Catalysis. Instructor: Dr. Tsung-Lin Li Genomics Research Center Academia Sinica

Transcription

1 Catalysis Instructor: Dr. Tsung-Lin Li Genomics Research Center Academia Sinica

2 References: Biochemistry" by Donald Voet and Judith G. Voet Biochemistry" by Christopher K. Mathews, K. E. Van Hold and Kevin G. Ahern "Protein Structure and Function" by George A. Petsko and Dagmar Ringe Introduction to Protein Structure by Carl Branden and John Tooze The Organic Chemistry of biological pathways by John McMurry and Tadhg Begley Organic Chemistry by Paula Yurkanis Bruice The Organic Chemistry of Enzyme-Catalyzed Reactions by Richard B. Silverman Medicinal Natural Products: A Biosynthetic Approach by Paul M Dewick Antibiotics: Actions, Origins, Resistance by Christopher Walsh

3 Catalyst A catalyst is a substance that increases the rate of a reaction without itself being consumed or changed A catalyst increases the rate of the reaction by lowering the ΔG of the reaction A catalyst can decrease ΔG of the reaction by one of three different ways

4 The Catalyst Converts the Reactant to a Less Stable Species

5 The Catalyst Stabilizes the Transition State

6 The Catalyst Changes the Mechanism of the Reaction

7 A catalyst can provide a more favorable pathway for an organic reaction by: increasing the susceptibility of an electrophile to nucleophilic attack increasing the reactivity of a nucleophile increasing the leaving ability of a group by converting it to a weaker base

8 Nucleophilic Catalysis Both the formation of the acyl imidazole and its subsequent hydrolysis are both faster than ester hydrolysis

9 An Acid-Catalyzed Reaction A proton is donated to the reaction

10 The acid increases the rates of both slow steps of the reaction

11 In specific-acid catalysis, the proton is fully transferred before the slow step of the reaction In general-acid catalysis, the proton is transferred during the slow step of the reaction

12 Compare Specific-Acid Catalysis with General- Acid Catalysis

13 A specific-acid must be a strong acid A general-acid can be a weaker acid

14 Base Catalysis A base catalyst increases the rate of the reaction by removing a proton from the reaction specific-base catalyzed dehydration

15 The rate of the reaction is accelerated by stabilization of the transition state In specific-base catalysis, the proton is completely removed before the slow step of the reaction

16 general-base catalysis In general-base catalysis, the proton is removed during the slow step of the reaction

17 Metal-Ion Catalysis A. The metal ion increases the susceptibility of electron attack B. The metal ion makes the leaving group a weaker base C. The metal ion increases the nucleophilicity of water

18 An Example of a Metal-Ion-Catalyzed Reaction

19 Metal-Ion-Catalyzed Decarboxylation

20 Metal-Ion-Catalyzed Ester Hydrolysis The metal-bound hydroxide is a better nucleophile than water The metal ion also decreases the basicity of the leaving group

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22 The relative rates are also called the effective molarity The effective molarity is the advantage given to a reaction The relative rate of reactant D is higher than the relative rate of B because the groups in D are less apt to adopt an unfavorable conformation for the reaction

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24 Putting a reacting group and a catalyst in the same molecule increases the rate of the reaction Intramolecular catalysis is also known as anchimeric assistance

25 The trans isomer reacts much faster than the cis isomer

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27 The rate of phenyl acetate hydrolysis is enhanced by an intramolecular general base catalysis

28 In the presence of nitro groups, the ortho-carboxyl substituent acts as an intramolecular nucleophilic catalyst

29 An Intramolecular Metal-Ion Catalysis

30 Most Biological Catalysts Are Enzymes The reactants are called substrates The substrate specifically fits and binds to the active site

31 Hexokinase undergoes a conformational change upon binding to a substrate red: before substrate-binding green: after substrate-binding

32 Important Features that Contribute to the Catalytic Ability of Enzymes Reacting groups are brought together at the active site in the proper orientation for reaction Some of the amino acids in the enzyme serve as catalytic groups; many enzymes have metal ions as catalysts Groups on the enzyme can stabilize the transition state of the reaction

33 Carboxypeptidase A catalyzes the hydrolysis of the C-terminal peptide

34 The binding pocket at the active site of serine proteases dictates substrate specificity

35 The Proposed Reaction Mechanism of a Serine Protease

36 Lysozyme Is an Enzyme that Destroys Bacterial Cell Walls

37 The amino acids at the active site of lysozyme are involved in binding the substrate

38 The Proposed Reaction Mechanism for Lysozyme

39 The ph-rate profile of an enzyme is a function of the pk a values of the catalytic groups in the enzyme a group is catalytically active in its basic form a group is catalytically active in its acidic form

40 Glucose-6-phosphate Isomerase

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44 The Organic Mechanisms of the Coenzymes

45 Cofactors An enzyme that has a tightly bound metal ion (Co 2+, Cu 2+, Fe 2+, Mo 2+, Zn 2+ ) is called a metalloenzyme in which metal-ion cofactor acts as a Lewis acid. Cofactors that are organic molecules are called coenzymes. Some coenzymes function as oxidizing and reducing agents, some allow electrons to be delocalized, some activate groups for further reaction, and some provide good nucleophiles or strong bases needed for a reaction. Holoenzyme vs apoenzymes

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47 Overall View of Metabolism catabolism: complex molecules simple molecules + energy anabolism: simple molecules + energy complex molecules

48 The Four Stages of Catabolism Digestion Hydrolysis TCA cycle Oxidative phophorylation

49 Glysolysis

50 TCA cycle

51 Niacin The coenzymes most commonly used by enzymes to catalyze redox reactions: oxidizing agents reducing agents

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53 The Components of NAD+

54 Oxidation of an Alcohol by NAD+

55 Reduction by NADH

56 All the chemistry of the pyridine nucleotide coenzymes takes place at the 4-position of the pyridine ring

57 Glyceraldehyde-3-phosphate dehydrogenase

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59 The Mechanism of Reduction by NADH (or NADPH)

60 A reducing enzyme can distinguish between the two hydrogens at the 4-position of the nicotinamide ring 156 dehydrogenase are known to transfer H a, 121 are known to transfer H b.

61 Flavin Another set of coenzymes in redox reactions

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64 Mechanisms for Flavin Nucleotide Coenzymes

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67 Unlike NADH, FADH 2 does not dissociate from the enzyme

68 The Coenzyme Form of Vitamin B1

69 Pyruvate Dehydrogenase Complex One source of acetyl-coa molecules for the citric acid cycle is oxidative decarboxylation of pyruvate, catalyzed by the pyruvate dehydrogenase complex. The complex is composed of three enzymes 1. Pyruvate decarboxylase (E1) 2. Dihydrolipoamide transacetylase (E2) 3. Dihydrolipoamide dehydrogenase (E3) and five coenzymes 1. Thiamine Pyrophosphate (TPP) 2. Lipoic Acid - lipoamide 3. FAD 4. NAD + 5. CoASH

70 Mechanisms of the pyruvate dehydrogenase complex

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72 Consider this reaction

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76 Thiamine pyrophosphate in the pyruvate dehydrogenase reaction

77 Biotin: Vitamin H

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79 In addition to requiring bicarbonate, biotin-requiring enzymes require Mg 2+ and ATP

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81 Pyridoxal Phosphate: Vitamin B 6 Required by enzymes that catalyze certain transformations of amino acids

82 In each of these transformations, one of the bonds to the α-carbon of the amino acid substrate is broken in the first step of the reaction

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87 Involvement of pyridoxal phosphate in transamination

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91 In the PLP-dependent reactions, the bond cleaved in the first step of the reaction depends on the conformation of the amino acid that the enzyme binds

92 Coenzyme B 12 Enzymes that catalyze certain rearrangement reactions require coenzyme B 12

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94 Coenzymes derived from vitamin B12

95 The intramolecular rearrangement catalyzed by methylmalonyl-coa mutase

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97 Folic acid Tetrahydrofolate is the coenzyme required by enzymes that catalyze the transfer of a group containing one carbon to their substrates

98 The Six Different THF-Coenzymes

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100 The Enzyme that Converts U s into T s

101 Relationship between thymidylate synthase and enzymes of tetrahydrofolate metabolism

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103 Conversion of Dihydrofolate Back to N 5, N 10 -Methylene-THF

104 5-Fluorouracil is a mechanistic-based inhibitor of thymidylate synthase used in cancer chemotherapy

105 Aminopterin and methotrexate competitively inhibit dihydrofolate reductase and are used as anticancer drugs

106 Vitamin K Vitamin K is required for proper clotting of blood

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110 Regeneration of Vitamin KH2