Bioenergetics-Quest for energy

Transcription

1 Bioenergetics-Quest for energy All cellular organisms need energy to grow and survive. The energy derived from catabolism of growth substrates is used to fuel anabolism (biosynthesis) and to fuel other cellular functions such as transport and motility. Two catabolic modes Phototrophy- energy from light Chemotrophy - energy from chemical reactions Chemotrophs catalyze thermodynamically favorable (exergonic) reactions and conserve part of the energy released, either as high energy ester bonds (such as ATP) or as an ion-motive force (usually protons). Bacteria and Archaea are incredibly versatile at conserving energy If there s a buck to be made some bug will do it...r. Wolfe (penny?)

2 Worth looking at Gottschalk, in library Great chapter on fermentations White, Drummond, and Fuqua 2012 Not in library - $ at Amazon Ed. much cheaper Lots of info not very user friendly Thauer, R. K., K. Jungermann, and K. Decker Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev. 41: Out of date, with nothing on chemiosmosis, but still a trove of information on fundamentals of anaerobic metabolism and killer tables at end

3 Free energy of reactions G ' = Gf products - Gf reactants glucose + 6O 2 6HCO H (0) 6(-586.9) + 6(-39.9) G ' = ( ) = kj/rxn (-237 kj/e - pair) glucose 2lactate - + 2H (-517.8) + 2 (-39.9) = kj/mol 4H 2 + HCO H + CH 4 + 3H 2 O 4(0) + (-586.9) +(-39.9) (-50.8) + 3(-237.2) = kj/rxn (-33.2 kj/e - pair - but actually less) Std conditions = 25 o C, 1 M solutes, 1 atm gases, aqueous (H M) For G o, H + is constant at 10-7 M (ph 7)

4 G f values in Manual Appendix 3 Most from Thauer 1977; Bact. Rev (MMBR) 41:

5 Balancing equations using H2

6 Example: Aerobic CH 4 oxidation Hydrogenation Eqn 27- is backwards Turn it around: Methane + 3H 2 O HCO H 2 + H kj/rxn Hydrogenation Eqn 43 need to balance hydrogens CH 4 + 3H 2 O HCO H 2 + H + 2O 2 +4H 2 4H 2 O CH 4 + 2O 2 HCO H + + H 2 O kj/rxn kj/rxn kj/rxn

7 Concentration affects the free energy of reactions... For a reaction: aa + bb cc + dd ΔG'= ΔG o '+RT ln (C)c (D) d (A) a (B) b At 25 o C: ΔG'= ΔG o '+5.7log (C)c (D) d (A) a (B) b Free energy form of the Nernst Equation...particularly important for anaerobes

8 Effect of H 2 partial pressure on methanogenesis H 2 typically atm in methanogenic habitats

9 Effect of H 2 partial pressure on G of 50 methanogenesis G' (kj/rxn) 0-50 slope = 22.8 (5.7 x 4) kj per 10fold change H 2 Partial Pressure (atm)

10 The electron tower

11 Substrate-level phosphorylation - ATP G o synthesis = kj/mol from ADP kj/mol under physiological conditions Five ATPs are hydrolyzed to ADP to form each amide bond in a protein

12 R. Thauer MD 2010

13 Substrate-level phosphorylation: highenergy phosphoester compounds Name 1,3-Diphosphoglycerate Phosphoenol pyruvate Acetyl phosphate Carbamyl phosphate Pyrophosphate Structure 2- O 3 P H H O 2- O C C C O PO 3 H OH OPO 3 2- G ' of hydrolysis (kj/mol) -52 H 2 C C COO -51 O H 3 C C O 2- PO 3-45 O H 2 N C O 2- PO O 3 P O PO 3-24

14 Substrate-level phosphorylation: acyl coenzyme A thioesters No resonance CH 3 -C O O Resonance

15 Acyl coenzyme A thioesters can be cashed in as ATP Fatty acid or succinate as fermentation product Acyl CoA was probably cashed in as ATP

16 Fermentation Latin: "fermentum" - brewing beverages - connotation of bubbling Alchemy: a process in which organic chemicals were transformed Still used by industrial microbiologists, e.g. the "penicillin fermentation Early 20 th century: metabolism of organics in the absence of oxygen Brock (13 th ): Anaerobic catabolism of an organic compound in which the compound serves both as electron donor and an electron acceptor and in which ATP is usually produced via substrate-level phosphorylation (SLP)

17 EMP pathway -ATP -ATP Aldehyde high energy Now easier to cleave +2ATP +2NADH +2ATP

18 Fermentation Another glycolysis pathway often used by microbes is the Entner Douderoff (ED) pathway, which only conserves 1 ATP/glucose There are many variations on these pathways especially in Archaea Selig et al. Arch Microbiol. 167:217 (1997)

19 Glycolysis diversity

20 Fermentation Net result of EMP is that glucose is converted to pyruvate with the production of NADH, which needs to be re-oxidized In aerobes and some anaerobic respirers, the electrons can go down the electron transport chain to the electron acceptor. Fermentative organisms don't have that option Must dispose of electrons from glycolysis Show three (and a half) solutions Glucose 2 ADP + 2P i 2 NAD + 2 ATP 2 NADH + 2 H + 2 Pyruvic acid

21 The simplest solution Dump electrons from NADH directly on pyruvic acid Lactic acid is produced by hypoxic animal tissues and tumor cells. Numerous microorganisms produce lactic acid Most prominent are the "Lactic Acid Bacteria in the Firmicutes Pyruvic acid Lactic acid O H 3 C C Lactate Dehydrogenase OH H 3 C C C O H OH C O OH NADH + H + NAD +

22 The alcoholic fermentation: the second simplest solution O 2 H 3 C C COOH Pyruvic acid Pyruvate decarboxylase (PDC) 2 CO 2 O 2 H 3 C C H Acetaldehyde Alcohol dehydrogenase (ADH) 2 NADH + H + 2 NAD + Pathway in yeast 2 OH H 3 C C H H Ethanol Glucose --> 2 Ethanol + 2CO 2 Also in Zymomonas mobilis, an Alphaproteobacterium Uses Entner Douderoff pathway and only gets 1 ATP/Glucose

23 Pyruvate-ferredoxin oxidoreductase: the clostridial solution S light yellow Fe dark yellow PFO and ferredoxin (Fd) are iron-sulfur (FeS) proteins Pyruvate is a powerful reductant (pyruvate/acetate couple = -680 mv) PFO can reduce Fd Model of Fd showing two 4Fe4S groups E o of Fd ~ -400 mv Close to H 2 (-414 mv) Clostridia are often vigorous H 2 producers

24 Hydrogenases Carry out the seemingly simple reaction: H 2 2e + 2H + Ribbon model of [FeFe] hydrogenase showing FeS centers leading to active site H 2 ase active sites From: Science 321:572, 2008

25 The phosphoroclastic reaction Thioclastic? HS-CoA Pyruvate:ferredoxin oxidoreductase CO 2 O H 3 C C COO - Fd ox H 2 Fd red 2H + Pyruvate Hydrogenase Phosphotransacetylase Acetate kinase O H 3 C C S-CoA HPO 4 2- HS-CoA O 2- H 3 C C OPO 3 ADP Acetyl-CoA Acetyl-phosphate O H 3 C C O - + ATP Acetate Pyruvate + ADP + Pi <----> Acetate + H 2 + CO 2 + ATP

26 Fermentation of glucose units by C. thermocellum 2 ATP 2 2 HS-CoA 2 CO 2 O H 3 C C COO - PFO Glucose Fd ox 2NADH 2H 2 4H + Fd red Glucose + 3ADP + 3Pi --> Ethanol + Acetate + 2H 2 + 2CO 2 + 3ATP O H 3 C C S-CoA PTA O 2- H 3 C C OPO 3 AK O H 3 C C O - HPO 4 2- HS-CoA HS-CoA ADP + ATP O H 3 C C S-CoA O H 3 C C H Aldehyde Dehydrogenase Alcohol Dehydrogenase OH H 3 C C H H

27 The homoacetate fermentation by Moorella thermoacetica Fermentation? Glucose ---> 3CH 3 COOH Respiration? Drake and Daniel, Res. Microbiol. 155:869 (2004) 4 ATP +

28 Butyrate fermentation in clostridia Also butanol and acetone Some Cl. ferment AAs Products include: putrescine, cadaverine, branched chain FAs, H 2 S, methyl mercaptan From Gottschalk

29 The E. coli solution: pyruvate-formate lyase HS-CoA O H 3 C C S-CoA O H 3 C C COO - H PFL Glycine radical at active site O 2 labile + HCOOH Formate-H 2 lyase Membrane bound Resembles Complex I H + H 2 + CO 2

30 The E. coli mixed acid fermentation - a little bit of everything glucose (100) = 600 mol C TCA cycle fumarate Fumarate (H) reductase H + succinate (10.7) Acetaldehyde (H) ethanol (49.8) oxaloacetate (H) CO 2 Acetyl-CoA Pi CoA Acetyl-Pi ADP acetate (35.5) ATP (H) ADP ATP PEP ADP ATP pyruvate CoA formate CO 2 H 2 H + (88.0) (75.0) (2.4) lactate (79.5) Products = 531 mol C After Gottschalk, Bacterial Metabolism, 1985

31 Fermentations: summary O 2 is limiting in many environments and organisms need to dispose their electrons One solution is fermentation, using the organic substrate as the electron acceptor Some facultative and aerotolerant anaerobes use simple fermentations producing lactate or ethanol as products Most true anaerobes increase their energetic yield by making acyl-coa intermediates which can be cashed in as ATP These pathways usually involve disposing of electrons as H 2 in the phosphoroclastic reaction or PFL

32 A controversial proposal

33 Proton motive force B H + H + H + H + H + H + H + H H + H+ H + + H + H + H + H + H+ Pump H + H + H + H H + H + + H + H + H + - A + H + H + H + H + H + H + H+ H + H + H + H + H + H + H + H + H + H + H + H + H + H + Protons are pumped from compartment A to B. Two forces can drive them back into A 1) the concentration difference ( ph) 2) electrostatic attraction ( Ψ). The H + concentration gradient component of the force can be expressed in volts as: RT/nF ln (H + out )/(H+ in ) = log (H + out )/(H+ in ) = ph The electrostatic force can be expressed in volts as: RT/nF ln (ions out )/(ions in ) = log (ions out )/(ions in ) = Ψ The total proton motive force ( p) is: p = Ψ ph In an actively metabolizing cell, p is typically mv ( v)

34 Rotary ion-pumping ATPases Three types: F 1 F o (mitochondria, chloroplasts, and many bacteria), A 1 A o (mainly Archaea, some bacteria), V 1 V o (acidify euk vacuoles) F 1 in cytoplasm (matrix in mitos), F o in membrane F 1 three alpha/beta dimers, each binds an (ADP + P i /ATP) c subunits in F o are proton channels, and along with the stalk rotate (100X/sec) relative to the other subunits F 1 Cytoplasm/matrix F o Membrane Outside/periplasm

35 F 1 F o in action Higher H + outside (PMF)

36 Rotary ion-pumping ATPases ATPases are reversible may help you to think of as an ATPpowered proton pump (fan vs windmill) Each alpha/beta dimer in F1 converts 1 ADP + Pi to ATP per 360 o rotation so there are 3 ATP altogether The question of how many H + /ATP (2,3,4?) was only settled by a crystal structure of a yeast mitochondrion ATPase It had 10 c subunits so that per rotation there are 10/3 or 3.33 H + /ATP Science 286:1700 (1999)

37 ATPase predicted stoichiometries Organism c subunits cation/atp Beef heart mitochondria Yeast mitochondria Escherichia coli Acetobacterium woodii Propionigenium modestum Thermus thermophilus 12 4 Spinach chloroplast Various cyanobacteria Methanopyrus kandleri

38 A Frankenstein-like reconstitution experiment In 1974 E. Racker at Cornell teamed up with some German Halobacterium researchers to perform a multi-organism reconstruction experiment Liposomes (membrane vesicles) from soybean lecithin ATPase from beef-heart mitochondria Bacteriorhodopsin from Halobacterium ATPase and BR inserted "backward into liposomes When light was shined a proton circuit led to ATP production

39 E. coli expressing proteorhodopsin gene

40 Sodium circuit in Propionigenium modestum O H H O H H O H + + C C C C H C C C + CO 2 O H H O H H O Succinate Propionate

41 Proton motive force and rotary ATPases p values in respiring organisms are typically 0.15 to 0.2 v, The production of ATP using 3.3 H + is energetically feasible G= -nfe = 3.3 x 96.4 x ( ) = kj/3.3 H + ATPases with higher ratios don t need as high p for 15 subunits and 100 mv = 5 x 96.4 (0.10) = 48 kj/atp Like gears on a bike but organisms can t change ATPases are reversible In fermentative heterotroph making ATP from SLP (e.g. Streptococcus) Low p and high ATP levels Needs p for transport and motility ATPase hydrolyzes ATP to pump protons and provide a p (or Na + )

42 Electron transport-carriers Couple E ' (v) H+/H Ferredoxin (Clostridium) NAD(P)/NAD(P)H FMN/FMNH2 in NADH dehydrogenase FeS centers in NADH dehydrogenase Free FAD/FADH Free FMN/FMNH Menaquinone/menaquinol Ubiquinone/ubiquinol cytochrome b cytochrome c Rieske iron sulfur protein cytochrome a cytochrome a O2/H2O Properties of e- carriers at the end.

43 Moving protons via electron transport

44 Complex I NADH/quinone oxidoreductase A proton pump Hydrophilic arm Cytoplasm ~280 kda 9 FeS centers 1e 2e Quinone reduction site cytoplasm Q + 2e + 2H + QH 2 ~95 Å Hydrophobic arm Membrane ~270 kda Periplasm From Nature 465:441 (2010)

45 Electron transport in aerobically grown E. coli Complex I Out (periplasm) 4H + Complex IV quinol oxidase b and o 3 are hemes Cu B is a copper site 2H + 2H + 8H + Q QH 2 QH 2 QH 2 QH 2 Q b 2e Cu B /o 3 4H + 2e 2H + 2H O 2 2H + H 2 O NADH + H+ In (cytoplasm) NAD+ 2.4 ADP + P 8H i 2.4 ATP +

46 Electron transport pathways in E. coli NDH I Complex I Normal O 2 O + 2H + b Cu B /o 3 Normal O 2 NADH + H + H 2 O NAD + NADH + H + NAD + FMN FeS 9 FAD 4H + NDH II High O 2 Succinate DH Complex II Succinate Fumarate + 2H + FMN FeS E o 0 v b 2H + Q 2H + bo 3 quinol oxidase bd quinol oxidase O + 2H + FMN FeS bd b H 2 O Nitrate reductase NO 3 + 2H + b FeS Mo Low O 2 Anaerobic + NO 3 NO 2 + H 2 O Fumarate + 2H + Anaerobic Succinate

47 Electron transport in aerobic Paracoccus denitrificans, an Alphaproteobacterium related to mitochondria Electron bifurcation Rhodobacter capsulatus Rhodobacter sphaeroides Paracoccus denitrificans Wolbachia pipientis Rickettsia rickettsii Rickettsia prowazekii Rhodospirillum rubrum } PNS (has respiratory system resembling mitochondria) Zea mays - mitochondrion } Part of an Alphaproteobacteria tree Obligate intracellular parasites

48 Electron transport in the aerobic Archaeon Sulfolobus Other Archaea have Complex I It lacks complex I, uses a different quinone, and Complexes III and IV form a "supercomplex" without free cyt c, Still, the electron transport chain is similar to those in Bacteria Was the ancestor of the Bacteria and Archaea an aerobe? Phylogenetic trees for the large subunit of copper oxidases are inconclusive

49 A truncated electron transport chain in Acidithiobacillus ferrooxidans Fe 2+ Fe 3+ Outer Membrane Cyc2? Periplasm RC cytc 553 Inner Membrane cyt aa 3 2H + O + 2H + H 2 O The lithotroph A. ferrooxidans (formerly Thiobacillus) grows aerobically at ph 2 by oxidizing Fe 2+ to Fe 3+ Fe 2+ is not a strong enough reductant (+0.65 v at ph 2) to reduce NAD + or quinones The electrons feed into the terminal oxidase through two high potential carriers (rusticyanin and cytc 533 ) in the periplasm

50 Summary F 1 F o ATPase H + Membrane Cell gaining ATP from SLP using its ATPase to generate a p Glucose 2 Pyruvate - 6 CO 2 NADH I ATP Biosynthesis transport, etc. Q III ADP +Pi H + H + H+ c Cytoplasm O 2 H 2 O IV Transporter H + Periplasm Respiratory cell with ET chain resembling that in Paracoccus/ mitochondria Solute

51 Volta 2013

52 Electron transport Organisms transport electrons through a chain of carriers, going energetically downhill from an electron donor to the final electron acceptor Some carriers carry only electrons, while others carry an electron plus a proton, the equivalent of an H atom Organisms can take advantage of this to develop a p across the cell membrane Electron donor red Carrier 1 ox Carrier 2 red Electron acceptor ox Electron donor ox Carrier 1 red Carrier 2 ox Electron acceptor red

53 Nicotinamide adenine dinucleotide (NAD + ) Carries 1 H + + 2e - (hydride) E o ' = v (-320 mv)

54 Flavins - flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD) Carry one or two H (H + + e - ) E o ' = -0.2 v (-200 mv) Usually serve as prosthetic groups in proteins (flavoproteins) E o ' in proteins can be as low as -0.4 v (flavodoxins) or as high as 0 v

55 Quinones Have long hydrocarbon chain that anchors them to the membrane Carry one or two H (H + + e - ) Ubiquinone commonly found in aerobes, E o ' = v Menaquinone more common in anaerobes, E o ' = v Plastiquinone found in chloroplasts and cyanobacteria, E o ' = 0 v Calderiellaquinone is found in Sulfolobus, a sulfur-oxidizing member of the Crenarchaeota, E o ' = +0.1 v H 3 CO H 3 CO H 3 CO H 3 CO H + + e - H 3 CO H 3 CO O O OH. O OH OH Ubiquinol CH 3 Ubiquinone H + + e - H + + e - CH 3 Semi-quinone radical R H + + e - CH 3 R H 3 C H 3 C O O Plastiquinone O O Menaquinone H R 4-8 S CH 3 R O SCH 3 R' O "Calderiellaquinone"

56 H 2 C COO CH 2 H 2 C COO CH2 Cytochromes H 2 C COO CH 2 H 2 C COO CH2 H 2 C H 3 C HC N N Fe N N CH 3 HC Heme b CH 2 CH 3 CH 3 H 3 C CH 3 N N Fe H 3 C N N CH CH 3 cys-s CH 3 CH cys-s CH 3 Heme c showing covalent links to protein Proteins containing heme prosthetic groups Fe complexed in various tetrapyrrole rings Can contain hemes a, b, d, o, or c (covalently linked) Carry a single electron reducing Fe 3+ to Fe 2+ E o ' of different cytochromes can vary greatly from -0.3 to v

57 Iron-sulfur proteins Iron sulfur (FeS) proteins have FeS clusters as electron carrying prosthetic groups Each cluster can carry a single electron (reducing an Fe 3+ to Fe 2+ ) and FeS proteins can have more than one FeS group FeS clusters are usually liganded by sulfur groups of cysteines except in the "Rieske" proteins, in which two of the ligands are Ns in histidine The E o ' for FeS proteins is typically reducing (-0.53 to 0) except for the Rieske type with a potential of The importance of FeS proteins was not appreciated because their light/uv spectrum doesn't change significantly on reduction. Can use EPR to detect. FeS proteins are probably ancient, derived from naturally forming FeS precipitates 2Fe/2S cluster Rieske 2Fe/2S cluster 4Fe/4S cluster