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

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

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.

(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

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

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

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

(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

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

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

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

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

(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

(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

(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

Adenine Phosphate groups Ribose Fig. 8-8 Figure 8.8 The structure of adenosine triphosphate (ATP) Ribose

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)

∆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

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

+ 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

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)

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

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

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)

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

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

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

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

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

(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

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

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

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

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)

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

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

Crystal structure of the DHFR domain of P. vivax. Crystal structure of the DHFR domain of P. vivax. (A) Structure of P. vivax DHFR complexed with NADPH and Pyr; α-helices are in red, and β-strands are in blue, including the Insert-1 loop and the Insert-2 α-helix. The carbons, nitrogen, oxygen, and chlorine atoms of Pyr and NADPH are shown in yellow, blue, red, and magenta, respectively. (B) Comparison of the DHFR domains from P. vivax (green) and P. falciparum (magenta). The superimposed structures demonstrate overall structural similarity with major deviation in the insert regions. Palangpon Kongsaeree et al. PNAS 2005;102:13046-13051 ©2005 by National Academy of Sciences

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

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