1. Chapter 8 An Introduction to Metabolism

2. Energy Flow Energy Flow in the Life of a Cell Energy: the capacity to do work Two type of Energy Kinetic: energy of movementKinetic Potential: stored energy Chemical Energy: PE available to be released in a chemical reaction

3. Organization of the Chemistry of Life into Metabolic Pathways Metabolic Pathway: Begins with a specific molecule, which is then altered in a series of defined steps resulting in a certain product.

4. Metabolic Pathway Enzyme 1 AB Reaction 1 Enzyme 2 C Reaction 2 Enzyme 3 D Reaction 3 Product Starting molecule

5. Types of Metabolic pathways Catabolic: breakdown pathways (Makes energy available) Downhill –Respiration: Breaks down glucose to produce carbon dioxide, water and ATP Anabolic: Consumes energy and builds molecules (Uphill) –Photosynthesis –Synthesis of a protein Bioenergetics: the study of how organisms manage their energy resources.

6. The Laws of Thermodynamics The 1 st Law is often called The Law of conservation of energy Assumes that the total amount of energy is constant. 2 nd law As energy is transferred through the system the amount of useful energy decreases. No process is 100% efficient Regions of great [energy] are regions of great orderliness. Entropy

7. Living things Use Energy to Organize Living things use solar energy to synthesize complex molecules and maintain orderly structures but do this at the expense of enormous loss of usable solar energy. Living systers increase the entropy of their surroundings so the entropy of the universe as a whole constantly increases. This means that the 2 nd law applies.

8. How Does Energy Flow in Chemical Reactions? Chemical reaction, reactants, products Exergonic (energy out) Endergonic (energy in)Endergonic Activation energy: the valence ē ‘s of the reactants must interact and overcome their natural (-) (-) replusion.

9. Coupled Reactions link Exergonic with Endergonic Reactions Endergonic reactions require energy. It gets this energy from exergonic reactions. Eg. Photosynthesis requires light which comes from the exergonic reaction occurring on the sun.

10. Examples of other coupled reactions ATPADP P + ATP Unflexedarm + P ADP + +

11. Concept 8.2: The free-energy changes of a reaction tells us whether the reaction occurs spontaneously Biologists want to know which reactions occur spontaneously and which require input of energy To do so, they need to determine energy changes that occur in chemical reactions

12. Free-Energy Change,  G A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell.

13. The change in free energy (∆G) during a process is related to the change in enthalpy, or change in total energy (∆H), and change in entropy (T∆S): ∆G = ∆H - T∆S Only processes with a negative ∆G are spontaneous Spontaneous processes can be harnessed to perform work

14. Free Energy, Stability, and Equilibrium Free energy is a measure of a system’s instability, its tendency to change to a more stable state During a spontaneous change, free energy decreases and the stability of a system increases Equilibrium is a state of maximum stability A process is spontaneous and can perform work only when it is moving toward equilibrium

15. LE 8-5 Gravitational motionDiffusionChemical reaction

16. Free Energy and Metabolism The concept of free energy can be applied to the chemistry of life’s processes

17. Exergonic and Endergonic Reactions in Metabolism An exergonic reaction proceeds with a net release of free energy and is spontaneous An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous

18. LE 8-6a Reactants Energy Products Progress of the reaction Amount of energy released (  G < 0) Free energy Exergonic reaction: energy released

19. LE 8-6b Reactants Energy Products Progress of the reaction Amount of energy required (  G > 0) Free energy Endergonic reaction: energy required

20. Equilibrium and Metabolism Reactions in a closed system eventually reach equilibrium and then do no work Cells are not in equilibrium; they are open systems experiencing a constant flow of materials A catabolic pathway in a cell releases free energy in a series of reactions Closed and open hydroelectric systems can serve as analogies

21. LE 8-7a  G = 0 A closed hydroelectric system  G < 0

22. LE 8-7b An open hydroelectric system  G < 0

23. LE 8-7c A multistep open hydroelectric system  G < 0

24. Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: –Mechanical –Transport –Chemical To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

25. The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cell’s energy shuttle ATP provides energy for cellular functions

26. LE 8-8 Phosphate groups Ribose Adenine

27. LE 8-9 Adenosine triphosphate (ATP) Energy PP P PP P i Adenosine diphosphate (ADP) Inorganic phosphate H2OH2O + +

28. The bonds between the phosphate groups of ATP’s tail can be broken by hydrolysis Energy is released from ATP when the terminal phosphate bond is broken This release of energy comes from the chemical change to a state of lower free energy, not from the phosphate bonds themselves

29. In the cell, the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic

30. The Regeneration of ATP ATP is a renewable resource that is regenerated by addition of a phosphate group to ADP The energy to phosphorylate ADP comes from catabolic reactions in the cell The chemical potential energy temporarily stored in ATP drives most cellular work

31. LE 8-10 Endergonic reaction:  G is positive, reaction is not spontaneous Exergonic reaction:  G is negative, reaction is spontaneous  G = +3.4 kcal/mol  G = –7.3 kcal/mol  G = –3.9 kcal/mol NH 2 NH 3 Glu Glutamic acid Coupled reactions: Overall  G is negative; together, reactions are spontaneous AmmoniaGlutamine ATP H2OH2O ADP P i + + +

32. LE 8-11 NH 2 Glu P i P i P i P i NH 3 P P P ATP ADP Motor protein Mechanical work: ATP phosphorylates motor proteins Protein moved Membrane protein Solute Transport work: ATP phosphorylates transport proteins Solute transported Chemical work: ATP phosphorylates key reactants Reactants: Glutamic acid and ammonia Product (glutamine) made + + +

33. Electron Carriers also Transport Energy Excited ē’s are created during photosynthesis and cellular respiration. These energized ē’s are captured by electron carriers and then donated to other molecules. Examples: NADP+, NAD+, FAD

34. How Do Cells Control Their Metabolic Reactions? 1.Cells regulate chemical reations through the use of enzymes. 2.Cells couple reactions. 3.Cells synthesize energy-carrier moleucles that capture energy from exergonic reaction and transport it to endergonic reactions.

35. Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers A catalyst is a chemical agent that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction

36. At Body Temperature, Spontaneous Reactions Proceed Too Slowly to Sustain Life Enzymes lower the activation energy but are not used up or permanently altered.

37. 3 Important Principles about Catalysts Catalysts speed up reaction Catalysts can speed up only those reactions that would occur spontaneously anyway, but at a much slower rate Catalysts are not consumed in the reactions they promote.

38. The Activation Energy Barrier Every chemical reaction between molecules involves bond breaking and bond forming The initial energy needed to start a chemical reaction is called the free energy of activation, or activation energy (E A ) Activation energy is often supplied in the form of heat from the surroundings

39. LE 8-14 Transition state CD A B EAEA Products CD A B  G < O Progress of the reaction Reactants C D A B Free energy

40. How Enzymes Lower the E A Barrier Enzymes catalyze reactions by lowering the E A barrier Enzymes do not affect the change in free- energy (∆G); instead, they hasten reactions that would occur eventually Animation: How Enzymes Work Animation: How Enzymes Work

41. LE 8-15 Course of reaction without enzyme E A without enzyme  G is unaffected by enzyme Progress of the reaction Free energy E A with enzyme is lower Course of reaction with enzyme Reactants Products

42. Substrate Specificity of Enzymes The reactant that an enzyme acts on is called the enzyme’s substrate The enzyme binds to its substrate, forming an enzyme-substrate complex The active site is the region on the enzyme where the substrate binds Induced fit of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction

43. LE 8-16 Substrate Active site Enzyme Enzyme-substrate complex

44. Catalysis in the Enzyme’s Active Site In an enzymatic reaction, the substrate binds to the active site The active site can lower an E A barrier by –Orienting substrates correctly –Straining substrate bonds –Providing a favorable microenvironment –Covalently bonding to the substrate

45. LE 8-17 Enzyme-substrate complex Substrates Enzyme Products Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. Active site (and R groups of its amino acids) can lower E A and speed up a reaction by acting as a template for substrate orientation, stressing the substrates and stabilizing the transition state, providing a favorable microenvironment, participating directly in the catalytic reaction. Substrates are converted into products. Products are released. Active site is available for two new substrate molecules.

46. Effects of Local Conditions on Enzyme Activity An enzyme’s activity can be affected by: –General environmental factors, such as temperature and pH –Chemicals that specifically influence the enzyme

47. Effects of Temperature and pH Each enzyme has an optimal temperature in which it can function Each enzyme has an optimal pH in which it can function

48. LE 8-18 Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) Temperature (°C) Optimal temperature for two enzymes 020 40 6080100 Rate of reaction Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) pH Optimal pH for two enzymes 0 Rate of reaction 1 23 45 67 8 910

49. Cofactors Cofactors are nonprotein enzyme helpers Coenzymes are organic cofactors

50. Enzyme Inhibitors Competitive inhibitors bind to the active site of an enzyme, competing with the substrate Noncompetitive inhibitors bind to another part of an enzyme, causing the enzyme to change shape and making the active site less effective

51. LE 8-19 Substrate Active site Enzyme Competitive inhibitor Normal binding Competitive inhibition Noncompetitive inhibitor Noncompetitive inhibition A substrate can bind normally to the active site of an enzyme. A competitive inhibitor mimics the substrate, competing for the active site. A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions.

52. Concept 8.5: Regulation of enzyme activity helps control metabolism Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated To regulate metabolic pathways, the cell switches on or off the genes that encode specific enzymes

53. Allosteric Regulation of Enzymes Allosteric regulation is the term used to describe cases where a protein’s function at one site is affected by binding of a regulatory molecule at another site Allosteric regulation may either inhibit or stimulate an enzyme’s activity

54. Allosteric Activation and Inhibition Most allosterically regulated enzymes are made from polypeptide subunits Each enzyme has active and inactive forms The binding of an activator stabilizes the active form of the enzyme The binding of an inhibitor stabilizes the inactive form of the enzyme

55. LE 8-20a Allosteric enzyme with four subunits Regulatory site (one of four) Active form Activator Stabilized active form Active site (one of four) Allosteric activator stabilizes active form. Non- functional active site Inactive form Inhibitor Stabilized inactive form Allosteric inhibitor stabilizes inactive form. Oscillation Allosteric activators and inhibitors

56. Cooperativity is a form of allosteric regulation that can amplify enzyme activity In cooperativity, binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits

57. LE 8-20b Substrate Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Cooperativity another type of allosteric activation Stabilized active form Inactive form

58. Feedback Inhibition In feedback inhibition, the end product of a metabolic pathway shuts down the pathway Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more product than is needed

59. LE 8-21 Active site available Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Enzyme 2 Intermediate A Isoleucine used up by cell Feedback inhibition Active site of enzyme 1 can’t bind theonine pathway off Isoleucine binds to allosteric site Enzyme 3 Intermediate B Enzyme 4 Intermediate C Enzyme 5 Intermediate D End product (isoleucine)

60. Specific Localization of Enzymes Within the Cell Structures within the cell help bring order to metabolic pathways Some enzymes act as structural components of membranes Some enzymes reside in specific organelles, such as enzymes for cellular respiration being located in mitochondria

61. LE 8-22 Mitochondria, sites of cellular respiration 1 µm

62. Cells control chemical reactions by 1.Regulating synthesis of enzymes 2.Producing inactive forms and activating only when needed.