The Urea Cycle

Hi, guys! I’m back with a heavily-edited version of a post I wrote last week! This one’s on a really fun subject—the synthesis of urea! You know you’re gonna love it.


Our bodies really hate ammonia. Like, really hate it. It’s something that we spend energy getting rid of, and our method of getting rid of it is as complicated as our method of obtaining energy from our food. That right there should tell you how much our bodies want to get rid of ammonia. They. Don’t. Like. It. They don’t.

It’s for that reason that we have lil’ nitrogen carriers like glutamine and alanine, two very common amino acids that happily carry nitrogen from other tissues to our livers. As I said in my post on nitrogen balance, we have a lovely bunch of enzymes that are more than happy to transfer nitrogen to and from our amino acids.

The enzymes that transfer nitrogen out of these carriers are present in our livers, perhaps unsurprisingly. In our liver cytosol, alanine is turned into pyruvate by alanine aminotransferase, and glutamine is made into glutamate by glutaminase. Glutamate can then be turned into alpha-ketoglutarate in the mitochondrial matrix using the enzyme glutamate dehydrogenase. This generates a heck-ton of ammonia, but it generates it in the liver.

That’s one of our liver’s jobs, after all—to take in ammonia (and ammonia sources) from our blood and metabolize it into something safe. In order to keep our blood ammonia levels low (10-50 micromolar), our livers routinely take in alanine, glutamine, bicarbonate and free ammonia, and metabolize them into a much safer nitrogen-containing molecule called urea. This can be kept at significantly higher concentrations in our blood—normal levels range from 1 to 6 millimolar (1ooo – 6000 micromolar).

urea.png

Lookatit! Shiny!

So, how do we accomplish this elegant conversion of highly toxic ammonia to (mostly) harmless waste product? Well, we use a little cycle called the urea cycle!

The urea cycle is a five-step cycle that converts free ammonia and bicarbonate into urea in liver cells. Here’s the general reaction:

HCO3 + NH4+ + Aspartate + 3 ATP + 3 H2O —> Urea + Fumarate + 2 ADP + 1 AMP + 4 Pi + 5 H+

There are a two main things we notice when we look at this net reaction. First, there’s a lot of chemical energy being used—four phosphoanhydride bonds’ worth, in fact. Second, we don’t just slap bicarbonate and ammonia together and call it a day; we have to also use aspartate in the process.

So, how does this work? Well, let’s look at the steps in detail, shall we?

Step 0: Activation of Bicarbonate and Carbamoyl-Pi Formation

In this preliminary step, which takes place in the mitochondrial matrix, carbamoyl-Pi synthetase I uses ATP to activate bicarbonate, generating carboxyphosphate. Ammonium then attacks this, knocking off a phosphate group and generating carbamoyl-phosphate. Although originally it was thought that this proceeded through a carbamic acid intermediate that was then converted to the carbomyl-Pi product using ATP, newer evidence suggests the chemical energy in the second ATP is used to change the conformation of the enzyme so that it can synthesize the final product directly.

urea cycle 0.1.png

Step 1: Condensation of Carbamoyl-Pi with Ornithine

In this step, the enzyme ornithine transcarbamoylase, a matrix enzyme, mediates the reaction of ornithine (lysine without one carbon) with the carbonyl of carbamoyl-Pi. This breaks a mixed anhydride bond, releasing enough energy to make this reaction spontaneous. The products of this reaction are inorganic phosphate and citrulline, an amino acid with an R-group that contains urea.

urea 1.png

Step 2: Condensation of Citrulline with Aspartate

Now, you’d think we’d just chop off that end bit, the urea bit, but nooooo. Apparently, that’s thermodynamically icky, so instead, we find a workaround. In the second step of urea synthesis, argininosuccinate synthetase, a cytosolic enzyme (yeh boys! We’re moving around!), uses ATP to facilitate the condensation of citrulline and aspartate into a molecule called argininosuccinate. This is named because it contains both arginine and succinate, but don’t get confused—we didn’t make it by joining arginine and succinate. It’s also worth noting that the ATP used in this reaction is made into AMP, which is more than enough energy loss to make this spontaneous.

urea cycle 2.png

Step 3: Lysis of Argininosuccinate

All right, now we can do something a little less cringy. In this reaction, a cytosolic enzyme called argininosuccinate lyase uses acid-base chemistry to cleave argininosuccinate into arginine and fumarate (oxidized succinate). This is, once again, a spontaneous reaction.

urea 3.png

It’s worth noting here that this reaction is a good source of arginine in adults, since the urea cycle is very active in adults. However, since it’s not nearly as active in children, arginine is considered an essential amino acid for developing children and young adults.

Step 4: Hydrolysis of Arginine

Finally, we’re ready to finish what we started. In the final step of the urea cycle, a cytosolic enzyme called argininase (manganese containing) facilitates the hydrolysis of arginine to ornithine and urea. Urea, our finished product, is released into the blood for the kidneys to take care of, and ornithine is funneled back into the cycle again.

urea 4.png

As you’ll notice from the cycle above, the nitrogens in urea didn’t just come from ammonia. Rather, they came from ammonia (often generated from alanine and glutamine) and aspartate. (Aspartate is replenished by first converting it into oxaloacetate using the citric acid cycle, and then transferring an amino group from other amino acids in the liver using aminotranferases.) Ultimately, though, all of the nitrogen comes from catabolism of amino acids.

All right, so we use alanine and glutamine to carry nitrogen to our liver while we’re catabolizing amino acids. Once our liver takes it up, we make urea by liberating ammonia from these amino acids and reacting it with bicarbonate. So what happens then?

Well, urea moves from the cytosol of our liver cells to our blood. Our kidneys take it up again by filtering it out of our blood. The urea is then eliminated in urine, where it’s kept at an average concentration of nearly ten grams per liter. Considering that two liters of urine are usually eliminated per day, roughly twenty grams of urea are eliminated per day.

Our livers take up glutamine too, to a small extent, and metabolize it to glutamate, liberating two ammonia in the process. This is also eliminated in urine, but in a much smaller amount—urine only contains 0.2-0.6 mg/L ammonia (in comparison to almost 10 g/L urea).

All right! That’s where our discussion of urea stops! Aren’t you glad it’s over with? I am, too. Although it’s an important (and simple!) cycle, I’d much rather talk about more interesting biomolecules. Thankfully, we didn’t spend all this time talking about nitrogen elimination for nothing—now we’re going to get to see where it all comes from. That’s right! We’re gonna talk about amino acids.


Yes, I know the images are inconsistent. I figured out how to do curly arrows earlier today, but I didn’t want to remake all those other images. I mean, look at ornithine. Look at it.

(I’ll probably edit them eventually.)

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