 Hello. Hello. So we're going to try out first here. I forgot my iPad, man. So I have to do the iPhone. So I'm going to be like this. Hi everybody. So we're going to try it. My eyesight is really bad. I'm a stubborn man and will not get glasses and I very much need them. So let's get started. So today, welcome all pre-medical students. We're going to be studying photosynthesis. And so it might be painful for some of you, but you're going to see some elegant examples of similarities to what we saw in electron transport. Remember that was the fuel that's keeping your core warm. So let's see what we can do. Hey, it works. So there's two parts today's lecture. One is making ATP and reduced cofactors using the energy of light transferring electrons from water molecules to NADH. You're like, oh, that's some crazy stuff. But then after that we're going to use that energy that we made ATP and NADH to assemble take carbon dioxide and turn it into a triose sugar. And so everything that you do, all the metabolism in you is dependent on the energy produced by the breakdown of sugar. Now we can make sugars through a process called gluconeogenesis but the energy to make that comes from the breakdown of sugars. And so we don't exist without these processes. You'll see some elegant examples of unintelligent design in one particular enzyme and you'll look at ways in which problems with enzymes can cause just massive difficulties for an organism. So if you look at the world, we're way out of equilibrium. If you go to a normal planet, you're not going to have all this oxygen here. And so this oxygen has a very high affinity for electrons. So it's rocket fuel. It's one component of rocket fuel. It's something that tends not to persist. And then we have a stable form of carbon, the carbon dioxide. But in our world there's all these sugars, these reduced sugars and fats floating around. So there's just, something is very strange here. And so rocket fuel typically dissipates. So you have oxygen here. It has one of the most high. Is that fuzzy over there or is it in my eyes? Does it look a little fuzzy? Oh good. All right. So you can't read it either. So oxygen is rocket fuel. And we guess it's going to want to grab some electrons from somewhere, right? And so there's this massive lack of equilibrium in our world. And the reason is because this is sort of explaining that it's logical that electrons would flow to the molecules that have the highest electron affinity. And so what's happening here is photosynthesis. It's creating this massive disequilibrium. This 20% of the atmosphere is oxygen. That's crazy. And so it's also making all these sugars. And this is providing the energy for us. We don't exist without this disequilibrium. We feed. We're a parasite on this disequilibrium. And so here's what we're talking about today is photosynthesis and carbon assimilation, a synthesis of sugars from carbon dioxide. And so you have photosynthetic cells producing reduced forms of carbon and carbohydrates are some examples and oxygen. And then the parasites, a.k.a. us, we're taking these molecules and putting them in a more stable state. So you're taking oxygen converting it from rocket fuel down to water and taking carbohydrates and burning them. So if you light a match on a tree the spontaneous thing to happen is what we're doing. And so this is magical. Wow. How are you sort of transforming this energy from the sun to create massive disequilibrium on a whole planet? So the magic occurs in these chloroplasts. And so there's various features of this chloroplast. You have a total of three membranes. And remember with mitochondria we had two membranes. The outermost was pretty permeable. Same situation here. Here you have this inner membrane here. And then you have thylakoid membranes. And so all photosynthesis is occurring on these thylakoid membranes. The most inner sanctum, like three levels in, is called the lumen. Remember we call that the matrix in mitochondria. So the inner part is called the lumen. And then all the space between these thylakoid membranes and this inner membrane on the outside here is called the stroma. And so we're going to be producing ATP and reduce cofactors in the stroma. And we're in the same exact location we're going to be fixing carving. We're going to take carbon dioxide and make sugar molecules. And so that minimizes the amount of transport that we need to do. Alright so the light reactions, which is the first part of the lecture is going to reduce cofactors. So we're going to take the energy of light and literally transfer electrons from water molecules onto NADP to make NADPH. We're also going to generate ATP. And we're going to do it in the exact same way we did it before by setting up a non-equilibrium of protons across a membrane. And in this case we're going to be pumping protons in to the lumen of these thylakoid membranes. And so it's a little bit upside down. Remember before we were in the mitochondria pumping protons out into the inner membrane space from the matrix. And so that gradient of protons is going to use the exact same enzyme to synthesize ATP. So the fuel instead of burning and synthesizing sugars, the fuel is the energy produced by the sun captured by in these light reactions. Then in the second part of the lecture we're going to take these short-term storage forms of energy, a reduced cofactor and ATP and we're going to put those into a safer storage form of energy. So remember we talked about the comparison of glucose monomers to polymers and the advantage of that having to do with the reliability and the reduction, the osmolality and osmolarity I should say. And so we have the same thing that we need to do here. We need to store a lot of energy and that's going to be this carbon assimilation part. Okay. But the power plant today is not the chemical oxidation of carbon atoms, it's the sun. And so you might be aware, many of you have taken physics class, that as the wave, there's an inverse relationship between the wavelength of light and the amount of energy there. So here it's expressed as kilojoules per Einstein, right? So it's increasing. Einstein gets some props in this process. And so as the wavelength decreases the energy increases. So anybody, it's a sunburn, that's the light over here causing that process. And so this light energy needs to be caught by plant cells. And this catching is done by pigments. So photons impact pigments not causing electrons to move between molecules like we saw in the last lecture, but instead to cause those molecules to become excited, to elevate electrons to a higher energy orbital. And so this excited molecule then is going to transfer that excitement to other pigment molecules, and we'll see how that happens in a moment. And so for each photon comes in that is able to excite one pigment molecule and when this photon disappears it's stored in the excited form of this pigment molecule and there's two options at this point. We can either release that energy in terms of fluorescence. So if you just take chlorophyll molecules and put them in a test tube, shine some light on it, a glow. And that's because we're releasing that in the form of fluorescence. But the other thing you can do is if you very precisely pack together molecules that are able to be excited in this way we can transfer energy without transferring electrons. So one molecule in its excited state as it relaxes back to its ground state it creates some kind of resonance in a very closely neighboring molecule to then go into its excited state. So we're not actually going to be transferring electrons, we're doing this exciton transfer. And so this is solid state, right? So there's no things moving between here. The change in the excitation state of a molecule going back to the ground state affects neighboring molecules. And so that's the antenna that we're going to be using. So these are the molecules that get excited. And so when we saw in our last lecture we saw the movement of electrons to some of these metal ions. Here we're not changing the oxidation state necessarily as metal ions, we're changing the excitement of this molecule. And so we're causing it to go from its ground state to the excited state. And what helps us to do that is all of this conjugation here. So the more conjugated the molecule is it affects what energies can be absorbed here. And so we have different forms of chlorophyll. I can't read that. So chlorophyll A is just the methyl group substituent, chlorophyll B is just tiny little change to the aldehyde functionality. And these are similar to what we saw before in these heme groups. So we saw examples where the heme group wasn't changing oxidation state in the globin, my globin, and we also saw it as an electron transport functionality where we're moving electrons to and from here. And so when we excite these molecules, again there's two options. Within 20 picoseconds of these things being excited if that energy is not removed to another molecule then it's going to be released as fluorescence. And so we need to be very very quick in the transfer of this energy. And so here's an example of a pigment molecule. And so it is a protein and all these prosthetic groups which are chlorophylls and these other conjugated molecules. And so as one of these pigments, so the chlorophylls receives a photon, it becomes excited. And then within a very short amount of time, if the molecules, if the excitable functionalities are close enough together, as one molecule returns to its ground state instead of releasing fluorescence, it transfers. It causes a neighboring molecule to become excited. And so this is an example of one of these pigment molecules. And so this is what sunlight looks like in terms of wavelengths. So the black line is at a particular time in day there'll be a profile of light. Generally the bluest wavelengths are the most abundant. But remember it's sunset and at dawn it's more of a red color, right? So we're from Rhode Island, red sky in the morning, silver take morning, you know some of these things. And so the color of the light coming onto plant cells is changing. And so there's got to be a way to adjust this. So look at these different chlorophyll molecules. So you have chlorophyll B, chlorophyll you might know looks green. So if you have a test tube full of chlorophyll and solution, it'd be green. Well that's because it's absorbing everything but green, right? So it's absorbing these blue frequencies and these red frequencies. So it appears green. The green is reflected back to you. Chlorophyll B has a similar but not identical set of absorbance spectra. And so that can absorb slightly different wavelengths. So those are some of the most common pigments in plant cells. But in various cyanobacteria you have different types of conjugated molecules due to the placement of different substituents and different amounts of conjugation they happen to absorb at different wavelengths. And so this particular one, these phycoproteins are absorbing in the central green part. And often these organisms can look red or purple. And so there's other molecules all listed here. So this is a handy table to come back to to get a sense. What we want to do is there's all this energy coming along. And we want to have sort of a mixture of different pigment molecules that can catch photons of different wavelengths. Right? So that'd be more efficient. So we need to have mixtures of these things in our plant cells. And so the way this works is literally like a radio telescope dish. We're focusing all this energy into one hot position. So in the radio telescope you focus the energy here, reflect it in, you take a look and you find Martians, right? But here you've got the thylakoid membranes and it's circular as well. And you've got the pigment molecules these proteins with attached prosthetic groups. And these pigment molecules can become excited. And through this process I was talking about, it's a mysterious process of exciton transfer. You can transfer you can cause neighboring pigment molecules to become excited. So you have one pigment molecule receives a photon, becomes excited. As it returns to its ground state, a neighboring pigment molecule then becomes excited. So this is like a funnel. It's catching the light. And you can have, for example, here we have green pigment molecules and yellowish-orange pigment molecules. These are absorbing different wavelengths. But this energy, once you've captured the photon, it's wavelength less, right? It's just energy. And so we can transfer that energy into the central core. It looks like some kind of reactor. And so this is a little bit confusing the way this is drawn. This is a reaction center. And it's important to realize that each color is a separate polypeptide. It's a separate protein. And so what we need to do here is to drive the synthesis of a reduced cofactor, we have to start separating electrons. Up to this point, we're just exciting molecules. And they're being excited. And the next one's being excited. But we have no redox change yet. So once, what the magic occurs in the reaction center, where we're going to convert this energy that's being transferred to this residence exciton transfer into a separation of electrons. And then we go right into an electron transport changes like we saw before. So let's look at this. So you have here, for example, starting in the pigment cell, say a distilled pigment cell receives a photon. And that causes it to go to the energy of the pigment molecule to be excited. And this energy can be transferred without the movement of anything at solid state. There's no electrons or anything moving, causing a neighboring molecule to become excited. So in our reaction center, we have all three of these polypeptides are in their ground state. But we're slowly coming in with the energized molecules. But then a pigment molecule right adjacent to the reaction center becomes excited. And when it returns to its ground state, you have transfer of electrons here. And so first, in one molecule in the reaction center, it becomes excited. But then here's the magic. An electron, because this is excited, it has a much lower affinity for electrons in its excited state. And we need the game here is we need to transfer that electron to a different polypeptide quicker than we release the energy as fluorescence. So we have about 20 picoseconds here to do this. So we need some special pairing to be able to accomplish this rapid transfer. And so now we have literally evacuated an electron from one of these reaction centers. And so now we have two electrons up here and we're missing one here. And you'll see processes today whereby we refill the electrons. We'll actually see electrons going in circles today. And it's pretty cool. They're recycled. And we'll be grabbing electrons from water, which is just sick. It just seems wrong, unethical. So here we have a light molecule. So this is what's happening in plants. You have these two chlorophyll molecules that are so intimately close to each other. Their orbitals are literally overlapping. When people first got the structure of this, they said how in the world is this like staying together? These orbitals are so tight together. And the closest in the molecules allows you to be able to transfer an electron. And so we have the precise, these things are not, if things are floating around then you just get excited and you can release some of that heat. It'll just, the molecule will vibrate. We got to hold these molecules, not allow them to vibrate so we can do something with this energy. So within three picoseconds, I believe it says three picoseconds, we transfer an electron from this special pair into this phycoerythrin, or a pheophyten molecule. And so now this is the moment in which we've transferred the energy of this exciton transfer in separated charge. We've started the process of creating reduced cofactors. And so this electron is first very, very rapidly, faster than this can decay back to its ground state in three picoseconds transfer the electron to this other molecule. And then we have an electron transport chain after that. So the electron is passing from one molecule to the next, moving to finally onto a quinone. Now there's two different types of quinones in these reaction centers. One is completely locked in place. It accepts the electron very quickly. So we get with each single photon that comes in, one electron is moved and only one. And so that one electron lands on the quinone turning it into the semiquinone. But then that electron can be transferred to a second quinone to turn it into a semiquinone. And then a second photon of light comes in, electrons are transferred here, you go to the semiquinone, and this goes to the quinol, the two electron reduced form. And so in electron transport, remember we talked about this ubiquinone. So it's a very similar molecule, it's called plastic quinone. And so I'll just say quinone, right, because it's the same thing. There's a oxidized state, one electron reduced semiquinone state, and a quinol, two electron reduced state. And so what we're doing here is accumulating two electrons on this mobile electron carrier, if that makes any amount of sense. Is this okay so far? It's a little bit mystical, like cytons, and we've now separated charge. It will become more familiar. Any questions so far? Okay, good. So here is the same exact reaction center. But pay close attention to these charts, almost always ask questions on these charts, and I think they're confusing. Ask me questions if you don't understand. And so on this axis here, the y-axis, we have E prime knot. What is this? So this is reduction potential, or another way of saying is electron affinity. Right, and so we have low electron affinity up here, negative numbers, and high electron affinity down here. So our exciton comes in and causes that special pair to become excited. And when it's in an excited state, that special pair of chlorophyll molecules now has a very low affinity for electrons. So that energy of the light is absorbed, causing the molecule to decrease its electron affinity. And now it's all downhill. We're just passing the electron to each subsequent molecule that has increasingly higher electron affinity. So you go first from this special pair to theophyten to a quinone. So we're accumulating a total of two electrons on the quinone. And then we have this cytochrome BC1, I believe it says complex. Sound familiar? What might happen here when we get our two electrons? So let me give you a hint. Whoa! Cytochrome C! That's a one-electron carrier. So we got to get that sick looking Q-cycle going on in this guy. And when we do the Q-cycle, we're going to be transporting four protons across the membrane. So we've now taken the light energy and transformed it into a disequilibrium of protons. And so this is one of the most primitive forms of photosynthesis. This is in purple bacteria. And all this thing does is sets up gradients. And we know we can plug all kinds of USP things into this charge across a bilayer, across a membrane. Or we can synthesize ATP. So F0, F1, ATP synthase can say cool. We've got a high concentration of protons in the lumen. I can let those pass back out into the stroma. And I'll synthesize ATP in this stroma. So this organism is all about just making ATP. Maybe it uses some other mechanism to make reduced cofactors such as the pentose phosphate pathway. Here's another type of bacteria. This is green sulfur bacteria. It has a reaction center here. Again, I haven't shown the Y axis, but this is according to decreasing reduction potential. So this is more negative. These have higher affinity for electrons. I might have mixed that up. So what we're doing here is we have again an excited special pair, which has a reduced affinity for electrons. And these electrons, you have a choice undoubtedly controlled through allosteric regulation. Choice one, make a gradient that culminates in synthesis of ATP amongst other useful things. Choice two, make a reduced cofactor. And so the way this works is we can transfer ferrodoxin FD as a one electron carrier. But this reduction requires two electrons. So we would need two photons to come in here. So each photon generates the movement of one electron. And we would accumulate those two electrons first on this enzyme, which then would be transferred to NAD to make NADH. Do you see a problem with this? So in the previous slide, what happens at the bottom? Or in the cyclic pathway? The cyclic pathway, the electron that came off here comes back in. But in this process, the electron that comes off here never comes back. It's sitting on this NADH molecule. And so this thing would grind to a halt. Once you're removed an electron, you're not going to remove another one out of there. And so we need some way to provide an electron back. If you were able to see the electron affinity, it's about, I believe, 0.5 here. And so the electron affinity of oxygen is one. We're not going to be pulling any electrons off a water molecule. Oxygen molecule has too high of an affinity. So what this organism uses is in its environments, in these volcanic environments in Yellowstone Park, and it uses hydrogen sulfide. So it actually pulls the electrons off of hydrogen sulfide making sulfur and eventually sulfate. And so it takes from what it has in its environment. Does that make sense how we need to replace this electronity with me on that? And now all we're going to do is compare these. And so you have the purple bacteria. We have only the cyclic pathway generating a proton gradient using what's analogous to complex 3 in electron transport. You've got a Q-cycle action going on there. And then there's this other bacteria, this green sulfur bacteria, has slightly different redox potentials. This one does two things, multipurpose. It can create a gradient, which doesn't cause problems with electrons being evacuated out of the reaction center, stopping the reaction center. But then it also does this reduction of NAD to NADH until we grab those electrons from another molecule. So all plants have done is combine these two. So these bacteria have different photosynthesis, they're very primitive. What plants have done is to combine these. So put a big star on this slide, circle it, you gotta understand this slide, ask your TAs if I do a bad job. So in this, in plant cells, you have two coupled photosystems. And just remember, photosystem two is on the left, it's a little bit lower. And then photosystem is on the right. Each of these becomes excited by different wavelengths. So this is more by blue light. So the pigment molecules that tend to associate here are more of the blue light type. And you could see that this reduction potential here is electron affinity is extremely high. So electron affinity acts, or redox potential of oxygen is like 0.8 I want to say. And this is one. So this is really as intense amount of electrons affinity. And so when we have photon comes into this first photosystem two, it goes into its excited state. And then can cause the movement of electrons to this pheophyton, to pqa plus toquinone A, going to the semiquinone, transfer it to this. This becomes semiquinone. Another photon comes in. Remember, these are not necessarily coupled, right? So when you have the mobile carrier, that's potentially being released and coming on. So you're not going to be taking two total electrons out of this single reaction center. You got to start from a reaction center that isn't already missing an electron. And so we have two electrons accumulating on our mobile plastic quinone. Those two electrons get transferred just like we saw an electron transport into this complex three analog, which pumps gradients, has a q-cycle. And then those electrons are transferred not on a cytochrome C, but on a photoplastocyanin. And that's a one electron carrier. So same sort of translation problem we have before. And this electron is then transferred to the other reaction center. So this is a filling up process. And this reaction center then can receive either through exciton transfer or through a photon. It can become excited into its excited state. And then the electrons can be transferred for a variety of cytochromes. These are all one electron transferred. Here's an iron sulfur cluster that's passing along electrons ferrodoxin. So when we get to ferrodoxin we have a choice. We can either go cyclic or we can go terminal deposition of the electron onto an electron carrier. So if we go cyclic, those electrons can be transferred into here, into the complex three analog. And that can drive a gradient of protons causing synthesis of ATP. But if we then the other choice we have, which is controlled by allosteric regulation is to transfer those electrons to this molecule NADP oxido reductase, which then can finally collect to one electron at a time for a total two electrons. And those two electrons can then at one fell swoopy transfer to NADP to make NADPH. But you see, so anytime we make an NADPH we have the same sort of problem we were seeing with the green sulfur bacteria we've removed an overall electron. So the electron that was here in this photo center is ending up here on this NADPH. So we need some way to replenish that electron. And the electron affinity of this photo center in photo system too has such a high affinity it literally pulls an electron off of water. So that's why on NASA you see water on a planet's life because that water can be used as a source of an electrons combined with solar energy to make an ATP and NADPH. So does this make any amount of sense? I think it's probably confusing. Alex, do we have any questions? We'll start it off there. No? I explained it well, no. It's not possible. Yes. Two's coming for one where. Yeah, so is there a reason why it's numbered backwards? I actually don't know the historic rationale. So these are endosymbionts. These cyanobacteria back a while ago went into plant cells and they made these chlorophyll. So the same like, basically these purple bacteria and your green sulfur bacteria are now inhabiting in plant cells and things have evolved since then but there's actually ribosomes in there, there's DNA in there. But yeah, it's a historic, that's a great question. I don't have a good answer. Does everybody understand? I think people are explaining to each other? You want me to go through it one more time? Sure, sure. So the idea here is that we need to be able to assemble carbon dioxide into sugars. We need two things. We need ATP and we need reduced cofactors. And so in this photo this reaction center, when we receive our exciton or when we receive a photon the electron affinity is greatly diminished in that special pair. That electron is then transferred to pheophyton, plastic quinone. Remember, I had that picture. We had the two plastic quinones. One is sort of glued in there and you transfer electrons pretty quickly to that one. And then the electrons are accumulated on the second plastic quinone going to the semi-quinone and then the quenol form. Those two electrons are then delivered to this one. We'll look at this in more detail in a moment. And then we have a translation from two electrons to a one electron carrier and a plastic ion. What's driving each of these transfers is electron affinity. We're on a chart here, right? So as we're going down we have more and more electron affinity and that's a favorable thing to move an electron to a center that has higher electron affinity. And we can this drives a gradient and this can replenish a depleted photosystem one, right? So this electron can come in and eventually be deposited here. So we're literally physically transferring electrons from water to NADPH. This has a similar thing, a exciton or photon is received, the molecule becomes excited, has greatly, vastly diminished electron affinity, releases its electron to some cytochromes and then to iron sulfur a cluster and then to ferritoxin. These are all one electron carriers and then we have this choice. We can either make more ATP or we can make NADPH. Right, I think we'll move on. Sorry, it's mystical. So these are the two confusingly named photosystem. Just remember, the second one's on the left, it's a little bit lower. It helps you to actually be able to draw this diagram. Okay, so here's photosystem two and look at where this is occurring. So remember this is occurring in thylakoid membranes. And so the lumen, that's the innermost sanctum rate of the thylakoid membrane. And so you have the electrons or the protons being pumped into the lumen. So this is sort of complex three upside down if you remember from our last lecture. Same exact stuff going on. The protons are being transferred when plastic quinone, in the case of complex three, it was ubiquinone, or ubiquinol. When that is bound, those electrons are transferred. One goes to another fully oxidized quinone, the other goes up to a carrier. Remember this, we're translating from two down to one. Instead of cytochrome C and other mobile carriers, we have a variety of ferrodox and plasticin. These are one electron carriers that can float around and then either interact with acetyl reductase to make NADPH or go into this cyclic pathway. And so this gradient, so we're accumulating protons in innermost sanctum of the thylakoids, the lumen. That gradient can come back out and drive synthesis of ATP strategically in the stroma, exactly where you need it to be to do your carbon assimilation. So we're making both NADPH and ATP in the stroma. No transport is necessary to do your carbon assimilation. This is very well designed. So this is the Q cycle, complex three analog. So you have your PQH2 coming in. One electron goes to your carrier. Today the role of cytochrome C is plus to a cyanin. So it's receiving that one electron. We're storing the other in a semi-quinone form that's available from the membrane. Remember there's the same sort of strategy, strategic. It's like, oh yeah, I think I'll grab that proton from the stroma and then eventually release it in the lumen. So we're strategically grabbing those protons from the right side of things. This is the same sort of Q cycle you saw before. So plants don't walk. There's some commercials where trees are running. I don't know if you've seen this recently. You wouldn't need this. What I'm about to show you, if the plant could say, dude, it's like real sunny and I'm going to go in a hut. The plant can't put sunscreen on. It's got to deal with, it's there. It's absorbing light. A wavelength is changing and the dawn there's nice red light and during the day it just gets blasted with more blue light and in the morning it's more red as well. And so each of these reaction centers is responsive, has a different constellation of these pigment molecules surrounding them. And so as the light changes, these two systems need to see in perfect sync. So for example as the light gets more blue during the midday, this photo system will start to go faster. It will see more useful photons or excitons. And so we'll begin to accumulate some PQH2. So if this is being excited at a faster rate than this molecule. So we need a way to rearrange our antenna. So when the station, you guys wouldn't know this, but before cable you'd have to point the antenna at the right place because some cloud came through. You have to do the same thing. And so this is where this is happening. There's a physical separation of these two photo systems in this pleated area of the membrane where you have different stretches of membrane. They're all on top of each other. And that's where photo system 2 hangs out. So light comes through all this stuff. It comes through this cell membrane. It arrives here in these photo systems but you have these light harvesting complexes where your pigments are surrounding. This is that dish. And all those little squares around them, those are the light harvesting complex. And so there's two different forms as it turns out of this light harvesting complex. The photo system 1 also has light harvesting complexes associated with it. They're not actually shown here. But there's a physical separation. The majority of these photo system 1s are in this so-called non-oppressed region of the membrane. And also ATP synthesis occurs in the non-oppressed region because that is where, if you put ATP synthase in here, it's hard to get the substrates in, the inorganic phosphate and ADP. So those are over here. And so what happens here is as the PQH2 builds up, that's a signal saying we're out of whack. These two systems are appearing at a different rate. And that signal is received by light harvesting complex 2, causing it to go from this configuration where it actually cross-links parts of the bilayer here and going into this bin, altered confirmation, that's not able to do this cross-linking. And these light harvest, the antennas move so they drift in the membrane to the non-oppressed region. So if you have all this intense light, we need to help these two photo systems to be operating at the same rate. And this is caused by a post-translational modification. So light harvesting complex 2 becomes phosphorylated on 3 anine and that kinase that does that is activated when PQH2 is an allosteric regulator of that kinase. And so that turns that kinase on causing this molecule, light harvesting complex, to change its confirmation and then increasing abundance aggregate with the photo system 1, the reaction center of photo system 1. And so instead of moving and walking to another place, you just change the configuration of the antenna to make sure there's perfect synchronicity between these two photo systems. Does that make sense so far? No? Sorry. Next slide. Okay. So this is, remember in our electron transport? So we were producing water molecules and we're moving electrons to oxygen molecules, making water molecules. This is the same exact thing in reverse. So this oxygen evolving complex that sits on photo system 2 on our bottom left, this thing is literally transferring electrons from water up into the photo system, replenishing the deficiency in electrons as that photo system has released each electron. And we have instead of a copper top battery that we saw in the other complex 4 in electron transport, we have a magnesium top battery. And magnesium has the ability instead of, we don't want to store electrons here like we did in the copper top battery in complex 4, we want to store a deficit of electrons. So we have a different type of ion, magnesium. There's actually calcium in here. Everything is positioned perfectly. And we build up an accumulation of a total of 4 positive charges. So we release an electron one at a time as needed into our special pair. And we accumulate 4 positive charges. And then in one fell swoop we convert 2 water molecules into an oxygen molecule. So the picture in Leninger is very, very confusing and so the same problems that existed in complex 4 exist here. We don't want free radicals. We don't want any kind of these reactive intermediates floating around. So we have to accumulate the lack of electrons. And then in one move, transfer those electrons back into this system here, replenishing these electron-depleted magnesium ions. So the same strategy is going on here. So that's electron oxygen evolving complex. Alright, so we have the F0, F1, ATV synthase, it's backwards. Instead of pointing into the matrix, like we saw in the mitochondria, it's pointing out from the thylakoid membranes into the stroma. So it's the same enzyme. Nothing has changed here. We got the camshaft. We got the boot going on. The binding of ATP is really, really tight. You throw in some inorganic phosphate, some label water, all the positions label. It's the same darn thing. The proton gradient, remember in plants we're accumulating protons in the lumen. And those protons are then driving the rotation of the camshaft with the boot on it and it's kicking out ATP molecules. So ATP is synthesized in the stroma strategically because that's exactly where we need it. And so this was the first evidence that these proton gradients could drive ATP synthesis. We didn't discover this in eukaryotic cells or in mitochondria. We discovered it in plants. So you can take some of these thylakoid membranes very carefully, remove them from the plant cells without causing them to fall apart. Drop them in a beaker that has a buffer. So say you put a page 4 buffer through many hours, you will have diffusion of protons across this bilayer. It's slow, but these bilayers are not 100% impervious to the movement of protons. So after a few hours you'll have the lumen of the thylakoid membrane will then have a negative charge that protons will have moved in. Then all you do is drop these pH 4 thylakoid membranes into another beaker. You can spin them down. I don't know what you do. You get them in a different beaker with a different pH. You throw in some ADP in organic phosphate and this thing just starts cranking out ATP. So you can literally watch it drive the gradient drive ATP synthesis. From what we've been saying so far, this is the overall picture. We also strategically place the oxygen-evolving complex in the lumen. One of the products is protons. That's helpful. It helps us to make a gradient of protons. Those protons combine with the protons generated by this Cytochrome B6F complex, I believe. You have 6 protons and those drive ATP synthesis. But then in Photosystem 1 we can shunt electrons from water all the way to NADPH to make reduced cofactors. So both ATP and NADPH are being synthesized in this stroma. Make sense so far? This is a summary slide. So it's just backwards. So here's mitochondria. Remember protons were going from the matrix into the inner membrane space, driving ATP synthesis in the matrix here. We're pumping them into the inner sanctum into lumen. We've got the protons accumulated there. And then we let them relax. This gradient relax and that drives the camshaft kicking out ATP molecules in the stroma. And so bacteria are also different. Also have F0, F1 ATP synthesis driven by proton gradients. Okay. So we have a lot to cover after this. I'm sorry. So I'm going to give you a strict 2 minutes. I can't hear you, sir. We're one-third through the lecture. We need to get going. Incredibly easy clicker question. You get negative points if you miss it. Okay. I need everybody to turn their thing in. Can you stop the... You can stop the polling. Everybody voted? Okay. This is just a break where we can relax. This question is not too painful. Equally is un-googlable, if that's a word. Alright. Let them finish business over there. What's the answer? Cover your ears. Don't listen. What's the answer? Yeah. I mean, chlorophyll. Right? I mean, you could have said you were like, well, which kind of quinone, right? We got the UVA quinone and plastic quinone. They're both quinones. We've made it through the exotic part of the lecture. Now, we're going to get some pathways. Remember pentose phosphate? It gets worse. That's mean to laugh, isn't it? Okay. So we've generated energy, but we have this osmolarity problem. Let's settle down. Thank you. We have an osmolarity problem. If we start accumulating tons of ATP molecules, the cell is going to start to swell with water. So we need a way to conveniently pack this energy away in a more compact form and in polymers of sugars. So you might have thought when you learned in junior high school or high school, photosynthesis say, yeah, you sensitize glucose. You don't synthesize glucose with photosynthesis. You synthesize triosphosphates. Eventually it can be converted into glucose, but typically you never heard of the triosphosphates. So what we're going to do here is take ATP and NATPH. We're actually going to need more ATP than NATPH. So that's why you have to have a cyclic pathway because you got to do some amount of, you know, you have to make, every time you do a cyclic pathway, you get some more protons moved and more ATP synthesized. And this is going to drive the synthesis of triosphosphates. And from there you can just elaborate adenosium with all kinds of anabolic pathways. You can do gluconeogenesis. We'll have a lecture dedicated to that where you can make hexoses and starches and disaccharides. You can make dreaded pintosis and those are important in a variety of different larger biopolymers. So what we want to do here is take carbon dioxide and accumulate three carbon dioxide molecules into a trios. And say, okay, how could this, like if I was designing things I'm nowhere of that intelligence. But yeah, just how can you put these together? I just take three CO2's and just provide some massive jolt of energy and just have a trios come out. Or could I do this in some other more creative way? And so this is the whole thing. Now this is a very huge sort of abbreviation of everything that's happening. But this is going to be a roadmap as we go through this. So there's three different stages that we'll be examining in more detail. The first stage is easy. We're taking this exotic ribulose 1,5-bisphosphate. So this is a ketose. Remember we said ribose before, that's an aldose. But this is ribulose ketose C2 position for those that remember the numbering. And we're going to take one carbon dioxide molecule, combine it with this five carbon ketose to make two three carbon molecules. And so the enzyme that synthesizes this is called Rubisco. It's a massive player in biochemistry. It drives all this assimilation of carbon dioxide. That is the most important enzyme I feel in the whole class, even if you are pre-medical. And so these three phosphoglycerates are then converted first making a better leaving group here, putting the phosphate and then reducing. So we're taking the carboxylic acid oxidation state and converting it into the aldehyde glyceraldehyde 3-phosphate. We know what to do with that. We saw that in glycolysis, right? So we can take that and shunt some of it off. So we can take glyceraldehyde 3-phosphate. We can actually run glycolysis and reverse the process called gluconeogenesis to make other sugars. But then if we want this to be a carbon neutral cycle, we'll need some way to recycle a 3-carbon sugar into a 5-carbon sugar. We've seen this problem before. Pintose phosphate pathway. So there's a lot of arrows in here. Details not important. Input and output important. So if you do the stoichiometry, you have three ribulose 1-phosphates combining with three carbon dioxide molecules making six of these three carbon sugars converted into a reduced form. Six of those. One is siphoned off. Three carbons in. One three carbon molecule going out. And then these five remaining three carbon sugars need to be converted into three five carbon sugars. Carbon neutral, right? 15 and 15 out. Okay. And so you can see we need more ATP than NATPH in this process. So this is it. This is the big daddy. Rubisco ribulose 1-5 bisphosphate carboxylase slash oxygenase. Now up to this point we haven't seen the slashee enzymes. So slashee enzymes this is actually because this enzyme catalyzes two entirely different reactions. One that's helpful. The other that is utterly useless. That is the appendix of this enzyme. This leftover from evolution wastes energy. Okay. And so we're going to be looking at both the carboxylase reaction which is first and then the oxygenase reaction. This enzyme is super essential. This is the thing that starts everything off in terms of making sugars storing energy from the light into stable forms. And so this enzyme is incredibly slow. So you're only able to convert three per second with this enzyme. So half the protein in the chloroplast is rubisco because it's so bad. It has such a low turnover number. But it's so critically essential that once evolution made it it's like dude if I change one amino acid life might stop. Life is dependent on this enzyme. So evolution stopped very early on here. So that's enough messing around with that. And so we're left with having to make tons of this protein in the cell. So let's look at the reaction. So here is our ketose, our ribulose 1-phibisphosphate. We're going to carboxylate here at the C2 position. And that carboxylate after we carboxylate we're going to break that carbon-carbon bonding making two, three phosphoglycerates. Pretty straightforward so far. So we're solving this problem, you know, it's not really chemically that desirable to take three carbon dioxide molecules and make a trios directly. Instead it's a lot easier to stick one carbon dioxide in this big molecule and then cleave it into two and have this sort of stoichiometry manipulation game that it's playing. And so this is the carboxylase reaction. Now we need to do that reduction, two electron reduction here from the three phosphoglycerate to the glyceraldehyde 3-phosphate. This picture is confusing. Why is it confusing? All the reactions occur in the stroma. It looks here like you're going in and out of the thylakoid membranes. No. They're in the background. Right? So this is, all of these reactions occur in the stroma. So these two red arrows are the two arrows down here. Okay? The rest of this is the yellow box. The other reactions, once you make your glyceraldehyde 3-phosphate here, you can convert that. You know, remember triosphosphate, I said that diffusion, that's a super fast enzyme. You can make your dihydroxyacetone phosphate, run glycolysis in reverse, make sugars that can be assembled into polymers. We can take things out of the chloroplasts into the cytosol. We can do a similar reaction. We can make more mobile forms of sugar that we can transfer sugar cane. That's where sucrose is hanging out. We can metabolize these in the cytosol using glycolysis. Yes, plants have glycolysis. Yes, they have mitochondria and aerobic respiration. That's where they're making oxygen and CO2. Yes, it's true. Okay. So these are the two reactions, these two arrows. And so we've put some ATP molecules in here, and we've also provided a reduced cofactor because the goal here is to take a carboxylic acid and reduce it to an aldehyde. So we need these NADPH and that's provided by the photosystems that I showed you a moment ago. Those electrons came from water and they're now being deposited on this trios. Okay, with me so far. So that's stage 2. The next stage is not fun. Big picture. Count the carbon atoms, right? So let's just look at this. So we have 2, 1, 2, 3, 4 glyceraldehyde 3-phosphate ish molecules. This one's convertible. Remember triosomerase can interconvert these. So it really is a 4 of these glyceraldehyde 3-phosphate. And then we have the usual transketolase catalyzed food fight where we're transferring carbons between molecules. How can we pronounce this? Don't worry about it. 4 or 3 carbons coming in here so far. Pintosphosphate, no ATP is used. Different. In the second part of this pathway, ATP is used. Why? Because in Pintosphosphate a monophosphorylated sugar, 5-carbon sugar, here we're making a diphosphorylated sugar. So we need, that's a more energetic form of the molecule and we need ATP to do that reaction. So here is our fifth 3-carbon sugar, 5-3-carbon sugar is coming in. Let's count the output. There should be 3. 1, 2, 3. So we have one neutral pathway, but we've used some ATP. Right? But these are useful. We have a, now we've regenerated our molecule that can then accept another carbon dioxide. So we're assembling carbon dioxide and ticklyceraldehyde 3-phosphate. It's a cyclic carbon neutral process driven by light energy that produces both ATP and NADPH. You with me so far? That's the whole thing. I am not going to say, okay, fill in the blank time. No. Just count the input output. Remember ATP is used where it is in Pintosphosphate. Remember where this is occurring. This is occurring in the stroma. Same location as ATP synthesis and NADPH synthesis. Okay? You with me so far? This is the bread of life. We siphon off our glyceraldehyde 3-phosphate. And so we have a total of three carbon dioxides coming in and one 3-carbon sugar coming out of this pathway. We've used more ATP than NADPH. So you only want to be doing this when the lights are on. If the lights go off, this needs to turn off. Because if the lights go off, then there won't be ATP and there won't be NADPH. That'll rapidly be used up. The thing that's producing ATP and NADPH is light. So we need a crosstalk between these pathways to communicate this. So here we have Calvin's cycle represented as Mickey Mouse. In Calvin's cycle, what the allosteric regulation here is the movement of protons. So we have in this case, protons moving into the lumen, higher concentration protons there, lower concentration there. There's actually a transporter magnesium. There's a pH dependent transporter. So the pH and the stroma increases from 7 to 8. And the magnesium concentration increases from 1 to 6 millimolar when there's light. And so that's the signal. That's the signal both to one of the Gluconeogenesis enzyme fructose, all 1,6 bisphosphatase, which is in here somewhere. And that's also the signal allosteric regulator. Both of those molecules are allosteric regulators of Rubisco. So when the light goes off, it all shuts down. And then it's just the mitochondria providing the fuel for the night. We're taking those sugars that were stored during the day and we're using them at night. We're not going to stop living at night. We need to keep going. pH regulation. This enzyme, the evolution stopped too soon. And so this enzyme can also do something, Rubisco, can do photo respiration, where oxygen molecule can bind at the exact same position that the carbon dioxide bound. And so when the oxygen binds there, instead of making two, three carbon sugars, we're not adding a carbon from carbon dioxide. So if we just break, we do a similar reaction where we break the same exact bond that we did when we added the carbon dioxide, we're going to end up obviously with a three carbon sugar and a two carbon sugar. And the problem is, this is not good for much. And so this three or two-phosphoglycolate, the plants like, I got to somehow convert this into something that's useful, like a three-phosphoglycerate. They say, okay, isn't there like this really helpful enzyme that in one step just adds a carbon dioxide to this? No. All we're doing here is adding a single carbon so we can take this byproduct and not, we don't want this byproduct just accumulating forever. We want to take it and feed it back into the Calvin cycle, right? We want to have our three-phosphoglycerate. And so here's the adaptation. It involves three organelles. It's like, I don't want to deal with this. You deal with this. So first we have the chloroplast. We have this enzyme that's screwed up, put in oxygen molecule and made a glycolate. And the chloroplast is like, I have nothing to do with that besides transport it out. And the peroxazone, a glyoxazone is a type of peroxazone. We have glycolate, gets moved in. We take another oxygen molecule. We're going in the reverse direction here. We're taking oxygen. We're dissipating it. So we take oxygen, making hydrogen peroxide. You know we wouldn't be doing this if we didn't have to. That's very reactive to make glyoxylate. It's like, oh, we could do our anoplarotic thing with glyoxyl yes. Or you could feed it into the Calvin cycle. So then we can say, you know, convert it to glycine, transaminate, like glyoxylate. We can take two glycines so we would need two glyoxylates, glyoclates to feed in to make two glycines. We can then combine two glycines while reducing and, or transferring electrons to NAD, making CO2, making serine. I mean it just is like absurd. This one simple little problem. And then we have serine. mitochondrists says, I don't know what to do with that. We pass it back to the glyoxazone. It comes in here, serine, gets converted to hydroxypyruvate, glycerate. And then we come back in and say, ah, three phosphoglycerate. That's where we want it to be. But we've wasted energy. So we're sort of neutral in this respect. We've made an NADH in one compartment. We used it up in another. So we might have to transport, waste some energy, moving things around. But here's the problem. We had to use an ATP. So we've just wasted energy because of a side reaction. Because of this side reaction, less carbon in the world is a symbol of reduced sugars. And so as it turns out, this screwed up reaction in Rubisco is heat sensitive. The more you warm up Rubisco, the more it screws up. The more oxygen-asectivity it has. And so this photo respiration is one way to deal with this. And something called a C3 plant. But there's this other type of plant, a C4 plant. And in the C4 plant it's hot. These plants occur in environments that are more hot. Where Rubisco is screwing up more frequently. And so we have more of this, we potentially would have more problems with the side reaction. And there's two strategies. In the C4 plants, we're going to hide the Calvin cycle from the environment. So we're going to have one that normally, the Calvin cycle occurs in cells that are exposed to air. But here what we're going to do is we're going to hide our carbon dioxide. We're going to bring our carbon dioxide in. And we're going to use an enzyme that has specificity. And we're going to stick that carbon dioxide on a 3 carbon sugar to make a 4 carbon sugar. Convert that into malate. And then we're going to take that malate and bring it into a place that's not exposed to air. So we're using the discrimination of this enzyme. This enzyme doesn't do anything with oxygen. Oxygen can come in and out of itself. That's not going to affect the synthesis of malate. Now, when we're protected from oxygen, we're going to release that carbon dioxide and that avoids the side reaction, the photorespirations. So now we have carbon dioxide feeding in the Calvin cycle. And this is an air type compartment. Option two is the cactus method. So in cam plants, cactus is other things that are, if it's really, really hot, maybe you just want to shut everything down during the day. So if it's really hot, plant cells have pores or plants have pores in them that allows moisture to come out. And also allows the exchange of gases. But in the desert, it's really hot. You want to shield, you want to close these pores. And that blocks the loss of water. But it also blocks the exchange of gases. And so in this plant, during the night, the pores open up. And carbon dioxide comes in. And we use that enzymatic specificity that Rubisco doesn't have that the same enzyme that we saw before does have. So we synthesize, we fix that carbon dioxide into oxaloacetate. And that is converted just as we saw in the C4 plants. Or I should say C3 plants. Now I'm mixed up. C4 plants. We have the same enzyme. We have malate. Instead, now we're going to put the malate in a vacuole and wait for day. Because we can't do Calvin cycle at night. But we're storing up there this carbon dioxide in the form of malate. It's sitting in a vacuole. When the light comes on, the malate is released, carbon dioxide is released and we can do the Calvin cycle. And so these are different ways that different organisms are adapting to this just pointless reaction. And so one philosophical question that comes up is, maybe we should fix it. You know, maybe we should make change do some kind of mutational analysis where we get around this problem with this side reaction. Okay, then the plants will grow faster. That's probably good, but you know, got to be careful when you start doing these kinds of things. So this is plants for today. Thank you. I think that's it. Any questions? I think that's it. Couple questions. One about water. If photosystem 2 is continually oxidizing water and nothing seems to ultimately regenerate water, is the planet being sucked dry? This awesome question. Whoever asks that, you get an A. Man, email me. It would be sucked dry if the parasites weren't around. So what happens in the parasites? Us. We make water. We're taking that oxygen converting it back to water. You know, 70% of you as a biochemical entity is water. That's a great question. And a question about light harvesting complex 2. If a structural change in the membrane activates the light harvesting complex 2, how does that push it toward photosystem 1? And there's a follow up to this. If you want me to ask that. Yeah, so it's just the conformational change causes that light harvesting complex 2 to not be able to cross-link membranes. And so then it just diffuses into this non-oppressed region. So diffusion is somewhat random. Things will go in every which direction. But it doesn't need, you know, when it's in the linear form, when it's not phosphorylated, it's stuck in place because it's cross-linking bilayer. So it's free to do whatever it wants. It simply diffuses to the other area. But not all of it. Just enough to balance the rate of synthesis of PQH2 to match the flux through photosystem 1. Okay. And the follow up was how does it notice start preferentially working for photosystem 1? Say it again. How does the light harvesting complex 2 know to preferentially work for photosystem 1? It doesn't. It just has the, it's being it's not that it's being drawn like a magnet to photosystem 1. It's trapped with photosystem 2 when it's cross-linking the bilayers. Because photosystem 1 only occurs in the non-oppressed membranes. Okay. And so when you release, you're basically pulling up the anchor, right? So when you phosphorylate that protein, it's now free to diffuse. When it's not phosphorylated, it's cross-linking the bilayers and that's the area where you have photosystem 2. Photosystem 2 stays in that area. These are good questions. Alright guys. Good job. Right. The person really seems convincing. Yeah.