An Introduction to Metabolism Chapter 8 An Introduction to Metabolism

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

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

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

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 Enzyme 1 Enzyme 2 Enzyme 3 A B C D Reaction 1 Reaction 2 Reaction 3 Starting molecule Product Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

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

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

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

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.

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

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

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

(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

Biological Order and Disorder Cells create ordered structures from less ordered materials Energy flows into an ecosystem in the form of light and exits in the form of heat Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

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

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

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

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

Free Energy and Metabolism The concept of free energy can be applied to the chemistry of life’s processes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

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

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

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

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

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

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

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

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)

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

∆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

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

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

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

+ 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

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

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)

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

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

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

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

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)

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

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

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 Each enzyme has an optimal temperature in which it can function Each enzyme has an optimal pH in which it can function Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Effects of Temperature and pH Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

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

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

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

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

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

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

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

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

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

(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

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

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

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

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)

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

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