1. Overview: The Energy of Life  The living cell is a miniature chemical factory where thousands of reactions occur  The cell extracts energy and applies energy to perform work  Some organisms even convert energy to light, as in bioluminescence © 2014 Pearson Education, Inc.

2. 10/15 Agenda Metabolism Vocab Laws of Thermodynamics

3. Vocab  Metabolism  Catabolism  Anabolism  Bioenergetics  Thermodynamics  System vs Surroundings http://entropysimple.oxy.edu/con tent.htm Open System vs Closed System Exergonic Endergonic Spontaneous Reaction

4. © 2014 Pearson Education, Inc. Figure 6.1

5. Concept 6.1: An organism’s metabolism transforms matter and energy  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 © 2014 Pearson Education, Inc.

6. Metabolic Pathways  A metabolic pathway begins with a specific molecule and ends with a product  Each step is catalyzed by a specific enzyme © 2014 Pearson Education, Inc.

7. Figure 6.UN01 Enzyme 1 Starting molecule Enzyme 2 Enzyme 3 Reaction 1 Reaction 2 Reaction 3 ProductDC B A

8.  Catabolic pathways release energy by breaking down complex molecules into simpler compounds  Cellular respiration, the breakdown of glucose in the presence of oxygen, is an example of a pathway of catabolism © 2014 Pearson Education, Inc.

9.  Anabolic pathways consume energy to build complex molecules from simpler ones  The synthesis of protein from amino acids is an example of anabolism  Bioenergetics is the study of how organisms manage their energy resources © 2014 Pearson Education, Inc.

10. Forms of Energy  Energy is the capacity to cause change  Energy exists in various forms, some of which can perform work © 2014 Pearson Education, Inc.

11.  Kinetic energy is energy associated with motion  Thermal energy is kinetic energy associated with random movement of atoms or molecules  Heat is thermal energy in transfer from one object to another  Potential energy is energy that matter possesses because of its location or structure © 2014 Pearson Education, Inc.

12.  Chemical energy is potential energy available for release in a chemical reaction  Energy can be converted from one form to another © 2014 Pearson Education, Inc. Animation: Energy Concepts

13. © 2014 Pearson Education, Inc. Figure 6.2 A diver has more potential energy on the platform. A diver has less potential energy in the water. Diving converts potential energy to kinetic energy. Climbing up converts the kinetic energy of muscle movement to potential energy.

14. The Laws of Energy Transformation  Thermodynamics is the study of energy transformations  An isolated system, such as that approximated by liquid in a thermos, is isolated from its surroundings  In an open system, energy and matter can be transferred between the system and its surroundings  Organisms are open systems © 2014 Pearson Education, Inc.

15. 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, but it cannot be created or destroyed  The first law is also called the principle of conservation of energy © 2014 Pearson Education, Inc.

16. Figure 6.3 (a) First law of thermodynamics (b) Second law of thermodynamics Chemical energy Heat

17. © 2014 Pearson Education, Inc. Figure 6.3a (a) First law of thermodynamics Chemical energy

18. © 2014 Pearson Education, Inc. Figure 6.3b (b) Second law of thermodynamics Heat

19. The Second Law of Thermodynamics  During every energy transfer or transformation, some energy is unusable and is often lost as heat  According to the second law of thermodynamics  Every energy transfer or transformation increases the entropy of the universe  Entropy is a measure of disorder, or randomness © 2014 Pearson Education, Inc.

20.  Living cells unavoidably convert organized forms of energy to heat  Spontaneous processes occur without energy input; they can happen quickly or slowly  For a process to occur without energy input, it must increase the entropy of the universe © 2014 Pearson Education, Inc.

21. Biological Order and Disorder  Cells create ordered structures from less ordered materials  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 © 2014 Pearson Education, Inc.

22. Figure 6.4

23. © 2014 Pearson Education, Inc. Figure 6.4a

24. © 2014 Pearson Education, Inc. Figure 6.4b

25.  The evolution of more complex organisms does not violate the second law of thermodynamics  Entropy (disorder) may decrease in an organism, but the universe’s total entropy increases  Organisms are islands of low entropy in an increasingly random universe © 2014 Pearson Education, Inc.

26. Concept 6.2: The free-energy change of a reaction tells us whether or not 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 © 2014 Pearson Education, Inc.

27. Free-Energy Change (  G)

28. 10/20 Free Energy 10/21 Enzyme Day CH 6 notes due 10/22 review and Quiz CH6 10/23 Ch 7 – Cell Resp and Fermentation *notes due  Today’s goals –  Focus on free energy  Weird concept of energy states  Energy coupling of reactions  ATP

29. In the energy diagram below, which of the energy changes would be the same in both the enzyme- catalyzed and uncatalyzed reactions? abcdeabcde

30. abcdeabcde

31. Free Energy  1.) Free Energy is the available energy to do work  2.) Chemical reactions proceed towards a more stable state  3.) If a reaction increases amount of free energy it is more likely to happen  4.) at Equilibrium there is the minimal amount of free energy  5.) Free energy increases when a system is pushed away from equilibrium  What does this result in?

32. Weird fact of the day  There is not a release in energy when bonds are broken!  Instead the new products have less free energy than the reactants

33. Free Energy  1.) Free Energy is the available energy to do work A cell does three main kinds of work Chemical Transport Mechanical

34. Free-Energy Change (  G), Stability, and Equilibrium  A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell © 2014 Pearson Education, Inc.

35. ∆G = G final state – G initial state  Only processes with a negative ∆G are spontaneous  Spontaneous processes can be harnessed to perform work © 2014 Pearson Education, Inc.

36. Figure 6.5 (a) Gravitational motion (c) Chemical reaction (b) Diffusion More free energy (higher G) Less stable Greater work capacity Less free energy (lower G) More stable Less work capacity In a spontaneous change The free energy of the system decreases (  G  0) The system becomes more stable The released free energy can be harnessed to do work

37. © 2014 Pearson Education, Inc. Figure 6.5a More free energy (higher G) Less stable Greater work capacity Less free energy (lower G) More stable Less work capacity In a spontaneous change The free energy of the system decreases (  G  0) The system becomes more stable The released free energy can be harnessed to do work

38. © 2014 Pearson Education, Inc. Figure 6.5b (a) Gravitational motion (c) Chemical reaction (b) Diffusion

39. © 2014 Pearson Education, Inc. Figure 6.6 (a) Exergonic reaction: energy released, spontaneous (b) Endergonic reaction: energy required, nonspontaneous Amount of energy released (  G  0) Amount of energy required (  G  0) Reactants Products Energy Progress of the reaction Reactants Products Energy Progress of the reaction Free energy

40. © 2014 Pearson Education, Inc. Figure 6.6a (a) Exergonic reaction: energy released, spontaneous Amount of energy released (  G  0) Reactants Products Energy Progress of the reaction Free energy

41. © 2014 Pearson Education, Inc. Figure 6.6b (b) Endergonic reaction: energy required, nonspontaneous Amount of energy required (  G  0) Reactants Products Energy Progress of the reaction Free energy

42.  A catabolic pathway in a cell releases free energy in a series of reactions  Closed and open hydroelectric systems can serve as analogies © 2014 Pearson Education, Inc.

43. Figure 6.7 (a) An isolated hydroelectric system  G  0  G  0  G  0 (c) A multistep open hydroelectric system (b) An open hydroelectric system

44. © 2014 Pearson Education, Inc. Figure 6.7a (a) An isolated hydroelectric system  G  0  G  0

45. © 2014 Pearson Education, Inc. Figure 6.7b  G  0 (b) An open hydroelectric system

46. © 2014 Pearson Education, Inc. Figure 6.7c  G  0 (c) A multistep open hydroelectric system

47. Concept 6.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions

48.  To do work, cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one  Most energy coupling in cells is mediated by ATP © 2014 Pearson Education, Inc.

49. Figure 6.8 (a) The structure of ATP Phosphate groups (b) The hydrolysis of ATP Adenine Ribose Energy Adenosine triphosphate (ATP) Adenosine diphosphate (ADP) Inorganic phosphate

50. © 2014 Pearson Education, Inc. Figure 6.8a (a) The structure of ATP Phosphate groups Adenine Ribose

51. © 2014 Pearson Education, Inc. Figure 6.8b (b) The hydrolysis of ATP Energy Adenosine triphosphate (ATP) Adenosine diphosphate (ADP) Inorganic phosphate

52. How the Hydrolysis of ATP Performs Work  the energy from the exergonic reaction of ATP hydrolysis can be used to drive an endergonic reaction  Overall, the coupled reactions are exergonic © 2014 Pearson Education, Inc.

53. Figure 6.9 (a) Glutamic acid conversion to glutamine Glutamic acid  G Glu   3.4 kcal/mol Glutamine (b) Conversion reaction coupled with ATP hydrolysis (c) Free-energy change for coupled reaction Ammonia Glutamic acid Glutamine Phosphorylated intermediate  G Glu   3.4 kcal/mol  G ATP  −7.3 kcal/mol  G Glu   3.4 kcal/mol  G ATP  −7.3 kcal/mol   G  −3.9 kcal/mol Net

54. © 2014 Pearson Education, Inc. Figure 6.9a (a) Glutamic acid conversion to glutamine Glutamic acid  G Glu   3.4 kcal/mol Glutamine Ammonia

55. © 2014 Pearson Education, Inc. Figure 6.9b (b) Conversion reaction coupled with ATP hydrolysis Glutamic acid Glutamine Phosphorylated intermediate Phosphorylated intermediate

56. © 2014 Pearson Education, Inc. Figure 6.9c (c) Free-energy change for coupled reaction  G Glu   3.4 kcal/mol  G ATP  −7.3 kcal/mol  G Glu   3.4 kcal/mol  G ATP  −7.3 kcal/mol   G  −3.9 kcal/mol Net

57.  ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant  The recipient molecule is now called a phosphorylated intermediate  ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind to another molecule © 2014 Pearson Education, Inc.

58. Figure 6.10 (a) Transport work: ATP phosphorylates transport proteins. (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. Transport protein Solute transported Solute Motor protein Vesicle Cytoskeletal track Protein and vesicle moved

59. © 2014 Pearson Education, Inc. Figure 6.11 Energy from catabolism (exergonic, energy- releasing processes) Energy for cellular work (endergonic, energy-consuming processes) The Regeneration of ATP

60. © 2014 Pearson Education, Inc. 10/21 Enzymes Focus on: 1.) Catalysts 2.) Activation Energy 3.) Induced Fit 4.) Allosteric Sites

61. Enzyme defined:  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 © 2014 Pearson Education, Inc.

62. Figure 6.UN02 Sucrase Sucrose (C 12 H 22 O 11 ) Fructose (C 6 H 12 O 6 ) Glucose (C 6 H 12 O 6 )

63. © 2014 Pearson Education, Inc. Figure 6.12 Transition state Reactants Progress of the reaction Products  G  0 Free energy A A A B C D B B C D CD EAEA

64.  Enzymes do not affect the change in free energy (∆G); instead, they speed up reactions that would occur eventually Enzymes catalyze reactions by lowering the E A barrier

65. © 2014 Pearson Education, Inc. Figure 6.13 Products  G is unaffected by enzyme Reactants Progress of the reaction Free energy E A with enzyme is lower E A without enzyme Course of reaction without enzyme Course of reaction with enzyme

66. Vocab: Substrate, enzyme-substrate complex, active site © 2014 Pearson Education, Inc.

67.  Enzymes change shape due to chemical interactions with the substrate  This induced fit of the enzyme to the substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction © 2014 Pearson Education, Inc. Video: Enzyme Induced Fit

68. © 2014 Pearson Education, Inc. Figure 6.14 Enzyme-substrate complex Enzyme Substrate Active site

69. How do you lower E A ?  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 © 2014 Pearson Education, Inc.

70. Orienting substrates correctly

71. Straining substrate bonds

72. Providing a favorable microenvironment

73. © 2014 Pearson Education, Inc. Figure 6.15-1 Substrates Enzyme-substrate complex Substrates are held in active site by weak interactions. Substrates enter active site. 2 1

74. © 2014 Pearson Education, Inc. Figure 6.15-2 Substrates Substrates are converted to products. Enzyme-substrate complex Substrates are held in active site by weak interactions. Substrates enter active site. 3 2 1

75. © 2014 Pearson Education, Inc. Figure 6.15-3 Substrates Substrates are converted to products. Products are released. Products Enzyme-substrate complex Substrates are held in active site by weak interactions. Substrates enter active site. 4 3 2 1

76. © 2014 Pearson Education, Inc. Figure 6.15-4 Substrates Enzyme Substrates are converted to products. Products are released. Products Enzyme-substrate complex Substrates are held in active site by weak interactions. Substrates enter active site. Active site is available for new substrates. 5 4 3 2 1

77. 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 © 2014 Pearson Education, Inc.

78. Figure 6.16 Temperature (  C) Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria (77  C) Optimal temperature for typical human enzyme (37  C) Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) (a) Optimal temperature for two enzymes (b) Optimal pH for two enzymes pH 120 100 80 60 40 20 0 9 10 86 4 2 0 7 5 3 1 Rate of reaction

79. © 2014 Pearson Education, Inc. Figure 6.16a Temperature (  C) Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria (77  C) Optimal temperature for typical human enzyme (37  C) (a) Optimal temperature for two enzymes 120 10080 60 40 200 Rate of reaction

80. © 2014 Pearson Education, Inc. Figure 6.16b Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) (b) Optimal pH for two enzymes pH 9 10 86 4 2 0 7 5 3 1 Rate of reaction

81. Cofactors  Cofactors are nonprotein enzyme helpers  Cofactors may be inorganic (such as a metal in ionic form) or organic  An organic cofactor is called a coenzyme  Coenzymes include vitamins © 2014 Pearson Education, Inc.

83. 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 © 2014 Pearson Education, Inc.

84. Figure 6.17 (b) Competitive inhibition (c) Noncompetitive inhibition (a) Normal binding Competitive inhibitor Noncompetitive inhibitor Substrate Enzyme Active site

85. The Evolution of Enzymes  Enzymes are proteins encoded by genes  Changes (mutations) in genes lead to changes in amino acid composition of an enzyme  Altered amino acids in enzymes may alter their substrate specificity  Under new environmental conditions a novel form of an enzyme might be favored © 2014 Pearson Education, Inc.

86. Concept 6.5: Regulation of enzyme activity helps control metabolism  Chemical chaos would result if a cell’s metabolic pathways were not tightly regulated  A cell does this by switching on or off the genes that encode specific enzymes or by regulating the activity of enzymes © 2014 Pearson Education, Inc.

87. Allosteric Regulation of Enzymes  Allosteric regulation may either inhibit or stimulate an enzyme’s activity  Allosteric regulation occurs when a regulatory molecule binds to a protein at one site and affects the protein’s function at another site © 2014 Pearson Education, Inc.

88. 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 © 2014 Pearson Education, Inc.

89. Figure 6.18 (b) Cooperativity: another type of allosteric activation (a) Allosteric activators and inhibitors Substrate Inactive form Stabilized active form Stabilized active form Active form Active site (one of four) Allosteric enzyme with four subunits Regulatory site (one of four) Activator Oscillation Stabilized inactive form Inactive form Inhibitor Non- functional active site

90. © 2014 Pearson Education, Inc. Figure 6.18a (a) Allosteric activators and inhibitors Stabilized active form Active form Active site (one of four) Allosteric enzyme with four subunits Regulatory site (one of four) Activator Oscillation Stabilized inactive form Inactive form Inhibitor Non- functional active site

91. © 2014 Pearson Education, Inc. Figure 6.18b (b) Cooperativity: another type of allosteric activation Substrate Inactive form Stabilized active form

92.  Cooperativity is a form of allosteric regulation that can amplify enzyme activity  One substrate molecule primes an enzyme to act on additional substrate molecules more readily  Cooperativity is allosteric because binding by a substrate to one active site affects catalysis in a different active site © 2014 Pearson Education, Inc.

93. 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 © 2014 Pearson Education, Inc.

94. Figure 6.19 Active site available Intermediate A End product (isoleucine) Intermediate B Intermediate C Intermediate D Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5 Feedback inhibition Isoleucine binds to allosteric site. Isoleucine used up by cell Enzyme 1 (threonine deaminase) Threonine in active site

95. 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  In eukaryotic cells, some enzymes reside in specific organelles; for example, enzymes for cellular respiration are located in mitochondria © 2014 Pearson Education, Inc.

96. Figure 6.20 Mitochondria The matrix contains enzymes in solution that are involved in one stage of cellular respiration. Enzymes for another stage of cellular respiration are embedded in the inner membrane. 1  m

97. © 2014 Pearson Education, Inc. Figure 6.20a The matrix contains enzymes in solution that are involved in one stage of cellular respiration. Enzymes for another stage of cellular respiration are embedded in the inner membrane. 1  m

98. © 2014 Pearson Education, Inc. Figure 6.UN03

99. © 2014 Pearson Education, Inc. Figure 6.UN04 Products  G is unaffected by enzyme Reactants Progress of the reaction Free energy E A with enzyme is lower E A without enzyme Course of reaction without enzyme Course of reaction with enzyme