1. An Introduction to Metabolism
Chapter 8
An Introduction to Metabolism

2. 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
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3. Fig. 8-1
Figure 8.1 What causes the bioluminescence in these fungi?

4. Metabolism is the totality of an organism’s chemical reactions
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 interactions between molecules within the cell
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5. 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
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6. Starting molecule Product
Fig. 8-UN1
Enzyme 1
Enzyme 2
Enzyme 3 A B C D
Reaction 1
Reaction 2
Reaction 3
Starting
molecule
Product

7. 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
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8. The synthesis of protein from amino acids is an example of anabolism
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
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9. Energy is the capacity to cause change
Forms of Energy
Energy is the capacity to cause change
Energy exists in various forms, some of which can perform work
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10. Animation: Energy Concepts
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
Animation: Energy Concepts
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11. Fig. 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.

12. The Laws of Energy Transformation
Thermodynamics is the study of energy transformations
A closed 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
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13. 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
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14. 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
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15. (a) First law of thermodynamics (b) Second law of thermodynamics
Fig. 8-3
Heat
CO2 +
Chemical
energy
H2O
Figure 8.3 The two laws of thermodynamics
(a) First law of thermodynamics
(b) Second law of thermodynamics

16. 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
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17. 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
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18. Fig. 8-4
Figure 8.4 Order as a characteristic of life
50 µm

19. 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
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20. 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
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21. 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
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22. Only processes with a negative ∆G are spontaneous
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 (T):
∆G = ∆H – T∆S
Only processes with a negative ∆G are spontaneous
Spontaneous processes can be harnessed to perform work
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23. 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
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24. Fig. 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
Less free energy (lower G)
More stable
Less work capacity
Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change
(a) Gravitational motion
(b) Diffusion
(c) Chemical reaction

25. More free energy (higher G) Less stable Greater work capacity
Fig. 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 8.5 The relationship of free energy to stability, work capacity, and spontaneous change
Less free energy (lower G)
More stable
Less work capacity

26. (a) Gravitational motion (b) Diffusion (c) Chemical reaction
Fig. 8-5b
Spontaneous
change
Spontaneous
change
Spontaneous
change
Figure 8.5 The relationship of free energy to stability, work capacity, and spontaneous change
(a) Gravitational motion
(b) Diffusion
(c) Chemical reaction

27. Free Energy and Metabolism
The concept of free energy can be applied to the chemistry of life’s processes
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28. 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
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29. Progress of the reaction
Fig. 8-6
Reactants
Amount of
energy
released
(∆G < 0)
Energy
Free energy
Products
Progress of the reaction
(a) Exergonic reaction: energy released
Products
Figure 8.6 Free energy changes (ΔG) in exergonic and endergonic reactions
Amount of
energy
required
(∆G > 0)
Energy
Free energy
Reactants
Progress of the reaction
(b) Endergonic reaction: energy required

30. Amount of energy released (∆G < 0)
Fig. 8-6a
Reactants
Amount of
energy
released
(∆G < 0)
Free energy
Energy
Products
Figure 8.6a Free energy changes (ΔG) in exergonic and endergonic reactions
Progress of the reaction
(a) Exergonic reaction: energy released

31. Amount of energy required (∆G > 0)
Fig. 8-6b
Products
Amount of
energy
required
(∆G > 0)
Energy
Free energy
Reactants
Figure 8.6b Free energy changes (ΔG) in exergonic and endergonic reactions
Progress of the reaction
(b) Endergonic reaction: energy required

32. 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 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
Closed and open hydroelectric systems can serve as analogies
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33. Figure 8.7 Equilibrium and work in isolated and open systems
(a) An isolated hydroelectric system
(b) An open hydroelectric
system
∆G < 0
Figure 8.7 Equilibrium and work in isolated and open systems
∆G < 0
∆G < 0
∆G < 0
(c) A multistep open hydroelectric system

34. (a) An isolated hydroelectric system
Fig. 8-7a
∆G < 0
∆G = 0
Figure 8.7a Equilibrium and work in isolated and open systems
(a) An isolated hydroelectric system

35. (b) An open hydroelectric system
Fig. 8-7b
∆G < 0
Figure 8.7b Equilibrium and work in isolated and open systems
(b) An open hydroelectric system

36. (c) A multistep open hydroelectric system
Fig. 8-7c
∆G < 0
∆G < 0
∆G < 0
Figure 8.7c Equilibrium and work in isolated and open systems
(c) A multistep open hydroelectric system

37. 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
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38. 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
For the Cell Biology Video Space Filling Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.
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39. Adenine Phosphate groups Ribose Fig. 8-8
Figure 8.8 The structure of adenosine triphosphate (ATP)
Ribose

40. Energy is released from ATP when the terminal phosphate bond is broken
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
For the Cell Biology Video Stick Model of ATP (Adenosine Triphosphate), go to Animation and Video Files.
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41. H2O P P P Adenosine triphosphate (ATP) P + P P + Energy
Fig. 8-9 P P P
Adenosine triphosphate (ATP)
H2O
Figure 8.9 The hydrolysis of ATP P + P P +
Energy i
Inorganic phosphate
Adenosine diphosphate (ADP)

42. Overall, the coupled reactions are exergonic
How 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
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43. ∆G = +3.4 kcal/mol Glutamic acid Ammonia Glutamine
Fig. 8-10
NH2
NH3 +
∆G = +3.4 kcal/mol
Glu
Glu
Glutamic
acid
Ammonia
Glutamine
(a) Endergonic reaction 1
ATP phosphorylates
glutamic acid,
making the amino
acid less stable. P +
ATP +
ADP
Glu
Glu
NH2 P 2
Ammonia displaces
the phosphate group,
forming glutamine.
NH3 + + P i
Glu
Glu
Figure 8.10 How ATP drives chemical work: Energy coupling using ATP hydrolysis
(b) Coupled with ATP hydrolysis, an exergonic reaction
(c) Overall free-energy change

44. The recipient molecule is now phosphorylated
ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant
The recipient molecule is now phosphorylated
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45. Membrane protein Solute Solute transported Vesicle Cytoskeletal track
Fig. 8-11
Membrane protein P P i
Solute
Solute transported
(a) Transport work: ATP phosphorylates
transport proteins
ADP
ATP + P i
Vesicle
Cytoskeletal track
Figure 8.11 How ATP drives transport and mechanical work
ATP
Motor protein
Protein moved
(b) Mechanical work: ATP binds noncovalently
to motor proteins, then is hydrolyzed

46. 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 chemical potential energy temporarily stored in ATP drives most cellular work
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47. + H2O Energy for cellular work (endergonic, energy-consuming
Fig. 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

48. An enzyme is a catalytic protein
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
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49. Sucrose (C12H22O11) Sucrase Glucose (C6H12O6) Fructose (C6H12O6)
Fig. 8-13
Sucrose (C12H22O11)
Sucrase
Figure 8.13 Example of an enzyme-catalyzed reaction: hydrolysis of sucrose by sucrase
Glucose (C6H12O6)
Fructose (C6H12O6)

50. 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 heat from the surroundings
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51. Progress of the reaction
Fig. 8-14 A B C D
Transition state A B EA C D
Free energy
Reactants A B
Figure 8.14 Energy profile of an exergonic reaction
∆G < O C D
Products
Progress of the reaction

52. How Enzymes Lower the EA Barrier
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
Animation: How Enzymes Work
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53. Progress of the reaction
Fig. 8-15
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 8.15 The effect of an enzyme on activation energy
Products
Progress of the reaction

54. 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
For the Cell Biology Video Closure of Hexokinase via Induced Fit, go to Animation and Video Files.
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55. Substrate Active site Enzyme Enzyme-substrate complex (a) (b)
Fig. 8-16
Substrate
Active site
Figure 8.16 Induced fit between an enzyme and its substrate
Enzyme
Enzyme-substrate
complex
(a)
(b)

56. 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
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57. Fig. 8-17
Substrates enter active site; enzyme
changes shape such that its active site
enfolds the substrates (induced fit). 1
Substrates held in
active site by weak
interactions, such as
hydrogen bonds and
ionic bonds. 2
Substrates
Enzyme-substrate
complex
Active site can lower EA
and speed up a reaction. 3
Active
site is
available
for two new
substrate
molecules. 6
Figure 8.17 The active site and catalytic cycle of an enzyme
Enzyme 5
Products are
released.
Substrates are
converted to
products. 4
Products

58. 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
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59. 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
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60. Optimal temperature for typical human enzyme Optimal temperature for
Fig. 8-18
Optimal temperature for
typical human enzyme
Optimal temperature for
enzyme of thermophilic
(heat-tolerant)
bacteria
Rate of reaction 20 40 60 80
100
Temperature (ºC)
(a) Optimal temperature for two enzymes
Optimal pH for pepsin
(stomach enzyme)
Optimal pH
for trypsin
(intestinal
enzyme)
Figure 8.18 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

61. 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
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62. 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
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63. Noncompetitive inhibitor
Fig. 8-19
Substrate
Active site
Competitive
inhibitor
Enzyme
Figure 8.19 Inhibition of enzyme activity
Noncompetitive inhibitor
(a) Normal binding
(b) Competitive inhibition
(c) Noncompetitive inhibition

64. 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
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65. 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
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66. 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
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67. Figure 8.20 Allosteric regulation of enzyme activity
Allosteric enyzme
with four subunits
Active site
(one of four)
Regulatory
site (one
of four)
Activator
Active form
Stabilized active form
Oscillation
Non-
functional
active
site
Inhibitor
Inactive form
Stabilized inactive
form
Figure 8.20 Allosteric regulation of enzyme activity
(a) Allosteric activators and inhibitors
Substrate
Inactive form
Stabilized active
form
(b) Cooperativity: another type of allosteric activation

68. Stabilized active form
Fig. 8-20a
Allosteric enzyme
with four subunits
Active site
(one of four)
Regulatory
site (one
of four)
Activator
Active form
Stabilized active form
Oscillation
Figure 8.20a Allosteric regulation of enzyme activity
Non-
functional
active
site
Inhibitor
Inactive form
Stabilized inactive
form
(a) Allosteric activators and inhibitors

69. 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
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70. (b) Cooperativity: another type of allosteric activation
Fig. 8-20b
Substrate
Inactive form
Stabilized active
form
Figure 8.20b Allosteric regulation of enzyme activity
(b) Cooperativity: another type of allosteric activation

71. Identification of Allosteric Regulators
Allosteric regulators are attractive drug candidates for enzyme regulation
Inhibition of proteolytic enzymes called caspases may help management of inappropriate inflammatory responses
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72. Hypothesis: allosteric inhibitor locks enzyme in inactive form
Fig. 8-21
EXPERIMENT
Caspase 1
Active
site
Substrate SH SH
Known active form
Active form can
bind substrate
Allosteric
binding site SH
S–S
Allosteric
inhibitor
Known inactive form
Hypothesis: allosteric
inhibitor locks enzyme
in inactive form
Figure 8.21 Are there allosteric inhibitors of caspase enzymes?
RESULTS
Caspase 1
Inhibitor
Active form
Allosterically
inhibited form
Inactive form

73. EXPERIMENT Allosteric binding site Allosteric inhibitor Caspase 1
Fig. 8-21a
EXPERIMENT
Caspase 1
Active
site
Substrate SH SH
Known active form
Active form can
bind substrate
Figure 8.21 Are there allosteric inhibitors of caspase enzymes?
Allosteric
binding site SH
S–S
Allosteric
inhibitor
Known inactive form
Hypothesis: allosteric
inhibitor locks enzyme
in inactive form

74. RESULTS Caspase 1 Inhibitor Active form Allosterically inhibited form
Fig. 8-21b
RESULTS
Caspase 1
Inhibitor
Figure 8.21 Are there allosteric inhibitors of caspase enzymes?
Active form
Allosterically
inhibited form
Inactive form

75. 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
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76. Fig. 8-22
Initial substrate
(threonine)
Active site
available
Threonine
in active site
Enzyme 1
(threonine
deaminase)
Isoleucine
used up by
cell
Intermediate A
Feedback
inhibition
Enzyme 2
Active site of
enzyme 1 no
longer binds
threonine;
pathway is
switched off.
Intermediate B
Enzyme 3
Intermediate C
Figure 8.22 Feedback inhibition in isoleucine synthesis
Isoleucine
binds to
allosteric
site
Enzyme 4
Intermediate D
Enzyme 5
End product
(isoleucine)

77. 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
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78. Fig. 8-23
Mitochondria
Figure 8.23 Organelles and structural order in metabolism
1 µm

79. Progress of the reaction
Fig. 8-UN2
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
Products
Progress of the reaction

80. Fig. 8-UN3

81. Fig. 8-UN4

82. Fig. 8-UN5

83. You should now be able to:
Distinguish between the following pairs of terms: catabolic and anabolic pathways; kinetic and potential energy; open and closed systems; exergonic and endergonic reactions
In your own words, explain the second law of thermodynamics and explain why it is not violated by living organisms
Explain in general terms how cells obtain the energy to do cellular work
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84. Explain how ATP performs cellular work
Explain why an investment of activation energy is necessary to initiate a spontaneous reaction
Describe the mechanisms by which enzymes lower activation energy
Describe how allosteric regulators may inhibit or stimulate the activity of an enzyme
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