Ch. 8 An Introduction to Metabolism organism’s chemical reactions emergent property of life - from interactions b/t molecules w/in the cell Each step - catalyzed by a specific enzyme Enzyme 1 A B Reaction 1 Enzyme 2 C Reaction 2 Enzyme 3 D Reaction 3 Product Starting molecule

Metabolic Pathways Catabolic release energy breaks down molecules -> simpler compounds (ex.) Cellular respiration Anabolic consume energy build complex molecules from simpler ones Synthesis of a protein

Energy Transformations of Life The First Law of Thermodynamics The Second Law of Thermodynamics Thermodynamics – study of energy transformations

The First Law of Thermodynamics energy of the universe is constant can be transferred/transformed cannot be created/destroyed principle of conservation of energy

The Second Law of Thermodynamics During transfer/transformation some energy is unusable, lost as heat every transfer/transformation inc. the entropy (disorder) of the universe

Free-Energy Change, G free energy energy that can do work when temperature/ pressure are uniform Cellular respiration: G = -686kcal/mol Releases energy processes w/ negative ∆G - spontaneous perform work

Free Energy, Stability, and Equilibrium as free energy dec., stability of a system inc. Spontaneous – occurs w/out an input of energy performs work (∆G <0) moves towards equilibrium Equilibrium - state of maximum stability (∆G = 0)

Movement to random Gravitational motion Diffusion Chemical reaction LE 8-5 Movement to random Gravitational motion Diffusion Chemical reaction

Free Energy & Metabolism exergonic reaction proceeds with a net release of free energy spontaneous endergonic reaction absorbs free energy from its surroundings nonspontaneous

ATP – energy source for the cell hydrolysis breaks bonds b/t phosphate groups energy is released: when terminal phosphate bond - broken from chemical ∆ to a state of lower free energy Actually, the high energy content is not the result of simply the phosphate bond but the total interaction of all the atoms within the ATP molecule. Phosphate groups Ribose Adenine

Adenine (nitrogen-base) LE 8-9 3 components of ATP: 3 Phosphate groups Ribose sugar Adenine (nitrogen-base) What does this molecule remind you of? A nucleotide! Adenosine triphosphate (ATP) Energy P i Adenosine diphosphate (ADP) Inorganic phosphate H2O +

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

Reactants: Glutamic acid NH2 Glu P i NH3 ATP ADP Motor protein Mechanical work: ATP phosphorylates motor proteins Protein moved Membrane protein Solute Transport work: ATP phosphorylates transport proteins Solute transported Chemical work: ATP phosphorylates key reactants Reactants: Glutamic acid and ammonia Product (glutamine) made + 3 types of cellular work: Mechanical Transport Chemical powered by hydrolysis of ATP phosphorylation – transferring a phosphate group to a reactant

The Regeneration of ATP LE 8-12 The Regeneration of ATP The Regeneration of ATP renewable resource – ADP + Pi potential energy -drives most cellular work P i ADP Energy for cellular work (endergonic, energy- consuming processes) Energy from catabolism (exergonic, energy- yielding processes) ATP +

Enzymes speed up metabolic reactions by lowering energy barriers are catalytic proteins Ex. Hydrolysis of sucrose by sucrase Sucrose C12H22O11 Glucose C6H12O6 Fructose C6H12O6

How Enzymes Lower the EA Barrier catalyze reactions by lowering the EA do not affect the change in free-energy (∆G) hastens reactions Animation: How Enzymes Work

Progress of the reaction 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

Enzyme-Substrate Complex active site - substrate binds Induced fit – specificity enhances fit Substrate Active site Enzyme Enzyme-substrate complex

Catalysis in the Enzyme’s Active Site Enzyme-substrate complex Substrates Enzyme Products 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 are converted into products. Products are released. Active site is available for two new substrate molecules.

Catalysis in the Enzyme’s Active Site active site can lower EA by Orienting substrates correctly Straining substrate bonds Providing a favorable microenvironment Covalently bonding to the substrate

Effects on Enzyme Activity temperature and pH changes certain chemicals enzymes have optimal levels

Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic (heat-tolerant bacteria) Rate of reaction 20 40 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 1 2 3 4 5 6 7 8 9 10 pH Optimal pH for two enzymes

Cofactors & Coenzymes Cofactors - nonprotein enzyme helpers Coenzymes are organic cofactors

Enzyme Inhibitors Competitive inhibitors Noncompetitive inhibitors Substrate Active site Enzyme Competitive inhibitor Normal binding Competitive inhibition Noncompetitive inhibitor Noncompetitive inhibition A substrate can bind normally to the active site of an enzyme. A competitive inhibitor mimics the substrate, competing for the active site. 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. Competitive inhibitors bind to the active site of an enzyme competing with the substrate Noncompetitive inhibitors bind to another part of an enzyme enzyme changes shape active site less effective

Allosteric Regulation a protein’s function at one site is affected by binding of a regulatory molecule at another site inhibit or stimulate an enzyme’s activity

Allosteric Activation/Inhibition Allosteric activator stabilizes active form. Allosteric enzyme with four subunits Regulatory site (one of four) Active form Activator Stabilized active form Active site (one of four) Non- functional active site Inactive form Inhibitor Stabilized inactive form Allosteric inhibitor stabilizes inactive form. Oscillation Allosteric activators and inhibitors polypeptide subunits active and inactive forms binding of an activator stabilizes the active form of the enzyme binding of an inhibitor stabilizes the inactive form of the enzyme

Cooperativity - another type of allosteric activation allosteric regulation that can amplify enzyme activity binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits Substrate Cooperativity another type of allosteric activation Stabilized active form Inactive form Binding of one substrate molecule to active site of one subunit locks all subunits in active conformation.

Feedback Inhibition end product shuts down pathway Active site available Initial substrate (threonine) Threonine in active site Enzyme 1 (threonine deaminase) Enzyme 2 Intermediate A Isoleucine used up by cell Feedback inhibition Active site of enzyme 1 can’t bind theonine pathway off binds to allosteric site Enzyme 3 Intermediate B Enzyme 4 Intermediate C Enzyme 5 Intermediate D End product (isoleucine) end product shuts down pathway prevents a cell from wasting chemical resources by synthesizing more product than is needed