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L20-23 - L20 start here Berg Tymoczko Stryer Biochemistry...

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1 Biochemistry Sixth Edition Chapter 8: Enzymes: Basic Concepts and Kinetics Berg • Tymoczko • Stryer Enzymes are responsible for the vast majority of biological functions e.g. Aequorin is responsible for oxidation of an aromatic compound by O 2 to release CO 2 and blue light (466 nm) Some properties of enzymes: 1.) Enzymes accelerate the rate of making and breaking of covalent bonds ( i.e. catalysis). 2.) Enzymes are highly specific: React with one substrate but not other (often very closely) related ones. 3.) Enzymes are not changed in the reaction. 4.) Enzymes catalyze many cycles (turnovers) of the reaction. 5.) Enzymes are usually proteins, but can be RNA which may have special evolutionary importance. 6.) Enzymes bind substrates in special regions called ‘active sites’. 7.) Enzymes function by stabilizing the transition state of the reaction (Pauling’s idea). •Therefore, enzymes catalyze the forward and reverse reactions to an equal extent. •Therefore, enzymes do not change the position of the equilibrium.
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2 8.1) Enzymes are powerful and highly specific catalysts carbonic anhydrase •The names of most enzymes end with ‘ase’. •Here the enzyme name is associated with the reverse reaction. •Even simple reactions are usually enzyme-catalyzed e.g. hydration of CO 2 to make carbonic acid •This reaction is one of fastest known: 10 6 turnovers/sec •Rate enhancement: 10 7 Enzymes typically show very large rate enhancements •a remarkable 10 17 -fold enhancement by the enzyme over the uncatalyzed reaction •enhancement is large, largely because k un is sooooo slow! ln2/ l big variation less variation / = Some enzymes are more specific than others: Example of proteases trypsin ( 2/20 sites) thrombin ( 1/20 2 sites papain Specificity: papain<trypsin<thrombin Structural basis has to do w/ binding pockets (more later) (all sites)
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3 A number of enzymes rely on cofactors for activity •Not unlike hemoglobin using a heme for its function, albeit a non-catalytic one. •Nomenclature: Apoenzyme + cofactor = holoenzyme •Coenzymes: Typically derived from vitamins 2 classes: Coenzymes and Metal ions •Metal ions: Exploring equilibria: Example of an isomerization reaction •See in-class notes for deriving the position of equilibrium •Enzymes do not affect the position of the equilibrium K eq -1.4 -1.4 -1.4 x10 x10 x10 •Each factor of 10 increase in K eq is worth an increment of -1.4 kcal/mol in Δ G o’
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4 Enzymes affect the rate at which equilibrium is achieved but not the position of the equilibrium -Enzyme=Slow + Enzyme=Fast •position of equilibrium is unaffected by the enzyme , or Yrs, or MYrs +enzyme (holds +/- enzyme) Pauling model for enzyme catalysis -enzyme Enzyme k f (s -1 )/ k r (s -1 ) = K - 10 -4 10 -6 100 + 10 2 1 100 8.3) Enzymes accelerate reactions by facilitating formation of the TS
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