Amino Acid Oxidation: Study with Video Lessons, Practice Problems & Examples

Amino acid oxidation involves the removal of nitrogen through the urea cycle, primarily occurring in the liver. The cycle begins with carbamoyl phosphate formation from bicarbonate and ammonium, costing 2 ATP. Glutamine, derived from glutamate, transports nitrogen to the liver, where it is converted back to glutamate and then to alpha-ketoglutarate, releasing ammonium. This ammonium feeds the urea cycle, while fumarate links to the citric acid cycle. Transaminases play a role in amino group transfer and can indicate tissue damage, particularly in the liver and heart.

Amino Acid Oxidation 1

Let's begin by talking about amino acid oxidation, which is how the body uses the carbon skeletons from amino acids to fuel the citric acid cycle. Before it can use those amino acid carbon skeletons, it needs to do something about the nitrogens. It needs to get rid of them, but it can't just cut them off and release them as ammonia to the cell because that would really mess with the cell's pH and also it could be toxic to the cell. It's a reactive species. Anyhow, what the cell is going to do is it's going to take those nitrogens and it's going to put them through the urea cycle, which is a cycle that occurs in the liver, so it's going to export this stuff to the liver. The cycle takes in 2 nitrogens and puts out 1 urea, and it costs 3 ATP to do this. So, we're going to take a look at the cycle right here, and the first step, or what you could think of as the first step which is right here, is going to occur inside the mitochondria. So, this here is inside the mitochondria matrix, and out here, we have the cytosol. What's going to happen is carbamoyl phosphate synthetase, this enzyme right here, is going to take bicarbonate, and this should be an ammonium because it's dissolved in the cell. So, this figure is a little mistake, but you can see that up here, it's ammonium. And it's going to take bicarbonate and ammonium, and at the cost of 2 ATP, form this molecule right here, which is carbamoyl phosphate. I'm just going to write carbamoyl P. It's carbamoyl phosphate. Now, ornithine is going to enter the mitochondria, and ornithine is this molecule right here. That's ornithine. It's going to enter the mitochondria and it is going to combine with carbamoyl phosphate, and that phosphate group is going to leave. You can see, it's inorganic phosphate, and they're going to combine to form this molecule right here, citrulline. Now, citrulline is actually going to then exit the mitochondria. So, a little back and forth in here. It's going to exit the mitochondria, and then things get a little interesting. What's going to happen is ATP is going to be broken down to pyrophosphate. Of course, pyrophosphatase is going to break this down to 2 inorganic phosphates. And citrulline is going to be combined with aspartate. What's actually happening, you see this AMP, let me jump out of the image here. My head is blocking it. You see this AMP right here. Basically, the AMP gets attached to the enzymatic intermediate. The aspartate is added, and the AMP leaves. So that's why you see the AMP coming off, a little later here before that pyrophosphate. So, these come together, and they form this molecule right here, argininosuccinate. Alright. Oh, I'm sorry, I'm not labeling my steps. So, we had step 1, this here was step 2, and this was step 3. Okay. So argininosuccinate is then cleaved into fumarate right here, and arginine right here. That is step 4. From there, arginine has urea removed from it, right? So basically, these nitrogens right here are coming off as urea, and what we're left with is ornithine again, right here. So, that is our final step of the cycle, Step 6. And then of course that ornithine will reenter the mitochondria combined with carbamoyl phosphate, and the cycle will repeat itself. So let's turn the page.

Amino Acid Oxidation 2

So how does the liver get amino acids to perform the urea cycle? Well, most amino acids are going to actually come in as glutamine. Basically, all the tissues in your body are capable of delivering glutamine to the liver to get rid of that nitrogen. So glutamine synthetase is the enzyme that makes glutamine to send to the liver. And basically, it will take glutamate and ATP and a nitrogen group and it will make glutamine and of course, you will be left with ADP and inorganic phosphate. And basically, the reason for this is that it is very easy for the cell to convert amino acids into glutamine this way. So that's how it's going to transport the majority of amino acids to the liver and it also can get rid of this extra nitrogen group by doing so. So glutamine enters the mitochondria and will actually get broken down into glutamate. So kind of undoing what happened up here and it'll cleave off that ammonium and this is carried out by an enzyme called glutaminase. Now, that glutamate will then be acted upon by glutamate dehydrogenase and it will be converted to alpha-ketoglutarate. Basically, glutamate dehydrogenase just cuts off that amino group and it comes off as ammonium and in the process, it's actually going to reduce NAD⁺ or NADP⁺ (that's why the 'p' is in parenthesis there; it's actually either or) and it's going to reduce that to NADH or NADPH. Now, these nitrogens that got cut off, those are going to be used to feed the urea cycle. Remember that the first step requires ammonium to form carbamoyl phosphate. It should be noted that some glutamate is actually used to add the ammonium instead of just cutting it and releasing it to the urea cycle. That ammonium is actually added to oxaloacetate and that forms aspartate. Now you might remember that during the urea cycle in step 3, we actually use aspartate. Guess what? That aspartate is this aspartate. So some glutamate is actually used to form the aspartate that is used during the urea cycle. And of course, the cell has to kind of regulate the amount of glutamate that it cleaves to provide ammonium and the amount it uses to form aspartate. And it's worth noting that this is going to happen in the mitochondria which should make sense because we have oxaloacetate. So then this aspartate has to actually be exported from the mitochondria into the cytosol for step 3 of the urea cycle. Now I said that most tissues or rather all tissues export glutamine but muscles, muscles actually can send alanine as well. This is called the glucose-alanine cycle. And this again only occurs in the muscles and basically muscles will send alanine to the liver. And the way they do that is by converting pyruvate into alanine and to provide the amino group for this, they're going to cleave glutamate, take the amino from glutamate. So glutamate is going to turn into alpha-ketoglutarate. Now that alanine gets transported through the blood to the liver and once in the liver, what happened in the muscle, what we just talked about up here, gets undone. That's a pattern in general that I hope you've started to notice and are going to notice, later that a lot of processes are done and then undone after some transport. Anyhow, so alanine gets converted back into pyruvate by sending that amino group over to alpha-ketoglutarate which reforms glutamate and then that glutamate ammonium to the urea cycle or by being used to make aspartate. Now, what's going to happen to that pyruvate? Well, remember, this is the liver, the site of gluconeogenesis, right? So we are going to use pyruvate or we can use pyruvate I should say for gluconeogenesis which is going to make glucose, right, and then guess where a lot of that glucose is going? Right back to the muscles. Right? Now this is why this is called a cycle because that glucose goes back to the muscles, it gets broken down into pyruvate and then we can use that pyruvate to make alanine and repeat this cycle. So, before moving on, I just want to get my fat head out of this picture and just zoom in on the liver for a second and show you what's going on here. So, we have alanine and glutamine being used to make glutamate to feed urea cycle. Of course, if you're using glutamine to make glutamate, you're going to cut off, a nitrogen from it which will be released as ammonium. And if you use glutamate, you can use it to either provide ammonium or aspartate, right, to the urea cycle. Alright. So you may have noticed that fumarate also came off of the urea cycle. Well, the urea cycle is connected to the citric acid cycle, right. It's happening in part in the mitochondria. So it's very easy for that fumarate to actually enter the citric acid cycle where it will be turned into malate and then oxaloacetate. And of course, that oxaloacetate as we previously discussed can be used to make aspartate, right? That is the aspartate that we saw right here. The aspartate that is used as part of the urea cycle. So in a sense, argininosuccinate is kind of the link citric acid cycle. Alright, the citric acid cycle. Alright. Last thing I want to talk about are transaminases. These are used throughout this process, right? Whenever we're moving an amino group from one molecule to another, we use transaminase. And what's interesting about these is they can actually be an indicator of tissue damage, a really easy indicator of internal tissue damage because if you have internal tissue damage, enzymes will be spilling out and you can assay for these transaminases to see where the tissue damage is depending on which transaminases you have. These transaminases right here GPT and GOT indicate liver damage and this S just means serum as in in the blood. And this, transaminase right here can be an indication of heart damage. So either, you know, imminent heart attack or heart attack or infection. Last thing I want to talk about before moving on is regulation of the urea cycle. So remember, step 1 is carried out by carbamoyl phosphate synthetase. This molecule N Acetylglutamate actually stimulates, that enzyme. So it can kick the urea cycle into gear. And the way that's going to happen is with this, basically it's like a regulatory enzyme sort of similar or kind of akin to what we saw with phosphofructokinase 2. So N Acetylglutamate synthase will take Acetyl CoA and glutamate and make N Acetylglutamate. This enzyme that produces the molecule that stimulates the urea cycle is stimulated by arginine. I hope that this makes a lot of sense to you. Why do you think arginine would stimulate the urea cycle in essence? It's a few steps removed but basically arginine can stimulate the urea cycle is what we're seeing. Arginine has a lot of nitrogen, doesn't it? Well, hopefully, you're putting 2 and 2 together and if you have a lot of nitrogen, you're going to want to kick that urea cycle into gear. Alright. Let's flip the page.

Here’s what students ask on this topic:

What is the urea cycle and how does it function in amino acid oxidation?

The urea cycle is a metabolic pathway that occurs primarily in the liver, responsible for removing excess nitrogen from amino acid oxidation. The cycle begins with the formation of carbamoyl phosphate from bicarbonate and ammonium, costing 2 ATP. This carbamoyl phosphate then combines with ornithine to form citrulline, which exits the mitochondria. Citrulline combines with aspartate to form argininosuccinate, which is then cleaved into fumarate and arginine. Arginine is further broken down to release urea and regenerate ornithine, completing the cycle. The urea produced is excreted in urine, effectively removing nitrogen from the body.

How does the liver obtain amino acids for the urea cycle?

The liver primarily obtains amino acids for the urea cycle in the form of glutamine. Tissues throughout the body convert amino acids into glutamine using the enzyme glutamine synthetase, which combines glutamate, ATP, and a nitrogen group. Glutamine is then transported to the liver, where it is converted back to glutamate by the enzyme glutaminase, releasing ammonium. This ammonium feeds into the urea cycle. Additionally, muscles can send alanine to the liver through the glucose-alanine cycle, where alanine is converted back to pyruvate and glutamate, providing another source of nitrogen for the urea cycle.

What role do transaminases play in amino acid oxidation?

Transaminases are enzymes that facilitate the transfer of amino groups from one molecule to another, playing a crucial role in amino acid oxidation. They operate by transferring an amino group from an amino acid to a keto acid, forming a new amino acid and a new keto acid. This process is essential for the deamination of amino acids, allowing the nitrogen to be funneled into the urea cycle. Transaminases are also used as biomarkers for tissue damage; elevated levels in the blood can indicate liver or heart damage, as these enzymes are released from damaged cells.

How is the urea cycle regulated?

The urea cycle is regulated primarily by the enzyme carbamoyl phosphate synthetase I, which catalyzes the first step of the cycle. This enzyme is activated by N-acetylglutamate, which is synthesized from acetyl-CoA and glutamate by N-acetylglutamate synthase. The production of N-acetylglutamate is stimulated by arginine, an amino acid rich in nitrogen. This regulatory mechanism ensures that the urea cycle is activated when there is an excess of nitrogen in the body, facilitating its removal. Additionally, the availability of substrates like ammonium and aspartate also influences the cycle's activity.

What is the connection between the urea cycle and the citric acid cycle?

The urea cycle and the citric acid cycle are interconnected through the molecule fumarate. During the urea cycle, argininosuccinate is cleaved to produce fumarate and arginine. Fumarate can then enter the citric acid cycle, where it is converted to malate and subsequently to oxaloacetate. Oxaloacetate can be used to form aspartate, which is a substrate for the urea cycle. This interconnection allows for the efficient use of intermediates and energy between the two cycles, integrating nitrogen metabolism with cellular respiration and energy production.