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Transamination, Deamination and Decarboxylation

Transamination, Amino keto acid, E-PLP complex, Mechanism, Double displacement type of bi-substrate reaction, Reactions in DNA that cause deamination.

Transamination

  • Nitrogen metabolism is one of the most important processes in amino acid synthesis.
  • An amino acid is transaminated when an amine group is attached and the amino acid is transformed into a keto acid (an amino acid without an amine group), thus creating two new amino acids.
  • Transamination occurs when amino acids are reversibly aminated and deaminated, and the amino group is redistributed among the amino acids.
  • Transaminases (aminotransferases) are a type of enzyme widely distributed in human tissues, especially in the heart, liver, kidney, and skeletal muscle.
  • Transamination generally causes the following reaction:

Concerned enzyme

  • A transaminase or an aminotransferase catalyzes the reaction.
  • L-amino acids are hydrolyzed by enzymes, but D-isomers are not.
  • The mitochondrial and cytosolic enzymes are separate.
  • Different transferases act on different amino acids and keto acids.

Amino keto acid

  • Amino acids naturally occur in a state of transamination.
  • Some exceptions include the basic amino acids lysine, hydroxyl amino acids, serine, and threonine, as well as the heterocyclic amino acids proline and hydroxyl-proline.
  • Some keto acids that are commonly involved include pyruvic acid, oxaloacetic acid, and α-ketoglutaric acid.
  • Transamination may also be mediated by glutamic and glyoxylate semialdehyde.

E-PLP complex

Transaminases are metabolized by pyridoxal phosphate (a derivative of vitamin B6) and involve the same reaction mechanism. Schiff bases are formed between an aldehyde group and an amino group within the pyridoxal phosphate molecule. The amino group holds the nitrogen atoms and the phosphate groups non-covalently.


Mechanism

The position of protons and electrons in a tautomer makes the difference between an isomer and a tautomer. Carbon has no differences in its skeleton. The process of proton transfer from one molecule to another inside a molecule is known as a tautomer.

Double displacement type of bi-substrate reaction

  • Pyridoxal phosphate binds to the enzyme through its cofactor, and enzyme-pyridoxal phosphate is formed.
  • Pyridoxal phosphate linked with enzyme binds to participant amino acid (1). A Schiff base I enzyme forms, and water is eliminated.
  • The enzyme Schiff Base I then tautomerizes to the ketamine form and dissociates as pyridoxamine-phosphate and keto acid (1) in the presence of water.
  • Following this, pyridoxamine phosphate linked to enzyme combines with the original participants’ keto acid (2).
  • Water molecule is emitted as a result of the formation of the enzyme Schiff Base II'.
  • The enzyme Schiff Base II' will then tautomerize from its ketamine to its aldimine forms, which will dissociate into a new amino acid (2) and enzyme pyridoxal phosphate upon reaction with water.

Deamination

A molecule becomes deaminated when an amine group is removed from it. Deamination is carried out by the liver. It is a reaction that breaks amino acids down. Ammonia is produced by eliminating the amino group from amino acids. Carbon and hydrogen form the rest of amino acids, which are recycled or oxidized for energy. In the urea cycle, enzymes convert ammonia to urea and uric acid by combining that ammonia with carbon dioxide molecules (which is not considered deamination). A person's urine contains uric acid and urea, which are safely excreted together.

Reactions in DNA that cause deamination

Cytosine

In the process of spontaneous deamination, cytosine is hydrolyzed into uracil, and ammonia is released. By converting cytosine to bisulfite in vitro, but not 5-methylcytosine, this can be achieved. Using this property, researchers have been able to distinguish methylated DNA from nonmethylated DNA (shown as uracil) by sequencing methylated DNA. The spontaneous deamination of cytosine in DNA is corrected by removing uracil (the product of the deamination of cytosine, not part of DNA) and replacing it with thymine.

5-methylcytosine

During spontaneous deamination of 5-methylcytosine, thymine and ammonia are produced. This reaction cannot be corrected in DNA since thymine is not recognized as an error by the repair mechanisms (in contrast to uracil), therefore the mutation will not be removed unless it impairs the gene's function. The absence of CpG sites in eukaryotic genomes is due to this defect in the repair mechanism.

Decarboxylation

Decarboxylation occurs when a carboxyl group is removed from a molecule and carbon dioxide is released. The act of decarboxylation involves the removal of a carbon atom from a chain of carbons by a reaction of carboxylic acids. Carbon dioxide is added to the compound during carboxylation, the first chemical step in photosynthesis. Decarboxylases are enzymes that catalyze decarboxylation.

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Ankur Choudhary is India's first professional pharmaceutical blogger, author and founder of Pharmaceutical Guidelines, a widely-read pharmaceutical blog since 2008. Sign-up for the free email updates for your daily dose of pharmaceutical tips.
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