Photorespiration

We have other videos that go into some depth on the Calvin cycle, and we'll refer to that in this video as the normal Calvin cycle. The focus of this video is really a quirk that diverts us from the normal Calvin cycle, and it's a quirk due to this enzyme right over here, whose shorthand name is rubisco.

So, to get an appreciation for that quirk, let's first do a very quick overview of a normal Calvin cycle. We could start at any point, but I'll start at the point that is typically started at, and we can start with this five-carbon molecule. We're visualizing just the carbons here for simplicity, so each of these gray circles represents a carbon. There are other atoms a part of this molecule, but we're not drawing them, and that's because the carbon accounting is what is interesting in, well, not only the Calvin cycle but also this variation, this diversion that we're going to see that we're going to call photorespiration.

So right over here, I've set it up so that I have six molecules of this. We call this ribulose 1,5 bisphosphate, but because it's a mouthful, the shorthand notation is RuBP. Sometimes people might say RuBP, or I guess you could even say RuP somehow, but each of these six RuBPs can then react with a carbon dioxide. So, if I have six RuBPs, well, they're going to react with six carbon dioxides.

One way to think about it is it's fixing the carbon in that carbon dioxide. It's taking this carbon that's part of this gaseous carbon dioxide and fixing it as part of an organic molecule. Now you might be tempted to say, well, it's going to create six six-carbon molecules, but then those will immediately become twelve three-carbon molecules. Notice, and it's important to keep doing this—pause the video if you need to— you can make sure that the carbons are all accounted for.

Right over here, how many carbons do we have? Well, we have 6 * 5, so that's 30 carbons right over here, and here we have 6 * 1 carbon, so that's six carbons right over here. So, if we want to account for all of our carbons, we should have 36 carbons right over here, and we do. We have twelve three-carbon molecules. These three-carbon molecules, when we go into some detail here in the video on the Calvin cycle, are called three-phosphoglycerate. But that's not what the focus is on in this video.

The focus of this video is the enzyme that actually does the fixing of the carbon along with the RuBP. That character, the character with the quirks that we're going to talk about, the shorthand name you could call it is ribulose 1,5 bisphosphate oxygenase carboxylase, but that's even more of a mouthful than RuBP, so people call it the nice friendly name, rubisco. Rubisco for short.

But you can learn a lot about what rubisco does from its name right over here, and you can even learn a little bit about its quirk that we're about to talk about. So, it obviously involves ribulose 1,5 bisphosphate, and it does indeed involve that. Then you see oxygenase and carboxylase. Well, the carboxylase is what tells us that it can deal with the carbon dioxide right over here. That carbon dioxide can be one of the substrates in a reaction with the ribulose 1,5 bisphosphate, and so that's exactly what it's doing in this reaction.

In a normal Calvin cycle, it's acting as a carboxylase. It is fixing that carbon, making it part of, if you view, you know, if you view that carbon—actually, I won't do it that way because here we have twelve as many—but it's taking these carbon molecules and it's fixing them into organic molecules, some of which can eventually be used to create glucose. That's what happens in a typical Calvin cycle. We use up some NADPH, we use up some ATP, and we go down through this cycle; eventually, we create some G3Ps, which are also three-carbon molecules. G3P is short for glyceraldehyde 3-phosphate for those of you who are interested.

Then, if we use this accounting of those twelve, ten go back through the Calvin cycle to regenerate our ribulose 1,5 bisphosphate, and two of them exit the Calvin cycle and then can be used to produce one six-carbon glucose. That’s what happens when everything is fine, and that’s what the Calvin cycle’s purpose is—to be able to have a store of energy in the form of glucose.

Now, you might have already gotten a little bit of the foreshadowing from rubisco’s name: well, maybe it sometimes acts as an oxygenase. So instead of fixing carbon, maybe sometimes it fixes oxygen, and that is indeed the quirk that I’m talking about of rubisco. So in photorespiration, instead of fixing carbon, it fixes oxygen along with the ribulose 1,5 bisphosphate.

You might say, why does it do that? The answer is, well, that's a really good question. Some folks think, well, that’s just one of these inefficiencies of a biological process. It really shouldn't do it. It's, in some ways, detrimental to the plant. It could be a side effect, a legacy feature, or a side effect from ancient evolution when there was very little oxygen in the atmosphere, and so this didn’t seem like that bad of an inefficiency. But it does happen.

In particular, the times where photorespiration is more likely to happen are with typical plants, often referred to as C3 plants. C3 is referred to because the first product when you fix the carbon is a three-carbon molecule. But this typically happens, or this happens with typical plants, in hotter than normal weather. So let me write this down, and I'll write it in a hot color: hot conditions.

That's where it typically happens with typical plants. And why hot conditions? Well, in hot conditions, first of all, rubisco has more affinity; rubisco's affinity to O2 increases. So under normal conditions, it tends to have more affinity for carbon dioxide. But under hot conditions, these proteins, or no protein is perfect; it can morph a little bit so it has more affinity to molecular oxygen.

Also, under hot conditions, plants are worried about conserving water, and so they will close their stomata. Stomata closed to preserve water, but when the stomata are closed, you have CO2 that can't diffuse in, can't diffuse in, and O2 that can't diffuse out, can't diffuse out. So your ratio of O2 to CO2 increases; the O2 to CO2 ratio increases.

So under hot weather, the rubisco just wants to work with the oxygen more. It typically wants to work with the carbon dioxide, and also, because this stomata is closed and you don't have as easy diffusion, well, this ratio is going to increase. So things are just more likely to react with the oxygen; especially the rubisco is more likely to bump into it in the right way than it is with the carbon dioxide.

But let's think a little bit about why this is inefficient. Well, in this case, it’s fixing the oxygen, and so it's not gaining those carbons like we just saw in the typical or the normal Calvin cycle. Here, you can account for the carbons; I encourage you to keep pausing the video and account for the carbons.

But here, you can't no longer produce your twelve three-carbon molecules because you’re not getting these six carbons over here. So instead, you can only produce six of those three-carbon molecules and then another six of the two-carbon molecule called phosphoglycolate. Once again, I'm not showing all the oxygens, and I'm not showing all the phosphates; I'm just accounting for the carbons.

So this seems like a pretty bad loss. You’re not able to use those carbons right over there. Well, evolution has given us pathways to at least start to salvage some of it, but it’s a pretty intense pathway to get back some of those carbons. The reason why it wants to get back some of those carbons is because remember, at the end of the day, you want to attempt to produce some glucose, and you want to have the typical or the normal Calvin cycle continue to happen.

But just so you get a sense of what the salvage pathway looks like, that phosphoglycolate, this two-carbon molecule right over here, has to go to glycolate. Then that has to go to the peroxisomes where it becomes glycine, to the mitochondria. You see this whole process here just to be able to salvage it into a few more of the three-carbon molecules.

That’s essentially what happens right over here. We get three more of the three-carbon molecules, but we do lose—for the way I've accounted it—three molecules of carbon dioxide. This is one reason for why it's called photorespiration. We use oxygen, and we produce carbon dioxide, and that's exactly what's happening. We're using oxygen, and we're producing carbon dioxide.

As you see this mechanism, it kind of makes the Calvin cycle disrupt it, or it makes it less efficient. So once again, why does this happen? Well, it could just be a biological quirk that has not been selected strongly enough against, or some people believe it actually has some not-so-well-understood mechanism and it somehow helps the plant in some way.

But it's a really interesting thing that goes on, and you know rubisco is not just some very fringe molecule. As you see, it's central to the Calvin cycle. If you look at plant matter, in particular plant leaves, it'll represent roughly 20% of the protein mass in those plant leaves. So it’s a very common protein, a very common enzyme, but it’s got this quirk that takes the plant down the path of photorespiration.