L24-28 - L24 start here Berg Tymoczko Stryer Biochemistry...

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1 1 Biochemistry Sixth Edition Chapter 9: Catalytic Strategies Berg • Tymoczko • Stryer 2 Trapped! Catalytic triad of a serine protease Substrate Chpt 9: Catalytic strategies: The organic chemistry of enzyme reactions Ser 195 His 57 Asp 102 3 Catalytic strategies: Four case studies 1.) Serine proteases--a slow uncatalyzed reaction 2.) Carbonic anhydrases--a very fast catalyzed reaction 3.) Restriction endonucleases--a highly specific reaction 4.) Nucleoside monophosphate (NMP) kinases--a need to prevent unwanted phosphoryl transfer to water Biochemical techniques used: 1.) Structural studies (Chpt 3) 2.) Site-directed mutagenesis (Chpt 5) 3.) Bioinformatics (Chpt 6) 4.) Enzyme kinetics (Chpt 8)
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2 4 Common catalytic strategies of enzymes 1.) Use of binding energy to drive catalysis •Promotes substrate binding and specificity •Drive an induced fit •Can be used to destabilize the ground state •Circe effect (term coined by Bill Jencks) : “The utilization of attractive forces to lure a substrate into a site in which it undergoes a transformation of structure.” “Circe was a goddess of Greek mythology. Circe lured Odysseus’s men to her house and then transformed them into pigs” p223. 2.) Covalent catalysis (section 9.1). 3.) General acid-base catalysis (sections 9.1-9.2). 4.) Catalysis by approximation (section 9.4). 5.) Metal ion catalysis. 3 types: as a base, an oxyanion hole, and a S-to-E bridge (sections 9.2-9.4) 5 9.1) Proteases facilitate a fundamentally difficult reaction A case study of Chymotrypsin: A Serine Protease The uncatalyzed reaction: Hydrolysis of a peptide bond •The uncatalyzed reaction is almost immeasurably slow at neutral pH. •See Table 8.1 (next slide) : 6 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 / =
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3 7 Why is k uncat so slow? The peptide bond is resonance stabilized! •Has stable double bond character •C of this carbonyl has reduced electrophilicity due to positive charge on neighboring nitrogen. 8 Chymotrypsin cleaves peptide bonds C-terminal to large hydrophobic amino acids •Bonds reactive to chymotrypsin •Specificity described by k cat / K m •See Table 8.6 (next slide) 9 k cat / K m is the specificity constant V o = ( k cat / K m ) [E][S] •Holds for all [S], large and small as compared to K m •For two substrates, A and B, where [A] o =[B] o , V o (B)/ V o (A) = ( k cat,B / K m,B ) / ( k cat,A / K m,A ) •1,000,000-fold specificity for Phe over Gly (to N-terminus of scissile bond)
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4 10 Overall, chymotrypsin uses a water to hydrolyze the peptide bond. BUT, water isn’t the first nucleophile. Serine IS! •Chymotrypsin contains one very reactive serine: Ser195 as judged by DIPF-mediated inactivation •Revisit Fig 8.23 11 A chromogenic substrate of chymotrypsin provides a convenient assay •Chromogenic substrate •Generates a chromophore upon cleavage p -nitrophenol •pK a 7 •A good leaving group •yellow color •Note that the scissile bond in the chromogenic substrate is an ester bond rather than an amide bond.
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