Decarboxylation Reaction

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The term decarboxylation means the removal of a carboxyl group (-COOH) from any reactant molecule. The chemical reaction where a carboxyl group (-COOH) gets eliminated and carbon dioxide (CO2) is released at the product end is called Decarboxylation. The liberation of CO2 makes the reaction almost irreversible in many cases. However, the reverse process i.e. Carboxylation is the addition of CO2. Carboxylation accounts for the very first step of Photosynthesis after the intake of CO2. Carboxylation results in the formation of Carboxylic acid. Most decarboxylation reactions involve carboxylic acids, where a carbon atom is broken off from the carbon chain. This carbon atom is released in the form of CO2.

Decarboxylation – Carboxylic acid

Carboxylic acids are the organic decarboxylation acids written as RCOOH, where R stands for an alkyl group or Hydrogen. The decarboxylation of a carboxylic acid is one of the oldest reactions discovered in organic chemistry. The reaction process involves the removal of -COOH group or a carboxylate salt of the given acid. The reaction gives the product RH along with CO2

RCO2H → RH + CO2

Decarboxylation reactions are observed with a slightly categorized form in many compounds. The following are some of them.

  • Krapcho Decarboxylation: This reaction involves activated esters with an electron-withdrawing group and halide anions. The ester is later replaced by a proton or an electrophile.

  • Hunsdiecker Reaction: It is a reaction where silver salts of carboxylic acid undergo decarboxylation to give an organic halide byproduct. It is also called the Halogenation reaction for the addition of halogen.

Decarboxylation Reaction Mechanism

  • The decarboxylation mechanism replaces the carboxyl group in a carboxylic acid with hydrogen. The reaction is facilitated by a group of enzymes called decarboxylases or carboxy-lyases. 

  • The regent that helps with the reaction is Soda-lime. It is a mixture of caustic soda and quick lime.

  • The mechanism of the reaction takes place in three steps. The first one begins with the removal of H+ ion from the carboxylic acid and the addition of Na. Na salt of carboxylic acid and water molecule was released in this step.

  • In the second step, a negative charge from Oxygen is moved in between the carbon-oxygen bond. So, the bond between the alkyl group(-R) and carbon breaks. CO2 is liberated in this step.

  • The third step takes place with help of the H2O generated in the first step. It breaks to give a proton ion that combines with an alkyl group to give an alkane.

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Decarboxylation Enzyme

The enzymes that help in the process of Decarboxylation of several organic acids are called decarboxylases or carboxy-lyases. They function in both adding and removing a carboxyl group from the organic compound. They are usually named according to the substrate they catalyze. Some examples of these enzymes are Ornithine decarboxylase, RuBisCO, Pyruvate decarboxylase, Histidine decarboxylase, etc.  

Decarboxylation of Amino Acids

Decarboxylation of amino acid results in the formation of an Amine by the removal of the carboxyl group (-COOH) from the amino acid. Due to the removal of the organic acid group, the byproduct moves up the pH scale for being of alkaline nature. The decarboxylase enzymes facilitate the decarboxylation mechanism i.e. removal of acidic groups. Deaminases, on the other hand, remove the amino groups to give out chemicals acidic in nature. 

Decarboxylation Tests

  • These are the biochemical tests involving the production of enzyme decarboxylase. So, they are also known as decarboxylase tests. 

  • The test is used to differentiate various members of Enterobacteriaceae that produce decarboxylase, from other gram-negative bacteria.

  •  Organisms that can metabolize amino acid by decarboxylation are identified by the formation of decarboxylase enzymes namely, arginine decarboxylase, ornithine decarboxylase, and lysine decarboxylase. 

  • The members are then further differentiated based on their abilities to produce these enzymes. 

  • The basal medium used in the test is Moeller’s formula. Meat peptones and beef extract present in the medium provide nitrogenous nutrition for bacterial growth.

  • Cresol red and Bromocresol purple are the pH indicators in the media.

  • Substrates like arginine, ornithine, and lysine are added to the medium to detect decarboxylation. 

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FAQ (Frequently Asked Questions)

1. Explain the decarboxylation of Histidine and Glutamate.

Histidine and Glutamate are both amino acids decarboxylated to form alkaline amine compounds on the body.   

  • Decarboxylation of Histidine: Histidine gets decarboxylated in presence of the enzyme histidine decarboxylase, catalyzed by a coenzyme B6-PO4. The reaction produces Histamine and CO2. The decarboxylation process takes place in Basophils, gut, gastric mucosa cell, and histaminergic neurons of the CNS.  Excessive release of Histamine occurs at the site of a wound, in injured tissues.

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  • Decarboxylation of Glutamate: Glutamate decarboxylation is catalyzed by glutamate decarboxylase enzyme with the help of coenzyme B6-PO4. The reaction forms the product γ-aminobutyric acid (GABA) along with the liberation of CO2. The reaction takes place in the grey matter of CNS. GABA acts as an inhibitory transmitter when released from axon terminals of neurons. 

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2. What are the uses and limitations of the decarboxylation test?

The following are the uses of the Decarboxylation test.

  • The test is efficient in differentiating members of the Enterobacteriaceae with similar physiological activities.

  • The decarboxylase test for lysine decarboxylase helps differentiate the bacteria Salmonella (+) and Shigella (-).

  • Arginine decarboxylase test results in the identification of Enterococcus species based on their Arginine metabolizing activity. 

There are some limitations to the test. They are:

  • The test is time-consuming. Results cannot be interpreted before 18-24 hours of incubation. Microorganisms that do not ferment glucose sometimes show weak decarboxylase activity.

  • The test fails to measure the intracellular amount of the enzyme. The enzyme presence is only detected by the change in pH.