prentice hall c2002chapter 61 principles of biochemistry fourth edition chapter 6 mechanisms of...
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Prentice Hall c2002 Chapter 6 1
Principles of BiochemistryFourth Edition
Chapter 6Mechanisms of Enzymes
Copyright © 2006 Pearson Prentice Hall, Inc.
Horton • Moran • Scrimgeour • Perry • Rawn
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Prentice Hall c2002 Chapter 6 2
Chapter 6 Mechanisms of Enzymes
• Mechanisms - the molecular details of catalyzed reactions
• Enzyme mechanisms deduced from:
Kinetic experiments
Protein structural studies
Studies of nonenzymatic model systems
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Prentice Hall c2002 Chapter 6 3
6.1 The Terminology of Mechanistic Chemistry
• A reaction mechanism describes the details of a reaction
• Reactants, products and intermediates are identified
• Enzymatic mechanisms use the same symbolism used in organic chemistry
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Prentice Hall c2002 Chapter 6 4
Nucleophilic substitution reactions
• Nucleophilic species are electron rich, and electrophilic species are electron poor
• Types of nucleophilic substitution reactions include:
(1) Formation of a tetrahedral intermediate by nucleophilic substitution
(2) Direct displacement via a transition state
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Prentice Hall c2002 Chapter 6 5
Two types of nucleophilic substitution reactions
• Formation of a tetrahedral intermediate
• Direct displacement
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Prentice Hall c2002 Chapter 6 6
Cleavage reactions
• Carbanion formation
• Carbocation formation
• Free radical formation
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Prentice Hall c2002 Chapter 6 7
Oxidation-reduction reactions
• Electrons are transferred between two species
• Oxidizing agent gains electrons (is reduced)
• Reducing agent donates electrons (is oxidized)
• Formaldehyde is oxidized by oxygen (below)
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Prentice Hall c2002 Chapter 6 8
6.2 Catalysts Stabilize Transition States
Fig 6.1 Energy diagram for a single-step reaction
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Prentice Hall c2002 Chapter 6 9
Fig 6.2 Energy diagram for reaction with intermediate
• Intermediate occurs in the trough between the two transition states
• Rate determining step in the forward direction is formation of the first transition state
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Prentice Hall c2002 Chapter 6 10
Enzymes lower the activation energy of a reaction
(1) Substrate binding
• Enzymes properly position substrates for reaction(makes the formation of the transition state more frequent and lowers the energy of activation)
(2) Transition state binding
• Transition states are bound more tightly than substrates (this also lowers the activation energy)
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Prentice Hall c2002 Chapter 6 11
Fig 6.3 Enzymatic catalysis of the reaction A+B A-B
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Prentice Hall c2002 Chapter 6 12
6.3 Chemical Modes of Enzymatic Catalysis
A. Polar Amino Acid Residues in Active Sites
• Active-site cavity of an enzyme is lined with hydrophobic amino acids
• Polar, ionizable residues at the active site participate in the mechanism
• Anions and cations of certain amino acids are commonly involved in catalysis
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Prentice Hall c2002 Chapter 6 13
Table 6.1
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Prentice Hall c2002 Chapter 6 14
Table 6.2 pKa Values of amino acid ionizable groups in proteins
Group pKa
Terminal -carboxyl 3-4
Side-chain carboxyl 4-5
Imidazole 6-7
Terminal -amino 7.5-9
Thiol 8-9.5
Phenol 9.5-10
-Amino ~10
Guanidine ~12
Hydroxymethyl ~16
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Prentice Hall c2002 Chapter 6 15
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Prentice Hall c2002 Chapter 6 16
B. Acid-Base Catalysis
• Reaction acceleration is achieved by catalytic transfer of a proton
• A general base (B:) can act as a proton acceptor to remove protons from OH, NH, CH or other XH
• This produces a stronger nucleophilic reactant (X:-)
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Prentice Hall c2002 Chapter 6 17
General base catalysis reactions (continued)
• A general base (B:) can remove a proton from water and thereby generate the equivalent of
OH- in neutral solution
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Prentice Hall c2002 Chapter 6 18
Proton donors can also catalyze reactions
• A general acid (BH+) can donate protons
• A covalent bond may break more easily if one of its atoms is protonated (below)
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Prentice Hall c2002 Chapter 6 19
C. Covalent Catalysis
• All or part of a substrate is bound covalently to the enzyme to form a reactive intermediate
• Group X can be transferred from A-X to B in two steps via the covalent ES complex X-E
A-X + E X-E + A
X-E + B B-X + E
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Prentice Hall c2002 Chapter 6 20
Sucrose phosphorylase exhibits covalent catalysis
Step one: a glucosyl residue is transferred to enzyme
*Sucrose + Enz Glucosyl-Enz + Fructose
Step two: Glucose is donated to phosphate
Glucosyl-Enz + Pi Glucose 1-phosphate + Enz
*(Sucrose is composed of a glucose and a fructose)
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Prentice Hall c2002 Chapter 6 21
D. pH Affects Enzymatic Rates
• Catalytic mechanisms are dependent upon the state of ionization of catalytic groups
• Plots of reaction velocity versus pH can indicate important ionizable catalytic groups
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Prentice Hall c2002 Chapter 6 22
Fig 6.4 pH-rate profile for papain
• The two inflection points approximate the pKa values of the two ionizable residues
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Prentice Hall c2002 Chapter 6 23
Fig 6.5
• Papain’s activity depends upon ionizable residues:His-159 and Cys-25
(a) Ribbon model(b) Active site residues
(N blue, S yellow)
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Prentice Hall c2002 Chapter 6 24
Fig. 6.6
Three ionic forms of papain. Only the upper tautomer of the middle pair is active
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Prentice Hall c2002 Chapter 6 25
6.4 Diffusion-Controlled Reactions
• Enzyme rates can approach the physical limit of the rate of diffusion of two molecules in solution
• Under physiological conditions the encounter frequency is about 108 to 109 M-1s-1
• A few enzymes have rate-determining steps that are roughly as fast as the binding of substrates to the enzymes
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Prentice Hall c2002 Chapter 6 26
Table 6.4
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Prentice Hall c2002 Chapter 6 27
A. Triose Phosphate Isomerase (TPI)
• TPI catalyzes a rapid aldehyde-ketone interconversion
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Prentice Hall c2002 Chapter 6 28
Role of active site residues in TPI catalysis
• TPI has two ionizable active-site residues
• Glu acts as a general acid-base catalyst
• His shuttles protons between oxygens of an enzyme-bound intermediate
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Prentice Hall c2002 Chapter 6 29
Fig 6.7 Proposed mechanism for TPI
• General acid-base catalysis mechanism (4 slides)
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Prentice Hall c2002 Chapter 6 30
Fig 6.7 TPI mechanism (continued)
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Prentice Hall c2002 Chapter 6 31
Fig 6.7 TPI mechanism (continued)
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Prentice Hall c2002 Chapter 6 32
Fig 6.7 TPI mechanism (continued)
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Prentice Hall c2002 Chapter 6 33
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Prentice Hall c2002 Chapter 6 34
Fig 6.9 Energy diagram for the TPI reaction
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Prentice Hall c2002 Chapter 6 35
B. Superoxide Dismutase
• Superoxide dismutase is a very fast catalyst because: (1) The negatively charged substrate is
attracted by a positively charged electric field near the active site
(2) The reaction itself is very fast
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Prentice Hall c2002 Chapter 6 36
Two step reaction of superoxide dismutase
• An atom of copper bound to the enzyme is reduced and then oxidized
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Prentice Hall c2002 Chapter 6 37
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Prentice Hall c2002 Chapter 6 38
6.5 Binding Modes of Enzymatic Catalysis
• Proper binding of reactants in enzyme active sites provides substrate specificity and catalytic power
• Two catalytic modes based on binding properties can each increase reaction rates over 10,000-fold :
(1) Proximity effect - collecting and positioning substrate molecules in the active site
(2) Transition-state (TS) stabilization - transition states bind more tightly than substrates
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Prentice Hall c2002 Chapter 6 39
Binding forces utilized for catalysis
1. Charge-charge interactions
2. Hydrogen bonds
3. Hydrophobic interactions
4. Van der Waals forces
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Prentice Hall c2002 Chapter 6 40
A. The Proximity Effect
• Correct positioning of two reacting groups (in model reactions or at enzyme active sites):
(1) Reduces their degrees of freedom
(2) Results in a large loss of entropy
(3) The relative enhanced concentration of substrates (“effective molarity”) predicts the rate acceleration expected due to this effect
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Prentice Hall c2002 Chapter 6 41
Effective molarity
k1(s-1)
Effective molarity =
k2(M-1s-1)
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Prentice Hall c2002 Chapter 6 42
Fig 6.11 Reactions of carboxylates with phenyl esters
• Increased rates are seen when the reactants are held more rigidly in proximity (continued next slide)
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Prentice Hall c2002 Chapter 6 43
Fig. 6.11 (continued)
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Prentice Hall c2002 Chapter 6 44
B. Weak Binding of Substrates to Enzymes
• Energy is required to reach the transition state from the ES complex
• Excessive ES stabilization would create a “thermodynamic pit” and mean little or no catalysis
• Most Km values (substrate dissociation constants) indicate weak binding to enzymes
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Prentice Hall c2002 Chapter 6 45
Fig 6.12 Energy of substrate binding
• If an enzyme binds the substrate too tightly (dashed profile), the activation barrier (2) could be similar to that of the uncatalyzed reaction (1)
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Prentice Hall c2002 Chapter 6 46
C. Induced Fit
• Induced fit activates an enzyme by substrate-initiated conformation effect
• Induced fit is a substrate specificity effect, not a catalytic mode
• Hexokinase mechanism requires sugar-induced closure of the active site
Glucose + ATP Glucose 6-phosphate + ADP
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Prentice Hall c2002 Chapter 6 47
Fig 6.13 Stereo views of yeast hexokinase
• Yeast hexokinase contains 2 domains connected by a hinge region. Domains close on glucose binding.
(a) Open conformation
(b) Closed conformation
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Prentice Hall c2002 Chapter 6 48
D. Transition-State (TS) Stabilization
• An increased interaction of the enzyme and substrate occurs in the transition-state (ES‡)
• The enzyme distorts the substrate, forcing it toward the transition state
• An enzyme must be complementary to the transition-state in shape and chemical character
• Enzymes may bind their transition states 1010 to 1015 times more tightly than their substrates
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Prentice Hall c2002 Chapter 6 49
Transition-state (TS) analogs
• Transition-state analogs are stable compounds whose structures resemble unstable transition states
• Fig. 6.14 2-Phosphoglycolate, a TS analog for the enzyme triose phosphate isomerase
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Prentice Hall c2002 Chapter 6 50
Fig 6.15 Inhibition of adenosine deaminase by a TS analog
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Prentice Hall c2002 Chapter 6 51
Catalytic antibodies
• Fig 6.16 Antibody-catalyzed amide hydrolysis
(a) TS analog antigen
(b) Reaction catalyzed by the catalytic antibody
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Prentice Hall c2002 Chapter 6 52
6.6 Lysozyme Binds an Ionic Intermediate Tightly
• Lysozyme binds polysaccharide substrates (the sugar in subsite D of lysozyme is distorted into a half-chair conformation)
• Binding energy from the sugars in the other subsites provides the energy necessary to distort sugar D
• Lysozyme binds the distorted transition-state type structure strongly
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Prentice Hall c2002 Chapter 6 53
Fig 6.17 Bacterial cell-wall polysaccharide
• Lysozyme cleaves bacterial cell wall polysaccharides (a four residue portion of a bacterial cell wall with lysozyme cleavage point is shown below)
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Prentice Hall c2002 Chapter 6 54
Fig 6.18 Lysozyme from chicken with a triaccharide molecule (pink)
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Prentice Hall c2002 Chapter 6 55
Fig 6.19 Conformations of N-acetylmuramic acid
(a) Chair conformation
(b) D-Site sugar residue is distorted into a higher energy half-chair conformation
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Prentice Hall c2002 Chapter 6 56
Lysozyme reaction mechanisms
1. Proximity effects
2. Acid-base catalysis
3. TS stabilization (or substrate distortion toward the transition state)
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Prentice Hall c2002 Chapter 6 57
Fig 6.20 Mechanism of lysozyme (2 slides)
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Prentice Hall c2002 Chapter 6 58
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6.7 Properties of Serine Proteases
A. Zymogens Are Inactive Enzyme Precursors
• Digestive serine proteases including trypsin, chymotrypsin, and elastase are synthesized and stored in the pancreas as zymogens
• Storage of hydrolytic enzymes as zymogens prevents damage to cell proteins
• Zymogens are activated by selective proteolysis
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Fig 6.21 Activation of some pancreatic zymogens
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Fig 6.22 Stereo view of the backbones of chymotrypsinogen and -chymotrypsin
Chymotrypsinogen (blue), -chymotrypsin (green)Catalytic Asp, His, Ser (red), Ile-16, Asp-194 (yellow)
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B. Substrate Specificity of Serine Proteases
• Many digestive proteases share similarities in 1o,2o and 3o structure
• Chymotrypsin, trypsin and elastase have a similar backbone structure
• Active site substrate specificities differ due to relatively small differences in specificity pockets
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Fig 6.23 Comparison of the backbones of (a) chymotrypsin (b) trypsin and (c) elastase
• Backbone conformations and active-site residues (red) are similar in these three enzymes
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Fig 6.24 Binding sites of chymotrypsin, trypsin, and elastase
• Substrate specificities are due to relatively small structural differences in active-site binding cavities
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C. Serine Proteases Use Both the Chemical and Binding Modes of Catalysis
• -Chymotrypsin active site groups include:
Ser-195 - identified by covalent DFP labeling
His-57 - identified by affinity labeling with TosPheCH2Cl
Asp-102 - identified by X-ray crystallography
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Fig 6.25 Stereo view of the catalytic site of chymotrypsin
• Active-site Asp-102, His-57, Ser-195 are arrayed in a hydrogen-bonded network (O red, N blue)
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Fig 6.26 Catalytic triad of chymotrypsin
• Imidazole ring (His-57) removes H from Ser-195 hydroxyl to make it a strong nucleophile (-CH2O-)
• Buried carboxylate (Asp-102) stabilizes the positively-charged His-57 to facilitate serine ionization
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Fig 6.27 -Chymotrypsin mechanism (8 slides)
Step (1): E + S
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Fig 6.27 (E-S)
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Fig 6.27 (E-TI1)
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Fig 6.27 (Acyl E + P1)
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Fig 6.27 (Acyl E + H2O)
(4)
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Fig 6.27 (E-TI2)
(5)
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Fig 6.27 (E-P2)
(6)
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Fig 6.27 (E + P2)