C a h p a t p e t r e r 6 E z n y z m y e m s

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1 Chapter 6 Enzymes

2 4. Examples of enzymatic reactions acid-base catalysis: give and take protons covalent catalysis: a transient covalent bond is formed between the enzyme and the substrate metal ion catalysis: metal ion participate in the catalysis

3 General Acid-base Catalysis Consider ester hydrolysis: O R O CH 3 O O + H-OH R OH + H + R + CH 3 OH OH O CH 3 Water is a poor nucleophile, and methanol is a poor leaving group Aqueous hydrolysis can be catalyzed either by acids or by bases Enzymes can do acid and base catalysis simultaneously

4 How a catalyst circumvents unfavorable charge development during cleavage of an amide. The hydrolysis of an amide bond, shown here, is the same reaction as that catalyzed by chymotrypsin and other proteases. Charge development is unfavorable and can be circumvented by donation of a proton by H 3 O + (specific acid catalysis) or HA (general acid catalysis), where HA represents any acid. Similarly, charge can be neutralized by proton abstraction by OH (specific base catalysis) or B: (general base catalysis), where B: represents any base.

5 Amino acids in general acid-base catalysis Many organic reactions are promoted by proton donors (general acids) or proton acceptors (general bases). The active sites of some enzymes contain amino acid functional groups, such as those shown here, that can participate in the catalytic process as proton donors or proton acceptors.

6 Covalent Catalysis In covalent catalysis, a transient covalent bond is formed between the enzyme and the substrate. Consider the hydrolysis of a bond between groups A and B: In the presence of a covalent catalyst (an enzyme with a nucleophilic group X:) the reaction becomes This alters the pathway of the reaction, and it results in catalysis only when the new pathway has a lower activation energy than the uncatalyzed pathway.

7 A representation of primary structure of chymotrypsin ( a serine protease), showing disulfide bonds and the amino acid residues crucial to catalysis.

8 Three-dimensional structure of chymotrypsin

9 A close-up of the active site of chymotrypsin with a substrate (mostly green) bound

10 Pre steady state kinetic evidence for an acyl-enzyme intermediate

11 Pre steady state kinetic evidence for an acyl-enzyme intermediate

12 The ph dependence of chymotrypsin-catalyzed reactions

13

14 Chymotrypsin Mechanism Step 1: Substrate Binding Hydrolytic cleavage of a peptide bond by chymotrypsin

15 Chymotrypsin Mechanism Step 2: Nucleophilic Attack

16 Chymotrypsin Mechanism Step 3: Substrate Cleavage

17 Chymotrypsin Mechanism Step 4: Water Comes In

18 Chymotrypsin Mechanism Step 5: Water Attacks

19 Chymotrypsin Mechanism Step 6: Break-off from the Enzyme

20 Chymotrypsin Mechanism Step 7: Product Dissociates General acid-base catalysis Covalent catalysis Transition-state stabilization

21 Peptidoglycan and Lysozyme Peptidoglycan is a polysaccharide found in many bacterial cell walls Cleavage of the cell wall leads to the lysis of bacteria Lysozyme is an antibacterial enzyme Cleavage of peptidoglycan by lysozyme: general acid-base catalysis + covalent catalysis

22 Ribbon diagram of lysozyme with the active-site residues Glu 35 and Asp 52 shown as blue stick structures and bound substrate shown in red

23 Reaction catalyzed by lysozyme

24 Cleavage of Peptidoglycan by Lysozyme: Two Successive Nucleophilic Displacement Reactions Asp 52 acts as a nucleophile to attack the anomeric carbon in the first S N 2 step Glu 35 acts as a general acid and protonates the leaving group in the transition state. Water hydrolyzes the covalent glycosyl-enzyme intermediate Glu 35 acts as a general base to deprotonate water in the second S N 2 step

25 Lysozyme reaction

26

27

28 Hexokinase Undergoes Induced Fit on Substrate Binding

29 Induced fit in hexokinase

30 Enolase Requires Metal Ions For Reaction

31 5. Regulatory Enzymes Exhibit increased or decreased catalytic activity in response to certain signals The first enzyme in most multienzyme systems Multisubunit proteins, with active site and regulatory sites on separate subunits Allosteric regulation by reversible, noncovalent binding of regulatory compounds called allosteric modulators or allosteric effectors Covalent regulation: reversible, covalent modification of one or more amino acids in enzyme Regulated steps are catalyzed by allosteric enzymes in many pathways

32 Factors that determine the activity of an enzyme

33 Factors that determine the activity of an enzyme

34 Subunit interactions in an allosteric enzyme, and interactions with inhibitors and activators. In many allosteric enzymes the substrate binding site and the modulator binding site(s) are on different subunits, the catalytic (C) and regulatory (R) subunits, respectively. Binding of the positive (stimulatory) modulator (M) to its specific site on the regulatory subunit is communicated to the catalytic subunit through a conformational change. This change renders the catalytic subunit active and capable of binding the substrate (S) with higher affinity. On dissociation of the modulator from the regulatory subunit, the enzyme reverts to its inactive or less active form.

35 Two views of the regulatory enzyme aspartate transcarbamoylase This allosteric regulatory enzyme has two stacked catalytic clusters, each with three catalytic polypeptide chains (in shades of blue and purple), and three regulatory clusters, each with two regulatory polypeptide chains (in red and yellow). The regulatory clusters form the points of a triangle surrounding the catalytic subunits. Binding sites for allosteric modulators are on the regulatory subunits. Modulator binding produces large changes in enzyme conformation and activity.

36 Feedback inhibition: The end product of a pathway inhibits the first enzyme of the pathway

37 Allosteric Enzymes Do Not Obey Michaelis-Menten Kinetics A homotropic enzyme: the substrate also serves as a positive (stimulatory) modulator, or activator Substrate-activity curves for representative allosteric enzymes Allosteric enzymes display a sigmoidal dependence of reaction velocity on substrate concentration.

38 The kinetic behavior of allosteric enzymes reflects cooperative interactions among enzyme subunits. Substrate-activity curves for representative allosteric enzymes The effects of a positive modulator (+) and a negative modulator ( ) on an allosteric enzyme in which K 0.5 is altered without a change in V max. The central curve shows the substrate-activity relationship without a modulator.

39 Substrate-activity curves for representative allosteric enzymes A less common type of modulation, in which V max is altered and K 0.5 is nearly constant

40 Some enzyme modification reactions

41 Protein phosphorylation and dephosphorylation

42 Regulation of muscle glycogen phosphorylase activity by multiple mechanisms

43 Multiple regulatory phosphorylations of glycogen synthase

44

45 Many proteolytic enzymes are synthesized as inactive precursors called zymogens, which are activated by cleavage of small peptide fragments. Activation of zymogens by proteolytic cleavage

46 Keywords catalytic capacity specificity K m V max allosteric regulation

47 Words of the week allosteric covalent competitive uncompetitive

48 Learning Goals To understand: why nature needs enzyme catalysis how enzymes can accelerate chemical reactions how to perform and analyze kinetic studies how to characterize enzyme inhibitors how chymotrypsin breaks down peptide bonds

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