Good evening, everyone! I’m back yet again, after a brief moment spent procrastinating by watching Hunter x Hunter fan videos on YouTube. (You never realize you want to spend a whole day doing something until you’re doing it instead of being responsible. Huh.)
Anyway! Time to get down to business. Let’s talk about protein metabolism~!
Amino acids are important for the synthesis of proteins. We know that much. They’re also important for making nitrogen-containing molecules (you know, other than proteins). Although we do take in plenty of amino acids daily (both essential and nonessential), our bodies are more than capable of generating a large number of them (the nonessential ones) without a lot of trouble.
So, how does a body start making an amino acid? Well, to make the nonessential amino acids, we need three primary components:
- Carbon Skeleton
- Nitrogen Source
- Heteroatom Source
The carbon backbones for the amino acids come from various sources depending on the amino acid, but all sources are intermediates in the pentose-phosphate pathway, the citric acid cycle, or glycolysis. The five primary carbon sources, as well as the amino acids that they are converted into, are listed below:
Pyruvate (3 C)—Alanine
Glycerol-3-Pi (3C)—Serine, Glycine, Cysteine
Oxaloacetate (C4)—Aspartate, Asparagine
alpha-Ketoglutarate (C5)—Glutamate, Glutamine, Proline, Arginine
Carbons are very important for the structure of the amino acids, but nitrogen sources are important to give them their “amino” essence (that is, to give them amine groups). Usually, the sources of nitrogen used in amino acid anabolism are other amino acids, like aspartate and glutamine.
Finally, heteroatoms (sulfur, really) are required for the synthesis of sulfur-containing amino acids (cysteine). The predominant source of sulfur in our body for biosynthesis is methionine, which is an essential amino acid. In this way, the biosynthesis of cysteine is dependent on dietary methionine consumption in the same way that the synthesis of tyrosine is dependent on phenylalanine consumption.
Now, before we move any further, there’s a rather important question worth addressing: why the heck are certain amino acids dietary essential? Did our bodies just go, “Eh, I feel like only making half of the amino acids I need to live?” Well, not exactly.
As far as biosynthetic pathways go, amino acids run the gamut. The number of steps it takes to make an amino acid can vary from one (alanine) to thirty-three (tryptophan). The energy requirements fluctuate, as well—glycine, the least energetic, requires 12 ATP to synthesize, while tryptophan, the most, requires seventy-eight. As you might expect, our bodies don’t like to run long, complicated, taxing biosynthetic pathways. Can you guess what that means?
Yup! It turns out that the amino acids that we make are the ones that require few steps and little energy. For example, all of the nonessential amino acids that we make, with the exception of histidine, proline and arginine, require fewer than six steps to make. (I kind of left tyrosine out because it’s made from phenylalanine using one reaction in our bodies.) We also emphasize low energy requirements: other than proline (39 ATP), most of our nonessential amino acids require less than 30 ATP to make.
All right, so we know that we can get amino acids from our diet and from our body, but what happens once we get them there? Yeah, we can make proteins (ho-hum, such a boring process), but they’re important for a lot more than that.
Turns out, amino acids alone are used to make all sorts of biomolecules:
- Coenzyme A
And that’s just if you’re using straight-up amino acids. If you use decarboxylases (PLP dependent), you can make another class of biomolecules called biological amines. Choose just a handful of these, and already, you’ll have found something important. For example, decarboxylate histidine, and what do you get? Histamine, which triggers an inflammatory response. Oxidize and decarboxylate tryptophan, and you get seratonin. Oxidize and decarboxylate tyrosine, and you get dopamine. The list goes on and on.
Here’s just a small sampling of the things that can be made from biological amines:
All right, so that’s what you make if you turn your amino acids into other biomolecules. But what if you want to make them into energy? Surely there’s way to do that, right? After all, we do pretend to get energy out of steak…
Well, as you saw up there, amino acids contain carbons with plenty of electrons. Theoretically, once we get rid of the nitrogen in these suckers (hello, urea cycle!), we can plug the carbons into their respective energy-generating cycles and get some ATP out of them.
Amino acids can either be glucogenic or ketogenic depending on where their carbons end up in metabolism. Of all of the amino acids, only lysine and leucine are ketogenic. All the others end up converted into glucose, which is then made into energy.
Two metabolites are strictly ketogenic: acetyl-CoA and acetoacetyl-CoA. All the others, however, are glucogenic. There are five primary glucogenic metabolites that result from amino acid catabolism:
- Pyruvate (Alanine, Serine, Cysteine, Glycine, Threonine, Tryptophan)
- Succinyl-CoA (Isoleucine, Valine, Methionine)
- Oxaloacetate (Aspartate, Asparagine)
- alpha-Ketoglutarate (Glutamine, Glutamate, Proline, Arginine, Histidine, Ornithine)
- Fumarate (Aspartate, Phenylalanine, Tyrosine)
All right, so, we didn’t have time to go over all of these in class, but we can take a look at how some of these metabolites arise from some of these amino acids. For starters, let’s look at how we interconvert alpha-ketoglutarate, glutamine and glutamate.
Under anabolic conditions, glutamate and glutamine are made using alpha-ketoglutarate as a carbon source. First, glutamate is reversibly made from alpha-ketoglutarate using an aminotransferase reaction (stealing amino groups from other amino acids that are in excess). (It can also be made from alpha-ketoglutamate using glutamate dehydrogenase, but that’s usually considered a less important reaction.) Glutamate and cellular ammonia are then made irreversibly into glutamine using ATP and the enzyme glutamine synthase.
Under catabolic conditions, glutamine is irreversibly hydrolyzed into glutamate using glutaminase. An aminotransferase then makes glutamate into alpha-ketoglutarate and other amino acids.
A very similar conversion occurs with aspartate, asparagine and oxaloacetate. This isn’t news to anyone, since we extensively covered this when we talked about nitrogen balance.
Now that we’ve got that established, we can look at some specific biosynthesis pathways. I’m going to go over the ones that we covered in class: the interconversion of proline and glutamate.
Catabolic: Proline to Glutamate
Step 1: Oxidation of Pyrolidine Ring
The first step in the conversion of proline to glutamate is the oxidation of its characteristic pyrolidine ring structure. This is mediated by a dehydrogenase enzyme that uses NADP+ as a cosubstrate.
Step 2: Hydrolysis of Schiff Base
Once the ring is reduced, it’s hydrolyzed into a linear structure called a glutamate semialdehyde.
Step 3: Oxidation of Aldehyde
The terminal aldehyde of the glutamate semialdehyde is oxidized to full-blown glutamate using another dehydrogenase enzyme. This is an irreversible reaction.
This reaction is favored under catabolic conditions because glutamate can be easily converted into alpha-ketoglutarate, which produces energy via the citric acid cycle. When this conversion occurs, the nitrogen from proline is trapped in urea.
Anabolic: Glutamate to Proline
Step 1: Phosphorylation of Glutamate
Under anabolic conditions, glutamate is generated from alpha-ketoglutarate. This molecule then accepts a phosphate group from ATP via a kinase, producing glutamyl-Pi.
Step 2: Reduction of Glutamyl-Pi
Glutamyl-Pi is then irreversibly reduced to that glutamate semialdehyde using NADPH. This is mediated by a reductase.
Step 3: Ring Closure
The alpha-amino group of this glutamate semialdehyde intermediate reacts with the aldehyde group, producing water and closing the ring. This forms a pyrroline-carboxylate.
Step 4: Reduction to Proline
Finally, this ring structure is reduced to the pyrolidine ring of proline using NADPH. This is mediated by a reductase.
[cries salty tears] All right, that about does it for amino acid metabolisms. I’d be lying if I said I enjoyed it, but really, it’s not too difficult. Don’t you agree? Now it’s time to move on to the final subject that I’ll ever cover for introductory biochemistry [looks sadly into the distance]—pyrimidine homeostasis! Don’t worry, it’s not nearly as difficult as it sounds.
Can you tell that I lost steam at the end? We may have kind of sort of ducked out for an hour to get pretzels…