CampBellBiology in focus06

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(1)CAMPBELL BIOLOGY IN FOCUS Urry • Cain • Wasserman • Minorsky • Jackson • Reece. 6 An Introduction to Metabolism. Lecture Presentations by Kathleen Fitzpatrick and Nicole Tunbridge © 2014 Pearson Education, Inc..

(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. © 2014 Pearson Education, Inc..

(3) Figure 6.1. © 2014 Pearson Education, Inc..

(4) Concept 6.1: An organism’s metabolism transforms matter and energy  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. © 2014 Pearson Education, Inc..

(5) Metabolic Pathways  A metabolic pathway begins with a specific molecule and ends with a product  Each step is catalyzed by a specific enzyme. © 2014 Pearson Education, Inc..

(6) Figure 6.UN01. Enzyme 1 Starting molecule. A. © 2014 Pearson Education, Inc.. Reaction 1. Enzyme 2 B. Reaction 2. Enzyme 3 C. Reaction 3. D. 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. © 2014 Pearson Education, Inc..

(8)  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. © 2014 Pearson Education, Inc..

(9) Forms of Energy  Energy is the capacity to cause change  Energy exists in various forms, some of which can perform work. © 2014 Pearson Education, Inc..

(10)  Kinetic energy is energy associated with motion  Thermal energy is kinetic energy associated with random movement of atoms or molecules  Heat is thermal energy in transfer from one object to another  Potential energy is energy that matter possesses because of its location or structure. © 2014 Pearson Education, Inc..

(11)  Chemical energy is potential energy available for release in a chemical reaction  Energy can be converted from one form to another. Animation: Energy Concepts © 2014 Pearson Education, Inc..

(12) Figure 6.2. A diver has more potential energy on the platform.. Climbing up converts the kinetic energy of muscle movement to potential energy. © 2014 Pearson Education, Inc.. Diving converts potential energy to kinetic energy.. A diver has less potential energy in the water..

(13) 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 isolated from its surroundings  In an open system, energy and matter can be transferred between the system and its surroundings  Organisms are open systems. © 2014 Pearson Education, Inc..

(14) 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. © 2014 Pearson Education, Inc..

(15) Figure 6.3. Heat. Chemical energy. (a) First law of thermodynamics. © 2014 Pearson Education, Inc.. (b) Second law of thermodynamics.

(16) Figure 6.3a. Chemical energy. (a) First law of thermodynamics. © 2014 Pearson Education, Inc..

(17) Figure 6.3b. Heat. (b) Second law of thermodynamics. © 2014 Pearson Education, Inc..

(18) 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 of the universe.  Entropy is a measure of disorder, or randomness. © 2014 Pearson Education, Inc..

(19)  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. © 2014 Pearson Education, Inc..

(20) 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. © 2014 Pearson Education, Inc..

(21) Figure 6.4. © 2014 Pearson Education, Inc..

(22) Figure 6.4a. © 2014 Pearson Education, Inc..

(23) Figure 6.4b. © 2014 Pearson Education, Inc..

(24)  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  Organisms are islands of low entropy in an increasingly random universe. © 2014 Pearson Education, Inc..

(25) Concept 6.2: 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. © 2014 Pearson Education, Inc..

(26) Free-Energy Change (G), Stability, and Equilibrium  A living system’s free energy is energy that can do work when temperature and pressure are uniform, as in a living cell. © 2014 Pearson Education, Inc..

(27)  The change in free energy (∆G) during a chemical reaction is the difference between the free energy of the final state and the free energy of the initial state ∆G = Gfinal state – Ginitial state  Only processes with a negative ∆G are spontaneous  Spontaneous processes can be harnessed to perform work. © 2014 Pearson Education, Inc..

(28)  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  At equilibrium, forward and reverse reactions occur at the same rate; it is a state of maximum stability  A process is spontaneous and can perform work only when it is moving toward equilibrium. © 2014 Pearson Education, Inc..

(29) Figure 6.5. • 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 (a) Gravitational motion. © 2014 Pearson Education, Inc.. (b) Diffusion. (c) Chemical reaction.

(30) Figure 6.5a. • 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. • Less free energy (lower G) • More stable • Less work capacity. © 2014 Pearson Education, Inc..

(31) Figure 6.5b. (a) Gravitational motion © 2014 Pearson Education, Inc.. (b) Diffusion. (c) Chemical reaction.

(32) Free Energy and Metabolism  The concept of free energy can be applied to the chemistry of life’s processes. © 2014 Pearson Education, Inc..

(33) Exergonic and Endergonic Reactions in Metabolism  An exergonic reaction proceeds with a net release of free energy and is spontaneous; ∆G is negative  The magnitude of ∆G represents the maximum amount of work the reaction can perform. © 2014 Pearson Education, Inc..

(34) Figure 6.6. (a) Exergonic reaction: energy released, spontaneous. Free energy. Reactants. Energy. Amount of energy released (G  0) Products. Progress of the reaction (b) Endergonic reaction: energy required, nonspontaneous. Free energy. Products. Reactants. Energy. Progress of the reaction © 2014 Pearson Education, Inc.. Amount of energy required (G  0).

(35) Figure 6.6a. (a) Exergonic reaction: energy released, spontaneous. Free energy. Reactants. Energy. Progress of the reaction. © 2014 Pearson Education, Inc.. Amount of energy released (G  0) Products.

(36) Figure 6.6b. (b) Endergonic reaction: energy required, nonspontaneous. Free energy. Products. Reactants. Energy. Progress of the reaction © 2014 Pearson Education, Inc.. Amount of energy required (G  0).

(37)  An endergonic reaction absorbs free energy from its surroundings and is nonspontaneous; ∆G is positive  The magnitude of ∆G is the quantity of energy required to drive the reaction. © 2014 Pearson Education, Inc..

(38) 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. © 2014 Pearson Education, Inc..

(39)  A catabolic pathway in a cell releases free energy in a series of reactions  Closed and open hydroelectric systems can serve as analogies. © 2014 Pearson Education, Inc..

(40) Figure 6.7 G  0. G  0. (a) An isolated hydroelectric system (b) An open hydroelectric system. G  0. G  0 G  0 G  0. (c) A multistep open hydroelectric system © 2014 Pearson Education, Inc..

(41) Figure 6.7a. G  0. (a) An isolated hydroelectric system. © 2014 Pearson Education, Inc.. G  0.

(42) Figure 6.7b. (b) An open hydroelectric system. © 2014 Pearson Education, Inc.. G  0.

(43) Figure 6.7c. G  0 G  0 G  0. (c) A multistep open hydroelectric system. © 2014 Pearson Education, Inc..

(44) Concept 6.3: ATP powers cellular work by coupling exergonic reactions to endergonic reactions  A cell does three main kinds of work  Chemical  Transport  Mechanical. © 2014 Pearson Education, Inc..

(45)  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. © 2014 Pearson Education, Inc..

(46) The Structure and Hydrolysis of ATP  ATP (adenosine triphosphate) is composed of ribose (a sugar), adenine (a nitrogenous base), and three phosphate groups  In addition to its role in energy coupling, ATP is also used to make RNA. Video: ATP Space-filling Model Video: ATP Stick Model © 2014 Pearson Education, Inc..

(47) Figure 6.8. Adenine. Phosphate groups. Ribose. (a) The structure of ATP. Adenosine triphosphate (ATP). Energy Inorganic phosphate. Adenosine diphosphate (ADP). (b) The hydrolysis of ATP © 2014 Pearson Education, Inc..

(48) Figure 6.8a. Adenine. Phosphate groups. (a) The structure of ATP. © 2014 Pearson Education, Inc.. Ribose.

(49) Figure 6.8b. Adenosine triphosphate (ATP). Energy Inorganic phosphate. Adenosine diphosphate (ADP). (b) The hydrolysis of ATP © 2014 Pearson Education, Inc..

(50)  The bonds between the phosphate groups of ATP 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. © 2014 Pearson Education, Inc..

(51) 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. © 2014 Pearson Education, Inc..

(52) Figure 6.9. GGlu  3.4 kcal/mol Glutamic acid. Ammonia. Glutamine. (a) Glutamic acid conversion to glutamine. Phosphorylated intermediate. Glutamic acid. Glutamine. (b) Conversion reaction coupled with ATP hydrolysis GGlu  3.4 kcal/mol. GGlu  3.4 kcal/mol  GATP  −7.3 kcal/mol Net G  −3.9 kcal/mol © 2014 Pearson Education, Inc.. GATP  −7.3 kcal/mol (c) Free-energy change for coupled reaction.

(53) Figure 6.9a. Glutamic acid. Ammonia. Glutamine. GGlu  3.4 kcal/mol (a) Glutamic acid conversion to glutamine. © 2014 Pearson Education, Inc..

(54) Figure 6.9b. Glutamic acid. Phosphorylated intermediate. Phosphorylated intermediate. Glutamine. (b) Conversion reaction coupled with ATP hydrolysis. © 2014 Pearson Education, Inc..

(55) Figure 6.9c. GGlu  3.4 kcal/mol. GGlu  3.4 kcal/mol  GATP  −7.3 kcal/mol Net G  −3.9 kcal/mol. © 2014 Pearson Education, Inc.. GATP  −7.3 kcal/mol (c) Free-energy change for coupled reaction.

(56)  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  ATP hydrolysis leads to a change in a protein’s shape and often its ability to bind to another molecule. © 2014 Pearson Education, Inc..

(57) Figure 6.10. Transport protein. Solute. Solute transported (a) Transport work: ATP phosphorylates transport proteins. Vesicle. Motor protein. Cytoskeletal track. Protein and vesicle moved. (b) Mechanical work: ATP binds noncovalently to motor proteins and then is hydrolyzed. © 2014 Pearson Education, Inc..

(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. © 2014 Pearson Education, Inc..

(59) Figure 6.11. Energy from catabolism (exergonic, energyreleasing processes). © 2014 Pearson Education, Inc.. Energy for cellular work (endergonic, energy-consuming processes).

(60) Concept 6.4: 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. © 2014 Pearson Education, Inc..

(61) Figure 6.UN02. Sucrase. Sucrose (C12H22O11). © 2014 Pearson Education, Inc.. Glucose (C6H12O6). Fructose (C6H12O6).

(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. © 2014 Pearson Education, Inc..

(63) Figure 6.12. A. B. C. D. Free energy. Transition state. A. B. C. D. EA. Reactants A. B G  0. C. D. Products Progress of the reaction © 2014 Pearson Education, Inc..

(64) 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. Animation: How Enzymes Work © 2014 Pearson Education, Inc..

(65) Figure 6.13. Free energy. Course of reaction without enzyme. EA without enzyme. EA with enzyme is lower. Reactants Course of reaction with enzyme. G is unaffected by enzyme. Products Progress of the reaction © 2014 Pearson Education, Inc..

(66) 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  Enzyme specificity results from the complementary fit between the shape of its active site and the substrate shape. © 2014 Pearson Education, Inc..

(67)  Enzymes change shape due to chemical interactions with the substrate  This induced fit of the enzyme to the substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction. Video: Enzyme Induced Fit © 2014 Pearson Education, Inc..

(68) Figure 6.14. Substrate. Active site. Enzyme. © 2014 Pearson Education, Inc.. Enzyme-substrate complex.

(69) 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. © 2014 Pearson Education, Inc..

(70) Figure 6.15-1. 1 Substrates enter active site.. Substrates. © 2014 Pearson Education, Inc.. 2 Substrates are held in active site by weak interactions.. Enzyme-substrate complex.

(71) Figure 6.15-2. 1 Substrates enter active site.. Substrates. 2 Substrates are held in active site by weak interactions.. Enzyme-substrate complex. 3 Substrates are converted to products. © 2014 Pearson Education, Inc..

(72) Figure 6.15-3. 2 Substrates are held in active site by weak interactions.. 1 Substrates enter active site.. Substrates. Enzyme-substrate complex. 4 Products are released. Products © 2014 Pearson Education, Inc.. 3 Substrates are converted to products..

(73) Figure 6.15-4. 2 Substrates are held in active site by weak interactions.. 1 Substrates enter active site.. Substrates. Enzyme-substrate complex. 5 Active site is available for new substrates. Enzyme. 4 Products are released. Products © 2014 Pearson Education, Inc.. 3 Substrates are converted to products..

(74) 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. © 2014 Pearson Education, Inc..

(75) 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. © 2014 Pearson Education, Inc..

(76) Figure 6.16. Rate of reaction. Optimal temperature for typical human enzyme (37C). 0. Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria (77C). 40. 80 60 Temperature (C) (a) Optimal temperature for two enzymes 20. Rate of reaction. Optimal pH for pepsin (stomach enzyme). 0. 1. 2. 3. 5 pH (b) Optimal pH for two enzymes © 2014 Pearson Education, Inc.. 4. 120. 100. Optimal pH for trypsin (intestinal enzyme). 6. 7. 8. 9. 10.

(77) Figure 6.16a. Rate of reaction. Optimal temperature for typical human enzyme (37C). 80 60 Temperature (C) (a) Optimal temperature for two enzymes 0. © 2014 Pearson Education, Inc.. 20. 40. Optimal temperature for enzyme of thermophilic (heat-tolerant) bacteria (77C). 100. 120.

(78) Figure 6.16b. Rate of reaction. Optimal pH for pepsin (stomach enzyme). 0. 1. 2. 3. 5 pH (b) Optimal pH for two enzymes. © 2014 Pearson Education, Inc.. 4. Optimal pH for trypsin (intestinal enzyme). 6. 7. 8. 9. 10.

(79) 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. © 2014 Pearson Education, Inc..

(80) 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. © 2014 Pearson Education, Inc..

(81) Figure 6.17. (a) Normal binding. (b) Competitive inhibition. (c) Noncompetitive inhibition. Substrate Active site Competitive inhibitor Enzyme. Noncompetitive inhibitor. © 2014 Pearson Education, Inc..

(82) 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 alter their substrate specificity  Under new environmental conditions a novel form of an enzyme might be favored. © 2014 Pearson Education, Inc..

(83) Concept 6.5: 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. © 2014 Pearson Education, Inc..

(84) 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. © 2014 Pearson Education, Inc..

(85) 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. © 2014 Pearson Education, Inc..

(86) Figure 6.18. (a) Allosteric activators and inhibitors Allosteric enzyme with four subunits. Active site (one of four). Regulatory site (one Activator of four) Active form. Substrate. Stabilized active form. Oscillation. Nonfunctional active site. Inactive form. © 2014 Pearson Education, Inc.. Inhibitor. (b) Cooperativity: another type of allosteric activation. Stabilized inactive form. Inactive form. Stabilized active form.

(87) Figure 6.18a. (a) Allosteric activators and inhibitors Allosteric enzyme with four subunits. Regulatory site (one of four). Active site (one of four). Activator Active form. Stabilized active form. Oscillation. Nonfunctional active site © 2014 Pearson Education, Inc.. Inactive form. Inhibitor. Stabilized inactive form.

(88) Figure 6.18b. (b) Cooperativity: another type of allosteric activation Substrate. Inactive form. © 2014 Pearson Education, Inc.. Stabilized active form.

(89)  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. © 2014 Pearson Education, Inc..

(90) 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. © 2014 Pearson Education, Inc..

(91) Figure 6.19. Active site available. Isoleucine used up by cell Feedback inhibition. Threonine in active site Enzyme 1 (threonine deaminase) Intermediate A Enzyme 2 Intermediate B Enzyme 3. Isoleucine binds to allosteric site.. Intermediate C Enzyme 4 Intermediate D Enzyme 5 End product (isoleucine). © 2014 Pearson Education, Inc..

(92) 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. © 2014 Pearson Education, Inc..

(93) Figure 6.20. Mitochondria. The matrix contains enzymes in solution that are involved in one stage of cellular respiration. Enzymes for another stage of cellular respiration are embedded in the inner membrane.. 1 m © 2014 Pearson Education, Inc..

(94) Figure 6.20a. The matrix contains enzymes in solution that are involved in one stage of cellular respiration. Enzymes for another stage of cellular respiration are embedded in the inner membrane.. 1 m © 2014 Pearson Education, Inc..

(95) Figure 6.UN03. © 2014 Pearson Education, Inc..

(96) Figure 6.UN04. Free energy. Course of reaction without enzyme. EA without enzyme. EA with enzyme is lower. Reactants G is unaffected by enzyme. Course of reaction with enzyme. Products Progress of the reaction © 2014 Pearson Education, Inc..

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