13 Cell MetabolismChapter 3 Cell Metabolism - review Student Learning Outcomes:• Describe central role of enzymes as catalystsVast array of chemical reactionsMany enzymes are proteinsRole of NAD+/NADH coenzyme carrying electrons• Explain how metabolic energy comes from breaking/ rejoining covalent bonds: ATP is energy currency• Glycolysis, fermentation or aerobic respiration• What goes into reactions, what comes out• Briefly explain biosynthesis of cell constituents (requires energy)Fig 3.1 Energy diagrams for catalyzed and uncatalyzed reactions Enzymes: catalysts increase rate of chemical reactions in cells (lower activation energy)• not consumed in reaction• not alter chemical equilibrium between reactants and productsConversion of substrate (S) to product (P):Fig. 3.1Enzymes bind substrates to form enzyme-substrate complex (ES)• S binds to active site of enzyme.• S converted to product, releasedFig. 3.2 Enzymatic catalysis of reaction between 2 substrates• Biochemical reactions often 2 or more substrates.ex: peptide bond joins 2 amino acids• Enzyme brings substrates together in proper orientation to favor transition state• Active sites: clefts or grooves from tertiary structure• Substrates bind active site:hydrogen bonds, ionic bonds, hydrophobic interactions.Fig. 3.2Fig 3.3 Models of enzyme-substrate interactionLock-and-key model:• substrate fits precisely active site.**Induced fit: • modifies configurations of both enzyme and substrate Specific side chains in active site may react with substrate and form bondswith reaction intermediatesFig. 3.32Fig 3.4 Substrate binding by serine proteasesEx. Chymotrypsin digests proteins by catalyzing hydrolysis of peptide bondsChymotrypsin digests adjacent to hydrophobic amino acidsTrypsin digests next to basic amino acids• Nature of active site pocket determinessubstrate specificityof different proteases• Active site amino acidsare involved in reactionFig. 3.4Fig 3.5 Catalytic mechanism of chymotrypsinChymotrypsin: Substrate binding orients peptide bond adjacent to serinein active site; catalytic reaction involves covalent join to serine.123The Central Role of Enzymes as Biological CatalystsSmall molecules binding in active sites assist catalysis.Prosthetic groups: small molecules bound to proteins - critical functional roles.Ex: myoglobin and hemoglobin, prosthetic group is heme, which binds O2.Ex. metal ions (zinc, iron)Coenzymes: low-molecular-weight organic molecules that work with enzymes to enhance reaction rates. Ex. NAD+works with many enzyme (carries electrons)Fig 3.6 Role of NAD+in oxidation–reduction reactions Nicotinamide adenine dinucleotide (NAD+): REDOX: coenzyme carries electrons in oxidation: reduction reactionsNAD+accepts H+and 2 e- from one substrate →NADH. NADH donates these e- to second substrate, re-forming NAD+.Fig. 3.6S1(red) + S2(ox) -> S1(ox) + S2(red)3Enzymes and coenzymesSome coenzymes are related to vitaminsFig 3.7 Feedback inhibitionEnzyme activity is often regulated• Ex. feedback inhibition, product of pathway inhibits an enzyme involved in its synthesis.Fig. 3.7Fig 3.8 Allosteric regulationFeedback inhibition is example of allosteric regulation: enzyme activity controlled by binding of small molecules to regulatory sites on enzyme (not at active site)• changes conformation of enzyme and alters active site.Fig. 3.8Fig 3.9 Protein phosphorylation**Enzyme activity can be modified by phosphorylation: addition of phosphate can stimulate or inhibit activity of an enzyme. Kinases addPhosphate(-OH of ser, thr, tyr)PhosphatasesremovePhosphateFig. 3.9 ex.phosphorylationactivates enzyme that degrades glycogen4Metabolic Energy• A large portion of cell’s activities is devoted to obtaining energy from environment, and using energy to drive energy-requiring reactionsMany reactions in cells are energetically unfavorable, can proceed only with energy input(especially biosynthetic reactions)ATP and NADH provide energy and reducing material (e-) for coupled reactionsFig 3.10 ATP as a store of energyAdenosine 5′-triphosphate (ATP) plays central role in storing, using free energy in the cell –Energy currency.Bonds between phosphates in ATP are high-energy bonds: Hydrolysis is accompanied by large decrease in free energy:powers coupled reactions.Fig. 3.10Metabolic EnergyHydrolysis of ATP drives energy-requiring reactionsEx: first step in glycolysis is unfavorable (∆G°′ = +3.3)ATP hydrolysis is energy yielding: (∆G °′ = –7.3 kcal/mol):Combined (coupled) reaction : (∆G°′ = -4.0) kcal/mol)Energy-yielding reactions - coupled to ATP synthesisEnergy-requiring reactions - coupled to ATP hydrolysis.Metabolic EnergyEx. complete oxidative breakdown of glucoseto CO2and H2O yields large amount of free energy: ∆G°′ = –686 kcal/mol.To harness this energy, glucose is oxidized in a series of steps coupled to ATP synthesisGlycolysis, citric acid cycle, e- transport chain(Krebs cycle), (oxidative phosphorylation)Energy-yielding reactions - coupled to ATP synthesisEnergy-requiring reactions - coupled to ATP hydrolysis.5Metabolic EnergyGlycolysis: common to all cells; does not require O2• Anaerobic organisms, can provide all metabolic energy (ex. E. coli, Streptococcus, yeast). • Aerobic cells, only 1st stage in glucose degradationGlycolysis:Breakdown of glucose -> 2 pyruvate, net gain 2 ATP• Enzymes that catalyze reactions are regulatory points: if adequate supply of ATP, glycolysis is inhibitedAlso converts 2 molecules of NAD+to NADH:• NADH must be recycled by donating e- for other oxidation–reduction reactions..Figure 3.11 Reactions of glycolysis Fig. 3.11Glycolysis: 1 glucose → 2 pyruvate, net gain of 2 ATP• First part of pathway consumes energy (2 ATP)• Second part generates energy (4 ATP)Also converts 2 molecules of NAD+to NADH:• NAD+is oxidizing agent that accepts e-• NADH must be recycled by donating e- for other REDOXpyruvateMetabolic EnergyIn eukaryotic cells, glycolysis in cytosol.NADH must be recycled, donate e- for other REDOX:• Anaerobic conditions, NADH reoxidized to NAD+by conversion of pyruvate to lactate or ethanol (fermentation):• Wasteful process reduces pyruvate, low ATP gain• Aerobic conditions, NADH donates e- to electron transport chain (oxidative respiration) (lot of ATP)• Pyruvate is transported into mitochondria, for complete oxidation (Krebs + electron transport chain)• (citric acid cycle)Fig 3.12