Friday, February 20, 2015

I guess I never thought about it like that...

By: Jason Johns

Today (2/17) I was sitting under a canopy of Oaks in the Los Osos Elfin Forest, talking to my BIO 114 class about taking a closer look at things they think they may already know. In our highly efficient lives we seldom find time to stop and think about how something works. Do you really know how your car works? Your washing machine? Yourself? Plants???

The plant guy is going to blog about plants. How novel and interesting.

It gets worse. He's going to blog about something that you can find in a regular ole Biology textbook. Photosynthesis. I'm imagining reactions from three different groups of people going on right now...

1. Last took Biology in high school:
"I already learned all I need to learn about it. Plants make food with their leaves. Not interested in your technical extras."

2. Biologists (or Biologists in training):
"I've learned photosynthesis at multiple levels, on multiple occasions. I'm not wasting my time with this."

3. Knowledge junkies:
"I may know a thing or two about photosynthesis, but what do you want to tell me? I don't know much about that C4 thing or whatever it's called." want to know about C4 photosynthesis? Good, because I did too. Remember, biologists, some of my friends and family are reading this too. We've gotta go over some basics so that Grandma Peg gets to join in on the fun.

Ok. Photosynthesis...
Light + Water + Carbon Dioxide = Plant food (sugar) + Oxygen

You've probably seen that before. I just spelled out one of the most "well-known" chemical reactions in nature. Have you really thought about it though? Plants are eating light. They have the machinery to take the energy from a particle of light and turn it into sugar. While they're at it, they'll just spit out some purified oxygen so that all of us can breathe. Can I get an A-Menn-ah!

I mentioned the word "machinery"in the previous paragraph and that was no metaphor. Contrary to what I once assumed, these particles of light, electrons, molecules, proteins, etc. don't just float around and react with each other. Look at the figure to your right. No need to understand it (yet)...just stare at it in awe. Does that look like a bunch of molecular gunk floating around to you? 

These are machines that exist in every cell that has chloroplasts (see Wikipedia for definition). Similar ones exist in every one of our cells that have mitochondria (again, Wikipedia). And yes, for the record, plants have mitochondria too. Sugar is no good unless the mitochondria can break it down to make some of that pure ATP: the energy currency of our cells. The little machines are not only incomprehensibly complex and fast, but they're frickin tiny. A poppy seed is roughly one million times as big as one of these machines.

This almost physically hurts to type this, but we're going to fast forward through all of the gorgeous light-harvesting reactions that occur within chloroplasts. Me skipping through that stuff is like fast-forwarding through the first 8 innings of Game 7 of the World Series to see the end. It aint Christian, but I don't have the space, and you might not have the attention span. KNOWLEDGE JUNKIES: watch this video before moving on.

Ok so you didn't have to watch that video but you DO have to check this image out below. It's an extremely simplified version of the process of turning light into sugar. One step at a time...

1. The light hits those green stacks: the photosynthesis factories in the chloroplast.

2. The symphony of reactions in the chloroplast spit out some ATP and some NADPH...both are basically Power Bars for the cell. But hang on, didn't you say the whole point of making sugar (glucose) is to go break it down into ATP? And we're using ATP to make glucose

The ATP made from the light reactions isn't enough to fuel the whole plant, so we've gotta use some energy to make more. Kinda like how your dog is. The more you work him out the more energy he's got. Or she...yeah, yeah, yeah.

3. Ok look again at that photosynthesis equation up top. Here's where the carbon dioxide (CO2) comes in. Plants take in that CO2 through their leaves so that they can attach it to another carbon-based molecule and send it through the Calvin cycle to make some glucose. The Calvin cycle is in blue on the right side of the image.

Let's focus in on #3. By this time we have our NADPH and some preliminary ATP, the energy sources necessary to make glucose that can then be stored or passed over to the mitochondria to get processed and turned into ATP

Basic rundown: we're taking an initial molecule, forget the name of it, and sending it through a crazy reaction machine (Calvin cycle) to spit out glucose. Ok so just know for now that the enzyme that makes this reaction happen is called RuBisCO (trust me that you don't want to know what that stands for). RuBisCO takes the initial molecule, mentioned above in whatever color this is and attaches a CO2 to it, making it a whole new molecule that eventually becomes glucose (after going through the Calvin cycle).

Here's the only problem...RuBisCO is a little slow in the head. We (and the plant) want it to react with CO2, but it can also react just as easily with gaseous oxygen (O2). When silly RuBisCO grabs an 02 molecule in stead of a CO2 molecule that's bad...mmmkayyy? When this happens the plant makes less sugar and we get less oxygen. It's called photorespiration and it sucks. Sorry stinks.

Fret not, my knowledge-loving brother or sister, the story doesn't end there. Some plants have developed the ability to take an enzyme normally used in a whole other part of the cell and use it here in the chloroplast to hide RuBisCO in a lower level of cells and save it from itself. The name of this microscopic hero is PEP carboxylase and guess only reacts with CO2. Look at the image to your right. In plants that use the "regular" (C3) photosynthetic mechanism, CO2 enters the leaves and goes straight to RuBisCO (blue box on left). In this case, O2 can just as easily meet up with RuBisCO and do bad things. Bad RuBisCO. Bad.

Check out the C4 plant on the right though. It sent RuBisCO down to a lower layer of cells (bundle sheath cells) and brought in the glorious PEP carboxylase to process the CO2 (in the mesophyll cell) and send it down to that bundle sheath cell where RuBisCO "the simpleton" is ready and waiting to process it and send it through the Calvin Cycle to make some sugar. 

Did you see what happened there? PEP carboxylase just swooped in and streamlined the whole process. What a bad butt.

Thank you for sticking with me all this way. This has been a long one. We're almost done, but this wouldn't a grad school blog if I didn't talk at least a little bit about something a lot of biologists don't even know about. So here it turns out some plants can actually switch back and forth between C3 and C4 photosynthesis depending on their environmental conditions. My heart rate is going through the roof. Yours too?

So how do these C3-C4 intermediates work? In case you missed it, photorespiration is the plant's equivalent of a hamster wheel. They waste a bunch of energy (that they worked hard to make) bouncing CO2 all over the place until it jut gets released out of the cell...all because RuBisCO was so dumb that it decided to grab an O2 in stead of a CO2. So these intermediates are still getting figured out, but it looks like they can actually use another molecule in the pathway (called glycine decarboxylase) to scoop up that CO2, and in stead of allowing all that hard work to go to waste, it directs the CO2 back to the Calvin cycle to go make some glucose (Ueno, 2011). This is real life. It's happening faster than your computer can send your tweet at 1 millionth of the size of a poppy seed. Oh yeah, and RuBisCo (ribulose-1,5-bisphosphate carboxylase oxygenase) is the most abundant enzyme on the planet. 

Obviously there's a whole lot more to know about all this. Believe it or not, Wikipedia is actually pretty darn accurate on all of this stuff. Let's be curious about the stuff that matters.

Ueno, O. 2011. Structural and biochemical characterization of the C3–C4intermediate Brassica gravinae and relatives, with particular reference to cellular distribution of Rubisco. Journal of Experimental Botany62(15), 5347–5355. doi:10.1093/jxb/err187


  1. A-Menn-ah!Speaking as someone from the first group - interesting read! Well written bud

  2. There's a certain pattern to your blogs that I plan on copying. Well done!