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Enzymes

Enzymes. Most biological catalysts are ____________ (some REALLY COOL ONES are folded RNAs!!!) Catalysts - Catalyst does not alter equilibrium. Nonenzymatic reaction rate (s -1 ). Enzymatic reaction rate (s -1 ). Enzyme. Rate enhancement. Carbonic anhydrase. 1.3 x 10 -1.

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Enzymes

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  1. Enzymes Most biological catalysts are ____________ (some REALLY COOL ONES are folded RNAs!!!) Catalysts - Catalyst does not alter equilibrium Nonenzymatic reaction rate (s-1) Enzymatic reaction rate (s-1) Enzyme Rate enhancement Carbonic anhydrase 1.3 x 10-1 1 x 106 7.7 x 106 Triose phosphate isomerase 4.3 x 10-6 4300 1 x 109 Staphlococcal nuclease 1.7 x 10-13 95 5.6 x 1014

  2. Enzymes E + S ES E + P Highly specific Reaction occurs in ___________ of enzyme Substance acted upon = __________ Resulting species = _____________ Enzyme acts on forward and reverse reactions Activity depends on protein’s native structure Regulated - by concentrations of substrate and substances other than substrate

  3. Enzymes Cofactors Functional groups of protein enzymes are involved in acid-base reactions, covalent bond formation, charge-charge interactions BUT they are less suitable for oxid-reduc and group-transfer reactions SO they use __________________ (inorganic ions) COFACTORS may be metal ions (Cu2+, Fe3+, Zn2+) trace amounts of metal needed in our diets

  4. Enzymes Cofactors COFACTORS can be organic or metalloorganic molecules --> COENZYMES Examples: NAD+ Heme Holoenzyme = Apoenzyme (inactive) + cofactor/coenzyme/metal ions

  5. Enzymes Coenzymes Coenzymes must be regenerated Many vitamins are coenzyme precursors Vitamins must be present in our diets because we cannot synthesize certain parts of coenzymes Human Disease Coenzyme Reaction mediated Vitamin source Cobalamin coenzymes Alkylation Cobalamin (B12) Pernicious anemia Flavin coenzymes Oxidation-reduction Riboflavin (B2) rare Nicotinamide coenzymes Oxidation-reduction Nicotinamide (niacin) Pellagra Pyridoxal phosphate Amino group transfer Pyridoxine (B6) rare Tetrahydrofolate One-carbon group transfers Folic acid Megaloblastic anemia Thiamine pyrophosphate Aldehyde transfer Thiamine (B1) Beriberi

  6. Enzymes Substrate specificity Types of complementarity between enzyme and substrate: Substrate binding sites undergo conformational change when substrate binds

  7. Enzymes Enzyme undergoes conformational change when substrate binds - induced fit Substrate a c b a + c b ES complex a c b Enzyme

  8. Enzyme-substrate complementarity Dihydrofolate reductase-NADP+(red)-tetrahydrofolate (yellow)

  9. Enzymes Stereospecific Why? Inherently chiral (proteins only consist of L-amino acids) so form asymmetric active sites Example: Protein enzyme Yeast Alcohol dehydrogenase (YADH) O YADH CH3CH2OH + NAD+ CH3CH + NADH + H+ Ethanol Acetaldehyde

  10. Enzymes Stereospecific Yeast Alcohol dehydrogenase (YADH) is stereospecific 1. If YADH reaction uses deuterated ethanol, NAD+ is deuterated to form NADD O D H NADD O NAD+ C H YADH NH2 C NH2 N + N O R R + CH3CD + H+ + CH3CD2OH (ethanol) (acetaldehyde) 2. Isolate NADD and use in reverse reaction to reduce normal acetaldehyde, deuterium transferred from NADD to acetaldehyde to form ethanol O OH D H YADH C Hpro-S Dpro-R C NH2 N CH3 O R +NAD+ + CH3CH + H+ 3. Enantiomer of ethanol - none of deuterium is transferred from this isomer of ethanol to NAD+ in the reverse reaction OH Dpro-S Hpro-R C CH3

  11. Enzyme activity Dependent on: [metal ion], pH, temperature, [enzyme], [substrate]

  12. Enzymes E + S ES E + P G’˚ < 0; favorable

  13. Enzymes Enzymes affect reaction rates, not ____________ Catalysts enhance reaction rates by lowering __________________ Rate is set by activation energy G‡ Higher activation energy --> _____________ Overall rate of reaction is determined by step with highest activation energy --> rate-limiting step

  14. Enzymes General acid-base catalysis General acid catalysis - partial proton transfer from an acid lowers free energy of reaction’s transition state Keto Transition state Enol R R R + - - C O H A H A C O C O H CH2 - CH2 CH2 H H A- H + General base catalysis - partial proton abstraction by a base lowers free energy of reaction’s transition state Keto Transition state Enol R R - R C O C O C O H - CH2 CH2 CH2 H H+ H + H B B + B

  15. Enzymes General acid-base catalysis

  16. Enzymes General acid-base catalysis Example: Ribonuclease A (RNase A) digestive enzyme secreted by pancreas into small intestine hydrolyzes RNA rate depends on pH, suggesting involvement of ionizable residues His12 and His119

  17. Enzymes Covalent Catalysis Transient covalent bond formed between E and S Accelerates reaction rate through transient formation of a catalyst-substrate covalent bond Usually covalent bond is formed by the reaction of a nucleophilic group on the catalyst with an electrophilic group on the substrate --> nucleophilic catalysis SA-SB + N: SA -N + SB SA + N: + SB H2O Example: Decarboxylation of acetoacetate (catalyst contains primary amine) acetone acetoacetate O O O CH3 C CH2 C CH3 C CH3 O- RNH2 + RNH2 + OH- OH- CO2 R H + R H R H .. + + H+ N O N N CH3 C CH2 C CH3 C CH2 CH3 C CH3 O- SCHIFF BASE (IMINE)

  18. Enzymes Covalent Catalysis R + HN NH Some amino acids with nucleophilic groups ROH Serine RSH Cysteine RNH3+ Lysine Histidine

  19. Enzymes Metal Ion Catalysis One-third of all known enzymes require metal ions --> metalloenzymes Fe2+, Fe3+, Cu2+, Zn2+, Mn2+, Co2+ (sometimes Na+, K+, Mg2+, Ca2+) Metal bound to enzyme (or substrate) What can it do? help orient substrate (or enzyme) for reaction stabilize charged reaction transition state mediate oxidation-reduction reactions (change metal’s oxidation state) Voet, p. 295 11-11, scheme

  20. Enzymes: Chymotrypsin Serine protease, very reactive serine residue in enzyme Digestive enzyme synthesized by pancreas Catalyzes cleavage of peptide bonds adjacent to aromatic amino acids Transition state stabilization General acid-base catalysis and covalent catalysis Catalytic triad = Ser195, Asp102, His57

  21. Enzymes: Chymotrypsin general base general acid general acid Covalent intermediate general base

  22. Enzymes: Chymotrypsin

  23. Enzymes: Chymotrypsin

  24. Enzymes: Chymotrypsin

  25. Enzymes: Chymotrypsin

  26. Enzymes: Chymotrypsin and other serine proteases

  27. Enzymes: Enolase catalyzes reaction step of glycolysis reversible dehydration of 2-phosphoglycerate to phosphoenolpyruvate Metal ion catalysis, general acid-base, transition state stabilization Lys345 = general base, abstracts proton from C-2 of 2-phosphoglycerate Glu211 = general acid, donates proton to -OH leaving group

  28. Enzymes: Enolase Metal ion catalysis 2 Mg2+ ions interact with 2-phosphoglycerate making the C-2 proton more acidic (lower pKa) and easier to abstract

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