Chapter 24 The Organic Chemistry of the Coenzymes, Compounds Derived from Vitamins Paula Yurkanis Bruice University of California, Santa Barbara

Cofactors Many enzymes need a cofactor in order to catalyze a reaction. A cofactor can be a metal ion or an organic molecule. A cofactor that is an organic molecule is called a coenzyme. Coenzymes are derived from vitamins.

The Substrate and the Coenzyme are Bound to the Enzyme’s Active Site

A Pyridine Nucleotide Coenzyme is Needed for Many Redox Reactions NAD+ and NADP+ are oxidizing agents. NADH and NADPH are reducing agents.

NAD+ is the Most Common Oxidizing Agent NADPH is the Most Common Reducing Agent

NAD+ is Composed of Two Nucleotides Linked Together by Their Phosphate Groups NAD+ = nicotinamide adenine dinucleotide The nicotinamide nucleotide is derived from vitamin B3. The adenine nucleotide is derived from ATP.

ATP

Metabolism Metabolism = the reactions cells carry out to obtain the energy they need and to synthesize the compounds they require. Metabolism can be divided into two parts. catabolism: complex molecule simple molecules + energy anabolism: simple molecules + energy complex molecule

NAD+ is an Oxidizing Agent A dehydrogenase is an enzyme that catalyzes an oxidation reaction. NAD+ and NADH are used in catabolic reactions. Catabolic reactions are primarily oxidation reactions, so NAD+ is the most common oxidizing agent. NADP+ and NADPH are used in anabolic reactions. Anabolic reactions are primarily reduction reactions, so NADPH is the most common reducing agent.

NADPH is a Reducing Agent

The Mechanism for Oxidation All the chemistry of the pyridine nucleotide coenzymes takes place at the 4-position of the pyridine ring.

Glyceraldehyde-3-Phosphate Dehydrogenase Glyceraldehyde-3-phosphate dehydrogenase is an example of an enzyme that uses NAD+ as an oxidizing agent. 13

The Mechanism 14

The Mechanism for Reduction All the chemistry of the pyridine nucleotide coenzymes takes place at the 4-position of the pyridine ring.

Most Enzyme-Catalyzed Reactions are Highly Selective The oxidizing enzyme can distinguish between the two hydrogens of ethanol. Only Ha is removed.

Most Enzyme-Catalyzed Reactions are Highly Selective The reducing enzyme can distinguish between the two hydrogens of NADH. Only Ha is transferred.

FAD is an Oxidizing Agent FAD = flavin adenine dinucleotide 18

FAD-Catalyzed Reactions Most oxidation reactions catalyzed by FAD do not involve a carbonyl group. 19

FAD is Reduced to FADH2 FAD is an oxidizing agent. FADH2 is a reducing agent. 20

The Mechanism for Dihydrolipoate Dehydrogenase 21

The Mechanism for Succinate Dehydrogenase

The Mechanism for D- or L-Amino Oxidase

Unlike NAD+ and NADH, FAD and FADH2 Do Not Dissociate From the Enzyme NAD+ is required to reoxidize the reduced cofactor.

Thiamine Pyrophosphate (TPP) TPP is the coenzyme required by enzymes that catalyze the transfer of an acyl group. 25

A Reaction That Requires TPP 26

The Reactive Part of TPP The TPP ylide is a good nucleophile. All enzyme-catalyzed reactions that require TPP start by forming an enamine.

The Mechanism for Pyruvate Decarboxylase

The Pyruvate Dehydrogenase Complex The conversion of pyruvate to acetyl-CoA requires five coenzymes: TPP, lipoate, coenzyme A, FAD, and NAD+.

Part Two of the Mechanism Part one of the mechanism is the reaction of the TPP ylide with pyruvate to form the same enamine that is formed from the reaction of the TPP ylide with pyruvate by pyruvate carboxylase. Lipoate is attached to its enzyme by forming an amide with a lysine side chain.

Part Three of the Mechanism

Coenzyme A

Biotin Biotin is required by enzymes that catalyze the carboxylation of a carbon adjacent to a carbonyl group. Biotin is attached to its enzyme by forming an amide with a lysine side chain.

Enzymes That Require Biotin

Activating Bicarbonate Biotin-requiring enzymes require Mg2+ and ATP.

Mechanism for Carboxylation

Pyridoxal Phosphate (PLP) Pyridoxal phosphate is attached to its enzyme by forming an imine with a lysine side chain.

PLP Catalyzes Reactions of Amino Acids

PLP Catalyzes Reactions of Amino Acids

PLP Catalyzes Reactions of Amino Acids

The Amino Acid Becomes Attached to PLP by Transimination In the reactant, the imine is between PLP and a lysine side chain of the enzyme. In the product, the imine is between PLP and the amino acid.

The First Step in All PLP-Catalyzed Reactions The first step of the enzyme-catalyzed reactions is breaking a bond attached to the alpha-carbon.

The Mechanism for Decarboxylation

The Mechanism for Racemization

The Mechanism for Transamination (Part 1)

The Mechanism for Transamination (Part 2)

Coenzyme B12

Enzyme-Catalyzed Reactions That Require B12 Enzymes that catalyze certain rearrangement reactions require coenzyme B12.

Y and H Change Places In an enzyme-catalyzed reaction that requires coenzyme B12, a group (Y) bonded to one carbon changes places with a hydrogen bonded to an adjacent carbon.

The Mechanism for a Reaction that Requires B12

Tetrahydrofolate (THF) THF is the coenzyme required by enzymes that transfer a group containing one carbon to their substrates.

THF Coenzymes

A Reaction That Requires THF The C-8 of purine comes from a THF coenzyme.

A Reaction That Requires THF

Sulfa Drugs (the first antibiotics) Sulfanilamide and p-aminobenzoic acid have similar structures. The sulfa drugs act by inhibiting the enzyme that incorporates p-aminobenzoic acid into folic acid (the enzyme binds sulfanilamide instead of p-aminobenzoic acid).

The Enzyme That Converts U into T The reaction reduces tetrahydrofolate (THF) to dihydrofolate (DHF).

The Mechanism

Conversion of Dihydrofolate Back to Tetrahydrofolate

Cancer Chemotherapy 5-fluorouracil is a suicide inhibitor of thymidylate synthase If a cell cannot make Ts, it cannot make DNA.

Competitive Inhibitors of Dihydrofolate Reductase Aminopterin and methotrexate are used as anticancer drugs. Trimethoprim is used as an antibiotic.

Vitamin K Vitamin K is required for proper clotting of blood. Vitamin K2 is the coenzyme.

Vitamin KH2 provides the strong base. The Enzyme That Catalyzes Carboxylation of the γ-Carbon of Glutamate Requires Vitamin KH2 The enzyme needs a strong base to remove the hydrogen from the γ-carbon. Vitamin KH2 provides the strong base.

making the strong base

Regenerating Vitamin KH2

These Compounds Prevent Blood Clotting These compounds are competitive inhibitors of the enzyme that converts vitamin K epoxide to vitamin KH2.