CEnzymes - Enzymes& Metabolism Enzyme characteristics...

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Unformatted text preview: Enzymes & Metabolism Enzyme characteristics Enzymes and Metabolic Pathways • Made of protein • Catalysts: – reactions occur 1,000,000 times faster with enzymes – Not part of reaction • Not changed or affected by reaction • Used over and over Why do cells need enzymes? • Not enough time to leave things to chance • Most probable reactions are not the required • Important molecules do not always occur in large quantities But since life processes are dependent upon enzymes, organisms cannot survive at high temperature – Heat denatures proteins Mechanism of Enzyme Action • (continued) Mechanism of Enzyme Action • Ability of enzymes to lower activation energy due to structure. • Each type of enzyme has has a highly-ordered, characteristic 3-dimensional shape (conformation). – Ridges, grooves, and pockets lined with specific amino acids. – Pockets active in catalyzing a reaction are called the active sites of the enzyme. Reactants must collide for reaction to occur Substrates have specific shapes to fit into the active sites (lockand-key model): – Substrate fits into active sites in enzyme. – Perfect fit may be induced: • Enzyme undergoes structural change. – Enzyme-substrate complex formed, then dissociates. – Products formed and enzyme is unaltered. Heyer 1 Enzymes & Metabolism Without enzymes, collisions are random An enzyme brings reactants together by binding to them Induced Fit Model Induced Fit Model 1. Enzyme binds substrate, forms complex 2. Substrates orient for productive collision Naming of Enzymes 3. Productive collision produces transition state 4. Reaction occurs, products are released Enzymes as Catalysts • Enzyme name ends with suffix “-ase.” • Name = substrate – action – “-ase” – E.g., glucose phosphory lase is an enzyme that adds a phosphate to glucose. – If the “action ” is left out of the name, assume the action is hydrolysis. E.g., a protease catalyzes the hydrolysis of proteins into oligopeptides or amino acids. • Different organs may make different enzymes (isoenzymes) that have the same activity. – Differences in structure do not affect the active sites. Heyer 2 Enzymes & Metabolism Regulation of Enzyme Activity • Rate of enzyme-catalyzed reactions measured by the rate that substrates (reactants) are converted to products. • Factors regulating enzyme activity: 1. Mass action: concentration of substrates and products. 2. Concentration of enzyme. • Gene expression. • Post-translational modification. • Proteolysis. Reversible Reactions • Some enzymatic reactions are reversible. – Both forward and backward reactions are catalyzed by same enzyme. carbonic anhydrase • H20 + C02 H2C03 • Law of mass action: 3. Alteration of enzyme structure. – Principal that reversible reactions will be driven from the side of the equation where concentration is higher to side where concentration is lower. • Activation. • Temperature. • pH. • But most biological reactions have complex organic substrates which require separate enzymes to catalyze the reverse reaction. 4. Cofactors and Coenzymes. 5. Inhibitors. Enzyme Activation Substrate Concentration • At a specific [enzyme], rate of product formation increases as the [substrate] increases. • Plateau of maximum velocity occurs when enzyme is saturated. • Additional [substrate] does not not increase reaction rate. • Enzymes may be produced in an inactive form. • Final post-translational modification occurs only when enzyme is needed. – In pancreas, digestive enzymes are produced as inactive zymogens, which are activated in lumen of intestine. • Part of the polypeptide is hydrolyzed off. • Protects against self-digestion. – In liver cells, enzyme is inactive when produced and is activated by addition of phosphate group. • Phosphorylation/dephosphorylation: Activation/inactivation of an enzyme. Enzyme Shape Effect of Temperature • Function of the enzyme is dependent on its shape • Destruction of shape destroys function – Heat – Acid (H +) • • • • Rate of reaction increases as temperature increases. Reaction rate plateaus, slightly above body temperature (37 o C). Reaction rate decreases as temperature increases. Enzymes denature at high temperatures. Optimal temperature for typical human enzyme Optimal temperature for enzyme of thermophilic Rate of reaction (heat-tolerant) bacteria 0 20 40 Temperature (C º ) (a) Optimal temperature for two enzymes Functional shape Heyer Denatured 80 100 Figure 8.18 3 Enzymes & Metabolism Enzyme helpers: Cofactors Effect of pH • Each enzyme exhibits peak activity at narrow pH range (pH optimum). • pH optimum reflects the pH of the body fluid in which the enzyme is found. • If pH changed, so is no longer within the enzyme range; reaction will decrease. • Alter shape or charge polarity of enzyme: makes active site available to substrate • Metal ions from dietary minerals. Substrate Active site Cofactors and Coenzymes Enzyme Inhibitors Enzyme • • • Competitive Inhibitors: Needed for the activity of specific enzymes. Cofactor: – Attachment of cofactor causes a conformational change of active site. – Participate in temporary bonds between enzyme and substrate. • Competitive inhibitor ß Shape at least partially fits in the enzymes active site È blocks substrate from binding. • Allosteric “different shape” Inhibitors: Coenzymes: ß Bind to a different location of the enzyme protein — the allosteric site È alters the shape of the protein È active site no longer fits substrates – Organic molecules derived from H20 soluble vitamins. – Transport H+ and small molecules from one enzyme to another. Allosteric inhibitor Figure 8.19 Most enzymes have allosteric regulation • Proteins change shape when regulatory molecules bind to sites. – Allosteric activators (cofactors) and/or inhibitors Allosteric enyzme with four subunits Allosteric activater stabilizes active from Active site (one of four) Ligand Regulatory site (one of four) Binding site Activator Active form Stabilized active form Oscillation Binding protein Allosteric inhibitor stabilizes inactive form Allosteric activators and inhibitors . In the cell, activators and inhibitors dissociate when at low concentrations. The enzyme can then oscillate again. Non-functional active site Heyer Enzymes are Binding Proteins • I.e., they function by binding to a substrate ( ligand ) • Other important biological regulation by means of binding proteins: • Receptors for hormones & neurotransmitters • Transporters across cell membranes • Carriers of low-solubility or fragile substances • Immune recognition Inactive form Inhibitor Stabilized inactive form Figure 8.20 All binding proteins have similar characteristics: 1. Specificity 2. Saturation 3. Competitive Inhibition 4 Enzymes & Metabolism Coupled Reactions •Catalysis of one reaction allows the catalysis of a second reaction by a different active site on the same enzyme. Substrate A Coupled Reactions: Bioenergetics Product B • Energy transfer from one molecule to another couples chemical reactions Product C Reaction 1 • Exergonic reaction: reaction releases energy • Endergonic reaction: reaction requires energy • Coupled bioenergetic reactions: the energy released by the exergonic reaction is used to power the endergonic reaction. Enzyme Substrate Y 2 Reaction Product Z •Both reactions must occur for either to occur. Free Energy & Entropy Bioenergetics More free energy (higher G ) • Less stable • work capacity • GreaterAt maximum stability • Flow of energy in living systems obeys: • 1st law of thermodynamics: • – The system is at equilibrium – Energy can be transformed, but it cannot be created or destroyed. A spontaneous change • The released free energy can be harnessed to do work • 2nd law of thermodynamics: – Energy transformations increase entropy (degree of disorganization of a system). – Only free energy (energy in organized state) can be used to do work. . Less free energy (lower G) • More stable (a) Gravitational motion. • Less work capacity Objects move spontaneously • • Systems tend to go from states of higher free energy to states of lower free energy. from a higher altitude to a lower one. Figure 8.5 Exergonic and Endergonic reactions in metabolism • An exergonic reaction – Is one that absorbs free energy from its surroundings and is nonspontaneous Products Amount of energy released (∆G <0) Energy Products Progress of the reaction (a) Exergonic reaction: energy released Free energy Free energy Reactants Energy Diffusion. Molecules in a drop of dye diffuse until they are randomly dispersed. (c) Chemical reaction. In a cell, a sugar molecule is broken down into simpler molecules. Coupled Reactions: Bioenergetics • An endergonic reaction – Proceeds with a net release of free energy and is spontaneous (b) Amount of energy released (∆G>0) Reactants • Cells must maintain highly organized, low-entropy state at the expense of free energy. – Cells cannot use heat for energy. • Energy released in exergonic reactions used to drive endergonic reactions. – Require energy released in exergonic reactions (ATP) to be directly transferred to chemicalbond energy in the products of endergonic reactions. Progress of the reaction (b) Endergonic reaction: energy required Figure 8.6 Heyer 5 Enzymes & Metabolism Endergonic and Exergonic Reactions • Endergonic : – Chemical reactions that require an input of energy to make reaction “go. ” • Products must contain more free energy than reactants. • Exergonic : – Convert molecules with more free energy to molecules with less. – Release energy in the form of heat. • Heat is measured in calories. Formation of ATP The Role of ATP: Energy transfer from one molecule to another couples chemical reactions A-P-P~P + glucose --> glucose-6~phosphate + A-P-P • Exergonic reaction: removing phosphate from ATP releases energy • Endergonic reaction: transfer of phosphate to glucose stores energy Forward reaction is exergonic Back reaction is endergonic • Formation of ATP requires the input of a large amount of energy. – Energy must be conserved, the bond produced by joining Pi to ADP must contain a part of this energy. • This energy released when ATP converted to ADP and Pi. • ATP is the universal energy carrier of the cell. • Cells use ATP by breaking phosphate bond and transferring energy to other compounds • Cells make ATP by transferring energy from other compounds to form phosphate bond Coupled Reactions: Redox Oxidation-Reduction Transfer of electrons is called oxidation-reduction • May involve the transfer of hydrogen atom [H+ + e–] rather than free electrons. • Reduced: – Molecule/atom gains electrons or hydrogen. • Reducing agent: – Molecule/atom that donates electrons or hydrogen. • Oxidized: – Molecule/atom loses electrons or hydrogen. • Oxidizing agent: – Molecule/atom that accepts electrons or hydrogen. • Reduction and oxidation are always coupled reactions. • AKA, Heyer Reduction–oxidation [“Redox”] – The reducing agent is oxidized. – The oxidizing agent is reduced. 6 Enzymes & Metabolism Coenzymes: Electron Carriers • Electron carriers: shuttles electrons (and hydrogen) between compounds • Used to transfer electrons to the electron transport chain • Carbon compounds are oxidized, carriers are reduced Coenzymes: Electron Carriers • NAD+ (nicotinamide adenine dinucleotide) – {Derived from vitamin B3: niacin} • NAD+ + H+ + 2e- ¤ NADH adenine dinucleotide) FADH+ (flavin – {Derived from vitamin B2: riboflavin} FADH+ + H+ + 2e- ¤ FADH2 • Reminder: Hydrogen = H+ + e- Oxidation-Reduction (continued) Metabolic Pathways Sequence of enzymatic reactions that begins with initial substrate, progresses through intermediates and ends with a final product. Inborn Errors of Metabolism Branched Pathways • End-Product Inhibition. • One of the final products in a divergent pathway inhibits the activity of the branch-point enzyme. – Prevents final product accumulation. – Results in shift to product in alternate pathway. Heyer • Inherited defect in a gene for enzyme synthesis. • Quantity of intermediates formed prior to the defect increases. • Final product formed after the defect decreases, producing a deficiency. 7 Enzymes & Metabolism Inborn Errors of Metabolism Example: phenylalanine metabolism Coupled Pathways: Bioenergetics • Energy transfer from one metabolic pathway to another by means of ATP. • Defective enzyme1 È phenylyketonuria [PKU] • Defective enzyme5 È alcaptonuria • Catabolic pathway (catabolism): breaking down of macromolecules. Releases energy which may be used to produce ATP. • Anabolic pathway (anabolism): building up of macromolecules. Requires energy from ATP. • Metabolism: the balance of catabolism and anabolism in the body. • Defective enzyme6 È albino Coupled Metabolic Pathways: via ATP ATP drives endergonic reactions • The three types of cellular work a re powered by the hydrolysis of ATP P i P Motor protein (a) Protein moved Mechanical work : ATP phosphorylates motor proteins Membrane protein ADP + ATP P P Solute (b ) Solute transported P NH 3 Reactants: Glutamic acid and ammonia (c) i i Transport work : ATP phosphorylates transport proteins Glu + Figure 8.11 P NH 2 Glu + P i Product (glutamine) made Chemical work : ATP phosphorylates key reactants Heterotrophic Organisms Heyer 8 ...
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