What is Nitrogen metabolism?

Nitrogen metabolism is the synthesis, utilization or uptake, breakdown, and excretion of nitrogenous compounds in the body. The nitrogen metabolism encompasses nitrogen fixation, biosynthesis, and the breakdown of amino acids, purines, and pyrimidine. Since nitrogen-containing compounds are required for various life processes, nitrogen is an important element of life.

Importance of nitrogen metabolism

Nitrogen is found in proteins, enzymes, amino acids, alkaloids, vitamins, and several growth hormones in living cells. Nitrogen is important for plants as it aids in their growth and development. Nitrogen metabolism mostly focuses on the removal of excess nitrogen from the body when the amino acids are broken down to provide energy. 

The main processes involved in the nitrogen metabolism

 The nitrogen metabolic pathway involves both anabolic and catabolic processes.

An anabolic process is a series of metabolic pathways that generate molecules from simpler components. These reactions are endergonic processes. There are three phases of anabolism. This metabolic pathway produces precursors such as monosaccharides, amino acids, nucleotides, and isoprenoids at the first phase. In the second phase, energy from ATP hydrolysis is used to activate these precursors. From these precursors, complex molecules such as polysaccharides, proteins, nucleic acids, and lipids are synthesized in the third phase.

The anabolic processes involved in the nitrogen metabolic pathway are:

• Nitrogen fixation.
• Protein synthesis.
• Synthesis of amino acids.

Catabolism is the process of breaking down molecules into smaller units that are then oxidized for energy or uptake in other metabolic pathways. Larger molecules like polysaccharides, nucleic acids, lipids, and proteins are broken down into monosaccharides, nucleotides, fatty acids, and amino acids during catabolism.

The catabolic processes involved in the nitrogen metabolic pathway are:

• Proteolysis and breakdown of amino acids.
• Nitrification.
• Denitrification.

Nitrogen cycle

In the environment, nitrogen is available in many different forms for the plant system, including nitrate, ammonia, organic nitrogen, and molecular nitrogen. The nitrogen cycle is defined as the constant interconversion of various forms of nitrogen from atmospheric nitrogen and vice versa through physical and biological processes to sustain life. Although air contains 78 percent nitrogen, most organisms are unable to use this nitrogen. Nitrogen fixation, nitrogen assimilation, ammonification, nitrification, denitrification, and sedimentation are some of the processes in the nitrogen cycle.

Nitrogen fixation

During the nitrogen fixation process, the nitrogen from the atmosphere is transformed into a form that plants may absorb through their root systems. Nitrogen fixation is divided into two categories: biological and non-biological nitrogen fixation.

Biological nitrogen fixation is the conversion of a small portion of gaseous nitrogen into a physiologically acceptable nitrogenous substance (NH₃) by microorganisms such as bacteria and others. This process involves two types of organisms, symbiotic and non-symbiotic nitrogen fixers. Some bacteria that live symbiotically in the leguminous root nodules can fix atmospheric nitrogen and makes it available to the plants in a process known as symbiotic nitrogen fixation (Rhizobium spp.). In non-symbiotic nitrogen fixation, some free-living bacteria convert nitrogen from the air into ammonia by forming a nitrogenase enzyme complex (Azotobacter, Clostridium).

In non-biological nitrogen fixation, atmospheric nitrogen reacts with oxygen to form nitrogen oxide during lighting and thunder. The nitrogen oxide is then dissolved in rainwater and reaches the ground, where it interacts with soil minerals to generate nitrates and ammonium ions. Haber process is used in industrial nitrogen fixation to produce ammonia for human use.

Nitrification

Nitrification involves ammonium oxidation followed by nitrite oxidation to form nitrate. The various sets of nitrifying bacteria are largely responsible for the conversion of ammonia to nitrate. Nitrification is a two-step process that converts NH₃/NH₄⁺ to NO₃^-. The soil bacteria Nitrosomonas and Nitrococcus convert NH₃ (ammonia) to NO₂^- (nitrite), which is then oxidized to NO₃^- (nitrate) by another soil bacterium, Nitrobacter. These transformations provide energy to the bacteria, and both reactions occur in the presence of oxygen.

Nitrogen Assimilation

The process through which animals and plants incorporate NO₃^- and ammonia produced by nitrogen fixation and nitrification is known as assimilation. These forms of nitrogen are taken up by plants through their roots and incorporated into plant proteins and nucleic acids. Because plants cannot absorb ammonium ions, they uptake nitrogen in the form of nitrate. The nitrate is again converted back to ammonia which is then incorporated into amino acids, chlorophyll, and nucleic acids. Amino acids are formed when nitrates are converted to ammonia, which is then combined with organic acids to generate amino acids.

Amino acids are used to synthesize the protein, which includes regulatory proteins as well as structural proteins. For protein synthesis, amino acids are transferred through the phloem to different parts of the plant.

The role of glutamine synthetase in nitrogen assimilation

One of the most important enzymes in metabolism is glutamine synthetase. Glutamine synthetase plays a major part in nitrogen metabolism in all organisms because it converts ammonium to amino acids, neurotransmitters. Isoforms of glutamine synthetase with highly conservative sequences have been found in different animals.

In plants, glutamine synthetase is the primary assimilatory enzyme for ammonia, which can come through N₂ fixation, ammonia supplementation, photorespiration, or protein and nitrogen transport component degradation.

Ammonification

Ammonification is one of the phases of the nitrogen cycle. It is the process by which some microbes release ammonia from organic molecules derived from plant and animal dead organic wastes, as well as animal excreta. Bacteria (Pseudomonas, Clostridium, Bacillus), fungus (Aspergillus, Penicillium, Mucor), and Actinomycetes can convert organic nitrogen compounds to ammonia.

Denitrification

Denitrification is the biological transformation of nitrite and nitrate to molecular nitrogen (gaseous form). Nitrate respiration is another term for it. Nitrate is first converted to nitrite, which is then converted to nitric oxide, which is then converted to nitrous oxide, and lastly to molecular nitrogen. Pseudomonas, Thiobacillus denitrificans, and other denitrifying bacteria are examples.

Urea cycle

The nitrogen excreted by animals is in the form of urea. Ammonia is a toxic byproduct of the nitrogen metabolism process that must be eliminated from our bodies. The urea cycle converts excess ammonia to urea in the liver mitochondrial cells. The urea produced is taken into the bloodstream, filtered by the kidneys, and finally excreted in the urine. Glutamine synthetase is an important enzyme in nitrogen metabolism that converts ammonium to amino acids. The cytosolic isoenzymes of glutamine synthetase absorb ammonium derived from primary nitrogen absorption and other internal nitrogen recycling activities.

Context and Applications

This topic is essential in the professional exams for both school level, undergraduate and postgraduate courses, especially for

• Bachelors of Science in Biochemistry
• Masters of Science in Biochemistry

Practice Problems

Question 1: In nitrogen metabolism pathway, the oxidation of  ammonium to nitrite, followed by the oxidation of nitrite to nitrate, is called as ________________.

1. Nitrogen fixation
2. Nitrification
3. Denitrification
4. None of the above

Answer: Option B is correct.  

Explanation: Denitrification is the method of converting nitrates to mostly inert nitrogen gas, which completes the nitrogen cycle. In denitrification, nitrate is first converted to nitrite, which is then converted to nitric oxide, which is then converted to nitrous oxide, and lastly to molecular nitrogen.

Question 2: An example of a non-symbiotic nitrogen-fixing bacteria is _____.

1. Nitrobacter
2. Rhizobium
3. Azotobacterium
4. None of the above

Answer: Option C is correct.

Explanation: There are two types of nitrogen-fixing bacteria. The cyanobacteria belong to the first group, free-living bacteria. Azotobacter, Beijerinckia, and Clostridium are among the genera of Anabaena and Nostoc. The symbiotic bacteria are the second type; examples include Rhizobium, which is connected with leguminous plants.

Question 3: Which of the following is important in the plant nitrogen metabolism?

1. Glutamine aminotransferase
2. Adenylyl transferase
3. Glutamate synthase
4. Glutamine synthetase

Answer: Option D is correct.

Explanation: In plants, glutamine synthetase is the primary assimilatory enzyme for ammonia, which can come through N₂ fixation, ammonia supplementation, photorespiration, or protein and nitrogen transport component degradation.

Question 4: The catabolic processes involved in the nitrogen metabolic pathway are ______.

1. Nitrogen fixation, protein synthesis, synthesis of amino acids
2. Proteolysis, nitrification, denitrification
3. Both A and B
4. None of the above

Answer: Option B is correct. 

Explanation: The catabolic processes involved in nitrogen metabolism are proteolysis, nitrification, denitrification, and amino acids breakdown.

Question 5: Nitrogen fixation is the transformation of_________________

1. Nitrogen to Nitrous oxide
2. Nitrogen into ammonia
3. Nitrogen to Urea

Answer: Option B is correct. 

Explanation: Biological nitrogen fixation is the conversion of a small portion of gaseous nitrogen into ammonia by biological microorganisms such as bacteria and others.