphate xidizes glucose to pyruvate 3a Transition step Yield 3b group and releases (s twice) x to proton motive force The Electron Transport Chain Generating roton Synthase arvesting the roton Motive Force to Synthesize Energy required to establish gradient Released when gradient is eased synthase allows protons to flow down gradient in controlled manner Uses energy to add phosphate group to AD formed from entry of 3 protons Calculating yields Based on experiments on rat mitochondria:. made per electron pair from NAD. made per electron pair from FAD xidizes glucose to pyruvate net gain = 0 NAD xidative Substrate-level 6 NAD xidative 6 x group and releases (s twice) 6 NAD xidative FAD xidative Substrate-level 8 The Electron Transport Chain Generating roton Calculating theoretical maximum yields In prokaryotes: : NADà 6 Transition step: NAD à 6 TCA Cycle: 6 NAD à 8 ; FAD à Total maximum oxidative yield = 3 Slightly less in eukaryotic cells NAD from glycolysis in cytoplasm transported across mitochondrial membrane to enter electron transport chain Requires per NAD generated 3

14 entose phosphate 3a Transition step 3b xidizes glucose to pyruvate x group and releases (s twice) to proton motive force The Electron Transport Chain Generating roton Yield of Aerobic in rokaryotes Substrate-level : (from glycolysis; net gain) (from the ) (total) xidative : 6 (from reducing gained in glycolysis) 6 (from reducing gained in transition step) (from reducing gained in ) 3 (total) Total gain (theoretical maximum) = 38 verview of Catabolism If cells cannot respire, will run out of carriers available to accept electrons will stop uses pyruvate or derivative as terminal electron acceptor to regenerate NAD can continue 6.. used when respiration not an option E. coli is facultative anaerobe Aerobic respiration, anaerobic respiration, and fermentation Streptococcus pneumoniae lacks electron transport chain only option -generating reactions are only those of glycolysis Additional steps consume excess reducing Regenerate NAD 3C (a) Lactic acid fermentation 3C C C C NAD NAD C 3C C C 3C C NAD Lactate NAD 3C C Acetaldehyde Ethanol (b) Ethanol fermentation

entose phosphate 3a Transition step 3b xidizes glucose to pyruvate x group and releases (s twice) to proton motive force NAD NAD 3 C C C 3 C C C Lactate (a) Lactic acid fermentation NAD NAD 3 C C C 3

15 entose phosphate 3a Transition step 3b xidizes glucose to pyruvate x group and releases (s twice) to proton motive force NAD NAD 3 C C C 3 C C C Lactate (a) Lactic acid fermentation NAD NAD 3 C C C 3 C C 3 C C Acetaldehyde Ethanol (b) Ethanol fermentation 6.. end products varied; helpful in identification, commercially useful Ethanol Butyric acid ropionic acid,3-butanediol Mixed acids Lactic acid Ethanol Butyric acid ropionic acid Mixed acids,3-butanediol Microorganisms Streptococcus Lactobacillus Saccharomyces Clostridium ropionibacterium E. coli Enterobacter End products Lactic acid Ethanol Butyric acid Butanol Acetone Isopropanol ropionic acid Acetic acid Acetic acid Lactic acid Succinic acid Ethanol (yogurt, dairy, pickle), b (wine, beer), (acetone): Brian Moeskau/McGraw- ill; (cheese): hotodisc/mcgraw-ill; (Voges-roskauer Test), (Methyl-Red Test): The McGraw-ill Companies, Inc./Auburn University hotographic Services 6.6. Catabolism of rganic Compounds ther than Glucose Microbes can use variety of compounds Excrete hydrolytic enzymes; transport subunits into cell Degrade further to appropriate precursor metabolites olysaccharides and disaccharides Amylases digest starch; cellulases digest cellulose Disaccharides hydrolyzed by specific disaccharidases Lipids Fats hydrolyzed by lipases; glycerol converted to dihydroxyacetone phosphate, enters glycolysis Fatty acids degraded by β-oxidation to enter roteins ydrolyzed by proteases; amino group deaminated Carbon skeletons converted into precursor molecules

lipases proteases amylases cellulases disaccharidases glycerol Amino acids deamination

glycolysis ß-oxidation removes -carbon units. x 6.7.

molecules (sulfate, nitrate) serving as terminal electron acceptors Important example of

Anabolic athways Synthesizing Subunits from recursor Molecules rokaryotes remarkably similar

product must be supplied Fastidious bacteria require many growth factors Lipid synthesis

16 Fig. 6. LYSACCARIDES DISACCARIDES LIIDS (fats) RTEINS Starch Lactose Maltose Cellulose Sucrose lipases proteases amylases cellulases disaccharidases glycerol Amino acids deamination monosaccharides fatty acids (simple sugars) N 3 entose phosphate Applies to both branches In glycolysis ß-oxidation removes -carbon units. x 6.7. Chemolithotrophs rokaryotes unique in ability to use reduced inorganic compounds as sources of energy E.g., hydrogen sulfide ( S), ammonia (N 3 ) roduced by anaerobic respiration from inorganic molecules (sulfate, nitrate) serving as terminal electron acceptors Important example of nutrient cycling Four general groups 6.0. Anabolic athways Synthesizing Subunits from recursor Molecules rokaryotes remarkably similar in biosynthesis Synthesize subunits using central metabolic s If enzymes lacking, end product must be supplied Fastidious bacteria require many growth factors Lipid synthesis requires fatty acids, glycerol Fatty acids: -carbon units added to acetyl group from acetyl- Glycerol: dihydroxyacetone phosphate from glycolysis Nucleotide synthesis DNA, RNA initially synthesized as ribonucleotides urines: atoms added to ribose -phosphate to form ring yrimidines: ring made, then attached to ribose -phosphate Can be converted to other nucleobases of same type 6

Title: Microbial Metabolism. Speaker: Amit Dhingra Created by: (remove if same as speaker) online.wsu.edu

Title: Microbial Metabolism. Speaker: Amit Dhingra Created by: (remove if same as speaker) online.wsu.edu Title: Microbial Metabolism Title: Instructor: What is Consetta the title Helmick of this lecture? Speaker: Amit Dhingra Created by: (remove if same as speaker) online.wsu.edu Microbial Metabolism Microbial