Nitrogen and urea cycle

Definitions & Key takeaways

The nitrogen cycle is the process by which nitrogen is converted between its various chemical forms. One important aspect of the nitrogen cycle is the urea cycle, which involves biochemical reactions that produce urea from ammonia. The urea cycle takes place primarily in the liver, and to a lesser extent in the kidney. Its main role is to convert excess nitrogen in the body into urea, which is then excreted in the urine.

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The human body generates a lot of waste products, and fortunately, our kidney is capable of getting rid of most of them.
However, there is one arch nemesis that the kidney can’t deal with on its own. So, the liver comes to the rescue.
The villain is ammonia. Ammonia is the major toxin that results from the metabolism of amino acids.
Amino acids are made of a nitrogen group, a carbon skeleton, and a side chain that is unique to each amino acid. When amino acids are metabolized, the nitrogen is formed into ammonia, and ammonia is toxic to the cells.
So the ammonia is shuttle over to the liver and sent through the urea cycle, which is a series of enzymatic reactions that convert ammonia into urea.
The urea cycle takes place within the mitochondria, so that it doesn’t affect proteins and organelles in our cytoplasm. Urea can then easily be dealt with by the kidney.
It’s a bit like how a mama bird might mash up a worm so that it’s easier for a baby bird to digest. In this case the liver is the mama bird, and the kidney is the baby bird.
Alright, so first, ammonia needs to get to the liver. And it has to be done carefully because it’s toxic.
So, much like a prisoner, it needs to be carried in the circulation by a police officer, to its prison, which is the liver mitochondria.
There are two ways this can happen. The first way is used throughout by cells throughout the body.
The enzyme glutamine synthetase adds ammonia to the amino acid glutamate forming glutamine. Glutamine can move into the blood, and essentially transport ammonia around the block, until it gets to a liver cell.
Once inside the mitochondria of a liver cell, an enzyme called glutaminase cleaves glutamine back into glutamate and ammonia, and the ammonia can then enter the urea cycle.
The second way to move ammonia around is done mostly by skeletal muscle cells. In skeletal muscle cells, the enzyme glutamate dehydrogenase incorporates ammonia into the molecule alpha-ketoglutarate and turns it into glutamate.
But unlike glutamine, glutamate can’t leave the cell on its own. It needs to somehow give its ammonia to an amino acid that can leave the cell, and that’s alanine.
So, the enzyme alanine transaminase, or ALT, converts glutamate and pyruvate into alpha-ketoglutarate and alanine. And alanine then moves into the blood, and ends up transporting ammonia to a liver cell, and once there it undergoes the reverse of the previous reactions.
The enzyme alanine transaminase converts alanine and alpha-ketoglutarate back to pyruvate and glutamate. At this point, the ammonia is now part of glutamate once again.
Okay, so now these two pathways both end up at the same point in the liver cell, which is in the form of glutamate. From there, glutamate has two possible outcomes.
The first is for glutamate to encounter the same enzyme that incorporated ammonia into glutamate; glutamate dehydrogenase, and to have the ammonia snatched away from glutamate, converting it back into alpha-ketoglutarate and a free ammonia the enters the urea cycle.
And since this reaction can happen in both directions, we call it a reversible reaction. The second outcome is for glutamate to encounter the enzyme aspartate transaminase, or AST, and combine with oxaloacetate to form aspartate and alpha-ketoglutarate.
As before, the amino acid aspartate is carrying the ammonia group, and aspartate will directly enter the urea cycle - in fact, it’s the only amino acid to do that!
Alright, now that we have ammonia in the liver, the urea cycle can begin. The urea cycle is made of a series of enzymatic reactions that modify the chemical structure of substrates within it until it ultimately results in the molecule urea.
Urea is made of 2 nitrogen groups and 1 carboxyl group. Think of the enzymes involved in the urea cycle as children playing around with clay, changing its shape until the clay looks like urea.
Sounds like fun! Okay so the first two steps of the urea cycle take place in the mitochondria, and the rest happens in the cytoplasm.
To kick things off, the participants in the first reaction are ammonia, carbon dioxide, and 2 adenosine triphosphate, or ATP molecules.
An enzyme called carbamoyl phosphate synthetase 1, or CPS1 converts these into a molecule called carbamoyl phosphate. If we breakdown the name of this molecule, “carb” refers to the carboxyl group provided by carbon dioxide, “-amoyl” refers to the nitrogen group provided by ammonia, and phosphate refers to the phosphate group that comes from one of the two ATPs molecules.
Now, this process can be sped or slowed down based on the affinity of carbamoyl phosphate synthetase 1 for ammonia. A molecule called N-acetylglutamate allosterically activates CPS1, meaning that it binds to the CPS1 on a site different from where ammonia binds.
When it binds, N-acetylglutamate modifies the physical shape of CPS1, so that it can process ammonia more efficiently, increasing the rate of urea synthesis.
Now N-acetylglutamate itself is made by a mitochondrial enzyme called N-acetylglutamate synthetases which combines glutamate and acetyl-CoA.
And having enough N-acetylglutamate around is crucial because without it, CPS1 has very low affinity for ammonia. In fact, having a genetic deficiency in N-acetylglutamate can lead to ammonia building up to toxic levels.
In the second step of the urea cycle, also in the mitochondria, the enzyme ornithine transcarbamoylase combines the molecule ornithine combines with the carbamoyl part of carbamoyl phosphate to form citrulline, releasing free phosphate in the process.
In fact, deficiency of ornithine transcarbamoylase is the most common genetic cause of increased ammonia levels, or hyperammonemia.
Next, citrulline goes from the mitochondria to the cytoplasm, where it meets up with aspartate. The enzyme argininosuccinate synthetase uses the energy of an ATP molecule to combine citrulline with aspartate to make argininosuccinate.
So now aspartate has provided the 2nd and final nitrogen group which will be part of the final urea structure. But we have to continue playing with clay until we get to urea.
Next, the enzyme argininosuccinate lyase breaks up argininosuccinate into two molecules - fumarate and arginine. Let’s start with fumarate.
Fumarate is first converted to malate , and then the enzyme malate dehydrogenase converts malate to oxaloacetate. Oxaloacetate and glutamate are converted to aspartate and alpha-ketoglutarate by the enzyme aspartate transaminase, or AST.
This regenerates aspartate, so that it may enter the next urea cycle. Next there’s arginine.
Arginine is broken down by arginase to make urea and ornithine. Urea exits the liver cell, enters the blood, and gets excreted by the kidneys.
Whereas ornithine heads the other way and enters the mitochondria, so that it may enter the next urea cycle. Alright, a quick recap.
All amino acids with the exception of aspartate are metabolized into a nitrogen containing toxic compound called ammonia.
In liver cells, aspartate and ammonia provide the 2 nitrogens necessary to make the less toxic urea in the urea cycle. In the liver mitochondria, carbomoyl phosphate synthetase 1 requires allosteric activation from N-acetylglutamate to bind ammonia.
Once urea is formed, it can go into the bloodstream and get excreted by the kidneys.