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Chapter 8

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Chapter 8

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  1. Chapter 8 An Introduction to Metabolism

  2. An organism’s metabolism transforms matter and energy, subject to the laws of thermodynamics • Metabolism is the totality of an organism’s chemical reactions

  3. 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

  4. LE 8-UN141 Enzyme 1 Enzyme 2 Enzyme 3 A B D C Reaction 1 Reaction 2 Reaction 3 Starting molecule Product

  5. Catabolic pathways release energy by breaking down complex molecules into simpler compounds • Anabolic pathways consume energy to build complex molecules from simpler ones • Bioenergetics is the study of how organisms manage their energy resources

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

  7. 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

  8. LE 8-2 On the platform, the diver has more potential energy. Diving converts potential energy to kinetic energy. Climbing up converts kinetic energy of muscle movement to potential energy. In the water, the diver has less potential energy.

  9. 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 • Energy cannot be created or destroyed • The first law is also called the principle of conservation of energy

  10. LE 8-3 CO2 Heat Chemical energy H2O First law of thermodynamics Second law of thermodynamics

  11. 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

  12. LE 8-6a Reactants Amount of energy released (G < 0) Energy Free energy Products Progress of the reaction Exergonic reaction: energy released

  13. LE 8-6b Products Amount of energy required (G > 0) Free energy Energy Reactants Progress of the reaction Endergonic reaction: energy required

  14. The Structure and Hydrolysis of ATP • ATP (adenosine triphosphate) is the cell’s energy shuttle • ATP provides energy for cellular functions

  15. LE 8-8 Adenine Phosphate groups Ribose

  16. 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

  17. LE 8-9 P P P Adenosine triphosphate (ATP) H2O + P P P + Energy i Adenosine diphosphate (ADP) Inorganic phosphate

  18. 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

  19. LE 8-10 Endergonic reaction: DG is positive, reaction is not spontaneous NH2 NH3 DG = +3.4 kcal/mol + Glu Glu Ammonia Glutamine Glutamic acid Exergonic reaction: DG is negative, reaction is spontaneous P ATP ADP DG = –7.3 kcal/mol H2O + + i Coupled reactions: Overall DG is negative; together, reactions are spontaneous DG = –3.9 kcal/mol

  20. How ATP Performs Work • ATP drives endergonic reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant • The recipient molecule is now phosphorylated • The three types of cellular work (mechanical, transport, and chemical) are powered by the hydrolysis of ATP

  21. LE 8-11 P i P Protein moved Motor protein Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP ATP + P i P P i Solute transported Solute Transport work: ATP phosphorylates transport proteins P NH2 NH3 P + + Glu i Glu Reactants: Glutamic acid and ammonia Product (glutamine) made Chemical work: ATP phosphorylates key reactants

  22. The Regeneration of ATP • ATP is a renewable resource that is regenerated by addition of a phosphate group to 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

  23. LE 8-12 ATP Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (energonic, energy- yielding processes) P ADP + i

  24. 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

  25. LE 8-13 Sucrose C12H22O11 Glucose C6H12O6 Fructose C6H12O6

  26. 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

  27. LE 8-14 B A C D Transition state EA B A Free energy D C Reactants B A DG < O C D Products Progress of the reaction

  28. How Enzymes Lower the EA Barrier • Enzymes catalyze reactions by lowering the EAbarrier

  29. LE 8-15 Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy Course of reaction with enzyme DG is unaffected by enzyme Products Progress of the reaction

  30. 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

  31. LE 8-16 Substrate Active site Enzyme-substrate complex Enzyme

  32. Catalysis in the Enzyme’s Active Site • In an enzymatic reaction, the substrate binds to the active site

  33. LE 8-17 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. • Active site (and R groups of • its amino acids) can lower EA • and speed up a reaction by • acting as a template for • substrate orientation, • stressing the substrates • and stabilizing the • transition state, • providing a favorable • microenvironment, • participating directly in the • catalytic reaction. Substrates Enzyme-substrate complex Active site is available for two new substrate molecules. Enzyme Products are released. Substrates are converted into products. Products

  34. 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

  35. 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

  36. LE 8-18 Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) Rate of reaction 40 0 20 60 80 100 Temperature (°C) Optimal temperature for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Rate of reaction 2 3 6 7 9 10 0 1 4 5 8 pH Optimal pH for two enzymes

  37. Cofactors • Cofactors are nonprotein enzyme helpers • Coenzymes are organic cofactors

  38. 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

  39. LE 8-19 A substrate can bind normally to the active site of an enzyme. Substrate Active site Enzyme Normal binding A competitive inhibitor mimics the substrate, competing for the active site. Competitive inhibitor Competitive inhibition A noncompetitive inhibitor binds to the enzyme away from the active site, altering the conformation of the enzyme so that its active site no longer functions. Noncompetitive inhibitor Noncompetitive inhibition

  40. Allosteric Regulation of Enzymes • Allosteric regulation is the term used to describe cases where a protein’s function at one site is affected by binding of a regulatory molecule at another site • Allosteric regulation may either inhibit or stimulate an enzyme’s activity

  41. 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

  42. LE 8-20a Allosteric activator stabilizes active form. Allosteric enzyme with four subunits Active site (one of four) Regulatory site (one of four) Activator Active form Stabilized active form Oscillation Allosteric inhibitor stabilizes inactive form. Non- functional active site Inhibitor Stabilized inactive form Inactive form Allosteric activators and inhibitors

  43. 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

  44. LE 8-20b Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation. Substrate Inactive form Stabilized active form Cooperativity another type of allosteric activation

  45. 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

  46. LE 8-21 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 can’t bind theonine pathway off Intermediate B Enzyme 3 Intermediate C Isoleucine binds to allosteric site Enzyme 4 Intermediate D Enzyme 5 End product (isoleucine)