Chapter 8: An Introduction to Metabolism

1. Chapter 8: An Introduction to Metabolism

2. Enzyme 1 Enzyme 2 Enzyme 3 A D C B Reaction 1 Reaction 2 Reaction 3 Startingmolecule Product Chapter 8: An Introduction to Metabolism • What is metabolism? • All of an organisms chemical processes • What are the different types of metabolism? • Catabolism – releases energy by breaking down complex molecules • Anabolism – use energy to build up complex molecules • Catabolic rxns – hydrolysis – break bonds • Anabolic rxns – dehydration – form bonds • How is metabolism regulated? • Enzymes

3. Chapter 8: An Introduction to Metabolism 4. What are the different forms of energy? - Kinetic – energy from molecules in motion - Potential – energy based on location or structure - water behind a dam - bonds in gas/oil/fats/starch - Chemical energy – bio speak for potential energy from release in a catabolic rxn

4. On the platform, a diver has more potential energy. Diving converts potential energy to kinetic energy. In the water, a diver has less potential energy. Climbing up converts kinetic energy of muscle movement to potential energy. Figure 8.2 Transformation between kinetic and potential energy

5. Heat co2 + Chemical energy H2O (b) (a) First law of thermodynamics: Energy can be transferred or transformed but neither created nor destroyed. For example, the chemical (potential) energy in food will be converted to the kinetic energy of the cheetah’s movement in (b). Second law of thermodynamics: Every energy transfer or transformation increases the disorder (entropy) of the universe. For example, disorder is added to the cheetah’s surroundings in the form of heat and the small molecules that are the by-products of metabolism. Chapter 8: An Introduction to Metabolism 5. What are the 2 laws of thermodynamics? - 1st law – Energy is constant. It can be transferred or transformed but it cannot be created or destroyed. - 2nd law – Every transfer or transformation of energy increases the entropy (disorder) of the universe.

6. Adenine NH2 C N C N HC O O O CH C N N –O O O O P P P CH2 O O– O– O– H H Ribose H H OH OH Phosphate groups Chapter 8: An Introduction to Metabolism • What is the difference between exergonic & endergonic rxns? - Exergonic – releases energy - Endergonic – require energy - Catabolic rxns – hydrolysis – break bonds – exergonic - Anabolic rxns – dehydration – form bonds – endergonic 7. Where does the energy come from to drive rxns in the body? - ATP

7. P P P Adenosine triphosphate (ATP) H2O Energy + P i P P Adenosine diphosphate (ADP) Inorganic phosphate Chapter 8: An Introduction to Metabolism 8. How does ATP provide energy? - hydrolysis of ATP +

8. Endergonic reaction: ∆G is positive, reaction is not spontaneous NH2 NH3 + ∆G = +3.4 kcal/mol Glu Glu Glutamine Glutamic acid Ammonia Exergonic reaction: ∆ G is negative, reaction is spontaneous ∆G = –7.3 kcal/mol + P ADP H2O ATP + Coupled reactions: Overall ∆G is negative; together, reactions are spontaneous ∆G = –3.9 kcal/mol Figure 8.10 Energy coupling using ATP hydrolysis

9. P i P Motor protein Protein moved (a) Mechanical work: ATP phosphorylates motor proteins Membrane protein ADP + ATP P i P i P Solute transported Solute (b) Transport work: ATP phosphorylates transport proteins P NH2 + + NH3 P i Glu Glu Reactants: Glutamic acid and ammonia Product (glutamine) made (c) Chemical work: ATP phosphorylates key reactants Figure 8.11 How ATP drives cellular work

10. ATP synthesis from ADP + P i requires energy ATP hydrolysis to ADP + P i yields energy ATP Energy from catabolism (exergonic, energy yielding processes) Energy for cellular work (endergonic, energy- consuming processes) ADP + P i Figure 8.12 The ATP cycle

11. Chapter 8: An Introduction to Metabolism 9. What is an enzyme? - biological catalyst made of protein 10. How do enzymes work? - lower energy of activation (EA) - EA - energy reactants must absorb before the rxn can start

12. Bonds break and new bonds form, releasing energy to the surroundings. The reactants AB and CD must absorb enough energy from the surroundings to reach the unstable transition state, where bonds can break. A B D C Transition state B A EA D C Free energy Reactants B A ∆G < O C D Products Progress of the reaction Figure 8.14 Energy profile of an exergonic reaction

13. Course of reaction without enzyme EA without enzyme EA with enzyme is lower Reactants Free energy ∆G is unaffected by enzyme Course of reaction with enzyme Products Progress of the reaction Figure 8.15 The effect of enzymes on reaction rate.

14. Substrate Active site Enzyme- substrate complex Enzyme (b) (a) Chapter 8: An Introduction to Metabolism • Some enzyme terms - substrate – what the enzyme works on – substrate specific - active site – where the substrate binds to the enzyme - induced fit – molecular handshake – when the enzyme binds to the substrate, it wraps around the substrate

15. 1 Substrates enter active site; enzyme changes shape so its active site embraces the substrates (induced fit). 2 Substrates held in active site by weak interactions, such as hydrogen bonds and ionic bonds. 3 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 6 Active site is available for two new substrate molecules. Enzyme 5 Products are Released. 4 Substrates are Converted into Products. Products Figure 8.17 The active site and catalytic cycle of an enzyme

16. Optimal temperature for enzyme of thermophilic Optimal temperature for typical human enzyme (heat-tolerant) bacteria Rate of reaction 100 60 0 80 40 20 Temperature (Cº) (a) Optimal temperature for two enzymes Optimal pH for pepsin (stomach enzyme) Optimal pH for trypsin (intestinal enzyme) Rate of reaction 4 1 0 7 2 3 5 6 8 9 10 pH Optimal pH for two enzymes (b) Optimal pH for two enzymes Chapter 8: An Introduction to Metabolism 12. What affects enzyme activity? - temperature - pH

17. Chapter 8: An Introduction to Metabolism 12. What affects enzyme activity? - temperature - pH - cofactors – non-protein helpers of enzyme activity (Zn, Fe, Cu) - coenzymes (vitamins) - inhibitors - competitive – compete w/ substrate for active site - non-competitive (allosteric) – bind remotely changing enzyme shape & inhibiting activity

18. A substrate can bind normally to the active site of an enzyme. Substrate Active site Enzyme (a) Normal binding A competitive inhibitor mimics the substrate, competing for the active site. Competitive inhibitor 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. (b) Competitive inhibition Noncompetitive inhibitor (c) Noncompetitive inhibition Figure 8.19 Inhibition of enzyme activity

19. Allosteric activaterstabilizes active from Allosteric enyzmewith four subunits Active site(one of four) Regulatorysite (oneof four) Activator Active form Stabilized active form Allosteric inhibiterstabilizes inactive form Oscillation Non-functionalactivesite Inhibitor Stabilized inactiveform Inactive form (a) Allosteric activators and inhibitors. In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again. Chapter 8: An Introduction to Metabolism 12. What affects enzyme activity? 13. How are enzymes regulated? - allosteric inhibitors - allosteric activators

20. Binding of one substrate molecule toactive site of one subunit locks all subunits in active conformation. Substrate Inactive form Stabilized active form (b)Cooperativity: another type of allosteric activation. Note that the inactive form shown on the left oscillates back and forth with the active form when the active form is not stabilized by substrate. Chapter 8: An Introduction to Metabolism 12. What affects enzyme activity? 13. How are enzymes regulated? - allosteric inhibitors - allosteric activators - cooperativity

21. Initial substrate(threonine) Active siteavailable Threoninein active site Enzyme 1(threoninedeaminase) Isoleucineused up bycell Intermediate A Feedbackinhibition Active site of enzyme 1 no longer binds threonine;pathway is switched off Enzyme 2 Intermediate B Enzyme 3 Intermediate C Isoleucine binds to allosteric site Enzyme 4 Intermediate D Enzyme 5 End product(isoleucine) Chapter 8: An Introduction to Metabolism 12. What affects enzyme activity? 13. How are enzymes regulated? - allosteric inhibitors - allosteric activators - cooperativity - feedback inhibition - compartmentalization in the cell