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Term Paper on Coenzymes and Prosthetic Groups

Term Paper Contents:

  1. Term Paper on the Introduction to Coenzymes and Prosthetic Groups
  2. Term Paper on Nicotinamide Nucleotides
  3. Term Paper on Adenine Nucleotides
  4. Term Paper on TetrahydrofoIic Acid
  5. Term Paper on Flavins
  6. Term Paper on Haem
  7. Term Paper on Metal Ions
  8. Term Paper on Pyridoxal Phosphate
  9. Term Paper on Thiamine Pyrophosphate
  10. Term Paper on Lipoic Acid
  11. Term Paper on Biotin
  12. Term Paper on Cobalamin

1. Term Paper on the Introduction to Coenzymes and Prosthetic Groups:

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These two classes of substances include non-protein compounds, often complex molecules, which participate in enzyme-catalysed reactions, but there is a fundamental distinction between them coenzymes do not remain permanently bound to the enzyme – having been acted upon by one enzyme (for example reduced, acylated or phosphorylated), a coenzyme then becomes the substrate for a different enzyme, which reverses the process.

Distinction between a Coenzyme and a Prosthetic Group

Coenzymes therefore act as the links between metabolic pathways; they exist in quite high concentrations in the cell, are found in two or more forms, and can be considered as special intracellular enzyme substrates. A prosthetic group, on the other hand, is a non-protein component of an enzyme which is a necessary part of its structure, usually in the active site.

Some prosthetic groups are covalently linked to proteins; others are less tightly bound and may be removed from the enzyme by dialysis or charcoal treatment to give the apoenzyme. Unlike coenzymes, they remain associated with the enzyme for a complete reaction cycle, and are not regenerated by reaction with different enzymes.

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2. Term Paper on Nicotinamide Nucleotides:

Two coenzymes, nicotinamide adenine dinucleotide (NAD) and nicotinamide adenine dinucleotide phosphate (NADP) are together known as nicotinamide nucleotides. They were previously called di- and triphosphopyridine nucleotides (DPN and TPN).

They are dinucleotides in that two mononucleotides (of adenine and nicotinamide) are linked by a pyrophosphate bond, and the coenzymes differ in the 2′-phosphate on the adenosine of NADP.

They are coenzymes for a large number of dehydrogenases, most of which are specific for one or the other, and although both are electron carriers, they have quite different metabolic functions – NAD is involved in oxidative degradation (glycolysis, the TCA cycle and degradation of acyl CoA) and NADP participates in reductive biosynthesis, such as the synthesis of fatty acids and sterols. For this reason NAD is maintained mainly in the oxidized form ([NAD+]/ [NADH] is about 100 in liver cytosol) while NADP is predominantly in the reduced form ([NADP+]/ [NADPH] is about 0.01).

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Reduction of the coenzymes occurs on the nicotinamide ring-dehydrogenases transfer two electrons and one proton from their substrates to the coenzymes, a second proton being liberated – 

NAD (P)+ + 2H ⇌ NAD(P)H + H+

The oxidized coenzymes have an absorbance peak at 260 nm, due to the adenine and nicotinamide rings; in the reduced coenzymes dihydronicotinamide absorbs maximally at 340 nm, so that interconnection involves a change in the spectrum and can be followed by measuring absorbance at 340 nm. This is the usual way to assay dehydrogenases.

Nicotinamide Nucleotide Coenzymes

The reduced coenzymes are also fluorescent, with an emission maximum at 450 nm, whereas the oxidized coenzymes are not, so fluorescence measurements can also be used in the assay of nicotinamide-nucleotide dependent dehydrogenases. The presence of a nicotinamide ring in these coenzymes is responsible for the dietary requirement for nicotinic acid (niacin).

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3. Term Paper on Adenine Nucleotides:

Adenosine triphosphate (ATP) functions as an energy store within the cell, linking exergonic reactions, to which its synthesis is coupled, and endergonic reactions, which are driven by the energy released during its hydrolysis. It is termed a ‘high energy compound’, because of its large free energy of hydrolysis (AGO = – 30 kJ/mol at pH 7)

ATP4- + H2O → ADP3- + HPO42- + H+

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The value for simple phosphate esters is much lower – DGO = 13.8 kJ/mol for the hydrolysis of glucose-6-phosphate, for example. The large free energy of hydrolysis derives from the electronic structure of the triphosphate group, and is similar for other nucleoside triphosphates. ATP is synthesized in degradative reactions such as glycolysis, and the oxidation of reduced coenzymes by the mitochondrial electron transport chain.

Site of Cleavage of Adenosine Triphosphate

The energy available from these reactions is used in energy-consuming processes such as muscle contraction, active transport across membranes and biosynthetic reactions. The free energy stored in ATP may be released by its hydrolysis either to ADP or to AMP and pyrophosphate –

ATP4- + H2O → AMP2-+ HP2O73- + H+

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For this reaction, ∆G0 = -32 kj/mol; since pyrophosphate is further hydrolysed to phosphate in vivo, the overall free energy of the process is even larger.

ATP may also act as a donor of phosphoryl, pyrophosphoryl, adenylyl or adenosyl groups – the points of cleavage of the molecule in these reactions are shown. A derivative of ATP, S-adenosyl methionine, functions as a coenzyme in methyl transfer.

Other Nucleoside Triphosphates:

The biosynthesis of complex lipids and polysaccharides utilizes nucleotide-linked intermediates, which are generated from nucleoside triphosphates. Thus CDPcholine, CDP-diglyceride and other intermediates occur in the synthesis of phospholipids, and UDP- and GDP-sugars in polysaccharide synthesis.

Hydrolysis of GTP provides the energy required by ribosomes for protein synthesis and nucleoside triphosphates are the substrates for all nucleic acid synthesis.

4. Term Paper on TetrahydrofoIic Acid:

This is the reduced form of the vitamin folic acid- it acts as a carrier of ‘one-carbon’ fragments, which are attached at N5, N10 or both together. After transfer to the coenzyme from a donor such as serine, the one-carbon residue can be oxidized or reduced before transfer to an acceptor.

The coenzyme contains a reduced pteridine ring, coupled to glutamate through 4-aminobenzoate – its synthesis in bacteria is inhibited by sulphonamides, which are structural analogues of 4-aminobenzoate. These simple compounds were among the first man-made antibiotics, and are still in use.

Tetrahydrofolic Acid

i. Pteridine Coenzymes:

Pteridines can act as electron-transferring coenzymes, in the same way as NAD; their use is limited to a very few enzymes, of which phenylalanine hydroxylase is one.

ii. Ubiquinone (Coenzyme Q):

Ubiquinone acts as a hydrogen carrier in mitochondrial electron transport, being reduced by a number of complex dehydrogenases and reoxidized by Complex III, in which the immediate electron acceptor is cytochrome b.

Oxidized and Reduced Forms of Ubiquinone

iii. Coenzyme A:

Coenzyme A is a carrier of acyl groups, which form a thiolester bond with the free sulphydryl of the coenzyme. Free fatty acids are lipid-soluble, and dissolve freely in membranes – esterification to CoA prevents this, and provides a nucleotide ‘handle’ which is recognized by enzymes of fatty-acid metabolism. The thiolester bond has a large free energy of hydrolysis (about 33.5 kJ/mol) and its formation by acyl-CoA synthetases requires the hydrolysis of ATP –

RCOOH + CoA—SH + ATP → RCO—S—CoA + AMP + P-Pi

Coenzyme A

Hydrolysis of succinyl-CoA is used to drive synthesis of nucleoside triphosphate.

The pantothenate residue of CoA cannot be synthesized in man, so there is a dietary requirement for pantothenic acid.

The coenzymes occur as substrates in a number of (sometimes very many) enzymic reactions. We now consider prosthetic groups, which, although they have essential functions in catalysis, never become separated from enzymes; from a kinetic point of view they can be treated as part of an enzyme.

5. Term Paper on Flavins:

There are two flavin derivatives- flavin mononucleotide (FMN), in which flavin is linked to ribitol phosphate, and flavin adenine dinucleotide (FAD). These are the prosthetic groups of a number of complex dehydrogenases, including those in mitochondria which transfer electrons to ubiquinone from NADH, succinate, acyl-CoA and glycerol-1-phosphate. They act as carriers of two hydrogen atoms.

Structures of the Flavin Prosthetic Groups

Flavoproteins frequently contain other prosthetic groups, such as iron, copper or molybdenum; the electron acceptors include haemoproteins, ubiquinone and oxygen. Synthesis of flavoproteins requires a dietary supply of riboflavin (vitamin B2). The prosthetic group is not usually covalently bound, and can often be removed by denaturation of the protein, or in some cases even by dialysis. An exception to this is succinate dehydrogenase, which contains FAD covalently bound to histidine.

6. Term Paper on Haem:

Haem is an iron-containing tetrapyrrole compound, found in haemoglobin and myoglobin, where its function is to bind oxygen, in cytochromes, where it acts as an electron carrier, and in some enzymes, such as tryptophan oxygenase, where it functions as a prosthetic group in the reduction of oxygen. Only in the c-type cytochromes is haem covalently linked to proteins.

Non-Haem Iron:

Some proteins contain iron linked to sulphur (either inorganic sulphur, or the side chains of cysteine) – they are known as iron-sulphur proteins, or non-haem-iron proteins. They are usually involved in redox reactions, although aconitase also contains one iron sulphur cluster, the function of which is unknown.

7. Term Paper on Metal Ions:

Ions such as Mg2+ often act as dissociable activators of enzymes; other ions may be tightly bound to proteins, fulfilling diverse catalytic roles. Enzymes with metal ions bound through amino acid side chains are called metalloproteins – Mn, Zn, Co, Cu, Mo and Ni have been found in various enzymes, although their function is not always clear. These involvements in enzyme activity account for the dietary requirement for these trace metals.

8. Term Paper on Pyridoxal Phosphate:

This is a derivative of pyridoxine (vitamin B6), and is the prosthetic group of a number of enzymes of amino acid metabolism, including transaminases, racemases and decarboxylases. The amino acid reacts directly with the prosthetic group to form an imine (‘Schiff’s base’) intermediate.

Decarboxylation occurs by cleavage of a C—C bond, and racemization (alteration of the stereo chemical configuration of the amino acid, for example D → L) by breakage and reformation of a C—H bond. Transamination occurs by hydrolysis of a C—N bond, releasing the oxoacid and leaving the prosthetic group as pyridoxamine phosphate.

Pyridoxine and its Derivatives

This can react with a different oxoacid in a reversal of the sequence, thereby converting it to the corresponding amino acid –

In transaminases the aldehyde group of pyridoxal phosphate is linked to the ԑ Ξ-NH2 of a lysine, and it is this conjugate that reacts with the incoming amino acid.

9. Term Paper on Thiamine Pyrophosphate:

This derivative of thiamine (vitamin B1) is involved in the oxidative decarboxylation of pyruvate, 2-oxoglutarate and the branched-chain amino acids, and in the transketolase reaction.

Thiamine Pyrophosphate

In these reactions the proton attached to C-2 of the thiazole ring dissociates, and the resulting anion attacks the substrate. In the metabolism of oxoacids, decarboxylation then occurs and the resulting group (R • CH(OH)—) is either released as the aldehyde, or transferred to lipoic acid for oxidation. In the transketolase reaction the group —CO • CH2OH is transferred, via thiamine pyrophosphate, in a similar way.

10. Term Paper on Lipoic Acid:

This disulphide derivative of octanoic acid is a prosthetic group in oxoacid dehydrogenases, where it is involved in the transfer of the substrate from thiamine pyrophosphate to coenzyme A.

During transfer the substrate is oxidized, with reduction of lipoic acid to a dithiol the prosthetic group is recycled, being oxidized back to a disulphide by FAD. Lipoic acid is covalently linked to protein, by an amide link to the ɛ-NH, of lysine.

Liopic Acid and its Derivatives

11. Term Paper on Biotin:

Biotin is the prosthetic group in a number of carboxylation reactions, and functions as a carrier of CO2. It is carboxylated in an ATP-dependent reaction and the carboxyl group is then transferred to the acceptor substrate.

Biotin and its Carboxylated Form

Typical biotin-dependent carboxylases are those for acetyl-CoA, propionyl-CoA and pyruvate. Biotin is covalently linked through its carboxyl to the ɛ-NH2 of a protein lysine.

12. Term Paper on Cobalamin:

The cobalamin prosthetic groups are derived from vitamin B12, containing Co2+ surrounded by a tetrapyrrole corrin ring. The fifth ligand to the metal ion is dimethylbenzimidazole, and the sixth is 5′-deoxyadenosine. In bacteria it is involved in a number of important reactions, including the reduction of ribonucleotides to deoxyribonucleotides and synthesis of methionine.

Cobalamin Prosthetic Group

In higher animals one reaction in which vitamin B12 is definitely known to be involved is methylmalonyl-CoA mutase; the bond between Co and the 5′-C of deoxyadenosine is replaced by another Co—C bond, to —CO—SCoA as it migrates. There also appears to be a link between B12 and folate deficiencies, which suggests that B12 could be involved in the metabolism of methionine.