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8 An Introduction to Metabolism

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1 8 An Introduction to Metabolism
8 An Introduction to Metabolism Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick

2 The Energy of Life The living cell is a miniature chemical factory where thousands of reactions occur The cell extracts energy stored in sugars and other fuels and applies energy to perform work Some organisms even convert energy to light, as in bioluminescence

3 Figure 8.1 Figure 8.1 What causes these breaking waves to glow?

4 Figure 8.1a Figure 8.1a What causes these breaking waves to glow? (part 1: bioluminescent fungus)

5 Concept 8.1: 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 orderly interactions between molecules

6 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

7 A B C D Starting molecule
Figure 8.UN01 Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting molecule Product Figure 8.UN01 In-text figure, generalized metabolic pathway, p. 142

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

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 energy flows through living organisms

10 Forms of Energy Energy is the capacity to cause change
Energy exists in various forms, some of which can perform work

11 Kinetic energy is energy associated with motion
Heat (thermal energy) is kinetic energy associated with random movement of atoms or molecules Potential energy is energy that matter possesses because of its location or structure Chemical energy is potential energy available for release in a chemical reaction Energy can be converted from one form to another

12 A diver has more potential energy on the platform than in the water.
Figure 8.2 A diver has more potential energy on the platform than in the water. Diving converts potential energy to kinetic energy. Figure 8.2 Transformations between potential and kinetic energy Climbing up converts the kinetic energy of muscle movement to potential energy. A diver has less potential energy in the water than on the platform.

13 Animation: Energy Concepts

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 unable to exchange energy or matter with its surroundings In an open system, energy and matter can be transferred between the system and its surroundings Organisms are open systems

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

16 Second law of thermodynamics
Figure 8.3 Heat CO2 H2O Chemical energy (a) First law of thermo- dynamics Figure 8.3 The two laws of thermodynamics (b) Second law of thermodynamics

17 First law of thermodynamics
Figure 8.3a Chemical energy Figure 8.3a The two laws of thermodynamics (part 1: conservation) (a) First law of thermodynamics

18 Second law of thermodynamics
Figure 8.3b Heat CO2 H2O Figure 8.3b The two laws of thermodynamics (part 2: entropy) (b) Second law of thermodynamics

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 (disorder) of the universe

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

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

22 Figure 8.4 Figure 8.4 Order as a characteristic of life

23 Figure 8.4a Figure 8.4a Order as a characteristic of life (part 1: sea urchin)

24 Figure 8.4b Figure 8.4b Order as a characteristic of life (part 2: succulent)

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

26 Concept 8.2: 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

27 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

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

29 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

30 • More free energy (higher G) • Less stable • Greater work capacity
Figure 8.5 • More free energy (higher G) • Less stable • Greater 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 Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change • Less free energy (lower G) • More stable • Less work capacity (a) Gravitational motion (b) Diffusion (c) Chemical reaction

31 • More free energy (higher G) • Less stable • Greater work capacity
Figure 8.5a • More free energy (higher G) • Less stable • Greater 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 Figure 8.5a The relationship of free energy to stability, work capacity, and spontaneous change (part 1: summary) • Less free energy (lower G) • More stable • Less work capacity

32 (a) Gravitational motion (b) Diffusion (c) Chemical reaction
Figure 8.5b Figure 8.5b The relationship of free energy to stability, work capacity, and spontaneous change (part 2: examples) (a) Gravitational motion (b) Diffusion (c) Chemical reaction

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

34 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

35 Exergonic reaction: energy released, spontaneous
Figure 8.6 (a) Exergonic reaction: energy released, spontaneous Reactants Amount of energy released (∆G < 0) Free energy Energy Products Progress of the reaction (b) Endergonic reaction: energy required, nonspontaneous Products Figure 8.6 Free energy changes (∆G) in exergonic and endergonic reactions Amount of energy required (∆G > 0) Free energy Energy Reactants Progress of the reaction

36 Exergonic reaction: energy released, spontaneous
Figure 8.6a (a) Exergonic reaction: energy released, spontaneous Reactants Amount of energy released (∆G < 0) Free energy Energy Products Figure 8.6a Free energy changes (∆G) in exergonic and endergonic reactions (part 1: exergonic) Progress of the reaction

37 Endergonic reaction: energy required, nonspontaneous
Figure 8.6b (b) Endergonic reaction: energy required, nonspontaneous Products Amount of energy required (∆G > 0) Free energy Energy Reactants Figure 8.6b Free energy changes (∆G) in exergonic and endergonic reactions (part 2: endergonic) Progress of the reaction

38 Equilibrium and Metabolism
Reactions in a closed system eventually reach equilibrium and then do no work

39 Figure 8.7 ∆G < 0 ∆G = 0 Figure 8.7 Equilibrium and work in an isolated hydroelectric system

40 Cells are not in equilibrium; they are open systems experiencing a constant flow of materials
A defining feature of life is that metabolism is never at equilibrium A catabolic pathway in a cell releases free energy in a series of reactions

41 ∆G < 0 ∆G < 0 ∆G < 0 ∆G < 0
Figure 8.8 (a) An open hydro- electric system ∆G < 0 ∆G < 0 ∆G < 0 ∆G < 0 Figure 8.8 Equilibrium and work in open systems (b) A multistep open hydroelectric system

42 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 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

43 The Structure and Hydrolysis of ATP
ATP (adenosine triphosphate) is the cell’s energy shuttle ATP is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups

44 Adenosine diphosphate
Figure 8.9 Adenine Triphosphate group (3 phosphate groups) Ribose (a) The structure of ATP Adenosine triphosphate (ATP) H2O Figure 8.9 The structure and hydrolysis of adenosine triphosphate (ATP) Energy Inorganic phosphate Adenosine diphosphate (ADP) (b) The hydrolysis of ATP

45 Triphosphate group (3 phosphate groups)
Figure 8.9a Adenine Triphosphate group (3 phosphate groups) Ribose Figure 8.9a The structure and hydrolysis of adenosine triphosphate (ATP) (part 1: structure) (a) The structure of ATP

46 Adenosine diphosphate
Figure 8.9b Adenosine triphosphate (ATP) H2O Energy Figure 8.9b The structure and hydrolysis of adenosine triphosphate (ATP) (part 2: hydrolysis) Inorganic phosphate Adenosine diphosphate (ADP) (b) The hydrolysis of ATP

47 Video: Space-Filling Model of ATP

48 Video: Stick Model of ATP

49 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

50 How the Hydrolysis of ATP Performs Work
The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP 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

51 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

52 i i ∆GGlu = +3.4 kcal/mol Glutamic acid Ammonia Glutamine
Figure 8.10 NH3 NH2 ∆GGlu = +3.4 kcal/mol Glu Glu Glutamic acid Ammonia Glutamine (a) Glutamic acid conversion to glutamine NH3 P 1 2 NH2 ADP ADP P i Glu ATP Glu Glu Glutamic acid Phosphorylated intermediate Glutamine (b) Conversion reaction coupled with ATP hydrolysis ∆GGlu = +3.4 kcal/mol Figure 8.10 How ATP drives chemical work: energy coupling using ATP hydrolysis NH3 NH2 ATP ADP P i Glu Glu ∆GGlu = +3.4 kcal/mol ∆GATP = −7.3 kcal/mol + ∆GATP = −7.3 kcal/mol Net ∆G = −3.9 kcal/mol (c) Free-energy change for coupled reaction

53 (a) Glutamic acid conversion to glutamine
Figure 8.10a NH3 NH2 Glu Glu Glutamic acid Ammonia Glutamine ∆GGlu = +3.4 kcal/mol (a) Glutamic acid conversion to glutamine Figure 8.10a How ATP drives chemical work: energy coupling using ATP hydrolysis (part 1: nonspontaneous reaction)

54 Phosphorylated intermediate Phosphorylated intermediate
Figure 8.10b P 1 ADP ATP Glu Glu Glutamic acid Phosphorylated intermediate NH3 P 2 NH2 ADP ADP P i Glu Glu Figure 8.10b How ATP drives chemical work: energy coupling using ATP hydrolysis (part 2: coupled reaction) Phosphorylated intermediate Glutamine (b) Conversion reaction coupled with ATP hydrolysis

55 i ∆GGlu = +3.4 kcal/mol ADP P ∆GGlu = +3.4 kcal/mol ∆GATP
Figure 8.10c ∆GGlu = +3.4 kcal/mol NH3 NH2 ATP ADP P i Glu Glu ∆GGlu = +3.4 kcal/mol ∆GATP = −7.3 kcal/mol + ∆GATP = −7.3 kcal/mol Figure 8.10c How ATP drives chemical work: energy coupling using ATP hydrolysis (part 3: free energy change) Net ∆G = −3.9 kcal/mol (c) Free-energy change for coupled reaction

56 Transport and mechanical work in the cell are also powered by ATP hydrolysis
ATP hydrolysis leads to a change in protein shape and binding ability

57 (a) Transport work: ATP phosphorylates transport proteins.
Figure 8.11 Transport protein Solute ATP ADP P i P P i Solute transported (a) Transport work: ATP phosphorylates transport proteins. Vesicle Cytoskeletal track Figure 8.11 How ATP drives transport and mechanical work ATP ADP P ATP i Motor protein Protein and vesicle moved (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed.

58 The Regeneration of ATP
ATP is a renewable resource that is regenerated by addition of a phosphate group to adenosine diphosphate (ADP) The energy to phosphorylate ADP comes from catabolic reactions in the cell The ATP cycle is a revolving door through which energy passes during its transfer from catabolic to anabolic pathways

59 ATP H2O Energy from catabolism (exergonic, energy-
Figure 8.12 ATP H2O Energy from catabolism (exergonic, energy- releasing processes) Energy for cellular work (endergonic energy-consuming processes) Figure 8.12 The ATP cycle ADP P i

60 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

61 Sucrase Sucrose (C12H22O11) Glucose (C6H12O6) Fructose (C6H12O6)
Figure 8.UN02 Sucrase Sucrose (C12H22O11) Glucose (C6H12O6) Fructose (C6H12O6) Figure 8.UN02 In-text figure, sucrose hydrolysis, p.151

62 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 (EA) Activation energy is often supplied in the form of thermal energy that the reactant molecules absorb from their surroundings

63 Progress of the reaction
Figure 8.13 A B C D Transition state A B EA Free energy C D Reactants A B Figure 8.13 Energy profile of an exergonic reaction ∆G < O C D Products Progress of the reaction

64 Animation: How Enzymes Work

65 How Enzymes Speed Up Reactions
Enzymes catalyze reactions by lowering the EA barrier Enzymes do not affect the change in free energy (∆G); instead, they hasten reactions that would occur eventually

66 Progress of the reaction
Figure 8.14 Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy Course of reaction with enzyme ∆G is unaffected by enzyme Figure 8.14 The effect of an enzyme on activation energy Products Progress of the reaction

67 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 reaction catalyzed by each enzyme is very specific

68 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

69 Substrate Active site Enzyme Enzyme-substrate complex Figure 8.15
Figure 8.15 Induced fit between an enzyme and its substrate Enzyme Enzyme-substrate complex

70 Video: Closure of Hexokinase Via Induced Fit

71 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 EA barrier by Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Covalently bonding to the substrate

72 Substrates enter active site. Substrates are held in active
Figure 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex Figure The active site and catalytic cycle of an enzyme (step 1)

73 Substrates enter active site. Substrates are held in active
Figure 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex Figure The active site and catalytic cycle of an enzyme (step 2) 3 Substrates are converted to products.

74 Substrates enter active site. Substrates are held in active
Figure 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex Figure The active site and catalytic cycle of an enzyme (step 3) 4 Products are released. 3 Substrates are converted to products. Products

75 Substrates enter active site. Substrates are held in active
Figure 1 Substrates enter active site. 2 Substrates are held in active site by weak interactions. Substrates Enzyme-substrate complex 5 Active site is available for new substrates. Figure The active site and catalytic cycle of an enzyme (step 4) Enzyme 4 Products are released. 3 Substrates are converted to products. Products

76 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

77 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 Optimal conditions favor the most active shape for the enzyme molecule

78 Optimal temperature for typical human enzyme (37C)
Figure 8.17 Optimal temperature for typical human enzyme (37C) Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria (77C) Rate of reaction 20 40 60 80 100 120 Temperature (C) (a) Optimal temperature for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Figure 8.17 Environmental factors affecting enzyme activity Rate of reaction 1 2 3 4 5 6 7 8 9 10 pH (b) Optimal pH for two enzymes

79 Optimal temperature for typical human enzyme Optimal temperature for
Figure 8.17a Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant) (37C) bacteria (77C) Rate of reaction Figure 8.17a Environmental factors affecting enzyme activity (part 1: temperature) 20 40 60 80 100 120 Temperature (C) (a) Optimal temperature for two enzymes

80 (b) Optimal pH for two enzymes
Figure 8.17b Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Rate of reaction Figure 8.17b Environmental factors affecting enzyme activity (part 2: pH) 1 2 3 4 5 6 7 8 9 10 pH (b) Optimal pH for two enzymes

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

82 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

83 (b) Competitive inhibition (c) Noncompetitive inhibition
Figure 8.18 (a) Normal binding (b) Competitive inhibition (c) Noncompetitive inhibition Substrate Active site Competitive inhibitor Enzyme Figure 8.18 Inhibition of enzyme activity Noncompetitive inhibitor

84 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 result in novel enzyme activity or altered substrate specificity Under new environmental conditions a novel form of an enzyme might be favored For example, six amino acid changes improved substrate binding and breakdown in E. coli

85 Two changed amino acids were found near the active site. Active site
Figure 8.19 Two changed amino acids were found near the active site. Active site Figure 8.19 Mimicking evolution of an enzyme with a new function Two changed amino acids were found in the active site. Two changed amino acids were found on the surface.

86 Concept 8.5: 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

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

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

89 (a) Allosteric activators and inhibitors
Figure 8.20 (a) Allosteric activators and inhibitors (b) Cooperativity: another type of allosteric activation Allosteric enzyme with four subunits Active site (one of four) Substrate Regulatory site (one of four) Activator Active form Stabilized active form Inactive form Stabilized active form Oscillation Non- functional active site Figure 8.20 Allosteric regulation of enzyme activity Inhibitor Inactive form Stabilized inactive form

90 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

91 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

92 Active site available Threonine in active site Enzyme 1 (threonine
Figure 8.21 Active site available Threonine in active site Enzyme 1 (threonine deaminase) Isoleucine used up by cell Intermediate A Feedback inhibition Active site no longer available; pathway is halted. Enzyme 2 Intermediate B Enzyme 3 Intermediate C Isoleucine binds to allosteric site. Enzyme 4 Figure 8.21 Feedback inhibition in isoleucine synthesis Intermediate D Enzyme 5 End product (isoleucine)

93 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

94 enzymes in solution that are involved on one stage
Figure 8.22 Mitochondria The matrix contains enzymes in solution that are involved on one stage of cellular respiration. Figure 8.22 Organelles and structural order in metabolism Enzymes for another stage of cellular respiration are embedded in the inner membrane 1 µm

95 enzymes in solution that are involved in one stage
Figure 8.22a The matrix contains enzymes in solution that are involved in one stage of cellular respiration. Figure 8.22a Organelles and structural order in metabolism (part 1: TEM) Enzymes for another stage of cellular respiration are embedded in the inner membrane. 1 µm

96 Figure 8.UN03a Figure 8.UN03a Skills exercise: making a line graph and calculating a slope (part 1)

97 Figure 8.UN03b Figure 8.UN03b Skills exercise: making a line graph and calculating a slope (part 2)

98 Progress of the reaction
Figure 8.UN04 Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy ∆G is unaffected by enzyme Course of reaction with enzyme Figure 8.UN04 Summary of key concepts: enzymes and activation energy Products Progress of the reaction

99 Figure 8.UN05 Figure 8.UN05 Test your understanding, question 11 (energy conversions)


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