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Biology notes


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Biology notes

  1. 1. Photosystems are functional and structural units of protein complexes involved inphotosynthesis that together carry out the primary photochemistry of photosynthesis: theabsorption of light and the transfer of energy and electrons. They are found in the thylakoidmembranes of plants, algae and cyanobacteria (in plants and algae these are located in thechloroplasts), or in the cytoplasmic membrane of photosynthetic bacteria.[edit] Reaction centersAt the heart of a photo system lies the Reaction Center, which is an enzyme that uses light toreduce molecules. In a photo system, this Reaction Center is surrounded by light-harvestingcomplexes that enhance the absorption of light and transfer the energy to the Reaction Centers.Light-Harvesting and Reaction Center complexes are membrane protein complexes that aremade of several protein-subunits and contain numerous cofactors. In the photosyntheticmembranes, reaction centers provide the driving force for the bioenergetic electron and protontransfer chain. When light is absorbed by a reaction center (either directly or passed byneighbouring pigment-antennae), a series of oxido-reduction reactions is initiated, leading to thereduction of a terminal acceptor. Two families of reaction centers in photosystems exist: type Ireaction centers (such as photo system I (P700) in chloroplasts and in green-sulphur bacteria) andtype II reaction centers (such as photosystem II (P680) in chloroplasts and in non-sulphur purplebacteria). Each photosystem can be identified by the wavelength of light to which it is mostreactive (700 and 680 nanometers, respectively for PSI and PSII in chloroplasts), the amount andtype of light-harvesting complexes present and the type of terminal electron acceptor used. TypeI photosystems use ferredoxin-like iron-sulfur cluster proteins as terminal electron acceptors,while type II photosystems ultimately shuttle electrons to a quinone terminal electron acceptor.One has to note that both reaction center types are present in chloroplasts and cyanobacteria,working together to form a unique photosynthetic chain able to extract electrons from water,creating oxygen as a byproduct.[edit] StructureA reaction center comprises several (>10 or >11) protein subunits, providing a scaffold for aseries of cofactors. The latter can be pigments (like chlorophyll, pheophytin, carotenoids),quinones, or iron-sulfur clusters.[edit] Relationship between Photosystems I and IIFor oxygenic photosynthesis, both photosystems I and II are required. Oxygenic photosynthesiscan be performed by plants and cyanobacteria; cyanobacteria are believed to be the progenitorsof the photosystem-containing chloroplasts of eukaryotes. Photosynthetic bacteria that cannotproduce oxygen have a single photosystem called BRC, bacterial reaction center.
  2. 2. The photosystem I was named "I" since it was discovered before photosystem II, but this doesnot represent the order of the electron flow.When photosystem II absorbs light, electrons in the reaction-center chlorophyll are excited to ahigher energy level and are trapped by the primary electron acceptors. To replenish the deficit ofelectrons, electrons are extracted from water by a cluster of four Manganese ions in photosystemII and supplied to the chlorophyll via a redox-active tyrosine.Photoexcited electrons travel through the cytochrome b6f complex to photosystem I via anelectron transport chain set in the thylakoid membrane. This energy fall is harnessed, (the wholeprocess termed chemiosmosis), to transport hydrogen (H+) through the membrane, to the lumen,to provide a proton-motive force to generate ATP. The protons are transported by theplastoquinone. If electrons only pass through once, the process is termed noncyclicphotophosphorylation.When the electron reaches photosystem I, it fills the electron deficit of the reaction-centerchlorophyll of photosystem I. The deficit is due to photo-excitation of electrons that are againtrapped in an electron acceptor molecule, this time that of photosystem I.ATP is generated when the ATP synthase transports the protons present in the lumen to thestroma, through the membrane. The electrons may either continue to go through cyclic electrontransport around PS I or pass, via ferredoxin, to the enzyme NADP+ reductase. Electrons andhydrogen ions are added to NADP+ to form NADPH. This reducing agent is transported to theCalvin cycle to react with glycerate 3-phosphate, along with ATP to form glyceraldehyde 3-phosphate, the basic building-block from which plants can make a variety of substancesPhotosystem II (or water-plastoquinone oxidoreductase) is the first protein complex in theLight-dependent reactions. It is located in the thylakoid membrane of plants, algae, andcyanobacteria. The enzyme captures photons of light to energize electrons that are thentransferred through a variety of coenzymes and cofactors to reduce plastoquinone toplastoquinol. The energized electrons are replaced by oxidizing water to form hydrogen ions andmolecular oxygen. By obtaining these electrons from water, photosystem II provides theelectrons for all of photosynthesis to occur. The hydrogen ions (protons) generated by theoxidation of water help to create a proton gradient that is used by ATP synthase to generate ATP.The energized electrons transferred to plastoquinone are ultimately used to reduce NADP+ toNADPH or are used in Cyclic Photophosphorylation.Structure
  3. 3. Cyanobacteria photosystem II, Monomer, PDB 2AXT.Photosystem II (of cyanobacteria and green plants) is composed of around 20subunits(depending on the organism) as well as other accessory, light-harvesting proteins. Eachphotosystem II contains at least 99 cofactors: 35 chlorophyll a, 12 beta-carotene, two pheophytin,two plastoquinone, two heme, one bicarbonate, 20 lipid, the Mn4CaO5 cluster (including chlorideion), and one non heme Fe2+ and two putative Ca2+ ion per monomer.[1] There are differentcrystal structures of photosystem II. The PDB accession codes for this protein are 3ARC,3BZ1,3BZ2(3BZ1 and 3BZ2 are monomeric structures of the Photosystem II dimer) [1] 2AXT, 1S5L,1W5C, 1ILX, 1FE1, 1IZL. Photosystem II Light Harvesting complex protein Identifiers Symbol PSII Pfam PF00421 InterPro IPR000932 TCDB 3.E.2 OPM superfamily 2
  4. 4. OPM protein 3arc [show]Available protein structures: Protein Subunits (only with known function)Subunit Function Reaction center Protein, binds Chlorophyll P680, pheophytin,D1 beta-carotene,quinone and manganese centerD2 Reaction center ProteinCP43 Binds manganese centerCP47PsbO Manganese Stabilizing Protein Coenzymes/CofactorsMolecule FunctionChlorophyll Absorbs lightBeta-Carotene quench excess photoexcitation energyHeme b559 also Protoporphyrin IX containing ironPheophytin Primary electron acceptorPlastoquinone Mobile intra-thylakoid membrane electron carrierManganese center also known as the oxygen evolving center, or OEC[edit] Oxygen-Evolving Complex (OEC)Proposed structure of Manganese CenterThe oxygen-evolving complex is the site of water oxidation. It is a metallo-oxo clustercomprising four manganese ions (in oxidation states ranging from +3 to +5) and one divalentcalcium ion. When it oxidizes water, producing dioxygen gas and protons, it sequentially
  5. 5. delivers the four electrons from water to a tyrosine (D1-Y161) sidechain and then to P680 itself.The structure of the oxygen-evolving complex is still contentious. The structures obtained by X-ray crystallography are particularly controversial, since there is evidence that the manganeseatoms are reduced by the high-intensity X-rays used, altering the observed OEC structure.However, crystallography in combination with a variety of other (less damaging) spectroscopicmethods such as EXAFS and electron paramagnetic resonance have given a fairly clear idea ofthe structure of the cluster. One possibility is the cubane-like structure.[2] In 2011 the OEC ofPSII was resolved to a level of 1.9 angstroms revealing five oxygen atoms serving as oxo bridgeslinking the five metal atoms and four water molecules bound to the Mn4CaO5 cluster; more than1,300 water molecules were found in each photosystem II monomer, some forming extensivehydrogen-bonding networks that may serve as channels for protons, water or oxygenmolecules.[3][edit] Water splittingWater-splitting process: Electron transport and regulation. The first level (A) shows the originalKok model of the S-states cycling, the second level (B) shows the link between the electrontransport (S-states advancement) and the relaxation process of the intermediate S-states ([YzSn],n=0,1,2,3) formationPhotosynthetic water splitting (or oxygen evolution) is one of the most important reactions on theplanet, since it is the source of nearly all the atmospheres oxygen. Moreover, artificialphotosynthetic water-splitting may contribute to the effective use of sunlight as an alternativeenergy-source.The mechanism of water oxidation is still not fully elucidated, but we know many details aboutthis process. The oxidation of water to molecular oxygen requires extraction of four electronsand four protons from two molecules of water. The experimental evidence that oxygen isreleased through cyclic reaction of oxygen evolving complex (OEC) within one PSII wasprovided by Pierre Joliot et al.[4] They have shown that, if dark-adapted photosynthetic material(higher plants, algae, and cyanobacteria) is exposed to a series of single turnover flashes, oxygenevolution is detected with typical period-four damped oscillation with maxima on the third andthe seventh flash and with minima on the first and the fifth flash (for review see [5]). Based onthis experiment, Bessel Kok and co-workers [6] introduced a cycle of five flash-induced
  6. 6. transitions of the so-called S-states, describing the four redox states of OEC: When fouroxidizing equivalents have been stored (at the S4-state), OEC returns to its basic and in the darkstable S0-state. Finally, the intermediate S-states [7] were proposed by Jablonsky and Lazar as aregulatory mechanism and link between S-states and tyrosine Z.Cyclic photophosphorylation is the production of some ATP in the light dependent stage ofphotosynthesis. No photoylsis of water occurs and therefore no reduced NADP is producedeither. Only photosystem one is involved here and as light is absorbed by the photosystem, twoelectrons are released which are accepted by the electron transfer chain. As the electrons aretransferred along the chain, energy is released which pumps protons across the thylakoidmembrane. A proton gradient forms and the protons diffuse through protein channels associatedwith ATP synthase enzymes, the proton motive force along with the enzyme combine ADP andinorganic phosphate atom to create ATP. The flow of protons which creates the ATP ischemiosmosis. The ATP can then be used in the light independent stage of photosynthesis or toactively transport potassium ions into the guard cells, so they become turgid as a result of waterentering by osmosis. This causes the stomata to open and carbon dioxide can readily diffuse in -increasing the rate of photosynthesisLight-Dependent and Light-Independent ReactionsThe light reactions, or the light-dependent reactions, are up first. We call them either and bothnames. The whole process looks a little like this:Do not freak out or fill your head with all the complicated names in that diagram. No—stop rightthere. All in all, the process is simpler than it looks. In the light-dependent reactions ofphotosynthesis, the energy from light propels the electrons from a photosystem into a high-energy
  7. 7. state. In plants, there are two photosystems, aptly named Photosystem I and Photosystem II,located in the thylakoid membrane of the chloroplast. The thylakoid membrane absorbs photonenergy of different wavelengths of light.Here again is our friend the chloroplast. All exposed the way he is, he kind of reminds us of a boatwith green checkers in it:Image sourceEven though the two photosystems absorb different wavelengths of light, they work similarly. Eachphotosystem is made of many different pigments. Some of these pigments can be described asabsorption pigments, and others are considered action pigments.The absorption pigments transfer the energy from sunlight to another pigment; at each transfer,the absorption pigments pass the photon energy to another pigment that absorbs a similar or lowerwavelength of light. Remember when we said that light is funky and acts like it has both particles andwaves? A photon is what we call the particle-like aspect of light. In other words, a photon is the basicunit of light.
  8. 8. Anyway, eventually, the energy makes it to the reaction center, or action pigment. At this point, thephotosystem loses a highly charged electron to adjacent oxidizing agents, or electron acceptors, inthe electron transport chain. TSince the photosystem has lost an electron, it no longer has aneutral charge and has instead become a positively charged photosystem.The positively charged photosystem creates a scenario similar to one that might occur if Twilightstars Robert Pattinson and Kristen Stewart made a surprise appearance at your local high school.You, like the electrons in the photosystem, would be attracted to their presence even if you hatedthem. (You would. Admit it.) The positively charged photosystem attracts electrons from water (H2O)that can then be excited by light energy. When exactly four electrons are removed from H2O, oxygen(O2) is generated. Why, you ask? If two water molecules have four hydrogens that lose fourelectrons, exactly four hydrogen ions (H+) and two oxygens are left. Dont believe us? Count it outfor yourself.4Side note: since hydrogen normally only has 1 proton and 1 electron, the four hydrogen atoms thathave each lost one electron are each referred to as H+. Since each H+ is now without an electron,there is only one proton remaining in the hydrogen atom. At some point, scientists became lazy andstarted equating H+ with the word proton. If you think about it, they are in fact equivalent.Back to regularly scheduled programming. The protons are then moved into the thylakoid lumen ofthe chloroplast using the power of the electron transport chain. This move results in a higherconcentration of protons in the lumen than in the stroma of the chloroplast.With so much positivity around, the protons get a little upset and try to equalize their distribution inthe chloroplast by moving from the lumen to the stroma to reach equilibrium (read: equal numbersof protons in both places). The rush of protons moving into the stroma is called a proton gradient.When protons move down the gradient, with down referring to the direction of the area containingfewer protons, the protons are grabbed by enzymes that bring the protons together with theelectrons from the electron transport chain. This event ultimately results in the making of adenosinetriphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADPH) from theadenosine diphosphate (ADP) and nicotinamide adenine dinucleotide phosphate ion (NADP+)that were hanging around nearby.Now that everyone is partying it up in the stroma, it becomes the perfect location for the next stageof photosynthesis, the light-independent reactions.Pictures are worth the thousand words that may or may not have just whizzed by your head as youwere reading. Here is a much-simplified version of the earlier picture:
  9. 9. Did you miss something, or do we just suck at drawing these pictures? Nope. Photosystem II isahead of Photosystem I. You might ask, "What the heck happened, Shmoop?" Well, scientistsactually discovered Photosystem II before Photosystem I, and instead of changing the names whenthey found the other photosystem, they just named them in reverse. We know; its very annoying.As you€™ve probably gathered by now, the light-dependent reactions fuel the second stage ofphotosynthesis called the light-independent reactions. Our good buddy carbon dioxide (CO2)provides an excellent source of carbon for making carbohydrates. However, conversion of one mole(one mole is an amount equal to 6.023 × 1023 molecules) of CO2 to one mole of the carbohydrateCH2O requires a lot of energy. And we mean a lot.Guess what? The ATP and NADPH generated in the earlier light Mreactions are strong reducingagents (electron donors) and are able to donate the necessary electrons to make carbohydrates.Altogether, the conversion of one mole of CO2 to one mole of CH2O requires two moles of NADPHand three moles of ATP. If you do the math, thats a heck of a lot of molecules. The cell then usesATP and NADPH to make carbohydrates in the Calvin cycle. We could use a Calvin and Hobbescartoon right about now.A key player in the Calvin cycle is ribulose-1,5-bisphosphate carboxylase oxygenase(affectionately called RuBisCo—thank goodness for nicknames), an enzyme that "fixes" CO2 to a
  10. 10. 5-carbon compound called ribulose-1,5-bisphosphate (RuBP). The oxygen in CO2 is released asH2O. Immediately after RuBisCo catalyzes the attachment of the carbon from CO2 to the 5-carbonRuBP, the new 6-carbon compound is broken down into two 3-carbon compounds calledphosphoglycerate (PGA, and no, it does not know how to golf). Since these 3-carbon compoundswere the first compounds to be identified in the plants, they were named C3 plants. It was originallythought that RuBisCo was catalyzing the attachment of carbon to a 2-carbon molecule to make a 3-carbon molecule. Oopsies. And we thought RuBisCo was a cookie company at first, too.RuBisCo is actually a poor enzyme. Sorry, RuBie. It is slow at catalyzing the attachment of CO2 toRuBP. To make matters worse, RuBisCo is also capable of catalyzing another less-than-beneficialreaction. This reaction is called photorespiration, and it occurs when the concentration of CO2drops too low relative to the concentration of O2 in the cell. Photorespiration begins when RuBisCouses O2 instead of CO2 and adds it to RuBP.While CO2 is eventually produced in this reaction, and O2 is consumed, the reaction does not seemto produce any useful energy forms. The origination and purpose of photorespiration is controversialand still under active study by scientists. In an attempt to overcome the deficiency of RuBisCo, theplant cell produces a whopping ton of the enzyme. If this sounds slightly masochistic, it kind of is,which is why photorespiration has been labeled an outdated evolutionary relic. However, RuBisCo isthought to be the most abundant protein on Earth.2Right…this not a moan fest about RuBisCo. We were explaining the Calvin cycle. When RuBisCocatalyzes the attachment of CO2 to the 5-carbon RuBP, the Calvin cycle begins. Reactions areinitiated to rebuild RuBP from PGA. In this process, 1 molecule of glyceraldehyde-3-phosphate(G3P), a 3-carbon sugar, is removed from the cycle. Altogether, 1 molecule of G3P is producedusing 3 molecules of CO2, 9 molecules of ATP, and 6 molecules of NADPH. This 3-carbon sugar canbe exported to the cytoplasm to make sucrose (a sugar and a carbohydrate), which is then movedthroughout the plant for energy use. Alternatively, sucrose can be converted into anothercarbohydrate, starch, and then stored in the chloroplast as a type of energy reserve
  11. 11. Brain SnacksThere are carnivores that undergo photosynthesis. Meat-eating plants do not eat for energy; they eatto obtain nutrients, such as nitrogen and phosphate, to build the proteins needed for photosynthesis.Living organisms besides plants do photosynthesis. One "biological masterpiece," the sea slugElysia chlorotica, is able to conduct photosynthesis by extracting DNA and chloroplasts from its plantfood source. Sneaky, sneaky.In seeded plants, chloroplasts do not develop unless the seedlings are exposed to light. Thisprocess is called photomorphogenesis.3Weed killers called herbicides work by targeting enzymes used in the light reactions ofphotosynthesis. Come here, little chloroplasts.The light-independent reactions of photosynthesis are chemical reactions that convert carbondioxide and other compounds into glucose. These reactions occur in the stroma, the fluid-filledarea of a chloroplast outside of the thylakoid membranes. These reactions take the light-dependent reactions and perform further chemical processes on them. There are three phases to
  12. 12. the light-independent reactions, collectively called the Calvin cycle: carbon fixation, reductionreactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.Despite its name, this process occurs only when light is available. Plants do not carry out theCalvin cycle by night. They, instead, release sucrose into the phloem from their starch reserves.This process happens when light is available independent of the kind of photosynthesis (C3carbon fixation, C4 carbon fixation, and Crassulacean Acid Metabolism); CAM plants storemalic acid in their vacuoles every night and release it by day in order to make this processwork.[1]Contents[hide] 1 Coupling to other metabolic pathways 2 Light-dependent regulation 3 Further reading 4 External links 5 References[edit] Coupling to other metabolic pathwaysThese dark reactions are closely coupled to the thylakoid electron transport chain as reducingpower provided by NADPH produced in the photosystem I is actively needed. The process ofphotorespiration, also known as C2 cycle, is also coupled to the dark reactions, as it results froman alternative reaction of the Rubisco enzyme, and its final byproduct is also anotherglyceraldehyde-3-P.TYHHHHHHHHHHHHT[edit] Light-dependent regulationMain article: Light-dependent reactionsDespite its widespread names (both light-independent and dark reactions), these reactions do notoccur in the dark or at night. There is a light-dependent regulation of the cycle enzymes, as thethird step requires reduced NADP; and this process would be a waste of energy, as there is noelectron flow in the dark.There are 2 regulation systems at work when the cycle needs to be turned on or off:thioredoxin/ferredoxin activation system, which activates some of the cycle enzymes, and theRubisco enzyme activation, which involves its own activase.The thioredoxin/ferredoxin system activates the enzymes glyeraldehyde-3-P dehydrogenase,glyceraldehyde-3-P phosphatase, fructose-1,6-bisphosphatase, sedoheptulose-1,7-
  13. 13. bisphosphatase, and ribulose-5-phosphatase kinas, which are key points of the process. Thishappens when light is available, as the ferredoxin protein is reduced in the photosystem Icomplex of the thylakoid electron chain when electrons are circulating through it.[2] Ferredoxinthen binds to and reduces the thioredoxin protein, which activates the cycle enzymes by severinga cystine bond found in all these enzymes. This is a dynamic process as the same bond is formedagain by other proteins that deactivate the enzymes. The implications of this process are that theenzymes remain mostly activated by day and are deactivated in the dark when there is no morereduced ferredoxin available.The enzyme Rubisco has its own activation process, which involves a more complex process. Itis necessary that a specific lysine amino acid be carbamylated in order to activate the enzyme.This lysine binds to RuBP and leads to a non-functional state if left uncarbamylated. A specificactivase enzyme, called Rubisco activase, helps this carbamylation process by removing oneproton from the lysine and making the binding of the carbon dioxide molecule possible. Eventhen the Rubisco enzyme is not yet functional, as it needs a magnesium ion to be bound to thelysine in order to function. This magnesium ion is released from the thylakoid lumen when theinner PH drops due to the active pumping of protons from the electron flow. Rubisco activaseitself is activated by increased concentrations of ATP in the stroma caused by its phosphorylation The light-independent reactions of photosynthesisThese involve the reduction of carbon dioxide using reduced NADP and ATP produced in the light-dependent reactions of photosynthesis.The reactions are known as the Calvin cycle, and they take place in the stroma of the chloroplast. Pass the mouse pointer over this diagram for more information.
  14. 14. =[Although the cycle is quite complicated, there are not too many compounds that need to be knownabout at this level: No of No of Compound C atoms phosphates Ribulose bisphosphate 5 2 (RUBP)
  15. 15. Glycerate 3-phosphate 3 1 (GP) Triose phosphate 3 1 (TP) Ribulose monophosphate 5 1 (RuP)There are effectively 3 stages to this process:1) Carbon dioxide fixationThis process is called fixation because carbon dioxide from the air is converted into an organiccompound which cannot move away.It is probably convenient to consider 6 molecules of carbon dioxide entering the cycle, so that the nextstep below occurs 6 times.Carbon dioxide reacts with ribulose bisphosphate RuBP.For this reason RuBP is called a CO2 acceptor.Yet another way of saying this is that RuBP is carboxylated.This occurs under the influence of the enzyme ribulose bisphosphate carboxylase (RUBISCO) which issaid to be the most abundant protein on the planet.Ribulose bisphosphate has 5 carbon atoms and 2 phosphate groups, and by accepting one more carbonatom from CO2 it should be converted into a 6 carbon, 2 phosphate compound. However ...This compound is immediately converted into 2 molecules of glycerate 3-phosphate (GP), whichcontains 3 carbons and one phosphate group.For every 6 molecules of CO2 entering the cycle, 12 molecules of GP are produced.This pathway is called C3 carbon fixation because the first product is a 3-carbon compound. Some plantshave an alternative pathway - C4 carbon fixation - in which the 4-carbon compound oxalacetate (OAA) isproduced and others have a CAM pathway.
  16. 16. 2) Carbon dioxide reductionThere are several published versions of this section, varying in complexity, and using differentterminology.This stage is so called because when CO2 reacts with H from reduced NADP it gains hydrogen and losesoxygen to become CH2O, the empirical (simplest) formula for carbohydrates. Reduction is loss of oxygen,or reaction with hydrogen, or gain of electrons. However the CO2 is now part of glycerate 3-phosphate(GP).Glycerate 3-phosphate (GP) is converted into triose phosphate (TP) using reduced NADP and ATP.The reduced NADP provides the reducing power (hydrogen) and is converted back to NADP which isthen reduced again in the light-dependent reactions.ATP is also used to provide energy for the conversion. It is converted into ADP + Pi, which arereconverted into ATP in the light-dependent reactions.Some of the triose phosphate (two molecules out of the twelve) is removed from the cycle, to beconverted into glucose, or other molecules such as starch, lipid or protein.3) Ribulose bisphosphate regenerationIn a complex series of reactions, the remaining ten molecules of TP are converted into 6 molecules ofthe 5-carbon compound ribulose monophosphate(10x3C=6x5C, but some phosphates are lost from the cycle).Ribulose monophosphate is converted into ribulose bisphosphate, using a phosphate group from ATP.Ribulose bisphosphate reacts with/accepts carbon dioxide/becomes carboxylated, to keep the cycleoperating again ...