October 2001: Photosystem ILook around. Just about everywhere that you go, you will seesomething green. Plants cover the Earth, and their smallercousins, algae and photosynthetic bacteria, can be found innearly every corner. Everywhere, they are busy convertingcarbon dioxide into sugar, creating living organic moleculesout of air using the energy of sunlight as power. This process,termed photosynthesis, provides the material foundation onwhich all life rests.

Capturing LightAt the center of photosynthesis is aclass of proteins termedphotosynthetic reaction centers.These proteins capture individuallight photons and use them toprovide power for building sugar.The example shown here isphotosystem I (PDB entry 1jb0 ), oneof the two large reaction centersused in cyanobacteria, algae andplants. Photosystem I is a trimericcomplex that forms a large disk. Incells, the complex floats in amembrane (the membrane isindicated by the two red lines in thelower picture) with the large flatfaces exposed above and below themembrane.

Colorful CofactorsEach of the three subunits of photosystem I is a complex of adozen proteins, which together support and position over ahundred cofactors. Some of these cofactors, shown here ingreen and orange, are exposed around the edge of thecomplex and many others are buried inside. Cofactors aresmall organic molecules that are used to perform chemicaltasks that are beyond the capabilities of pure proteinmolecules. The cofactors in photosystem I include many small,

October 2001: Photosystem Ibrightly-colored molecules such as chlorophyll, which is brightgreen, and carotenoids, which are orange. The colors are, infact, the reason that these molecules are useful: the colors arean indication that the cofactors absorb other colors strongly.For instance, chlorophyll absorbs blue and red light, leavingthe beautiful greens for us to see. The energy from theseabsorbed colors is then captured to perform photosynthesis.

The Electron Transfer ChainThe heart of photosystem I is an electron transfer chain, achain of chlorophyll (shown in green), phylloquinone (shown inorange) and three iron-sulfur clusters (yellow and red at thetop). These cofactors convert the energy from light into energythat the cell can use. The two chlorophyll molecules at thebottom capture the light first. When they do, an electron isexcited into a higher energy state. Normally this electronwould quickly decay, releasing heat or releasing a new photonof slightly lower energy. But before this has a chance tohappen, photosystem I passes this electron on, up the chain ofcofactors. At the top, the electron is transferred to a smallferredoxin protein (not shown here), which then ferries it on tothe other steps of photosynthesis. At the bottom, the hole leftby this wandering electron is filled by an electron from anotherprotein, plastocyanin.

October 2001: Photosystem IThis may seem rather mundane until you see the trick that thephotosystem is performing. The proteins at both ends of thisprocess, ferredoxin and plastocyanin, are carefully chosen.Because of the special design of their own cofactors, it is moredifficult to add an electron to ferredoxin than it is toplastocyanin--normally, the flow would be in the oppositedirection. But photosystem I uses the energy from light toenergize the electron, moving it in a difficult direction. Then,since the electron is placed in such an energetic position, itcan be used to perform unfavorable duties such as theproduction of sugar from carbon dioxide.Photosynthetic CousinsDifferent photosystems are used by different photosyntheticorganisms. Higher plants, algae, and some bacteria have thephotosystem I shown here and a second one termedphotosystem II. A low resolution structure of photosystem II isavailable in PDB entry 1fe1 (not shown here). Photosystem IIuses water instead of plastocyanin as the donor of electrons tofill the hole left when the energized electron is passed up thechain. When it grabs electrons from a water molecule,photosystem II splits the water and releases oxygen gas. Thisreaction is the source of all of the oxygen that we breathe.Some photosynthetic bacteria contain a smaller photosyntheticreaction center, such as the one shown on the right (PDB entry1prc ). As in photosystem I, a stack of chlorophyll and othercofactors transfer a light-energized electron up to an energeticelectron carrier.

October 2001: Photosystem IHarvesting LightOf course, plants do not rely on the slim chance of a photonrunning into one tiny chlorophyll molecule in the middle of thereaction center. As with all things in life, cells have found aneven better way. Photosystem I, shown here looking from thetop, contains an electron transfer chain, colored here in brightcolors, at the center of each of the three subunits. Each one issurrounded by a dense ring of chlorophyll and carotenoidmolecules that act as antennas. In this picture, the protein istransparent so that only the cofactors are seen. These antennamolecules each absorb light and transfer energy to theirneighbors. Rapidly, all of the energy funnels into the threereaction centers, where is captured to create activatedelectrons.

October 2001: Photosystem IExploring the StructureYou can look at the many photosystem I cofactors of theelectron transfer chain and the antenna in PDB entry 1jb0 . Onlyone of the three subunits is included in the file, but you willfind that this is complicated enough. If you display only thecofactors, you will get a picture like the one shown here. Thispicture shows the electron transfer chain at the center, drawnin spacefilling spheres. Two special chlorophyll molecules,residues 1140 and 1239, are also shown in spheres andcolored green. These two chlorophyll molecules act as a bridgebetween the reaction center in the middle and the manymolecules in the surrounding antenna. The many antennacofactors are shown here in bond representation with smallspheres for the magnesium ions at the center of eachchlorophyll.

November 2004: Photosystem IIThree billion years ago, our world changed completely. Before then,life on Earth relied on the limited natural resources found in thelocal environment, such as the organic molecules made bylightning, hot springs, and other geochemical sources. However,these resources were rapidly being used up. Everything changedwhen these tiny cells discovered a way to capture light and use it topower their internal processes. The discovery of photosynthesisopened up vast new possibilities for growth and expansion, and lifeon the earth boomed. With this new discovery, cells could takecarbon dioxide out of the air and combine it with water to createthe raw materials and energy needed for growth. Today,photosynthesis is the foundation of life on Earth, providing (with afew exotic exceptions) the food and energy that keeps everyorganism alive.The Colors of PhotosynthesisModern cells capture light using photosystem proteins, such as theone pictured here from PDB entry 1s5l . These photosystems use acollection of highly-colored molecules to capture light. These light-absorbing molecules include green chlorophylls, which arecomposed of a flat organic molecule surrounding a magnesium ion,and orange carotenoids, which have a long string of carbon-carbondouble bonds. These molecules absorb light and use it to energizeelectrons. The high-energy electrons are then harnessed to powerthe cell.

November 2004: Photosystem IIEnergetic ElectronsPhotosystem II is the first link in the chain of photosynthesis. Itcaptures photons and uses the energy to extract electrons fromwater molecules. These electrons are used in several ways. First,when the electrons are removed, the water molecule is broken intooxygen gas, which bubbles away, and hydrogen ions, which areused to power ATP synthesis. This is the source of all of the oxygenthat we breathe. Second, the electrons are passed down a chain ofelectron-carrying proteins, getting an additional boost along theway from photosystem I. As these electrons flow down the chain,they are used to pump hydrogen ions across the membrane,providing even more power for ATP synthesis. Finally, the electronsare placed on a carrier molecule, NADPH, which delivers them toenzymes that build sugar from water and carbon dioxide.The Reaction CenterThe heart of photosystem II is thereaction center, where the energy oflight is converted into the motion ofenergized electrons. At the center isa key chlorophyll molecule. When itabsorbs light, one of its electrons ispromoted to a higher energy. Thisenergized electron then hopsdownward, through several otherpigmented molecules, on toplastoquinone A, and finally over toplastoquinone B. When it getsenough electrons, this small quinoneis released from the photosystem,and it delivers its electrons to thenext link in the electron-transferchain. Of course, this leaves theoriginal chlorophyll without anelectron. The upper half of thereaction center has the job ofreplacing this electron with a low-energy electron from water. Theoxygen-evolving center strips anelectron from water and passes it toa tyrosine amino acid, which thendelivers it to the chlorophyll, makingit ready to absorb another photon.

November 2004: Photosystem IIHarvesting LightOf course, this whole process wouldn't be very efficient if plantshad to wait for photons to hit that one special chlorophyll in thereaction center. Fortunately, the energy from a light-excitedelectron is easily transferred through the process of resonanceenergy transfer. Thanks to the mysteries of quantum mechanics,the energy can jump from molecule to molecule, as long they areclose enough to each other. To take advantage of this property,photosystems have large antennas of light-absorbing moleculesthat harvest light and transfer their energy inwards to the reactioncenter. Plants even build special light-harvesting proteins that sitnext to the photosystems and assist with light collection. Thepicture shows a top view of photosystem II (PDB entry 1s5l ),showing all of the light-absorbing molecules inside. The centralchlorophyll molecule of the reaction center is shown with the arrow(notice the second reaction center in the bottom half--photosystemII is composed of two identical halves). The little triangularmolecules at top and bottom, stuffed full of chlorophyll andcarotenoids, are light-harvesting proteins (PDB entry 1rwt ).

November 2004: Photosystem IIExploring the StructureThe oxygen-evolving center of photosystem II is a complicatedcluster of manganese ions (magenta), calcium (blue green) andoxygen atoms (red). It grips two water molecules and removes fourelectrons, forming oxygen gas and four hydrogen ions. The actualbinding site of the two water molecules is not known for certain,but in the PDB structure 1s5l a bicarbonate ion is bound to thecluster, providing a clue for location of the active site. The pictureshows two oxygen atoms from this ion (colored blue): one is boundto a manganese ion, the other is bound to the calcium ion. Noticethat the oxygen-evolving center is surrounded by histidines,aspartates and glutamates, which hold it in place. The tyrosineshown in the middle forms a perfect bridge between the water siteand the light-capturing chlorophyll.