Cofactors, Coenzymes, biosynthetic intermediates

In general, a cofactor is any substance required to cooperate with an enzyme that catalyzes a specific reaction. Cofactors are non-proteinaceous substances that assist enzymes in performing catalytic actions. Cofactors may be cations (metal ions) or organic molecules known as coenzymes (vitamins).

Cofactors may be altered temporarily during the reaction which they assist, but they return to their original state after participating in catalysis, so they are not ultimately changed by the reaction.

Cofactors may be loosely or tightly bound to the enzyme. Organic, loosely bound cofactors are called coenzymes, and play an accessory role in enzyme-catalyzed processes, often by acting as a donor or acceptor of a substance involved in the reaction. When combined with an inactive apoenzyme, coenzymes form a complete, active enzyme called the holoenzyme. ATP and NAD⁺ are common coenzymes, and are loosely bound to the enzyme. Many coenzymes are phosphorylated water-soluble vitamins. Heme is tightly, covalently bound, and as such is a prosthetic group.

Prosthetic groups differ from cofactors in being tightly (often covalently) bound to a particular enzyme molecule. Haem is an example of a prosthetic group found in cytochromes and haemoglobin, which carries electrons and/or oxygen.

In molecular genetics, cofactors are proteins that interact with transcription machinery, transducing regulatory information between core RNA polymerase machinery and gene-specific transcription factors. 'Mediator' is the most universal cofactor known today – it is a modular complex serving as the interface between gene-specific RNA pol II machinery. Mediator is also needed for response to other regulatory proteins such as activators and repressors of transcription.

Many molecules are important intermediates in biochemical pathways.

• acetyl-CoA • NADH : NAD+ : NADPH : NADP+ : Nicotinamide adenine dinucleotide : • pyruvate • • •

Acetyl Co-Enzyme A

The main function of coenzyme A is transfer of acyl groups, such as the acetyl group, or of thioesters. A molecule of coenzyme A carrying an acetyl group is also referred to as acetyl-CoA.

Coenzyme A is sometimes referred to as 'CoASH' or 'HSCoA' because when it is not attached to an acetyl group, it is attached to a thiol group, -SH. CoA is adapted from β-mercaptoethylamine, panthothenate and adenosine triphosphate.

The coenzyme is a very important biological intermeditate in the synthesis and β-oxidation of fatty acids and in generation of pyruvate for the citric acid cycle.

Acetyl Co-A is chiefly employed to convey the carbon atoms of the acetyl group to the citric acid cycle to be oxidized for energy production. Acetyl-CoA is the precursor to HMG CoA, which is a vital component in cholesterol and ketone synthesis. Acetyl C0-A contributes an acetyl group to choline in the synthesis of acetylcholine, in a reaction catalysed by choline acetyltransferase.

NADH

Nicotinamide adenine dinucleotide
is an important cofactor. NADH is the reduced form, while NAD⁺ is the oxidized form. Phosphorylation through an ester linkage at the 2' position of the adenosyl nucleotide yields NADP.


Phototrophs obtain NADPH (along with ATP) through the noncyclic fom of photophosphorylation during the light-reactions of photosynthesis (image Z-scheme). A photon is absorbed by Photosystem II and the two resultant excited electrons are passed to Photosystem I, which employs a second photon to further boost their energy for the overall reaction: NADP⁺ + H⁺ + 2e^- → NADPH. Non-phototrophic organisms manufacture NADH during oxidative phosphorylation, where NADH & FADH2, the energy carrier molecules generated by the citric acid cycle enter an electron transfer chain that generates a proton gradient by pumping protons (H⁺) across the membrane. Glycolysis generates the energy carrier molecules ATP and NADH in addition to intermediates (3-C or 6-C) for biosynthetic pathways.

Nicotinamide adenine dinucleotide phosphate (NADP) is employed in anabolic reactions, such as fatty acid biosynthesis and nucleic acid synthesis, which require NADPH as a reducing agent.

In chloroplasts, the light-reactions of noncyclic photophosphorylation produce both ATP and NADPH, which act as energy-transfer, reducing agents in the light-independent (“dark”) reactions of the Calvin cycle.

MH2 + NAD⁺ → NADH + H⁺ + M: + energy, where M is a metabolite.

Two hydrogen ions (a hydride ion and an H⁺ ion) are transferred from the metabolite. One electron is transferred to the positively-charged nitrogen, and one hydrogen attaches to the carbon atom opposite to the nitrogen.

NAD is synthesized from the vitamin niacin in the form of nicotinic acid or nicotinamide. At right is adenine.

Left: space fill molecule of NADH

C black : H white : O red : P orange : N blue

oxaloacetate

oxaloacetate

pyruvate

Left: pyruvic acid -click to enlarge image.

Pyruvate is the carboxylate anion of the alpha-keto acid. As the output compound of glycolysis, where one molecule of glucose yields 2 pyruvate, pyruvate is an important intermediate in metabolism. Pyruvic acid unites several key metabolic reactions because it can be converted to carbohydrates via gluconeogenesis, to fatty acids, to energy through acetyl-CoA, to the amino acid alanine, and to ethanol.

Provided that sufficient O2 is available, pyruvic acid is converted to acetyl-CoA, which enters the Krebs cycle. Pyruvate is also converted to oxaloacetate in an anaplerotic reaction, and ultimately yields 4 molecules of CO2.

In anaerobic conditions, pyruvic acid is converted to lactic acid and ethanol by plants. Pyruvate generated by glycolysis is converted by anaerobic respiration (lactate fermentation) to lactate using the enzyme lactate dehydrogenase and the coenzyme NADH. Pyruvate is converted, in alcoholic fermentation, to acetaldehyde and then to ethanol.