1. Essential Knowledge 2A.1b. Living systems do not violate the second law of thermodynamics, which states that entropy increases over time. Evidence of student learning is a demonstrated understanding of each of the following: 1. Order is maintained by coupling cellular processes that increase entropy (and so have negative changes in free energy) with those that decrease entropy (and so have positive changes in free energy). 2. Energy input must exceed free energy lost to entropy to maintain order and power cellular processes. 3. Energetically favorable exergonic reactions, such as ATP→ADP, that have a negative change in free energy can be used to maintain or increase order in a system by being coupled with reactions that have a positive free energy change.

2. Energy and Matter converted from concentrated to less concentrated forms… Simple Molecule Concentrated Energy More ordered molecule Heat Entropy of universe increased

3. Previous slide Picture can be summarized by the following: Cells create ordered structures from less ordered materials using energy Organisms also replace ordered forms of matter and energy with less ordered forms Energy flows into an ecosystem in the form of light and exits in the form of heat Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

4. ∆G = ∆H – T∆S ∆G: The change in free energy during a process ∆H: change in total energy, or enthalpy ∆S: change in entropy (disorder) T: temperature in Kelvin. Spontaneous processes have a negative ∆G (-∆G ) To be spontaneous reactions must give up ENERGY (-∆H), ORDER (T∆S) or BOTH! Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Free energy: how much energy is available to do work from a given reaction.

5. Free energy is a measure of a system’s instability, its tendency to change to a more stable state (equilibrium) A process is spontaneous and can perform work only when it is moving toward equilibrium During a spontaneous change, free energy decreases and the stability of a system increases Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Free Energy, Stability, and Equilibrium

6. Fig. 8-5 (a) Gravitational motion (b) Diffusion(c) Chemical reaction More free energy (higher G) Less stable Greater work capacity In a spontaneous change -∆G The system becomes more stable The released free energy can be harnessed to do work Less free energy (lower G) More stable Less work capacity

7. Free Energy and Metabolism The concept of free energy can be applied to the chemistry of life’s processes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Exergonic reaction: release free energy, (-∆G ) and is spontaneous Catabolic pathways Endergonic reaction: absorbs free energy, (+∆G ) and is nonspontaneous Anabolic pathways Spontaneous in the direction shown

8. Fig. 8-6 Reactants Energy Free energy Products Amount of energy released (∆G < 0) Progress of the reaction (a) Exergonic reaction: energy released Products Reactants Energy Free energy Amount of energy required (∆G > 0) (b) Endergonic reaction: energy required Progress of the reaction Exergonic and Endergonic Reactions Example Glucose 686 kcal/ mol

9. Equilibrium and Metabolism Reactions in a closed system eventually reach equilibrium and then do no work Cells are open systems and never reach equilibrium Example: The catabolic pathway of breaking down glucose into CO 2 and H 2 O Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

10. ∆G < 0∆G = 0 ∆G < 0 Fig. 8-7 (a) An isolated hydroelectric system (b) An open hydroelectric system (c) A multistep open hydroelectric system Analogy for catabolic pathways

11. Concept 8.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions A cell does three main kinds of work: – Chemical – Transport – Mechanical Energy coupling: the use of an exergonic process to drive an endergonic one ATP is used for most coupling in cells. Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

12. The Structure and Hydrolysis of ATP ATP (adenosine triphosphate) is the cell’s energy shuttle ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Phosphate groups Ribose Adenine

13. Fig. 8-9 Inorganic phosphate Energy Adenosine triphosphate (ATP) Adenosine diphosphate (ADP) P P P PP P + + H2OH2O i Hydrolysis of ATP releases energy

14. How ATP Performs Work Cellular work is powered by hydrolysis of ATP The energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction Overall, the coupled reactions are exergonic Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

15. Fig. 8-10 (b) Coupled with ATP hydrolysis, an exergonic reaction Ammonia displaces the phosphate group, forming glutamine. (a) Endergonic reaction (c) Overall free-energy change P P Glu NH 3 NH 2 Glu i ADP + P ATP + + Glu ATP phosphorylates glutamic acid, making the amino acid less stable. Glu NH 3 NH 2 Glu + Glutamic acid Glutamine Ammonia ∆G = +3.4 kcal/mol + 2 1

16. Fig. 8-11 (b) Mechanical work: ATP binds noncovalently to motor proteins, then is hydrolyzed Membrane protein P i ADP + P Solute Solute transported P i VesicleCytoskeletal track Motor protein Protein moved (a) Transport work: ATP phosphorylates transport proteins ATP

17. Fig. 8-12 P i ADP + Energy from catabolism (exergonic, energy-releasing processes) Energy for cellular work (endergonic, energy-consuming processes) ATP + H2OH2O The Regeneration of ATP

18. Essential knowledge 4.B.1: Interactions between molecules affect their structure and function. a. Change in the structure of a molecular system may result in a change of the function of the system. b. The shape of enzymes, active sites and interaction with specific molecules are essential for basic functioning of the enzyme. Evidence of student learning is a demonstrated understanding of each of the following: – 1. For an enzyme-mediated chemical reaction to occur, the substrate must be complementary to the surface properties (shape and charge) of the active site. In other words, the substrate must fit into the enzyme’s active site. – 2. Cofactors and coenzymes affect enzyme function; this interaction relates to a structural change that alters the activity rate of the enzyme. The enzyme may only become active when all the appropriate cofactors or coenzymes are present and bind to the appropriate sites on the enzyme. c. Other molecules and the environment in which the enzyme acts can enhance or inhibit enzyme activity. Molecules can bind reversibly or irreversibly to the active or allosteric sites, changing the activity of the enzyme. d. The change in function of an enzyme can be interpreted from data regarding the concentrations of product or substrate as a function of time. These representations demonstrate the relationship between an enzyme’s activity, the disappearance of substrate, and/ or presence of a competitive inhibitor.

19. Concept 8.4: Enzymes speed up metabolic reactions by lowering energy barriers A catalyst is a chemical that speeds up a reaction without being consumed by the reaction An enzyme is a catalytic protein Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Sucrose (C 12 H 22 O 11 ) Glucose (C 6 H 12 O 6 )Fructose (C 6 H 12 O 6 ) Sucrase

20. The Activation Energy Barrier Chemical reactions rearrange bonds The energy needed to start a chemical reaction is called the activation energy (E A ) Activation energy is often supplied in the form of heat from the surroundings Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Progress of the reaction Products Reactants ∆G < O Transition state Free energy EAEA DC BA D D C C B B A A

21. 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) or the point of equilibrium, instead, they hasten reactions that would occur eventually Animation: How Enzymes Work Animation: How Enzymes Work Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

22. Fig. 8-15 Progress of the reaction Products Reactants ∆G is unaffected by enzyme Course of reaction without enzyme Free energy E A without enzyme E A with enzyme is lower Course of reaction with enzyme

23. Substrate Specificity of Enzymes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings Substrate Enzyme-Substrate Complex Induced fit, enzyme shape changes to fit the substrate better Product (s) Enzyme

24. Fig. 8-16 Substrate Active site Enzyme Enzyme-substrate complex (b)(a) This shows the induced fit of the enzyme- substrate complex.

25. Catalysis in the Enzyme’s Active Site In an enzymatic reaction, the substrate binds to the active site of the enzyme 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

26. Fig. 8-17 Substrates Enzyme Products are released. Products Substrates are converted to products. Active site can lower E A and speed up a reaction. Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. Substrates enter active site; enzyme changes shape such that its active site enfolds the substrates (induced fit). Active site is available for two new substrate molecules. Enzyme-substrate complex 5 3 2 1 6 4

27. Conditions that effect enzyme activity An enzyme’s activity can be affected by anything that alters the 3D structure of the protein. – Temperature – pH Many enzymes will not work without Cofactors or Coenzymes – Cofactors are nonprotein enzyme helpers – Cofactors may be inorganic (such as a metal in ionic form) – Coenzyme is an organic cofactor Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

28. Fig. 8-18 Rate of reaction Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria Optimal temperature for typical human enzyme (a) Optimal temperature for two enzymes (b) Optimal pH for two enzymes Rate of reaction Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Temperature (ºC) pH 54 3210 678910 0 20 40 80 60100

29. 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 Examples of inhibitors include toxins, poisons, pesticides, and antibiotics Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

30. Fig. 8-19 (a) Normal binding (c) Noncompetitive inhibition (b) Competitive inhibition Noncompetitive inhibitor Active site Competitive inhibitor Substrate Enzyme

31. Concept 8.5: Regulation of enzyme activity helps control metabolism Cells regulate enzyme function by – Switching on or off the genes that encode specific enzymes – Regulating the activity of enzymes Allosteric Regulation of Enzymes: – May inhibit or activte an enzyme’s activity – What happens: Regulatory molecule binds to a protein at one site and affects the protein’s function at another site Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

32. Fig. 8-20a (a) Allosteric activators and inhibitors Inhibitor Non- functional active site Stabilized inactive form Inactive form Oscillation Activator Active formStabilized active form Regulatory site (one of four) Allosteric enzyme with four subunits Active site (one of four) 1. Each enzyme has active and inactive forms 2. The binding of an activator stabilizes the active form of the enzyme 3. The binding of an inhibitor stabilizes the inactive form of the enzyme

33. 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings (b) Cooperativity: another type of allosteric activation Stabilized active form Substrate Inactive form

34. 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 Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

35. Fig. 8-22 Intermediate C Feedback inhibition Isoleucine used up by cell Enzyme 1 (threonine deaminase) End product (isoleucine) Enzyme 5 Intermediate D Intermediate B Intermediate A Enzyme 4 Enzyme 2 Enzyme 3 Initial substrate (threonine) Threonine in active site Active site available Active site of enzyme 1 no longer binds threonine; pathway is switched off. Isoleucine binds to allosteric site

36. Interpreting Enzyme Activity Graphs Enzyme activity is measured by concentration of substrate and/ or product.

38. Michaelis Menten Plot A graph of enzyme kinetics Vmax represents the maximum velocity of the enzyme when all available active sites are bound with substrate Km of the Michaelis constant, the point at which ½ of the active sites are bound with the substrate A LOW km indicates that relatively low amounts of substrate are needed to bind ½ the active site and thus a HIGH affinity for the substrate A HIGH km indicates that a high amounts of substrate are needed and a LOW affinity for the substrate

39. How would a competitive inhibitor change the MM plot?

40. Competitive inhibitors change the km of the enzyme Explanation: The competitive inhibitor competes with the substrate for binding to the active site. As the amount of substrate increases there is more substrate proportionally than inhibitor to bind with the active site. Eventually the amount of substrate overwhelms the competitive inhibitor and the same Vmax is reached as was observed without the inhibitor present. Thus Vmax is not shifted, but the graph is shifted to the right because more substrate is necessary to reach Vmax.

41. Allosteric affects on enzyme kinetics: Allosteric regulation affects the shape of the active site and will change the km, but not Vmax

42. Answer C

43. Answer A

44. Answer D

45. Review Questions 1.Distinguish between the following pairs of terms: A.catabolic and anabolic pathways; B.kinetic and potential energy; C.open and closed systems; D.exergonic and endergonic reactions 2.In your own words, explain the second law of thermodynamics and explain why it is not violated by living organisms 3.Explain in general terms how cells obtain the energy to do cellular work Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

46. 4.Give three examples of how ATP performs cellular work and explain. 5.Explain why an investment of activation energy is necessary to initiate a spontaneous reaction 6.Describe the mechanisms by which enzymes lower activation energy 7.Explain the parts of a M-M plat including substrate concentration, Vmax, ½ Vmax and km. 8.Why does the M-M graph level off when substrate concentration is high? 9.Describe how competitive inhibitors affect enzyme function (Draw a picture) and the km of a M-M plot (Draw a picture). 10.Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme (Draw a picture) Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

47. Fig. 8-UN5 11. What is the process shown in the diagram below? Why do cells use this type of regulation? 12. What would happen to the production of substance R and S if there was an abundance of substance Q? 13. Which reaction would prevail if both Q and S were present in the cell in high concentrations?