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MCB+102+F10 lecture 09

MCB+102+F10 lecture 09 - Enzymes are catalysts Catalysts...

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Unformatted text preview: Enzymes are catalysts Catalysts promote chemical reactions Catalysts are not consumed or used up?) Catalysts are restored alter reaction and can be re-used repeatedly Nenenzymatic Untatalyzed rate Catalyzed rate Rate enhancement Enzyme half-life (knur‘l lkmr‘l 0MP decerhoxylase E] 78,000,000 years 2.0 X 10'“ 39 Staphylocetcal nuclease 130.000 years 1.7 X 10"13 95 AMP nucleesidase 69.000 years 1.0 X 10'" 60 Carboxypeptidase A 7.3 years 3.0 X 10" 578 Ketestereld isomerase 7 weeks 1.7 X 10" 66.000 Triese phosphate isomerase 1.9 days 4.3 X 10" 4.300 Cherismete mutase 7.4 hours 2.6 X 10'5 50 tethenit anhydrase 5 seconds 1.3 X 10'1 1 X10‘ h rear some catal icall -activ R Am le LII 3 $3551? 63% air” 9 1 Ion Nearly All Enzymes Are Proteins nee n O C ozymes, mos noa ii @‘WJSE'ELE éfimr .I I Examples of Enzymes Requiring the Ion Cu1+ Cytochrome oxidase Fe2+ or Fe3+ Cytochrome oxidase, catalase, peroxidase K‘“ Pyruvate kinase, proprionyl-CoA carboxylaee l'lilg2+ Hexokinase, glucose 6-phosphatase, pyruvate kinase, Eco RV lllllir'i1+ Arginase, ribonucleotide reductase, superoxide diemutaee Mo Dinitrogenase, nitrate reductaee I'lii2+ Urease Se Glutathione peroxidase Zn“ Carbonic anhydraee, alcohol dehydrogenase. carboxypeptidases A and B Many enzymes need complex cofactors: Coenzymes and Prosthetic Groups Such cofactors serve as transient carriers of electrons, specific atoms, or functional groups Coenzyme A 5’-Deoxyadenosyicohaiamin {coonzyme B11] Flavin adenine dinucieotide Lipoato Dietary preosrsor in mammals Biotin Group carried co2 Pantothenic acid and other compounds Acyi groups Vitamin Eu Riboflavin {vitamin BI} Dietary sulfur Hicotinamide adenine dinucleotide Hicotinic acid {niacin} Pyridoical phosphate Tetrahydrofolate Thiamine pyrophosphate Heme Guide RNA Pyfldostine {vitamin HG} Foiate Thiamine {vitamin Ed Fe2+ Dietary nitrogen H atom: and alkyl groups Electrons Electrons and acyi groups Hydride ion {:H'} Amino groups I.‘1ine-cariilion groups Aldehydes Electrons cRNA Example Enzyme Pyruyate ca rbcxylase Acetyl-CoA carbcxylase Methylmalcnyl mutase Monamine oxidase Pyruyate dehydrogenase Lactate dehydrogenase Asp aminotransferase Thymidylate synthase Pyruyate dehydrogenase Cytochrome c Telomerase Hallmarks of enzyme-mediated catalysis (1) Tremendous rate enhancement. (2) Occurs under mild (physiological) conditions, (pH 7, 37C, aqueous solution, low concen- tration of the reactants). (3) Precise reaction: highly selective forsubstrates; stereo-specific products formed in high yield. (4) Subject to metabolic regulation. How do Enzymes Work? ngng mes%§cfi§elegrate refi (ficéfilfistgym [giliitgting [E fie dfiectfofi ofitfie reatci‘fin34%g state + Enzyme Churismate mutase 1;, @m £2: No enzyme 3 thin-III AGD I a. for biochemical I reacflons Seconds Hours Time —a~» How do e TriéstefiYrMéNé‘fitififi IBEFrierfit EIEX GI)? FORMATI N OF THE ENZYME-SUBSTRA E COMP The chemistry takes place in the' 'active site” Substrate How does an active site expedite a chemical reaction? (1) Entropy gain from substrates shedding water of solvation and displacing water bound in the active site “2° “2° H20 H20 H20 H20 H20 H H20 H20 Hf) H20 H O H D 2 “1H202 H20 2 H20 H20 How does an active site expedite a chemical reaction? (2) Molecular complementary— geometry of the pocket "fits" the substrates and maximizes van der Waals contacts How does an active site expedite a chemical reaction? (3) H-bonds and salt bridges between groups on the substrates and side chains in the active site are stronger in the absence of competition from or shielding by water Active site How does an active site expedite a chemical reaction? (4) Binding at the active site holds the substrates in close proximity (raises their effective local concentration) A + B—rC; v = k [A] [B] Active How does an active site expedite a chemical reaction? (5) Binding at the active site holds the substrates in a precise orientation (promotes productive encounter) How does an active site expedite a chemical reaction? (6) Some binding energy used to introduce strain or polarization into the bonds in the substrates THE ACTIVE SITE IS MOST COMPLEMENTARY TO THE REACTANTS IN THEIR TRANSITION STATE Both the enzyme and its substrates change— Wnducede' Enzymes use binding energy to lower the barrier to reach the transition state [a] No enzyme _ ——~ -—- I ‘ Substrate Transition state Products irnetal stick] {bent stick] [broken stick} [b] Actiye site of the enzyme most complementary to substrate Magnets _ “tr—t ES [:1 Active site of the enzyme most complementary to transition state eta—Aw Covalent catalysis: in many enzymes, a group in the active site can participate transiently in the chemistry of the reaction catalyzed, but the enzyme is always regenerated __ HP“ :' a //O Acylatiun I?“ Deacylatien f OH + R'fl—c\ T» e—c\‘ ——» OH + H0 —C / \R R'DH / R / \R Preduct #1 Prnduct #2 Enzyme Marl-enzyme Enzyme intermediate Hydrolysis of an ester by an esterase Even though there are many thousands of different enzymes known, the chemical tranformations catalyzed can all be categorized as one of just six types of reactions Class no. Class narne Type of reaction catalyzed 1 Oxidoreductases Transfer of electrons [hydride ions or H atoms} 2 Transferases Group tra nsfor reactions 3 Hydrolases Hydrolysis reactions {transfer of functional groups to water) 4 Lyases Addition of groups to double bonds, or formation of double bonds by removal of groups 5 Isomerases Transfer of groups within molecules to yield isomeric forms 6 Ligases Formation of C—C, C—5, C—0, and {2—H bonds by condensation reactions coupled to cleavage of ATP or similar cofactor ...
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