 Okay, so we are at 10-01 Pacific Standard Time, so that seems as good a time as any to start. I'm using a roomcaster slide show today. It's got a bit of a different hud, so excuse me if things seem a little bit weird as I'm getting used to it. So today I'm going to try and present a informal discussion of some bioprocesses that use light and title is green and purple. I've got green and purple things all through the talk and basically I'm going to tell you about two different biosystems that use green pigments and purple pigments that end up being able to harvest energy from sunlight. So yeah, there's all sorts of big scary molecules around me. I'll talk about that my little friend over there later in the talk if it's a kind of a benty chlorophyll. So without further ado, hey here's an abstract. You know basically I'm going to talk about light-driven biological processes. They are very complicated. I'm not a biochemist so I'm going to try to reduce them down to very simple behavior. The fundamental thing that these systems will do is that they'll take in light, they'll absorb that energy, that will move some electrons around and end up moving hydrogen ions, H pluses around, so as to accomplish tasks within cells. And one of these tasks is vision which plants don't have. I hope not. They don't really want them watching me too much but which we do. One of the things I'm struck by when we talk about photosynthesis and the similar mechanisms is just how complicated many of these processes are. The structures themselves rival Rube Goldberg machines and their complexity. So we'll take a look at some of them. That's what I'll focus on primarily today. Okay so what are the green and purple in the title? Well green will be photosystem one and two. Let's see if I can add some animation to what's going on. Maybe not. Green. Okay so I can move around on slides but I'm not getting very quick drawing on the slides. Okay well talking about photosystems one and two. They're in plants, cyanobacteria. Also going to talk about rhodopsin and related species which are in bacteria. Let's start with the purple ones. They're rhodopsins. Talking about Rube Goldberg machines. Here's a sketch of one I've given the image credit below. I'm still trying to make little squares and circles and things and it was working right before the seminar so that's something that we'll have to fix. So there's a recent CBS story and I can give you the URLs as I'm speaking. There you are. Okay so that's not working right now either. Okay very well. There's the URLs. I'll be able to send those to people later. Maybe I can try one last thing. There we go. Okay that's the URL for more on Rube Goldberg machines. Very complicated as we say. So first thing I'm going to talk about is a bacterial rhodopsin and it comes from this halo bacterium selenarium. And so the halo bacterium selenarium ends up living in very salty waters. Very salty waters. And there is an article on them at this link. Okay that's working better. And these are a few of the denizens that live in such salty waters and very salty lakes. And this little rod shaped one that I've got the arrow pointing to is actually the halo bacterium selenarium. This was featured as a bacterial rhodopsin from this organism was featured as a molecule of the month about a decade ago I think on the protein database. I'll talk about that in a little bit. Essentially what it does is it pumps hydrogen ions H plus across bacterial cell membranes. And this action causes a pH difference inside the cell versus outside the cell. And that is what allows a molecule called ATP to be synthesized. Okay this ends up being a way for the cell to store energy. All right that's a mouthful and I'm not here to try and be intimidating about all of these structures. I will provide a direct link. Here's a direct link to the actual page that I'm showing you. If you haven't seen it the protein database has these molecules of the month and it is a really lovely introduction to structural biology and they bring it down to a level that even a poor interganate chemist like myself can understand. Next slide. So the whole point of what the rhodopsin does is to move the H plus around. Okay so on one side of the cell you've got high concentrations of H plus right you think of H plus as being acid. You've got low concentrations of H plus on the other side of the cell because there is a light driven pump that moves these ions. As a result this slide can happen where on the left I'm showing you adenosyl ribo-diphosphate. I think that's what it's called. Again I'm not a biochemist. The point is if you look at where I say have diphosphate labeled there's two phosphorus atoms with a bunch of oxygen atoms. There's a little enzyme in how that spans a cell membrane that will take and add to this diphosphate stuff another phosphorus atom with some oxygen. It takes energy to do that but that energy can be released reversibly so this is an energy storage mechanism. Okay let's see. So one can access a little bit more on that from LibraTex. These are open source textbooks out of the University of California system. That's where I got the figures from. So how ATP synthase works is going to be a story for another day. I'm going to go back to the rhodopsin. Next slide. So here's a structure of the rhodopsin from the halobacterium salinarium. It presents as a complex of three of these of three of these little structures. There we go. So on this slide on the figure in the lower right you see three of the proteins from above going forward. This is a view from the side. The rods I'm still trying my pointers and stuff. I have a pointer. Okay so the rods that are showing up from the the top and bottom of this figure that I've just put arrows on will represent the cell membrane. This thing spans a cell membrane. What are the coils? Okay well the coils are actually protein. Protein is basically a chain of amino acids. What does that mean? Well it's basically like one long molecule that's linked with little Lego bricks essentially that you can make into different shapes. There's a particular amino acid that if you repeat it over and over and over again will turn into these spirals. These are structural. They're essentially the building blocks of the they're essentially to keep all of the important machinery in place. They're basically the building in which the chemistry takes place. I've got the same structure lurking out behind the screen. I'm going to shrink it down and bring it in front of you. Because if I don't shrink it down it's going to get kind of big and intimidating. It's almost like something from HB Lovecraft. Let's stretch, make you a little bit smaller and move you in front of the screen. And when I said a little bit smaller it really meant just just a tiny bit smaller. Okay so hopefully I haven't engulfed anybody in in there. Okay it looks looks looks pretty good. This is the same structure. Essentially what you see is the pink spirals and those span the cell membrane. Those are very good at keeping the protein in place in a specific place in the cell. There's some loose-looking spaghetti ends at the top. There's some loose-looking spaghetti ends at the bottom. These represent the protein chain that aren't spiraling. And you'll notice some blue stuff kind of hanging out in the middle. And I don't know if you can zoom in on the blue stuff. These are molecules called retinol. Every three spirals represents one of the proteins and these proteins always occur in trimmers of three. And each retinol molecule is the pump. So what happens is that the blue like that blue blue array of molecules inside this protein gets hit by light changes shape and that shape change drives an H plus being moved from the top of all the spirals down through a channel and out out the bottom. Okay so I'll show you this on I'll show you what happens on the the slideshow screen. In the meantime let's edit this guy and move him out of the way. All right, goodbye. Okay I always have stage directions on my slide. C structure model here at Science Circle. I got to do that or else I forget what I'm doing and go off on to science and start talking to you more about my cats. I've got cat pictures later of course. So here's here's more pictures of bacteria or dops and remember I said Luke Goldberg machine you would expect that the H plus kind of starts at the top and moves down out the bottom in a logical flow. But there's five steps to moving the H plus and the step one right here right in the middle is where that retinol molecule was. Absorption of a photon causes retinol to change its shape and it basically shuttles an H plus from one place to another and in reaction to that an H plus is kicked out of the bottom and in reaction to that an H plus gets sucked further in and recharges the retinol followed by an H plus being sucked in from the rest of the cell and finally an H plus moves into position to be ejected when the next photon arrives. So this isn't like one two three four five in a like a logical sequence from from one end of the structure to the other. There is a logical sequence and all of these things have to happen but it's started off by the proton pumping action of the retinol. Hey retinol is in your eyes. I'm going to show you that in a second. Okay I actually like this loom cast screen. I like making arrows. There's an arrow. So what happens in the bacterial rhodopsin? Well that's the structure of the molecule. For those of you who aren't familiar with organic chemistry jargon I guess every every vertex right? So if I maybe circle one of these guys every vertex represents a carbon atom. So the one I've just put a square around is a carbon atom. You see two lines well carbons tend to have four things attached to them. You see two lines. Those are the bonds to other carbons. There's four things attached. The ones you don't see are assumed to be hydrogen. So what I've just put a square around is a CH2. This guy with the next square has oh four lines. There are no hydrogens attached to that one. The places where we see two parallel lines are referred to as double bonds. And when you have a pattern of single bond, double bond, single bond, double bond then you have some electronic mobility through a chain. So the electron mobility gives us some special features. Like having a chain that long with maybe a nitrogen at the end allows the molecule to absorb light. One of the things that happens when the molecule absorbs light is that the bonding becomes a bit looser. These double bonds tend to be rigid. They tend to basically keep the things attached to the carbon in a particular geometry. Happens to be a planar geometry. When you get into an excited state by absorbing an electron that ends up being loosened. And you can have rotations happening. So very simple thing. Very simple molecule. This retinal derivative is not quite retinal because it's actually attached to the protein in this case. But it's essentially the same molecule. In your eye, in your eye, oh I always forget this slide. Okay so I kind of explained why does the molecule change shape. You know in in molecules we've got electrons that are holding nuclei together. And the electrons where they're allowed to go is determined by quantum mechanics. I won't scare you with that. Essentially what happens is that the molecules arrange their electrons into states where you have low energy states and you have high energy states. My squares have gone away again. Oh no there we are. So I circled the high energy state. There's so high energy that the electrons avoid them. There's no electrons in there. Until the molecule absorbs some light. Each new is light. And then an electron can show up up here leaving a hole down there. This reduces the strength of interactions between neighboring carbon atoms. And that's what lets the free rotation start to happen. So orbital change reflects a change in the energy state of the electron. Absolutely yes. Because this is basically the same as taking a bucket of water and climbing a hill with it. You could do some work with the potential energy that you have invested in water in the bucket. I don't throw it at someone whose politics differ from yours or something like that. Okay that was meant to be a joke. So in your eye we have similar molecules. Here's retinal. Oh that's not what I wanted to do. Click. Here is retinal. And you know I keep saying retinal. It says retinilidine. All that's happening is that we're kind of changing kind of just changing this little bit there depending on what is connected to it. Okay so in your eye in your eye we have some recharging of the retinal that happens in the dark state. That's stuff down here. Okay my ability to draw comes and goes. Okay that's that's down in the lower block. And in the upper block this is what happens when light absorption occurs. That bit in red is exactly what happens when light absorption occurs. I'm going to zoom in on it. Okay notice how we get a structure change. What's the importance of the internal rotation? So essentially you move this H plus from one position in the protein to another position in the protein and or to another position in space. And that allows it to be transferred along a chain. In your eye this ends up developing a potential that can be trigger a nerve to fire. Okay so this is what happens in the rods in your eye. This structural change triggers H plus flow. Since H plus is a charged species movement of ion is the same thing as an electrical current. So that can trigger nerves to fire. And all the rest of what I had on the slide was the recharging. It takes about half an hour after this structural change to occur for the compound to go back. One of the things I'll just point out in your eye we are moving that bond but in the bacteria rhodopsin it's moving that the bond adjacent to it. And part of that is going to be determined by the space left in the protein and carefully managed by the protein. It's exactly like a conveyor belt. Let's see next slide. 16. Okay so the purple part was the bacteria rhodopsin and the visual purple it was called that's in the rods of your eye. I'm going to talk a little bit about photosystems one and two the green part of the title. And thank you for indulging me. These are some pictures from my garden we've got some purple cone flowers going on. I think these are some lavender and some blue bells and they just happen to be purple flowers and with green in the background. Otherwise no relevance to the talk so thank you for your indulgence. Taking a slight detour because I am an inorganic chemist and we like to look at biochemistry and structural biology and get inspiration for how to do things that might be useful for society. This is an early structure you'll call it bio-inspired inorganic chemistry. It's a molecular photovoltaic an example from 2004. If you take the photosystems in that values for photosynthesis and distill them down to their essence you have parts of the molecule that are antennas. Actually in photosystem one and photosystem two as I'll show you these molecule the molecules aren't actually joined to each other they're just in proximity held by the protein scaffolding. So anyway you have an antenna which helps photons which don't actually hit the active site. The donor which I've circled in green here helps channel their energy to the active site and increases the efficiency of absorption. Why donor? Well what happens like I described way back on the molecular orbital slide what happens when a molecule absorbs light is that an energy or is that an electron gets promoted from a low energy state to a high energy state. Most of the time that electron just falls back into the hole at left and the energy is released as useless heat. If you set things up right the electron in the high energy state can make it sell or can make its way somewhere else and be trapped there and avoid recombination. So it's still high energy oh and there's a low energy hole and now we've got an energy difference that can be used to drive some chemistry. Let's see when the electron returns to the cis energy state the shape returns to the cis form from the transform until it forms another photon is that it? So here's the thing the one form will turn into the different form on absorption of energy. The the energy can be transferred somewhere somewhere else the proton can be can be moved through the protein chain or whatever it does take some time for the molecule to relax back into the initial state. So in the rods in your eye there's a constant movement of the retinal from the light absorbing kind of tip of the rod back into the I'm going to just call it the lower portion where there are processes that actually reset the shape and manage the shape and then inject it back. So it's not instant it may take 10 to minutes to half an hour. Sometimes photon absorption doesn't excite an electron it can induce internal rotations and vibrations absolutely. So it does depend on the wavelength of light so usually visible light has the enough energy to promote electrons from low energy states to higher energy states but if you're looking at infrared light that tends to excite molecular vibrations it leaves the electrons alone and microwaves tend to be appropriate for exciting rotations molecules. But yeah all of those all of those are like fascinating techniques. Okay let's see back to this slide the three things you need to make photosynthesis happen are antennas are donor sites and acceptor sites and then some other chemistry to do some energy or do some useful work with the separated charges and their associated energy. Okay here's an example so Dan Nosira is at Harvard and he's done some lovely work this is a paper I saw last week or from a paper I saw last week from accounts of chem research and it talks about some of his work from the last 12 years. On this slide I've got one of his figures it's a comparison between natural photosynthesis and artificial photosynthesis and as we'll see later in my slides there's a thing called photosystem two there's a thing called photosystem one they both absorb energy photosystem two is where oxygen is evolved that plants and these things drive a couple of other processes that end up taking carbon dioxide and adding hydrogen to it and making biomass. So the artificial photosynthesis relies on a silicon chip or a silicon wafer and the silicon wafer can absorb light and cause charge separation as I've been describing and what the clever thing they've done is to put a surface on one side of the silicon chip that will be favorable for turning water into oxygen and H plus it happens to be a cobalt phosphate it's oh it's delightful because when the cell is running it's self healing any damage to the surface actually gets repaired as part of the dynamic chemistry of the process so it pretty much got no time limits on to its lifetime. On the other side you need H plus to turn into H2. There's lots of things that'll do that for you platinum is especially good but anything that will turn H plus into H2 at fairly low voltages has a problem with oxygen O2 molecules from the air can be turned into reactive oxygen species related to hydrogen peroxide well that's a problem because on this hydrogen side of the silicon wafer you want a colony of bacteria to live and if you're generating hydrogen peroxide it kind of bleaches them into death so the particular surface he came up with it says it says COP and that's confusing because the other one other side says COP the green side is a cobalt phosphate it's a salt the pink side is a cobalt phosphorus alloy and that has the property of allowing this H plus to H2 thing to happen but it suppresses the oxygen making reactive oxygen species happen the upshot is this cell operates pretty close to its ideal value and pretty much every photon that I should say every photon one out of every four photons that hits this thing it's got 25 efficiency ends up making these reactions go who cares well the bugs that are engineered use the hydrogen to fuel their metabolism right so they do they do all the same things that the the the regular leaf would do including taking carbon dioxide and turning it into biomass and they can be engineered to make methanol ethanol or biopolymers that are useful this was wonderful work it said really just appeared in his last sentence or I'm sorry in his last paragraph in this he said oh by the way we've also engineered the we've also engineered the bacteria to fix nitrogen and you know the nitrogen containing biomass also has pulled carbon dioxide from the air and if you spread that on on fields then you know you'll enrich the spoil with carbon organic matter and fertilizer at the same time in what should be a process that depletes the atmosphere of carbon dioxide this sounds to me like a wonderful thing because as some of you know night ammonia fertilizers are made by the Haber process which requires 500 degree iron powder at I think 200 atmospheres or something like that it's essentially responsible for one percent of the carbon dioxide formation on this planet or commercial activity so it's a huge contributor to climate change so having having bionic leaves do that work for us without having to burn any fossil fuels to make fertilizers that would be awesome I'll remind you that without fertilizers without the Haber process to make fertilizers there would not be enough food to feed all the people on this planet so let's see I'm going to catch up with the feed for a sec I kind of get too focused on what's happening inside my head to always look at the feed so sorry about that let's see can't see high energy gamma rays we will I love that one and the alloy so it's cobalt and phosphorus as the alloy I think it's a very small amount of phosphorus in cobalt they in in their paper they were also using a I think it's a nickel zinc tin alloy as well for that they started with but found that the cobalt phosphorus one worked and you know it's like steel steel is iron and carbon but the amount of carbon and steel is really really tiny but very significant so yes yes Haber process has been very important and here's the here's here's the actual reference I'll copy the URL so you can read the abstract to it no one's mostly behind the paywall okay and you know if you are actually wanting some much better information about photosynthesis than than I'm going to provide here here's here's a link to a beautiful paper I found this is in Journal of Chemical Education the article itself is probably behind the paywall but the supplementary material is not and in the supplementary material you've got zip file containing an executable file that has a wonderful set of animations that show dynamically how how photosynthesis let's see so I keep saying things about blue goldberg machines fundamentally the photosynthesis that you're used to runs by something called the z scheme and here the z is on its side you know essentially essentially this essentially that thing can look like a letter z or z if you happen to be Canadian if you rotate it by 90 degrees clockwise or counterclockwise and this is actually a lovely little slide to summarize because what happens at one end of the process is that hydrogen and or that water has electrons stolen from it and and is turned into oxygen that happens at a manganese cluster and photosystem two paradoxically I'm going to talk about photosystem two first photosystem two is that bit takes four photons and promotes four electrons to a higher energy level and then these electrons are allowed to come down in energy they drive some chemical reactions along the way and then they're stored in photosystem one which also absorbs some photons these nice little rg biv h news are the photons it absorbs four photons that essentially take h plus and turn into h2 the h2 is stored in nadh another energy storage molecule short-term energy storage molecule in cells and ultimately it's used to take carbon dioxide and turn that into carbohydrate turns out that co2 to carbohydrates is nearly thermo neutral right so costs very little energy to do that although the pathway has to be catalyzed to make it happen so that's the I like that picture that that gets the idea across here's another picture that kind of tells you a little bit more detail of what's going on there's a manganese part of the photosystem the electrons from the water are stored at a very low energy level light promotes them up and then like a slinky these electrons cascade through a series of molecule alone or in pairs no just just single electron transfers they cascade through these various structures doing some work along the way making ATP from ADP things that your cells need to live things that everyone's cells need to live the ATP until they're stored in another place where they can be promoted again and then there's a whole bunch of stops along the way I'm going to show you some of these structures okay so here's a structure of photosystem 2 again it was a molecule of the of the month in I think 2004 it's a big molecule so I'm going to show you different views of it click okay so this is from the molecule of the month page the photosystem 2 ends up being a dimeric photo protein so it shows up as dimers it spends membranes so one is still trying to get things to work eventually it will so it spends the protein membrane that's this gray area on the left hand side of the slide oh there we go there's a gray area there's a lot of chlorophyll molecules that act as antennas and direct energy towards the central bit okay and all of this is held in place by the scaffolding of the probe of the coils the alpha helices okay let's see is there this is there evidence that in certain cases there are additional photosystems 3 4 and 5 there may be there's a lot of structural there's a lot of structural diversity in photosystem 1 and photosystem 2 if you go to different organisms but I think that the core of them involve the manganese as the oxygen generating center and the chlorophyll in fact there's several different types of chlorophyll A chlorophyll B there tend to be letters so yeah you know what I'm showing you isn't V for the system it is A for the system let's see so changing colors going over here so that little section is shown more detail on this side of the slide the right hand slide so erasing those we tend to have as I said a lot of antenna chlorophylls they direct their energy down into this part of the molecule chlorophyll ends up being where charge separation takes place and the electrons make their way down through this part of the molecule while the holes i.e. where the electrons came from come from that oxygen evolving center let's look at that guy in a little more detail the oxygen evolving center ends up being a cluster of manganese atoms and calcium you'd think it a cube of manganese oxygen and calcium um like with one vertex of the cube being a calcium and then there's another manganese kind of capping one of the faces I'll show you that in more detail in a 3d structure but that's where the water gets stripped of its protons and the oxygen atoms somehow come together there's a number of variety of hypotheses as to how the how the oxygens come together and it basically makes the O2 molecule oh um a ligand yeah these things are coordinated by the protein right so metal atoms metal atoms don't just float around in solution naked they're very shy what you think of as maybe a copper solution like nice blue copper solution is usually a copper two plus ion that has six water molecules attached to it usually a common number of things attached to transition metals especially six but it can vary from um well it can vary from two to nine in fact um if i'm going to be real pedantic about it but six is um the normal number i'm reminded reminded of something from multi python about five being the number of the counting i'm following along on my powerpoint at home and i'm trying to make sure that i know what i'm going to talk about um so at this point i can talk about some of the some of the structures i've got hidden here there and everywhere um let's see i think way above us i've got uh something that i will let's see if i click on it it gives me a note card yay uh let's edit it and make it a bit smaller rich click click click click i really enjoy giving these talks i actually double dip because i will be using um i will be using um this this talk actually i'll send my students in my bio and organic class to watch it as homework let's see again i hope i haven't crushed anyone with a protein there we go okay so that thing that thing let's move it down a little bit more i wish i could do this in real life like have rhino sized molecules just kind of hovering in front of my students so um this this thing is a um i won't say uh photosystem two from a different molecule i think this one's from a cyanobacterium uh the black spheres well there used to be spheres in blender but i got rid of a lot of um details so i could upload them without crashing the sim the black spheres are carbon atoms red are oxygen atoms um green is magnesium and in the center of this maybe i can rotate this so that the chlorophyll unit faces front now since the chlorophyll is actually buried within kind of harder harder to see okay that's that's not bad um if you um if you pan in on the chlorophyll the green atom surrounded by four blue atoms those are nitrogens uh you'll see you'll see the actual chlorophyll this is an antenna chlorophyll um and um it's actually got antennas around it the um most of this kind of um um black and red molecules that's your beta carotene beta carotene um has a lot of those double bonds it makes it like a wire um ends up funneling energy towards the magnesium or towards the chlorophyll sites um which then is used um by the rest of the photosystem too so yay um one thing you'll notice let me move this guy out of the way edit and then back up into the sky with you back i say there we go you know make sure he's high enough so that he doesn't interfere in any recordings okay so um one thing that you'll know this is um similarities between things like heme and here's a molecule of heme i'll bring it to the uh front in front of the screen um heme is found in your blood heme is found in hemoglobin heme is found in your liver in cytochrome p450s heme is found uh in plants in photosystem one photosystem two as an electron transfer uh destination um heme is found everywhere the little brown atom in the middle of the square of the four uh green atoms that's iron um um heme looks a lot like chlorophyll but there are some important differences and those differences have to do with um in the lower half of this molecule uh you have more double bonds in heme than you do in chlorophyll okay otherwise they look structurally very similar um and i've actually got a um kind of weird looking um chlorophyll molecule on my other side so let's let's move you out of the way and move you back into focus here yeah okay so move move that one up a little bit one of the things you'll notice on this particular chlorophyll is that um where the magnesium atom is i should rotate that where the magnesium atom is and bring you in the front is not planar it's not flat it's like a shape like a saddle right so where that green atom is the four nitrogens look as if they're in a tetrahedron rather than a square plane around so that's unusual uh usually the chlorophyll magnesium part is really flat and that's just that's just one of the like weirdest things i've seen uh recently um the um it kind of shows some of the power of the structural biology this this these models i show you are from x-ray crystallographic studies uh they are faithful representations of where the atoms actually are in these molecules they have been measured uh right they're not an artist conception or anything they're um have pretty much the validity of photographs of um you know photographs of mars i mean they are the data essentially uh so you know to find find a structure that's a little bit unusual um kind of uh requires some requires some explanation so i have no explanation as to why this one is is is weird looking you will notice that it reminds me of the um it reminds me of the um um molecular photovoltaic that i showed you earlier in that there's this long chain um attached to a donor site in this case the chain doesn't have double bonds in it though so i think it's more for positioning than for electronic purposes a heme theme yeah i think there's an evolutionary similarity because i think making these um hemes um is uh something that's been coded for um in genes and you know there's a um um conservation of um conservation of genes to generations especially if they're important for living things but they can be adapted for other purposes i think making a heme and then adding um functionality to the heme molecule and then shoving a magnesium in instead of an iron allows um you know is um you know probably um an efficient reuse of that machinery although i gotta say um usually i usually if i say something like that i'm wrong okay um moving on with some more let's see i'm gonna move this guy out of the way boom boom boom boom and hopefully i'm gonna yeah that's fine okay next slide is there click down one there we go all right so here's some structures i talked about those structures um beta carotene uh i think i've got a picture beta carotene somewhere at chlorophyll a i showed you uh chlorophyll molecule i showed you a heme i showed you the antenna structures and here's some cats uh these uh all of these guys over here um passed away this was taken about a month ago and um they had the window open and there were birdies outside so dad dad there's birds dad and then the two little girl cats are um really looking at one neurotic bird um hey cat so um photosystem 2 basically um takes the electrons ultimately away from water that makes h plus which gets used for things uh makes o2 which is a useful byproduct for us the h plus makes its way to other um uh rhub goldberg machines we'll call them um enzymes and the electrons get shunted through into photosystem one here's photosystem one um or actually here's some more pictures that i thought i would share with you uh some of the cats uh got some tiger lilies hey it's purple and green and uh we actually have on my campus a um calendar or um it's a it's a it's a sundial sculpture and during the summer we have deer that roam around this is actually right outside the science building uh so um you know this is uh two minutes away from my office it's actually quite lovely okay so photosystem one um doesn't look like my cats uh here's a structure again from molecules of the month from a cyanobacterium called uh now i have to pronounce it right uh cynicococcus elongatus um it's a trimer if you look at the um structure this would be a view from above it's actually got three repeating units um that are all pointing in i was circling that but um it's not it's not coming up for me right now oh there it is okay but basically basically yeah well that's that's part of one of the trimmers you can kind of see there's there would be three of them um where am i next slide so this is actually what it looks like when it's uh in the when it's in this membrane i keep saying cell membrane but i should say that for the synthesis happens uh in chloroplasts so this is a membrane that is um on the chloroplast which is within the cell right so there's going to be um ph differences inside the chloroplast versus outside the chloroplast that's going to drive some um energy storing chemistry and the cells are small or small and transparent enough so that light can penetrate into them to make these processes happen okay so the the red and blue indicate where the cell membrane go uh kind of reminds me of an iceberg because there's um chunk of stuff that is um that is uh kind of happening like within within the ribosome no not ribosome chloroplast there we go here's the business end of photosystem one remember photosystem two had manganese in it photosystem one has these iron clusters in those iron clusters are where the equivalents of electrons get stashed while um the molecules are waiting for um light to come in and promote them so um we've got let's see we've got the iron sulfur um clusters that i've already uh circled in orange um there's electron transports change so these are molecules in gray where um electrons uh can um flow towards um towards the chlorophyll molecules that are in green uh that um uh are where the charge separation uh takes place well notice there's all these little um green atoms each one of those represents the center of an antenna molecule that happens to be a chlorophyll so are we now it's like 31 i think so if we put all of this together if we put all of this together um we can um usually find uh four types of uh super complexes um in the in close vicinity on the membranes of the ribosomes right so we have a photosystem two um lovely little a lovely little uh von von Neumann machine right that acts as we've described it basically takes some uh photons it destroys water liberates h plus which gets used over here in um i haven't really talked about this this is a cytochrome uh type of molecule um and it uses h plus and some of those electrons to to make some work happen it recharges some of these um nadhs i think maybe it's just flavonoid over here we have photosystem one which is definitely making some nadh and over here we have the ATP synthase just like the one i talked about earlier let's see i don't always get i don't always get to circle things for this one of this viewer so you know when we think of ruby goldberg machines we think of very complicated machinery that makes something simple happen well the simple thing that happens is that we take some water and carbon dioxide and rearrange some atoms to make oh something like glucose or some some carbohydrate um but it goes through a lot uh steps to get there and you know each one of these organic structures those um biochemical structures is a little machine on its own okay so i've uh i've got just a couple of more things to say i was hoping to be a little more quicker than i am uh um from a pea plant okay so on these panels over here let me just show you let's see edit let's move them into the metal they are actually taking up quite a bit of quite a bit of space uh so for me i actually shut off my media these actually show you 3d rotating cross-eyed gifts or stereograms so let's see i'm clicking on my media to make make those happen and takes a little bit to load in the meantime i will open up a file and give you give you some links let go while i let those load so what are we looking there well these are crystal structures these are crystal structures of um the uh super complex um all of the um photosystem uh two from a pea plant there's only so much ram in my head um so i'm actually um hunting down hunting down a document i wanted to share in text on dates click here we go uh so the bottom panel shows the entire protein so if you zoom in on it you zoom in on it and our um you know not too far away if you click on it it'll just like um dominate your whole screen so you know press escape just zoom in on it with your mouse camera um for some people not everybody if you cross your eyes and overlay the images um you can see the rotation happening in three dimensions the very bottom panel is the complete um protein plus all of the machinery you can see how it's put together the alpha helices the little pink spirals kind of i mean they look like hamburgers to me um they basically provide a scaffolding for all of the other stuff to be in the correct position to make the chemistry happen um up here in the middle um i've deleted all the machinery and just shown you the protein itself this is one molecule right it's one molecule but like like a like when you're doing knitting it's basically one strand of um wool for example and it's knitted into all of these shapes this means that somewhere in this mess there is a beginning end and a end end i guess so this is all one shape and what it does if you look in the top panel is it holds and i got rid of a lot of stuff i got rid of all the beta carotines that we we don't actually need to look at um it has the chlorophylls plus all of the intermediate stages that you need to get electrons um out of the iron sulfur clusters to the to the chlorophylls in the photosystem one i guess it is um the little bright yellow orange dots are the iron sulfur clusters and you can see there's kind of some molecules that bridge towards where the green dots are and those those are basically the electron transport chain um so let's see moving to my next slide um i've got oh yeah well i'm almost i'm almost done here let me move the um panels out of the way i guess i've gotten myself hidden behind one there we go um i made a whole bunch i made a whole bunch of these 3d rotating stereograms and viewed in second life they're not as interesting um because you know second life has a little bit of uh lag to it um so um here's links to the uh rest that i made enter there you go um and uh if you open those in something like uh chrome um some of them are 30 megabyte rotate like single gift files so it might take a little bit to open but if you open them in chrome you can kind of see things in a little more detail and you can expand them uh so yeah feel free to copy the chat um nearby chat for quick so at this point i'm going to conclude okay so um hope you've enjoyed seeing some structures seeing some data uh kind of getting a sense for how things work for um in uh photosynthesis um and um you know i want to thank uh um students uh members science circles shantal and jess especially for everything they do everyone in the board as well i thank my students and uh colleagues and nsf for um their generous support of my current research um you know the dp all c for hosting my animated gifts that that i gave you um and all my cats for their patience because i take lots of pictures of my cats so i okay i saw scissors he asked the question how exactly are the colors green and purple central to these processes it's more of a byproduct um the rhodopsin happens to be um purple uh and that of course is a um um consequence of the um light profile that they absorb uh and actually you know i heard once upon a time that uh in the early earth the rhodopsin um you know under low oxygen conditions um was a um early and dominant uh photosystem so it may have been and and i've heard it suggested that it may have been that uh photosynthetic plants um evolved to absorb green or you know evolved their um absorption uh profile because there was complementary to rhodopsin i i don't know the validity of of this but i do offer it as an explanation because um if you actually look at the absorption profiles the uvb spectra of these things uh there is a complementarity so the light that the um rhodopsin using molecules um organisms uh wasn't using was available um as maybe an evolutionary niche for the um plants that eventually came to dominate so i don't know um but you know that is a possibility uh let's see zoom in closely 3d rotating yes excellent um and let's see i've had a couple of messages as well from from people and uh yeah um so uh let me move forward a slide here's some resources um essentially what i do is i take i use jmail um which is available there i'll actually put the links in um in local local chat here we go there's another drawing of my cats we'll see so source for jmail is that um and it's a nice molecular um drawing program um you can get x-ray crystal structure data for um biological um molecules um for inorganic molecules for minerals uh from uh these sites let's see um crystallography dot net small molecules uh rough does um more minerals it didn't come up with everything that i had copied so let's try that again weird okay um oh i didn't copy the actual thing all right well anyway and i use blender basically um basically i just uh take um export the uh structure from jmail as x3d files imported into blender do some editing like you can get rid of like if there's a sphere inside a sphere no i'll get rid of the inner sphere um and then um um you know combine all of the objects into one mesh decimate the mesh so that it's not so big and then it can be uploaded as a dae final into second life so so yeah um anyway so uh that's my talk hope you enjoyed it i'm um happy to answer any questions as always so um hey all right well um if uh if if there aren't many questions then uh i'm going to wish everyone a happy thanksgiving because uh that's happening this week i get a week off from classes so i'll actually be traveling for some collaboration next week and my cats didn't eat well no they're sitting there asleep although i've got one that was grabbing my foot during uh during my talk and now she's inside um inside this little box that i have next to my feet awesome well um i'm going i'm going to sign off uh i'll uh tidy up some of these things later today and tomorrow for the next speaker and uh i thank you all for your attention