Weene Sunes airs mares > Types of catalysis Covalent Catalysis > nucleophilic catalysis > formation of covalent bond between: * nucleophilic group on E * electrophilic group on S > General reaction of Nucleophilic substitution: RX + Nu: > R-Nu + X fee Mechanism of Enzyme Action > Types of catalysis Covalent Catalysis > uncatalyzed AB >A+B > catalyzed E-Nu: + AB > E-Nu:A + B > E-Nu: +A +B T \w/ nucleophilic group (eg. -OH, amino) covalent bond formed Tara > Types of catalysis Covalent Catalysis ° Y ——GH + HO—C R © Rady Remigio> Types of catalysis General Acid-Base Catalysis > transfer or protons in the transition state by molecules other than HzO. > ionizable side chain (Asp, Glu, His, Cys, Tyr, Ser, Thr. Lys) > Acid catalysis [E-RH* +B > E-R + BH* > Base catalysis: |E-R + HA > E-RH* +A ae Mechanism of Enzyme Action > Types of catalysis General Acid-Base Catalysis © Rady Remigio ene Mechanism of Enzyme Action > Types of catalysis Metal-lon Catalysis ® Can occur by: * binding of $ for proper orientation * stabilizing negative charge * polarizing bonds * providing nucleophiles * participating in redox reactions> Types of catalysis Metal-lon Catalysis > Orientation & stabilization of negative charge by a Zn? ion in thermolysin v 1 Po ll EL wot ba Ocenia ran (as ‘op H ‘oH SF © Rady Remigio > Types of catalysis Metal-lon Catalysis » Generation of “OH nucleophile by a Zn?* ion in carbonic anhydrase L Coz oS ‘0 © Rady Remigio > Types of catalysis Metal-lon Catalysis > Polarization of carbonyl group by a Zn2* ion in carboxypeptidase i ° an nest fl oF: a cua c~ wr I, : “ oF Ly C—coo’ cua CPN, ii ee Pca HO = H (© Rady Remigio> Types of catalysis vy vv Catalysis through Proximity & Orientation > bringing substances closer > Aligning substrates & catalytic groups » Freezing out motions > Electrostatic stabilization of transition state > Auxiliary amino acid residues CHYMOTRYPSIN proteolytic enzyme; serine protease secreted in pancreas cleaves peptide bonds via hydrolysis selective: C-terminal of Phe, Tyr, Trp ch catalytic triad: Ser 195, His 57, Asp wmotrypsin 102 Seuekol CHYMOTRYPSIN Catalytic triad at the active site» CHYMOTRYPSIN » STAGE 1 aD) Ne ox om Wd, * coe ET Sa: vata peennee Ferman of terahectt » CHYMOTRYPSIN » STAGE 1 ) : 1 Py a ee . Sante SS Substrate binding Protonation by Mls Ceara tonal » CHYMOTRYPSIN B STAGE 1 = \ : Dae Na ‘ — wit 5 oF cane aA io Se ear cacy oT eae. eee a ‘tonation by bi eae of CoN 6 colare of» CHYMOTRYPSIN b STAGE 2 i? ; Bh 2 of C-N& collapse of intermediate aaa fem foe et Nucleophilic attack by HO Examples of Enzymes » CHYMOTRYPSIN b STAGE 2 philic attack by HjO Collapse of tetrahedral intermediate ae Collapse of tetrahectal intermediate Deacylation/Release of carboxy! group PAPAIN > > > > > > > cysteine protease derived from papaya meat tenderizer insect sting remedy heat resistant cleavage: hydrophobic—Arg or Lys-not Val catalytic triad: Cys 25, His 159 & Asn 175/Asp 158PAPAIN > subsequent steps similar to serine . protease Riese R * nucleophilic attack by Ser NH ara * tetrahedral intermediate un? Sn * protonation by His & collapse of at th a il intermediate * release of amino group & = = formation of acylenzyme * nucleophilic attack by water * release of carboxyl group amples of Enzym: > CITRATE SYNTHASE > Catalyzes an addition reaction > aldol-like addition of acetyl CoA to oxaloacetate to give citrate > fist step of TCA or citric acid cycle > binding: sequential, ordered fashion > binding of oxaloacetate leads to creation of a binding site for acetyl CoA > active site: 3 ionizable side chains resm—! Jy os +e ye. visa ee ° Teal Pm Xo scon = Hac] son peepee na \ ee -< + HI oN coo Ox 600" * — wkae ears au ae Examples of Enzymes > CITRATE SYNTHASE, Ho C7 tb WoL + HS-CoA coc” cti-coo"™ trate Senos ees etomsaties > CITRATE SYNTHASE it Hh 1 C7 ™scoa Il re : a ciate synthase Hc~ 0 + Ho + HSCon ox coo < Ser ‘o0c” cH,~coo ee Crete