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by: Thurman Wilderman


Thurman Wilderman
GPA 3.66


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This 31 page Class Notes was uploaded by Thurman Wilderman on Saturday September 12, 2015. The Class Notes belongs to CHEM 3100 at University of Georgia taught by Staff in Fall. Since its upload, it has received 8 views. For similar materials see /class/202587/chem-3100-university-of-georgia in Chemistry at University of Georgia.




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Date Created: 09/12/15
BCMBBIOLCI EM 3100 Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis AcidBase catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced fit Serine Proteases Energy diagrams show the progress ofa reaction 39l39rzlminnn mu energy unstable state in which a molecule is best suited to undergo a chemical reaction state in which chemical bonds are being broken and formed Lifetime 10 to 10 13 sec Ammuun cumgy Subumlc glmmd quit Htc cncm Chung in am hcrwcrn mu 2 r r 7 and product l rmlucl Fig 61 Energy diagram CUHNU for a singlestep reaction R quot39quotquot quot quotquot m a or Fig 62 Energy diagram for reaction with intermediate occurs the Tr1msl0n miles trough between the two transition states 0 Lifetime gt NI 03914 to 103913 sec Intermediate Free energy In this case the rate determining step in the forward direction is P formation of the first transition state Reacllun coordinate Fig 63 Enzymatic catalysis of the reaction AB gt AB Transition sta e stabilization lowers activation energy Proximity effect prop er p ositioning of ub strate c humg Imuml m tin1 Tr mm mm Trmiuon m AB kvwmm mamm Wm wurdlmuc What is the enzyme active site A few polar residues and H20 molecules are found at the otherwise hydrophobic active site of an enzyme polar amino acids that undergo changes during enzymatic catalysis Ionic side chains are involved in two types of chemical catalysis 1 2 Table 61 TABLE 61 Catalytic functions of reactive groups of ionizable amino acids Net charge Amino acid Reactive group at pH 7 Principal functions Aspanat C009 71 Canon binding proton transfcr Glutamate C006 7 1 Canon binding proton transfer I39listldinc Imidazolc Near 0 Proton transfer Cysminc CIizSiI Near 0 Covalent binding of acyl groups Tyrosine Phenol 0 Hydrogen bonding to ligands Lysme 7NH I Anion binding proton transfer Argininc Guanidinium l Anion binding Scrine CHZOH U Covalenl binding of acyi groups Note pKa of ionizable groups of amino acids in proteins vary from pKa of free amino acids com pare Table 32 to Table 62 Table 62 pKa Values of amino acid ionizable groups in proteins Group pKa Terminal occarboxyl 34 Sidechain carboxyl 45 Imidazole 6 7 Terminal ocamino 759 Thiol 895 Phenol 9510 sAmino 10 Guanidine 12 Hydroxymethyl 16 Chapter 6 Mechanisms of Enzymes 0Energy diagrams Chemical modes of enzyme catalysis AcidBase catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transiti0n state analogs Induced t Serine Proteases Chemical modes of enzyme catalysis AcidBase catalysis Covalent catalysis acceleration of a reaction by transfer of a protein B base proton acceptor BH conjugate acid proton donor A general base B can act as a proton acceptor to remove protons from OH NH CH or other XH This produces a stronger nucleophilic reactant X7 XH 3399 Hit 67 J R9 OHO Sim General base catalysis reactions continued A B can remove a proton from water and thereby generate the equivalent of OH39 in neutral solution 0 r 0 ll Vi f H CiN g iC iN 4 iciorI HN r l r HO 5 A HUH H i l 68 Proton donors can also catalyze reactions BH can donate protons A covalent bond may break more easily if one of its atoms is protonated below He 7 R70H a R70H B R 10 69 He part or entirety of S forms covalent bond with E and then with second S All or part of a substrate is bound to the enzyme to form a Group X can be transferred from AX to B in two steps via the covalent ES complex XE AX E Z XE A 610 XE B BX E 611 Sucrose phosphorylase exhibits covalent catalysis 611613 og a glucosyl residue is transferred to enzyme Sucrose Enz GlucosylEnz Fructose mm Glucose is donated to phosphate GlucosylEnz Pi Glucose 1phosphate Enz Sucrose is composed of a glucose and a fructose Fig 64 pHrate pro le for papain of an enzyme can give information about ionic residues at the active site A simple bellshaped curve can result from two overlapping titrations of active site amino acids The two inflection His15 points approximate z 3 4 5 6 7 s 9 0 I the pKa values of P the two ionizable residues Fig 65 a Papain s activity depends upon ionizable residues His159 and Cys25 a Ribbon model b Active site residues N blue 8 yellow Fig 66 e w pKa 0f Cys in We papain34 Three ionic forms W quot 7 of papain Only H the upper tautomer y of the middle pair 39 is active H pKa 0r His in u r W papain83 hmum39 Fastest Reactions are Diffusion Controlled Reactions rates approach rate of diffusion 108 to 109 M39ls39l speed of binding of substrates to the enzyme Table 64 TABLE 64 Enzymes with secondorder rate constants near the upper limit Enzyme Substrate k thm Mquot squot Catalase H202 4 x 107 Carbonic anhydrase CO2 12 X 108 Acetylcholineslemse Acelyicholinc 16 X 10 Fummse Fumamre 16 X 10 Triose phosphale isomerase u Giyeeraldehyde 3phmphale 4 x 105 Supcmxidc dismulasu 326 2 x 109 Th r vi 1e K E P For these enzymes me farmation of the ES complex can be the sluwcst step A Triose Phosphate Isomerase TPI TPI catalyzes a rapid aldehydeketone interconversion H O I CH OH Trlose C 3 phosphate Isomerase 3 f O a H i C OH quotCHQOPOQ CH20POQ 615 Dihydroxyacetnne DGlyceraldehyde phosphate 3phosphale DI IAP G3 Fig 67 Proposed mechanism for TPI General acidbase catalysis mechanism 4 slides ivoi When nliiiydrm mum pilusphulc himlx quot quot m carlmnyl 0 1mm 1 hydragcn quot 0 band wi he neulrui imldumie group ul I it V H P HisNS The curhmylmc group nl39Glu 5 H C 0 remmm u pmhm I39rnm ll ui lhc L 39CHJOPU suluuulr 10 um un cncdinlulu inwnncdiulc Giurl Hi 5705 Orms a slum ma C72 0 en at lt Lh39N oxygen mum Fig 67 TPI mechanism continued myde bun o n d v of he cncdinlnle GIurl S Eucdlnh e Emenuediam H5795 C quotK 0H c N H 01 Icio culopof J chL lic imidaminlc mm 01 His M a s uctxzipmmn mm m m on and shunlcs me pr n umms pm hydmx clan hem L ncmg nnnlhcr Me encdmlalc inlenncdinle Fig 67 TPI mechanism continued IJH Glurlhi ncdinl illtcrlncdinlc Fig 67 TPI mechanism continued Haws 7 CH 0 n xvi Gluri dnmtcsupmmnmCrZ E H N prnducing Dglycsruldehydc 3phmphum C C 7 0 H7 CHEOPO L 3 5 Encdmlale mm mtdldie His95 H l U H 0 C N N H H k on LC CHZOPOJ CID65 Fig 69 Energy diagram for the TPI reaction Enzyme with E gtD mutation 4 gtw El 2 5 Wild type r 2 LL enzyme I l I EDHAP EDHAP Encdiol EGSF EG3P intermedialc Reaction unurdinule Fig 612 Excessive ES stabilization would create a thermodynamic pit and give little or no catalysis I if E binds S too tightly dashed pro le the activation banier 2 wimpyquot tmylvm l lc could be similar to that 7777777777777777777777777 r 7 of the uncatzlyzed 391 reaction 1 Fm mag most Km values substrate dissociation constants indicate weak binding to enzymes Radian cmmmm Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis AcidBase catalysis Covalent catalysis Binding modes of enzyme catalysi Proximi ec Transition state stabilization n Transition state analogs Induced fit Serine Proteases TransitionState TS Stabilization increased interaction of E with S in transitionstate ESI E distorts S forcing it toward the transition state E must be complementary to transitionstate in shape and chemical character E binds transition states 1010 to 1015 times more tightly than S Basis for enzymatic catalysis 1 eg acidbase amp covalent catalysis gt 10100 T 2 quotweakquot binding 01 M of S to active site raises the effective concentration of S and favors more frequent transition states 104105 T effective molarity enhanced relative concentration of reactants due to binding to E greater binding of transition states than S or P to E lower activation energy 104105 T Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis AcidBase catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced t Serine Proteases Wolfenden amp Lienhard 19705 showed that chemical analogs of are enzyme inhibitors In Emil Fisher s lockandkey model for SE binding the Binding of S to E distorts S to transition state The transition state must be stabilized for catalysis to occur Transition state analogs can catalytic antibodies Transitionstate TS analogs Fig 614 2Phosphoglycolate a T8 analo enzyme triose phosphate isomerase 39l H l ou on k NH 1R 7 trim Cr 009 C70 H E u yCH PUQ 0qu63 mm xlc 39I39mlemu SlillL 279m hogly Hmmilluxlrslillc ululiug Transitionstate analogs are stable compounds whose structures resemble unstable transition states 1huhmmccmuc phmnlmm uuhsrmrur g for the by a TS analog 112 6 Hz 9 NHK x 7 x T X i HNr39 4 i sN Ri busc Adenosinc Covalent hydrate substrch b H 713 0 It Ull K1 3x10 M N5 N N K A N N L N N ILO ermsc ermsc Pnrmc rilmnuclmsidc Trilllsilinnrslzllc subsuqu analog Fig 615 Inhibition of adenosine deaminase Ribnse lnosine product Ki 5 x 10 6 M ll H HNquot is i N 7 N Ribmc Dihydmpurinc rrmmucrumiuc compullmu inhibitor Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis AcidBase catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced t Serine Proteases Induced Fit substrate induced cleft closing Daniel Koshland 19505 activates an enzyme by substrate initiated conformation effect Induced t is a substrate speci city effect not a catalytic mode Hexokinase mechanism requires sugarinduced closure of the active site Other examples pyruvate kinase phosphoglycerate kinase phosphofructokinase Stereo views of yeast hexokinase Yeast hexokinase contains 2 domains connected by a hinge region Domains close on glucose binding a Open conformation b Closed conformation Glucose ATP gt Glucose 6phosphate ADP Chapter 6 Mechanisms of Enzymes Energy diagrams Chemical modes of enzyme catalysis AcidBase catalysis Covalent catalysis Binding modes of enzyme catalysis Proximity effect Transition state stabilization Transition state analogs Induced fit Serine Proteases Properties of Serine Proteases Digestive serine proteases including and are quot 39 39 and stored in the pancreas as zymogens are inactive enzyme precursors that must be covalently modified to become active Storage of hydrolytic enzymes as prevents damage to cell proteins Pancreatic zymogens are activated by The pancreatic zymogens are also regulated by enzyme inhibitors eg trypsin inhibitor Kd 10 13 M H Fig 621 Activation of some pancreatic zymogens Enzyme cascades rapid signal amplification Trypsinogen The protease zymogens are synthesized in the pancreas Enlcropcpudase gt 1w and activated in the I duodenum l l I I l I I I I I Chymotrypsinogen Proclasrase Elastase Cleaves on the carbonyl side of hm x p aawithsmall uncharged side Chymmrypsin Elaslase chains Fig 622 The backbones of chymotrypsin blue trypsin yellow and elastase green Backbone conformations and activesite residues red are similar in these three enzymes Fig 624 Binding sites of chymotrypsin trypsin and elastase a Chyummpun b Trypin c mm n ALI Vul Thr Substrate specificities are 0 due to relatively U er d mp 0mm small structural age 1 WW differences in 0 quotwequot activesite binding cavities 20 Fig 626 of chymotrypsin Imidazole ring His57 removes H from Ser195 hydroxyl to make it a strong nucleophile CH2O39 Buried carboxylate Asp102 stabilizes the positively charged His57 to facilitate serine ionization Hixr His57 LIV SCHUS Scrri lfi U V 3 39 H H H W 32539 3 Catalytic triad of serine proteases Asp His Ser Fig 627 a Chymotrypsin mechanism 8 slides 1 Nurrl Step 1 E S Hmv i u m Lil ii H u H w i H H H t My WI m2 IL 4 lt K Spw my pocket H pep debond I x 39Iwmi um 21 Fig 627 ES 2 Fig 627 ETIl 3 Tetrahedral inhermediahe m thH mm mmlwm InkHIme n M7 mum mcmhvrmu7l mud K UdugnhumMhmMclmmHu luugm WWquot 39 quot r K m W m y unm 1an Tim allow llu Impatle 39 u dn lt u A m n m mmun m le mlmhcdm micrmcdmlc w mrm m A H H I HUImlyuuumHHHIMLLAHC nu H I I mylumuhu Mmuu hum I R m mm nhumhw lmcpugmdu mm m w H 7le mm m Glyrl H um mums Hm mndmmnm mm m mm an m nu ma mmlyikdoummg n pmmn w Hn unmcu m m mun mum mm mm Mcmmmg m dmmgc m mm gnmp mun me Venn1e rum Wham mm wn cw m puxlnmxgmh u rmedmle mam um mm Kln um um tum mm mm m 7 mm 6 mm mm un lrnuum w m M r 1 Fig 627 Acyl E P1 4 Acidibase amp covalent catalysis vaI I HrsS7 I f H II M H o 1 K R m l n m mmlt mummy Hm7 u n H l l H o r v 7 H 0 R my L H mz 39 Hydrolysis Fig 627 Acyl E H20 5 4 My Hydmlw dcdcylmwr or he 1 qu rx m wwwmnmmwwuwhm ml E Aspml and Hum again form 3 MW 0 banner Mdmgcu how 397 V L ml H1 mwvcs u pmmu I m c 1 L w mo ccuk u Wm In one W m mka m Irbouyl 9mmquot quotmmy Fig 627 ETIZ 6 5 sums lt n H H 1 whiny quot H llx ammgmmnummzahummn immumpmlnu c Hg ammunw u V wequot t H E I mmMuummwumnnmmmm 537 m H Tetrahedral We de rummmmmu 4m mined and duhed 13 intermediate wwwva Flg 627 EPz 7 6 mm H 39 A i li H r H u H v Hmwumd VHMUMll39 iJUHKHNplIdA39 n V H mm H Um mhm Immunw Im mml 1 IL x u Fig 627 E P2 8 Sam Hum R H l H H n 31 n m VH H n 44 V39 n EH My N o 102 x C iRl 397 h unhoxym mum my 6 The cArbmylulc piuducl is misused nom Lhc um sun and m dummrypmv u m man Additional material to aid in learning the material covered in the chapter Review of Chemical Mechanisms l Nucleophilic Substitution Reactions ionic reaction where both electrons stay with one atom gt ionic intermediate leaving group ionic reactions have nucleophile electrophile Formation of tetrahedral intermediate Direct displacement two molecules react to form a five group transition state Two types of nucleophilic substitution reactions Formation of a tetrahedral intermediate quotif i9 ii C be R cix gt c x9 R X I LA R Y 51 ye Direct displacement R Rl R R R R x e C XWCWY C Y i U 62 Y R x Rg Transition slate 26 2 Cleavage reactions most common when both electrons stay with one atom formation of a carbanion C retains both 6 formation of carbocation ion C loses both 6 Carbanion formation 9 R3 C H gt R3 C H 53 Carbanion Proton Carbocation formation 9 e Rs C H gt R3 C 11 Carbocation Hydride ion 64 3 Cleavage reactions less common when one electron remains with each product gt two free radicals Free radical formation RIO 0R2 gt RIO 0R2 65 27 4 Oxidationreduction reactions Oxidation addition of oxygen removal of hydrogen removal of electrons Electrons are transferred between two species Oxidizing agent gains electrons is reduced Reducing agent donates electrons is oxidized Enzymes lower the activation energy of a reaction 1 Substrate binding Enzymes properly position substrates for reaction makes the formation ofthe transition state more frequent and lowers the energy of activation 2 Transition state binding Transition states are bound more tightly than substrates this also lowers the activation energy 28 Binding Modes of Enzymatic Catalysis Proper binding of reactants in enzyme active sites provides substrate specificity and catalytic power Two catalytic modes based on binding properties can each increase reaction rates over 10000fold 1 Proximity effect collecting and positioning substrate molecules in the active site 2 Transitionstate TS stabilization transition states bind more tightly than substrates Binding forces utilized for catalysis 1 Chargecharge interactions 2 Hydrogen bonds 3 Hydrophobic interactions 4 Van der Waals forces 29 A The Proximity Effect 0 Correct positioning of two reacting groups in model reactions or at enzyme active sites 1 Reduces their degrees of freedom 2 Results in a large loss of entropy 3 The relative enhanced concentration of substrates effective molarityquot predicts the rate acceleration expected due to this effect Fig 611 Reactions of carboxylates with phenyl esters Increased rates are seen when the reactants are held more rigidly in proximity continued negtltt slide Mm WWW V Fx 7 m 7 704 ea In 7 j i39 4 5 v 4 Br I In L 0139 HI L is 39m gt Br lxm Fig 61 1 continued Ix m gtle B Weak Binding of Substrates to Enzymes Energy is required to reach the transition state from the ES complex Excessive ES stabilization would create a thermodynamic pitquot and mean little or no catalysis Most Km values substrate dissociation constants indicate weak binding to enzymes


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