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Reading - Chapter 8
Practice problems - Chapter 8: (not yet assigned); Enzymes extra problems
Introduction
Kinetics
For the reaction A + B → products, v = k[A][B]. This is a second order reaction (there are two
reactants).
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Reaction Rate Theory
Catalysis
Enzymes
• Enzymes are highly effective catalysts that carry out complex chemical transformations
under mild conditions (water, neutral pH).
• Enzymes show great specificity with regard to the reactions they catalyze and the substrates
they react with.
• Enzymes can be regulated.
• Enzymes carry out their catalytic role by binding the substrate to a specific area of the protein
called the active site (Companion: Enzymes/Enzyme Kinetics).
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• Several amino acid side chains comprise the active site.
Coenzymes are small organic molecules, derived from vitamins that participate in the chemical
reactions catalyzed by many enzymes.
Summary of factors responsible for the rate enhancement seen with enzyme catalysis
Enzyme Kinetics
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The rate of the enzymatic reaction is:
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For determination of KM and Vmax a linear
transformation, the Lineweaver-Burk plot, is
useful.
Turnover Number
Enzyme Efficiency
• When [S] << KM, then kcat/KM is a second order rate constant, and is a measure of the
efficiency of the enzyme at low [S].
• The maximal value of kcat/KM is 108-109, which is diffusion-controlled.
For different substrates, kcat/KM is also the best way to determine the specificity of an enzyme.
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For hydrolysis of a peptide bond by the proteolytic enzyme
chymotrypsin, the nature of the R1 sidechain is critical.
.
R1 kcat/ KM (M-1sec-1)
Gly 1.3x10-1
Val 3.6x102
Leu 3.0x103
Phe 1.0x105
Enzyme Regulation
• Multisubunit enzymes
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• Heteroallostery - regulation by effector
molecules, which can be positive or negative.
• Allosteric effectors bind at a site different from
the active site.Allosteric effectors can activate
(favor R state) or inhibit (favor T state).
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Enzyme Inhibitors
• The use of enzyme inhibitors can often provide valuable information about an enzymatic
mechanism. Many drugs are based on the use of enzyme inhibitors, e.g., penicillin inhibits
an enzyme involved in bacterial cell wall synthesis.
• A competitive inhibitor competes with the substrate for binding at the active site, increasing Km.
• A noncompetitive inhibitor binds to a site other than the active site and inhibits product
formation. Noncompetitive inhibitors decrease velocity, including Vmax, by decreasing kcat.
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Covalent Inhibition
Effect of pH
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• This pH-rate profile suggests that a protonated
lysine is involved in the catalytic step.
Note that the apparent pKa derived from inspection of kinetic data may be significantly
different than the actual pKa of the sidechain. More sophisticated analysis is required to obtain
an accurate estimation of the pKa in the enzyme.
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