MCB 3020, Spring 2005

1. MCB 3020, Spring 2005 Chapter 5: Nutrition and Metabolism I

2. The Generation of Energy: I. Metabolism (metabolic reactions) II. Nutrients III. Energy IV. Review of free energy V. Enzymes VI. Energy generation: oxidation and reduction reactions

3. I. Metabolism (metabolic reactions) • all of the biochemical reactions in a cell • includes catabolic (degradative) and anabolic (biosynthetic) reactions

4. 1. Catabolism ENERGY • the breakdown of complex molecules into simpler compounds with the release of energy 2. Anabolism • the biosynthesis of complex molecules from simpler compounds with the input of energy

5. B. Catabolic reactions generate ATP. ATP is used for biosynthesis and cell maintenance. small molecules macromolecules (polymers) Anabolism waste products energy source Catabolism ATP, reductant

6. C. ATP is called the energy currency of the cell. • catabolic reactions release energy and store it as ATP. • anabolic (biosynthetic) reactions require energy in the form of ATP. ATP = $$

7. II. Nutrition A. Nutrients chemicals taken up from environment and used for cellular reactions 1. macronutrients 2. micronutrients 3. growth factors

8. 1. Macronutrients: chemicals taken up and required in relatively large amounts C H O N P S K+ Mg2+ Na+ Ca2+ Fe2+/Fe3+

9. Where do macronutrients occur in cells? C H O N P S Fe many organic molecules amino acids, nucleic acids, cell walls, etc. nucleic acids, phospholipids cysteine, methionine, vitamins like CoA Electron transport proteins

10. • examples Co (the metal center of vitamin B12) Cu (found in electron transport proteins) Se (found in selenocysteine) Ni, Zn, Mn, V, W 2. Micronutrients: inorganic chemicals required in small amounts • also called trace elements • usually metals in metabolic enzymes

11. 3. Growth factors: organic chemicals required in small amounts by some (but not all) cells a. Examples: vitamins, like B1, B6, B12, biotin some amino acids purines, pyrimidines

12. b. Many vitamins are precursors of coenzymes used in metabolism. Vitamin Coenzyme B2 (riboflavin) FAD, FMN niacin (nicotinic acid) NAD, NADP B12 cobalamin folate tetrahydrofolate Coenzymes are molecules that work together with enzymes to catalyze chemical reactions.

13. ? B. Cells can be grown in laboratory cultures. Two classes of culture media 1. Chemically defined medium exact chemical composition is known; contains precise amounts of pure chemicals added to distilled water 2. Complex (undefined) medium exact chemical composition is not known; contains digests of milk proteins, yeast, soybeans, etc. that have growth factors

14. Different organisms can have vastly different nutritional requirements. Escherichia coli can grow on a simple defined medium. It can synthesize most of the organic molecules required for biosynthesis. Leuconostoc mesenteroides needs added amino acids, purines, pyrimidines, and vitamins for growth because it cannot synthesize these molecules by itself.

15. Laboratory growth medium for E. coli (NH4)2SO4 Glucose K2HPO4 CaCl2 MgSO4 H2O minerals KH2PO4 Growth medium for L. mesenteroides Glucose, H2O, K2HPO4, KH2PO4, NH4Cl, MgSO4, Na acetate, alanine arginine asparagine, aspartate, cysteine, glutamate, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, valine, adenine, guanine, uracil, xanthine biotin, folate, nicotinic acid, pyridoxal, pyridoxamine pyridoxine, riboflavin, thiamine, pantothenate, para-aminobenzoic acid, trace elements (don't memorize)

16. III. Energy Why do cells need energy? Where do organisms get energy? How do cells use energy sources? ENERGY the ability to do work

17. nutrients polysaccharides A. Why do cells need energy? • growth and biosynthesis • motility • nutrient uptake • reproduction • maintenance, etc.

18. Phototrophs light Chemotrophs chemicals Chemoorganotrophs organic chemicals (eg. sugars) Chemolithotrophs inorganic chemicals (eg. H2, NH3, H2S) B. Where do organisms get energy?

19. C. How do chemotrophs derive energy from energy sources? Remember: oxidation is the loss of electrons Organisms capture energy that is released when an organic or inorganic chemical is oxidized. glucose + 6 O2 6 CO2 + 6 H2O G°’ = - 686 kcal/mol

20. D. Units of energy How many kcal in a snickers bar in a teaspoon of sugar used by human in a day used by a microbe to grow? kcal (kilocalorie) • a unit of energy • amount of heat energy required to raise the temperature of 1 kg of water 1°C Who cares about a kcal? Want to give students idea of how much energy we’ll be talking about in the biochemical rxns • 1 kcal = 4.184 kilojoules (kJ) • 1 kcal = 1 “nutritional” calorie

21. Review from General Chemistry: G = H - T S change in entropy change in enthalpy (total energy) change in free energy IV. Review of free energy (G) • energy that is available to do useful work

22. For biological reactions, the standard conditions for measuring the change in free energy (G°’ ) are • 25°C • pH 7 • reactants and products initially present at 1 M concentration

23. A. The  G°’ can tell us about the direction a reaction tends to occur. A + B C + D Free Energy  G°’ is negative Progress of reaction If G°’ is (-) products have lower free energy than substrates  A + B C + D

24. 1. If  G°’ is negative • free energy is released • the reaction is exergonic • the reaction tends to occur in the direction written Examples: H2 + 1/2 O2 H2O - 57 kcal/mol glucose + 6 O2 6 CO2 + 6 H2O - 686 kcal/mol ATP + H2O  ADP + PO4- - 7.3 kcal/mol

25. 2.If  G°’ is positive • energy input is usually required • the reaction is endergonic If  G°’ is (+) products have higher free energy than substrates C + D Free Energy G°’ is positive A + B Progress of reaction • the reaction does not tend to occur in the direction written

26. B. Coupled reactions DGo’ = +20 kJ/mole A B Reaction 1 DGo’ = -30 kJ/mole C D Reaction 2 DGo’ = -10 kJ/mole A + C B + D Reactions 1 and 2 coupled Exergonic reactions (-DG°’) can be used to "drive" endergonic reactions (+DG°’) to make the overall "coupled" reaction favorable.

27. C. Equilibrium A + B C + D • equilibrium occurs when the rates of the forward and reverse reactions are equal • usually at equilibrium, the concentrations of the products and reactants are not equal

28. C. Equilibrium (contd.) A + BC + D • if the DG°’is large and negative, equilibrium lies towards product; very little of the reactants remain

29. Because before water is formed, chemical bonds have to be broken. D. “Activation energy” is required to break bonds. H2 + 1/2 O2 H2O DG°’= - 57 kcal/mol If H2 andO2 are mixed without a catalyst, no detectable amount of water is formed in our lifetime. Why?

30. Activation energy Free Energy H2 + 1/2 O2 H2O Progress of reaction Activation energy: energy required to bring molecules to the reactive state

31. E. Catalysts Activation energy of catalyzed reaction Free Energy H2 + 1/2 O2 DG H2O Progress of reaction chemicals that increase the reaction rate by lowering the activation energy

32. Properties of catalysts • increase the rate of the reaction, • but DO NOT change the DG, •DO NOT change the equilibrium • many reactions in living organisms are catalyzed by biological molecules called enzymes

33. V. Enzymes • biological catalysts • most enzymes are proteins, a few are nucleic acids (ribozymes or catalytic RNAs) • most enzymes catalyze specific reactions or sets of reactions

34. P Substrates (S): reactants, starting materials S E Substrate(s) first combine with the enzyme to form an enzyme-substrate (E-S) complex. S E A. Enzyme catalysis Enzyme (E): usually a protein Products (P): ending materials

35. S P P E E E Enzyme-substrate complex S E At end of reaction, the enzyme returns to its original form B. Typical enzymatic reaction sequence: E + S  E-S  E-P  E + P

36. C. Important notes on enzymes • Enzymes DO NOT alter the equilibrium of the reaction. • Enzymes can catalyze exergonic and endergonic reactions. • Substrates bind at the enzyme active site. • Many enzymes contain nonprotein components: coenzymes (loosely bound) or prosthetic groups (tightly bound).

37. Important notes on enzymes (contd.) • Enzymes tend to be sensitive to pH and temperature. • Enzymes are often named after the substrate or the reaction catalyzed, plus the ending “-ase” (eg. cellulase breaks down cellulose, ATP synthase makes ATP).

38. D. Sometimes enzymes change shape when substrates bind (“induced fit”) glucose + hexokinase (a protein used in glycolysis) Active site

39. CH2OH O OH HO OH OH E. Metabolic reactions are catalyzed by enzymes. glucose 12 enzymes ethanol + CO2 glucose fermentation (anaerobic)

40. Respiration of glucose (aerobic) glucose + 6 O2 ~36 [ADP + Pi] ~30 enzymes ~36 ATP 6 CO2 + 6 H2O What is O2 used for?

41. VI. Energy generation: A. Oxidation and reduction reactions For chemotrophs, utilization of a chemical energy source involves oxidation and reduction reactions (redox reactions).

42. Loss of Electrons = Oxidation H2  2 H+ + 2 e- Glucose (C6H12O6)  12 H+ + 12 e- + 6 CO2 Gain of Electrons = Reduction 1/2 O2 + 2 H+ + 2 e- H2O Oxidation and reduction reactions “LEO says GER”

43. B. Complete redox reactions can be divided into oxidative and reductive half reactions. e- donor e- acceptor Oxidative half-reaction: H2 2 H+ + 2 e- Reductive half-reaction: 1/2 O2 + 2 H+ + 2 e- H2O Complete reaction: H2+ 1/2 O2H2O H2 and H+ are called a redox couple.

44. an electron donor (eg. H2) and primary electron donor terminal e- acceptor an electron acceptor (eg. O2) C. Because electrons do not typically exist alone in solution, complete redox reactions need glucose + 6 O2 6 CO2 + 6 H2O

45. D. Energy is released when an energy source is oxidized. ENERGY Oxidative half-reaction H2  2 H+ + 2 e- DG°’ H2 + 1/2 O2 H2O - 57 kcal/mol glucose + 6 O2 6 CO2 + 6 H2O - 686 kcal/mol

46. E. Cells oxidize energy sources and harness the energy released to make ATP. H2 Hydrogen atoms separated into protons & electrons 2 H+ 2 e- ATP = $$ Some released energy is harnessed to make ATP Electron transport system 2 e- 2 H+ 1/2 O2 H2O H2 1/2 O2 Explosive release of energy as heat can't be harnessed to do work H2O H2 + 1/2 O2 H2O DG°’= - 57 kcal/mol Starr & Taggart, Figure 6.15

47. Study Objectives 1. Understand metabolism, catabolism, anabolism, and the role of ATP in metabolism. 2. Know the differences between macronutrients, micronutrients, and growth factors. Know where they occur in biological molecules and the examples presented in class. 3. Contrast defined and complex media. Know one reason why nutritional requirements differ among organisms. 4. Give examples of energy-requiring processes in the cell. 5. Define chemotrophs, phototrophs, chemoorganotrophs, chemolithotrophs. (eg. chemotrophs are organisms that use chemicals as an energy source.) Given an energy source (eg. NH3), be able to identify the type of catabolism being used (eg. chemolithotrophy). 6. Understand the terms kcal and free energy. What predictions can be made from the Go' value of a reaction. What is reaction coupling and how can it be used by the cell?

48. 7. Understand equilibrium, activation energy, catalysts and their properties. Understand the effect of catalysts on equilibrium. Can catalysts make a nonspontaneous reaction spontaneous? 8. Understand enzymes and all the properties presented in class. What is the function of enzymes in the cell? 9. Define oxidation, reduction, half reactions, redox couples, electron donor, electron acceptor. 10. Describe how cells derive energy from an energy source. What are the roles of the primary electron donor and the terminal electron acceptor?

49. Energy generation and glycolysis I. Oxidation of the energy source II. Reduction of NAD+ III. Making ATP through substrate level phosphorylation IV. Glycolysis V. Reoxidation of NADH

50. I. Oxidation of the energy source: A. Energy released when an energy source is oxidized can be conserved in the form of high energy chemical bonds. ENERGY oxidation waste products glucose ATP ADP + Pi chemicals with high energy bonds