Enzymes and Enzyme Kinetics I. Dr. Kevin Ahern

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1 Enzymes and Enzyme Kinetics I Dr. Kevin Ahern

2 Enzymatic Reactions

3 Enzymatic Reactions

4 Enzymatically Catalyzed Reactions Background Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase Enzyme

5 Enzymatically Catalyzed Reactions Background Enzyme Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase Enzyme

6 Enzymatically Catalyzed Reactions Background Substrates Enzyme Substrate(s) Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase Enzyme

7 Enzymatically Catalyzed Reactions Background Enzyme Substrate(s) Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase Enzyme

8 Enzymatically Catalyzed Reactions Background Enzyme Substrate(s) Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase Enzyme

9 Enzymatically Catalyzed Reactions Background Enzyme Substrate(s) Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase Enzyme

10 Enzymatically Catalyzed Reactions Background Enzyme Substrate(s) Active Site Active Site Substrates Bound at Active Site of the Methylene Tetrahydrofolate Reductase Enzyme

11 Substrate Binding / Active Site Lysozyme

12 Substrate Binding / Active Site Substrate Lysozyme

13 Substrate Binding / Active Site Substrate Lysozyme Substrate Binding Site

14 Substrate Binding / Active Site Substrate Active Site Lysozyme Substrate Binding Site

15 Enzymatic Reaction

16 Enzymatic Reaction

17 Enzymatic Reaction Enzyme

18 Enzymatic Reaction Substrate A Enzyme

19 Enzymatic Reaction Substrate A Substrate B Enzyme

20 Enzymatic Reaction Substrate A Substrate B Enzyme

21 Enzymatic Reaction Substrate A Substrate B Enzyme ES Complex

22 Enzymatic Reaction Enzyme Changes Result in Reaction Between Substrates A and B

23 Enzymatic Reaction Enzyme Changes Result in Reaction Between Substrates A and B ES* Complex

24 Substrates Affect Enzymes on Binding Background A Has Become C B Has Become D Part of A Has Moved to B

25 Substrates Affect Enzymes on Binding Background A Has Become C B Has Become D Part of A Has Moved to B EP Complex

26 Substrates Affect Enzymes on Binding Background Product C Product D Released Released Enzyme Freed to Bind More Substrates

27 Substrates Affect Enzymes on Binding Background Product C Product D Released Released Enzyme Freed to Bind More Substrates E + P

28 Steps In Catalysis Background E + S <=> ES Free Enzyme & Substrates Substrate Binding Reversible <=> ES* <=> EP <=> Reaction Product Formation E + P Release of Products

29 Enzymes Mechanistics A Serine Protease

30 Enzymes Mechanistics Binding Specificity A Serine Protease

31 Enzymes Mechanistics Binding Specificity Flexibility A Serine Protease

32 Enzymes Mechanistics Binding Specificity Flexibility Electronic Environment A Serine Protease

33 Enzymes Mechanistics Binding Specificity Flexibility Electronic Environment Coenzymes A Serine Protease

34 Substrate Binding

35 Substrate Binding

36 Substrate Binding

37 Enzymes Catalysis Considerations - Models Concerted Model of Catalysis

38 Enzyme Action Free Energy of Substrate(s) Activation Energy Necessary for Uncatalyzed Reaction Overall Free Energy Change Free Energy of Product(s)

39 Enzyme Action Free Energy of Substrate(s) Activation Energy Necessary for Uncatalyzed Reaction Reaction Reverses Reaction Goes Forward Overall Free Energy Change Free Energy of Product(s)

40 Enzyme Action Activation Energy Necessary for Uncatalyzed Reaction Free Energy of Substrate(s) Activation Energy Necessary for Catalyzed Reaction No Overall Free Energy Change Free Energy of Product(s)

41 Enzyme Action Activation Energy Necessary for Uncatalyzed Reaction Free Energy of Substrate(s) Activation Energy Necessary for Catalyzed Reaction Reaction Reverses Reaction Goes Forward No Overall Free Energy Change Free Energy of Product(s)

42 Enzymatic Reactions

43 Enzymatic Reactions Enzymes lower activation energy

44 Enzymatic Reactions Enzymes lower activation energy Enzymes catalyze reversible reactions

45 Enzymatic Reactions Enzymes lower activation energy Enzymes catalyze reversible reactions Enzymes do not change overall energy

46 Enzymatic Reactions Enzymes lower activation energy Enzymes catalyze reversible reactions Enzymes do not change overall energy Enzymes do not change equilibrium concentrations

47 Enzymatic Reactions Enzymes lower activation energy Enzymes catalyze reversible reactions Enzymes do not change overall energy Enzymes do not change equilibrium concentrations Enzymes speed achieving equilibrium

48 Enzymatic Reactions

49 Enzymatic Reactions A <=> B

50 Enzymatic Reactions A <=> B At equilibrium,

51 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5

52 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly,

53 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly, [B]T0 = [B]T+5

54 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly, [B]T0 = [B]T+5 At any amount of time X after equilibrium has been reached,

55 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly, [B]T0 = [B]T+5 At any amount of time X after equilibrium has been reached, [A]T0 = [A]T+5 = [A]TX

56 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly, [B]T0 = [B]T+5 At any amount of time X after equilibrium has been reached, [A]T0 = [A]T+5 = [A]TX and

57 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly, [B]T0 = [B]T+5 At any amount of time X after equilibrium has been reached, [A]T0 = [A]T+5 = [A]TX and [B]T0 = [B] T+5 = [B]TX

58 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly, [B]T0 = [B]T+5 At any amount of time X after equilibrium has been reached, [A]T0 = [A]T+5 = [A]TX and [B]T0 = [B] T+5 = [B]TX However, unless ΔG = 0, it is wrong to say

59 Enzymatic Reactions A <=> B At equilibrium, [A]T0 = [A]T+5 Similarly, [B]T0 = [B]T+5 At any amount of time X after equilibrium has been reached, [A]T0 = [A]T+5 = [A]TX and [B]T0 = [B] T+5 = [B]TX However, unless ΔG = 0, it is wrong to say [A]T0 = [B]T0

60 Substrate Binding

61 Substrate Binding Types of Reactions

62 Substrate Binding Types of Reactions Single Substrate - Single Product : A B

63 Substrate Binding Types of Reactions Single Substrate - Single Product : A B Single Substrate - Multiple Products : A B + C

64 Substrate Binding Types of Reactions Single Substrate - Single Product : A B Single Substrate - Multiple Products : A B + C Multiple Substrates - Single Products : A + B C

65 Substrate Binding Types of Reactions Single Substrate - Single Product : A B Single Substrate - Multiple Products : A B + C Multiple Substrates - Single Products : A + B C Multiple Substrates - Multiple Products : A + B C + D

66 Substrate Binding Types of Reactions Single Substrate - Single Product : A B Single Substrate - Multiple Products : A B + C Multiple Substrates - Single Products : A + B C Multiple Substrates - Multiple Products : A + B C + D Ordered

67 Substrate Binding Types of Reactions Single Substrate - Single Product : A B Single Substrate - Multiple Products : A B + C Multiple Substrates - Single Products : A + B C Multiple Substrates - Multiple Products : A + B C + D Ordered Random

68 Substrate Binding Types of Reactions Single Substrate - Single Product : A B Single Substrate - Multiple Products : A B + C Multiple Substrates - Single Products : A + B C Multiple Substrates - Multiple Products : A + B C + D Ordered Random Ping-Pong

69 Multiple Substrate Binding

70 Multiple Substrate Binding NADH + Pyruvate Lactate + NAD + Lactate Dehydrogenase

71 Multiple Substrate Binding Ordered NADH + Pyruvate Lactate + NAD + Lactate Dehydrogenase

72 Multiple Substrate Binding Ordered NADH + Pyruvate Must bind first Lactate + NAD + Lactate Dehydrogenase

73 Multiple Substrate Binding Ordered NADH + Pyruvate Creatine + ATP Must bind first Lactate + NAD + Lactate Dehydrogenase Creatine phosphate + ADP Creatine Kinase

74 Multiple Substrate Binding Ordered NADH + Pyruvate Random Creatine + ATP Must bind first Lactate + NAD + Lactate Dehydrogenase Creatine phosphate + ADP Creatine Kinase

75 Multiple Substrate Binding Ordered Random Must bind first NADH + Pyruvate Lactate + NAD + Lactate Dehydrogenase Creatine + ATP Creatine phosphate + ADP Creatine Kinase No order to binding

76 Multiple Substrate Reactions - Double Displacement

77 Multiple Substrate Reactions - Double Displacement Two things are happening

78 Multiple Substrate Reactions - Double Displacement Two things are happening

79 Multiple Substrate Reactions - Double Displacement Two things are happening

80 Enzymes Ping-Pong Catalysis

81 Enzymes Ping-Pong Catalysis Enzyme Flips Between Two States

82 Enzymes Ping-Pong Catalysis Enzyme Flips Between Two States Enzyme Flips Between Two States

83 Enzymes Kinetic Considerations E+S <=> ES <=> ES* <=> EP <=> E+P

84 Enzymes Kinetic Considerations Rate of Formation of Product of Primary Interest E+S <=> ES <=> ES* <=> EP <=> E+P

85 Enzymes Kinetic Considerations Rate of Formation of Product of Primary Interest E+S <=> ES <=> ES* <=> EP <=> E+P If We Assume in the Simple Case that ES Proceeds Directly to E+P,

86 Enzymes Kinetic Considerations Rate of Formation of Product of Primary Interest E+S <=> ES <=> ES* <=> EP <=> E+P If We Assume in the Simple Case that ES Proceeds Directly to E+P, Kƒ E + S E S E + P Kr Kcat

87 Enzymes Kinetic Considerations Rate of Formation of Product of Primary Interest E+S <=> ES <=> ES* <=> EP <=> E+P If We Assume in the Simple Case that ES Proceeds Directly to E+P, Kƒ E + S E S E + P Kr where kf, kr, and kcat refer to the rate constants for formation of ES, reversible breakdown of ES, and conversion of ES to E+P, respectively Kcat

88 Enzymes Kinetic Considerations Rate of Formation of Product of Primary Interest E+S <=> ES <=> ES* <=> EP <=> E+P If We Assume in the Simple Case that ES Proceeds Directly to E+P, Kƒ E + S E S E + P Kr where kf, kr, and kcat refer to the rate constants for formation of ES, reversible breakdown of ES, and conversion of ES to E+P, respectively Kcat

89 Metabolic Melody

90 The Way They Work (To the tune of "The Way We Were") Copyright Kevin Ahern Enzymes Mighty powerhouse peptides Cause reactions to go faster In the cell s insides Tiny substrates Bring about an induced fit Enzyme structure is affect-ed By what binds to it Can it be that it s just simple zen? How the enzymes activate If they bind effector, will they go To an R-State, T-State? Folding Gives the mechanistic might To three-d arrangement Of the active site Enzymes Have a bias they can t hide Hydrophobic side chains are Mostly found inside Recording by David Simmons & Liz Bacon Download HERE So it s the structure For celebrating Whenever there s debating The way they work The way they work

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