The Science of Everything Podcast - Episode 101: Photosynthesis Part I

Episode Date: February 27, 2020

An overview of photosynthesis, including the structure of chloroplasts, phototransduction of energy by chlorophyll, the macromolecular complexes of the thylakoid membrane. I also discuss the mechanisms of electron transfer along the electron transport chain, and the role of ATP synthase in generating ATP. Recommended pre-listening is Episode 75: Cellular Respiration, Episode 32: Light and Optics, and Episode 18: Biochemistry Basics. If you enjoyed the podcast please consider supporting the show by making a paypal donation or becoming a patreon supporter. https://www.patreon.com/jamesfodor https://www.paypal.me/ScienceofEverything

you're listening to the Science of Everything podcast episode 101, photosynthesis, part one. And I'm your host, James Fodor. So, in this episode, we are going to discuss photosynthesis, as the title suggests. In particular, I'm going to talk about the main structures of the plant cell that support photosynthesis, so the thylacoid membrane and the granum,

which exists inside the chloroplast. I'm going to talk about the overall chemical reactions that occur as part of photosynthesis, so the reaction of carbon dioxide and water to produce sugar and oxygen, and how that fits into plant metabolism. But then we're going to go through and talk in some detail about the different biological complexes and protein complexes that support photosynthesis, so Ferdosystem 2, the cytochrome complex, photosystem 1, NADP reductase, the ATP synthase, and the various complexes and molecules that connect them together. So we'll go through at a fairly fine grain of analysis through the process of light absorption by chlorophyll and the other pigments, and then how the electrons move through the different complexes in the chloropath membrane.

Particularly we're going to focus on electron flow and how the energy is. is gradually extracted from the electrons to produce NADP, NADPH, and ATP, which is the main sort of energy products of photosynthesis as a process. So there's quite a lot to get through, and it's difficult to describe a lot of this without using diagrams or visualizations. So as usual, I will do my best. Recommended pre-listing for this podcast is a bit wide-ranging, because we're going to talk about quite a few issues here.

Episode 75 on cellular respiration is the single most relevant episode because that's sort of the flip side to this. Cellular respiration is basically the process of using sugar and oxygen to produce energy, whereas we're looking at the process of forming those sugar and oxygen products from sunlight and carbon dioxide and water. So there's a lot of commonality in terms of the overall structure, and so it will be helpful for you to have some background in cellular respiration before looking, at this episode. Episode 32 on light and optics will also be somewhat relevant because we're talking about the absorption of light. And episode 18, biochemistry basics also is relevant because you will need some degree of background about, you know, the cell membrane and proteins and

some other things like that, just to understand some of the pieces of the puzzle that we will be investigating. All right, so all that being said, let's make a start and get into the topic of photosynthesis. So fundamentally, what we're talking about is how plants turn to the sunlight, carbon dioxide and water into useful scores of energy and sugar. So plants actually grow by taking carbon dioxide from the air and also combining it with water and using sunlight to turn that carbon dioxide and water into physical plant matter. So if you look at plants, the substance that they're made of are basically long sugar chains of long polysaccharides, so chains of sugars. And those are made through metabolic processes which are

ultimately fueled by photosynthesis. So there's a number of processes here. There's the process of energy production, producing the energy molecules, NADPH and ATP that are necessary to fuel this process. There's that side of things. And there's also what's called carbon fixation. This is the process by which carbon dioxide from the air is incorporated into a form, is fixed as the phrase is, into a form that can be used by plants to produce plant matter. So all of these polysaccharides that actually make up most of the physical substance of the plant. So it's quite a remarkable process

that plants are literally able to turn air, water, and sun into plant matter and wood and leaves and all of the greenery that we see around us. I'm going to be focusing on photosynthesis in eukaryotes, so basically in plants. There are a number of other organisms that engage in photosynthesis or similar metabolic functions as well in bacteria and algae and so forth. But I'm going to mostly focus here on plants,

just because that's what we're most familiar with and sort of most interesting in some sense. And it's sort of the most highly evolved complex version of photosynthesis. Okay, so that's a broad background. More specifically, as I've said, photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy, which can then be in turn used to fuel their organisms, activities, and metabolic processes. So the chemical energy is stored in the form of carbohydrate molecules or sugars, and these in turn are synthesized from carbon dioxide and water. So that's where the name comes from photosynthesis. It's the synthesis of sugar products using the energy from sunlight. So photosynthesis occurs in two distinct stages.

These are sometimes called the light dependent reactions and the light independent reactions. First of all, let's talk about the light-dependent reactions. The light-dependent reactions, as the name indicates, rely on sunlight, so they can only occur during the day. And basically, their purpose is to produce energy. They take water, NADP and ADP. So, if you recall, NADP and ADP are the like de-energized forms of the energy molecules, NADPH and ATP. These are the sort of two main energy molecules that cells use. I talked about them at some length in the cellular respiration episode 75, so look back to that if you want more about them. I won't talk about them in great depth here. But the basic idea is that the high energy forms of these molecules are obtained by either adding a hydrogen in the case of NADP. So NADP is the de-energized form. You add a hydrogen. It's that becomes the energized form.

ADP, or adenosine diphosphate, is turned into its high energy form by adding a phosphate group. so that forms ATP, adenosine trifosate. I liken this in the cellular respiration episode to compressing a spring downwards by adding something that then locks it into place. So you can think of adding the phosphate or adding the hydrogen as like loading the spring. And so it will stay in its loaded position until sort of something triggers it off. And when it does, you get that sort of spring action which releases the energy, which can then be used in other forms. That's not too inaccurate as to the basic making.

of what's happening here. So these high energy molecules, NADPH and ATP, are sort of the spring-loaded versions that have the energy that is then used to perform various functions within the cell. And these are not specific to photosynthesis, NADPH and ATP are used in a wide range of metabolic functions, but photosynthesis is a way of producing them using sunlight. If you recall from cellular respiration episode, heterotroves, so that's like humans and really all other animals, get their NADPH and ATP, ultimately from consuming existing matter, either plant matter or other animal matter. And so basically they break down the sugars in these plant or animal matter that they're consuming

and then use the energy released in that process to produce NADPH and ATP. Plants are different because they can produce their own NADPH and ATP without having to consume existing plant or animal matter. They produce it directly from sunlight, and so they are what's called autotropes. They can make their own energy from, they can produce their own. their own energy without requiring existing organic matter. So that's how they're quite distinctive from animals. But anyway, the point to get across here is that the light-dependent reactions

involve the process of producing energy from the sunlight. So you need some water. That's ultimately where the hydrogens come from that are loaded onto the NADP molecules to produce their high-energy form NADPH. You also need some phosphate, which then you load onto your adenosine-difosate to produce the high energy and it's in triphosphato ATP form.

That's the key light-dependent reactions. It's loading up these NADP and ADP molecules to their high-energy versions using water and phosphate. So that's all about energy production.

There's no carbon fixation that occurs there. Carbon fixation occurs during the light independent reactions. And this is the process by which the plants actually use the energy

that they've produced in the first in the light-dependent reactions. They actually use that now to produce the organic molecules that they need to grow and to fulfill their metabolic functions. So in the light independent reactions, they take ATP and NADPH, the high energy molecules that they produced in the light dependent stage.

And they also take carbon dioxide. Carbon dioxide is critical as the source of carbon. And then they convert these essentially into the de-energized forms, the ADP and the NADP, and the inorganic phosphate that's sort of ejected off by the ATP as it releases its energy. and also a three-carbon compound, which is, it goes by a number of different names, but I'm just going to call it a C-3 compound. The point of it is that it's then fed into further metabolic processes that are used to build up, making six-carbon, you know, sugar molecules, which then combined into chains to make polysaccharides,

which, you know, then are used to form the structure of the plant and to store energy and all sorts of other things like that. So we won't talk about those reactions in too much detail. I'll talk a little bit more about them near the end. But all I want to emphasize is that the initial photosynthesis, light independent reactions, produce a three-carbon-long compound, which I'm just going to call a C-3 compound, and then further metabolic processes used to convert that into longer and longer sugars, essentially. So the light-dependent reactions, that's for extracting energy,

the light-independent reactions using that extracted energy to fix carbon into organically accessible and usable forms. So that's the fundamental logic of what's happening here. Of course, the light independent reactions don't depend on sunlight, so they can occur at any time. The light dependent reactions require sunlight, and so they occur during the day. Now, I'm sure everyone knows that chloroplasts are the organelles in plant cells that conduct photosynthesis. So photosynthesis occurs in these special organelles that are found in many plant cells. And this is where the enzymes and other key proteins are found that carry out the functions of photosynthesis. The number of chloroplasts in each plant cell varies, but they can be up to 100 in some plant

cells. So we're talking a few dozen to maybe 100 or so chloroplasts per cell. Within each of these chloroplasts are basically membrane sacks. And this interior membrane is called the phylochoid membrane. So if we just take a step back for a moment, there's quite a few layers of membranes that you have to get your head around here. First of all, there's the membrane around the cell itself, around the whole plant cell, right? Plants also have cell walls, but that's another thing. Again, we won't talk about that, but the cell has a cell wall around it. Then within that, you've got the organelle, which is the chloroplast. The chloroplast actually has two layers of membranes, an outer membrane and an inner membrane. And it's thought that the reason for

that is because of a process called endosymbiosis. Basically, it's thought that chloroplasts were originally free-living bacterial cells, or sort of like bacterial cells, which had a membrane surrounding them. And then they were kind of eaten endocytos by, well, they wouldn't have been plant cells at the time, but they were eaten by other cells, right? And so if you can imagine the membrane sort of from the bigger cell comes and surrounds the membrane from the smaller cell. And therefore what previously had one membrane now has two membranes surrounding it. So anyway, that's why, in order to go from the external extracellular matrix into the interior of a chloroplast, you need to pass through three membranes, the membrane of the cell itself,

then the outer membrane of the chloroplast, and then the inner membrane of the chloroplast. So we've already got three different distinct membranes. And remember, there's multiple chloroplasts in a given cell. But even once we get into the interior matrix of the chloroplast, there's yet another membrane layer that we have to pass through. And this is the thylacoid membrane. The thylacoid is basically a series of sacks, or little sort of disks, which sit on top of each other in stacks called granite, or granum is the singular. Because they look a bit like granaries, right? That's sort of the idea.

And these are just little disks of membrane. They look a little bit like red blood cells, the sort of squished in the middle kind of thing, that are stacked on top of each other several high in the cell. And there's, you know, so there's multiple of these sort of stacks of thylacoids that exist in each chloroplasts, and, of course, multiple chloroplasts in each plant cell. Now, all of this membrane counting is important because the photosynthesis, the key reactions of photosynthesis, particularly the ones will be mostly focusing on the light-dependent reactions. Remember, those are the ones that actually generate the energy,

or convert the energy from sunlight into chemical energy. These reactions occur in protein complexes which sit on the thylacoid membrane. These reactions don't just occur in the cytosol of the plant cell, nor do they just occur sort of floating around inside the chloroplast, but they occur embedded in the thylacoid membrane. And there are stacks of these thylacoid membranes called, again, granum, or granum, singular granopural, which exist inside the chloroplas.

So we've got all these stacks of disks, and sitting in the membrane of the disks are these protein complexes which are carrying out photosynthesis. So hopefully you can visualize the situation here. We've got, obviously, a plant has lots of cells. Within each of those cells, there's a bunch of chloroplasts, these little organelles.

Within those, you've got these stacks of little membrane disks, and embedded and sort of studded throughout the membrane of each of these little disks, the phylochoid membranes, the protein complexes which carry out photosynthesis. And it's these protein complexes that we're mostly going to be talking about. Photosystem 2, cytokrome complex, photosystem 1, NAD reductase, and so on. So these are all studded in the thylacoid membranes.

Okay, so that's the basic picture of how this setup works. Now, what I'm going to do is spend quite a while talking through the system by which light energy is actually converted into chemical energy. And remember the two forms of chemical energy that we're interested in. NADPH and ATP. Those are the two energy molecules that the cell uses, and I've talked about their role. So that's fundamentally what we want to do.

We want to generate NADPH and ATP from sunlight. In order to do that, what we have to do is basically we need high-energy electrons. High-energy electrons are needed because we need to get the energy from those electrons and then use it, sort of convert it into chemical bonds that exist, high-energy bonds that exist in the NADPH and the ATP molecules. So this is, high-energy electrons are sort of how we convert from electromagnetic energy, which is the form of energy that exists in light, in photons, and chemical energy, which exists in the bonds of NADP-H and ATP.

We convert between the two because electrons obviously relate directly to chemical bonds, which involves electrons in atoms, right, and molecules, but also electrons are charged particles, and so they can interact with light. So fundamentally, it's electrons that are critical to mediate between the light energy and the chemical energy, and that's why we're going to be focusing on the electron flow and changes in energy levels of the electron as we go throughout this process. So, that's our goal, is to produce NAD, pH, and ATP from these high-energy electrons. The high-energy electrons, in terms of are excited by absorption of photons.

That's the basic structure. And what happens is the electrons are excited to a high energy level, and then they pass through a very complicated series of proteins and other structures that are embedded in the thylacoid membrane that gradually fall down from a high energy level back to the low energy level, and in the process their energy is extracted to do things that ultimately leads to the storage of that energy

in chemical form, in chemical bonds, of the NADPH and ATP. So that's our goal. I should also emphasize that, kind of like in the case of cellular respiration, the photosynthesis apparatus that exists in cells is a bit of a Rube-Goldberg machine. It's very complicated, and it's basically all just bits that, like, interact with other bits to do other things that then leads to this and leads to that, which finally results in the production of NADPH and ATP.

So it's very indirect. And so don't feel too bad if you find that this is kind of confusing and, you know, why doesn't it just happen more directly? This is ultimately a product of evolution, right? So it's not designed by someone who's trying to rationally engineer it, although it's very efficient. It's not really a weakness, but it does mean that it's kind of indirect and complicated. So bear that in mind. I'll try to go through this bit by bit and then summarize it, go back over it as an overall summary at the end, so you can see how the pieces fit together. But I want you to have some understanding from this episode as to how this actually works at a molecular level.

So, you know, it's not just magic. There's actual chemical, physical, opinions of what the plants are doing here. Okay. To make a start, let's talk about chlorophyll, which you probably heard of. It's the prime pigment molecule that exists in plants, and it's the mechanism by which the plants absorb photons absorb sunlight for then subsequent conversion into chemical energy. There's two main types of chlorophyll called chlorophyll A and chlorophyll B. They're very similar to each other, so I'm not really going to bother about the distinction between them too much. I'll just talk about chlorophyll as if there's only one type.

so I'm not going to worry too much about that. There are also other pigment molecules, beta-carotin, for example, which also absorb sunlight, and plants use a, actually, they don't just use chlorophyll, they use a wide range of pigments to absorb a wider range of sunlight,

so that can help them be more efficient, basically, absorb a wider range of wavelengths from the electromagnetic spectrum. But again, I'm going to be mostly focusing on chlorophyll because it's sort of the most important one, and just to keep things fairly simple, rather than talking about a bunch of different molecules, I'll just focus on chlorophyll. But I have said chlorophyll as a pigment, and I haven't really defined what a pigment is.

A pigment is basically just a molecule or a substance. In this case, we're talking about a molecule, that absorbs light. Some sense, like nearly everything absorbs light, right? But the point of a pigment in this case is that we want to absorb light in order to convert the energy into chemical form. So the idea here is that we need to absorb the energy of the photon in order to essentially transduce the energy into chemical forms, right?

Now, people probably know that plants are green, right? It's actually chlorophyll that's green. What does that mean? It means that chlorophyll reflects green light, and it specifically reflects green light. So that means that of the, you know, all of the colors that exist in the electromagnetic spectrum, and I'm assuming you sort of know about the electromagnetic spectrum, if not have a look at light and optics episode 32.

Of all of the colors in the visible light in the electromagnetic spectrum, chlorophyll absorbs most of the blue and much of the red regions of the spectrum. Slightly different depending on whether it's chlorophyll A and B and blah, blah, blah, blah. But particularly it reflects light in the sort of yellow-green region of the spectrum. That means that's what we see, right? We don't see the colors that it absorbs because it absorbs those and the light doesn't reach our eyes. We see what it reflects, so it reflects mostly green light, then that is what reaches our eyes and we see, oh, look, the plant is green. Most of animal and plant cells are actually

transparent, right? So it's only particular pigments that are found in specific tissues that will give it color. So, for example, melanin is a pigment that's found in human skin that gives human skin color. There are other pigments like the hemoglobin that has a reddish pigment, is a reddish pigment that's found in human blood cells. That also gives color to humans. In the case of plants, much of the color that we see is the result of the reflection of light from chlorophyll, which reflects green light. So that means it absorbs in the blue and the red ends of the spectrum. Okay, but how exactly does this absorption process work? We know that there are photons that are constantly hitting the leaf and the, you know, pass through most of the transparent layers of the cells and

ultimately reach the thylacoid membrane, where the chlorophyll molecules are all sitting. So there's a bunch of these photons and some of them don't have the right energy, so some of them are green, for example, and they generally won't be absorbed. Some of them are blue and red, and those may be absorbed. But how does this absorption process actually work, and how does it lead to particularly high-energy electrons? High-energy electrons is what we want to sort of fuel the rest of the photosynthesis process. So how do we go from the photon to the high-energy electron? Well, the basic idea is what I've talked about in previous episodes relating to the ball model of the atom, right? So we have an atom, a bunch of

protons and neutrons in the nucleus, different energy levels of the electrons in orbit around it, electrons fill up the lowest energy levels first, and then as you add more electrons, they feel progressively higher and higher energy levels, because each energy level can only accommodate a certain number of electrons. That's fundamentally what's happening here. Fundamentally, there's more complication, but basically what's happening is there's a bunch of electrons that are in their energy levels. One of these electrons absorbs a photon, and is promoted to a higher energy level, because it's gained the energy to jump the gap to the higher energy level. And this is how we get a high energy electron, because it's absorbed that energy

from the photon, and so it's got more energy now, and it's at a higher energy level. But there are complications here, because we're not actually talking about the energy levels of a single atom anymore. We're actually talking about the energy levels of the whole molecule, the whole chlorophyll molecule, or at least the main part of the chlorophyll molecule. And now is where I need to talk about the actual structure of the chlorophyll molecule. So a chlorophyll molecule is comprised of a magnesium ion that's encased in a large ring structure called a chlorine ring. So this ring is literally a ring of mostly carbon and also some nitrogen atoms, which surrounds the magnesium ion and sort of holds it in place.

These sorts of cyclic rings are quite common in biochemistry, as they can often form quite stable structures, and they're good for surrounding and what's called coordinating with metal ions, and these are quite common in biology. It's very similar to the overall structure of the heme group, which is basically a ring of carbon atoms which surrounds iron, and this is what holds on to the oxygen atoms throughout bloodstream. So this is not some sort of freak, this is a very common type of structure in biology, basically a ring of carbons and maybe some nitrogen surrounding, and sometimes sulfur, there's sometimes some other things in there,

but basically carbon surrounding a central metal ion. Okay, so that's the main part of chlorophyll. There's also a long tail of mostly carbon atoms and some oxygens that extends out from one side of it. So it sort of looks like a ball on a stick. The ball being the metal, the magnesium ion surrounded by the ring and then the long tail

being the stick part. It's the sort of the ball part, the ring surrounding the metal iron that we're most interested in, the chlorine ring. Now, the critical thing about this chlorine ring is that it is what is called a conjugated system, or another way of describing this is it's a cyclic aromatic compounds. Now, I'm pretty sure I would have talked about this in

one of my organic carbon, sorry, organic chemistry or biochemistry episodes. I don't specifically remember which one, possibly in biochemistry basics, but the basic idea of a conjugated system is that you have, so remember carbon is a very flexible molecule, that's why it's found in biology, because it can form four bonds. And in the case of these rings, basically you can think of it as carbon forms one bond with carbon on either side, and there's usually one bond left over for a hydrogen or maybe a random carbon or an oxygen or something or other, but there's still one bond left over. So it forms, basically what the carbon does is it forms one double bond with one of its neighbors, then a single bond with the other of its neighbors. And if this pattern is repeated around the ring, as it often

is, this is called a conjugated system, because it's a regular pattern of single bond, double bond, single bond, double bond, and so on. And these conjugated systems are particularly important because they form what are called resonance structures. Basically, the electrons become delocalized, and they don't actually just exist on this carbon or that carbon, but they can spread out through around the whole ring. It's because of their ability to resonate, which essentially means that there's this sort of symmetrical pattern.

It's not just that there's a double bond here, and then at a random place later on there's another double bond. It's because they're in this regular arrangement, it allows the electrons to delocalize and spread around the ring as a whole. You need more organic chemistry and a bit of physics to understand why this works the way it is. So look back at some of the previous episodes I've done on this to get more details on that. But if it doesn't obviously make sense, just kind of take my word for it, that when you have this conjugated double-bond, single-bond, double-bond, system, you get this resonance which allows the electrons to sort of delocalize.

And they form a series of discrete energy levels. the more carbon atoms you have in the conjugated system, the more energy levels you form. So in particular, if you have two carbon atoms, they'll form two energy levels. If you have four in your resonant structure, they'll form four energy levels and so on. Now, this is important because it means that the energy levels that we're talking about don't just exist on one carbon atom, but they're spread across the whole ring, and so that the gap between the energy levels is different compared to the gap between the energy levels in a single atom.

This matters a lot because if we relied on absorbing photons in a single atom that would require much higher energy levels this would have to be ionizing radiation which is actually dangerous to those forms of life and that's not what plants are doing they don't rely on ionizing radiation

to excite the electrons in a single atom instead they have this delocalized conjugated aromatic system where the energy levels are the electrons are spread across many carbon atoms and therefore the energy level levels, the energy levels are closer together so that there's a small energy gap that you have to excite the electron through. And so you don't need as high energy photons to excite that.

So that's essentially why we use these conjugated compounds. And having them in a ring format is convenient as well because it's a stable structure. Although they're not always in a ring. Structure, we'll see later on, there are versions where you just have these aromatic carbons in a long tail, and that's actually the bit of the molecule that absorbs the photon. But in the case of chlorophyll. It's basically the, I mean, it's really the molecules a whole, but it's mostly the conjugated carbons in the ring bit that actually absorb the photon. But it's not, it's important to understand, it's not a single carbon that absorbs a photon. It's sort of, the absorption is spread across the whole ring system because that's where the energy levels are. There are a combination

of, um, of, um, of the orbitals of the individual atoms. Now, so like all orbitals, they're, they have different energy levels. And as you move up the energy levels, the, electron in that sitting in the energy level has up a higher energy. I mean, not surprisingly, right? And this ultimately relates to the fact that the wave, because an electron is a standing wave, right? It's actually formed by a wave function, which represents the probability of finding the electron in a particular location, and that wave function has a particular wavelength, and as that wavelength gets smaller, as it gets wavyer, essentially, its energy increases, and this is represented by sort of more complicated orbital arrangements.

So it's easy to show these in diagrams where you start off with sort of slow waves and then an increasing number of nose, antinodes. As the wavelength increases, you get sort of you pack more and more vibrations into the same finite space around the ring. And these represent higher and higher energy levels. So basically what's going on when the electrons are excited in the energy levels in the ring here, in the chlorophyll molecule, is that they're moving from states where they can kind of, if you like, have relatively long wavelengths. Their vibrations are kind of more leisurely slower, if you like. They're moving from those states into states where they have to, where they can only exist at higher energy,

more rapid vibrations. And so more rapid vibrations is sort of directly related to sort of the same thing as a higher energy. So that's fundamentally what's going on. They're actually moving into physically different orbitals, which, because of their physical distinctive nature of having a shorter wavelength, of being more sort of variable, therefore have higher energy levels. Don't worry about that if it doesn't make a whole lot of sense. Hopefully it makes some sense if you got some idea about the relationship between wavelength and energy. A shorter wavelength means higher energy, basically. And that's what happens as a result of these energy levels that exist in the ring and the chlorophyll. Okay, so the delocalized electrons across the ring,

at the various energy levels, are able to absorb a photon and then excite, which excites the electron to the next energy level. What's actually physically happening when the photon comes in is, obviously, the photon needs to pass close enough to a particular chlorophyll molecule, but it also has to have the right energy. Now, you've probably heard before that in order for an atom to absorb a photon and excite the electron to a higher energy level, the incoming photon needs to have just the right energy level to bridge the gap from the low energy level, from the electron's low energy to its higher energy level, and therefore promote the electron to the higher level. You can't have a little bit of energy left over. You have to have just

the right amount of energy to bridge that gap to promote the electron up. Now, that would actually be a bit of a problem for plants if that were literally true and carried over to the case of chlorophyll because that would mean that plants would only be able to absorb exactly one wavelength of light. And that means that they'd be very inefficient at utilizing all of the wavelengths that are emitted by the sun. The sun is pretty close to a black body, which means it emits all wavelengths. The amount of different wavelengths depends on the temperature of the sun, but the point is it emits a continuous spectrum of energy across a wide range of wavelengths. And therefore, if it's going to take advantage of that, the plant needs to be able to

also absorb energy across a range of wavelengths, not at exactly just this or that wavelengths, even if it had a few different pigments to absorb different wavelengths. Still, a few tiny sort of pinpricks of wavelengths that you can absorb across the whole spectrum is not really going to help very much. So this idea of requiring exactly the right amount of energy to promote the electron from low to high energy is not really going to work. And in fact, that's not how it works. And fundamentally, this comes down to the Heisenberg Uncertainty Principle.

The basic idea is that excited states, so when you promote the electron to the higher energy level, they have a finite lifespan. Eventually, the excited state is unstable. The electron will go back to its lower energy level, and often there will be an admission to release that energy, or sometimes it's converting into other forms. But the basic point is that the excited snake doesn't last forever. It doesn't usually last very long. Because of that limit on its lifetime, that places a limit on the wavelength,

that the, on the frequency, and therefore on the wavelengths that the emitted light or that the electron itself can have, and therefore that also places a limit on its energy. Basically, the idea is that if you restrict time, that means you restrict frequency, because that's related to time. If you restrict frequency, you restrict wavelength, which is related to frequency, you know, the frequency of vibrations, and if you restrict wavelength, you restrict energy, because that's directly related to the frequency of something, basically how rapidly it's vibrating. That, representation of its energy. So again, if that doesn't make full sense, don't worry too much about it. I've talked about this before in some of my physics and chemistry episodes. The basic point, though,

is because of this finite lifetime, the allowable energies actually spread out. There's not just a single defined energy that the photon is allowed to be. It's allowed to be across some range, depending on the lifetime of the excited state. And so actually atoms are able to absorb photons over some range of energy spectrums. It's a fairly narrow range, so the energy of the photon has to be fairly close to the gap in energy levels, but it doesn't have to be exact. It can be over some range. Now, that's the case for chlorophyll molecules as well. But there are still other processes operating to allow plants to absorb energies from a wider range of frequencies.

In particular, I've been talking about the absorption of light as if it happens at just one of these, a single chlorine ring on a single chlorophyll molecule. and although that's a simple way to think about it to start off with, that's not actually the case. That's not how it works. In fact, these chlorophyll molecules exist in combination with other chlorophyll molecules, so in pairs or groups of four or eight or even more. They exist in systems. Therefore, they don't typically act as single molecules, but they act as interacting complexes, which absorb electrons together in the form of what are called excitons. So basically the way to think about this is that it's, I talked about how multiple,

carbon atoms within the ring sort of combined together to form energy levels that then can absorb the photon. But it's actually even more complicated than that because multiple chlorophyll molecules can combine together to form multiple energy levels of these things called excitons. Just sort of like a delocalized electron

kind of... It's a representation of the energy that's been absorbed by the combined multiple chlorophyll molecule system and has its own energy levels even distinct from those of the carbon atoms in the aromatic ring itself. So it gets quite complicated.

The point, though, is that the exact energy levels of these excitons that exist in these sort of sets of chlorophyll molecules, the exact energy levels depend upon the number of chlorophyll molecules you've got there, which can vary from one, two, four, and so forth. It also depends on their relative orientation and their distance from each other and other factors like that. So this means that the energies that can be absorbed by plants vary over some range, over some range of like a few dozen nanometers in terms of wavelengths. So the visible spectrum of wavelengths extends roughly from 400 to 750 nanometers, and this is where most of the absorption of energy occurs in plants.

As I said, there are sort of peaks around the 450 and the sort of 650 regions where most of the energy is absorbed, but there's still some width to these peaks. They're not just like a point at exactly one particular wavelength, which is what you'd expect if you just looked at the naive energy gap model of absorption. but they spread over a range of a few dozen nanometers, perhaps. And as I said, part of the explanation for this is because of the fact that excited states don't last forever. They have a limited lifetime, and therefore that leads to a spreading of the energy levels that can be absorbed. But it's also in part due to the fact that the chlorophyll molecules don't operate in isolation most of the time,

but they operate together in systems, and therefore the energy levels of each sort of little system depend upon the orientation and the distance and the number of chlorophyll molecules involved. And so there's some spreading there of the energy levels. So these factors is what enables plants to actually absorb a reasonable proportion of incident sunlight and not just like tiny pinpricks of specific energies. Okay, so we've talked about the absorption process. The phonon comes in, it interacts with a chlorophyll or a couple of chlorophyll molecules and is able to excite the electron in these aromatic rings of the chlorophyll to a higher energy level.

And that's where the high energy electrons come from. Okay, but what do we do with these high energy electrons? We want to pass them ultimately through a complicated system of protein complexes so that they can be used to convert this high energy electron into chemical energy. Remember the NADPHs and ATPs that we're trying to get to. So we need to do this. In order to explain how that process works, I need to introduce some of the big players here. So photosystem 2, the cytochrome complex, and photosystem 1, I'll focus on at this stage.

Now, you can think of these as embedded in the membrane into sort of a sequence. It's actually not quite so simple as this. They kind of move around and come close to each other and then move away again, but we'll just think of them as if they're like a production line, a linear sequence. That makes things easier. So first up is Photosystem 2. This is a big complicated complex of proteins and other elements that are all sort of combined together. So this is a really big complicated mess.

There are like dozens of proteins all connected to each other plus other compounds and cofactors and so on that are all stuck together kind of in this big complicated system which we'd just call a complex that's embedded in the thylacoid membrane. So there's photosystem 1 and then we've got the synachrome complex that's sort of conceptually similar, big complex of proteins and cofactors and other things that's stuck in there. Then we've got photosystem 1. Again a different photo system. So it's set up differently but similar basic architecture with lots of proteins and cofactors and other things that's stuck in there. but similar basic architecture with lots of proteins and co-factors bound together, and they all do different things. The important thing to keep in mind is the order. Photosystem 2, cytochrome complex, photosystem 1. You might wonder why Photosystem 2 comes before Photosystem 1. The reason for that is essentially historical. Photosystem 1 was discovered first, before Photosystem 2. And they were discovered before we knew sort of the relative order of the electrons flowing through the system. So that's just how it

works, just have to remember, Photosystem 2 comes before Photosystem 1. Okay, so what are these complexes do, and how do they work, and how does chlorophyll fit into this? So the chlorophyll molecules that are doing the absorbing are found in Photosystems 2 and Photosystem 1. So they're not found in the cytochrome complex, but they are found in Photosystems 2 and once, hence the names, right?

So actually what happens is that the system kind of gets two jolts of energy, if you like. There's one sort of zap of energy when a photon is absorbed in photosystem 2, then that produces a high energy electron which flows to the system and eventually gets the photosystem 1, and then it gets another zap of energy. So it's kind of like a two zap process if you like, one at photosystem 2 and one at at photosystem 1. There are some forms of bacteria and algae in someone that only have one or other of these photosystems or like relatives of them, because you can get away with just having one. It's just having two of them allows you to get a sort of bigger bang

for your buck sort of, but you can get more energy out of it because you've got those sort of two zaps, the two absorption processes. Okay, but let's start with photosystem two, because that occurs first in the process. This is where we have the first absorption event and the first excitation of the electron. And here again, I have to introduce another complexity, because it would be nice and simple if there was just one or a couple of these chlorophyll molecules which absorbed the light and then produced a high-energy electron, which was then passed off to the different parts of the photo system.

but it's not quite that simple because it's not just one chlorophyll molecule or even like a pair of chlorophyll molecules or a bunch of four or something. There's actually dozens of them that exist as what are called antenna pigment molecules, and they all surround what's called the reaction center. So you can think of it like this. There's a special pair of chlorophyll molecules that exist in the reaction center, and these are the ones that actually excite the electrons that we need to fuel the process of photosynthesis, right? So these are kind of the workhorse ones. but they can't absorb the light all by themselves in part because the actual physical surface area

that we have available for absorption affect how efficient we're going to be at absorbing the incoming photons because they actually have to hit, they have to pass quite spatially close to the chlorophyll molecules in order to be absorbed. So if we just have these one pair of chlorophyll molecules that can do the absorbing, you know, most of the light's going to miss them. So to increase the surface area, we have these what are called antenna pigment molecules. which are basically just pairs or quads or whatever of the chlorophyll molecules that are spread around in a kind of a disc surrounding the reaction centre. And what they do is, they absorb photons in the same way that I've just talked about, the energy levels and promoting and so forth. But they don't directly do anything with the electrons. They just pass the electrons on to a neighbouring pair of chlorophyll molecules, which then pass the electrons, the high energy promoted electrons to a neighbour and so on.

resonance pattern, and eventually the high-energy electrons will reach the chlorophylls of their reaction centre, and that's when the sort of interesting stuff happens. So the antenna pigment molecules, their only purpose is to increase the sort of surface area, the overall photo system. They don't do anything themselves with the high-energy electrons. They just pass them onto a neighbor, which then passes them onto a neighbor and so on and so forth until eventually they get to their reaction center. This resonance sort of transfer process is actually quite complicated. It's the mechanism is called the Forster resonance energy transfer, and relates to the fact that the the energy levels kind of overlap with each other,

and so the electrons can kind of jump across the barrier from one to the other, and it's quite a complicated quantum process. So we won't get into the details of that, but just bear in mind that there are all of these antennae pigment molecules which absorb light and then pass it on to the reaction center, and that's where the action happens. So here there's a special pair of chlorophyll molecules, which receive the excited electrons from all the antennae molecules,

and then pass it on through a series of co-factors. So these are other essentially molecules that are bound in and form part of the photosystem 2 complex. It's kind of like an assembly line in a sense or a pass-the-passal kind of thing where one of these molecules or sometimes atoms, sometimes it's a residue from the protein. It's all sorts of different things. The electrons pass from one thing to another thing to another thing, gradually losing energy in the process because each of these transfers has to be energetically favorable, right? So you can think of it as if the electrons falling down a series of steps where each step represents a different molecule. or residue of the protein or sometimes it's a metal ion, anything that can hold the electron, basically.

And the fact that it's going down the steps is representing the fact that the electrons gradually losing that energy that it gained when the photon excited it. It's going down the energy hill, so to speak. So once the electrons have been excited by the chlorophyll molecules in the reaction center, or they've reached the chlorophyll molecules in the reaction center

after having been passed to it by the antenna, Pinapegna-pigna molecules, then they're passed through a series of sort of intermediary compounds, including a compound called Phaephyton, which is very similar to chlorophyll. It just lacks the magnesium ion in the center of the carbon ring. So it passes it to that. Then it passes it to a molecule called quinone, which basically has a long tail of conjugated bonds that is able to absorb the electron, you know, because remember it's the conjugated bonds that form the energy levels that the electron is able to sort of exist in.

So whereas chlorophyll has these conjugated bonds in a ring surrounding the magnesium ion, quinone just has them in a linear long tail of the molecule. So it's passed to quinone, and then it's passed over to an iron atom, and then it's passed over onto a carrier molecule, which is not part of photosystem to, but exists inside the phylocord membrane. This molecule is called plaster quinone, so it's very similar to quinone. Again, it has a long tail of conjugated bonds, a linear tail, and the electron is able to, again, be passed onto this tail,

so it exists in one of the excited energy levels there. So what we see is a sort of a pass-the-passal mechanism of the electron being passed from one of these components to another, and usually it exists in a sort of conjugated set of bonds, usually around 10 carbon atoms, because this will produce the right energy levels for the electron to exist in, and it's passed from compound to compound. Sometimes it changes the oxidation state of an iron atom or other metals, as we'll see later.

But either way, it's passed from sort of one carrier to another in this complicated chain until it eventually is passed on to Plasterquinone, which then diffuses through the membrane and passes the high-energy electron onto the next component, the next complex that is embedded in the membrane. And this is called the Cytochrome Complex, or the Cydchrome BF Complex. I'll just call it the Cydicrome Complex. So again, this is the complex, the protein and co-factor complex that sits between photosystem 2 and photosystem 1, and within the cytokrome complex, the high-energy electron is once again passed through a series of intermediaries.

In this case, it's a different one, you know, it's a different set to photosystem 2, but similar sort of idea. So it's passed through a number of heem groups. Again, it's found in the blood, as I mentioned before. In plants, in this case, it occurs as just a mechanism of storing electron, basically. So it's just an iron ion, which is surrounded by a ring of carbons and a few nitrogen. So once again, it has this carbon resonance structure of the alternating double and single bonds. So once again, it's able to hold the electron.

So again, you see that's a common feature of these systems. It's also passed, the high-energy electron is also passed to something called an iron sulfur cluster, a bound network of iron and sulfur atoms, which is able to, I believe, change the redox state in accepting and donating the electron, passes on to more heen groups, and eventually passes the high-energy electron off to a compound called Plasticionin.

But we're getting ahead of ourselves here, so before I describe Plastercyon in and then talk about the high-energy electron being passed over to the final of the three complexes, Photosystem 1, I need to talk about what is achieved through this, past the parcel of the high-energy electron from one compound to another. What is the point of all of this? Essentially the point is that the point becomes evident in the cytocrine complex,

because as the high-energy electron is being passed around between these heen groups and the iron-sulfer cluster and other things, this sequence of transitions is all sort of cleverly set up, obviously by evolution, so that a couple of hydrogen atoms, or hydrogen ions rather, diffuse out of the complex into the intermembrane space. So this is the internal membrane of the thylacoid. So within the thylacoid membrane space, the hydrogens are essentially diffuse into this interior space. Now, why do we care about that? Well, we care about that because this leads to a buildup of charge inside the thylcoid membrane with positively charged hydrogen ions from the outside being progressively pumped into the thylacoid space

and therefore increasing the hydrogen concentration, and leading to a charge differential over the membrane. This charge differential is effectively a storage of energy, both due to the increased concentration of hydrogen and also due to its electric charge. So there's actually two effects there, but they reinforce each other. So basically what's happened is that the high-energy electron that was excited originally, in photosystem 2 has been passed around from, you know, one heem group or one iron cluster, ion sulfur cluster, or one chlorophyll molecule or phyaphyton molecule, whatever it is,

from one of these to another. And in the process, in the process of all this, four hydrogen ions are pumped from the outside to the inside of the thylacoid membrane, from the low hydrogen concentration side to the high concentration side. So they're pumped across their concentration and charge gradient, which obviously is something that works against the ordinary operation. Things ordinarily molecules move down their concentration gradient and are repulsed by charge concentrations. And so this is something that is a process that requires energy,

and that energy, of course, ultimately comes from the high-energy electrons. So for each, I think it's for every, as far as I can be able to tell, for every two photons that are absorbed, four of these hydrogen ions are pumped across into the thylacoid interior membrane space. This is also called the lumen, but I'll just talk about being inside the thylacoid membrane. So this is really the whole point of Photosystem 2 and the cytochrome complex is to pass this high-energy electron around in such a way so that it leads to or enables the pumping of these four hydrogen ions

from the outside to the inside of the thylacoid membrane. These hydrogen ions then form essentially a battery. They're a concentration of charge. They're a form of energy, and they then flow back down their concentration gradient later on, so they flow from the inside to the outside of the thylcoid space, back down the concentration gradient, and down there in the direction that they are propelled

by the electrochemical gradient, as a result of the buildup of positive charge from inside the thylquoid space. But in doing so, they pass through the ATP synthase, which I talked about in the previous episode of cellular respiration, this is effectively a, it's like a generator, effectively. The hydrogens pass through it, flowing down the concentration gradient. As they do, energy is released, and that energy is extracted by the design of the ATP complex, and the energy is stored by essentially clicking into place the extra phosphate group

onto ADP, turning into ATP, and then by storing the energy as that extra sort of spring-loaded phosphate group. So that's really the entire purpose of these initial two complexes, is to generate a gradient of hydrogen ions, which then flow back down the concentration gradient, releasing energy in the process, and storing that energy or transferring that energy to make ATP. And so that's the first way in which photosynthesis is able to extract energy from light. So it's quite a complicated process. It goes from the energy goes from being in the photon to being in the high-energy electron, which is then gradually shuffled from one compound to another.

And in the process, this sort of shuttling is so arranged that hydrogen ions are transferred at just the right place and in just such a way that hydrogen ions are pumped from the outside to the inside of the space. So the energy is then converted from the potential energy of the electron to the potential energy of the hydrogen ions and is then in. turn it transferred into the chemical energy of the high-energy bond of the phosphate, which is sort of clicked into place in the spring loading of the adenosine triphosphate molecule. So there's quite a complicated process there, but this is the first stage or the first

manner in which the plant is able to convert sunlight into chemical energy. So although we haven't finished our story about photosynthesis, I'm going to break the episode off here because it's gone long enough already, and we'll pick up. by talking about the oxygen evolving complex serving as the source of electrons for the photosynthesis process in the second part in the next episode. So thank you very much for listening. I hope you found this interesting. If you would like to get in touch with me, you're welcome to send me an email. My email address is FODs12 at gmail.com. That's F-O-D-S-1-2 at gmail.com.

You can also support the podcast by becoming a patron on Patreon. You can find my podcast website by just going to Patreon and searching for The Sides of Everything podcast. You can support the podcast at various dollar amounts for each episode that I release. It's done per episode. And that's entirely voluntary, but any support that you can provide is very much appreciated. So thank you very much for listening, and I'll talk to you next time.