PHA111 Enzyme Catalysis PDF

MPharm Programme Enzyme Catalysis Dr. Mark Gray Slide 1 of 28 MPharm PHA111 Enzyme Catalysis Recap: Protein Structure Slide 2 of 28 MPharm PHA111 Enzyme Catalysis Why do we need catalysis? O R1 OH + R2 O R3 X O R2 O R1 + HO R3 • Conversions of esters to other products e.g. o...

MPharm Programme Enzyme Catalysis Dr. Mark Gray Slide 1 of 28 MPharm PHA111 Enzyme Catalysis Recap: Protein Structure Slide 2 of 28 MPharm PHA111 Enzyme Catalysis Why do we need catalysis? O R1 OH + R2 O R3 X O R2 O R1 + HO R3 • Conversions of esters to other products e.g. other esters, acids, amides etc. necessary for some metabolic processes. • However, if an ester and an alcohol / water are mixed the reaction does not occur spontaneously. Slide 3 of 28 MPharm PHA111 Enzyme Catalysis So why is that reaction so bad? Nucleophilic Attack Transition State 1 (TS1) d OH O R2 H O O R1 R3 Transition State 2 (TS2) MPharm PHA111 O R R2 O 3 d O H R1 d OH d R R2 O 3 O H R1 Slide 4 of 28 Tetrahedral Intermediate (TI) Enzyme Catalysis R2 H O O R1 O R2 O H R1 O Conjugate Acid/Base Products R3 R3 Base-catalysed version is much better…. • Transition states and intermediates are much more stable. • When hydroxide is the attacking species: specific base catalysis. Nucleophilic Attack R2 MPharm PHA111 Tetrahedral Intermediate (TI) d O O O R3 R2 O R1 d O R2 O R1 • For all other bases: general base catalysis Slide 5 of 28 Transition State 1 (TS1) O R3 R2 Od R1 O O R1 O d R 3 O Transition State 2 (TS2) Enzyme Catalysis O R2 O R1 O Products R3 R3 ….as is acid-catalysed version! Nucleophilic Attack H B O R2 O O R3 H O R2 R2 Transition State 1 (TS1) d H O H O R3 R2 O O R3 R2 O Od H R1 Transition State 2 (TS2) O O O H R1 O R3 H R3 R2 H R O 3 O R H BH 1 B: d H O H O O H R1 R2 H Od R1 O R1 R3 Tetrahedral Intermediate (TI) R2 H O :B R1 H O H B O R2 O R1 H R3 O R3 Products • This reaction has more steps, called proton transfers. • The catalyst is always regenerated at the end of the mechanism. • Again, if H3O+ is involved it is specific acid-catalysis, otherwise the catalysis is termed general acid-catalysis. Slide 6 of 28 MPharm PHA111 Enzyme Catalysis Another example Uncatalysed Od O OR O OR d OR Specific Acid-catalysed d OH2 H OH2 O OR O Slide 7 of 28 MPharm H O R PHA111 O d H O OR OH2 O d OH2 H Od R Enzyme Catalysis Od H O R H O d R OH3 O O R A reaction co-ordinate diagram of the uncatalysed reaction. Slide 8 of 28 MPharm PHA111 Enzyme Catalysis Catalysis stabilises transition states. Slide 9 of 28 MPharm PHA111 Enzyme Catalysis But, that’s all very well in the lab…. • Available in Laboratory • Human Body • Strong Acids + Bases • Extreme temperatures • Extreme pressures • pH ~ 7 • 37 °C • 1 atmosphere So, to get reactions to work in the body we need very good catalysts: ENZYMES Slide 10 of 28 MPharm PHA111 Enzyme Catalysis Enzymes: Proteins with catalytic activity Slide 11 of 28 MPharm PHA111 Enzyme Catalysis Amino acids side chains can take part in Acid / Base catalysis Slide 12 of 28 MPharm PHA111 Enzyme Catalysis Often, sides chains aren’t enough Slide 13 of 28 MPharm PHA111 Enzyme Catalysis Sometimes, pre-made small organic molecules help out too……. Slide 14 of 28 MPharm PHA111 Enzyme Catalysis Slide 15 of 28 MPharm PHA111 Enzyme Catalysis So, how good is that, really? O O H N HO O N H N O N H Orotic Acid H O + CO2 Uracil t1/2 (uncatalysed) = 78 million years at RT t1/2 (catalysed) = 1 ms with orotidine 5'-phosphate decarboxylase Slide 16 of 28 MPharm PHA111 Enzyme Catalysis Chymotrypsin • Member of the serine protease enzyme family. • Disulphide linkages: yellow, Catalytic Groups, red. Slide 17 of 28 MPharm PHA111 Enzyme Catalysis A closer look at the active site… • Ser195 and His57 give chymotrypsin its catalytic activity. • Chymotrypsin cleaves peptides containing aromatic residues. Slide 18 of 28 MPharm PHA111 Enzyme Catalysis Enzymes have strong affinity for the transition states of reactions. Slide 19 of 28 MPharm PHA111 Enzyme Catalysis The chemistry of chymotrypsin Slide 20 of 28 MPharm PHA111 Enzyme Catalysis A more detailed look Slide 21 of 28 MPharm PHA111 Enzyme Catalysis Slide 22 of 28 MPharm PHA111 Enzyme Catalysis Slide 23 of 28 MPharm PHA111 Enzyme Catalysis Slide 24 of 28 MPharm PHA111 Enzyme Catalysis Slide 25 of 28 MPharm PHA111 Enzyme Catalysis Slide 26 of 28 MPharm PHA111 Enzyme Catalysis Slide 27 of 28 MPharm PHA111 Enzyme Catalysis Summary • The prevalent conditions in the human body make it a poor vessel for chemical reactions. • To overcome this, nature has developed protein based catalysts called enzymes. • Enzymes are selective for particular substrates. • Enzymes have strongest affinity for the transition state of the reactions they catalyse. Slide 28 of 28 MPharm PHA111 Enzyme Catalysis