bk_ch6_09_19_06_71pp

bk_ch6_09_19_06_71pp - Biological Kinetics K. Dane Wittrup...

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Biological Kinetics K. Dane Wittrup & Bruce Tidor September 19, 2006
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Contents 6 Enzyme kinetics 1 6.1 Enzymes are catalysts. ................................ 1 6.2 Enzymatic rate laws. ................................. 5 6.2.1 Michaelis–Menten rate law. ......................... 5 6.2.2 Bisubstrate kinetics. ............................. 1 8 6.2.3 Substrate inhibition. 2 0 6.2.4 Cooperative enzymes. ............................ 2 3 6.2.5 pH effects. .................................. 2 3 6.3 Enzyme Inhibition . 2 6 6.3.1 Reversible inhibitors . 2 6 6.3.2 Pharmacological inhibition. 3 6 6.3.3 Tight-binding inhibitors . .......................... 3 9 Case Study 6-1 “Mechanism of inhibition of HIV-1 reverse transcriptase by nonnucleoside inhibitors.” R. A. Spence, W. M. Kati, K. S. Anderson, and K. A. Johnson. Science, 267 : 988–993 (1995). ............... 4 0 6.4 Signaling pathways. 4 4 6.4.1 Tyrosine kinases . .............................. 4 4 6.4.2 Trimeric G proteins and G protein coupled receptors . ........... 4 7 6.5 Metabolism . ..................................... 4 9 6.5.1 Flux control coef±cients . 4 9 6.5.2 Constraint based models . 5 0 6.6 Hydrolytic regulatory enzymes. ........................... 5 2 6.6.1 Caspases . 5 2 6.6.2 Blood coagulation cascades . ........................ 5 4 Case Study 6-2 “A Model for the Tissue Factor Pathway to Thrombin.” K. C. Jones, K. G. Mann. textitJ. Biol. Chem., 269 : 23367–23373 (1994). .... 5 5 6.6.3 Extracellular metalloproteases . ....................... 6 3
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ii CONTENTS
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Chapter 6 Enzyme kinetics “Enzymes are things invented by biologists to explain things which otherwise require harder thinking.” Jerome Lettvin Enzymes are biological catalysts that ensure that required chemical reactions occur at the proper time and place to convert metabolic energy, build biopolymers and cellular structures, transmit signals culminating in altered gene expression, and carry out most other biological events involving covalent transformations. In this chapter we will consider mathematical expressions useful for understanding the rates of enzyme-catalyzed reactions at varying concentrations of reactants and inhibitors. The integration of enzymatic reactions in signal transduction and metabolism will be considered as well. 6.1 Enzymes are catalysts Enzymes are protein or nucleic acid catalysts that accelerate chemical reaction rates through par- ticipation in the reaction without being progressively consumed. A chemical catalyst is deFned by the following properties: 1. Accelerates a reaction by lowering its activation energy. 2. Is not progressively consumed or created by the reaction. 3. Does not alter the overall thermodynamics of the reaction (i.e., the equilibrium of the overall reaction.) These properties are graphically reflected in the reaction coordinate diagrams in ±igure 6.1. The word “enzyme” comes from the latin term for “in yeast”, because it was Frst discovered that extracts of yeast could catalyze fermentation in the absence of living cells. The great majority of
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2 CHAPTER 6. ENZYME KINETICS &REE %NERGY 2EACTION PROGRESS 2EACTANTS 0RODUCTS #ATALYST LOWERS ACTIVATION ENERGY Figure 6.1. A catalyst lowers the activa- tion energy for a reaction without chang- ing the energy states of the reactants or products; hence the equilibrium is not al- tered,but the rate of interconversion be- tween the states is accelerated.
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bk_ch6_09_19_06_71pp - Biological Kinetics K. Dane Wittrup...

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