CHAPTER 6

1. CHAPTER 6 AN INTRODUCTION TO METABOLISM

2. Figure 6.1  The complexity of metabolism Metabolism is the sum total of all of an organism’s chemical reactions. It is an emergent property That arises from interactions between molecules within the cell.

3. Enzymes (biological catalysts) direct matter through the metabolic pathways by selectively accelerating each step. We’ll learn all about enzymes in a minute… • In the next class we will perform a lab dealing with enzymes… LAB #2: enzyme catalysis. You must let me know if your lab manual hasn’t arrived yet so I can photocopy the first lab for you. Pick it up from me tomorrow so you can do your HW. • HW: pre-read the lab and do the lab bench exercise for lab #2. PopQUIZ next class on the procedure!!!

4. METABOLISM all the rxns… • Catabolic pathways (catabolism) = degradative processes that release energy by breaking down complex molecules into simpler ones. Ex. Cellular respiration Glucose or Amino Acids -> CO2 + H20 + ATP (energy) • Anabolic Pathways (anabolism) = processes that consume energy to build complicated molecules from simpler ones. Ex. Synthesis of Protein from amino acids or glucose by PhotoS Forming peptide bonds requires energy • Energy released from “downhill” reactions of catabolism (ATP ADP) is used to drive the “uphill” reactions of anabolism (polymerization) = “coupled reaction”

5. THIS IS CALLED COUPLING!!!! (ewwww. How cute.)

6. BIOENERGETICS & ENERGY • Energy- the capacity to do work… to move matter against the forces of gravity and friction. • What are the three forms of energy?

7. BIOENERGETICS & ENERGY • What are the three forms of energy? Potential, Kinetic, Chemical Water stored Behind a dam. (potential energy) Water rushing out Of the dam. (kinetic energy)

8. Cheetah… also, potential & kinetic energy.How is the cheetah storing it’s potential energy???

9. CHEMICAL ENERGY • A form of potential energy • Stored in molecules as a result of the arrangement of the atoms in the molecules. • Big molecules like glucose and proteins have a lot of stored chemical energy. • Small molecules like carbon dioxide, oxygen and water have little stored energy. • Enormous molecules like glycogen, starch (amylose & amylopectin) and lipids have even more chemical energy.

10. THERMODYNAMICS • The study of energy transformations that occur in a collection of matter. • 1st law = energy can be transferred and transformed but not created nor destroyed. • 2nd law = every energy transfer increases the entropy (randomness) of the universe. Ex. messy room, random molecular motion, macromolecules to small ones.

11. How do these pictures exemplify the 2 laws of thermodynamics?

12. How do these pictures exemplify the 2 laws??? Octane, a hydrocarbon, is reduced to CO2 and H2O when burned, transferring energy from chemical to kinetic… increasing the entropy of the environment

13. THE QUANTITY OF ENERGY IN THE UNIVERSE IS CONSTANT… BUT THE QUALITY ISN’T.

14. Considering the laws of thermodynamics… how do we explain the orderliness of life?

15. Considering the laws of thermodynamics… how do we explain the orderliness of life? Organisms are open systems! Matter & energy are transferred between the system & it’s surroundings. There is a constant source of energy. Ex. Cells take in starch, protein, lipids & release energy (ATP) CO2 and water.

16. Figure 6.7 Disequilibrium and work in closed and open systems

17. A. FREE ENERGY (G) • Free energy is a measure of a system’s instability- it’s tendency to change to a more stable state. • FYI- big molecules w/ lots of covalent bonds are unstable. Small molecules like CO2 are stable. • Thus, free energy is the portion of a system’s energy that is available to perform work. Equation: Free energy (G) = total energy - entropy (temp K) • What about heat? • Temperature amplifies the entropy of a system so the higher the temperature, the less free energy there is left available (because you have to subtract this from the total energy.)

18. The amount of free energy at the beginning and end of a reaction (sG change in free energy) predicts whether a reaction will occur spontaneously or not. sG = free energyfinal - free energyinitial • TO OCCUR SPONTANEOUSLY The system must give up order, energy, or both. It will have a negative value. • Ex. Cellular Respiration has a negative sG. • Ex. Glucose + O2 CO2 + H20 + 38 ATP energy

19. More free energy LESS STABLE Stretched slinky Girl at top of slide Glucose molecule Less free energy MORE STABLE Compact slinky Girl at bottom of slide CO2 & H20

20. Biochemical reactions can be 1) exergonic or 2) endergonic

21. Figure 6.6  Energy changes in exergonic and endergonic reactions you may have learned the terms Exo and Endothermic Exergonic Rxns have a - sG. Endergonic Rxns have a + sG.

22. EXERGONIC “energy outward” • sG is negative • Why? Because the chemical mixture loses free energy. • Energy is released. • The reaction is spontaneous. Ex. C6H12O6 + 6 02 --> 6 CO2 + 6 H20 sG = -686 kcal/mol The products have 686 kcal less free energy than the reactants. We’ll learn that the energy is converted to ATP molecules (and lost as heat).

23. Figure 6.12 Energy profile of an exergonic reaction

24. 2. ENDERGONIC = “energy inward” • sG is positive • Why? Because this reaction stores free energy in larger molecules. • Energy is absorbed from its surroundings. • The reaction is non-spontaneous. • sG is the amount of energy required to drive the reaction. • Ex. Photons + 6CO2 + 6H20 --> C6H12O6 + 6O2

25. Many biological pathways rely on energy coupling, using the free energy released from an exergonic process to drive an endergonic one. ALL reactions are coupled with the degradation OR synthesis of ATP

26. ATP adenosine-tri-phosphate • Made of: adenine + ribose + 3 phosphates (basically, an Adenine RNA nucleotide w/ 3 not 1 P) • When the terminal phosphate bond is broken, a molecule of inorganic phosphate leaves the ATP and ADP is left • Phosphorylation = transferring a phosphate group from ATP to some other molecule. • This makes the molecule more reactive (less stable) than the original molecule.

27. Figure 6.9  Energy coupling by phosphate transfer

28. B. ACTIVATION ENERGY (Ea) • the initial investment of energy “energy hump” needed for starting a reaction (energy needed to break the bonds of the reactant molecules) • Activation energy prevents spontaneous reactions from going forward (occurring)

29. What would happen to biochemical reactions and high-energy molecules without activation energy? What would happen to you???? (discuss)

30. What would happen to biochemical reactions and high-energy molecules without activation energy? What would happen to you???? • Complex molecules of the cell (ie. proteins, DNA, carbs) would decompose spontaneously because they are rich in free energy. • The laws of thermodynamics favor their breakdown.

31. How can cellular reactions overcome activation energy? • Heat • Enzyme (biological catalyst)

32. Figure 6.11 Example of an enzyme-catalyzed reaction: Hydrolysis of sucrose

33. C. CATALYSTS • What do they do? • Speed up chemical reactions. • How do they do it? • by lowering the amount of activation energy needed.

34. ENZYMES • Are globular proteins • Names ending in -ase • Enzymes act on substrates How do enzymes recognize specific substrates? • Specificity is a result of it’s shape- Protein… structure/function

35. The “lock and key” model - substrate is the key - enzyme is the lock • the active site is a restricted region of the enzyme molecule that actually binds to the substrate. (the key hole)

36. THE INDUCED FIT MODEL Like the clasping of a handshake, brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction.

37. Figure 6.15 The catalytic cycle of an enzyme

38. Figure 6.16 Environmental factors affecting enzyme activity TEMPERATURE cold- little movement of Substrate to enzyme Increased temperature Increases # collisions Too HIGH denatures enzymes. No RXN. pH Deviations from optimal pH denature the enzymes & make them inactive

39. Some enzymes are assisted by prosthetic groups called: • Cofactors are non-protein helpers for catalytic activity that may be inorganic (like: zinc, iron, and copper). • Coenzymes are cofactors that ARE organic molecules. (vitamins)

42. Figure 6.21 Organelles and structural order in metabolism

43. D. CONTROLLING ENZYME ACTIVITY • COMPETITIVE INHIBITION molecular mimics bind to the active site, thus reducing productivity of enzymes by blocking substrates from binding the active sites. Ex) Penicillin blocks the active site of an enzyme bacteria use to make their cell walls.

44. 2. NONCOMPETITIVE INHIBITION Molecules bind to a part of the enzyme that is not the active site (allosteric site) causing the enzyme to change its shape, making the active site useless. Ex) DDT, parathion are inhibitors of main enzymes of the nervous system.

45. Figure 6.17 Inhibition of enzyme activity

46. 3. FEEDBACK INHIBITION Switching off of a metabolic pathway by its end-product, which acts as an inhibitor of an enzyme within the pathway. Negative feedback.

47. 4. ALLOSTERIC REGULATION • Allosteric enzymes are typically made of 2 or more polypeptide subunits, each having its own active site. (ex. Of quaternary structure) • Allosteric enzymes have 2 conformations (shapes): • Active form • Inactive form

48. Figure 6.18 Allosteric regulation of enzyme activity • ACTIVATOR MOLECULES stabilize the “active form” of the allosteric enzyme. • INHIBITOR MOLECULES stabilize the “inactive form”.

49. 5) COOPERATIVITY One substrate molecule primes the enzyme to accept additional substrate molecules more readily.

50. DESIGN AN EXPERIMENT TESTING THE RATE OF ENZYME ACTIVITY and ONE TO TEST THE EFFECT OF ENVIRONMENT ON ENZYMES • What materials will you need? • What will the control group be? • What will your independent and dependent variables be? • What variables will you control? • What will the resulting graph look like?