Enzymes reduce the activation energy

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1 Enzymes reduce the activation energy Transition state is an unstable transitory combination of reactant molecules which occurs at the potential energy maximum (free energy maximum). Note - the ΔG of the reaction is not changed

2 Catalytic Mechanisms 1. Acid-Base Catalysis 2. Covalent Catalysis 3. Metal Ion Catalysis 4. Proximity and Orientation Effects 5. Preferential binding of the transition state

3 Catalysis through Proximity and Orientation Enzymes bring their substrates together in proper spatial relationships for reactions to occur Simply Binding Substrates Facilitates Rnxs in 4 Ways 1. Bring substrates into contact with each other and catalytic groups 2. Enzymes bind substrates with a specific orientation that aligns the substrates and catalytic groups 3. Charged groups may stablize the transition state 4. Enzymes freeze out the relative transitional and rotational motion of their substrates and catalytic groups

4 Catalysis by Preferential Transition State Binding Enzymes may bind the transition states with higher affinity than its substrates or products which increases the concentration of the transition state and therefore proportionally increases the reaction rate. Transition state analogs are potent inhibitors of enzymes that bind to the transition state

5

6 Catalytic Mechanisms 1. Acid-Base Catalysis 2. Covalent Catalysis 3. Metal Ion Catalysis 4. Proximity and Orientation Effects 5. Preferential binding of the transition state

7 Acid-Base Catalysis Side chains Asp, Glu, His, Cys, Tyr, and Lys ph sensitive

8 Covalent Catalysis Accelerates the reaction rate through transient formation of substrate - catalyst covalent bonds Steps 1. Nucleophilic reaction forming covalent bond 2. Withdrawl of electrons by now electrophilic catalyst 3. Elimination of catalyst

9 Metal Ion Catalysis 1/3 of all known enzymes require metal ions for catalytic activity Metals 1. Most common cofactors - iron, copper, magnese and cobalt 2. Structural ions - sodium, potassium and calcium 3. Both - magnesium and zinc 3 Ways metal ions participate in the catalytic process 1. Orientation of substrates 2. Oxidation -reduction 3. Electrostatic stablization

10 Example of Enzyme Mechanism - Serine Proteases Serine proteases - cleave at reactive Ser digestive enzymes, development, blood coagulation, inflammation chymotrypsin, trypsin, and elastase Digestive enzymes chymotrypsin - bulky hydrophobic residue trypsin - positively charged residues elastase - small neutral residues Are synthesized in an inactive form and are then activated when they reach the digestive tract - proenzyme (specific to proteolytic enzymes is the term zymogen)

11 Example of Enzyme Mechanism - Serine Proteases chymotrypsin - bulky hydrophobic residue trypsin - positively charged residues elastase - small neutral residues

12 Example of Enzyme Mechanism

13 Different Types of Reactions Reaction Order determined by the molecularity of the reaction how many molecules must simultaneously collide to generate the product First order - unimolecular reaction described on the previous slide Second order - bimolecular reactions 2A P v = k[a] 2 A+B P v = k[a][b] * watch the units for k, 2nd order M -1 s -1

14 Initial Velocity

15 Effect of [S] on Initial Velocity

16 Michaelis-Menton Equation Vo = V max [S] K M + [S]

17 V o = initial velocity Some Important Terms V max = maximal velocity K M = substrate concentration at which the reaction velocity is half maximal = measure of the affinity of the enzyme for its substrate (small Km achieves maximal catalytic efficiency at low [S] so high affinity) K cat = V max /[E] T = catalytic constant = turnover number (# of reaction processes that each active site catalyzes per unit time) K cat /K M = measure of catalytic efficiency

18 Lineweaver - Burke or double reciprocal plot

19

20 Enzyme Inhibition Inhibitors are substances that reduce an enzyme s activity Influence binding of substrate or turnover number Mechanism Irreversible bind to the enzyme so tightly they permanently block activity reagents that chemically modify residues Reversible structurally resemble substrate but not reactive may affect catalytic activity but not substrate binding some affect both

21 Evidence for an acyl-enzyme intermediate

22 ph dependence

23 Effects of small structural changes in the substrate on kinetic parameters

24 Three Types of Inhibition Competitive Inhibition - a substance competes directly the normal substrate for binding Uncompetitive Inhibitiona substance binds directly to the enzyme-substrate complex but not to the free enzyme Mixed Inhibition (noncompetitive inhibition) a substance affects both substrate binding and catalytic activity

25 Competitive Inhibition a substance competes directly the normal substrate for binding 1. Resembles the substrate but does not react 2. Product may compete for binding to active site 3. Transition state analog may compete for binding site

26 Competitive Inhibition a substance competes directly the normal substrate for binding 1. Resembles the substrate but does not react

27 Competitive Inhibition Product may compete for binding to active site Alcohol dehydrogenase converts alcohols into aldehydes

28 Competitive Inhibition 3. Transition state analog may compete for binding site

29 Competitive Inhibition The apparent K M = αk M α= 1 + [I]/K I S competes with I, at high [S] still reach the same V max

30 Uncompetitive Inhibition Inhibitor binds directly to the ES complex but not to the free enzyme Does not need to resemble the substrate Alters the active site rendering the enzyme inactive

31 Uncompetitive Inhibition The apparent K M = K M/ α The apparent V max = V max / α α = 1 + [I]/K I Adding S does not reverse the affects of the inhibitor as it does in competitive inhibition Inhibitor affects catalytic function of the enzyme not substrate binding V max changes unlike competitive Slope does not change - apparent K M /V max = K M /V max

32 Mixed Inhibition or Noncompetitive substance affects both substrate binding and catalytic activity The term mixed inhibition comes from the modulation of V max and K M in the MM equation Apparent V max = V max / α Apparent K M = (α / α ) K M

33 Summary of V max and K M changes

34 Regulation of Enzyme Activity 1. Control of enzyme availability 2. Control of enzyme activity product inhibition structural alterations substrate binding catalytic activity Allosteric Interactions - ligand binding at one site affects the binding of other ligands at other sites

35

36 Example of Allosteric Regulation Feedback inhibition of ATCase Regulates Pyrimidine Synthesis

37 Example of Allosteric Regulation Feedback inhibition of ATCase Regulates Pyrimidine Synthesis

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