1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Focus What does an enzyme do that causes a reaction to occur more quickly? What portion of a nucleotide contains the “information”

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics Metabolism is the totality of an organism’s chemical reactions Metabolism is an emergent property of life that arises from interactions between molecules within the cell The metabolism can never be at equilibrium or the organism is dead.

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Organization of the Chemistry of Life into Metabolic Pathways A metabolic pathway begins with a specific molecule and ends with a product Each step is catalyzed by a specific enzyme

4. LE 8-UN141 Enzyme 1 AB Reaction 1 Enzyme 2 C Reaction 2 Enzyme 3 D Reaction 3 Product Starting molecule

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Catabolic pathways release energy by breaking down complex molecules into simpler compounds Anabolic pathways consume energy to build complex molecules from simpler ones Bioenergetics is the study of how organisms manage their energy resources

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The First Law of Thermodynamics According to the first law of thermodynamics, the energy of the universe is constant – Energy can be transferred and transformed – Energy cannot be created or destroyed The first law is also called the principle of conservation of energy

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Second Law of Thermodynamics During every energy transfer or transformation, some energy is unusable, often lost as heat According to the second law of thermodynamics, every energy transfer or transformation increases the entropy (disorder) of the universe

8. LE 8-3 Chemical energy Heat CO 2 First law of thermodynamicsSecond law of thermodynamics H2OH2O

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The free-energy change 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

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

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

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

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

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cell’s energy shuttle ATP provides energy for cellular functions

18. LE 8-8 Phosphate groups Ribose Adenine

19. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

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

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

23. LE 8-12 P i ADP Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (energonic, energy- yielding processes) ATP +

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

25. LE 8-13 Sucrose C 12 H 22 O 11 Glucose C 6 H 12 O 6 Fructose C 6 H 12 O 6

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

27. 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

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

29. 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

30. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Endergonic Reaction

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

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

33. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

34. 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.

35. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

36. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

37. 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

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

39. 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.

40. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

41. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

42. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

43. 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

44. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

45. 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

46. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

47. 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)

48. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings 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

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