Catalysis Instructor: Dr. Tsung-Lin Li Genomics Research Center Academia Sinica
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
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
The Catalyst Converts the Reactant to a Less Stable Species
The Catalyst Stabilizes the Transition State
The Catalyst Changes the Mechanism of the Reaction
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
Nucleophilic Catalysis Both the formation of the acyl imidazole and its subsequent hydrolysis are both faster than ester hydrolysis
An Acid-Catalyzed Reaction A proton is donated to the reaction
The acid increases the rates of both slow steps of the reaction
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
Compare Specific-Acid Catalysis with General- Acid Catalysis
A specific-acid must be a strong acid A general-acid can be a weaker acid
Base Catalysis A base catalyst increases the rate of the reaction by removing a proton from the reaction specific-base catalyzed dehydration
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
general-base catalysis In general-base catalysis, the proton is removed during the slow step of the reaction
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
An Example of a Metal-Ion-Catalyzed Reaction
Metal-Ion-Catalyzed Decarboxylation
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
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
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
The trans isomer reacts much faster than the cis isomer
The rate of phenyl acetate hydrolysis is enhanced by an intramolecular general base catalysis
In the presence of nitro groups, the ortho-carboxyl substituent acts as an intramolecular nucleophilic catalyst
An Intramolecular Metal-Ion Catalysis
Most Biological Catalysts Are Enzymes The reactants are called substrates The substrate specifically fits and binds to the active site
Hexokinase undergoes a conformational change upon binding to a substrate red: before substrate-binding green: after substrate-binding
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
Carboxypeptidase A catalyzes the hydrolysis of the C-terminal peptide
The binding pocket at the active site of serine proteases dictates substrate specificity
The Proposed Reaction Mechanism of a Serine Protease
Lysozyme Is an Enzyme that Destroys Bacterial Cell Walls
The amino acids at the active site of lysozyme are involved in binding the substrate
The Proposed Reaction Mechanism for Lysozyme
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
Glucose-6-phosphate Isomerase
The Organic Mechanisms of the Coenzymes
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
Overall View of Metabolism catabolism: complex molecules simple molecules + energy anabolism: simple molecules + energy complex molecules
The Four Stages of Catabolism Digestion Hydrolysis TCA cycle Oxidative phophorylation
Glysolysis
TCA cycle
Niacin The coenzymes most commonly used by enzymes to catalyze redox reactions: oxidizing agents reducing agents
The Components of NAD+
Oxidation of an Alcohol by NAD+
Reduction by NADH
All the chemistry of the pyridine nucleotide coenzymes takes place at the 4-position of the pyridine ring
Glyceraldehyde-3-phosphate dehydrogenase
The Mechanism of Reduction by NADH (or NADPH)
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.
Flavin Another set of coenzymes in redox reactions
Mechanisms for Flavin Nucleotide Coenzymes
Unlike NADH, FADH 2 does not dissociate from the enzyme
The Coenzyme Form of Vitamin B1
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
Mechanisms of the pyruvate dehydrogenase complex
Consider this reaction
Thiamine pyrophosphate in the pyruvate dehydrogenase reaction
Biotin: Vitamin H
In addition to requiring bicarbonate, biotin-requiring enzymes require Mg 2+ and ATP
Pyridoxal Phosphate: Vitamin B 6 Required by enzymes that catalyze certain transformations of amino acids
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
Involvement of pyridoxal phosphate in transamination
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
Coenzyme B 12 Enzymes that catalyze certain rearrangement reactions require coenzyme B 12
Coenzymes derived from vitamin B12
The intramolecular rearrangement catalyzed by methylmalonyl-coa mutase
Folic acid Tetrahydrofolate is the coenzyme required by enzymes that catalyze the transfer of a group containing one carbon to their substrates
The Six Different THF-Coenzymes
The Enzyme that Converts U s into T s
Relationship between thymidylate synthase and enzymes of tetrahydrofolate metabolism
Conversion of Dihydrofolate Back to N 5, N 10 -Methylene-THF
5-Fluorouracil is a mechanistic-based inhibitor of thymidylate synthase used in cancer chemotherapy
Aminopterin and methotrexate competitively inhibit dihydrofolate reductase and are used as anticancer drugs
Vitamin K Vitamin K is required for proper clotting of blood
Regeneration of Vitamin KH2