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METABOLISM part A BACKGROUND

1. METABOLISM part A BACKGROUND. A. METABOLISM refers to all the chemical reactions which occur in life. These reactions are: 1. CATABOLIC - degradative reactions which:

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METABOLISM part A BACKGROUND

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  1. 1 METABOLISM part A BACKGROUND

  2. A. METABOLISM refers to all the chemical reactions which occur in life. These reactions are: 1. CATABOLIC - degradative reactions which: a. Convert food into twelve, key, low molecular weight intermediates (which can be converted in anabolic reactions into low molecular weight precursors of proteins, polysaccharides, lipids, and polynucleotides). b. Oxidize food, generating NADH + H+, which transfers electrons to the electron transport chain, with resulting ATP generation. c. Convert food into low molecular weight compounds which can serve to generate ATP by substrate level phosphorylation. 2. ANABOLIC - biosynthetic reactions which generate amino acids, fatty acids, monosaccharides, and mononucleotides and polymerize them into proteins, lipids, polysaccharides, and polynucleotides. B. PATHWAYS. Sets of reactions in which the product of one reaction serves as the substrate for the next reaction are called PATHWAYS. For example, compound A might be converted into compound E by four, successive reactions. C. ENZYMESare necessary to catalyze most biochemical reactions so that the reaction reaches equilibrium within a time scale useful for life. Enzymes usually are proteins; they usually catalyze one, specific reaction; usually every reaction requires catalysis by one specific enzyme. Although a given reaction, such as A + B = C + D, might come to equilibrium, in the test tube, with only slightly more C + D formed than the amount of A + B remaining, in living organisms, this reaction usually goes to completion. This is possible because C or D is removed by, for example, conversion to some other product -if C or D is not removed, the reaction comes to equilibrium. D.GLYCOLYSISis the oxidation/conversion of glucose to pyruvate (also called the Embden-Meyerhoff Pathway): NAD+ is converted into NADH+ H+ ATP is generated by substrate level phosphorylation E. RESPIRATION converts pyruvate to CO2 (Kreb’s cycle, citric acid cycle, Tricarboxylic acid cycle) and in the process: NADH + H+ are formed, FAD is converted into FADH2, GDP is converted into GTP. The reducing compound pool reduces the electron transport chain, generating a pH gradient across the Cytoplasmic membrane, the resulting proton motive force is used by ATP synthase to convert ADP + Pi into ATP (Oxidative Phosphorylation) A terminal electron acceptor is required to accept electrons from the electron transport chain. In aerobic respiration O2 accepts electrons and is converted to H2O. F. FERMENTATION is a process by which glucose oxidation (glycolysis) can+ be sustained in the absence of a terminal electron acceptor. That is the oxidation/reduction reactions are internally balanced. Pyruvate is reduced to lactate or ethanol by NADH H+, regenerating NAD+. G. Microbes have evolved to occupy many niches. Four modes of respiration include aerobic, anaerobic, chemolithotrophic, and photosynthetic. 2

  3. OVERVIEW - ANABOLISM, CATABOLISM ENERGY Free Energy Change, Exergonic, Endergonic ENZYMESEnzymes - Catalysts, Lower Activation Energy Bind substrates Strain specific bonds in substrates; help form bonds COENZMES Low molecular weight compounds, Function with enzymes Apoenzymeplus coenzyme = holoenzyme OXIDATION/REDUCTION REACTIONS - REDOX Oxidation - loss of electron - electron donor Reduction - gain of electron - electron acceptor Coupled Oxidation/Reduction reactions ELECTRON CARRIERS Nicotinamide adenine dinucleotide [NAD] - coenzyme involved in oxidation/reduction NAD+ plus 2e- plus 2H+ < > NADH plus H+ Oxidized Reduced [Reducing Power] HIGH AND LOW ENERGY BONDS Esters - low energy glucose-6-phosphate Anhydrides -high energy ATP, adenosine triphosphate - Universal source of high energy 1,3-diphospho glyceric acid - (1,3-diphospho glycerate) 3

  4. CARBON/ENERGY GLUCOSE BYPRODUCTS H2O; CO2 4 G-6-PO4 ATP LOW MOLECULAR WEIGHT BUILDING BLOCKS MACROMOLECULES AMINO ACIDS FATTY ACIDS MONOSACCHARIDES MONONUCLEOTIDES PROTEINS-ENZYMES; FLAGELLIN; RIBOSOMES ETC. PHOSPHOLIPIDS POLYSACCHARIDE [PEPTIDOGLYCAN] DNA/RNA [t,r,m] CHEMICAL SYNTHESIS; FOOD TRANSPORT [MOTILITY]

  5. A + B C + D LARGE -DG SMALL -DG 5 G - FREE ENERGY - ENERGY RELEASED IN FORM ABLE TO DO WORK DG°' CHANGE IN FREE ENERGY UNDER STANDARD CONDITIONS AND pH NEGATIVE DG - EXERGONIC = FREE ENERGY RELEASED = REACTION OCCURS SPONTANEOUSLY = EQUILIBRIUM FAVORS RIGHT

  6. 1/2O2 + H2 H2O DG = -237 kj/mole [4.2 KILOJOULES = 1 KILOCALORIE] POSITIVE DG - ENDERGONIC = FREE ENERGY REQUIRED = REACTION WILL NOT OCCUR SPONTANEOUSLY = EQUILIBRIUM FAVORS LEFT 6 DG VALUE - DOES NOT PREDICT HOW LONG WILL BE REQUIRED TO REACH EQUILIBRIUM

  7. ENZYMES 108 - 1020 x RATE • BIND SUBSTRATE(S) • HOLD SUBSTRATE IN ENZYME CATALYTIC SITE-STRAIN BONDS OR HELP FORM BONDS • REDUCE ACTIVATION ENERGY 7 NO ENZYME NO ENZYME DG PLUS ENZYME G + ENZYME ACTIVATION ENERGY SUBSTRATE PRODUCT (Not a time scale) ENZYME DOES NOT CHANGE: • FREE ENERGY OF SUBSTRATE/PRODUCT • EQUILIBRIUM; DG IS THE SAME +/- ENZYME

  8. 8 ENZYME - TURN OVER NUMBER - NUMBER OF MOLECULES OF REACTANT (SUBSTRATE) CONVERTED TO PRODUCT PER MOLECULE OF ENZYME PER UNIT OF TIME (e.g., SECOND) TYPICAL: 2,000 / SECOND = 120,000 / MINUTE

  9. ALDOLASE 359 a.a.; MW = 39,147 9 APPRECIATE ! ENZYME - ALDOLASE + ENZYME - SUBSTRATE COMPLEX FRUCTOSE-1,6- BISPHOSPHATE DI-HYDROXY ACETONE PHOSPHATE + + GLYCERALDEHYDE -3-PHOSPHATE

  10. APPRECIATE ! 10 ENZYME - ALDOLASE + ENZYME - SUBSTRATE COMPLEX ALDOLASE SPLITS HERE BREAKS TWO BONDS FORMS TWO MOLECULES FRUCTOSE-1,6- BISPHOSPHATE DI-HYDROXY ACETONE PHOSPHATE ALDOLASE 359 a.a.; MW = 39,147 + + GLYCERALDEHYDE -3-PHOSPHATE

  11. H2- ELECTRON DONOR H2 2e- + 2H+ 1/2O2- ELECTRON ACCEPTOR 1/2O2+2e- O- - H2 + 1/2O2 H2O NET CHANGE : 2H+ + O- -H2O 1/2O2- OXIDIZING AGENT - ACCEPTS ELECTRONS - BECOMES REDUCED H2- REDUCING AGENT - DONATES ELECTRONS - BECOMES OXIDIZED OXIDATION - LOSS OF ELECTRON REDUCTION - GAIN OF ELECTRON 11 REDUCING AGENT OXIDIZING AGENT SUMMARY:

  12. 12 • COENZYMES – • LOW MOLECULAR WEIGHT, NON-PROTEIN • MOLECULES WHICH PARTICIPATE WITH ENZYMES • IN METABOLIC REACTIONS. • ESSENTIAL FOR THOSE REACTIONS. • LESS SPECIFICITY THAN ENZYMES. • RECYCLE.

  13. NAD + 2e + 2H NADH + H IS REDUCED OXIDIZED STATE; OXIDIZES FOOD PICKS UP 2e- and 2H+ FROM FOOD; REDUCING AGENT REDUCED STATE 13 NICOTINAMIDE ADENINE DINUCLEOTIDE NADH + H NAD + 2e + 2H IS OXIDIZED OXIDIZED STATE TRANSFERS e- TO OTHER E.T.C. TO GENERATE ATP REDUCED STATE; REDUCES ELECTRON TRANSPORT CHAIN

  14. NAD+ NADH + H+ 14 +H +2e +2H REDUCED OXIDIZED APPRECIATE ! NICOTINAMIDE ADENINE DINUCLEOTIDE

  15. 15 • HIGH AND LOW ENERGY BONDS – • FOOD OXIDATION – MAIN EVENT - ENERGIZES THE CYTOPLASMIC • MEMBRANE; • PERMITS FORMATION OF HIGH ENERGY BONDS - ANHYDRIDES • HYDROLYSIS OF HIGH ENERGY BONDS • RELEASES LOTS OF ENERGY WHICH CAN BE USED TO DRIVE WORK: • ANABOLISM (CHEMICAL SYNTHESIS) • FOOD TRANSPORT

  16. 16 b-D-GLUCOSE-6-PHOSPHATE ESTER LOW ENERGY ADENOSINE TRIPHOSPHATE ANHYDRIDE HIGH ENERGY 1,3 DIPHOSPHO GLYCERIC ACID ANHYDRIDE HIGH ENERGY

  17. METABOLISM B - ENERGY FROM FOOD OXIDATION GLYCOLYSIS - glucose conversion to pyruvate [Embden-Meyerhoff Pathway] NADH plus H+ generated Substrate level phosphorylation RESPIRATION - pyruvate conversion to carbon dioxide plus water [in aerobic respiration] Tricarboxylic acid cycle generates NADH plus H+, FADH2, GTP Flow of electrons to Electron Transport Chain ELECTRON TRANSPORT CHAIN (SYSTEM) ENERGIZED MEMBRANE – CHEMIOSMOSIS – PROTON MOTIVE FORCE pH Gradient; H+ and OH- ATP Synthase - Oxidative Phosphorylation Terminal Electron Acceptor (Oxygen in aerobic respiration) REDUCTION; DELTA Eo’; DELTA G FERMENTATION - Pyruvate> Lactic Acid (lactate) Pyruvate> Ethanol plus CO2 GLYCOLYSIS PLUS FERMENTATION: Allow glucose conversion to lactate or ethanol with internally balanced redox reactions. Do not require terminal electron acceptor. Result in only partial oxidation of glucose carbons. Yield only small amount of potential energy of glucose. Allow ATP generation by substrate level phosphorylation. Permit growth in absence of oxygen. 1

  18. GLYCOLYSIS NAD+ NADH + H+ ADP ATP SUBSTRATE LEVEL PHOSPHORYLATION CITRIC ACID CYCLE NAD+ NADH + H+ FAD FADH2 GDP GTP ELECTRON TRANSPORT CHAIN NADH + H+ NAD+ ADP ATP [OXIDATIVE PHOSPHORYLATION] 6O2 6H2O TERMINAL ELECTRON ACCEPTOR GLUCOSE 2 2 PYRUVATES 6CO2 RESPIRATION (AEROBIC)

  19. GLUCOSE NAD+ 2 LACTATES OR 2 ETHANOLS +2 CO2 NADH + H+ NAD+ NADH + H+ NADH + H+ PYRUVATE FERMENTATION 3 NOTE: NAD RECYCLES

  20. WAYS TO GENERATE ATP 4 SUBSTRATE LEVEL PHOSPHORYLATION ATP (PLUS LOW MOLECULAR WEIGHT COMPOUND) LOW MOLECULAR WEIGHT - PO4 CONTAINING COMPOUND + ADP OXIDATIVE PHOSPHORYLATION • NADH + H+ TRANSFER ELECTRONS TO ELECTRON TRANSPORT CHAIN • ELECTRON FLOW IS COUPLED TO ATP SYNTHESIS ADP + Pi ATP • REQUIRES TERMINAL ELECTRON ACCEPTOR e.g., O2

  21. SUBSTRATE LEVEL PHOSPHORYLATION 5 APPRECIATE !!! PHOSPHO - ENOL PYRUVATE ENZYME - PYRUVATE KINASE PYRUVATE

  22. CH2 O PO3H2 HC O C O HC OH CH2OH CH2 O PO3H2 GLYCOLYSIS GLUCOSE ATP 6 ADP GLUCOSE-6-PO4 FRUCTOSE-6-PO4 ATP ADP FRUCTOSE-1,6-BISPHOSPHATE 4 5 DIHYDROXY ACETONE PHOSPHATE GLYCERALDEHYDE -3-PHOSPHATE

  23. H C O H C OH H C O PO3H2 H O O O Pi C O P OH OH H C OH H C O PO3H2 C OH H H C OH H C O PO3H2 H GLYCOLYSIS GLYCERALDEHYDE -3-PHOSPHATE 7 NAD+ e- NADH + H+ REDUCING POWER 6 SUBSTRATE LEVEL PHOSPHORYLATION 1,3 BISPHOSPHO-GLYCERATE ADP ATP 7 3-PHOSPHO-GLYCERATE

  24. O O C OH OH H C O PO3H2 C O P OH H C OH H C O H ADP ATP GLYCOLYSIS 8 8 9 C OH OH HIGHER ENERGY THAN ANHYDRIDE C O P 2-PHOSPHO GLYCERATE OH O H C 10 PHOSPHOENOL PYRUVATE O PYRUVATE C OH SUBSTRATE LEVEL PHOSPHORY-LATION C O CH3

  25. AEROBIC RESPIRATION 9 PYRUVATE NAD+ CoA NADH + H+ CO2 CoA Q OXALO- ACETATE CITRIC ACID (C6)

  26. 10

  27. ENERGY YIELD FROM PYRUVATE OXIDATION 11 1 PYRUVATE 3 CO2 1 NAD+ 4 NADH & H+ 12 ATP 1 FAD 1 FADH2 2 ATP 1 GDP + 1 Pi 1 GTP1 ATP 15 ATP EQUIVALENT TO APPRECIATE !!!

  28. 12 ELECTRON TRANSPORT CHAIN (SYSTEM) 1. ACCEPTS e- FROM DONORS NADH & FADH2 2. USES ENERGY RELEASED IN OXIDATION/ REDUCTION REACTIONS TO ENERGIZE MEMBRANE AND SYNTHESIZE ATP RE-DOX ENZYMES • NADH DEHYDROGENASES • FLAVO PROTEINS • IRON-SULFUR PROTEINS • QUINONES (NON - PROTEINS) • CYTOCHROMES

  29. REDUCTION POTENTIAL E'O 13 ENERGY RICH -0.4 SUBSTRATES, AS GLYCERALDEHYDE-3-PHOSPHATE -0.3 NADH, NADH DEHYDROGENASE -0.2 FLAVOPROTEIN -0.1 IRON SULFUR PROTEINS QUINONES 0 CYTOCHROMES +0.4 NO3- NO2- +0.8 OXYGEN O2 ENERGY POOR

  30. CHEMIOSMOSIS - GENERATES PMF (PROTON MOTIVE FORCE) 14 NDH = NADH DEHYDROGENASE OUTSIDE INSIDE pH GRADIENT; ENERGIZES CM; PMF GENERATED

  31. ENERGIZED MEMBRANE - SYNTHESIZES ATP [ROTATES FLAGELLA] 15 OUTSIDE THE MEMBRANE H+ H+ H+ H+ H+ H+ H+ H+ OH- OH- OH- OH- ADP + Pi ATP ATP SYNTHASE INSIDE THE MEMBRANE

  32. ATP SYNTHASE – TINIEST BIOMOLE- CULAR MOTOR IN WHOLE UNIVERSE NANO METERS 9-12 SUBUNITS ATOMIC FORCE MICROSCOPY CYTOPLASMIC MEMBRANE SHAFT CYTOPLASM

  33. ROTOR – INCLUDES SHAFT STATOR – THE MOTOR PROTON GRADIENT ALLOWS MOTOR TO ROTATE ROTOR WITH SHAFT ROTATING SHAFT CHANGES CONFORMATION OF F1 SUBUNITS CHANGES ALLOW: ADP + Pi TO ENTER; BIND BETA CATALYTIC SITE; ATP TO BE SYNTHESIZED; ATP TO BE RELEASED H+ TRANSPORTED INSIDE PREVENT F1 SUBUNITS FROM ROTATING

  34. ATP SYNTHASE 16 ADP + Pi + H+ ATP + H2O ANHYDRIDE

  35. Eo - REDUCTION POTENTIAL - TENDENCY TO DONATE ELECTRONS; i.e., TO OXIDIZE SOMETHING UNDER STANDARD CONDITIONS (I MOLAR) MEASURED IN VOLTS MUST BE MEASURED RELATIVE TO STANDARD STANDARD IS HYDROGEN: H+ + e- > 1/2H2Eo = 0 VOLTS (BY CONVENTION) CONSIDER: MATERIAL X + e- > X- WHAT IS REDUCTION POTENTIAL? CHAMBER A CHAMBER B X + e- > X- BRIDGE H+ + e- > 1/2H2 ELECTRONS FLOW TO H+, Eo IS NEGATIVE X HAS LOWER AFFINITY FOR e- THAN H+ ELECTRONS FLOW TO X, Eo IS POSITIVE X HAS HIGHER AFFINITY FOR e- THAN H+ VOLTMETER MEASURES VOLTAGE

  36. Eo’ BIOLOGY pH = 7.0 H+ + e- > 1/2H2 -0.42 NAD+ + 2e- + 2H+ > NADH + H+ -0.32 STRONG REDUCER 1/2O2 + 2e- + 2H+ > H20 +0.82 STRONG OXIDIZER

  37. DELTA G OF REACTION DETERMINED BY DELTA Eo’ OXIDANT + e- > REDUCTANT (a) 1/2O2 + 2e- + 2H+ > H20 +0.82 (b) NAD+ + 2e- + 2H+ > NADH + H+ -0.32 DELTA Eo’ = (a) - (b) = +0.82 - (-0.32) = 1.14 DELTA G = - n x F x DELTA E n = NUMBER OF e- [2 IN THIS EXAMPLE] F = FARADAY CONSTANT IN CALORIES 23.062 Kcal/volt.mol DELTA G IS NEGATIVE AND = - 53 Kcal/MOLE THIS PATHWAY IS EXERGONIC SUPPOSE FINAL ELECTRON ACCEPTOR IS NITRATE?

  38. YIELD - GLYCOLYSIS + RESPIRATION 17 GLYCOLYSIS 1 GLUCOSE 2 PYRUVATES INPUT:2ATPYIELD SUBSTRATE LEVEL PHOSPHORYLATION 4 ATP 2 NADH ETC 6 ATP AEROBIC RESPIRATION 2 PYRUVATES + 6O2 6CO2 + 6H2O 8 NADH 24 ATP 2 FADH2 4 ATP 2 GTP [EQUIVALENT] 2 ATP GROSS 40 ATP NET 38 ATP APPRECIATE !!

  39. REDUCING POWER (FROM FOOD OXIDATION) LIGHT ENERGY (PHOTOSYNTHESIS) PROTON MOTIVE FORCE (ENERGIZED MEMBRANE) ADP + Pi ATP 18 ACTIVE TRANSPORT (FOOD) FLAGELLA ROTATION

  40. O C OH H C OH O CH3 C OH C O CH3 LACTIC ACID FERMENTATION 19 PYRUVATE NADH + H+ REDUCED NAD+ e- NET: GLUCOSE 2 LACTATE 2 ADP + 2 Pi 2 ATP LACTATE

  41. NET: GLUCOSE 2CO2 + 2 ETHANOL 2 ADP + 2 Pi 2 ATP PYRUVATE H ACETALDEHYDE H C OH NADH + H+ e- REDUCED TO CH3 O H C O NAD+ C OH CH3 C O ETHANOL CH3 ETHANOL FERMENTATION 20 + CO2

  42. METABOLISM - PART C MODES OF NUTRITION AND RESPIRATION - BIODIVERSITY Aerobic respiration, Anaerobic respiration Chemolithotrophic metabolism Phototrophic metabolism NITROGEN FIXATION CATABOLISM – ANABOLISM INTERACTIONS ANABOLISM - BIOSYNTHESIS Low Molecular Weight Building Blocks (Precursors of Macromolecules) Twelve key, central metabolites Pentoses Amino Acids - Alanine (from Pyruvate) Tryptophan (from Phosphoenolpyruvate and erythrose-4-phosphate) 1

  43. NUTRITION AND RESPIRATION MODES 2 FOOD ELECTRON ACCEPTOR O2 H2 O NO3- NO2- NO2- N2 SO4-- SO3-- SO3-- H2S O2 H2 O NO TERMINAL e- ACCEPTOR e- FLOW IS CYCLIC MODE AEROBIC ANAEROBIC CHEMO-LITHOTROPHIC PHOTO-TROPHIC CARBON ORGANIC COMPOUNDS ANABOLISM ORGANIC COMPOUNDS CO2 ALL ORGANIC COMPOUNDS CO2 ALL ORGANIC COMPOUNDS ENERGY ORGANIC COMPOUNDS OXIDATION TO CO2 ORGANIC COMPOUNDS H2 H2S NH3 LIGHT PROVIDES ENERGY

  44. PHOTOTROPHIC NUTRITION AND RESPIRATION [PLANTS AND CYANOBACTERIA - OXYGENIC, EVOLVE OXYGEN FROM H2O] ANOXYGENIC PHOTOSYNTHETIC BACTERIA - DO NOT GENERATE O2 - HAVE BACTERIOCHLOROPHYLL 3 EXCITED B Ch P PROTON DONORS [H2S; SUCCINATE] LIGHT PROTON GRADIENT- PROTON MOTIVE FORCE ATP SYNTHESIS BACTERIO-CHLOROPHYLL [B Ch P]

  45. ORGANIC NITROGEN N2 ATMOSPHERIC NH3 AMMONIA NITROGEN FIXATION 4 RHIZOBIUM - LEGUMES AZOTOBACTER - FREE LIVING

  46. ORGANIC COMPOUNDS (GLUCOSE) 5 BY-PRODUCTS (WASTE) CATABOLISM ATP SIMPLE COMPOUNDS [12 KEY, CENTRAL METABOLITES] ANABOLISM LOW MOLECULAR WEIGHT PRECURSORS OF MACROMOLECULES ANABOLISM CELLULAR CONSTITUENTS

  47. ORGANIC COMPOUNDS 6 HETEROTROPHS GLUCOSE-6-PHOSPHATE FRUCTOSE-6-PHOSPHATE RIBOSE-5-PHOSPHATE ERYTHROSE-4-PHOSPHATE DIHYDROXY-ACETONE PHOSPHATE 3-PHOSPHOGLYCERATE PHOSPHOENOL PYRUVATE PYRUVATE ACETYL-CoA aKETOGLUTARATE SUCCINYL-CoA OXALOACETATE MONO AND DISACCHARIDES AMINO ACIDS POLY- SACCHARIDES PROTEIN FATTY ACIDS MONO-NUCLEOTIDES LIPIDS RNA, DNA VITAMINS LIST IS NOT ASSIGNED AUTOTROPHS CO2

  48. PENTOSE BIOSYNTHESIS 7 GLUCOSE-6-PHOSPHATE RIBOSE-5-P CO2 GLUCOSE-6-P RIBULOSE-5-P RING STRUCTURE - RIBOSE-5-P

  49. NH4 AMMONIUM ALANINE SYNTHESIS 8 TRANSAMINASE PYRUVATE L-ALANINE L-GLUTAMATE a-KETO-GLUTARATE

  50. TRYPTOPHAN (AN AMINO ACID) SYNTHESIS A. CHORISMATE FROM "KEY METABOLITES" 9 PHOSPHOENOL PYRUVATE ERYTHROSE- 4-PO4 + 6 REACTIONS AND 6 ENZYMES APPRECIATE ! CHORISMIC ACID (CHORISMATE)

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