My related essay on Cell Energy is here: Cell Energy
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Reference
         Typical values
** World's best photosynthesis block diagram
Short photosynthesis Q&A
Things (almost) no one tells you
Mysteries
Overview
How many types of photosynthesis?
       Basic photosynthesis -- Full Z
       Half Z
       'Energy only' photosynthesis
       Cyclic photo-phosphorylation
Why is it plants throw net oxygen into the air?
Light reactions
       Manganese 'water oxicizing' complex
Dark reactions- calvin cycle
       Calvin cycle steps
       Discussion ---Does the Calvin cycle run at night?
Cool animations of Calvin cycle and light reactions
Evolutionary aspects
       Photosynthetic bacteria
Chloroplasts & leaf structure
       Mitochondria
Molecular energy molecules and machines
Thylakoid membrane
Bond energy
       fuel energy
       methane oxidation
Efficiency
Key molecules and enzymes
       Chlorophyll vs Hemoglobin  structure
Modified photosynthesis -- C4 and CAM
       Pre-CO2 processing -- C4 pathway
       Pre-CO2 preprocessing -- CAM

Appendix
Marine cyanobacteria
       Sallie Chisholm's tiny prochlorococcus (cyanobacteria)
Tiny photosynthetic eukaryote, ostreococcus
       Flow cytometer
       Chlorophyll world wide distribution
       Diatom gallery
       (my) winogradsky columns
Misc photosynthesis topic
       Osmosis overview
       Perspective on ATP energy
Idiot photosynthesis
Amino acids  (an aside)
       What other elements do photosynthetic cyanobacteria need?

        Photosynthesis is (arguably) the most important biological process on earth. Virtually all life depends on it for food, oxygen to burn the food, and organic compounds to build the body. It's the source for practically all the O2 in Earth's atmosphere. Not just plants do it but bacteria too, and therein lies an evolutionary tale. Some of the details are amazing, like a high speed rotary turbine machine spun by flowing protons. Yet the inputs for this life process are only CO2, water, sunlight, and a few inorganic minerals.

        All the photosynthesis machinery was developed in bacteria. One to two billion years ago in a major evolutionary advance photosynthesis was acquired by non-bacteria when an early eukaryotic cell completely engulfed a photosynthetic bacterial algae cell. This ultimately led to the chloroplast, the organelle with its own genes inside the cells of plants where photosynthesis is done.

       To build organic material (like glucose C6H12O6) from inorganic CO2 requires a source of hydrogen & energy. Free hydrogen is extremely rare on earth, so photosynthesis uses the energy of sunlight to pull apart water (H2O) or hydrogen sulfide (H2S) to get at the hydrogen and to boost the potential energy of the electrons in the final product.

        It's almost impossible (I found) to learn photosynthesis from the vague little diagrams biologists draw. I got my arms around photosynthesis by drawing up a detailed top level diagram in the manner of the engineer. It is, I modestly claim, the world's best photosynthesis diagram. The obscuring of photosynthesis by biologists is too bad, because I found in photosynthesis some great surprises.
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Reference
        1 ) 1 ev = 23.1 kcal/mol = 96.5 kj/mol
        2)  bright sunlight = 2,000 microEinstein (2,000 micromole of  photons per m^2 per sec)
                                  [(2,000 x 10^-6) x (6.0 x 10^23) = 12 x 10^20 photons per m^2 per sec]
        3)  Ein (photons) for one C6H12O6 (glucose) = 48 photons @ 1.8 ev (av) = 86.4 ev
        4)  Eout (oxidation) of one  glucose = 2,870 kj/mol = 29.7 ev
        5)  Efficiency (theoretical) of photosynthesis = 29.7 ev/86.4 ev = 34%
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Typical values
           chloroplast                                           5 micron
           prochlorococcus  (smallest               0.6 micron  (For ref the smallest known living
                photosynthetic cyanobacteria)                 organism is nanoarchaea at 0.4 micron dia)
           mitochondria                                        0.5  to 5 micron
           reaction center (PSII or PSI)             11 nm
           thylakoid membrane (thickness)        10 nm
          ATP synthase (rotary machine dia)      9 nm
          photoreceptive molecule spacing       6 to 7 nm centers
           electron chain response time             5 msec (> 200 sec^-1)  (process 200 photon/sec)
           chlorophyll molecule (one)               8 to 10 photons/sec absorbed @ 2,000 uEinstein
                                                                             (1 photon/sec @ 200 uEinstein)
            reaction center (w/antenna)               x 200 to 300 chlorophyll matches photon absorption
                                                                             rate @ 200 uEinstein to electron chain response
                                                                             time [200 x 1 photon/sec = 200 photon/sec]
           grana (dia)                                            500 to 800 nm (typ)
           # grana/chloroplast                               20 to 100
           leaf stoma (size)                                   10 to 20 micron
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Introduction
        I set out to teach myself photosynthesis from the web. My starting point was the generally excellent technical resource, Wikipedia, but here I ran into some problems. Online photosynthesis lectures I found were generally very basic and professional papers usually hidden except for abstracts. At the more advanced level a good resource was the ability to search into some photosynthesis books via Google books and Amazon books. It took a lot of searching to answer a specific question, if the information could be found at all. Occasionally I would sit down for a few minutes with real books too, though my favorite technical bookstore (at MIT) carried only one book with photosynthesis in the title.

        I approached this as an electrical engineer with no college biology and one year of college chemistry long forgotten. I found learning photosynthesis this way (without a guru) initially very difficult. I've made two passes at it, the first time abandoning the effort for a year when it didn't jell. On a 2nd pass I have made much more progress largely because I was able to pull together tidbits of info from many sources into what I (modestly) claim is the world's best photosynthesis diagram (see below).

World's best photosynthesis diagram
        Photosynthesis 'Z' light and dark reactions drawn in the style of a circuit diagram.  (higher resolution .pdf)

Overview of the diagram
        Z cycle photosynthesis, used by most plants, runs 24 times to create one molecule of glucose. Each cycle is powered by the absorption of TWO photons, one in the PS2 complex and one in the PS1 complex, so in total 48 photons (min) must be absorbed for each molecule of glucose produced.

                PS2 -- Most of the energy from red (680 nm) photons is used to rip apart 12 water (freeing H+ and e-) with the remaining PS2 photon energy used to pump H+ across a membrane creating a proton gradient. The proton gradient runs rotary turbines (ATP Synthase) that move the stored PS2 energy into ATP (8.6 ev) for use in the dark cycle. All the oxygen freed from the water in the light cycle is released in gaseous form (6 O2).

               PS1 -- Energy from slightly redder (700 nm) photons is used to add hydrogen and electrons to NADP+ to create energy rich NADPH. NADPH (26.5 ev) transports the hydrogen and energy to the dark cycle, which runs in the (aqueous) stroma.

               Dark cycle -- Powered mostly by oxidation of NADPH, the dark cycle combines all the carbon from 6 CO2 with half the hydrogen freed from the water and half the oxygen from the CO2 to create a single molecule of glucose (C6H12O6). Glucose is an energy rich hydrocarbon sugar that releases 29.7 ev when 'burned' (oxidized). The excess 12 hydrogen from the water and 6 oxygen from the CO2 are combined in the dark reactions to create water (6 H2O). This dark cycle output water (6 H2O) diffuses back to the light reaction area (path not shown on the diagram) and provides half the 12 H2O needed as an input, so only 6 H2O of water externally is needed for a molocule of glucose.

        Efficiency -- Idealized (max) efficiency of photosynthesis is 34%, since 86 ev from 48 absorbed photons is (in principle) sufficient to store 29.5 ev of usable energy in one glucose molecule. (This breaks down into 85% efficiency for the dark reactions and 40% for the light reactions.) However in the real world the efficiency of photosynthesis is much lower. The most efficient crops like sugar cane are only able to capture about 1% of the energy in sunlight.

 Comment
        There is much confusion about the source of the oxygen released by students and even teachers as the equations and block diagrams of photosynthesis are complex and do not make it clear. I saw a question on a biology forum. A questioner thinks it's clear from the equations that all the oxygen released to the atmosphere must come from the CO2, and in fact this what early researchers assumed. An 'expert' answers him with a long tutorial on photosynthesis and concludes "O2 in natural photosynthesis always come from the water".
Technically this is right, but if by 'water', the expert is implying ground water, then both are wrong.

        What is very poorly documented, and hence widely misunderstood, is that there is a feedback path for oxygen from CO2 to the light reactions. The dark reactions make 6 (new) water molecules from half the oxygen in the 6 CO2 by combining it with 12 protons and electrons received from the light reactions. The combining of half the 24 hydrogen from the light reactions with half the 12 oxygen freed by ripping apart 6 CO2 to make 6 H2O is a major source of energy to power the dark reactions (19.6 ev of 35.2 ev).

        The definitive tests that resolved where oxygen goes used a heavy isotope of oxygen (O18) as a tracer, substituting it in separate tests in the CO2 and the H2O. None of the heavy O18 from water was found in the glucose, it was all released into the atmosphere. However, the heavy O18 from CO2 was found equally in both the glucose and released oxygen. (Even in an excellent, detailed, popular book on photosynthesis ['Eating the Sun, How Plants Power the Plant' by Oliver Morton] this key point is not made clear. A footnote (p72) says only that when algae were grown in normal water and CO2 enriched with O18, the released oxygen contained "much less O18" compared to the reverse experiment of normal CO2 and water rich in O18.) Bottom line is 6 of the 12 oxygen atoms from 6 CO2
go into the glucose with the other 6 into the atmosphere, and all of the 6 oxygen atoms from 6 external H2O also go into the atmosphere.

Light and Dark reaction viewpoint --- a detailed explanation
        Photosynthesis takes place in two closely adjacent physical areas always labelled Light and Dark reactions. Water enters and is torn apart in the light reaction area. CO2 enters and is torn apart in the dark reaction area. All photosynthesis references detail how the only atom (net) to cross from from the light reactions to the dark reactions is hydrogen (in the form of free protons (H+) and as H (plus an electron) added to reduce NADP+ to NADPH). Thus it is fairly easy to see, our 'expert' in the story understood this, that all the oxygen stripped from H2O must be exported, allowed to diffuse away as gaseous oxygen.

        Less easy to see is how the excess oxygen stripped from the CO2 is handled. The reason for the confusion I believe is that in my research I found many reference texts use the reduced (simplified) set of photosynthesis equations where water output is viewed as a detail and subtracted out. In the dark reaction area the excess oxygen stripped from the CO2 merges with excess free protons (hydrogen) diffusing over from the light reactions (and electrons stripped from NADPH as it is oxidized to NADP+) to make water molecules. The hydrogen stripped in the oxidation of NADPH to NADP+ makes its way into the glucose.

        The key to the confusion about how the excess oxygen stripped from CO2 is handled arises because the water feedback path from the dark reaction area to the light reaction area is missing in block diagrams based on the reduced equations. This is probably the reason our 'expert' may not have understood that half of the water being being ripped apart in the light reaction area has (in effect) been created in the dark reaction area and is carrying half the oxygen atoms the dark machinery stripped from the 6 CO2. Thus the light area machinery, somewhat surprisingly, is exporting to the atmosphere (as 6 O2) not only all the oxygen stripped from ground water (6O), but also (in effective) half the oxygen stripped from carbon dioxide (6O).

                    However, it is true that released oxygen from photosynthesis has over billions of years built up the amount of oxygen in the atmosphere
                          from virtually nothing to 21% (by vol) today, but this is because there is a slight unbalance causing a tiny bit more oxygen
                          (extracted half from water and half from CO2 by photosynthesis) to be put into the atmosphere than the oxidation (burning process)
                          of dead plants and photosynthesizing bacteria by microbes pulls out of the atmosphere. The primary reason for the imbalance is not
                          all dead plant and bacteria gets broken down. If after death they end up in an oxygen deficient region, say by sinking to the bottom
                          of the sea, their carbon can end up buried in the earth.

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Objectives
        My original objective in this essay was to give my own overview of photosynthesis with an emphasis of the how the energy of the incoming photon is made to do useful work, hopefully clearer and more quantitative the usual write ups written by biologists.

        What I basically wanted was a narrative that starts with light photons coming in and ends with glucose going out. The supply of CO2 and water are generally predictable, but not photons. It's photon rates that are the big variable in photosynthesis, and of course photons are what make photosynthesis unique. How many photons a second come into a light capture center, with what energy,  how fast can the system respond, where are the bottle necks, etc? My search for a narrative like this came up blank. I don't think such a narrative, or anything like it, exists! So gathering a dimension here, a rate there, I have set out to pull it together into a coherent picture, hence my list of typical values above and annotated block diagram. Since my numbers come from various sources (nearly all from different plants and bacteria), the best that can be hoped for is a rough approximation, but that's much better than exists now.

        As I went along I got attracted by related fields, so the essay has sections on the evolutionary story of photosynthesis, the world's smallest most common photosynthetic bacteria (prochlorococcus), the relationship between the organelles chloroplast and mitochondria (one uses ATP to make glucose while the other uses glucose to make ATP). And I ran into wonderful surprises, which when I started I was totally unaware of, like the high speed double rotating machine (ATP synthase) that makes ATP in photosynthesis and mitochondria.

        Another surprise was that there is a vastly simpler form of photosynthesis, a one protein photo driven proton pump, in archaea and recently found to be widespread in bacteria too. Some reference claim this is not true photosynthesis, but it does convert sunlight into usable chemical energy. This type of photosynthesis requires just one membrane bound protein (different in bacteria and archaea), which when coupled to the light sensitive molecule retinal, acts to pump up a concentration gradient of protons. The proton gradient is then usable by pre-existing ATP synthase rotary turbine (to make ATP) or to rotate flagella via its proton driven rotary turbine.

Mysteries
        I also ran into major mysteries, which kept me interested, but also slowed me down. It seemed like every set of equations and figure I saw was different, and even worse a lot of the equations did not appear to be balanced!  I think I have now figured out how to decode the unbalanced equations, but I still don't understand the thinking or rational for using them in reference or teaching material.

Why is photosynthesis so little understood?
           Why is photosynthesis so little understood?  Three possible reasons: One, it's newly understood, two, it's very complex. To understand it, even at an elementary level, requires some knowledge of biology, chemistry, and physics. And three, biologists (I have come to realize) are almost totally incapable of coherently explaining anything!

        Much of photosynthesis has been figured out only fairly recently with photosynthesis researchers wining a bunch of Nobel prizes (for chemistry) in the 80's and 90's. The details about how water is split into hydrogen and oxgyen (water oxidizing complex) was only figured out about five years ago. Some details of photosynthesis, like how much H+ flow is needed to make ATP, are still not well understood. Research into photosynthesis must be difficult, because chloroplasts are tiny, the proteins are complex and varied, and many of the reactions are incredibly fast (10^-12 sec, few pico seconds or even faster). In fact much photosynthesis research has been done on photosynthetic bacteria where the light reactions are only half as complex as in plants (& algae).

        An interesting new line of research is artificial photosynthesis, the development of (non-living) photosynthetic systems. The newly understood details about how photosynthetic organisms can efficiently split water into hydrogen and oxgyen at room termperature is providing guidence for how to design organisms to function as photo driven hydrogen generators. Here's an excellent overview of photosynthesis in considerable detail in a very readable 2005 paper by German researchers, Photosynthesis: a blue print for solar energy capture and biohydrogen production technologies.

        http://www.rsc.org/delivery/_ArticleLinking/DisplayArticleForFree.cfm?doi=b506923h&JournalCode=PP

        Photosynthesis is not only complex, but is a mixture of biology, chemistry, physics (& even electrical engineering)! Descriptions of photosynthesis for the non-expert often tend to skimp on one or more of these aspects, likely reflecting the background of the author. There's also the difficulty of how deep an explanation should go, because it's nested problem with many layers (like an onion).

Things (almost) no one tells you about photosynthesis
        I found that an amazing number of facts about photosynthesis are very poorly documented. While all my weeks of research of work on photosynthesis were still fresh in my head, I scribbled out this list in a few minutes. Almost no one tells you:

        * Size of reaction center, i.e. antenna complex with chlorophyll centers
                    (nearly impossible # to find)
        * How many photons/sec arrive at a reaction center (say in bright sunlight)?
                    How many are absorbed? (after much digging I found two references
                    without any calculation that stated the estimated number of photons
         absorbed in bright sunlight by a single chlorophyll molecule is about
                    10/sec. Since antenna complexes are 200 to 300 molecules, this
                    translates into 2,000 to 3,000 photons/sec per reaction center.
                    Almost no one tells you this directly!)
        * What is the average light intensity seen by chloroplasts in leaves, what's a
                    typical intensity gradient though a leaf of grana stack. How much is
                    reflected, transmitted?  How much shielding is there in leaves and
                    grana stacks? What's the purpose of grana stacks, to improve efficiency
                    by capturing some transmitted photons? (I have been able to find
                    virtually nothing on this.)
        * Most of the energy from light reactions to dark reactions is carried by
                    NADPH not by ATP. 12 NADPH (@) 2.12 ev) brings in 26.52 ev
                    (75% of total) vs 8.64 ev brought in by 18 ATP (@ 0.48 ev)
                    (no one tells you NADPH is the primary intermediate energy carrier,
                    you must calculate it yourself!)
        * No clean comparison of chloroplasts and mitochondria, in terms of
                    size, H+ gradient, membrane voltage, electron transport chains, etc
                    (This is curious because the parallels and differences are illuminating)
        * No one tells you if the hydrogen transported from the lumen by NADPH
                    goes into the glucose or into water.
        * How often does a reaction center run? At what light intensity is efficiency
                    maximum? Where are the bottlenecks? (It takes a lot of digging in
                    textbooks to find any of this info, which is all spread out, and usually
                    obscurely stated.)
        * How many glucose per second can be made by one reaction center and by
                    one chloroplast? (no one tells you this. This is related to optimum light
                    levels and system bottlenecks.)
        * How many ATP synthase are needed per reaction center? (no one tells you
                    this! Since ATP synthase is a rotary machine, in relative terms it is slow,
                    and it runs off the proton gradient so it's not tightly coupled to photons.
                    I have calculated it twice. My first value was many ATP are needed per
                    reaction center, which is not good, because it crowds out the antenna
                    complexes. Second calculation using lower light levels and stacking of
                   chloroplasts gave a much more reasonable value of one ATP synthase
                    shared by several reaction centers.)
        * There is no significant long term (chemical) energy storage between the light
                    and dark reactions, so this means that dark reactions must run pretty much
                    concurrent with light reactions. Dark reactions do not run at night. (details
                  here) (almost no one tells you this)
                            There is a CO2 storage mechanism in desert plants that allows uptake
                            of CO2 at night (to minimize water loss) for use during the day, known
                            as CAM photosynthesis, but this is a preprocessing step, so in desert
                            plants too light and dark reactions proceed simultaneously.
        * Standard textbook ratios of NADPH (12) and ATP (18) per glucose are only valid
                    at lower light levels, when the process runs smoothly without bottle necks.
                    (no one tells you this. Digging deeply into various photosynthesis textbooks
                    it appears the optimum efficiency light levels are probably quite low, something
                    like 5% to 10% of full sunlight.)
        * How is photon energy in the light reactions divided, specifically how much for proton
                    pumping, how much for ripping water apart, how much for reducing
                    NADP+? (no one tells you this. Can be estimated from the energy contained
                    in intermediate products NADPH and ATP)
        * What are the potential requirements for oxidizing water? (I find it variously referred
                    to as redox potential of +0.83 V, sometimes +1.3 V. There are references to
                    mid-potential with uncertain estimates about overdrive. (It turns out that +0.83 V
                    is the H2O/O2 redox voltage for a pH of seven, but the pH in the lumen is lower,
                    meaning a higher concentration of H+, and this increases the water redox
                    voltage to more like +0.95V. no one tells you this!)
        * Is the electrolysis potential of water 1.23V relevant to, or useful in understanding, the
                    oxidation of water in photosynthesis? (seems like an obvious question, but no one
                    ever mentions this)
        * The the various energies quoted for water oxidation all appear to be well below
                    the 1.8 ev a single PHII photon provides. So why is it that bacteria with only
                    PHII photosynthesis (first half Z cycle) are unable to oxidize water. (It's always
                    just stated, but no one explains why. Too much energy loss?)
        * What are the constraints in low light since two (sequential) photons are needed to run
                    The Z cycle? This translates into what are the 'hold' times relative to photon arrival
                    times. This likely applies to an electron coming out of PHII which must wait around
                    for a 2nd photon to run PSI, and also to the water oxidizing complex which needs to
                    hold oxidation states while four PHII photons come in.
                    (no one ever tells you this. I don't know the answer to this. So if maximum
                    efficiency is at (say) 10% full sunlight, will the system run at 1/10 capacity at 1%
                    full sunlight?)
        * Why are photosynthesis equations so very different in various references. And even more
                    importantly, why are so many not balanced? (I have never seen an explanation, even
                    as an aside, for what appears (to me) to be unbalanced equations.)
        * Why do only a tiny number of references show water as a dark reaction output, and why
                    is there no explanation of where the excess oxygen in CO2 goes?
                    (In a reduced single photosynthesis equation water is normally shown as net only
                   on the input side. But separate equations for light and dark reactions should show
                    water input for light reactions, where it provides the output O2, and water output
                    for the dark reactions, where it carries off the excess O in CO2. Why the water
                    output is so rarely shown as a dark reaction output is still a major mystery to me.)
        * It's not generally made clear how it is that bacteria with only one photosystem are able
                    to generate the two high energy molecules (ATP and NADPH) required to run the
                    dark reactions Calvin cycle. The 'pussle' arises because the two photosystems in
                    plants (Z cycle) are specialized with the first (PSII) making ATP and the second
                    (PSI) NADPH. (The answer is a single photosystem in some bacteria is more
                    complicated than in plants allowing it to switch between generating ATP (cyclic
                    mode) and NADPH (non-cyclic mode).
        * Why is 'energy only' photosynthesis dismissed as not "true photosynthesis"? True it
                    doesn't fix carbon, but it is a means for organisms (archaea & bacteria) to convert
                    sunlight into usable chemical energy, and its simplicity provides a good starting
                    point for the teaching of photosynthesis.
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Mysteries
        I ran into a strange mystery with photosynthesis. I must have looked at the description of the back end of photosynthesis, known as the dark reactions or calvin cycle, in 15 different (detailed) references including lectures and books (one an MIT textbook). The dark reactions are where the energy temporarily stored in two chemicals by the front end 'light reactions' is used to fix carbon from CO2 into sugar.

        The dark reactions are a long chain of complicated biological/chemical reactions, something like ten steps in series all catalyzed by protein, however, it's well understood. Calvin in the 1940's used CO2 tagged with radioactive C14 to figure it out. Most introductory photosynthesis references focus on the light reactions and say relatively little about the dark reactions. Generally they just give an overview of the dark reactions with an input-output equation and/or figure. Here is where I ran into trouble:

        Problem #1 is almost all the equations and/or figures are different!

but it gets worse

        Problem #2 is virtually  every dark reaction and back end summary equation I find is unbalanced. And no one even comments on this. The equations don't balance in oxygen or hydrogen. And I find they don't agree on the phosphate group with some implying Pi =  PO3H, others PO3H2 and even PO3 and PO4 versions. (The explanation on phosphate I find out later is very likely that it has several variants in equilibrium, and the dominant one depends on pH. The body's pH typ is pretty close to neutral (7.4), so at this pH the phosphate group is PO3H.)

Where does the oxygen go?
        The heart of the mystery in the dark reactions is oxygen. CO2 comes in bringing two oxygen for every carbon. It's clear that the captured CO2 provides all the carbon and oxygen needed for the sugar and that hydrogen needed for the sugar comes from ripping water apart. The problem is that there is extra oxygen in the CO2 to dispose of. The output sugar, whether the end product glucose (C6 H12 O6), or the intermediate 3 carbon sugars (which have an extra H hiding the phosphor Pi complex), have a specific ratio of C, H, O. In sugars there is the same number of oxygen as carbon atoms plus twice the hydrogen atoms. This means that only half the oxygen coming in with the carbon of CO2 is used in the sugar. It doesn't appear to come off as gaseous oxygen. All the references agree that the oxygen emitted by photosynthesis comes only from the light reactions where water is ripped apart. This is because experiments that run only the light reactions find the full oxygen output. So what I couldn't figure out was:

                Where (the hell) does the excess oxygen go!

Is water an output?
        A couple of references showed water as an output of the Calvin cycle, but most didn't. One reference said in text that water was an output, but in its equation it showed water only as in input. Good grief! I kept thinking that water might be a hidden reactant, but to carry away extra oxygen as water I need extra hydrogen. At first I tried to provide the extra hydrogen by increasing the quantity of the NADPH, but then the CO2 to NADPH ratio disagreed with every reference. Not a single reference even hints that O2 emerges from dark reactions. O2 emission is always shown coming only from the light reactions (from the manganese water oxidizing group attached to the input photosystem II reaction center).

       To verify I wasn't nuts (about the mystery) after doing my block diagram I went back and looked again at a $150 MIT introductory biology textbook on the cell, and sure enough the photosynthesis equations were not balanced!

 Hidden assumptions?
        The day after I drew a draft of my block diagram, I had a dental appointment, so I asked my dentist about hidden assumptions. He is only two years out of dental school and said he specialized in biochemistry. He said a lot of (biological) reactions have a little water as output, so it is sometimes just assumed. Well, OK, but I would argue that writing unbalanced equations (without explanation) in descriptive material for non-specialists and students is really dumb.

Example of water omitted for 'clarity'
        Maybe my dentist is right. I came across below, which I have copied exactly (including the 'actually' line). Here's a case where water output is omitted in the 2nd line leading to an unbalanced equation (which I noticed). The reason clearly is for clarity, to allow a clean comparison with the equation above. But apparently the author then had qualms about the equation being unbalanced (finally!) and added the follow up line with the correct balanced equation including the water output.
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(Three lines below copied from a biology source on Winogradsky columns )
        6 CO2 + 6 H20 = C6H12O6 + 6 O2     (plant photosynthesis
        6 CO2 + 6 H2S = C6H12O6 + 6 S         (bacterial anaerobic photosynthesis)
        Actually, the balanced equation is: 6 CO2 + 12 H2S = C6H12O6 + 6 H20 + 12S
------------------

        The text says "The immediate product of the Calvin cycle is glyceraldehyde-3-phosphate (G3P) and water." So far so good, but here is the Wikipedia Calvin cycle equation (I've doubled it, to be compatible with my block diagram):

    6 CO2 + 12 NADPH + 10 H2O + 18 ATP => 2[C3H5O3 - (PO3)(2-)] + 4 H+ + 12 NADP+ + 18 ADP + 16 Pi

        Yikes, text says water output and equation shows water input. (Note sugar is not CxH2xOx form, but if you put the 4H+ into the sugar and PO3 you get the standard sugar and PO3H phosphate.) There is 10 water at the input and no water at the output, looks inconsistent with the text to me. Not balanced in H and O and assuming [Pi = PO3H]. What is going on? I have seen this pattern (far too much water at input) in text books too. What is going on?

Confirming the mystery
        I checked 6th edition of an MIT biology textbook (didn't note the author but it may be 'Molecular Cell Biology' by Lodish etc.) This book has similar equation for dark reactions as above, but of course not exactly the same. Lots of extra water at input (in this case 12 H2O) and more H+ output (in this case 12H+). I see no way this equation is balanced. There is no output to accomodate all the O and H the high input water provides.

        It's hard to see how a major textbook in its 6th edition could be in error, but what the explanation is I have not a clue! (Well, 12 H2O at the input is possible clue, since the light reactions have 12H2O at the input, so maybe this equation is some sort of mixture of light and dark reactions, but it's still not balanced!)

        I counted up the unbalance in O and H and noticed something interesting. The O and H 'missing' on the output side were 18 O and 18 H. There are, of course, also 18Pi on the output side. So if Pi is [PO3H + 'OH'], then all the missing O and H are accounted for! My guess is this is what is going on, but why the strange definition of Pi?  Of course neither book defines Pi in the photosynthesis section and Pi is not in the books' indexes either.

My equations
        I finally cracked the problem when I tried supplying the hydrogen needed to make the water by bringing in H+ (protons) from the light reactions. Now everything worked, water is indeed an output of the dark reactions! It carries off the excess oxygen (see my block diagram). I think the output equation of calvin cycle (excluding post processing) is

    6 CO2 + 18 ATP + 12 NADPH + 12H+  => 2[C3H6O3 - (PO3H)]  + 18 ADP + + 16 Pi + 12 NADP+   + 6 H2O
                                                            where
                                                                    Pi = PO3H      (phosphate group)
                                                               ATP = ADP + Pi
                                                         NADPH = NADP+ + H+ + 2e-

My 'unreduced' equations
        When I worked through the chemical equations of all the molecules in the Calvin cycle, I found the above equation is a reduced equation. The non-reduced dark equation has an extra 6H2O on both sides.

  6 CO2 +18 ATP +12 NADPH + 12H+  + 6 H2O => 2[C3H6O3 - (PO3H)] + 18 ADP + 16 Pi + 12 NADP+  +12 H2O

        The extra 6H2O on both sides is a minor H2O loop in the forward path of the Calvin cycle. The chemical formulas show that when a CO2 is fixed into RuBP, an H2O from the stroma (liquid) is incorporated too. This H2O is then spit out back into the stroma at the point where the NADPH come into the forward path, one H2O for each two NADPH. The net 6H20 output from dark reactions, shown in the reduced equation, results from 6O (half the oxygen from the CO2) combining with the 12H+ ions that diffuse over from the lumen (inside of thylakoid membrane) plus 12e- released by the oxidation of NADPH.

Confirm fix of  water with CO2 (3/28/09)
        In the MIT textbook on BioChemistry there was a detailed section on the Calvin cycle. Those diagrams showed one H2O coming in the very next step after one CO2 comes in! Just what I found. And they explained what the H2O does. The unstable six carbon that first forms breaks apart (into two three carbon sugars) when it is hydrologized. In other words it is the the water that breaks apart the 6 carbon sugar. This is the first reference I have seen to this.
-----------------
        My equations (see block diagram lower left corner) are balanced atomically and in charge. I have water in the output and H+ at the input, which is the reverse of the two mystery equations above. The 24H from 12 H2O ripped apart come into the calvin cycle in two ways: 12H carried by the 12 NADP+/NADPH transporter and 12H as protons that flow out of the lumen through the ATP synthase rotary machine. Half the 12 O in 6CO2 goes into the 'sugar' 2[C3H6O3 - (PO3H)] and half into the 6 H2O output.

Confirming my equations (2/21/09 update)
        Weeks after my block diagram and equations were finished I checked out the equations in the only book carried by the MIT bookstore with photosynthesis in the title (Aquatic Photosynthesis, 2nd edition, 500 pages, by Falkowski & Raven, 2007, Princeton Univ Press). I was pleased to find their light & dark equations agree exactly with my equations (balanced both atomically and in charge).

        The whole thing is very strange.

Confirm #2 (3/28/09)
        Weeks after I worked out my equation (above), I checked the Photosynthesis entry in Wikipedia. It, of course, has an entirely different equation for the Calvin cycle than the Calvin entry in Wikipedia (above). Gone are the water at the input, this one has water in the output. Here is the Photosynthesis equation doubled, and what do you know, it is exactly the same as my equation!

    6 CO2 + 18 ATP + 12 NADPH + 12 H+  => 2[C3H6O3-phosphate] + 18 ADP + 16 Pi + 12 NADP+ + 6 H2O

My complete photosynthesis block diagram (2/09)
        My new block diagram has balance in elements and charge. Its key ratios, the ratios of ATP and NAPDH to sugar and the ratio of protons diffusing through the ATP complex to make ATP, all agree with most references. The exact ratio of H+/ATP is not known exactly. I have drawn the diagram for a ratio of 4, but noted how the alternate ratio of 4.67 is easily accommodated by just changing the number of circulating pumped H+.

        My new block diagram of photosynthesis, while not pictorially pretty, is (I think) far better and far more complete than any block diagram I have seen in accurately & quantitatively showing the showing atomic and charge flows. After I had the layout and quantities right, I decided to annotate the hell out of it, adding equations, bond energy, redox energy and efficiency. It's photosynthesis drawn the way an electrical engineer draws block diagrams.

Correct summary equations
       From my figure above the terms crossing the dotted line allow the equations summarizing light and dark reactions to be easily written. These equations, unlike most of the published equations that I have seen, are balanced and (I believe) accurate.

Where does the O2 gas come from?
       The light reactions equation shows all the hydrogen from the ripped apart input water is passed to the dark reactions. All the oxygen from the water is output as a gas. The dark reactions equation shows to make glucose all the carbon from CO2 is needed but only half of the CO2 oxygen and half of the hydrogen from the water (via the light reactions). The surplus hydrogen and oxygen combine to make water, which is an output of the dark reactions.

        The definitive experiment to figure out where which oxygen went where was done using a stable isotope of oxygen (O18) that was substituted in separate tests in water and CO2. When water was made using O18, the released oxygen gas was found to be all O18. When CO2 was made from O18, O18 was found in the sugar and water. I had initially assumed that the oxygen tracer isotope would be radioactive because it makes tracing easy, and I knew radioactive C14. which became available after WW2, was used used to figure out the dark cycle of photosynthesis, but Wikipedia shows all radioactive isotopes of oxygen have short half lives, the longest (O15) is only 2 minutes, so expermimentation with them would be very difficult.

                     where
                            NADPH = NADP+ + H+ + 2e-      (hydrogen & energy transport)
                                  ATP = ADP + Pi                        (energy transport)
                                      Pi = PO3H                              (phosphate group)
                                                                                            (one reference says PO3H2?)

Adding the two equations and cancelling terms.

          48 photons (@ 1.8 ev) + 6 CO2 + 12 H2O => C6H12O6 + 6 H2O +6 O2

Above is the best single summary equation because the 12 left water are all ripped apart by the light reactions inside the membrane and the right 6 water are ouput by the dark reactions outside the membrane. But ignoring this and combining the water terms gives the classic super simple photosynthesis summary formula.

         Light + 6 CO2 + 6 H2O => C6H12O6 + 6 O2
 

Classic 'Oxidation is Reverse of Photosynthesis'

        Note oxidation of glucose is the reverse of photosynthesis with the difference in input/output bond energies exactly the same. This is commonly explained in introductory photosynthesis texts, but I think my hand drawn sketch (above) makes this point clearer. For the making of one glucose the bond energy difference is the (minimum) light energy input needed to make the reactions go, whereas for oxidation of one glucose it is the heat/work released by the reaction.

        This figure shows the six O2 released into the atmosphere by photosynthesis 'manufacture' of one molecule of glucose (C6H12O6) are all extracted from the atmospher to burn (oxidize) the glucose molecule to extract its stored energy. Hence from this idealized textbook view it is not clear why [photosynthesis + oxidation] would net release oxygen to the atmosphere.
======================================================
Overview
Photosynthesis yields glucose
        Photosynthesis in plants and bacteria captures the energy of photons and puts (a fraction of it) in the form of chemical energy into the sugar molecule glucose (C6H12O6), the starting material for glucose being two simple inorganic molecules (CO2 and H2O) obtained from the environment. Glucose not only 'feeds' the plant, but its hydrocarbon molecule can be reconfigured into the plants' structural material. So in a sense, glucose is the basic energy molecule of life.

        Photosynthesis in plant cells and eukaryotic algae occurs in organelles called chloroplasts, which are thought to have evolved from engulfed (endosymbiotic) cyanobacteria (i.e. blue-green algae). Chloroplasts have their own DNA with 50 genes or so. Within the chloroplasts are stacked-up folds of the thylakoid membrane, where the light photons are actually captured and the first part of photosynthesis process takes place.

        From the photosynthesis summary equation [6 CO2 + 6 H2O + (photon energy)  => C6H12O6 + 6 O2] it appears that photosynthesis probably works like this:

 First Idea?
        Energy from captured solar photons is used to break apart six carbon dioxide (obtained from the atmosphere). The freed carbon is combined with six water to form an energy rich molecule, the simple sugar glucose (C6H12O6), and the oxygen freed from the carbon dioxide is thrown off (into the atmosphere) as six dual oxygen.

                         6 CO2     +  6 H2O   +  48 hv    => C6H12O6 + 6 O2                       (reduced)
                       6 CO2     +  12 H2O   +  48 hv    => C6H12O6 + 6 O2 + 6 H2O       (Wikipedia)
                                                                where
                                                                    hv = photon energy
                                                                    C6H12O6 = glucose

        A simple way to look at the (net) photosynthesis reaction is to make one glucose you take all the hydrogen from six H2O and combine with all the carbon from six CO2. There is more oxygen than needed for the glucose (C6H12O6), so 1/3rd of the oxygen goes into the sugar and 2/3rd of the oxygen is thrown off as a gas.

        In detail photosynthesis is quite complex and the equation above is really the net equivalent reaction of what in detail is a complex sequence of reactions, the sequence being triggered by an electron knocked free by the photon. Oxidation of a glucose molecule has a free energy output of 2,870 kJ/mol (or 29.7 ev). All this energy came from the photons. The 48 photons needed to make the glucose had an average energy of about 1.8 ev, which totals to 86ev. This makes the theoretical efficiency of the photosynthesis process about 34% = [29.7 ev/86 ev].

        Cells in the plant later use the energy stored in the glucose by pulling oxygen from the air to oxidize the glucose (generating carbon dioxide and water as waste products). This equation is basically the reverse of the photosynthesis equation.

                      C6H12O6 + 6 O2 =>  6 CO2  +  6 H2O

Cellulose
        Cellulose is a major structural molecule used in plants and algae for cell walls. Cellulose is the most common organic compound on Earth with lignin a close second. Cellulose is the primary component of paper, and cotton is mostly cellulose. Wood is half cellulose and a third lignin. Cellulose can't be digested by humans but it can be by ruminants and termites using microbes who live in their guts.

        Cellulose is a carbohydrate like glucose. In fact from its chemical formula each link in the cellulose chain looks like [glucose - water] = [C6H12O6 - H2O = C6H10O5]

        -- (C6H10O5)n, a polysaccharide consisting of a linear chain of several hundred to over ten thousand linked D-glucose units.

Hemicellulose & lignin
       -- Hemicellulose is a polysaccharide related to cellulose that comprises ca. 20% of the biomass of most plants. In contrast to cellulose, hemicellulose is derived from several sugars in addition to glucose, including especially xylose but also mannose, galactose, rhamnose, and arabinose. Hemicellulose consists of shorter chains - around 200 sugar units.

        -- Lignin is a huge, cross-linked, hydrocarbon, macromolecule with molecular masses in excess of 10,000. Lignin fills the spaces in the cell wall between cellulose, hemicellulose, etc. The sketch below gives an indication of the complexity of lignin.

How many types of photosynthesis?
       There are several different types of photosynthesis. The Z type found in plants and cyanobacteria has a double light gathering structure and carbon fixing process. This is classic photosynthesis. It is by far the most complicated requiring dozens of different proteins. A somewhat simpler version with the same carbon fixing process but only half the light structure of the Z process is used by some bacteria, some using the first half of the Z light process and some the second half.

        There is also a vastly simpler type of photosynthesis, energy only photosynthesis, that basically uses only one protein. It can convert light energy to chemical energy, but cannot fix carbon. Archaea, and many bacteria too it recently was discovered, do this type of photosynthesis. Its photo-driven proton pumping protein is different enough in archaea and bacteria that this type of photosynthesis may have evolved separately in each group.

Basic photosynthesis -- Full Z
        The full Z (photosystem II and photosystem I) photosynthesis is found in 99% of cells: all plants, diatoms, algae, and many common aerobic bacteria (cyanobacteria, prochlorococcus). There are two different structures that work sequentially to extract energy from light photons, it uses water as an input, has oxygen as byproduct, converts the light energy first into two forms of chemical energy (NADPH and ATP), then uses the NADPH and ATP to fix carbon from (inorganic) CO2 into sugars (and later into organic structure). If you understand how the classic (full Z) photosynthesis works, then you easily understand the other types, because they are all just simplified versions of Z.

Half Z
        There are two types of 'half Z' photosynthesis found in a few (anaerobic) bacteria (non-sulfur) bacteria use the first half of the Z (photosystem II), and green sulfur bacteria use the second half of the Z (photosystem I). The 'half Z' light processing works with the energy from only one photon,  rather than two as in the full Z. As a consequence this type of photosynthesis does not have the energy to rip apart (oxidize) water to get at the electrons, so the inputs used are materials easier to oxidize like hydrogen sulfide (or hydrogen or ferrous iron).  Purple sulfur bacteria get electrons from either sulfide or elemental sulfur, and purple non-sulfur bacteria typically use hydrogen. They are, however, able to fix carbon into sugar from CO2. Because the input is not the water, the byproduct is not oxygen, but typically sulfur. These half Z photosynthesis reactions are thought to predate the full Z photosynthesis.

Wikipedia on half Z bacteria
        -- The other two major groups of photosynthetic bacteria (besides cyanobacteria), purple bacteria and green sulfur bacteria, contain only a single photosystem and do not produce oxygen. (They are optimized for wavelengths below visible light (775 nm and 790 nm) in the near infrared where the sun radiates most strongly.)

        -- Purple bacteria and green sulfur bacteria occupy relatively minor ecological niches in the present day biosphere. They are of interest because of their importance in precambrian ecologies, and because their methods of photosynthesis were the likely evolutionary precursors of those in modern plants.

        -- Researchers have theorized that some purple bacteria are related to the mitochondria. (ATP producing organells found in nearly all eukaryotic cells (blood cells are an exception) that are thought to have arisen from engulfing symbiotic bacteria.) Comparisons of their protein structure suggests that there is a common ancestor.

        The answer (confirmed by a textbook for at least one bacteria) is that 'half z' bacteria are able to switch their one photosystem back and forth between cyclic and non-cyclic modes. In cyclic mode a proton gradient is pumped up, which allows ATP to be made. In non-cyclic mode electrons and hydrogen are obtained by ripping apart hydrogen sulfide (H2S), or other hydrogen material easier to rip apart than water, and the electron and hydrogen are used to reduce NADP+ to NADPH. With both ATP and NADPH available the calvin cycle, or one of the other carbon fixing cycles, which also require ATP and NADPH, can run.

'Energy only' photosynthesis
        There is also a vastly simpler type of photosynthesis, energy only photosynthesis, found only in bacteria and archaea, and remarkably it needs only one protein to work! It's possible to be so simple because it uses some of the machinery already in place in the cell for respiration and movement. The key is that almost all cells, both prokaryotic and eukaryotic, use proton gradients across a membrane as part of their respiration system. Respiration (aka, burning of food) typically builds up the proton concentration. The proton gradient is then used to make energy molecule ATP by allowing the protons to flow down their concentration gradient spinning the rotary turbine of ATP synthase. In cells with flagellum 'motors' they too are spun by turbines working off the proton gradient.

        In 'energy only' photosynthesis the photosensitive protein sits in the membrane, and when illuminated is able to use photon energy to pump protons across the membrane increasing the proton concentration gradient (across the membrane). In this way light energy can be used to provide an energy boost to a microbe that may normally 'eat' for a living. Some people don't consider this 'real' photosynthesis, because it does'nt fix carbon. Thus you see the claim (in Wikipedia Archaea) that archaea don't 'do' photosynthesis, but they do do 'energy only' photosynthesis.

Archea --- bacterio-rhodopsin
        There's a type of photosynthesis found only in archaea. It's a less efficient one photon photosynthesis that also does not using water as input and is unable to fix carbon from CO2. It functions as a light driven proton pump, which uses bacteriorhodopsin to capture light, and from the proton concentration ATP is made. Hence it provides only supplemental energy, requiring archaea to 'eat' other creatures or organic molecules to get the energy and structure they needs to live. The archaea type of photosynthesis is thought to have evolved separately.

Bacteria --- proteo-rhodopsin
        Until the year 2000 proton pumping 'energy only' photosynthesis was thought to exist only in archaea, but in 2000 proteorhodopsin was found in bacteria. Research showed proteorhodopsin, like bacteriorhodopsin, was also a light driven proton pumper allowing ATP to be made or flagella to rotate. (Flagella whips, like ATP synthase, are spun by proton gradient driven rotary turbines.)

        In 2005 everyone was amazed when the genomes of wild marine bacteria were tested and the gene for proteorhodopsin was found in 13% of the bacterial species tested. What was so surprising was that no photosynthetic activity was known in most of these bacteria, so what were they doing with a gene for a photosynthesis protein in their genome?  When researchers went looking, they found bacteria with this gene had a previously unknown backup (energy only) backup photosynthesis system, they were able to switch over (or supplement) their food input with light. Clearly having a backup energy system like this could provide a huge evolutionary advantage.

DNA leads the way
        Note what's interesting here is decoding DNA is becoming a major research tool in the study of bacteria. If you know what genes a bacteria has, you've have a good handle on how it probably lives. (Apparently) only fairly recently did it become possible to do genomic analysis on mixed populations. This is essential for studying wild populations of bacteria which always include a lot of types mixed together.

        "Here, we show that when cellular respiration is inhibited by depleting oxygen or by the respiratory poison azide, Escherichia coli cells expressing proteorhodopsin (PR) become light-powered. Illumination of these cells with light coinciding with PR's absorption spectrum creates a proton motive force (pmf) that turns the flagella motor, yielding cells that swim when illuminated with green light.

        We quantify the coupling between light-driven and respiratory proton currents, estimate the Michaelis–Menten constant (K m) of PR (10^3 photons per second/nm^2), and show that light-driven pumping by PR can fully replace respiration as a cellular energy source in some environmental conditions." (2006 paper @ http://www.pnas.org/content/104/7/2408.full)

        -- Ion channels and pumps (Wikipedia):

        -- Rhodopsins found in prokaryotes and algae act as light-gated ion channels, and can be further distinguished by the type of ion they channel. Examples are bacterial sensory rhodopsins, channel-rhodopsin, bacterio-rhodopsin, proteo-rhodopsin, and halo-rhodopsin. Bacteriorhodopsin and proteorhodopsin function as proton pumps, whereas halorhodopsin acts as a chloride pump. Their functions range from bacterial photosynthesis to driving phototaxis (channelrhodopsins in flagellates). Signal transduction in phototaxis involves depolarization of the cell membrane.

Light gated, single protein, ion channels are used by motile algae (with flagella) to sense light
and move accordingly (phototaxis)
Optogenetics inserts the genes for these proteins into animal nerve/brain cells to allow light flashes to
control neuron response (Scientic American, Nov 2010)

        -- Bacteriorhodopsin is a protein used by archaea, most notably halobacteria. It acts as a proton pump, i.e. it captures light energy and uses it to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy.

        -- Proteorhodopsin is a photoactive retinylidene protein in marine bacterioplanktons. Just like the homologous pigment bacteriorhodopsin found in some archaea, it consists of a transmembrane protein bound to a retinal molecule and functions as a light-driven proton pump.

        The only product of this type of photosynthesis is ATP, made by the rotary machine ATP synthesis as the H+ flow down their concentration gradient. No reduction of NADP+ occurs. There is no carbon fixing. This type of photosynthesis if used exclusively provides only supplemental energy, not organic materials for structure.

        Some organisms, however, can do both cyclic (ATP) and non-cyclic (NADPH)  photophosphorylation shifting back and forth between them. Wikipedia below implies strongly that plants can do this, but other references talk of cyclic photosynthesis only in the context of bacteria with one photosystem. I have seen references that say cyclic photophosphorylation only occurs in PSI, but then I find it shown in PSII. Where exactly you find cyclic photophosphorylation is not very clear.

        -- The concentration of NADPH in the chloroplast may help regulate which pathway electrons take through the light reactions. When the chloroplast runs low on ATP for the Calvin cycle, NADPH will accumulate and the plant may shift from noncyclic to cyclic electron flow. (Wikipedia -- photophosphorylation)

Cyclic and non-cyclic animation
        Here's an excellent animation with voice (below screen captures) that shows both cyclic and non-cylic (Z cycle) photophosphorylation from McGraw Hill. Cyclic photophosphorylation is here identified as bacterial, and electrons are shown being excited and moving through the transport chains one at at time.

         http://highered.mcgraw-hill.com/olc/dl/120072/bio12.swf

Definitions
       -- Photo-phosphorylation is the process of using the energy of photo excited electrons to make ATP by first pumping up a proton gradient. Phosphorylation refers to the fact that ATP releases useful energy by popping off a phosphate molecule [Pi = PO3H (nom)] when it is exposed to water.

        -- Chemi-osmosis is the process of using proton diffusion (down its gradient) thru a rotary turbine (called ATP synthase) to reattach the phosphate molecule (Pi) to ADP forming ATP.

        -- Cyclic photo-phosphorylation is using the energy of photo excited electrons cycling (physically) around an electron transport chain back to where they started to pump up the proton gradient, which is used to make ATP. This process is used in 'half Z' photosynthetic bacteria with only one photosystem.

        -- Non-cyclic photo-phosphorylation is using the energy of photo excited electrons moving through an electron transport chain and out of the enclose space by crossing the thylakoid membrane. This process is used in 'full Z' photosynthetic organism like plants and cynobacteria. The 'lost' electrons are constantly replaced by oxidizing (ripping apart) water (or sulfur, hydrogen, iron, etc in the casse of certain bacteia.
        -- Autotrophs -- 'Most phototrophs are autotrophs'. Translation: most photosynthetic organisms can live autonomously, i.e light & CO2 plus a few inorganic materials are all they need to live. They use light energy to fix carbons.

Photosynthesis is biology, chemistry, & physics
         Biology --- Photosynthesis reactions are controlled by (about) 30 different proteins. Light sensitive proteins can quickly change shape when hit by a photon of visible light. An electron (in key bonds) of the light sensitive proteins can pop out of its bond when it absorbs the energy of a photon. The 'breaking' of the bond triggers the protein to change shape (which can do work), and the energized free electron is able to move to nearby proteins that are designed to extract more energy from it (electron transport chain).

         Chemistry --- The so-called 'dark reactions', which can occur when there is no light (surprise), involve processing the two intermediate (energy storage) molecules into a sugar (glucose) that can feed the plant.

         Physics --- The capture of photons of light by electrons is the domain of quantum physics. Understanding energy flows, electric fields, concentration gradients, and diffusion is as much physics/electrical engineering as it is biology/chemistry. It's not uncommon to read in introductory photosynthesis write ups about how a reaction occurs when photons knock out two electrons. But photons come in fairly slowly (msec apart in bright sunlight per reaction center), so electrons are energized (from P680) one at a time (one photon energizes one electron) jumping into the electron transport chain. It may be though (it's not fully understood) that the electron transport chain does not (fully) run until two electrons arrive, the so-called 'two electron gate'.

        P680 then gets its (one) missing electron back by pulling it (oxidizing) from a nearby manganese molecule. When the P680 reaction has run four times (four photons have come in) and the manganese molecule has lost four electrons, the manganese molecule then gets its four electrons back by ripping apart two water molecule (2H2O), essentially pulling the four electrons from the four hydrogen atoms (releasing them as proton ions inside the membrane) and allowing the two oxygen atoms to join (O2) (in a covalent bond where they share two electrons).

If plants both put out and take in oxgen, this brings up an interesting question:

Question --- Why is it plants throw net oxygen into the air? In other words why doesn't the oxygen plants pull from the air for their own energy needs (to grow and make structure) cancel out the oxygen their photosynthesis puts into the air?

(Update July 2014)
       Short answer --- According to PBS Nova the explanation may be that some of the carbon pulled from the air by photosynthesis is not returned to the air because it goes into a carbon sink. Mostly this is ocean photosynthetic bacteria and diatoms that don't get eaten and die sinking to the bottom of the ocean. Carbon that goes into a sink never gets oxidized, so it means that photosynthesis taken as a whole (plants and bacteria) output net oxygen to the atmosphere.

Some perspective on net oxygen output
       School textbooks simply say plants output oxygen, but it's not enough to point out that photosynthesis throws off oxygen, which it certainly does as only 1/3rd of the oxygen from disassembled CO2 and H2O molecules ends up in glucose with the remaining 2/3rd released as gaseous oxygen, without looking at the oxygen intake of plants as they oxidize the sugar they have made to get useful energy. The idealized equations of photosynthesis are the reverse of oxidation. Isn't this saying that the oxygen released when CO2 and H2O are converted to sugar is just the amount of oxygen that must be extracted from the air to 'burn (oxidize) sugar back to CO2 and H2O?

        A major (2 hr) PBS Nova show on satellite views of the dynamic earth throws some perspective on this. Satellite views of the Amazon rain forest shows it outputting huge quantities of oxygen during part of the day only to have nearly all this oxygen sucked back in later in the day. The shows claims the net (daily) oxygen output of the Amazon rain forest into the atmosphere is nearly zero, it is almost a 'closed system'.

        The shows explanation for the largest flow ("more than half") of net oxygen into the atmosphere come from satellite views of huge blooms of photosynthetic bacteria and diatoms. When the bloom is growing the output of oxygen is large. A bloom like this is the base of the ocean food chain attracting many fish, so much of it is eaten, but it's not all eaten. The dead bacteria and diatoms sink to the bottom of the ocean where it builds up in a huge layer, a geological carbon sink. Without of course giving numbers (this is TV) the show implies this imbalance is substantial. They say "more than half" the oxygen entering the atmosphere comes from this source. (Of course, a large imbalance is consistent with those who argue that fertilizing the ocean would be a practical way to pull carbon from the atmosphere.)

Here's my guess --- I suspect there are two answers
                    --- No process is 100% efficient. The plant must take in more (solar) energy than it stores (in glucose). Each time glucose transforms there is an energy loss. When the plant uses the glucose, some of its energy is lost. Hence oxygen output, being near the start of the process chain, exceeds oxygen usage, which is at the end of the process chain.

                  --- Some of the energy captured by the photosynthesis process is used not for cellular respiration, but to make cellulose and other structural components of the plant. When the plant dies, its structure becomes food for other organisms, so at that time some of the 'excess' oxygen is than pulled from the air to break it down.

        I found this interesting reference about C4 plants. (search 'CO2 compensation concentration')
       --        (C4 plants) have a low CO2 compensation concentration (ambient CO2 concentration at which the rate of CO2 uptake (photosynthesis)is balanced by the rate of CO2 evolution (respiration)
======================================================
All the light reactions occur in membranes?
        Yup, membranes are one of the keys to understanding photosynthesis. Of course, one purpose of the folded internal membrane of the chloroplasts is likely that it provides structure and a controlled geometry for the collection of light. But probably much more important is that a membrane supports both a concentration gradient (of ions) and a voltage across the membrane. The membrane voltage and concentration gradient across the membrane play important roles in photosynthesis light reactions.

        Concentration gradients are sort of like rechargeable batteries. Pump up the ion concentration inside the membrane and you can store energy. Allow ions to flow down the concentration gradient, and you can extract useful work from the gradient. Both of these mechanism happen in chloroplasts. Light activated electrons cause H+ concentrations to be is pumped way up in the center, then concurrently (or later) this energy is extracted by allowing H+ to flow down the concentration gradient (through the membrane). Proteins capture some of the energy of the ions flowing down the concentration gradient and use it to make the energy rich molecule (ATP).

        If there is a voltage, there is an electric field (or E field) present (units of E fields are volt/meter). E fields exert forces on (free) electrons, so it is likely that the E field of the membrane helps direct the light energized electrons as they jump from protein to protein (electron transport chain).  In the case of nerve cells the membrane releases and pumps ions to modulate the membrance voltage high/low, in this way transfering signals from nerve cell to nerve cell.

Photosynthesis Outline
Energy flow
        photon ==> energitic electron
        electron (generated from H2O pulled apart) ==> flows across membrane doing work
                    waste product from pulled apart H2O is O2 (inside inner cell)
                    (waste) O2 diffuse through the cell membranes to air
        energetic electrons(s) ==>  used to make  two (recylable?)  'internal food' molecules (ATP and NADxxx)
                        a) NADxxx generated from a protein powered by an energetic electron
                        b) ATP is made in two steps
                                    1) proteins powered by energetic electrons pump up (very high)
                                                    concentration of H+ (hydrogen nuclei) in the cell
                                    2) High concentration gradient of H+ used to power a protein
                                                    that makes ATP (chemogradient)
        ATP and NADxxx ==> (straight chemistry) make glucose (primary output)
                                CO2 gas pulled from air is pulled apart to use the carbon in the glucose
                                glucose has in it only the atoms of carbon, hydrogen, and oxygen?
                    This is the dark reaction (Calvin cycle) occurs outside the inner cell

how well understood
        very fast, much of it learned from bacteria (1/2 as complex)
when understood
         lots of nobel prizes in 890, & 90's
dark reactions
            just chemistry, outside the inner cell
Speed
    much is amazingly fast (1/1000 speed of fast computer gate)
    some is slow msec
Rates
    bright light 1-10 times a sec for center molecule (chlorophyll), maybe 300 times sec with
           antenna feed
Muddled
    photons are discreet only (pretty sure) only can excited one electron
         (much of discussion is muddled or simplified because it talks of two or four electrons being processes)

Introduction
        Photosynthesis is (very) complex and for the non-biologist (or non-chemist) difficult to understand. Photosynthesis in plants uses nearly 30 distinct proteins that work within a complicated membrane structure to produce a sugar molecule of sucrose. Much of the detail of these molecular structures has only been figured out in the last 20 years.

        My first attempts to dig into it using Wikipedia left me baffled. I found to get anywhere I first needed to do some homework. I found I needed at least a modicum (I like this word) of understanding of topics like, chemical bonds, membrane potentials, oxidation, electronegativity values, osmosis, ion channels, ion pumps, and electrochemical potential.

       I tried to hack a path though the (astounding) complexity of cellular mechanism by focusing on energy flows. How do cells get energy, store energy, and use energy?  How are the electric fields and concentration gradients across cell membranes involved?  What's the deal with electron flows? Does it make sense to think of electrons flows as currents?  In photosynthesis, of course, the key questions are how (at least in overview) is the the energy of (individual) light photons captured and used to form energy rich molecules and with what efficiency?

        Best readable description of photosynthesis I found is here:

         http://www.life.uiuc.edu/govindjee/paper/gov.html

Capturing photons
        The way plants capture photons for photosynthesis is somewhat like a type of solar power collector. There is a type of desert solar power collector that has central tower surrounded by a field of mirrors. The mirrors concentrate the sunlight on the tower. The tower contains the machinery to convert the energy of the concentrated sunlight into useful power (typically by heating a fluid that expands and turns an electric generator).

        Scattered throughout the membranes of the chloroplasts are the tower-like analogs (called photosystems) each containing a light sensitive chlorophyll molecule that is coupled to other molecules (called a reaction center) that extract useful work from photon energized electrons released by the chlorophyll. In the same way that the tower is surrounded by mirrors that direct photons to it, each chlorophyll molecule is surrounded by a large array (300 or so) of so-called antenna molecules. The antenna molecules, which are composed of five different pigments, can absorb photon energy (into their electrons) over a wide frequency range and are able to efficiently (by resonance energy transfer) pass that energy to a nearby chlorophyll molecule in a photosystem (tower) for processing. The energy transfer process is so efficient because its a quantum effect (involving excitons which are quanitized quantums of vibration).

Excellent 26 chapter online (pre-university) chemistry course (should read through)

        http://www.chem.ox.ac.uk/vrchemistry/foundation.html

**        -- Carotenes are assistants to chlorophyll in photosynthesis. They absorb light of wavelengths that chlorophyll does not, and transfer the energy in the form of excited electronic states to chlorophyll molecules. They are called antenna molecules, and the different numbers of electrons in their delocalized systems represent a "tuning" of the antenna.

(for email to dekay?) carotenes carbon  congugate structure sets
        http://www.chem.ox.ac.uk/vrchemistry/chapter19/page23.html

**        -- The relationship between the extent of delocalization systems and wavelength of light absorbed applies here.
               * b-Carotene (in plants & algae) has 11 electron pairs and absorbs blue
                * spirilloxanthin (in purple bacteria) has 13 electron pairs and absorbs yellow green
                * isorenieratene (in green bacteria)  has 15 electron pairs and absorbs red.
As their electronic energy-level spacings become progressively smaller, they absorb at lower frequencies. The three molecules (above) absorb in the blue-violet, the green, and the purple-red regions of the visible spectrum, respectively, so the molecules are coloured yellow-orange, purple, and green by the unabsorbed wavelengths.

        -- In a congujate carbon chain the carbons are usually shown as having alternating single and double bonds. But tests show (& carbon spacing and energy level indicate) that energy level is between one and two bonds (closer to two bonds).

        --  b-Carotene has 11 double bonds in one long conjugated chain, and hence contributes 11 electron pairs, or 22 electrons, to a delocalized electron system.  Spirilloxanthin from purple bacteria has 13 double bonds and 26 delocalized electrons, and isorenieratene from green bacteria has the largest delocalized system of the three: 15 double bonds and 30 delocalized electrons.

How much CO2 is used?
        While each year more than 10% of the total atmospheric carbon dioxide is reduced to carbohydrate by photosynthetic organisms, nearly all of this reduced carbon is returned to the atmosphere as carbon dioxide by microbial, plant and animal metabolism, and by biomass combustion.
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Light reactions
Z diagrams
        Here's an excellent introduction to the Z system (non-cyclic photophosphorylation) with animation and a voice that pronounces all the intermediate enzymes (2nd animation from McGraw Hill). The text of the screen captures show the intermediate proteins.

         http://highered.mcgraw-hill.com/olc/dl/120072/bio13.swf

Photosynthesis light capture overview
        The photosynthesis light capture machinery in all plants (and algae) is two step process. There are two light capture mechanisms, called photosystem II and photosystem I, in cascade (named backwards because PSI was found first). Below is one of the better figures I found showing (qualitatively) the sequence of reactions involved in light capture (see also the other light capture figures further below).

        There's another whole set of molecular machinery of photosynthesis, called dark reactions, which in spite of their name do not run (for the most part) in the dark, but run in parallel during sunlight. They takes the energy rich molecules from the light reactions (ATP and NADPH) and use them to break apart CO2 and combine (fix) the freed carbon with freed hydrogen making sugar (glucose). Molecules thrown off by the dark reactions (ADP, Pi and NADP+) are recycled back to the light reactions to be used as raw materials to make ATP and NADPH.

First step -- photosystem II
        The sequence is as follow:  A photon energizes an electron in the P680 reaction center and it flys out. It cascades in energy down an 'electron transport chain' (plastoquinone, cytochrome b6-f) ending in plastocyanin where it awaits another photon.

        Some of the energy extracted from this electron is used to rip apart (oxidize) water in the oxygen-evolving complex into oxygen H+ and e-, in a process called photolysis. (Similiar to electrolysis of water, but using light energy instead of current). The oxygen from the split water diffuses out into the atmosphere (or water). The split water provides an electron to replace the missing electron in P680 and H+ builds up the H+ concentration inside (lumen).

        The remainder of the PSII excited electron energy is extracted in its electron transport chain and used to pump protons (H+) into the center (lumen) further building up the proton gradient across the (thylakoid) membrane. The proton pumps are proteins (cytochrome b6-f complex) within the electron transport chain.

        -- In photophosphorylation, light energy is used to create a high-energy electron donor and a lower-energy electron acceptor. Electrons then move spontaneously from donor to acceptor through an electron transport chain.

PhII electron transport chain
        The heart of the PhII electron transport chain is the b6-f complex. It's built around iron and sulfur (FeS4), and it's the main proton pump in the thylakoid membrane. It extracts some of the electron's energy using it to pump protons from outside (stroma) to a high concentration inside (lumen). This pumping converts the (some of) the local electron's energy into potential energy of a high concentration of protons in the lumen (inside the thylakoid membrane).

        The other two stages in the PHII electron transport chain are plastoquinone at the beginning and plastocyanin at the end. Compared to the b6-f complex these are (I think) small molecules or small molecules bound to a protein.

        The job of plastoquinone is to quickly accept the high energy electron freed from the PHII reaction center by a photon, so it doesn't fall back into the reaction center and waste its energy as heat. (Wikipedia says plastoquinone also pumps protons, but this seems to be a minority view. Maybe it's a matter of definition with Wikipedia maybe considering it to be part of the b6-f complex.)

Fluorescence time constant
      Blankenship explains that excited electrons always have a fluorescence decay path (emitting a photon to radiate away the excess energy) that is in 'parallel' with other reactions. With parallel reaction paths the reaction with the faster time constant dominates. The fluorescence time constant is on the order of a few nsec, so the reduction of plastoquinone (grabbing of the light activated electron from the reaction center) has to be sub-nsec to keep the transfer efficient. These are first order time constants, so to keep the loss to 1% the time constant would need to be on the order of a tens of psec. Note the need for sub-nsec speed rules out diffusion being involved. In a sense the need for speed 'explains' why electron transport chains exist. They can move electrons via the quantum mechanism of overlapping orbits.

Two electron gate disagreement
       It's pretty clear there must be a two electron gate somewhere in the light reactions, because at the termination of the light reactions two electrons are needed to convert NADP+ to NADPH. Notice in my figure the 24 turns of the Z cycle bring 24 electrons through the cycle, but at the termination only 12 NADPH are made. The reason it takes two electrons to make one NADPH is that in addition to the one electron needed to neutralize the plus ion (NADP+) another electron is needed to pair up with the proton picked up from the stroma fluid to make H. But where is the two electron gate? This is where references disagree.

Plastoquinone or ferredoxin
       The book 'Acquatic Photosynthesis' (2007) explains in some detail that the first stage in the PHII electron transport chain (plastoquinone) holds one electrons and waits for a second electron (from the reaction center) before releasing them. In other words it identifies plastoquinone as a 'two electron gate', but Blankenship's book (2002) says nothing about plastoquinone being a two electron gate. Blankenship does include a two electron gate, but instead of being at the beginning of PHII electron transport chain he has it at the end of the PHI electron transport chain (ferredoxin).

--  The semiquinone at the Qi-site is much less stable (Em < -50 mV for Q/SQ couple), so that reduction by cyt bH does not occur significantly, and the site operates effectively by transferring two electrons only when both b-cytochromes are reduced. (http://www.life.illinois.edu/crofts/bioph354/lect24.html. Lots of good, detailed photosynthesis info at this siite)

        Don't know if this disagreement is due to time. Acquatic Photosynthesis was published five years after Blankenship's book, which is now 8 years old. Or maybe the where the two electron gate is is just not settled. I found one paper online proposing a 'A MODEL OF THE TWO ELECTRON GATE IN CHLOROPLASTS' showing plastoquinone. It seems that the two electron gate is better understood in bacteria, because a Google search finds a lot of references to a two electron gate in bacteria.

        What's not shown on the Z diagram is that the reaction centers of PHII and PHI are spacially separate. Blankenship shows that in chloroplasts the PHII reactions centers are in the grana (center stacks) whereas most of the PHI reactions centers are on the outside layers or in the interconnecting stroma lamellea. Plastocyanin is a mobile protein that has to diffuse a long way (hundreds of nm says Blankenship) to bring the PHII electron near the PHI reaction center.

        The second complication to coupling an electron from PHII to PHI is that run at different times, i.e. they are time separate. Plastocyanin has to hold its spare electron until a photon hits the PHI reaction center oxidizes it (pops out an electron to the PHI electron transport chain), then the PHI reaction center will be positively charged and it will pull the electron it needs from plastocyanin.

        For a long time I thought this presented timing problems. Specifically, under low light when the time between photons stretch out, that the 'hold' time of plastocyanin would be exceeded and its extra electron would (somehow) leak away. While I have not read this anywhere, it now seems reasonable to me that the plastocyanin extra electron can probably be held a long time, because it's likely at a low energy since most of the photon excited electron energy was (likely) extracted in the previous b6-f proton pump.

                plastoquinone -- (abrev Pq) H+ pump, powered by electron energy

        cyctochrome -- H+ pump, powered by electron energy. A hemeprotein (bound to a heme)
                            with a central iron atom whose change in oxidation state allows it to accept or
                            donate an electron
        plastocyanin -- (abrev Pc) transfers an electron via a copper atom

PhI electron transport chain
       ferredoxin -- (abrev Fd) electron carrier built around two iron and two sulfur

        In essence this process converts a fraction of the energy of the two photons hitting PSII and PSI reaction centers into chemical energy stored in the bonds of NADPH. NADPH is one of the two intermediate molecules used to transfer energy from the light reactions to the dark reactions.

One or two electrons?
        There is no question that it takes two electrons arriving at the end of PSI electron transport chain (ferredoxin-NADP reductase) to reduce NADP+ and make NADPH, but do the electrons arrive one at a time or two at a time? My working assumption has been that they arrive one at a time, but some references seem to imply that electrons move though the electron transport chain in pairs. It's unclear.

        In essence this process converts more of the energy of the photons hitting PSII (not PSI), temporarily stored as potential energy of a proton concentration gradient (proton motive force) across the thylakoid membrane into chemical energy stored in the bonds of ATP. ATP is the second of the two intermediate molecules used to transfer energy from the light reactions to the dark reactions.

Electron transport chain
        -- The electron transport chain is remarkable similar from the simplest organisms to the most complex. The discovery of these fundamental similarities was one of the crowning achievements of 20th century biology. The underlying unity of these seemingly unrelated processes (photosynthesis, mitochondrial ATP production, lithotrophy) motivates modern research in energy metabolism, one of the most exciting fields in biology.

Lithotrophy
        Lithotrophic bacteria get energy to live by oxidizing inorganic materials. Using this energy some lithotrophic bacteria make both ATP and NADPH allowing them to run the calvin cycle and fix carbon. In other words lithotrophic bacteria have much of the same molecular machinery as photosynetic bacteria, but it's driven by oxidation of inorganic materials like hydrogen, sulfur, or iron rather than light! (There is even a gold reducing lithotrophic bacteria.)

Subsurface (deep underground) bacteria
       -- Heterotrophic anaerobic microbial communities exist in relatively permeable sandstone or sandy sediments, located adjacent to organic-rich deposits. These microorganisms appear to be maintained by the consumption of organic compounds derived from adjacent deposits. Sources of organic material serving as electron donors include lignite-rich Eocene sediments beneath the Texas coastal plain, organic-rich Cretaceous shales from the southwestern US, as well as Cretaceous clays containing organic materials and fermentative bacteria from the Atlantic Coastal Plain.

        Additionally, highly diverse microbial communities occur in regions where a source of organic matter is not apparent but where igneous rock is present. Examples include the basalt-rich subsurface of the Columbia River valley and the granitic subsurface regions of Sweden and Canada. These subsurface microbial communities appear to be maintained by the action of lithotrophic bacteria growing on H2 that is chemically generated within the subsurface.

        Other deep-dwelling microbial communities exist within the deep sediments of oceans. These systems often rely on anaerobic metabolism and sulfate reduction. Microbial colonization extends to the depths below which high temperatures limit the ability of microbes to survive. Energy sources for the organisms living in the oceanic subsurface may originate as oceanic sedimentary deposits.

        P680 is nothing more than four chlorophyll molecules that are in some way coupled together and act as one entity. It's probably built from chloropyll 'a' molecules because chlorophyll 'a' has a sharp peak in its response curves (see curves below) at 680 nm. (This is one biological item that is rationally named!)

        Photosystem II is the only known protein complex that can oxidize water, resulting in the release of O2 into the atmosphere. Despite years of research, little is known about the molecular events that lead to water oxidation. Energetically, water is a poor electron donor.  The oxidation-reduction potential of water is +0.82 V but the oxidizing potential of P680/P680+ is estimated to be +1.2 V.

        When the P680 rips away two electrons from a water molecule (oxidizes the water), what is left is two bare protons, H+ (two hydrogen minus their electrons) and a free oxygen atom. The freed H+ further build up the concentration of H+ inside the cell. The free oxygen atom soon meets another free oxygen, and they join up forming a molecule of molecular oxygen, which as a waste product, diffuses out of the cell and finds its way to the atmosphere.

Manganese 'water oxidizing' complex
        Manganese (not magnesium) at Z = 25 is just below iron in the periodic table. Manganese is the universal metal for catalyzing water splitting in all oxygenic phototrophs. Researchers have tried replacing manganese with other elements for photosynthesis, but nothing else works, concluding "manganese may be truly unique for biological water splitting."

        So the high Z atom that sucks the electrons out of water appears to be manganese. Photosynthesis II has a "metalloenzyme core containing four atoms of manganese" (Wikipedia). When looked at in detail, of course, its complicated. It's actually four magnesium atoms coupled to calcium. Magnesium has a partially filled 3d shell and the four atoms together have a bunch of energy combinations involving various spin configurations. The difference in energy levels with 3d orbits is small.

        Below P680+is photon activated P680, meaning it is P680 which has been hit by one photon that knocked out one electon (which moves 35 angstums across the membrane). P680+ has an estimated ionization potential of 1.3V to 1.4V enough to oxidize water. Notice the figure shows P680+ entering the four manganese complex and stripping off one electron. The little P680+ shows it being restored (reduced, given back its missing electron). (The times given appear to be the times required for the state change, rather than the hold time, which is what I want to know.)

        -- "The spacial distribution and energies of the electrons in the various S states are vital to understanding the water splitting chemistry."

        -- Photooxidation of a second Mn is catylized by a reaction product of the first photooxidation of Mn. (In other words the system is more sensitive to a photon coming in after the first.)

        -- Production of O2 by the oxidation of water within photosynthetic organism is a striking signature of life on earth.

        -- By using water as an inexhaustable source of electrons and protons, it enabled the proliferation of phototrophic life everywhere on the planet.

        -- O2 is a byproduct of water into electrons and protons (in photosynthetic oxygen-bacteria and eukaryotes (green algae and higher plants)

        -- Emergence of atmospheric O2 premitted the development of respiratory metabolism with its vastly more efficient energy production.

***        -- Every known O2 producing (oxogenic) phototroph uses exactly the same four magnesium + calcium cluster. Its gene is highly conserved, "an extraordinary feature not found anywhere elese in biology." The authors emphasize that in 2-3 billion years of evolution mother nature has been able to invent only this one biological blueprint for water splitting.

*        -- Photosystem II accomplishes a complex task of converting one electron photoexcited state of chlorophyll into the four electron (all or nothing) oxidation of two water molecules

        -- Basic data for a four cycle state is that when chroloplasts are flashed repeatedly O2 release peaks every four flashes. The models assume that each flash removes one electron, i.e each flash advances the oxidative state of two water molecules. This is known as the S-state cycle (see below)

        -- The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions and a calcium ion; this oxygen-evolving complex binds two water molecules and stores the four oxidizing equivalents that are required to drive the water-oxidizing reaction.

        -- Photosystem II is the only known biological enzyme that carries out this oxidation of water.

Key to photosynthesis! ???
        After working bond energy calculations (see below), I have come to realize that the catalyzing Mn complex (see fig below) is a critical element in making photosynthesis work! The highly oxidizing photon energized P680 works though this Mn complex to oxide water. Without this Mn complex energy supplied by photons would not be enough to break apart the water molecule to extract the electrons (& protons).

        I have skimmed dozens of reference and papers on photosynthesis and I don't remember anyone making this point! Everyone just blithely says that oxygen is the byproduct of (normal) photosynthesis. In more detailed references they may say that O2 comes out after four state changes in the Mn complex, but no one I have seen points out this is not a detail. It is absolutely critical from an energy viewpoint in making photosynthesis work, in matching the energy oxidation requirements of water to the energy available in photons of visible light!

        The trick (to making photosynthesis work) is that the electron bond energy in the so-called waste or byproduct O2 (molecular oxygen with two bonded oxygen atoms) is something like 90% of the energy of the electron bond energy in water. In other words the net energy required to break apart water is reduced by nearly an order of magnitude, from something like 4.8 ev to 0.5 - 0.8 ev if the output is O2 rather than just electrons, protons and O. This is critical, because red P680 nm photons only supply 1.8 ev of energy.

        A very serious complication in taking advantage of the potentially huge net O2 energy savings is that it's only available if two water (H2O) molecules are dismembered freeing two oxygen atoms. Since photons arrive one at a time and since four photons are needed to remove the four electrons from two water molecules, how does this work?

        The Mn complex below makes it work. It somehow stores up the energy from four photons, as it cycles through states S0 to S4, then all at once it works on two water molecules, freeing four electrons and four protons (4H+) and releasing one O2 molecule. When tested with flashing light (presumed to only deliver one photon per flash), pulses of oxygen only come out on every fourth light flash!

Details of Mn4Ca cluster (four manganese atoms plus one calcium)
showing four state changes (S0 to S4) due to four photons (hv)
One electron per flash is snatched from two water (H2O) molecules
with O2 released only after four photons have arrived.
source ---' Manganese: the Oxygen-evolving Complex and Models'
in Encyclopedia of Inorganic Chemistry
http://mrw.interscience.wiley.com/emrw/9780470862100/eic/article/ia128/current/pdf

 Notes from reading encyclopedia article (above link) on the Manganese complex
        The Mn oxygen-evolving complex, also called the WOC (water oxidizing complex) and OEC (oxygen evolving complex), is believed to have evolved between 2 and 4 billion years ago, because it is the oxygen output by this complex as part of photosynthethetic single celled organisms that oxygenated the earth's atmosphere.

        It's inorganic core (Mn4Ca1OxCl1), is almost exactly the same in every known oxygen producing photosynthetic organism, whether bacteria or algae or plants, and the DNA sequence of its key gene is highly conserved. It's the only known biological way to split water and appears to have been invented only once.

        The understanding is that energy of one photon in P680 'advances the oxidation state of WOC by removing one electron', meaning it pulls out more electron, advancing the oxidation state from S0 to S4, then at state S4 WOC oxidized two water molecules (2H2O) with the release of four electrons, four protons (H+) and one O2.

        There's even another intermediate oxidizing step:  P680 actually oxidizes tyrozine (which is indicated by Yz in the figure) that in turn oxidizes the Mn complex WOC.

        The encylopedia reference on WOC (15 pages) simply says that the oxidation potential of P680 (estimtated as 1.3 - 1.4V) exceed tha required for water splitting. They do not explain that the bond energy of O2 being only slightly lower the bond energy of water, is what really the Mn WOC to work its water splitting magic with an energy input from P680 less than that provided by one visible light photon per electron.

'Two electron gate' explanation?
        The way P680 is activated looks like it may provide an explanation as to how the photosynthesis process can wait for msec's for a second photon to come it before starting. It must be that the time constant of P680 minus one electron is longer than the average time between photons (locally collected). (One technical article has a time constant of 1 msec for changes in energy of four manganese atoms)

        Note this is another of these critical for life parameters. A shorter time constant of single photon activated P680 could drastically reduce the efficiency of photosynthesis, so probably we wouldn't be here!

Oxidize water
        A double photon activated P680 must have open electron orbits down deep in one (or two) high Z atoms, manganese (Mn Z = 25) is the key atom, in the P680 complex for two electrons to fall into. What keeps two hydrogen atoms and an oxygen atom together in a water molecule are the two shared hydrogen atoms, so when the shared electrons are ripped away, the molecule falls apart and the three atoms separate.

Manganese (Mn Z = 25)

        We review the atomic structure of the metalloenzyme, the photosystem II water splitting complex (PSII-WOC), as revealed by X-ray diffraction and spectroscopic techniques. We describe: 1) The electronic structure of its inorganic core, Mn4Ca1OxCl1–2(HCO3). The chemistry of photosynthetic water splitting is energetically demanding and mechanistically complex.

Artificial photosynthesis
        One goal of artificial photosynthesis is to do what photon activated P680 does, which is to break apart water to release hydrogen and oxygen (for energy). But I read on a Swedish Univ site, where they are working on this, that so far it has never been achieved in man-made molecular systems.

Generating ATP
         The light reactions ion pumping and water oxidation build up a large H+ concentration inside the cell across the membrane, storing a lot of energy in this concentration gradient. A complex in the membrane (ATP-Synthase) (later?) allows the excess H+ inside to escape to the outside, and as the H+ flows down its concentration gradient it does work making the energy storage molecule (inside cell) ATP.

        The energy stored in the proton electrochemical potential is used to covalently attach a phosphate group to adenosine diphosphate (ADP), forming adenosine triphosphate (ATP). The energy stored in ATP (phosphate group-transfer energy) can be transferred to another molecule by transferring the phosphate group.

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Dark reactions -- calvin cycle
        The NADPH and ATP formed by the light reactions provide the energy for the dark reactions of photosynthesis, known as the Calvin cycle or the photosynthetic carbon reduction cycle. The reduction of atmospheric CO2 to carbohydrate occurs in the aqueous phase of the chloroplast. The carbon reduction cycle is a complex series of redox reactions catalysed by enzymes, which break apart CO2 and add hydrogen obtained from the water to make the sugar glucose (C6H12O6). Glucose not only serves as a fuel for respiration (food), but as a raw material for cellulose (& lignin) building the structure of the plant.

       All plants and algae remove CO2 from the environment and reduce it to carbohydrate by the Calvin cycle. The Calvin cycle is used by almost all organisms that fix atmospheric carbon, including some photosynthetic bacteria like purple bacteria, but there is another way to fix CO2 used by a few bacteria. Green sulfur bacteria fix carbon without RuBisCo using the reverse (reductive) TCA (Tricarboxylic acid) cycle. Sill in evolutionary terms dark reactions have been remarkably conserved. There is somewhat more variation in light reactions where there are three major variants, some bacteria have a version of half the Z cycle of plants.

Decoding the Calvin cycle
        In my early readings of the Calvin cycle (dark reactions of photosynthesis) I found it a nearly impenetrable thicket of complexity. It was step after step of enzyme catalysed reactions, each molecule having  a very long name and the enzymes having even longer names. I decided it was too complicated for anyone but an expert to follow and basically gave up trying to understanding it in detail.

        I began collected calvin figures, when I noticed they were almost all different and not consistent, and virtually none of them showed the water output, which I was sure was there! How complicated is this process when most people writing about it can't seem to keep it straight!

        The aim of most Calvin references was to follow the carbon through the process, a few followed the phosphate group too, but none paid any attention to O & H, so it was impossible to figure out where the water output, which  I knew must be there, came out. Also I was unsure how to show the (simplified view) of the calvin cycle in my block diagram because I couldn't figure out if the hydrogen in the glucose came in via NADPH, the hydrogen carrying intermediate between light and dark reactions, or if it came from H+ ions that diffused out of the lumen.

Cracking the Calvin cycle
        After a couple of months, I took another whack at the calvin cycle, and I found a way to crack it, meaning a way  to figure out the inputs and outputs of each step in the process.

        The trick I found was to use Wikipedia to look up the chemical formulas of all the molecules in the process (ignoring the catalysing enzymes). It turns out all those molecules in the process carrying the carbon with the forbiddingly long names are actually relatively simple (just four elements with < 30 atoms total). By making one assumption (phosphate group = PO3H), I found the chemical differences from step to step could be explained by the inputs or outputs shown on most Calvin figures plus inputs and outputs of water. Everything worked! I have seen nobody do an analysis like this.

What I found in the Calvin cycle -- water loop
        What I found is very interesting and gave insight into a long standing mystery. What I found is effectively a water loop in the forward part of the Calvin cycle. Water enters at the same time as the CO2, i.e. one molecule of water is fixed with every molecule of CO2. Just before the sugar output 12 NADPH come in bringing 12 hydrogen. At this point the 6 water picked up with the CO2 exit along with the 6 extra oxygen from the CO2 and 6 hydrogen. This water loop (6 H2O in/out) is in addition to the 6 H2O output of the forward path of the Calvin cycle.

H2O confirm  (6/10)
       Blankenship's photosynthesis book confirms water comes in with CO2. The carboxylation step in his Calvin figure (p176) shows CO2 + H2O entering.

H discrepancy
        A count of atoms in in Blankenship's Calvin molecular diagrams generally agrees with what I show in table (from Wiki and other sources) except that that Blankenship H is generally two lower?? Blankenship in the regeration phase twice shows H2O twice entering followed immediately with HOPO3 exiting. This is equivalent to picking up one (or two) H as Pi exits.

        There are weird differences. The RuPB ball and stick figure in Wikipedia shows H12, but Blankenship's RuBP figure shows only H8! (Half of this H difference may be due to Pi. Blankenship shows no H on his phosphate groups, whereas I am using PO3H. (C, O, and P all agree).

Calvin cycle steps
        Most references including many of the calvin figures in this essay just name the molecules of the various steps (without the formula), and some show the quantity too. In the table below I include the formulas I obtained from Wikipedia. (In one case the formula was missing so I counted the atoms in the stick and ball figure, and later confirmed this formula from another reference.) With the chemical formulas of each step I can figure the input and outputs at various points in the cycle.

        My assumption is that the phosphate group, which come in with ATP and breaks off to release energy, is Pi  = PO3H, so when a P comes and goes in the formula it takes O3H with it. My quantities in column 2 are for one molecule of glucose (C6H12O6 with post processing).
 

Calvin cycle regeneration path details
        Morton in his book  (Eating the Sun: How Plants Power the Planet) has a nice summary of the details of the regeneration (feedback) part of the calvin cycle. Nowhere else have I seen it explained so simply, certainly not in Blankenship, who just says there are a lot of intermediates and who doesn't label quantities.

        Morton's numbers are for the case where three CO2 are input combining with three rubisco yielding six three carbon phosphoglycerate.  One of the three carbon phosphoglycerate is split off as output (later to become half a glucose). The other five three carbon phosphoglycerate molecules are used to regenerate the five carbon rubisco that got chopped up after CO2 bonded with them. The job of the calvin regeneration path is to 'rejigger' the five three carbon molecules (phosphoglycerate) into three five carbon molecules (RuBP).

        The details of the rejiggering are this: Two of the five three carbon are combined to make a six carbon, which splits into a four carbon and two carbon. This four carbon and two carbon are then each combined with a three carbon making a seven carbon and a five carbon. One of the five carbon is now made. The seven carbon splits into a five carbon and a two carbon, so a 2nd five carbon is now made. Finally the two carbon is added to the one remaining three carbon making the 3rd of the five carbon rubisco molecules.

Water loop
        The change in the chemical formula before and after CO2 (Step 0 to 2) show that 6H2O must come in with 6CO2. In other words when a CO2 is fixed into RuBP it looks like a water picked up from the stroma fluid and is incorporated into the molecule too. This maybe (probably?) explains why some textbook refererences show a large water term on the input side of the dark reaction equations.

Tracking Pi through the cycle (6/10)
        Reading Blankenship's book and rereading Wikipedia photosynthesis entries some of the details of the Calving cycle have come into focus, for example, tracking Pi around the loop. When water pulls Pi off of ATP, energy is released that can do work, but what also happens in the Calvin cycle is that the released Pi from ATP gets incorporated into the product (briefly or permanently).

a) Six RuPB that grab CO2 each have two Pi. The resulting unstable six carbon product separates into twelve three carbon molecules each getting one Pi.

b) The Pi count in the reduction phase briefly goes up one and then down one. In the reduction phase (step 4) ADP exits, but Pi (for a brief time) remains attached to the three carbon product (it gets phosphorylated) increasing its Pi from one to two. When the NADPH comes in to do the reduction (reduce the oxygen), those 'extra' 12 Pi, which came from the 12 ATP, are now removed (it is dephosphorylated) and they exit, so the three carbon 'sugar' at the cycle output and entering into the regeneration phase each have only one Pi.

c) In the regeneration phase the first thing that happens (step 10) is that the 10 three carbon (each with one Pi) reconfigure into six five carbon (RuP) also each with one Pi. This means there are four Pi left over and they are released into solution (they exit). When six ATP come in in the regeneration phase to provide energy their Pi is also incorporated (permanently) into the RuPB product. It is phosphorylated increasing its Pi's from one to two.

d) The remaining two Pi that came in with the 18 ATP into the cycle are recovered (exit into solution) in the post processing phase where the two three carbon 'sugar' (each with one Pi) that come out of the Calvin cycle are combined to make glucose.

        a) 12H picked up earlier (step 2) from water go into the sugar and the 12H released by
                NADPH join with 6O (of 12O released) and exit as water, or

        b) 12H released by NADPH 'swap' with 12H picked up earlier from water. So the 'new'
                12H from NADPH go into the sugar, and the 'old' 12H join with 6O (of 12O released)
                and exit as water

While I admit that a) seems more logical, b) is (I think) equivalent and is easier to draw and lends itself to a simple interpretation in the form of local water loop, so this is the version I have included in my block diagram. In the table below I summarized what I find to be the inputs/outputs of the Calvin cycle organized by molecule and atom.
 

Discussion ---Does the Calvin cycle run at night?
        Does the calvin cycle run at night?  The short answer is no. The calvin cycle runs during the day in parallel with light reactions using the hydrogen and ATP the light reactions generate, but how long after the sun goes down and light reactions shut down will NADPH and ATP be available to power the calvin cycle?  No reference I've found ever seems to directly address this question, so I did some spade work.

        What would it take for the Calvin cycle to run at night?  The Calvin cycle needs a continual input of ATP and NADPH to run, both to provide the energy to power it and bring in the hydrogen for the sugar. A look at the detailed block diagram of photosynthesis in this essay shows that if light photons suddenly stop coming in, NADPH production stops immediately because it is powered by one of the electron transport chains, and ATP production will (likely) stop soon thereafter, because after the high H+ density inside the small thylakoid membranes bleeds down and the ATP generating rotary pumps (ATPsynthase) will stop. Thus the only way the Calvin cycle can continue to run for any sustained time after the sun goes down is if the light reactions have built up a large surplus of NADPH and ATP in the stroma (fluid outside the thylakoid membrane) during the daytime.

        How likely is that?  Not likely. For one thing ATP is a low energy molecule (details here) widely used to shuttle energy around inside cells. It is not used for bulk energy storage. The lifetime of the average ATP molecule is seconds to minutes depending on the metabolic activity. (A number widely quoted is while a person may use 75 kg of ATP during a day, he has only (75 mg) or 1/1,000th of this amount in his body at any one time!) ATP needs to be regenerated all the time (from ADP) when energy flows occur. It is very, very unlikely that there is enough ATP/ADP molecules within a photosynthetic cell to hold energy for more than a few minutes of Calvin cycle operation.

Shuttle molecules
        ATP and NADPH are both small molecules that shuttle back and fourth between the light and dark reactions. To move energy and hydrogen around they need to be regenerated all the time. Pop the phosphate group off ATP in the stroma and it makes a little useful energy available to the calvin cycle, but then it need to run through a light reaction ATPsynthase turbine again to be recharged by having a phosphate group reattached. Same thing with NADPH. Oxidize it in the stroma and it drops off its hydrogen atom and makes available a little useful energy to help run the calvin cycle, but then for it to be useful again it's back to the light reactions to be recharged (reduced). ATP and NADPH are shuttle molecules, there will be relatively little of them in the cell. They are spectacularly unsuited for long term energy storage, which is what would be required if the calvin cycle was to run all night.

Plants demonstrate daily in/out CO2 flows
        There's hard data too showing CO2 flows in/out of plants have a daily cycle. After much searching I found some hard field data that makes a convincing case that photosynthesis typically shuts down after sunset. In the water of ponds with lots of algae and water plants there can be large day/night pH cycles (see graph below). The cause of the pH cycle are net flows of CO2 in and out of algae and water plants, since CO2 dissolved in water makes the water more acidic (carbonic acid). When the calvin cycle is not running, the algae and water plants output CO2 into the water as they respire, burning their stores of glucose to live as do all organisms. When the calvin cycle is running well, say on a sunny day, the flow of CO2 reverses, the photosynthetic fixing of carbon exceeds CO2 respiration, so now the algae and water plants are net consumers of CO2 from the water, the acidity falls and pH rises. I found the figure below from a pond management group that advises acquaculture farmers that shows just this, a pH rise during the day and a fall during the night. This is hard proof that the calvin cycle of the algae and water plants in the pond is only running during the day and not at night.

        Something similar is seen in the air of the sealed Biosphere2 dome out in the desert. CO2 levels in the air in Biosphere2 show a similar large day/night cycling (600 ppm) with CO2 levels falling strongly during the daytime. The plants (and soil microbes) inside this large dome were clearly net consumers of CO2 during the daytime when calvin cycles were running, and net exporters of CO2 at night when calvin cycles shut down and respiration continued.

        -- During daylight algae and underwater plants remove CO2 from the water as part of the sunlight driven process of photosynthesis. ... During the day photosynthesis usually exceeds respiration so pH rises as (net) carbon is extracted from the water. As the sun begins to set in the late afternoon, photosynthesis decreases and eventually stops, so pH falls throughout the night as respiring organisms add CO2 to the water.

Biosphere2 CO2 cycle
        -- Daily fluctuation of carbon dioxide dynamics was typically 600 ppm (huge!) because of the strong draw down during sunlight hours by plant photosynthesis, followed by a similar rise during the night time when system respiration dominated. (Wikipedia Biosphere2) (I visited Biosphere2 on a trip to Arizona)

Terminology --- ['dark' reactions' => 'light independent reactions']
        The terminology for the binary division of photosynthesis into 'light reactions' and 'dark reactions' is changing. 'Light reactions' and 'dark reactions' has a nice symmetry, but more and more I see the phrase 'dark reactions' being replaced by 'light independent reactions'.  Why? I would suggest the following reasons:

        1) Does not accurately reflect lab data and current good understanding of photosynthesis
        2) Cause unnecessary confusion when teaching photosynthesis to students

        When students are told the two sections of photosynthesis machinery called 'light' and 'dark' reactions, is it any surprise that many assume one runs in the light (daytime) and the other runs in the dark (night time). Of course, this is only half right. The photosynthetic machinery that tears apart water and puts out oxygen runs on the energy extracted from light photons, so light is continuously required here, but the photosynthetic machinery that takes in CO2 and outputs glucose (Calvin cycle) doesn't need light to run, at least not directly. Tests on chloroplasts in a test tube show that as long as a source of ATP and NADPH is provided CO2 will be taken up and fixed, meaning the Calvin cycle is running, light or no light. Hence the phrase  'light independent reactions' is more accurate than 'dark reactions' and avoids the implication that the Calvin cycle runs only at night.

        One of the most efficient crop plants is sugar cane, which has been shown to store up to 1% of the incident visible radiation over a period of one year. However, most crops are less productive. The annual conversion efficiency of corn, wheat, rice, potatoes, and soybeans typically ranges from 0.1% to 0.4%

Membrane potential
        The voltage across the membrane in photosynthetic chloroplasts is reversed from other cells. In most cells, due to modulated transport of potassium and sodium (Na+/K+ ATPase transporter -- 3Na+ out and 2K+ in) the voltage inside a cell is kept negative with respect to the outside. But in a chloroplast (when light is falling), there is strong pumping of protons (H+) into the cell for the purpose of making ATP as they flow out. Pumping up H+ (positive ion) concentration inside the chloroplast organelle relative to the outside (x100 typ) apparently causes the inside membrane voltage to be slightly positive with respect to the outside.

Ion pumps and membrane voltage
        Predicting the polarity (& certainly magnitude) of membrane voltage from the dominant ion pump is risky. Often there is no info about electron flows, and there can be several types of ion pumps. There can also be hidden cycles. For example the animation (below) of  the Na+/K+ transporter for normal cells (below) shows three Na+ going out for each K+ coming in, but at the end shows some of the Na+ cycles in again in a glucose transporter.

        That said the dominant ion pump is most cells is Na+/K+ ATPase transporter, which is a net positive charge flow out, and the normal cell voltage is negative. In mitochondria the dominant ion pump is H+ out of the center into the intermembrane volume and again the inside membrane voltage is negative. In chloroplasts the dominant pump is H+ inward and the inside membrane voltage is (slightly) positive. However, maybe this is a coincidence, because from my block diagram you can see the all the pumped H+ just circulates!
        http://www.stolaf.edu/people/giannini/flashanimat/transport/secondary%20active%20transport.swf

        Although the voltage across the photosynthetic membrane in chloroplasts can be as large as 100 mV, under normal conditions the proton gradient dominates.  During photosynthesis there is x100 more H+ inside than outside, which is equivalent to 120 mV.

        It is very likely that the positively charged reaction center complex is immobile in the membrane, so it would appear an E field (likely due to the membrane voltage) is needed at the reaction center to push the electron away and guide it into the electron transport chain.

            The problem I (think) I see is that with the inside of the thylakoid membrane positive the E field points from inside to outside, but isn't this the wrong way? So while an outward pointing E field would push protons out through the ATP synthase channel, it pulls electrons in! The reaction centers are on the inside and simplified sketches seem to show (at least for PH 1) the electron in the electron transport chain traveling from inside to outside. (puzzled)
-----------------------------------------
        -- The missing electron on P680+ is recovered, ultimately, from water molecules on the left bottom of the diagram via an amino acid tyrosine (a specific one in a protein of PSII, also referred to as Yz in the literature) and a tetra-nuclear manganese (Mn) cluster. These reactions also require a few milliseconds. (Some reactions between P680 and P700 also take a few msecs, whereas some of these reactions occur virtually instantlyly (femoseconds.))

        -- A total of 8 quanta (photons) of light (4 in PSII and 4 in PSI), are required to transfer 4 electrons from 2 molecules of water to 2 molecules of NADP+. This produces 2 molecules of NADPH and 1 molecule of O2
======================================
        -- Photoexcited electrons travel though the cytochrome b6f complex to photosystem I via an electron transport chain set in the thylakoid membrane. This energy fall is harnessed, (the whole process termed chemiosmosis), to transport hydrogen (H+) through the membrane to provide a proton-motive force to generate ATP. If electrons only pass through once, the process is termed noncyclic photophosphorylation.

        -- During plant photosynthesis, two molecules of glycerate 3-phosphate (GP) are produced by the first step of the light-independent reactions when ribulose 1,5-bisphosphate (RuBP) and carbon dioxide are catalysed by the rubisco enzyme. The GP is converted to D-glyceraldehyde 3-phosphate using the energy in ATP and the reducing power of NADPH as part of the Calvin cycle. This returns ADP, phosphate ions Pi, and NADP+ to the light-dependent reactions of photosynthesis for their continued functioning. RuBP is regenerated for the Calvin cycle to continue.

        -- G3P ( C3H7O6P) is generally considered the prime end-product of photosynthesis and it can be used as an immediate food nutrient, combined and rearranged to form monosaccharide sugars, such as glucose, which can be transported to other cells, or packaged for storage as insoluble polysaccharides such as starch.
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Cool animations of Calvin cycle and light reactions
        Here's a link to a cool Calvin animation that nicely follows the carbon through the three Calvin steps showing (quantitatively) NADPH and ATP coming in and doing their thing and Pi's attaching and disattaching. (These links looks like Smith college biology course notes. The original source of animations is not identified.)

         http://www.science.smith.edu/departments/Biology/Bio231/calvin.html

        Here's a link on same site to an animation of light reactions. (Both animations are pretty accurate.)

         http://www.science.smith.edu/departments/Biology/Bio231/ltrxn.html

        Same site also has an animation of electron transport chain, but in mitochondria. Mitochondria too pump protons to make ATP using the same ATP synthase rotary machine as in photosynthesis, but notice in mitochondria the protons pump the other way. The protons are pumped out of the inner (mitochondria) space into the narrow intermembrane space.

         http://www.science.smith.edu/departments/Biology/Bio231/etc.html

Evolutionary aspects
            All plants and eukarotic photosynthetic organism have the same type of photosynthesis: full Z cycle (PSII and PSI). They employ non-cyclic photophosporlation,  ripping apart water (freeing oxygen), make NADPH and use ATP and NADPH to make sugar from CO2.

        Bacteria (prokaryotic cells) have three variants of the Z process. Only cynobacteria has the full Z process. The other two major groups of photosynthetic bacteria, purple bacteria and green sulfur bacteria, contain only a single photosystem and do not produce oxygen. Both purple and green sulfur bacteria can run their single type of reaction center (PSII or PSI) two ways: cycliclly to make ATP or non-cyclicly to make NADPH.

            * Cynobacteria --- Cynobacteria  have the full Z process. Wikipedia says, "Unlike plants and algae, cyanobacteria are prokaryotes. They do not contain chloroplasts. Rather, they bear a striking resemblance to chloroplasts themselves. This suggests that organisms resembling cyanobacteria were the evolutionary precursors of chloroplasts."

        -- Cynobacteria light-harvesting system is different from that found in plants (they use phycobilins, rather than chlorophylls, as antenna pigments), but their electron transport chain is essentially the same as the electron transport chain in chloroplasts.

        -- Cyanobacteria are the only bacteria that produce oxygen during photosynthesis.

        -- The Earth’s primordial atmosphere was anoxic. Organisms like cyanobacteria produced our present-day oxygen containing atmosphere.

            * Purple bacteria --- Purple bacteria have a photosynthetic structure close to PHII. It's reaction center, called P870, is optimized for wavelengths below visible light in the near infrared where the sun radiates strongly. Purple bacteria make ATP running it PHII like struture cyclicly, the energy from the transport chain pumping protons. They make NADPH non-cyclicly using a non-water electron donor like hydrogen or sulfur, etc. The can vary the ratio of ATP to NADPH by varying the cyclic and non-cyclic operation of its PSII like reaction center.

           * Green sulfur bacteria --- Green sulfur bacteria photosynthetic structure close to PHI. The reaction center in green sulfur bacteria is known as P840. It's one reaction center (PSI) also can be run cycliclly (pumping protons to make ATP) or non-cycliclly (making NADPH).

        -- Purple bacteria and green sulfur bacteria occupy relatively minor ecological niches in the present day biosphere. They are of interest because of their importance in precambrian ecologies, and because they were the evolutionary precursors of modern plants.

Photosynthesis in archaea
        Archaea also do photosynthesis, but, not surprisingly, in their own unique way. Photosynthetic archaea are called halobacteria. Photosynthesis in archaea is quite different from the systems in other domains of life. Photosynthetic archaea ( halobacteria) use the pigment bacteriorhodopsin (not chlorophyll) which acts directly as a proton pump when exposed to light.  Halobacteria appear reddish, from the pigment bacteriorhodopsin, related to the retinal pigment rhodopsin. This pigment is used to absorb light (there are no antenna pigments in archaea) and provides energy to create ATP. Halobacteria also possess a second pigment, halorhodopsin, which pumps chloride ions in the cell in response to photons, creating a voltage gradient and assisting in the production of energy from light.

         It can be argued that halobacteria do not perform true photosynthesis. The extra energy they obtain from light is mostly used to maintain their ionic balances (& generate some ATP?). They are unable to generate the reducing power to fix carbon from CO2, so they can't generate structure or sugars. Halobacteria need a source of organic food, they need to eat. They are are heterotrophs, as opposed to true photosynthesizes, which are autotrophs, able to live on light, water, CO2 and inorganic minerals. (This explains why Wikipedia's Photosynthesis article starts by saying archaea do not do photosynthesis.)

        The photosynthesis in halobacteria (bacteriorhodopsin based system) is so different from chlorophyll based photosynthesis, which does carbon fixation for structure and energy, that it is thought likely that photosynthesis independently evolved at least twice, once in bacteria and once in archaea.

Purple sulfur bacteria
        -- All other photosynthetic systems in bacteria, algae and plants use chlorophylls or bacteriochlorophylls rather than bacteriorhodopsin. (These also produce a proton gradient, but in a quite different and more indirect way involving an electron transfer chain consisting of several other proteins.) Bacteriochlorophylls is used (in place of chlorophyll) by photosynthetic bacteria and archaea that do not produce oxygen, like purple bacteria and green sulfur bacteria. They do not produce oxygen because the reducing agent is not water, in other words they do not break apart water. The reducing agent (source of electrons) is typically a sulfur compond, typically hydrogen sulfide, so their byproduct output is sulfur.

        -- The purple sulfur bacteria and the green sulfur bacteria use hydrogen sulfide as electron donor in photosynthesis, thereby producing elemental sulfur.  Green and purple sulfur bacteria are anaerobic. Besides using sulfides some use ferrous iron as reducting agents.  (In fact, this mode of photosynthesis is older than the mode of cyanobacteria, algae and plants which uses water as electron donor and liberates oxygen.)

        Purple sulfur bacteria are anaerobic that fix CO2 using hydrogen sulfide as an electron donar and many are also nitrogen fixers.

        -- Bright green (naturally occurring) blooms are (typically) blue-green algae, which are actually bacteria (cyanobacteria).
======================================================
Photosynthetic bacteria
        There are five phyla of prokaryotes that have photosynthetic members:
 

Photosynthetic cynobacteria bacteria
        There is a type of true bacteria, called cyanobacteria (formerly but misleadingly called blue-gree algae), that have plant like double reaction centers and use water for electrons, and so output waste oxygen. (In anaerobic conditions, they are also able to use only PS I  with electron donors other than water like hydrogen sulfide, thiosulphate, or even molecular hydrogen.) Cynobacteria are thought to be the microbes that oxygenated the earth's atmosphere.

        Cyanobacteria are often still referred to as blue-green algae, although they are in fact are true bacteria with a simple prokaryote cell. Fossil traces of cyanobacteria have been found from around 3.8 billion years ago. Cyanobacteria's ability to perform oxygenic (plant-like) photosynthesis is thought to have converted the early reducing atmosphere into an oxidizing one, which dramatically changed the life forms on Earth and provoked an explosion of biodiversity (Oxygen Catastrophe).

        Chloroplasts, the organelle in eukaryotes (algae and higher plants) which houses the photosynthetic machinery, likely evolved from an endosymbiotic relation with cyanobacteria.

        Phytoplankton in the ocean is made up of algae and oxygenic photosynthetic bacteria. Most photosynthesis in the ocean is due to phytoplankton, which is an important source of food for marine life. Scientific American (1/09) says that microbial communities (doesn't specify which) conduct most of the world's photosynthesis.

Intro to photosynthetic purple bacteria & green sulfur bacteria
        Plants, of course, have eukaryotic cells with a nucleus and organelles, but some bacteria, which have the much simpler prokaryotic cells, are also photosynthetic. It turns out that there are two types of photosynthetic bacteria, now rather rare, known as purple bacteria and green sulfur bacteria, that have only a single light capture mechanism (single photosystem). These organisms are of ancient origin, presumed to have evolved before oxygenic photosynthetic organisms

        Curiously, the light capture and processing mechanism in purple bacteria is similar to photosystem II and in green sulfur bacteria is similar to photosystem I. Hence, even though the light detecting molecules in bacteria differ from those in plants (and repond to different regions of the spectrum), it's quite possible that photosynthesis light capture and processing mechanisms in plants evolved from these two bacteria.

         Purple and green photosynthetic bacteria do anoxygenic photosynthesis. These single reaction center bacteria get their electrons not from water, but from hydrogen sulfide (H2S) or even organic matter. In their making of sugars (food) from light they do not output oxygen as a waste product, hence this type of bacteria did not oxygenate the atomosphere of earth.

        The designation 'sulfur' or 'non-sulfur' in the name of purple or green bacteria just indicates whether they do or don't (typically) oxidize sulfur compounds as part of light reactions.

Purple bacteria do calvin
        The light capture and processing mechanism in purple bacteria is similar to PsII. Purple bacteria use the same calvin cycle as higher plants to fix CO2. The calvin cycle is the back end of photosynthesis, also known as the dark reactions, where CO2 is 'fixed' into sugar. It is a very complex bit of chemistry and biology with 10 stages mostly catalyzed with proteins and its needs ATP (18) and NADPH (12) for every glucose made.

        Thus the purple bacteria light reactions with only its one photosystem must generate both ATP and NADPH the calvin cycle needs to run. Very likely this is an organism that switches its one photosystem back and forth from cyclic (ATP) and non-cyclic operation (NADPH). (It is of course possible to made ATP by oxidizing fuel (respiration), but this probably makes no sense here when the purpose of the calvin cycle is to make fuel!)

        -- They are pigmented with bacteriochlorophyll a or b, together with various carotenoids. These give them colours ranging between purple, red, brown, and orange. Photosynthesis takes place at reaction centers on the cell membrane, which is folded into the cell to form sacs, tubes, or sheets, increasing the available surface area.  The electron donor material is sulfur (or sulfide) in some purple bacteria and hydrogen in other purple bacteria.

        -- Bacteriochlorophylls are photosynthetic pigments that occur in various bacteria. They are related to chlorophylls, which are the primary pigments in plants, algae, and cyanobacteria. Groups that contain bacteriochlorophyll conduct photosynthesis, but do not produce oxygen. They use wavelengths of light not absorbed by plants.  The bacteriochlorophyll pigments absorbs light in the extreme UV and infra-red parts of the spectrum which is outside the range used by normal chlorophyll.

Green sulfur bacteria
        The light capture and processing mechanism in green sulfur bacteria is similar to PsI. Green sulfur bacteria can also fix CO2, but they do it using a different cycle without RuBisCo, which is the Calvin cycle CO2 capture enzyme.

        Green sulfur bacteria use mostly bacteriochlorophylls instead of chlorophyll, shifting its light gathering to lower frequencies. The green sulfur reaction center is called P840 (opimized at 840 nm). Green bacteria (same as green sulfur bacteria?) live deep in the water, so their light collection is optimize for low light levels and red light.

        --- They engage in photosynthesis, using bacteriochlorophylls c, d, and e in vesicles called chlorosomes attached to the membrane. They use sulfide ions as electron donor, and in the process the sulfide gets oxidized, producing globules of elemental sulfur outside the cell, which may then be further oxidized. (By contrast, the photosynthesis in plants uses water as electron donor and produces oxygen.)

Heliobacteria
        -- Heliobacteria have a PSI type reaction center. The primary pigment involved is bacteriochlorophyll g, which is unique to the group and has a unique absorption spectrum; this gives the heliobacteria their own environmental niche. Phototrophy takes place at the cell membrane, which does not form folds or compartments as it does in purple phototrophic bacteria.

        -- Heliobacteria are photoheterotrophic, requiring organic carbon sources (meaning they cannot fix carbon). They are exclusively anaerobic. They are avid nitrogen fixers and are probably important in the fertility of rice paddy fields.

Speculations on evolutionary developments
        (from Journal Photosynthesis and the Origin of Life, 1998, Springer books)
        -- The origin and evolution of photosynthesis is considered to be the key to the origin of life.

        -- Cyanobacteria (Z cycle) have been formed by the horizontal transfer of green sulfur bacterial
photoreaction center (PsI)  genes by means of a plasmid into a purple photosynthetic bacterium (PsII).

        -- The fixation of carbon dioxide is considered to have evolved from a reductive dicarboxylic acid cycle (Chloroflexus), which was then followed by a reductive tricarboxylic acid cycle (Chlorobium), and finally by the reductive pentose phosphate cycle (Calvin cycle).

        -- The evolutionary developments that led to the ability of photosynthetic organisms to oxidize water to molecular oxygen are discussed. Two major changes from a more primitive non-oxygen-evolving reaction center are required: a charge-accumulating system and a reaction center pigment with a greater oxidizing potential. Intermediate stages are proposed in which hydrogen peroxide was oxidized by the reaction center, and an intermediate pigment, similar to chlorophyll d, was present.

        -- The evolution of O(2)-producing cyanobacteria that use water as terminal reductant transformed Earth's atmosphere to one suitable for the evolution of aerobic metabolism and complex life. The innovation of water oxidation freed photosynthesis to invade new environments and visibly changed the face of the Earth. We offer a new hypothesis for how this process evolved, which identifies two critical roles for carbon dioxide in the Archean period. First, we present a thermodynamic analysis showing that bicarbonate (formed by dissolution of CO(2)) is a more efficient alternative substrate than water for O(2) production by oxygenic phototrophs. This analysis clarifies the origin of the long debated "bicarbonate effect" on photosynthetic O(2) production. We propose that bicarbonate was the thermodynamically preferred reductant before water in the evolution of oxygenic photosynthesis.

        -- Second, we have examined the speciation of manganese(II) and bicarbonate in water, and find that they form Mn-bicarbonate clusters as the major species under conditions that model the chemistry of the Archean sea. These clusters have been found to be highly efficient precursors for the assembly of the tetramanganese-oxide core of the water-oxidizing enzyme during biogenesis. We show that these clusters can be oxidized at electrochemical potentials that are accessible to anoxygenic phototrophs and thus the most likely building blocks for assembly of the first O(2) evolving photoreaction center, most likely originating from green nonsulfur bacteria before the evolution of cyanobacteria.

Tree of life web project
        -- Green plants as defined here includes a broad assemblage of photosynthetic organisms that all contain chlorophylls a and b, store their photosynthetic products as starch inside the double-membrane-bounded chloroplasts in which it is produced, and have cell walls made of cellulose (Raven et al., 1992). In this group are several thousand species of what are classically considered green algae, plus several hundred thousand land plants.
        Link to Tree of Life (many bacteria web references)
        200 photos of cynobacteria
-----------------------
        -- Present knowledge of photosynthesis is almost exclusively based on data derived from cultivated species but genone studies of wild bacteria may very well reveal new organisms with novel combinations of photosynthetic and phototrophic components. Metagenomics has already shown how the relatively simple phototrophy based upon rhodopsins has spread laterally throughout Archaea, Bacteria and eukaryotes.

Chloroplasts & leaf structure

Organelles
        Organelles in eukaryotic cells (cells of everything except bacteria and archaea) are sort of like cells within cells. Wikipedia says, "an organelle is to the cell what an organ is to the body." Organelles are small regions of the cell, isolated from the rest of the cell with a membrane, that do specific jobs for the cell, and even have their own DNA.

        Examples of organelles are chloroplasts, which do photosynthesis, and microchondria, which oxidize fuels to make energy for the cell. There can be a huge number of organelles in a cell. Plant cells are full of chloroplasts (see image below). A typical eukaryotic cell contains about 2,000 mitochondria (about 20% of its volume).  A good case can be make that chloroplasts (and microchondria too) were originally free living bacteria (cynotbacteria) that got captured (technically, endosymbiosis) by plant cells (see link below for details).

        http://www.biology.iupui.edu/biocourses/N100/2k2endosymb.html

Chloroplasts
        Photosynthesis occurs in tiny, green colored organelles within plants cells called chloroplasts. Chloroplasts are typically a few microns in dia (micron = 1/1,000  mm). Most chloroplasts are located in specialized leaf cells, which often contain 50 or more chloroplasts per cell. Photosynthesis inputs, water and CO2, and waste product, O2, are all small neutral molecules that are able to pass freely (diffuse) through the membranes of the chloroplasts.

        Inside each chloroplast is another huge membrane (thylakoid membrane) that is folded up into what looks like a stack of pancakes enclosing an area in the center that has a high concentration of H+ (protons). The internal chloroplast (thylakoid) membrane is a key structure because light is captured and all the light reactions take place inside the membrane. Dark reactions (which make sugar from CO2) occur in the region of the chloroplast between its outer membrane and the thylakoid membrane.

Leaf structure
        Relevant to photosynthesis efficiency is the structure of a leaf. Here's a good crosssection. Most of the chloroplasts (tiny green dots) are in the long cylindrical cells (palisade parenchyma) near the top of the leave with some more in the so-called spongy cells in the middle. Note only are the grana within chloroplasts stacked vertically, but also, as shown below, the chloroplasts themselves are clearly stacked many deeps inside vertically oriented cells. The result must be that sunlight intensity at reaction centers must be quite variable and probably quite attenuated at the lower chloroplasts. Leaves are somewhat translucent, but I would estimate that no more than 10% of light passes through a leaf.

        It's hard to find data on leaf thickness, but a typical number appears to be a 1/4 of a mm, or a few hundred microns. With a chloroplast only 5 micron in size a lot of them can be stacked up inside a leaf.

Stoma (not stroma)
         Carbon dioxide cannot pass through the protective waxy layer covering the leaf (cuticle). Plant leaves let in CO2 through really tiny openings to the outside called stoma (plural: stomata), which are mostly on the bottom of leaves. [Stoma is to be distinguished from stroma.  Stroma is the region of a chloroplast where dark reactions occur, the region outside the grana.] Oygen produced by photosynthesis inside the chloroplasts also passes out of the leaf via the stoma. (I have seen no reference on whether the outgoing oxygen changes the composition of the inside air to any significant extent.)

        A stoma is just a gap (10 to 20 micron long) between two cells, so as a consequence in scanning electron microscope pictures it tends to look like a little eye. Stoma are opened and closed by the two cells adjusting their internal K+ concentration, which osmotically affects internal water pressure and hence the amount the cells swell.

        Here's a great electron microscope picture of stomata from Wikipedia. The tiny little eye shaped openings at the bottom are the stomata. (There's no scale on this picture, but if a stoma is 10 to 20 microns in size, we can estimate that the picture shows about one mm square of leaf surface, and that spacing between stoma is on the order of 100 micron or so.)

Fluorescence & phosphorescence
        About 3-6% of the light absorbed by plants is dissipated by fluorescence.

Mitochondria
        Mitochondria are sort of the inverse of chloroplasts. Both are organelles, small structures within eukaryotic cells. Chloroplasts make glucose (photosynthesis) and mitochondria burn it (cellular respiration). Without mitochondria cells are able to extract some energy from sugar using fermentation, but this type of respiration is very wimpy, extracting only about 1/13th of the energy that mitochondria can extract from the same amount of glucose.

        Both have their own DNA and an outer membrane, which separates them from the rest of the cell. Both are thought to have evolved from captured (engulfed) prokaryotic cells, called endosymbiotic hypothesis, about two billion years ago, a case argued for years by Lynn Margulis. Clearly the case for endosymbiotic inclusion in both cases is strong as new cellular machinery gained (potentially) provided the cells with an enormous evolutionary advantages.

       Chloroplasts take in CO2, H2O (& light) and output glucose a storable energy. Chloroplasts take in glucose and oxidize it, generating waste products CO2 and H2O, using the released energy to make ATP needed to power many cell functions. Both build up proton gradients using energy from an electron transport train, and then use the gradients to make ATP with ATP synthase rotary machines. The inner membrane where the ATP synthase and most of the working proteins reside has a large surface area packed into in a small volume. In chloroplasts this is done by shaping (folding) the thylakoid membrane into stacked disk structures (grana). In mitochondria it's done with many long narrow projections of the inner membrane space, called cristae, into the mitochondria volume

ATP in cells
        ATP (references say) is main energy transfer molecule in the cell. So what does this mean?  Cells import energy molecules in the form of sugars and other fuel molecules (fats etc) and oxidize (burn) them to release energy. But depending on the cell type, there are tricky requirements as to where and when the energy is needed, so various energy transport and storage means are needed within the cell. A good example is muscle cells. A calcium flow may initiate a contraction, but the molecules that actually move (slide) get their energy from ATP (converting it as usual to ADP + Pi), so muscle cells (& most cells) need a way to make ATP from ADP + Pi using the energy they obtain from oxidizing their fuel molecules.

Building on photosynthesis
        Interestingly once you know about how photosynthesis works you know a lot about energy flows within cells too. Cells use exactly the same ATP synthase rotating molecular machine to make ATP, and it's powered basically the same way as in photosynthesis, by a proton flow spinning the ATP synthase turbine. The need for a proton gradient is why ATP generation is done (in eukoratic cells) within enclosed membrane organelles called  mitochondria. It supports the proton gradient. (See figure below). Also similar to photosynthesis are proton pumps powered by an electron transport chain to maintain the proton gradient. However, in cells the electron transport chain gets its high energy electrons by pulling them off oxidized NADH (nearly the same as NADHP), which in turn were created by the burned fuel molecules.

        But note in mitochondria the proton gradient is reversed from chloroplasts. In chlororplasts the proton density is kept high inside by the proton pumps that point inward and the protons flow out through the ATP synthase rotary machine. In mitochondria everything is flipped (sort of). The proton pumps pump point outward and keep the proton density inside low, so protons then flow down their gradient  through the ATP synthase rotary machine into the center region of the mitochondria. The result of the flip is that ATP is now make inside the mitochondria so (presumably) it needs to diffuse out into the cell.

'Flipped'
        As seen below mitochondria of eukaryotic cells have two outside membranes with a small space (red) in between called the inter-membrane space. It is in the inter-membrane space that H+ is pumped up, so from this view there is no real flip. The large operating part of the mitochondria where oxidation and its genome sits is probably near neutral (PH7). It is the small inter-membrane space where H+ is pumped up and storing the H+ potential energy seems to be its main job. ("The main function of the inter-membrane space (in mitochondria) is oxidative phosphorylation." Wikipedia)

Leaky (update)
        It turns out that the outer membrane in mitochondria is very porous. So while the proton pumps pump into the inter-membane space the proton density there does not really rise very much. What happens is that the pumping of protons from the center region of the mitochondria drives the voltage on the inside of the inner membrane negative. (-180 mv). Most (est are 3/4th) of the proton motive force that causes protons to flow inward through ATP synthase is energy stored in the membrane voltage.

        -- Wiki says the outer membrane of mitochondria is very porous allowing free diffusion of small molecules. Because of channels in the outer membrane of the mitochondria, the content of the intermembrane space is similar to that of the content of the cytoplasm."

        --  Every "turn" of the citric acid cycle (Krebs Cycle) produces two molecules of carbon dioxide, one molecule of the ATP equivalent guanosine triphosphate (GTP), three molecules of the reduced coenzyme NADH, and one molecule of the reduced coenzyme FADH2. Both of these latter molecules are recycled to their oxidized states (NAD+ and FAD, respectively) via the electron transport chain, which generates additional ATP by oxidative phosphorylation.

Mitochondria folded inner membrane
        Mitochondria have the same problem with ATP synthase as do chloroplasts. ATP synthase, being a mechanical (rotary) machine, is slow.  It makes ATP slowly, so mitochondria need a lot of it. Since ATP synthase sits on the inner membrane, a lot of membrane area is needed in small volume. The mitochondria solution is to heavily fold the inner membrane. You can see in the figure below. Notice all the red projections,  called crista, of the inner membrane space into the blue matrix (center). The crista are covered with ATP synthase rotary machines. The mitochondria of muscle cells have an extra amount of cristae (folding) to make the large amounts of ATP muscle cells need.

======================================================
Molecular energy molecules and machines
ATP
        ATP is made up of the nitrogenous base adenine, the five-carbon sugar ribose and three phosphate groups. Three phosphate units (triphosphate), each made up of one phosphorus atom and four oxygen atoms, are attached to the ribose. The two (covalent) bonds between the three phosphate groups are relatively weak and yield their energy readily when split by enzymes.

        Inside a cell the ATP molecule is split at one of the high energy bonds, releasing the energy to power cellular activities. Adenosine diphosphate (ADP) and phosphorus group (Pi) are produced in the process. With the release of the end phosphate group, 7.3 kcal/mol of energy become available for work.

                        ATP + H2O ==> ADP + Phosphate + 7.3 kcal/mol  (0.316 ev)

        ATP needs to be regenerated continuously by the recombining  of ADP and Pi.

        -- ATP synthase, also called complex V, is the final enzyme in the oxidative phosphorylation pathway. This enzyme is found in all forms of life and functions in the same way in both prokaryotes and eukaryotes.

ATP generation runs in reverse too --- like a rechargable battery
**         In other words the mechanically rotating 'rotor' in ATP synthase functions as a geneator, extracting energy from an H+ gradient, or as a motor pumping up the H+ gradient.

        -- This phosphorylation reaction is an equilibrium, which can be shifted by altering the proton-motive force. In the absence of a proton-motive force, the ATP synthase reaction will run from right to left, hydrolyzing ATP and pumping protons out of the matrix across the membrane. However, when the proton-motive force is high, the reaction is forced to run in the opposite direction; it proceeds from left to right, allowing protons to flow down their concentration gradient and turning ADP into ATP

        -- ATP synthase is a huge enzyme! 600 kilodaltons, I think this is 600,000 atomic weight or about 30,000 atoms assuming an average weight of 20

        --  Rubisco can take in O2 as well as CO2. This lowers the efficiency of photosynthesis. At air levels of carbon dioxide and oxygen, the ratio of the reactions is about 4 to 1 (CO2 to 2 input), which results in a net carbon dioxide fixation of only 3.5. Thus the inability of the enzyme to prevent the reaction with oxygen greatly reduces the photosynthetic potential of many plants.

        -- The energy used by human cells requires the hydrolysis of 100 to 150 moles of ATP daily which is around 50 to 75 kg. Typically, a human will use up their body weight of ATP over the course of the day.[26] This means that each ATP molecule is recycled 1000 to 1500 times during a single day (100 / 0.1 = 1000). ATP cannot be stored, hence its consumption closely follows its synthesis.

Making ATP in mitochondria
        -- The energy released as electrons flow through this electron transport chain is used to transport protons across the inner mitochondrial membrane, in a process called chemiosmosis. This generates potential energy in the form of a pH gradient and an electrical potential across this membrane. This store of energy is tapped by allowing protons to flow back across the membrane and down this gradient, through a large enzyme called ATP synthase. This enzyme uses this energy to generate ATP from adenosine diphosphate (ADP), in a phosphorylation reaction.

*        -- Unusually, the ATP synthase is driven by the proton flow which forces the rotation of a part of the enzyme—it is a rotary mechanical motor, and can spin up to 12,000 RPM (!) making 3 APT molecules on every turn.

*        -- This gradient has two components: a difference in proton concentration (a pH gradient) and a difference in electric potential, with the N-side having a negative charge. The energy is stored largely as the difference of electric potentials in mitochondria, but also as a pH gradient in chloroplasts.

        -- ATP is used by all life, even viruses. ATP is a big molules weighing about 500 atomic mass units.

        -- ATP poses a big evolutionary problem, since it is required for all life. What simpler versions are there. One reference says none is known.

        -- Cells need energy to drive reactions. The molecule that supplies the energy is ATP (This reaction is called ATP ). When the third phosphate is removed by hydrolytic cleavage, 7 kcal of energy is released per mole of ATP.

        ATP + H2O ---> ADP + Phosphate + Energy (7 kcal)

When the second phosphate is removed, the same amount of energy is released.

      ADP + H2O ---> AMP + Phosphate + Energy (7 Kcal)

The bonds between the two phosphates are not strong bonds.  In fact, these bonds are easily broken releasing 7Kcal of energy per mole. 7 Kcal of energy is enough to drive endergonic reactions in the cell. All the energy does not come from the moving of electrons to a lower energy level. In fact, the rearrangement of electrons in other orbitals (i.e..ATP ---> ADP) result in a structure with less energy.

        --    ATP is the chemical equivalent of a loaded spring; the close packaging of the three negatively charged phosphate groups ia an unstable, energy-storing arrangement (like charges repel).  The chemical “spring” tends to “relax” from the loss of terminal phosphate.  The cell taps this energy source by using enzymes (kinases) to transfer phosphate groups from ATP to other compounds, which are then said to be phosphorylated.  Adding the phosphate primes a molecule to undergo some kind of change that performs work, and the molecule loses its phosphate group in the process.

        -- ATP (Adenosine triphosphate)  It is the most important "molecular currency" of intracellular energy transfer. (C10H16N5O13P3).  It is produced as an energy source during the processes of photosynthesis and cellular respiration and consumed by many enzymes. This large release in energy makes the decomposition of ATP in water extremely exergonic (-20.5 kJ / mole, with a change in free energy of 3.4 kJ/mole). The overall process of oxidizing glucose to carbon dioxide is known as cellular respiration and can produce up to 30 molecules of ATP from a single molecule of glucose

        -- The system of ATP and water under standard conditions and concentrations is extremely rich in chemical energy; the bond between the second and third phosphate groups is loosely said to be particularly high in energy. Strictly speaking, the bond itself is not high in energy (like all chemical bonds it requires energy to break), but energy is produced when the bond is broken and water is allowed to react with the two products. Thus, energy is produced from the new bonds formed between ADP and water, and between phosphate and water.

        -- The phosphate ion is a polyatomic ion with the empirical formula PO4 and a molar mass of 94.973 g/mol; it consists of one central phosphorus atom surrounded by four identical oxygen atoms in a tetrahedral arrangement. It has a charge of -3.

        -- This gradient is composed of both the pH gradient and the electrical gradient. The pH gradient is a result of the H+ ion concentration difference. Together the electrochemical gradient of protons is both a concentration and charge difference and is often called the proton motive force (PMF).

        -- In mitochondria the PMF (proton motive force) is almost entirely made up of the electrical component but in chloroplasts the PMF is made up mostly of the pH gradient. In either case the PMF needs to be about 50 kJ/mol for the ATP synthase to be able to make ATP.

ATP/[ADP + Pi]
        ATP has a phosphate group (PO3H nominally), known as Pi, that attaches and disattaches. The breaking of the phosphate bond releases energy, nominally quoted (under standard conditions as 7.3 cal/mol (0.316 ev), but is estimated to be more like 10 to 12 kcal/mol in cells. This is 0.433 to 0.519 ev, so I used the average 0.48 ev for ATP transfer energy in my block diagram.  In photosynthesis it's one of two molecules that transfer energy from the light reactions to the dark reactions. In cells of the body it part of pathway of burning fuels and using the energy to do useful work like causing muscle contraction.

        Removing a phosphate group from ATP (adenosine triphosphate) changes it to ADP (adenosine biphosphate). The equations are

                  ATP => ADP + Pi + energy release (0.48 ev nom in a cell)
                  ADP + Pi + energy in => ATP
                            where
                                  ATP = C10 H16 N5 O13 P3
                                  ADP =C10 H15 N5 O10 P2 = ATP - PO3H
                                  Pi = phosphate group (PO3H nominally)

        One reason ATP is so useful is that the reaction to release the energy is very simple. ATP reacts directly with water (hydrolysis) to break the phosphate bond and release the work/heat. Typically ATP and [ADP + Pi] loop around carrying energy from place to place. ATP is made (from ADP and Pi) by the enzyme ATP synthase, which is an amazing molecule, and a creationist reference (but it could very well be accurate) said ATP gets reconstituted from ADP about 3 times a minute.

        From various sources the following ATP numbers body are thrown around

                ATP in human body                                    50 grams
                ATP turnover per day in body                    weight of body

Combining the above [100kg/0.05 kg = 2,000] and there are [60 x 24 = 1,440 min/day], so on average all the ATP in the body recycles, is used and recreated from [ADP + Pi], every 40 seconds!

Check
        Actually there's a rough (order of magnitude) way to check these numbers. I'll make a seat of the pants guess is that half the energy in ATP is lost as heat and maybe half the heat generated in the human body comes from ATP losses. Reference say human body heat output is about 130 watts.

ATP release energy (in cell)               0.48 ev  x 1.6 x 10^-19 joule/ev
ATP (mol)                                             507 gram
ATP turnover/sec                                  50 gram/40 sec = 1.25 gram/sec

Power =  [(1.25g/507g) x 6 x 10^23] ATP/sec x [0.48 ev  x 1.6 x 10^-19 joule]/ATP
            = 1.48 x 10^21 x 0.77 x 10^-19 joule/sec
            = 1.14 x 10^2 joule/sec
            = 114 watts                            OK (within factor of four of my seat of pants guess)

ATP Synthase (rotary machine)
        ATP synthase enzyme is (literally) a rotary turbine and rotary motor. It is one of only two rotary molecular motors known, the other being the rotary motor that spin flagellum. ATP synthase is actually two separate rotary machines on the same shaft, one machine handles protons (H+) and the other ATP. It runs efficiently forward and backward. In photosynthesis and mitochondria the proton machine works as a turbine and the ATP machine makes ATP. Run the other way the ATP machine powers rotation by taking in and splitting ATP and the proton machine does work pumping protons uphill thermodynamically.

        The enzyme is about about 9-10 nm in dia with about a 2 nm dia rotor that can spin at speeds as high as 100 to 200 rev/sec (6,000 to 12,000 RPM). The rotor has three fold symmetry and processes one ATP[ADP + Pi] for a rotation of 120 degrees (3 ATP molecules per rev). One ATP synthase machines can output 600 ATP/sec, which since it takes 18 ATP per gluose molecule is about 33 glucose/sec (30 msec/gluose).

ATP synthase is slow
       Almost no reference mentions this, but an important point is that ATP synthase is slow. Being a true mechanical (rotating) machine it works very slowly compared to the speed of most chemical reactions. It takes 30 msec at top speed (12,000 RPM) for 6 revolutions to make the 18 ATP needed for one glucose. When I worked number (above), I found one 5 um chloroplast makes hundreds of millions of glucose molecules per sec processing the energy from tens of billions of photons. It takes 30 msec for one of these machine to do its job for one glucose, while it's not so slow as RuBisCo, which at 300 to 500 msec per glucose is about ten times slower, it still means that the thykaloid membrane must be jam packed with ATP synthase machines! (a fact I have never seen mentioned.

        Only in 1994  when a 3d model of ATP synthase was built did the rotating aspect of the two machines (proton and ATP) on the same shaft of ATP synthase begin to be reasonably understood. Even today the specifics of the F0 proton machine are not well understood, this is why the ratio of H+/ATP is not known exactly. When slowed way down (in lab) by low concentrations, ATP synthase begins to rotate like a stepper motor pulsing in 120 degree (single ATP) increments. Over a wide range of loads its torque measures to be pretty constant. Constant torque motors tend to spin up until their torque dies, so it may very well be that ATP synthase machines, when working, run most all the time near their top speed (200 rev/sec, 12,000 RPM).

How torque was measured
        ATP synthase at 9 nm dia is far too small to be seen through a microscope (well marginally, I read that electron microscopes can go down to 4 nm and specialized interferometer optical microscopes down to 20 nm), so how was its rotation and torque measured? It was done by attaching a long 1 um 'whip' (thread) to the rotor. 1 um at about x100 dia is really long for such a tiny motor, and dragging it around through fluid put a heavy, calculable, torque load on the motor. The whip (thread) fluoresced, so using a a sequence of photographs taken with a fluorescence microscope the speed of rotation was measured.

        The heavy load slowed rotation down from its normal 200 rev/sec to around 6 rev/sec. Surprisingly (to me) there exists a formula that calculates the the torque load from the characteristics of the fluid and parameters of a tiny thread. When the numbers were crunched, the torque came out to about 40 pN nm (T = r x F), which agrees nicely with the chemical energy numbers if the efficiency of the machine approaches 100%.

ATP synthase 1 um whip rotating
pictures 33 msec apart, 1.3 rev/sec
source --- Japanese paper "Rotary Molecular Motor that can work at near 100% Efficiency"
http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1692765&blobtype=pdf

measured ATP synthase rotation at driven by ATP at two different ATP concentrations in lab
left: high concentrations 320 rev/sec
right: at low ATP concentrations stepwise motion visible
source -- http://www.pnas.org/content/102/5/1333.full.pdf

ATP synthase animation
        Here's a cool flash animation of ATP synthase driven by protons and making ATP. (minor quibble -- it shows the proton machine turning smoothly and the ATP machine moves in jumps. The shaft connection between the machines is generally described as rigid. As shown here it would be spring like. The ATP machine motion was probably slowed down for clarity.)

         http://www.iubmb-nicholson.org/swf/ATPSynthase.swf

Check of torque value
    Energy = torque x angle, and 1/3 rev makes one ATP (0.48 ev in cells)

        40 pN nm = 40 x 10^-12 x 10^-9 nm
                          = 40 x 10^-21 nm
        E rotation = 40 x 10^-21 nm x 2 pi/3 radian
                          = 8.4 x 10^-20 joule
              E ATP = 0.48 ev x (1.6 x 10^-19 joule/1ev)
                          = 7.7 x 10^-20 joule                          about 90% of E rotation, checks

       The proton machine spans a membrane and rotates with proton flow across the membrane. The ATP machine resides on one side of the membrane. In turbine mode (as in photosynthesis) the flow of protons (H+) down a concentration gradient powers the machine and it makes ATP. In motor mode the energy released by ATP powers the machine and it pumps protons (H+) uphill increasing the H+ concentration gradient.

        In photosynthesis the concentration of H+ is high (Ph = 4 to 5) inside the volume enclosed by the thylckoid membrane. It's high inside for two reasons. One, inside is where water is oxidized releasing H+ and two, more importantly, many protons are pumped in from the outside by pumps run by energy from the electron transport chain. The flow of protons down its gradient through the ATP synthase proton machine causes shaft rotation and provides the energy for the other machine on the shaft, located on the outside of the membrane, to reattach Pi to ADP making ATP.

        It's not known exactly how many protons need to flow thorough the ATP turbine to make one ATP molecule. Previously the H+/ATP ratio was estimated to be three, but most experiments now measure 4 with a few at 4.67. I have drawn my block diagram for a ratio of 4 and noted the flow change in the pumps to accomodate 4.67. Basically my block diagram can accomodate any ratio by just changing the number of H+ pumped around in a loop by the electron transport chain.

Detailed, readable paper on ATP synthase motor
        Single molecule, 10 nm in size, "smallest rotary motor known". The rotor may only be 2 nm in dia (1 nm radius). This detailed article on the motor references the maximum (unloaded) rotation rate at 100 rev/sec (6,000 RPM), which is half of what other references say (200 rev/sec, 12,000 RPM).  Energy obtained from hydrolysis of one molecule of ATP is estimated to be 90 to 100 pN nm in cells depending on ADP concentrations. Thus the motor efficiency comes out close to be 80 to 90%, "close to 100%" says text and abstract. It's a constant torque motor over a wide range of conditions. they have photos of rotation with flourescent 1 um filament attached (which slows it way down)

         http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1692765&blobtype=pdf

ATP synthase motor efficiency (in mitochondria)
                    Power = torque x w
                    Work = torque x angle = 40 pN nm (torque) x 2 pi/3 (120 per ATP molecule)
                                                            = 80 pN nm
                              E = 80 pN nm = 80 x 10^-12 x 10^-9 joules
                                                       = 8 x 10^-20 joules  [6.24 x 10^18 ev/1 joule]
                                                      = 50 x 10^-2 ev
                                                      = 0.5 ev            OK (ATP est to be 0.519 ev in other ref)

Run in reverse as a proton pump
        ATP synthase can run in reverse taking in ATP for energy from its turbine section (run as a motor) and using its proton rotator as a proton pump. References are not totally clear, but it looks like a proton pump known as 'proton ATPase' or 'H+-ATPase' is probably the ATP synthase molecular motor/turbine running in reverse. One reference puts it this way:

"Proton ATPase runs in reverse to synthesize ATP in mitochondrial and chloroplast membranes"

        Proton ATPase is used as a proton pump in cell walls. It's clearly not the proton pump in photosynthesis and mitochondria, because these proton pumps runs on energy from an electron transport chain. Curiously proton ATPase appears only in plants and very simple eukaryotic cells like fungi. In animals the same job is done by Na+/K+-ATPase transporter.

Cells make ATP too
        Cells need ATP to power respiration, run ion pumps, and as an energy molecule for doing work. ATP is not transported around the body, so cells need to make it locally. In eukoratic cells ATP is made in organelles called mitochondria. And what do you know, just like in photosynthesis a proton gradient (more generally a 'proton motive force' that also includes membrane voltage) across a membrane drives the ATP synthase 'turbine' to make the ATP. In mitochondria the immediate source of energy to build up the proton gradient and membrance voltage comes from the oxidation of NADH (this molecule from an energy view point is the same as NADPH). Operation of ATP synthase in cell mitochondria is shown in the figure below.

        While a lot of the cellular machinery in the mitochondria figure below is common to photosynthesis, there are some interesting differences. Sugars diffuse in and are oxidized and converted to NADH. The oxidation of NADH inside provides high energy electrons to an electron transport chain (replacing the light excited electrons in photosynthesis) that run proton pumps that pump protons out of the center of the mitochondria. These protons cycle around and diffuse down their gradient through the ATP synthase turbine back into the mitochondria making ATP inside, which presumably need to diffuse out to do work.
eukaryote

Is there a proton gradient in mitochondria?
       Note if a proton gradient is to develop the mitochrondia membrane must be relatively impermeable to tiny proton and yet somehow permit the much larger molecules of glucose in and ATP out. This seems a difficult requirement and it may not be satisfied. Also mitochondria have two outer membranes and the protons are pumped from the inside into the small inter-membrane space between them, but I read the outer membrane is very porous.

        Mitochondria  can use the proton gradient just to make (body) heat without making ATP. This is done by opening (non ATP-synthase) channels that allow protons to diffuse into the mitochondria.

======================================================
Thylakoid Membrane
Membrane voltage and the nernst equation
        The shorthand is that the proton gradient causes the flow of protons through ATP synthase, but in fact the membrane voltage helps too. Most cell and organelles regulate ion flow in/out such there there is nearly always a voltage across the membrane. Thus when there is a density gradient of an ion (like protons) across a membrane, the flow of the ion through an open channel is a function of the density gradient and the membrane voltage.

        When the direction of the two currents is opposite, a single open channel can lead to a steady state condition where the two currents are equal and opposite. For example suppose inside proton density (and charge) are low compared to outside. Protons will then diffuse down an open channel to the inside, but if there no charge canceling mechanism, this builds up positive charge (& positive voltage) inside producing an outward pointing E field that opposes the diffusion flow. Steady state is reached when the outward electric current and the inward diffusion current are equal and opposite. This is one way equivalent 'voltage' to be assigned to the diffusion gradient.

        The equivalent voltage of relative ion concentration gradients can also be calculated directly from the nernst equation. Wikipedia gives the nernst equation as the first equation below. The 2nd version is @ 25C and in 'log' form.

                            V =    (RT/F)     x    l n [(ion density inside)/(ion density outside)]
                            V = (59.2 mv)   x    log [(ion density inside)/(ion density outside)]

Looks pretty obscure, but after playing around with it for a while, I realized it's just the diode equation in disguise! Here's the diode equation:

                                        I = I0 e^(qV/kT)
solve for voltage
                            ln (I/I0) = (qV/kT) x ln(e)
                                       V = (kT/q) ln (I/I0)

But cancel the (delta t)'s in current ratio (I/I0) and you get a charge density ratio and
                        (kT/q) = (RT/F) = 25.7 mv @ 25C

Changing ln => log we need to scale up 25.7 mv by [ln x/log x = 2.30], so 25.7 mv => 59.2 mv
so bottom line we get 59.2 mv for each factor of 10 density difference across a membrane.

        If there is a membrane voltage (V0) and a density difference, the net voltage seen by an open (diffusion) channel across the membrane is

                        Vnet = V0 + (59.2 mv) log [(ion density inside)/(ion density outside)]

For an open channel with no net flow Vnet =0, so
                            V0 = - (59.2 mv) log [(ion density inside)/(ion density outside)]
                                        where
                                                V0 is membrane voltage (relative to outside)

so for example a positive ion (say K+) pumped up inside (relative to outside) by x100 will have no net open channel conduction flows when the inside membrane potential (relative to outside) is V0 = - 2 x 59.2 mv = -118.4 mv.

Photosynthesis membrane voltage exception
        Note the membrane potential in photosynthesis is not at all like the K+ example (above). In a 'normal' a pumped up K+ ion density inside causes the inside voltage to be negative. In photosynthesis while the proton density inside is way up inside by x100 to x1,000 the membrane potential is positive. The membrane potential does not oppose the ATP synthase proton flow it enhances it!  Very interesting.

ATP synthase and membrane voltage
        However, in photosynthesis (chloroplasts) and respiration (mitochondria) the diffusion proton flow through the ATP synthase is assisted (not opposed) by the membrane voltage. In photosynthesis the proton pumps pump up the inside concentration of protons and also the inside positive charge, hence the inside of the membrane is positive with respect to the outside, so the E field pushes the protons outward. The situation is basically the same with mitochondria except everything is reversed. The proton pumps point outward causing the inside proton density inside to be low and the inside positive charge is depleted. The result is that inside of the membrane voltage is negative with respect to the outside, thus both diffusion and E field cause protons to flow inward.

        I read that mitochrondria and chloroplasts are so small that no one is able to measure the membrane voltage directly (seems suspect to me), so various estimates float around as to what the membrane voltages are. The consensus seems to be that with photosynthesis the diffusion voltage is dominant (maybe 75%), so it is correct to say the protons flow is down the diffusion gradient. However, with mitochondria the consensus view is that the membrane voltage is dominant (maybe 75%), and I see mitochondria membrane voltage estimates of 180 to 200 mv.
-----------------------------

  In xxxxx the same ATP synthase molecule runs as a motor. Here ATP enter the ATP machine releasing Pi and energy spinning the proton machine. The proton machine now acts as a pump, pumping protons uphill increasing the inside H+ concentration gradient.

Pumped water storage analogy
        Note in both photosynthesis and in mitochondria energy is stored in proton (H+) gradient across enclosed membrane volumes. How long this storage is good for depends on proton leakage through the membranes. Finding number (sec, min, hours?) in references is rare.

        This means of energy storage is similiar to a pumped water storage system. In a pumped water system when energy is available it's used to run the turbines backwards pumping water up to a high reservoir increasing its potential energy. When energy is needed, the water is allowed to flow out of the high reservoir through the turbines recovering most of the pumped energy.

        In the chloroplasts and mitochondria  is works basically the same. When energy is available the potential energy of protons is pumped up by increasing its concentration, and when the energy is to be recovered the potential energy of the protons is released as they diffuse down their gradient through the ATP synthase turbine. While ATP synthase rotoary machine can work as a motor it doesn't workd this in chloroplasts and mitochondria. They have separate pumps across the membrane that pump up (or down) the proton concentrations.

        One paper on the ATP synthasis turnbine (with ATP generation) attempted to measure the efficiency of the process. They attached one micron flourescent filaments to the 2 nm rotor and photographed its rotation. From fluid drag coefficient they found the torque put out by the ATP synthase rotation and from there figured the efficiency. They argued it approached 100%, probably at least 80 to 90 %.

Storing energy (briefly)  in ATP
        Almost all forms of life carry out oxidative phosphorylation to produce ATP (so says Wiki). In other words almost all life oxidizes (burns) fuels or food to store energy in ATP by attachine a phosphate group to ADP. The figure below shows how ATP is generated in microchondria of most cells. H+ pumped by an electron transport chain and ATP synthase driven by a proton gradient! Looks a lot like photosynthesis, except the proton gradient is reversed (and a different form of NADP is used). Notice the H+ concentration is low inside, not high, so the H+ flow is into the membrane enclosed space.

Excellent overview of ATP and its energy role (anti-evolution site)
         http://www.trueorigin.org/atp.asp

        While its true that ATP stores energy, it really just moves energy about (between enzymes). It's created moves through water and then destroyed. The human body only has 50 mg (!) at any one time, so it's clearly not used for storage.

Oxidation of glucose to make ATP
**        -- If glucose is simply burned in air, all of this energy is released as heat.

                   C6H12O6 + 6 O2 => 6 CO2 + 6 H2O + 686 kcal/mol (29.7 ev)

In a cell, however, oxidation of glucose is coupled to the synthesis of ATP from ADP in the following reaction:

                    C6H12O6 + 6 O2 + 36 ADP + 36 Pi  => 36 ATP + 6 CO2 + 6 H2O

Efficiency of this reaction
        Oxidizing one molecule of glucose in air yields 29.7 ev of heat. When glucose is oxidized to make ATP (from ADP + Pi) we get 36 ATP (plus 6 O2 and 6 H2). The available energy in ATP (when transformed to ADP + Pi) is 7.3 kcal/mol (0.316 ev). So efficency of turning glucose energy into ATP energy is

                            [ 36 x 0.316 ev (ATP)]/29.7 ev (glucose) = 38.3%

Ref not too clear but above is apparently for equal concentrations of ATP and ADP. ATP concentration in cells can by x5 or x10 ADP, then 7.3 kcal/mol can rise to 12 kcal/mol, which increases efficiency from 38% to 50% or so (number not right).
 

        -- Note that ATP is an energy-coupling agent and not a fuel. It is not a storehouse of energy set aside for some future need. Rather it is produced by one set of reactions and is almost immediately consumed by another.

        --  Generally, ATP is connected to another reaction—a process called coupling which means the two reactions occur at the same time and at the same place, usually utilizing the same enzyme complex

        -- ATP is not excessively unstable, but it is designed so that its hydrolysis is slow in the absence of a catalyst. This insures that its stored energy is “released only in the presence of the appropriate enzyme”

*        -- The ATP synthase revolving door resembles a molecular water wheel that harnesses the flow of hydrogen ions in order to build ATP molecules. Each revolution of the wheel requires the energy of about nine hydrogen ions returning into the mitochondrial inner chamber (Goodsell, 1996, p.74). Located on the ATP synthase are three active sites, each of which converts ADP to ATP with every turn of the wheel. Under maximum conditions, the ATP synthase wheel turns at a rate of up to 200 revolutions per second, producing 600 ATPs during that second.  (Actually the H+/ATP ratio is not known exactly. Goodsell here is saying three, but as of 2009 the favored number is 4 or 4.67)

            From an energy viewpoint each ADP +Pi processed to ATP has 0.316 ev more energy. If three H+ flows are needed this would translate into an (equivalent) membrane voltage of 316 mv/3 = 105 mv (@ 100 % efficiency)

Here is a good ATP bond energy ref (with neat animated graphics)
         http://www.blobs.org/science/article.php?article=30

    ** -- Mitchell (1978 Nobel prize for Chemistry) realised that the movement of ions across an electrochemical membrane potential could provide the energy needed to produce ATP. He knew that living cells had a membrane potential; interior negative to the environment. The movement of charged ions across a membrane is thus affected by the electrical forces (the attraction of plus to minus charges). Their movement is also affected by thermodynamic forces, the tendency of substances to diffuse from regions of higher concentration. He went on to prove that ATP synthesis was coupled to this electrochemical gradient.

        -- Mitchell's theory was confirmed by the discovery of ATP synthase, a membrane-bound protein that uses the potential energy of the electrochemical gradient to make ATP. Mitchell's chemiosmotic theory turned out to be one of the two seminal discoveries in biology in the 20th century (DNA being the other)

        -- Hydrogen ions (protons) will diffuse from an area of high proton concentration to an area of lower proton concentration. Peter Mitchell proposed that an electrochemical concentration gradient of protons across a membrane could be harnessed to make ATP. He likened this process to osmosis, the diffusion of water across a membrane, which is why it is called chemiosmosis.

        -- ATP synthase is the enzyme that makes ATP by chemiosmosis. It allows protons to pass through the membrane using the kinetic energy to phosphorylate ADP making ATP. The generation of ATP by chemiosmosis occurs in chloroplasts and mitochondria as well as in some bacteria.

        --  Although the many forms of life on earth use a range of different nutrients, almost all carry out oxidative phosphorylation to produce ATP, the molecule that supplies energy to metabolism.

        -- Equation for diffusion of gas across a cell membrane (Ficks first law)
                    Rate of Diffusion  = k (A/d) (presssure difference)
                        Note this is like a current equation (i = V/R = V/(resistivity x length/area),
                        so flow x pressure diff must be power.
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RuBisCO
        A key protein (enzyme) in photosynthesis is nicknamed RuBisCo. RuBisCo catalyzes CO2's entry into the sugar making dark reactions. RuBisCo's fixing of CO2 is a slow process, only three CO2 per second per protein molecule, whereas some enzyme catalyzed reactions run in less than a msec. The result of the slowness is that there needs to be lot of the RuBisCo in a chloroplast or photosynethic bacteria. In fact RuBisCo may be the most abundant protein on earth!

        (excerpts from Wiki article RuBisCo)
        -- Ribulose-1,5-bisphosphate carboxylase/oxygenase, most commonly known by the shorter name RuBisCO [1] , is an enzyme. RuBisCO catalyzes either the carboxylation or oxygenation of ribulose-1,5-bisphosphate (also known as RuBP) with carbon dioxide or oxygen. (Translation --- RuBisCo acts to join carbon (in form of CO2) or oxygen (in form of O2) into RuBP. The latter is a competing reaction, so it's important for plants to minimize oxygen reaching RuBP.)

        -- RuBisCo is used in the Calvin cycle to catalyze the first major step of carbon fixation, a process by which the atoms of atmospheric carbon dioxide are made available to organisms in the form of energy-rich molecules such as sucrose.

        -- RuBisCO is very important in terms of biological impact because it catalyzes the most commonly used chemical reaction by which inorganic carbon enters the biosphere. RuBisCO is also the most abundant protein in leaves, and it may be the most abundant protein on Earth[2].

        --  Some enzymes typically can carry out thousands of chemical reactions each second. However, RuBisCO is slow, being able to "fix" only 3 carbon dioxide molecules each second.

        -- The ultimate rate-limiting factor of the Calvin cycle is RuBisCO that cannot be ameliorated in short time by any other factor. Since RuBisCO is often rate limiting for photosynthesis in plants, it may be possible to improve photosynthetic efficiency by modifying RuBisCO genes in plants

        --  Since carbon dioxide and oxygen compete at the active site of RuBisCO, carbon fixation by RuBisCO can be enhanced by increasing the carbon dioxide level in the compartment containing RuBisCO (chloroplast stroma)

-----------------------------------------------------------
        -- Osmosis is the net movement of a solvent across a semipermeable membrane from a region of high solvent potential to an area of low solvent potential. (Note it is the solvent that moves not the solute!) It is a physical process in which a solvent moves, without input of energy, across a semipermeable membrane (permeable to the solvent, but not the solute) separating two solutions of different concentrations. Osmosis releases energy, and can be made to do work. In plant cells, water enters the cell until the inside and outside water potential is equal.

       -- Cellular respiration is a process that describes the metabolic reactions and processes that take place in a cell to obtain chemical energy from fuel molecules. Energy is released by the oxidation of fuel molecules and is stored as "high-energy" carriers. The reactions involved in respiration are catabolic reactions in metabolism. Fuel molecules commonly used by cells in respiration include glucose, xx, and a common oxidizing agent (electron acceptor) is molecular oxygen (O2).

        -- The energy released in respiration is used to synthesize molecules that act as a chemical storage of this energy. One of the most widely used compounds in a cell is adenosine triphosphate (ATP). Most of the ATP produced by cellular respiration is by oxidative phosphorylation??   Chemiosmotic hypothesis (1961) --- The theory suggests essentially that most ATP synthesis in respiring cells comes from the electrochemical gradient across the inner membranes of mitochondria.

        --  The energy available in the electrons is used to pump protons from the matrix across the inner mitochondrial membrane, storing energy in the form of a transmembrane electrochemical gradient. The electrons and protons at the last pump in the ETC are taken up by oxygen to form water.

        -- Chemiosmosis is the diffusion of ions across a membrane. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane. It allows protons to pass through the membrane using the kinetic energy to phosphorylate ADP making ATP. The generation of ATP by chemiosmosis occurs in chloroplasts and mitochondria as well as in some bacteria.

        -- (the proton circulate in and out of the cell. In driven by the electrochemical potential to make ATP and then some of the energy available is used to pump them out again restrong the potential. And some protons inside are oxidized to water). The energy available in the electrons (from metabolized glucose)is used to pump protons from the matrix across the inner mitochondrial membrane, storing energy in the form of a transmembrane electrochemical gradient. The protons move back across the inner membrane through the enzyme ATP synthase

        -- The Light reactions of photosynthesis generate energy by chemiosmosis.  Chlorophyll loses an electron when energized by light. This electron travels down a photosynthetic electron transport chain ending on the high energy molecule NADPH. The electrochemical gradient generated across the thylakoid membrane drives the production of ATP by ATP Synthase. This process is known as photophosphorylation.

        -- ATP is made by an enzyme called ATP synthase. The structure of this enzyme and its underlying genetic code is remarkably similar in all known forms of life. ATP synthase is powered by a transmembrane electrochemical potential gradient, usually in the form of a proton gradient. The function of the electron transport chain is to produce this gradient.

        -- Electron transport chains produce energy in the form of a transmembrane electrochemical potential gradient. This energy is used to do useful work. The gradient can be used to transport molecules across membranes. It can be used to do mechanical work, such as rotating bacterial flagella. It can be used to produce ATP and NADPH, high-energy molecules that are necessary for growth.

        -- It catalyzes a reaction that splits water into electrons, protons and oxygen.  The electrons are transferred to special chlorophyll molecules (embedded in PS II) that are promoted to a higher-energy state by the energy of photons.

        -- The transfer process (exciton transfer) is extremely efficient, due to the ability of antenna proteins to transfer their excitation energy to neighboring molecules in a quantum, all-or-none fashion. This is one of two core processes in photosynthesis, and it occurs with astonishing efficiency (greater than 90%) because, in addition to direct excitation by light at 680 nm, the energy of light first harvested by antenna proteins at other wavelengths in the light-harvesting system is also transferred to these special chlorophyll molecules.

        -- This is the second core process in photosynthesis. The initial stages occur within picoseconds, with an efficiency of 100%. The seemingly impossible efficiency is due to the precise positioning of molecules within the reaction center. This is a solid-state process, not a chemical reaction. It occurs within an essentially crystalline environment created by the macromolecular structure of PS II.

        -- (summary) PS II is a transmembrane structure found in all chloroplasts. It splits water into electrons, protons and molecular oxygen. The electrons are transferred to plastoquinone, which carries them to a proton pump. Molecular oxygen is released into the atmosphere.

        -- The emergence of such an incredibly complex structure, a macromolecule that converts the energy of sunlight into potentially useful work with efficiencies that are impossible in ordinary experience, seems almost magical at first glance. Thus it is of considerable interest that essentially the same structure is found in purple bacteria. It is noteworthy that PS I closely resembles photosynthetic structures found in green sulfur bacteria, just as PS II resembles structures found in purple bacteria.

        -- PS II, PS I and cytochromeb6f are found in chloroplasts. All plants and all photosynthetic algae contain chloroplasts, which produce NADPH and ATP by the mechanisms described above. Essentially the same transmembrane structures are also found in cyanobacteria.

        -- Unlike plants and algae, cyanobacteria are prokaryotes. They do not contain chloroplasts. Rather, they bear a striking resemblance to chloroplasts themselves. This suggests that organisms resembling cyanobacteria were the evolutionary precursors of chloroplasts. One imagines primitive eukaryotic cells taking up cyanobacteria as intracellular symbionts.

    **   -- Cyanobacteria are the only bacteria that produce oxygen during photosynthesis. The Earth’s primordial atmosphere was anoxic. Organisms like cyanobacteria produced our present-day oxygen containing atmosphere. The other two major groups of photosynthetic bacteria, purple bacteria and green sulfur bacteria, contain only a single photosystem and do not produce oxygen.

        -- Purple bacteria and green sulfur bacteria occupy relatively minor ecological niches in the present day biosphere. They are of interest because of their importance in precambrian ecologies, and because they were the evolutionary precursors of modern plants.

        -- The eventual electron donor is water, liberating molecular oxygen, and the ultimate electron acceptor is carbon dioxide, which is reduced to sugars.

        -- the number of pigments associated with each photochemical complex. The intensity of sunlight is sufficiently dilute so that any given chlorophyll molecule only absorbs at most a few photons per second. The vast majority of the pigments in a photosynthetic organism are not chemically active, but function primarily as an antenna

        -- The heart of photosynthesis as it occurs in most autotrophs consists of two key processes:
                * removal of hydrogen (H) atoms from water molecules
                * reduction of carbon dioxide (CO2) by these hydrogen atoms to form organic molecules
                *   2H2O => 4e-  +  4H+  +  O2  (water becomes electrons, protons, and molecular oxygen)

        -- The removal of electrons from water molecules and their transfer to NADP+ requires energy. The electrons are moving from a redox potential of about +0.82 volt in water to ?0.32 volt in NADPH. Thus enough energy must be available to move them against a total potential of 1.14 volts. Where does the needed energy come from? The answer: Light.

   **     -- Absorption of 1 photon of light by Photosystem II removes 1 electron from P680. With its resulting positive charge, P680 is sufficiently electronegative that it can remove 1 electron from a molecule of water.
When these steps have occurred 4 times, requiring 2 molecules of water, 1 molecule of oxygen and 4 protons (H+) are released

        -- The P680 molecule is involved in noncyclic electron flow. Light striking P680 excites electrons which rush off to fill the electron "holes" in the P700 chlorophyll. The P680 with its electron "holes" is a strong enough oxidizing agent to oxidize water, filling its electron holes and producing O2.

    **    -- P680+ is such a strong oxidant that it is able to pull away electrons from the quite electronegative oxygen atom. Intermediate is a manganese molecule. When manganese has lost four electrons to P680, the manganese (via most electropositive reaction in nature) pulls the four electrons from water (breaking it apart).

        -- The energy released as electrons pass down the gradient between photosystem II and photosystem I is harnessed by the cytochrome b6/f complex to pump protons (H+) against their concentration gradient from the stroma of the chloroplast into the interior of the thylakoid (an example of active transport).

    **    -- This process (cyclic photophosphorylation) is truly cyclic because no outside source of electrons is required. Like the photocell in a light meter, photosystem I is simply using light to create a flow of current. The only difference is that instead of using the current to move the needle on a light meter, the chloroplast uses the current to help synthesize ATP.

        -- Antenna Pigments --- Chlorophylls a and b differ slightly in the wavelengths of light that they absorb best (although both absorb red and blue much better than yellow and green). Carotenoids help fill in the gap by strongly absorbing green light. The entire complex ensures that most of the energy of light will be trapped and passed on to the reaction center chlorophylls.

        -- (osmosis) Water is never transported actively; that is, it never moves against its concentration gradient. However, the concentration of water can be altered by the active transport of solutes and in this way the movement of water in and out of the cell can be controlled.

        Online biology textbook (by Harvard prof)
         http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/W/Welcome.html

pn junctions ---electric field and diffusion gradients
        A pn junction is formed in a semiconductor when the fixed dopant atoms in the crystal change (over a very short distance) from acceptor (P type) to donar (N type). The resultant pn junction has steep charge gradients of mobile positive (holes) and negative (electrons) carriers across the junction and an intrinsic voltage across the junction that opposes charge flow along the gradients. This voltage across the junction is initially set up by a small amount of positive charge (holes) from the P side diffusing to the N side, and a small amount of negative charge (electrons) diffusing from the N side to the P side. The holes and electrons that cross the junction annihilate each other (electrons fall into holes) expose in a thin region (depletion region) spanning the junction the underlying non-mobile charge in the crystal, which is positive on the N side of the junction and negative on the P side.

        The non-mobile exposed charge forms an electric field that points from the N to the P side. This electric field in the depletion region sweeps holes back to the P side and electrons back to the N side, thus keeping the depletion region free of mobile charge and (in effect) preventing charge from moving along the diffusion gradients. Summarizing, across a pn junction there exists two strong charge moving mechanisms, diffusion and an E field, that are opposed, and if undisturbed quickly come into balance preventing any net charge motion across the junction.

        Small changes to the junction field by an external voltage can induce large diffusion of charge carriers across the junction. For example: current in a diode increases exponentially if the voltage across the diode (P side positive with respect to N) is increased even slightly above the what is known as the diode forward voltage (typ 700 mv for a silicon diode). An analogy (from a 50's Scientific American article) is a dam with an overflow spillway. A slight lowering of the dam height (junction voltage) causes a large flow of water (diffusing charges) across the dam.

        Consider what happens when light falls on a pn junction (solar cell). Electron/hole pairs are generated by each photon of light and the charges are accelerated (in opposite directions) by the voltage across the junction. The holes driven by the electric field to the P side and the electrons to the N side. This raises the potential of the P side with respect to the N side, so if wires are attached to the P and N materials and resistor connected between them current will flow from the P material through the resistor to the N material. The power dissipated in the resistor has come from the energy of the photons via the electric field across the junction.
        I wonder --- Does understanding the energy physics of pn solar cells help us understand how photosynthesis works, how a plant is able via photosynthesis to capture the energy of solar photons?

Do cell membranes act like semiconductor pn junctions?
        Question: Do cell membranes act like pn junctions? ---  Yes, somewhat. Cell membranes usually have across them ion grandients and if the membrane pores are 'open' (to diffusion), then an electric field soon forms that blocks further ion (potassium, sodium, hydrogen) diffusion through the membrane.

        In a common case the resting potential across a membrane is set up by (a few) potassium (K+) ions diffusing out of the cell (and negative ions diffusing in). The tendency of K+ to flow down the diffusion gradient out of the cell is balanced by the voltage across the membrane driving K+ into the cell. The membrane is spoken of a have a membrane capacitance and the voltage across it is due to the excess charges next to the membrane. The diffusion channel of a membrane is modeled as a resistor with a different ohms for each type of ion. Note the ion channel in the membrane must be open for the voltage to appear. The resting membrane voltage generated by potassium is -80 mv. Typical capacitance is 66 pf and typical resistance is 33 Mohm (RC = about 2 msec). A neuron cell fires for 2 msec passing a current of 3.3 na. (see 'membrane potential')

Energy mechanisms in cells (excerpts from Wikipedia)
        As a motor control engineer, I have a good understanding of motion and energy. The terminology of energy generation, tranport, and usage in cells is very complex. Using Wikipedia (following links when I hit a new term) I have been trying to gain a general understanding of cell energy. For example, what (really) does it mean to say (useful) energy is obtained by a cell when a material (called food) is oxidized.

        -- Only two sources of energy are available to living organisms: oxidation-reduction (redox) reactions and sunlight (photosynthesis). Organisms that use redox reactions to produce ATP are called chemotrophs. Organisms that use sunlight are called phototrophs. Both chemotrophs and phototrophs utilize electron transport chains to convert energy into ATP. (ATP is a key energy storage/transport molecule.)

        Translation --- When molecules are oxidized (oxygen is added), you get energy out. (This is burning or metabolizing food. The general name for this is (apparently) cellular respiration.) To unoxidize (reduce) a molecule (oxygen is removed) you must put energy in. In other words you do work to rip oxygen out of molecules (redox) and you get that energy back when oxygen reattaches itself (oxidizes).

        -- The overall purpose of the electron transport chain is to create ATP using energy contained in high-energy electrons. This is achieved through a three step process: (1) Gradually sap energy from a high-energy electron in a series of individual steps. (2) Use that energy to forcibly unbalance the proton concentration across the membrane, creating an electrochemical gradient. (3) Use the proton concentration's drive to rebalance itself as a means of producing ATP.

        Translation --- My guess is that hydrogen in a cell is ionized, so proton refers to the positive hydrogen ion. Essentially it's the biological equivalent of a hole in a semiconductor. It seem that high energy or high speed electrons are able to separate protons (holes) across a membrane. The protons can then sit there as form of potential energy ready to do work (at some later time) moving charged stuff across the membrane.

        -- Electron transport chains produce energy in the form of a transmembrane electrochemical potential gradient. This energy can then be harnessed to do useful work. In all living organisms, a series of redox reactions are used to produce a transmembrane electrochemical potential gradient. The gradient can be used to transport molecules across membranes. In biological processes the direction an ion will move by diffusion or active transport across membrane is determined by the electrochemical gradient.

        Translation --- Energy is pulled from high energy (high speed?) electrons to separate charges across a membrane barrier. The voltage across this membrane is then able to do work on charged molecules passing through it, (somehow) generating the energy tranport molecule ATP.  There can also energy stored in an ion concentration gradient across the membrane. This is called chemical potential. Electrochemical potential is the sum of the two potentials.

        -- Redox reactions are chemical reactions in which electrons are transferred from a donor molecule to an acceptor molecule. The transfer of electrons from a high-energy molecule (the donor) to a lower-energy molecule (the acceptor) can be spatially separated into a series of intermediate redox reactions. This is an electron transport chain.

        -- Biological macromolecules that catalyze a thermodynamically unfavorable reaction if and only if a thermodynamically favorable reaction occurs simultaneously underlie all known forms of life.
======================================================
Bond energy, redox voltages, electrolysis of water
        Wikipedia (Photophosphorylation) has many useful observations on energy in photosynthesis and biological system generally:

        --  Only two sources of energy are available to living organisms: sunlight and oxidation-reduction (redox) reactions. All organisms produce ATP, which is the universal energy currency of life.

        -- In photophosphorylation, light energy is used to create a high-energy electron donor and a lower-energy electron acceptor. Electrons then move spontaneously from donor to acceptor through an electron transport chain.

        -- Redox reactions are chemical reactions in which electrons are transferred from a donor molecule to an acceptor molecule. The underlying force driving these reactions is the Gibbs free energy of the reactants and products. The Gibbs free energy is the energy available (“free”) to do work. Any reaction that decreases the overall Gibbs free energy of a system will proceed spontaneously.

        -- The fact that a reaction is thermodynamically possible does not mean that it will actually occur. A mixture of hydrogen gas and oxygen gas does not spontaneously ignite. It is necessary either to supply an activation energy, or to lower the intrinsic activation energy of the system, in order to make most biochemical reactions proceed at a useful rate. Living systems use complex macromolecular structures (proteins, enzymes) to lower the activation energies of biochemical reactions.

 Hyperphysics site
        -- Obtaining energy output from a fuel typically involves oxidation of the fuel, and if the fuel is more reduced to start with, this would imply that more energy can be obtained from it if we could fully oxidize it.

        -- Viewing a molecule that is more reduced as being in a higher energy state with respect to its totally oxidized state is useful for biological energy processes like cellular respiration.

        Figure below is a useful visualization of carbon reduced/oxidized state. In high energy methane electrons are pulled more closer to C than H, so in a sense C has (partial) electrons to give away. When C is oxidized (CO2), O has pulls hard on electrons, pulling them down into a potential energy well, thus releasing energy. C has been oxidized in the sense that it has lost (partial) electrons.

        As I look at it, energy is released going rightward because O pulls electrons harder than H. Here are the electron negative element values. Elements with higher electronegative values pull electrons closer (in a covalent bond). However, these values are not volts, Pauling electronegativity is dimensionless. (I can't find any quantitative relationship between electronegativity and redox voltages.)

                                                    H        2.20            (many elements are lower, Ca = 1.00)
                                                    C        2.50            (C is between H and O)
                                                    O        3.44            (2nd highest of all elenents)

Fuel energy -- Toward an intuitive feel for why burning (or oxidizing) of fuels outputs energy
        In the paragraphs below I look at fuel energy in several different ways, but after doing this work I see the basic answer as to why fuels give out energy and how much is very simple.

        The lowest number (by far) in the bond energy table below is 58 kcal/mol for 1/2 O=O in gaseous (or dissolved) O2, so if any significant amount of O2 appears on the input side of the equation, bond energies on the output side almost for sure will be higher and energy will be released. Oxygen bonds with carbon in CO2 (C=O) and and hydrogen in H2O (H-O) outputs have almost twice the energy (93.5, 110 kcal/mol) as oxygen-oxygen bonds in O2 inputs (58 kcal/mol).

                                 CH4 + 2O2 => CO2 + 2H2O
                         [4 x 98 + 4 x 58]  -  [4 x 93.5 + 4 x 110] = 4 x 47.5 = 190

Methane oxidation sketch
        The oxidation of methane (equation above) is a classic case of fuel oxidation. Methane is a CH fuel (no oxygen) with just one carbon. Carbon's four valence electrons are each attached to a hydrogen atom (four C-H bonds). It is so important it deserves a little sketch, so I drew one (below). In a C-H fuel all the oxygen in the CO2 and 2H2O in the output is pulled from the air. The single C in the fuel required one CO2 and the four H in the fuel require two H2O. I have drawn the ouput molecules from the point of view of oxygen, the heaviest atom. Oxygen pulls in other atoms close, so its bonds have high energy. The two valence electons of the two oxygen in CO2 are attached to a single carbon (two O=C bonds). In two water the oxygen valence electrons are all attached to hydrogen (four O-H bonds).

        It is interesting to note that none of the energy output of methane oxidation comes from reconfiguring the four bonds of its single carbon from four hydrogen to two oxygen. In fact it costs energy, the bond energy of output CO2 (374) is less than fuel CH4 (392). The energy output of the reaction can be viewed as really coming from making water, where one O2 from the air is needed to sop up the four hydrogen from the CH4 fuel. The bond energy of the one the two H2O (2O-H = 2 x 110 = 220) is almost enough to break the bonds of both of the two O2 pulled from the air (2O=O = 2 x 116 = 232).

Less oxygen => higher energy output
        The energy output of the fuel is higher the less oxygen it contains. This is true for two reasons. One, most of the oxygen in the outputs CO2 and H2O comes from O2 with its low energy bonds. Fuels like glucose (C6H12O6) with a lot of oxygen are (in a sense) already partially oxidized. Less external oxygen is needed to burn them because they provide (in higher energy form) some of the output oxygen. There are three oxygen bonds in the table (O-H, C=O, C-O). The first two of these are in the outputs water and CO2, so contribute nothing toward energy output. The third (C-O) at 78 contributes a little because in CO2 the (double) carbon-oxygen bond has a somewhat higher energy (93.5 per electron).

        Oxygen at atomic weight 16 is relatively heavy, so it can increases the weight of a fuel substantially (53% of the weight of glucose C6H12O6 is oxygen) while contributing little to the energy output. So from a weight perspective, the more oxygen in a fuel the lower the energy output per unit weight of fuel.

excellent bond energy table
John W. Kimbal (retired Harvard biology prof) online Biology book
source -- http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BalanceSheet.html
(source moved to -- http://www.biology-pages.info/B/BalanceSheet.html
which includes the bond energy analysis of glucose oxidation and photosynthesis)

        Biological fuels (food) are mostly carbon, hydrogen, and oxygen and contain a mixture of bond types among these atoms. Fossil fuels are mostly hydrogen and carbon (hydrocarbons). For example, glucose has C-C, C-H, C-O, and O-H bonds, but no double C=O bonds and no double C=C bonds. The hydrocarbon series: methane, ethane, propane, butane, pentane, hexane are all a linear carbon chain, so have only C-O and C-H bonds.

        The outputs of oxidation of all C,H,O fuels are just CO2, which is oxygen double bonded to carbon (C=O), and H2O, which is oxygen single bonded to hydrogen (H-O).  Of course oxidation requires additional oxygen input, which if gaseous requires breaking double oxygen bonds (O=O). (oxygen in water?)

        At first I though I could understand the nature of fuels by understanding the energy differences when oxygen replaces hydrogen or carbon, but I found there are a lot of combinations [ H-C to H-O, C-C to C=O, C-O to C=O, C-H to C=O]. This means that oxidations could not usually be broken down into a series of simple swaps, so this method appears to have limited use, but there is another way I realized.

Focus on input bond energy and source of oxygen
        Energy released in an oxidation can be figured by differencing the energy in the output bonds (bonds made) and the energy in the input bonds (bonds broken). In the oxidation of C,H,O fuels there are only two types of output bonds C=O (in CO2) and H-O (in water). A good guess is that the key to getting high energy out of fuels is that the input side bond energy be low, and looking at the bond table the 1/2 O=O bond has by far the lowest energy. Another whole different perspective is gained by looking at bond energy per atomic weight.

        All the hydrogen ends up in water, all the carbon in CO2. Each C needs two O and each H needs 1/2 O, so the external O needs can be figured by subtracting off the O contained in the fuel. The less O inside the better because the bond energy of O2  (@ 58 kcal/mole  for 1/2 O=O) is much lower than C-O, H-O, and 1/2 C=O. Also oxygen in a fuel can substantially increase its weight, while simultaneously decreasing the energy output.

Kimbal's view of fuel energy
        Harvard professor Kimbal argument as to why oxidation of glucose releases energy goes like this. Electronegativity: (O   3.44, C  2.55,  H   2.20)

Outputs H2O and CO2
            * Difference in electronegativity between their atoms (oxygen to carbon and hydrogen) is high, so they form "strong bonds" (polar covalent bonds with high bond energies)
                    * broken with difficulty
                    * releasing large amount of energy when they form    delta electronegativity
                    * O=C           93.5 x 2  kcal/mol                                           .89
                       O-H           110          kcal/mol                                         1.24

Inputs glucose and oxygen
            * Differences in electronegativity between their atoms tend to be lower, so they form
                                    (covalent) bonds that (on average) have relatively low bond energy
                    * broken with relative ease                                        delta electronegativity
                    * O=O          58 x 2      kcal/mol                                              0
                       O-C            78            kcal/mol                                             .89
                       C-C            80            kcal/mol  (carbon chain & loop)        0
                       C-H            98            kcal/mol                                             .35
                       O-H (same as water)

        Clearly the correlation between differences in electronegativity and bond energy is only approximate!

                            CH4 + 2O2 => CO2 + 2H2O  + 890 kj/mole (9.22 ev)

bond energy             4 C-H + 2 O=O => 2 C=O + 4H-O
                           4 x 98 + 2 x (2 x 58) => 2 (2 x 93.5) + 4 x 110
                                            392 + 232 => 374 + 440
                                                       624 => 624 + 190 (8.22 ev)

Single vs average bond energy
        A complication with bond energy calculations is that the energy to break (seemingly identical) C-H bonds is not quite the same. For example, it takes more energy to break the first C-H bond in methane than the remaining C-H bonds. The simplification normally used is to use the average bond energy to break all the C-H bonds. Average bond energy is what is listed in the tables.

        -- 104.1 kcal/mol is required to break a single C-H bond for a mole of methane, but breaking all four C-H bonds for a mole of methane requires 397.8 (4 x 99.5) kcal/mol. (In other words it takes 5% more energy to break the first C-H bond in methane than the average to break all four.)

    CH4 (four 1/2 C=O bonds in CO2, four H-O bonds in water) in output from four input C-H bonds and four 1/2 O=O bonds
                         4 x (93.5) + 4 x (110)  - 4 x (98)  - 4 x (58)  = 4 x 47.5 = 190 kcal/mole

        In glucose (C6H12O6) oxidation, which yields 6CO2 + 6H2O), 1/3rd of the oxygen in the output comes from glucose.

Weight perspective
        In the outputs each H contributes only one (H-O) bond at 110 vs C which contributes 4 (1/2 C=O) bonds at 93.5. Making the four bonds of a carbon atoms yields x3 to x4 times as much energy as making the one bond of hydrogen, but carbon weighs x 16 times more than hydrogen. Thus in fuels hydrogen contributes much more energy by weight than carbon!

        In contrast oxygen in fuel not only has bonds quite a bit more difficult to break than free gaseous oxygen, but it can increase the weight of the fuel substantially. Oxygen has atomic weight of 16 vs 12 for carbon and one for H. Glucose (C6H12O6) has a weight of 180 and more than half of that (6 x 16 = 96) is oxygen. As shown below, if equal weights of glucose and methane are oxidized, methane puts out 350% more energy than glucose.

                   CH4 weight               = 16            9.22 ev
                   C6H12O6 weight     = 180         29.7 ev
      (11.25 CH4 weight               = 180        103.7 ev)

Carbohydrate vs fat
       Burning dried food in a calorimeter allows the energy content to be measured. These results (I'm pretty sure) are similar to the energy obtain when the food is (slowly) oxidized in the body. Below are values I find in a book. What's interesting is fat has over twice the energy (per gram) as carbohydrate, which is the main source of energy in the human diet. But it's also suggestive of why the body carries its energy stores in the form of fats.

                 carbohydrate                    17.2 kj/gram            C6H12O6 (glucose)
                 protein                              22.2 kj/gram            C44189 H71252 N12428 O14007 S321
                 fat                                      38.5 kj/gram            C55H98O6 (triglycerides)

        'Fuel Rule' -- High energy per weight means high hydrogen and, even more importantly, low oxygen

Why is fat's energy density so high?
        Fat has a little lower ratio of H to C than glucose (1/78 vs 2, bad), but a much lower ratio of O to C (0.109 vs 1, good). So very likely the high energy obtained from the oxidation of fat (vs sugar) per unit weight is mostly because fat is virtually a hydro-carbon with only about 1/10th the oxygen of glucose. Initially I didn't see it, but I now think it's pretty clear the reason fat has double the energy output per unit weight compared to glucose is that its weight is nearly halved by having only about 1/10th the oxygen. This also explains why proteins are midway between carbohydrates and fats. N has atomic weight 14, pretty close to 16 for O, so the ratio of (O + N) to C in proteins is 0.56 (vs 1 for glucose and 0.109 for fat) putting it midway between them in energy stored per unit weight. A good guess is that the net energy contribution of fat's slightly lower H and higher O2 input (vs glucose) roughly cancel.
Fat in human diet
        Wikipedia (Food Energy) gives the energy value for fat (37 kj/gram) very close to above. Fat being mostly a hydrocarbon has an energy density in the range of hydrocarbon fuels, for example, gasoline is 47 kj/gram and coal is 27 kj/gram. So how many food calories (kcal) are stored in a lb of fat!

                                37 kj/gram x (1 kcal/4.184 kj)  = 8.84 kcal/gram
                   8.84 kcal/gram x (1,000 gram/2.205 lb) = 4,001 kcal/lb

Body efficiency
        Wikipedia says humans (on average) are able to extract about 85% of the energy value stored in food they eat. An interesting question is what is the efficiency of the body in burning its fat stores? How many kcal does the body obtain when it 'burns' a lb of stored fat?

        Efficiency from respiration ('burning' of food) to mechanical (muscle) work out in the human body is low, roughly 20-25%. The biggest loss is [respiration to ATP], where only 40% of the food energy makes it into ATP, the remaining 60% presumably lost as heat. Roughly half of the ATP energy is output by the muscles as useful work, the remaining ATP energy is lost as heat (exercising muscles get warm).

Oxidation of glucose
        In a balanced equation the number of shared electrons is the same in the input and output side (because atoms are the same, so total valence electrons are the same). For example, in the oxidation of glucose the number of shared electrons on each side is 36. On input side 24 shared electrons in one glucose (see the 3d model of glucose) and 12 shared electrons in 6O2 (two per oxygen). On the output side 6CO2 has 24 shared electrons (four per carbon) and 6H2O has 12 shared electrons.

                                  C6H12O6 + 6O2 => 6CO2 + 6H2O + 686 kcal/mole (29.7 ev)

        Looking at the table above we can make the following observations:

Fuel oxygen bonds
                * H-O bonds in fuel are a wash (no net energy contribution). They are cancelled
                            by H-O bonds in water
                            (5 of glucose's 24 bonds are H-O bonds)

                * C=O bonds in fuel are a wash (no net energy contribution). They are cancelled
                            by C=O bonds in CO2
                            (none of glucose's 24 bonds are C=O bonds)

                * C in fuel bonded to oxygen with a single bond (C-O) releases moderate energy
                            when it rebonds to O as half of a double bond (1/2 C=O) in CO2
                            (7 of glucose's 24 bonds are C-O bonds)
                            (93.5 - 78 = 15.5 kcal/mole per electron)

Not bonded to oxygen in fuels
               * H and C in fuel bonded together (H-C) releases a lot of net energy when
                            C and H rebond to oxygen. (1/2 C=O, H-O)
                            (7 of glucose's 24 bonds are H-C bonds)
                            (110 +93.5 - 98 - 58 = 47.5 kcal/mole per electron)

                * Carbon in fuel single bonded to itself (C-C) releases a lot of energy when
                            both C rebonds to oxygen (1/2 C=O) as half of a double bond in CO2
                           (5 of glucose's 24 bonds are C-C bonds)
                            (93.5 +93.5 - 80 - 58 = 49 kcal/mole per electron)

                * Carbon in fuel double bonded to itself (C=C) releases a very large amount
                            of energy when both C rebond to oxygen (1/2 C=O) in CO2
                            (none of glucose's bonds is C=C)
                            (93.5 +93.5 - 72.5 - 58 = 56.5 kcal/mole per electron)

Glucose structure and bonds
        Glucose is a (simple) sugar (technically a monosaccharide), but it is also a carbohydrate.  A carbohydrate has the general formula Cm(H2O)n, which fits C6H12O6. A carbohydrate is a 'hydrate' of carbon, basically a 'watered' carbon. However, then I found this caveat: "Molecules have been labeled as hydrates for historical reasons. Glucose, C6H12O6, was originally thought of as C6(H2O)6 and described as a carbohydrate, but Wikiped addes that this is a very poor description of its structure as known today." (Wikipedia: 'Hydrate', Organic chemistry)

        -- (In a hydrate water often breaks up into OH (hydroxyl group) and H. All the center carbons of the glucose chain have side chains of OH and H, so they can be seen as having a 'water' attached.)

        -- Carbohydrate is most common in biochemistry, where it is a synonym of saccharide. The carbohydrates (saccharides) are divided into four chemical groupings: monosaccharides, disaccharides, oligosaccharides, and polysaccharides. In general, the monosaccharides and disaccharides, which are smaller (lower molecular weight) carbohydrates, are commonly referred to as sugars. (Wikipedia: Carbohydrate)

        "Every living organism on earth eats glucose" (NASA), hence it was used in the famous Mars life experiment as a nutrient for microbes. But on earth only the right handed form (D-glucose) is eaten and can provide energy. Left handed glucose (L-glucose) has been proposed as a no calory sweetner and as a colon cleaner.

        Surprisingly finding out the structure and bond energy of glucose is not so simple. References differ. Prof Kimbal of Harvard shows the basic structure of glucose as a 'hex loop' (five carbon + one oxygen) and uses it to calculate the bond energy of glucose and the energy released when oxidized. But Wikipedia shows the structure of glucose as six carbon chain (d_glucose chain). Wikipedia mentions a loop form, but says it's not used in life as life cannot oxidize it.

Kimbal's details of glucose bond energy and oxidation are here:
         http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BalanceSheet.html

Glucose starting from an ideal chain
       Draw a chain of six carbon each with an -H and -O-H side chains (like the inner carbon above). All the atoms are there, but the end carbons have a problem: end carbons are one (valence) electron short.

           a) The easiest way to fix the ends (it would seem) would be to tie the ends together with a C-C bond (making a hex C-C loop), but I don't see this so it must be unstable or not favored energetically.

           b) The chain form of glucose is just the ideal chain with basically one tweak: At one end C-O => C=O, which frees up the hydrogen that was on the oxygen. The free hydrogen now joins up with the carbon at the other end (C-H), so both end end carbons are now happy.

        c) In the loop form of glucose one end of the ideal chain is fixed by folding back to join an oxygen (C-O), which frees the hydrogen that was on the oxygen. The freed hydrogen then fixes the carbon at the other end (C-H). Note (on paper) these fixes work by looping back to join any of the six oxygen. In fact the C=O bond at the end of chain glucose can be viewed as a special case of looping back. In this case the end carbon just 'loops back' to its own oxygen!

        The chain form with its one double C=O bond has 1.4% more bond energy (= 31 kcal/mol)/(2,182 kcal/mol) than the loop form with its replacement two C-O bonds. (Why is everything so complicated in biology!) There's probably some equilibrium between forms and is seems likely that the loop form is most common since its energy is a little lower.

        The loop form has five carbon and an oxygen in the loop. Looking at the chain I could see how to get the [5C + O] loop by connecting a carbon one end to an oxygen near the other end. The chain to loop conversion requires removing two hydrogen to free up the two ends and shifting the two hydrogen to the remaining carbon side chain, which requires that its C=O double bond reconfigure to the lower energy form with one C-O bond. I sketched it up.

        -- In organic chemistry, a carbonyl group is a functional group composed of a carbon atom double-bonded to an oxygen atom: C=O. When an H is attached to the carbon in a C=O bond at the end of a carbon chain, it's called an aldehyde, so the right end of the glucose chain ends in an aldehyde.)

        -- Monosaccharides with three carbon atoms are called trioses, those with four are called tetroses, five are called pentoses, six are hexoses, and so on.

Where the oxidation energy in glucose comes from?
               All we need do is to add up the increase in energy from rearrangement of the 24 electron bonds listed above and subtract off the energy needed to crack open 12 electron O=O bonds in O2 and we should have the net energy output of the reaction.

start from output  (5 H-O bonds in glucose 'transfer' to water)

        24  1/2 C=O bonds form              24 x 93.5 = 2,244
          7 (of 12 total) H-0 bonds form     7 x 110 =    770
                                                                            ------------------------
                                                                          total   3,014 kcal/mol

36 bonds must break (5 H-O bonds in glucose 'transfer' to water)

         12  1/2 O=O                                        12 x 58 = 696
           5 C-C                                                    5 x 80 = 400
           7 C-H                                                    7 x 98 = 686
           7  C-O                                                   7 x 78 = 546
                                                                               --------------
                                                                         total     2,328 kcal/mol

Check:  3,014 - 2,328 = 686 kcal/mol (stated energy released by oxidation)

        12 1/2 O=O to 1/2 C=O        12 x (93.5 - 58) = 426            62.1%

          7 C-O to  1/2 C=O                   7 x (93.5 -78) = 108.5        15.8%
          7 H-C to 7 H-O                        7 x (110 - 98) = 84              12.2%
          5 C-C  to 1/2 C=O                  5 x (93.5 - 80) = 67.5             9.8%
                                                                           ----------------------------
                                                                                total 686 kcal/mol

        From this perspective 62% of energy output comes (loosely speaking) from an energy 'upgrade' of the low energy oxygen-oxygen bonds to high energy carbon-oxygen bonds. (Not sure how useful this viewpoint is, since the need for external oxygen is intimately tied up with how many bonds of glucose are non-oxygen.)

Carbon backbones
        The backbone of fuels (& most organic molecules) is carbon. Carbons want to share (if possible) four electrons. This makes for four types of carbon backbones: single bonds, alternating double/single bonds, all double bonds, and (potentially) triple/single bonds.

                         |    |   |   |    |              |    |    |    |    |
                      -C-C-C-C-C-         =C-C=C-C=C-         =C=C=C=C=C=      -C(triple)C-C(triple)-
                         |    |   |   |    |

1st type: Single bonded carbon chains (& loops) have two side chains on each carbon. In a carbohydrate (a hydrated carbon) it's possible to (in effect) hang a 'water' in the form of an 'H' and 'OH' side chain on each carbon. Glucose basic structure is a hydrated single bonded carbon chain.

2nd type: Alternating double/single bonds. A lot of carbon hex loops have this structure. Each carbon here has one side chain.

3rd type: Each carbon double bonded to next carbon. Here the backbone provides each carbon with the four electrons it wants, so there are zero side chains on the carbons.

4th type: Alternating triple/single bonds. This also would have no side chains. Not sure if this long chains of this type exist, but two short versions are acetylene H-C(triple)C-H and propyne (see below) H-C(triple)C-CH3.

Alkane (C-C) hydrocarbon family
       The 1st type (C-C) hydrocarbons have names ending in -ane. As a group they are alkanes. One carbon is methane, two carbon is ethane, eight carbon is octane, etc. Alkanes (C-C chain with H sides) as a family have a remarkable property. As the number of carbon goes up the boiling point monotonically increases! Wikipedia ('Alkanes') has a table from one carbon (methane) to fifty carbon (pentacontane) with the boiling points going from -162 C to 575 C. Low carbon C-C chain hydrocarbons (like methane and ethane) are gases. At five carbon (pentane) the boiling point is a little above room temperature so these are liquids, and at twenty carbon and higher the materials are solids.

Types of fuel or 'fuel jargon'
        In a book on synthetic fuels I found an overview of basic carbon molcules (fuels) and all the confusing names applied to them. A key distinction is made between those that are saturated hydrocarbons and those that are reactive (unsaturated hydrocarbons). Reactive to fuel chemists seems to mean a substance is easier to alter, like oil is 'cracked' a change with heat, pressure, and/or additives. The implication being that reactive molecules are less stable than saturated molecules. Surprisingly whether a carbon molecule is reactive or saturated seems to depends only on its carbon backbone.

         Saturated                                          C-C
                   Not Saturated (Reactive)                C=C or C(triple)C

Saturated fuels
       I think I now understand this emphasis on saturated vs unsaturated from a fuel engineers perspective. An unsaturated molecule has a carbon backbone that is double bonded (=C=C=C=), so it has no side chains (except for the ends). When burned, each carbon atom pulls in O2 from the atmosphere to form one CO2. Fuel engineers can upgrade the fuel energy of unsaturated fuels by changing them to saturated, i.e. changing their backbone from (=C=C=C=)to(-C-C-C-). Now each carbon has two side chains, typically H's, which don't weigh much.

        Intuitively it's clear a saturated fuel is a better fuel. Each carbon in a saturated fuel when burned outputs (as before) one CO2, but two H side chains add one H2O. More energy is released per kg of fuel burned.

        As a check I looked at gasoline, which is a mixture of many different molecules. Some of its major components have a linear saturated backbone with H side (like alkanes), and some (like toluene) are only partially saturated. Toluene being a carbon ring of alternating single double bonds (C-C=C-C=) with one side chain per carbon.

                               single C-C                     348 kj/mol   (83.3 kcal/mol)
                               double C=C                   614 kj/mol   (73.5 kcal/mol per electron)
                               triple C(triple)C           839 kJ/mol   (67 kcal/mol per electron)

Comment on 'bond energy'
        'Bond energy' is potentially confusing because it can be looked at two ways. The reference above says the triple carbon bond has the highest energy. Clearly this is true experimentally, because separating a mole of carbons takes 839 kJ if the carbons are triple bonded vs 348 kJ if they are single bonded.

       But if looked at on a per electron basis the situation is reversed! The per electron basis (it seems to me) is what is important in reactions, because when you break a triple carbon bond each carbon can make three new single bonds. It's triple bonded propyne that is a potential rocket fuel.

Comment on 'bond length'
        Bond length is another confusing term. Firstly, it's not really a measure of the electron bond length at all, it's just the distance between the nuclei of bonded atoms. Secondly, the above reference says the bond energy (tends to) go up as the bond distance goes down. For example the bond distance for single, double, triple carbon bonds are

                      C-C                        154 pm       (348 kJ/mol)
                      C=C                       134 pm       (614 kJ/mol)
                      C(triple)C             120 pm       (839 kJ/mol)

OK, so carbons triple bonded are closer, but it takes three electrons to do this. (120 pm is 1.2 Angstrom.)

Propyne with C(triple)C
        Consistent with the fact that molecules with C(triple)C bonds are reactive is the case of propyne C3H4 a simple molecule with one C(triple)C bond:

                                            H-C(triple)C-CH3

The European Union is considering this as (liquid) rocket fuel when combined with liquid oxygen. Suffix -yne indicates a triple carbon bond.

Bond energy vs distance
        Here's a cool graph showing how H-H bond energy varies as the distance between the two hydrogen nuclei (bond length) varies. This shows several interesting things. The basis for (thermal) oscillations, restoring force vs distance, is clear. The slope at the bottom of the energy well is zero, so just a tiny amount of thermal energy will cause some motion. Once nuclei are separated about x3 times the normal bonding distance the bond is pretty much broken.

Oxidation of propyne
        Oxidation of potential rocket fuel propyne with it's one triple carbon bond. (In a balanced equation the number of shared electrons is the same in the input and output side (because atoms are the same, so total valence electrons are the same).

                                            H-C(triple)C-CH3 + 4O2 => 3CO2 + 2H2O

                           4C-H + C(tripleC) + C-C   + 4O=O =>  6C=O + 4H-O
            4C-H + 3 1/3 C(tripleC) + C-C + 8 1/2 O=O =>  12 1/2 C=O + 4H-O            (16 bonds each side)
                   4 x 98 + 3 x 67 + 1 x 80      +    8 x 58     => 12 x 93.5      + 4 x 110         (kcal/mol)
                                                                             1,137  => 1,137 + 425  kcal/mol

It's so easy to double count
        When I first counted bonds I got: On input side 12 (3 carbons x 4 bonds per carbon) shared electrons in propyne and 8 shared electrons in 4O2 (two per oxygen) for a total of 20 shared electrons. On the output side 3CO2 has 12 shared electrons (four per carbon) and 2H2O has 4 shared electrons. Whoops, 20 on input side and 16 on output side?? The problem is the single and triple bonds in the carbon backbone of propyne have been double counted. Propyne has four H bonds and four carbon to carbon bonds (C-C and C(triple)C)).

        Note on the input side because the carbons are bonded with each other the count is only 8 carbon bonds, yet on the output side, where carbon is only bonded to oxygen (in CO2), the carbon bond count is 12.

        One way to get the count right just count looking at the 3d (ball) structure.

                  methane      (CH4)                 190 kcal/mol             fuel  weight = 16        11.9 kcal/gram
                  glucose       (C6H12O6)       686 kcal/mol             fuel  weight = 180        3.8 kcal/gram
                  propyne       (C3H4)              425 kcal/mol             fuel  weight = 40        10.6 kcal/gram

        Propyne puts out a little less energy per unit weight than methane, but methane is a gas while propyne is a liquid. Both hydrocarbons (no oxygen) put out about x3 more energy than glucose per unit weight.
--------------
Ethanol energy
        Ethanol (fuel) is interesting. It's made from glucose by fermentation (done by yeast). Fermentation from an energy point of view an inefficient 'burning' of a fuel, which is why the residue, ethanol, still has a lot of energy than can be extracted by oxidation. The formula to make ethanol from glucose is below. Note while CO2 comes out (plus heat) no oxygen goes in! All the O comes from the glucose.

                    C6H12O6 => 2 C2H6O + 2 CO2 + heat

Alcohol
        Ethanol the fuel (without denaturing, i.e  without added poison) is exactly the same as drinking alcohol (ethyl alcohol). Alcohol is just a hydrocarbon with an H replaced by an OH (radical). To get ethyl alcohol think ethane (C2H6), which is the two carbon 'version' of methane (technically a two carbon -ane chain), and replace an H with an OH (C2H5-OH). The OH makes it an alcohol. This change makes the molecule 50% heavier and converts a gas (ethane) into a liquid (ethyl alcohol).

                                    C6H12O6                          2 C2H6O + 2 CO2
                                    ------------                         -----------------------
           C-H                 7 x 98 = 686                       10 x 98 = 980
            C-C                  5 x 80 = 400                         2 x 80 = 160
            C-O                  7 x 78 = 546                         2 x 78 = 156
            O-H                5 x 110 = 550                       2 x 110 = 220
            C=O               0 x 187 = 0                            4 x 187 = 748
                               ---------------------                  ---------------------
                                       2,182 kcal/mol                 2,264 kcal/mol

        The energy released (lost as heat) from fermentation of glucose to ethanol is [2,264 - 2,182 = 82 kcal/mol], which at 1 ev = 23.1 kcal/mol is 3.55 ev. Since oxidation of glucose to H2O and CO2 yields 29.7 ev, about 88% [= 26.2 ev/29.7 ev] of the glucose enengy remains in ethanol.

                        C2H6O + 3 O2 => 2 CO2 + 3 H2O + (ethanol oxidation heat)

        Ethanol oxidation heat (above) is 2,818 kj/mol (29.2 ev) (Wikipedia) and 2,656 kj/mol (27.5 ev) in another reference. Bond energy only provides an estimate of release energy and everyone bond energies are slightly different, so this agreement. Below confirms that energy density of ethanol is higher than glucose.

           Energy density of ethanol  = (23.4 to 26.8) kj/gram
            Energy density of glucose = 15.5 kj/gram

Bottom line --- Most (88%) of the  energy in glucose is transferred into ethanol in the fermentation process and as a bonus the energy density is increased by the removal of oxygen.

Brewing
        Brewing has the same formula as above [C6H12O6 => 2 C2H6O + 2 CO2] except the output is described as 'Ethyl alcohol', but Wikipedia says "Alcoholic beverages are defined as beverages that contain ethanol (C2H6O)."  The complex transformation takes weeks using yeast (plant fungi), which in brewing proceeds anaerobic. (Actually yeast will oxidize glucose all the way to CO2 and H2O if you give them oxygen, so oxygen is cut off so they proced anaerobically yielding ethanol and CO2.) Interestingly how high the alcohol level goes is self limiting because high alcohol levels kill yeast cells. This happens at 6% to 21% alcohol depending on the yeast strain. For example, wine yeast can tolerate alcohol levels up to about 12%. (Bacteria do fermentation too, I guess yeast, which is a eukarotic cell, is used for practical reasons.)

                                                    H3C-CH2OH + 3 O2 => 2 CO2 + 3 H2O
                            5C-H + C-C + C-O + O-H + 3O=O =>  4C=O + 6H-O                 (14 bonds each side)
                           5 x 98 + 80 + 78 + 110 + 3 x 2 x 58 => 4 x 2 x 93.5  + 6 x 110          kcal/mol
                                                                              1,106 => 1,106 + 301 (13.0 ev)           kcal/mol

        Ferementation of glucose (C6H12O6) yields two ethyl alcohol molecules (2 C2H6O), so energy from oxidation of ethyl alcohol (ethanol) (2 x 13 ev = 26 ev) is 88% of the energy release from oxidizing glucose (29.7 ev).   Checks
--------------
Getting fat and doing work
**      -- If you eat an 'extra', meaning above your energy needs, pound of fat (or equivalently two pounds of carbohydrates), then assuming about 30% "digestion efficiency" (from some reference) you add to your weight 1/3 of a pound (of fat). (Wow, this is simple! Eat an extra pound of fat and you increase your weight 1/3 of a pound. I wonder how accurate this is?)

        -- If you are working hard and putting out 150 watts of work (say measured by a stationary bicycle), then a muscle and system efficiency of about 12.5% means you must be oxidizing about 1,200 watts of fuel. You generating 80% of the energy of a 1,500 watt room heater! (This is consistent with a fact I heard on 'Animal Planet'. The reason a cheater has to stop running quicky (in a 1/2 mile or so) is not that he has run out of fuel, but because he overheats.)

        -- Only carbohydrates (including fiber), fats, proteins, organic acids, polyols (sugar), and ethanol contain food energy. All foods are made up of a combination of these five nutrients.(Wiki -- Food energy)
------------------------
Overview of redox potentials
        I find the various listings of standard redox potentials to be a quite a mess. There are multiple confusions: name/definition, conditions (pH) and sign.

Which potential?
             Reduction potentials (Er)      --- voltage measured relative to a standard hydrogen
                                                                            electrode (SHE) under standard conditions
                                                                            which is defined at 0 volts
                                                                            (Wikipedia says measured values "seldom
                                                                              correlate with calculated values", so are
                                                                              table values measured or calculated?
             Oxidation potentials (Eo)      --- negative of Reduction potentials (US convention)
             Redox potentials                     --- shorthand for Reduction potential
              Redox state                            --- ratio of NADP+/NADPH

        The more positive the redox voltage the harder it sucks electrons, so oxygen is very positive and lithium very negative. An element will pull away electrons (oxidize) from any element will a lower redox voltage.

Polarity
        An 'environment' that accepts electrons from a normal hydrogen electrode is a half cell that is defined as having a positive redox potential, so an environment that favors oxidation reaction, such as free oxygen, will have a high positive voltage.

Example of redox reaction (Wiki)
            Hydrogen combines with florine to make hydrogen floride. Insight into why this reaction goes is seen by breaking the equation into two steps, and oxidation and reduction step. Florine is the most powerful oxidizer known so it accepts electrons. (I guess the message is that the reaction goes because F- and H+ attract with, of course e- cancelling out.)

                        F +e- => F-                     florine accepts an electron
                              H => H+ + e-            hydrogen give up an electron
                   ---- -------------------
                  H2 + F2 => 2HF

Standard conditions or pH?
        There seem to be two sets of standard (or quasi-standard) conditions in use: ph=0 and pH=7 with a difference between them of about 413 mv. This is very confusing. Hyperphysics site says 'standard' conditions are pH = 0, but standard conditions prime are for pH = 7 (neutral water). The figure below the correction vs pH. The correction for pH is -59 mv/pH, or 7 x -59 mv = -413 mv.

       -- The redox potential of the hydrogen is zero at pH=0, but for tabulations a pH=7 is used for the hydrogen and under those conditions its redox potential is -0.421 volts. (well as long as its used for tablulations...)

        -- For biochemical reactions, it is convenient to reference the change in Gibbs free energy (delta G) at some standard set of conditions.

                        Standard Conditions
                       T = 25°C = 298K
                        P = 1 atm
                        [C]=1 M, all reactants
                        Water 55.6M
                         H+ conc = 10-7M (pH=7.0)

        'Standard redox potentials' (E0 prime) from hyperphysics site (from [2H+ +2e- <=> H2] it's clear that these conditions are pH=7.

                NADP+ + 2H+ +2e- <=> NADPH + H+             -0.324 V
                   1/2 O2 + 2H+ +2e- <=> H2O                          +0.816 V
                    2H+ +2e- <=> H2                                               -0.421 V

Ionization energy (formerly ionization potential)
         --  Work required to remove to infinity the topmost electron in the atom or molecule when the gas atom or molecule is isolated in free space and is in its ground electronic state.

        -- The greater the ionization energy, the more difficult it is to remove an electron.

Applying redox equations to photosynthesis
        An easy way to estimate a reaction energy input/output is use of (standard) redox potentials times number of electrons transferred. Breaking up an equation into separate oxidation and reduction equations can show how many electrons transfer, i.e. how many e- are in the equation. I think it's an estimate because redox potentials are tabulated at standard conditions (pH, pressure, etc), so correction terms may be needed.

pH correction
        A common correction term for redox voltage (appears to be) pH (H+ concentration). In general the change in electrochemical potential per factor of ten (H+ only?) concentration is 59 mv. pH is a decimal logarithmic measure of H+, hence the pH correction term for redox voltage is just -[59 mv x pH]. For example, the standard reduction potential of water is 1.23 V, but at pH of 7 (neutral), it is 1.23 V - [7 x 59 mv] = 0.817 V.

source --- (book) An Indroduction to Plant Biology by James Mauseth (Google books)
(Note H2O potential here of +0.82V agrees with the table above, so this table must be for pH=7)

Basic redox equations

 Redox jargon -- In a chemical reaction a single electron (cloud) shifts away from one atom toward another. This one shift is referred to as two 'half reactions', the atom that 'loses' the electron is oxidized and the atom that 'gains' the electron is reduced.

        All redox equations can be reversed, just flip the arrow and sign of Er. Typically redox equations are scaled and added to cancel the electrons. The key to combining redox equations is that when equations are added, the Er's are added too. Combining simple redox equations is how to find the Er for more complex reactions.

        Energy flow --- A negative Er means the electrons need to be pushed against the potential, so an energy input is needed to run the reaction. The lower two equation (ripping apart of water and fixing CO2 into glucose) require energy input, so have negative Er. Whereas the first equation (breaking apart of NADPH) clearly outputs energy and so has a positive Er.

                                        12 NADPH => 12 NADP+ + 12 H+ + 24e-          Er = +0.32 V
                                                6H2O  => 6O + 12H+ +12e-                          Er = -0.82 V
                                     12H+ + 12e- => 12H                                                   Er = 0.00 V
                        6CO2 + 24H+ +24e- => C6H12O6 + 6H2O                         Er = -0.40 V

                                        12H+ + 12e- => 6H2                                                Er = -0.41 V @ pH = 7

and
            O2   + 2e- => 2O^2-                                    +0.81V
           2H+ + 2e- =>  H2                                         -0.41 V
Above (see right) are the practical limits in water. An oxidizer above 0.81 will start rippping apart water and the oxygen will consume the oxidizer, below -.41 hydrogen is released and consumes reducer.

        -- It is impossible to measure the absolute potential of an ion to gain or lose an electron.
                            (but it's calculaable isn't it?)
                    so an arbitrary reference is chosen:
                            1/2 H2 => H+ + e-                                            Er =0.00 V @ standard conditions
                                        Standard conditions are 1 atmosphere (so H2 is a gas)  and 25C

    There only  a little overlap between above and Wiki Standard potentials. Here are Wiki voltages

                           K+ + e- <=> K(s)                                       -2.93 V
                    2H2O + 2e- <=> H2(g) + 2OH-                     -0.8277 V
                       2H+ + 2e- <=>  H2(g)                                    0.00 V            -0.41 V @ pH7
            C(s) +4e- + 4H+ <=> CH4(g)                                +0.13 V
            S(s) +2e- + 2H+ <=> H2S(g)                                 +0.14 V
        O2(g) + 4e- + 4H+ <=> 2H2O                                   +1.23 V             +0.81 V @ pH7

Combination redox equations
        The three basic redox equations (above) can be recombined in three ways (below) which gives good insights into some of the localized photosynthesis drivers.  To make clear which pair of the three equations above (or their reverse) have been added, I show Er (below) as the sum of two terms.

1) NADPH oxidation redox
                                        12 NADPH => 12 NADP+ + 12 H+ + 24e-          Er = +0.32 V
                                     12H+ + 12e- => 12H                                                   Er = 0.00 V
                           6O + 12H+ + 12e- => 6H2O                                               Er = +0.82 V
              ---------------------------------------------------------------------------------------------------
               12 NADPH  + 12H+ + 6O => 12 NADP+ 12H  + 6H2O              Er = +0.82 V + 0.32 V
                                                                                                                                  = +1.14 V

**          In other words the oxidation of each molecule of NADPH (plus an extra H+) releases energy of 2 (electrons) x 1.14 V = 2.28 ev, so the oxidation of the twelve NADPH used in photosynthesis (for one molecule of glucose) releases 12 x 2.28ev = 27.4 ev.

        This is consistent with the energy release I show on my block diagram being carried via NADPH from light reaction to dark reactions (26.5 ev). The redox equation show that 72% of this energy is obtained by the coming together of oxygen, hydorgen ions and electrons to make water.

2) Dark reactions (minus ATP) redox
         12 NADPH + 12H+ + 6CO2 => C6H12O6 +12 NADP+ + 6H2O     Er = +0.32 V +  -0.40 V
                                                                                                                                    = -0.08 V
yes!!          24 electrons x -0.08 V = -1.92 ev

**        In other words from standard potentials the dark reactions, excluding the ATP transfers, needs only an input of 1.92 ev of energy per molecule of glucose to run. ATP provides the needed 1.92 ev plus a little more (8.64 ev at lumen pH or about 5.7 ev at standard conditions). The ATP provided excess 3.8 to 6.7 ev of energy vs the 29.7 ev of glucose makes the dark reaction efficiency 81 to 88%.

3) Photosynthesis summary redox
                               6CO2 + 6H2O  => C6H12O6 + 6O2                               Er = -0.82 V + -0.40 V
                                                                                                                                  = -1.22 V

        Four electrons (per O2) move against a potential of 1.22 V, hence energy input need to make this reactions go with one glucose (C6H12O6) and 6 O2 and 6 H2O as output is [6 (O2) + 4 (electrons) x 1.22 V (sum of Er)] = 29.3 ev. This agrees nicely with the energy figured from (total) bond energy calculations on my block diagram (and shown below).

Redox energy is consistent with bond energy calculations
        You get the same result doing a subtraction of total bond energies (see my photosynthesis block diagram). Here the numbers are

                      Input bond energy     -     Output bond energy
                     [6CO2 + 12 H2O]      -    [C6H1206 + 6O2 +6 H20]
           [6 x 16.2ev + 12 x 9.52ev]  -  [94.5ev + 6 x 5.02ev + 6 x 9.52ev]
                                    [211.4 ev]    -    [181.7 ev] = 29.7 ev

Electrolysis of water

        Electric current disassociates water into H+ and OH- ions.
        At cathode hydrogen ions (H+) accept electrons (reduced)
        At anode hydroxide ions (OH-) give up electrons (oxidized)

        Standard potential of water electrolysis cell = -1.23V @ 25C

        H2SO4 (sulfuric acid) is used as electolyte because its competing oxidation at anode does not occur because SO4 (2-) is so difficult to oxidize. There is no competing reduction at the cathode with an acid because it puts H+ ions in solution, same as water.

        At reducing electrode an OH bond in water breaks creating H+ and OH-, then electron (e-) from electrode adds to H+ to make H. Two H pair up releasing H2 gas. Release of H2 gas puts OH- ions in water at that electrode.

        At oxidizing electrode there is initially H+ and OH- in liquid. The OH- gives up it's electron (e-) to electrode making OH (neutral), then OH separates into H+ and O-. O- gives up its electron (e-) to electrode becoming O. Two O pair up releasing O2 gas.

All these equations below (from several references) look consistent.

        Standard electrode potentials
                                        2H2O  + 2e- <=> H2(g) + 2OH-                           -0.8277 V
                                        O2 (g) + 4H+ +4e- <=> 2H2O                            +1.23 V
reversing presumably     2H2O   <=>    O2 (g) + 4H+ +4e-                      -1.23 V
                                            H2(g) + 2e- <=> 2H-                                         -2.25 V

    oxidation at anode        2H2O (aq) => O2(g) +4H+(aq) +4e-            Eox    -1.23V
    oxidation at anode       2H2O (aq) => O2 + 4H+ (aq) + 4e-             Ered = -1.23 V
                                           2H2O - 4e- =>O2 + 4H+
       h+ are holes?          2H2O (aq) + 4h+ => O2(g) + 4H+ (aq)          1.23 V  NHE
    equivalent to?             2H2O (aq) - 4e-  => O2(g)  +4H+ (aq)           1.23 V  NHE

    oxidation                        4 OH- (aq) => O2 (g) + 2H2O (aq) + 4e-
    oxidation at anode        2SO4 (2-) => S2O8 (2-) +2e-                    Eox    -2.05V

    reduction at cathode   2H+ (aq) + 2e- => H2(g)                            Ered    0.00V   (ref point)
                                            2H+ (aq) +2e- => H2(g)                              0.00 V  NHE
    reduction at cathode    2H2O (g) + 2e- =>H2(g) + 2OH-(aq)       Ered    -0.83V

check
                                        2H2O  + 2e- <=> H2(g) + 2OH-                           -0.8277 V
                                        4H2O  + 4e- <=> 2H2(g) + 4OH-                           -0.8277 V
   oxidation                           4 OH- (aq) => O2 (g) + 2H2O (aq) + 4e-
   add (OH- & 4e- cancel)         2H2O <=> 2H2(g) +O2 (g)                       OK

Photosynthesis water oxidizing complex equation is one of above
    oxidation at anode              2H2O (aq) => O2(g) +4H+(aq) +4e-       Eox    -1.23V
                                        2H2O (aq) - 4e-  => O2(g)  +4H+ (aq)               1.23 V  NHE

        So it looks like the oxidizing potential of water is 1.23V    (or is it?)
Many references quote 0.83 V as the redox potential for water, comparing P680's 1.2 V +/- 0.1 V to it. But from table above 0.83 V is the value for breaking one O-H bond and releasing H2. In the water oxidizing complex what we want is the voltage for breaking water bonds and releasing O2. This looks to be 1.23V. But then there seems to be a problem because P680's +1.1 V to + 1.3V is not strong enough??

Water redox mystery?
        The vast majority of references refer to the redox potential of water in reference to photosynthesis as 0.83V, which to me based on standard reduction potentials doesn't seem right because it for H2 output. I finally found a reference that looks at it more like my intuition. This is a 2008 paper given at the 14th International Photosynthesis conference by five Japanese researchers from two univ including Univ of Tokyo. They think the standard model of P680 at 1.2V reducing 0.83V water is not right.

        They identify the redox potential for water in photosynthesis as H2O/O2, (not H2) which is right! And they give this formula for H2O/O2 redox:

                                    E =  1.23V - 59 mv x  pH  vs SHE (standard hydrogen electrode)
                                        =  1.23 V - 0.32 V         @ PH = 5.5 (lumen)
                                        =  0.91 V

        -- SHE (standard hydrogen electrode) is the defined 0.0V reference of redox potentials.
        -- Any system or environment that accepts electrons from a normal hydrogen electrode is a half cell that is defined as having a positive redox potential (Wikipedia). The redox voltage general formula is related to pH, the general from being: E = E0 - 59mv x pH, so the higher the pH the lower redox potential.

        The Japanese guys idea is that feedback from the PSII electron transport chain raises the redox potential of the Mn water complex to about +1.25V to + 1.5V high enough over the +0.91V to provide enough overdrive to get the reaction to go.

OK, so it's 1.23 V, but with a gradient correction (note this absolute PH, not relative to PH = 7)

Explanation for 0.82V for water?
        Notice that at pH =7 the correction term (59 mv x 7 pH = 413 mv, which reduces 1.23V to 1.23 - 0.413 = 0.82V. This is common value people use to oxidize water, but it's really the same equation at neutral pH 7! The Japanese guys get a higher voltage of 0.91 V because pH is lower than 7 in the lumen, where the water is split. The big uncertainty is in the overdrive voltage.

Overdrive voltage
        They further state that these are equilibrium potentials. To make the reaction go an 'overdrive potential' is needed, which they estimate at 300 mv.

        Here's a confirming figure (sort of) from Univ of Arizona. They are looking at oxidizing water into H2 and O2 for fuel, so use the electrolysis value of 1.23V and estimate a 300 to 400 mv needed for overdrive. They are asking s this possible sometime in future using 1.8 ev (nom) photons.

Finally the two water redox values make sense
        Notice the equations in the figure:
                                        2H+  + 2e- => H2                    redox     -0.42V
                                4H+  +4e- +O2 => 2H2O               redox     +0.82V

Finally everything makes sense. Both of these redox potentials fall out of the equation (see Wikipedia)

                                       E = E0 - 59 mv x pH (@ ph =7).

For H2 out E0 = 0.0V (it's the ref standard), so the -59 mv x 7 pH correction term give -0.42V. For O2 out E0 = +1.23 V and with the - 0.42 correction it comes out +0.82 V. Notice inverting and doubling the first equation and then adding to cancel terms gives the classic electrolysis equation.

                            2H2 + O2 => 2H2O                  redox = +0.42V + 0.82V = +1.23V
-----------------------------------------------------------
Relationship of redox potential to bond energy
        After a lot of work I think I finally understand the relatioship between redox voltage and bond energy. The energy input or output of a reaction can be figured by differencing the the (total) bond energies of the input and outputs of the reaction. Redox (reduction potential) voltage also tells you the energy input or output, because it's the effective (or average) voltage difference 'seen' by the electrons in the reaction. So energy input or output (in ev) is just # of electrons x redox voltage.

        For example, here is the bond energy analysis of the oxidation of hydrogen, which is just the reverse of electrolysis of water.

bond energy method
                          2H2              +         O2     =>         2H2O
             [2 x 4.48 ev = 8.96 ev] + 5.12 ev => [2 x 9.52 ev = 19.04 ev]
                                                     14.08 ev  => 19.04 ev     delta 4.96 ev released as heat/work

redox method
        The redox voltage of this reaction is 1.23V, and it's the 'open circuit' voltage of water electrolysis. Four H electrons break bonds to H and make bonds to O, so the total energy released is 4 x 1.23 ev = 4.92 ev
-----------------------------------------------------------------------
easy
    oxidation at anode               2H2O (aq) => O2(g) +4H+(aq) +4e-       Eox    -1.23V
    but   (reference point)           2H+ (aq) + 2e- => H2(g)                         Ered    0.00V
    x2 and combine                2H2O (aq) => O2(g) + 2H2(g)                    Eox   -1.23V

          The bond energy of water net over 2H2 and O2 is just 4 x 1.23V = 4.92 ev . Externally in electrolysis you add -1.23 ev to each of four bonds in water broken and end up with one O2 and 2H2.
-----------------------------
Standard reduction potential polarity
        With an understanding of the definition of 'standard reduction potential' the polarity is easily figured out.

        Def: Reduction potential (also known as redox potential, oxidation / reduction potential or ORP) is the tendency of a chemical species to acquire electrons and thereby be reduced.

        Polarity: A (chemical) solution with a higher (more positive) reduction potential than the new species will have a tendency to gain electrons from the new species (i.e. to be reduced by oxidizing the new species).

        In other words, it's simple, electrons are attracted more strongly by a more positive voltage. When two chemicals react, the one with the more positive reduction potential will pull the electrons from the material with the lower reduction potential. The more positive the reduction potential the stronger the reducer, the better it is at gaining electrons pulling them from other chemicals.

        For example, here the entries for flourine (most powerful oxidizing agent known) and oxygen gas as listed in the standard reduction potential (in Wikipedia table):

                                     F2(g) + 2e- <=> 2F-                    +2.87 V
                        O2(g) + 4e- + 4H+ <=> 2H2O                +1.23 V
------------------------------
Practical water electrolysers
        I read that practical water electrolyzers, which use a cobalt based catalyst, are only about 70% efficient at storing energy, meaning the energy available from the combusion of hydrogen is only 70% of the power put into the electrolyzer. Or put another way while the theoretical voltage for splitting water is 1.23V the practical voltage is more like 1.8V. Not sure where all this voltage goes, but apparently some of it is ohmic drop across the electrolytes in solution.
------------------------------
        The electrolysis of water provides a direct measurement of the energy required to rip water apart. Running DC current through water (with some added ions to increase conductivity) causes oxygen gas (bubbles) to form at the positive electrode and hydrogen gas (bubbles) at the negative electrode.  The equations are

        Anode (oxidation):                     2 H2O(l) => O2(g) + 4H+(aq) + 4e-
        Cathode (reduction):                 4 H+(aq) + 4e- => 2H2(g)
        Terminal voltage (@ 25C)        1.23 V

bond energies (oxidation of hydrogen to make water)
                        2 H2   +        O2       =>  2H2O
                  2 x 4.46 ev  +   5.02 ev  =>     4 x 4.76 ev
                                          13.94 ev  =>    19.04 ev          5.1 ev difference (5.1/4 = 1.275 V per bond)
                                                                                            pretty close to 1.23 V

Wikipedia Standard Electron Table (I think these are redox potentials)

             2H+  + 2e- <=> H2 (g)                                 0.00 V (reference point)
                     2 H2O <=> O2(g) + 4H+ + 4e-         +1.23 V (electrolosis of water value)

What is rodox potential?
        It seems like redox voltage (if there is one) for a reaction is shorthand way of calculating the energy out (or in) of the reaction. It's a measure of the energy differences per bond between the two sides. It appears to be an alternate to the more tedius method subtracting all the bond energies of one side from the other side.
---------------------------
 So the 4H+ and 4e- are intermediates, by extension I could consider the net output to be O2 + [HO in minus H2O out]  but that makes the output 6 water vs 12 water in, so net mn reaction is

in                12 H2O in + 6 CO  = 114.2 ev +  6 x8.34 =164.3
out             6 O2    +6 H2O        =  30.1 ev +57.1          = 87.2
light                                                                        77.1 ev/24 = 3.21 ev per electron?? seems high, but with energy from PHII and PHI 3.6 rv we make it. in the range of most references and well within the 1.8 ev available from PHII. (not sure this is valid because 6O come in fomr CO2 so the reactions are cross linked. Well a good guess in added input is 6CO bonds Two values for CO 358 kj/mol single line and 805 kj/mol double line. I'll guess is 358 nope, doesn't work for dark. Lets try 805  8.34 ev because 12 x cO bond = 100 ev pretty close to 97.1 ev for 6 CO2
This leaves 6 CO in for sugar       48.6 or 49.3
sugar                                                    94.5
this reaction runs because output is higher than input. 45.9 surplus. subtracting 45.9 surplus off 77.1 deficetof step 1 leaves with a net light input of 77.1 -45.9 = 31.2 OK 29.7.
The above simply amounts to dividing the CO2 energy in half. with half to light reaction and half to dark reactions.
------------------------------
        Here's a picture of what happens. Every four electrons flowing out of the positive terminals (current in) come from two water molecules ripped apart at that terminal. The four H+ ions released into the water then flow across, this of course being positive current flow through the liquid, to the negative terminal where they meet returning electrons from the external circuit. Each H+ in liquid accepts an electron from the negative electrode and for every two electrons a diatomic molecule of hydrogen (H2) forms at the electrode.

        But notice the top equation (anode) is exactly the same equation as the input/output equation for the water evolving complex. Wikipedia gives the oxidation potential of the anode as - 1.23V, and interestingly the reduction potential (just the negative of oxidation potential) as O V. This is because 2 H+ + 2e- => H2 is the reference standard for oxidation potentials chosen to be 0V. So bottom line, it seems we can neglect the H2 formation, and electrolysis of water is telling us that the (average) energy needed to rip each electron out of water is 1.23 V, so this must be the voltage the manganese water evolving complex puts out!

Bond energy & photosynthesis
        The energy of a molecule is (approx) the sum of the energy of its atom-to-atom electron bonds. Bond energies are usually negative (free electrons have zero energy). The more negative the more stable  Note oxygen to oxgyen (-116) is loosely bound. Oxygen much prefers bonding to carbon (-190) or hydrogen (-220 = 2 x 110). CH2O is a carbohydrate. (all units are Kcal/mole, but mole of what?)

                CO2        C to O -190 (twice)                                  total -380
                H2O       O to H  -110 (twice)                                  total -220
total for inputs to photosynthesis -380 + (-220) = -600 Kcal/mole

                O2        O to O     -116                                               total -116
                CH2O    C to O    -190       C to H -92 (twice)       total  -374
total for outputs of photosynthesis -374 + (-116) =  -490 Kcal/mole

        Note the outputs of photosynthesis are less stable than the inputs (energy from light has been added to make the output bond energies less negative). The difference between -490 - (-600) = 110 Kcal/mol is the energy stored (added to bond energy) in photosynthesis and is the same energy released (taken out of bond energy) in respiration.

        You can view the bond energy changes across photosynthesis (110 Kcal/mole) this way: About 2/3 of the energy of light (74 Kcal/mole) goes into separating an oxygen atom from carbon (breaking CO2, where it is tightly bound) and connecting it to another oxygen (making O2, where it is loosely bound). About 1/3 of the energy (36 Kcal/mole) goes into separating two hydrogen from oxygen (breaking water) and connecting the two hydrogen to carbon (making a carbohydrate).

               major term   -- O to C (-190)  => O to O (-116)  yields +74 delta
               minor term   -- O to H (-220 = 2 x -110) => C to H (-184 = 2 x -92) yields +36 delta

Check
        Breaking apart one water frees two electrons to flow through the membrance potential (guess: 100 mv), let's assume it flows across twice (photosystem I & II), so figuring energy electrically we get
                2 x 2 x 0.1 ev = 0.4ev = 0.4 x 1.6 x 10^-19 joule  =0.64 x 10^-19 joule

        From a bond energy point of view the energy is given as 110 Kcal/mole above for one water. I am not sure if this is a mole of electrons, but maybe it doesn't matter since a mole of anything has 6 x 10^23 (Avogadro's number) of particles.
               {110 x 4.2 x 10^3 joule}/(6 x 10^23) = 77 x 10^-20 = 7.7 x 10^-19 joule

        Well not grossly different, but the electrons pumped agains the membrane potential seems to only provide 1/10th the gain in bond energy. Is something is wrong? Or does this mean that maybe the cell chemical voltage (due to the proton gradient) is more like one volt? If so this would make the numbers agree.

            In a molecular biology text book I find that the two light reactions have redox potentials of about 1.5 to 1.7 volts. OK, this explains the bond energy, but I am not sure what rodox potential is. Other references do confirm that the membrane potential in choroplasts is in the range of 125 mv or so with the proton potential dominating.

Bond energy (general)
        Good bond energy ref (MIT chemistry series)

        http://www.sciencegateway.org/resources/biologytext/chem/review.html

Covalent bond energy
       -- Covalent Bonds are the strongest chemical bonds, and are formed by the sharing of a pair of electrons. The energy of a typical single covalent bond is ~80 kilocalories per mole (kcal/mol). However, this bond energy can vary from ~50 kcal/mol to ~110 kcal/mol depending on the elements involved. Once formed, covalent bonds rarely break spontaneously. This is due to simple energetic considerations; the thermal energy of a molecule at room temperature (298 K) is only ~0.6 kcal/mol, much lower than the energy required to break a covalent bond.

        -- Oxygen, because of its high electronegativity, attracts the electrons away from the hydrogen atoms in water, resulting in a partial negative charge on the oxygen and a partial positive charge on each of the hydrogens.  The possibility of hydrogen bonds (H-bonds) is a consequence of partial charges

Hydrogen bonds
        -- Hydrogen bonds are formed when a hydrogen atom is shared between two molecules.Hydrogen bonds have polarity. A hydrogen atom covalently attached to a very electronegative atom (N, O, or P) shares its partial positive charge with a second electronegative atom (N, O, or P). One example, shown above, involves the hydrogen bonding between water molecules.

        -- Hydrogen bonds are ~5 kcal/mol in strength. These bonds are frequently found in proteins and nucleic acids, and by reinforcing each other serve to keep the protein (or nucleic acid) structure secure. But, since the hydrogen atoms in the protein could also H-bond to the surrounding water, the relative strength of protein-protein H-bonds vs. protein-H2O bonds is smaller than 5 kcal/mol. (Ionic bond, like in table salt NaCl, are in the same range 4-7 kcal/mol.)

Solubility in water
        -- Nonpolar molecules cannot form H-bonds with H2O, and are therefore insoluble in H2O. These molecules are known as hydrophobic (water hating), as opposed to water loving hydrophilic molecules which can form H-bonds with H2O.

        -- Hydrophobic molecules tend to aggregate together in avoidance of H2O molecules; hydrophobic interactions are clearly demonstrated when you put an oil drop on water. This attraction/repulsion is known as the hydrophobic (fear of water) force. To understand the energetics driving this interaction, visualize the H2O molecules surrounding a "dissolved" molecule attempting to form the greatest number of hydrogen bonds with each other. The best energetic solution involves forcing all of the nonpolar molecules together, thus reducing the total surface area that breaks up the H2O H-bond matrix.

Energy conversion
        Reaction energy is often given in Kcal/mole (where mole = 6 x 10^23) or kj/mole. These can be converted into electron-volts. (1 kcal = 4.2 x 10^3 joule) (1 kj = 1 kcal/4.2) (A mole of photons (6.02 x 10^23) is called an Einstein.)

             100 kcal/mol = 100 x 4.2 x 10^3 joule}/(6.2 x 10^23) = 68 x 10^-20 joule
                                1 ev = 1.6 x 10^-19 joule
                        68 x 10^-20 joule /1.6 x 10^-19 = 4.34 ev
so
                                1 ev  <=> 23.1 kcal/mol  <=> 96.5 kj/mol

Atomic bonds -- Electronegativity
        Atoms bond into molecules by overlapping their electronic orbitals. Whether this is called 'sharing'  or 'donating/accepting' electrons, it's really the same thing. Wikipedia link on Electronegativity (see below) is a good introduction to atomic bonding. Electronegativity is a measure of the ability of an atom or molecule to attract electrons in the context of a chemical bond. The link has a periodic chart showing the electronegativity value of every element (ranges from about 1 to 4) with oxygen at 3.44 having the 2nd highest value (fluorine is highest at 3.98). (Electronegativity is so important even my supermarket sells it!  Yes indeed, I was able to buy a periodic chart with all the negativity values in my supermarket -- part of a plastic 'crib notes' series for students).

        When bond is made between only two atoms, it's typically an atom from the left side of the periodic table, which have a few excess (outside a full shell) electrons, joining an atom from the right side of the table, which are just a few electrons shy of completing an electron shell. When multiple atoms bond, there are a lot of different ways to fill a shell. For example, in CH4 (methane) carbon gets the four extra electrons it needs to fill its shell by sharing with four hydrogen. From the hydrogen perspective it gets the one extra electron it needs to fill its shell by sharing one of the carbon electrons. (Note, shell filling is just a set of 'rules of thumb' that make it easy to remember the lower energy orbit states.)

Atomic bonds -- Covalent vs ionic
       There are two (idealized) types of chemical bonds, Covalent and Ionic, but really they shade into each other with the key parameter being the relative electronegativity. This is nicely shown pictorially in this link:

        http://www.chem.ox.ac.uk/vrchemistry/electronsandbonds/bondsperatom1.htm

        Covalent  --- If  electronegativity values are close, in a sense the atoms pull on (shared) electrons equally. When the difference in the relative electronegativity is not too great (< 1.7), the electron bond formed is called a covalent bond. This type of bond is conventionally described as the atoms sharing electrons. If the relative electronegativity values is < 0.4, then the bond is balanced, so these are non-polar covalent bonds. If the relative electronegativity values is 0.4 to 1.7, then the bond is unbalanced, so these are polar covalent bonds. Obviously bonds between identical atoms, like diatomic oxygen, are perfectly balanced, so these bonds are pure (non-polar) covalent.

        Ionic --- If  electronegativity values are far apart ( > 1.7),  then one atoms pulls on (shared) electrons much harder than the other. This type of bond is called an ionic bond. This type of bond is conventionally described as one atom donating an electron to another atom that accepts it. The force between the atoms created by this bond is then spoken of as being an electrostatic attractive force between the positive (donating) ion and the negative (accepting) ion.

        A dipole moment is an electrical force that is generated because of the unequal distribution of the bonding electrons between the two bonded atoms. In the case of an ionic bond that unequal distribution is extreme. The dipole moment of an ionic bond is quite large compared to polar bonds of the covalent bond. Ionic bonds (can be) about as strong as covalent bonds.

        Salt (sodium cloride) is a classic ionic bond. Most metals (like sodium) have only a few valence electrons hence relatively low ability to attract electrons and low electronegativity values. Sodium (atomic number 11) has only one valence electron, so it has a very low electronegativity value of 0.93. Many non-metals like nitrogen, chlorine, oxygen, fluorine have nearly full shells missing one or two electrons (nitrogen is missing three), so have high electronegativity values. Chlorine (atomic number 17) has a seven valence electrons, so it has a very high electronegativity value of 3.16.

        When salt dissolves in water,  the sodium and clorine atoms come apart (why? see below) as charged ions, so here (at least) the sharing & loss of the electron must be 100%.

        --    Hydrogen and oxygen in water are covalently bonded. Water is a polar molecule, because it has partial positive and partial negative ends. The hydrogen atoms of the water molecule can now form bonds with other slightly negative (polar) compounds. Each hydrogen of this water molecule can form hydrogen bonds with oxygen atom of other water molecules. Hydrogen bonds are 20 times weaker than covalent bonds. But hydrogen bonding between molecules is very important with organic compounds.

        -- Water is able to dissolve anything polar due to polarity. Water separates ionic substances. Many covalently bonded compounds have polar regions, the covalent compounds dissolve in water and are called hydrophilic (water loving) compounds. Nonpolar substances do not dissolve in water and are called hydrophobic (water fearing).

        --  Due to hydrogen bonds water is attracted to itself (more than the air above it) forming surface tension. To change water from a liquid to a gas (boil it), a lot of energy must be added to break the hydrogen bonds between the water molecules.

        -- The bond strengths are expressed in terms of energy (kilocalories or kilojoules per mole) that must be supplied to break the bonds under standard conditions of temperature and pressure.

        -- Carbon backbone  Carbon can form covalent bonds directly with one to four atoms since it as four valence electrons. In many biological molecules carbon atoms form long chains. Carbon is unique in that it can form single, double, and triple covalent bonds with itself and other atoms.

         http://en.wikipedia.org/wiki/Electronegativity

Nitrogen
        Nitrogen has two stable isotopes: N14 (7 neutrons, 99.6%) and N15 (8 neutrons, 0.4%). Nitrogen is atomic number 7, between carbon (6) and oxygen (8). It has five electrons in its outer shell and is therefore trivalent in most compounds. Nitrogen is a nonmetal, with an electronegativity of 3.0.

        The triple bond in molecular nitrogen (N2) is the strongest in nature. The resulting difficulty of converting (N2) into other compounds, and the ease (and associated high energy release) of converting nitrogen compounds into elemental N2, have dominated the role of nitrogen in both nature and human economic activities.

Oxidation
        Simple, gereral view
                * Oxidizer pulls away electrons, so to be oxidized is to losean electron
              * Reducer gives electrons, so to be reduced is to gain an electron

        Oxidation is a slippery term. From its name you would think it means adding oxygen, but this is only one type of oxidation. Oxidation is also used in a loose sense to mean 'burn'. But there is an electrochemistry definition and it appears to be totally different. So what is oxidation really? And why does oxidizing something yield energy?

        (My thinking now is this)
         Oxidize --- A molecule is oxidized when an atom from the right side of the periodic table (an oxidant like oxygen, fluorine, or chlorine) bonds to the molecule causing electrons to be sucked (to some degree) from the molecule to the oxidant atom using them to fill the oxidant's shell. The energy stored in the combined molecule is less than the sum of its parts (due to the filled shell), so this reaction (always?) puts out energy.

        Oxidation example: In a fuel cell gaseous oxygen (O2) is used to oxidize gaseous hydrogen (H2) forming water. This puts out useful work in the form of electricity + some heat.

         Reduce --- A molecule is reduced when an atom from the left side of the periodic table (a reductant like hydrogen, or sodium) bonds to the molecule causing electrons to be added (to some degree) to the molecule from the reducer. The energy stored in the combined molecule is more than the sum of its parts (even though the reductant is down to a filled shell), so this energy need to added to make this reaction go.

        Reduction example: Electrolysis of water into gaseous oxygen and hydrogen. This is the reduction of hydrogen (putting back the electrons that the oxygen sucked away), and for it to occur energy must be added in the form of running electricity through the water.

As stated in Wikipedia:
        "Oxidation is the loss of electrons by a molecule, atom or ion"
        "Reduction is the gain of electrons by a molecule, atom or ion"

        When a carbon atom 'loses' (shares) two electrons to each of two oxygen atoms it bonds with, Wikipedia speaks of this as 'oxidation' of carbon to yield CO2. Yet when carbon joins with four hydrogen, Wikipedia refers to this as 'reduction' of carbon by hydrogen to yield methane (CH4).

       Is it oxidation of carbon when it joins with an atom with a higher electronegativity value (like oxygen), and reduction when it joins with an atom with a lower electronegativity value (like hydrogen)?

        Yes!   Here (I think) is the key --- When electrons are shared, they are pulled spatially toward the atom with the higher electronegativity value. So higher electronegativity atoms (oxidants) suck away electrons from the bonding molecule, and it is the loss of electrons by the molecule that is (technically) the definition of oxidation. It is correct (if confusing) to speak of carbon being reduced by hydrogen, because carbon being the higher electronegativity atoms sucks the electrons from the hydrogen to itself, thus technically since carbon has gained electrons it has been reduced! It's clearer I think to speak of it as carbon oxidizing the hydrogen.

              element                  electronegativity
            -------------             ---------------------
                oxygen                            3.44
                carbon                             2.55
                hydrogen                        2.20

        My guess is that oxygen's so-called high affinity for attracting electrons (its high electronegativity value) means that the oxygen atom when it bonds with other atoms that bring two electrons to share with it, drops into a lower energy state and (somehow) releases energy in the form of heat and useful work like current (fuel cells), electrons flows, and ion pumping.

         My model is gravity. When an object is attracted to a body by gravity, energy is released either as useful work or as heat. Is the oxygen atom like this? Is energy released when two electrons 'fall into' orbitals of oxygen allowing it to complete its electron shell?

Redox or oxidation/reduction
        Redox reactions are simple. A redox reaction is just a transfer of ectron(s) between atoms. The atom that loses electron(s) is oxidized, and the atom that gains the electron(s) is reduced. The redox potential (Vr) for a reaction is just the net voltage diffence through which the transfer electron(s) flow. Hence a transfer electron see an energy change of ev (in this case eVr). The total energy output of a reaction is just eVr x # of electrons transferred..

        But the idiot biologist can never state things simply, they don't use ev for energy. Instead you find this:

                            delta G (free energy) = n x 23.1 kcal x (redox potential difference)
                                                    where
                                                                n is # of moles of electrons transferred

Of course (23.1 kcal/mol = 1 ev), but the biologist don't mention this!

    Wikipedia excerpts
        -- Oxidant removes electrons from another substance, and is thus reduced itself.
            (mnemonic) "OIL RIG" -- Oxidation Is Loss, Reduction Is Gain.

        -- Oxygen is an oxidant, but not the only one. Despite the name, an oxidation reaction does not necessarily need to involve oxygen.

        -- The gain of oxygen, loss of hydrogen and increase in oxidation number is also considered to be oxidation, while the inverse is true for reduction.

        --  Oxidants are usually chemical substances with elements in high oxidation numbers (e.g., H2O2, MnO4-, CrO3, Cr2O72-, OsO4) or highly electronegative substances that can gain one or two extra electrons by oxidizing a substance (O, F, Cl, Br).

        -- Photosynthesis involves the reduction of carbon dioxide into sugars and the oxidation of water into molecular oxygen.

        -- The oxidation state of an ion is the number of electrons it has  donated (+) or accepted (-) compared to its neutral state (which is defined as having an oxidation state of 0).

        --Oxidation state explanation

    (from a textbook) 'Oxidation state' is a figurative description. In CO2 the carbon is said to have a +4 'oxidation state'. Each oxygen is viewed as having pulled two electrons (almost completely) away from the carbon. This is of course an exaggeration. These bonds are covalent, not ionic, the electron clouds just spends more time near the oxygen nucleus than the carbon nucleus. (In carbohydrates oxygen 'pull electrons' away from both carbon and hydrogen, so the oxidation state of the oxygen is raised by the same amount as the oxidation state of the C and H are lowered.)

        -- Electrochemical process are redox reactions where energy is produced by a spontaneous reaction which produces electricity, otherwise electrical current stimulates a chemical reaction. In a redox reaction, an atom's oxidation state changes as a result of an electron transfer.

        -- A spontaneous electrochemical reaction can be used to generate an electrical current, in electrochemical cells. This is the basis of all batteries and fuel cells. For example, gaseous oxygen (O2) and hydrogen (H2) can be combined in a fuel cell to form water and energy (a combination of heat and electrical energy, typically).

        -- Conversely, non-spontaneous electrochemical reactions can be driven forward by the application of a current at sufficient voltage. The electrolysis of water into gaseous oxygen and hydrogen is a typical example.

        --  Photosystem II and Photosystem I have their own distinct reaction center chlorophylls, named P680 and P700, respectively. These pigments are named after the wavelength (in nanometers) of their red-peak absorption maximum.

         -- The function of the vast majority of chlorophyll (up to several hundred per photosystem) is to absorb light and transfer that light energy by resonance energy transfer to a specific chlorophyll pair in the reaction center of the photosystems.

        -- The charged reaction center chlorophyll (P680+) is then reduced back to its ground state by accepting an electron. In Photosystem II, the electron which reduces P680+ ultimately comes from the oxidation of water into O2 and H+ through several intermediates

        -- NADPH a universal reductant used to reduce CO2 into sugars as well as for other biosynthetic reductions.

        -- The different chlorophyll and non-chlorophyll pigments associated with the photosystems all have different spectra, either because the spectra of the different chlorophyll pigments are modified by their local protein environment, or because the accessory pigments have intrinsically different absorption spectra from chlorophyll. The net result is that, in vivo the total absorption spectrum is broadened and flattened such that a wider range of red, orange, yellow and blue light can be absorbed by plants and algae.

Glucose bonds
        From the above structure we can count the glucose bonds and find the bond energy. Notice earch white (H) has one connection, red (O) has two connections, and green (C) has four connections. This means each connection shown is a single shared electron (one electron bond). I count as follows: (bond energy ref:http://www.wou.edu/las/physci/GS361/Energy_From_Fossil_Fuels.htm)

                      white (H) <=>  red (O)                 5         O-H      460 kj/mol     5 x 4.77 ev = 23.83
                      white (H) <=>  green (C)            7         C-H      410 kj/mol      7 x 4.25 ev = 29.74
                      green (C) <=>  red (O)                 7         C-O      360 kj/mol      7 x 3.73 ev = 26.11
                     green (C) <=>  green (C)             5         C-C      347 kj/mol       5 x 3.60 ev = 17.98
                                                                              --        C=O     799 kj/mol   (8.28 ev)
                                                                             --         C=C     611 kj/mol (or 519 aromatic)
                                                                             --         H-H     432 kj/mol   (4.48 ev)
                                                                             --         O=O     494 kj/mol  (5.12 ev)
                                                                 -------------                                                             -------------
                    total (single electron) bonds       24                                 total bond energy     97.66 ev

        Counting shared electrons in C6H12O6 you get [6 x 4 +12 +2 x 6] = 48, but the (single electron) bond count is half of this or 24 consistent with count above. For example H-O bond is (loosely speaking) H losing its electron to O which accepts it. Using this table of bond values above;

        Oxidation of glucose (reverse of photosynthesis)

                C6H12O6 +        6 O2               =>           6 CO2             +         6 H2O
                 97.66 ev + [6 x 5.12 = 30.71] => [6 x 16.56 = 99.36] + [6 x 9.53 = 57.20]
                                                        128.37 => 156.56     delta 28.2 ev released as heat/work (29.7 ev other ref)

        Oxidation of methane
                               CH4         +       2O2                    =>  CO2    +        2H2O
                   [ 4 x 4.25 =16.99]  + [2 x 5.12 = 10.24] => 16.56 + [2 x 9.53 = 19.06]
                                                                            27.23  => 35.62    delta 8.39 ev released as heat/work

        Oxidation of hydrogen (reverse of electrolysis of water)
                                2H2              +   O2 =>         2H2O
                       [2 x 4.48 = 8.96] + 5.12 => [2 x 9.53 = 19.06]
                                                        14.08 => 19.08     delta 5.00 ev released as heat/work
                                                                                            (or 1.25 ev/bond)

Note 1.25ev/bond is (just about) the electrolysis (redox) value of water (1.23V)

        Oxidation of carbon (diamond). Diamond does in fact burn. LaVoise demonstrated this. In diamond each carbon has four C-C bonds with neighbors, but each two carbon share a bond, so energy per carbon is (I think) that of 2 C-C bonds.
                                C (in a lattice)             +   O2 =>    CO2
                [2 C-C bonds.,  x 3.60 = 7.20]   + 5.12 => 16.56
                                                                     12.32 =>  16.56    delta 4.24 released as hear/work

Comparison
                                              Energy release/atomic weight                        Energy release/input bond energy
                                            ------------------------------------                     --------------------------------------
C-H, C-C
C-O, H-O  glucose                        28.2 ev/[180 + 6 x 32] = 0.0758                    28.2/128.37 = 22.0%
C-H           methane                       8.39 ev/[16 + 2 x 32]   = 0.1049                    8.39/27.23    = 30.8%
H-H           hydrogen                      5.00 ev/[4 +32]            = 0.1389                   5.00/14.08    = 35.5%
C-C           carbon (diamond)       4.24 ev/[12 +32]          = 0.0963                     4.24/14.08    = 34.4%

Why is glucose lowest % energy release?
       (my explanation) In glucose (C6H12O6) about half the C and H are already oxidized (C-O and H-O) bonds, hence the heat released is lower than when pure C-H bonds (methane) or H-H or C-C are oxidized.

Electronegativity
        Definition --- A measure of the ability of an atom (in a molecule) to attract electrons towards itself in a covalent bond. Electronegativity is not a voltage, but a sqrt of energy differences (see below). Its real utility appears to be in relative terms. An element with a higher electronegativity pulls electrons closer (to its nucleus) thus releasing more potential energy as heat/work.

                O           3.44
                C            2.55
                H            2.20

        Above explains why oxidation, the pulling by oxygen of electrons off carbon and hydrogen (to itself), releases energy. Oxygen's electronegativity is the 2nd highest of all elements. Chlorine is highest at 3.98 and potassium is near bottom at 0.82. Noble gases have no electronegativity value.

Electronegativity formula
        Relative electronegativity is calculated from the square root differences in disassociation energy (in ev). It's technically dimensionless only because sqrt{ev} is put in the denominator. Formula for atoms a and b.

        [delta electronegativity (a -b)] = sqrt{E(ab) - (1/2) [E(aa) + E(bb)]}
                                            where
                                                    E = dissociation energy (essential bond energy) in ev

        What this formula says is that the electronegativity difference is positive (meaning reaction goes) if the bonds of a-b is more than the average of a-a and b-b. For example, the bond energy of O-H is higher than the average of H-H and (1/2) O=O, so O2 and H2 will split and rejoin as H2O.

check
        Assume a is O, b is H, then

                    E(ab) = O-H                4.77 ev
                    E(aa) = O=O               5.12 ev    (2.56 per single bond)
                    E(bb)= H-H                4.48 ev

        [delta electronegativity (a -b)] = sqrt{E(ab) - (1/2) [E(aa) + E(bb)]}
                                 3.44 - 2.20    =? = sqrt{4.77 - (1/2)[ 2.56 + 4.48}}       (note using single bond of O=O)
                                             1.24  =?= sqrt{4.77 - 3.52}
                                             1.24  =?= sqrt{1.25}
                                             1.24 =?= 1.12            ?? somewhat off. Wikipedia example shows sqrt{} works

Energy bond calculation
        To get a feel for bond energy my idea is to start with the simplest case I can think of:

                               no bond => one bond

        In the essay on atoms (?) I have solved this problem doing the integration of the electron falling in from infinity to the bohr radius. The result is that the electron coming in falls though a voltage difference of 27.2 volts, so losing 27.2 ev of its potential energy. The electron in the Bohr orbit of hydrogen moves at about 1% of the speed of light with 13.6 ev of kinetic energy, which is exactly half the loss in potential energy. So half the potential energy of the electron has been converted to its kinetic energy and that must mean that the other half of lost potential energy is given off (presumably radiated away as heat) as the electron comes in.

        Let's do this with one gram (one mole) of ionized hydrogen and matching number of electrons and calculate the energy release. A mole of ionized hydrogen has 6 x 10^23 (Avogadro’s number) atoms.

        Eout = 6 x 10^23 (# of electron)  x 13.6 ev (energy loss per electron) x [1.6 x 10^-19 joule/1ev]
                =  1.30 x 10^6 joule   (or watt-sec)

        Wow, if this comes out quickly its going to be quite a bang! The forming of simple electron-proton bonds in this tiny amount of hydrogen (1 gram) releases 1.3 Mw for one second, or if it comes out slowly enough energy to run a 1.5 Kw room heater for almost 15 minutes.

        In terms of energy density our simple hydrogen (H not H2) bonding (moving in electrons from infinity through a voltage drop of 13.6 volts) is

        Energy density = 1,300 kj/mol      or (1,300 kj/gram)  or (1,300 Mj/Kg)

       One mole of electrons (6 x 10^23) dropping through 1 volt
                               1 mole x 1 ev = 6.022 x 10^23 x 1.602 x 10^-19 joule
                                                        = 9.65 x 10^4 joule
                                                        = 96.5 kj
so
                                                 1 ev = 96.5 kj/mol                  (agrees with references)

        Wikipedia 'Energy Density' has a table of energy density by mass (Mj/Kg). All the chemical energy  densities are below 20 Mj/Kg. For example, the military explosive Octanitrocubane, which is x2.7 more powerful than TNT by weight, is 8.5 Mj/Kg, and Nitromethane, used as fuel in Top Fuel Drag racing, is 11.3 Mj/Kg or roughly 1% of our hydrogen bond value.

        The above high energy explosive and fuel are made up mostly of carbon, nitrogen and oxygen, with atomic weight roughly x15 higher than hydrogen. Let's guess that 1 to 2 electron bonds per atom rearrange during the energy output. The higher molecular weight (compared to hydrogen) means fewer bonds per kg of mass, so higher energy change per bond.

        Putting it all together this means that even in very powerful explosives and burning of high energy fuels the potential energy change per electron bond reconfigured (energy output per valence bond change) is on the order of 10% of the bond energy.

Conversion                                kcal/mol x 4.184 = kj/mol
                                                                 ev x 96.5 = kj/mol
                                                                 ev x 23.1 = kcal/mol

                          H2  bond        4.48 ev           432 kj/mol       (104 kcal/mol)
                    water OH bond     4.76 ev           459 kj/mol (av)
                                                                               (493.4 1st OH bond or 5.11 ev)
                                                                               (424.4 2nd OH bond or 4.40 ev)
                O2 double bond       5.12 ev          494 kj/mol    (for two shared electrons/atom)
                     O2 one bond        1.47 ev          142 kj/mol

        Not sure how bond energy is defined. For example in H2 each atoms shares one electron, but in O2 each atoms shares two electrons. From reference it looks like bond energy is the energy required to rip away one atom from the molecule. So with H2 your breaking one bond, whereas with O2 your breaking two.
A mole here probably still means 6 x 10^23 bonds, so for removing a hydrogen from water (459 kj/mol/1,300 kj/mol) x 13.6 ev = 4.8 ev. This is too high.

        Another example, disassociate water into H2 and O2 by running current though ions in solution. When O2 and H2 burn (explode), its the same energy value, except it's energy out. (from ref link below)

                                energy in = 2 H2O - [2 H2 + O2]
                              energy in = [2 x (2 x 459)] - [2 x (432)  + 494]
                                             = 1,836 (two water) - 864 (two H2) - 494 (O2)
                                             = 478 kj/mol      (4.95 ev)     agrees with ref below

So as applied to photosynthesis Mn complex, its the same except there's no H2 bonds
               photon energy in = 2 H2O - O2 - 4 H
                                             = 1,836 (two water) - 494 (O2) - 0?
                                             = 1,342 kj/mol     (13.9 ev = 4 x 3.48 ev)   too high!!

***         I don't understand the energy equation of how the Mn water splitting works! The number is much worse than above, because it seems like we need to also pull the electron off four hydrogen and that is 13.6 ev per hydrogen. All the descriptions have bare protons going one way and electrons the other. Does having everything in solution change the picture?? These values are absurdly too high. Confused!!
 

------------------------------
see for input/output bond energies, water, photosysnthesis, respiration

        http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BalanceSheet.html

water and carbon dioxide
            * differences in electronegativity between their atoms are high
                        (can you calculate bond energy from electronegativity?)
            * so they have polar covalent bonds with high bond energies
             * these are strong bonds
                    broken with difficulty and
                    liberating copious amounts of energy when they form
glucose and oxygen
            * differences in electronegativity between their atoms tend to be lower
            * so they form covalent bonds with average bond energies on the low side
           * these are broken with relative ease

photosynthesis of a mole of glucose requires the input of 686 kcal (2,870 kj) of energy.
                (if all O2 comes from Mn complex??, then complex runs four times for every O2,
                        this is 24 runs of Z cycle for 6 O2 with each Z cycle taking two photons)
                           686 kcal/(23.06 kcal per ev) = 29.75 ev
                                           29.75 ev/48 photons = 0.62 ev per photon (av)
                                                                                        seems too low

    48 photons +  6 CO2 +  6 H2O        =>  6 O2  +  C6H12O6

To make this balance we can set bond energy negative and photon energy positive, then
                             +29.7 ev photon - 154.3 ev  = - 124.6 ev

**    29.7 ev is exactly the energy released when glucoe is burned (oxidated)

Z runs 24 times. Looks reasonable. Requires for each gluose molecule 12 water are ripped apart at input and 6 water spit out of dark reactions for a net of 6 water consumed. In this scenario all the O2 comes from the front end.
                    Mn reactions
                                       12 H2O + 24 photons => 24 H+ + 24 electrons + 6 O2
                                        114.2                                                                           30.1
how does the energy balance here. Seems like each H+ and separate electron would have 13.6 ev???

           possible dark reactions
                        24 electrons + 6 CO2 + 24 H+  + xxx photons   =>   C6H12O6 + 6 H2O
                                                   30.1 ev                                                         94.5        57.1
--------------------------------
Figures show following
       front end
                        photons + H2O  + [ADP +P + NADP+ + H+]  => ATP + NADPH +  O2
or                    photons + 6 H2O  + [ADP +P] + [NADP+ + H+]  => ATP + NADPH + 6 O2
or                    photons + 6 H2O  + 6 [ADP + PO3] + 6 [NADP+]  => 6 ATP + 6 NADPH + 3 O2
more likely is that the whole phosphate group PO3+ cycles back (probably what Pi means) and hydrogens don't cycle back!!, then from 6 water, 6 hydrogens go to ATP and 6 hydrogens go to NADPH and the NADPH soak up two electrons each molecule (12 total) from the 6 split water). Problem is output is only 3 O2 instead of 6 O2??? (can't make the charges work!)
 

ATP   Adenosine triphosphate    C10 H16 N5 O13 P3
ADP  Adenosine diphosphate     C10 H15 N5 O10 P2  confirm diagrams show phosphate group = P O3
so (ATP - ADP) = H O3 P

NADPH     Nicotinamide adenine dinucleotide phosphate          C21 H29 N7 O17 P3
NADP+     oxidized form of NADPH = NADPH + H+ - 2e-      C21 H28 N7 O17 P3
NADP+ + 2e- + H+ = NADPH
so (NADPH - NADP+)  = H+ + 2 electrons = (H + 1 electron)
       back end

                        ATP + NADPH + CO2 => C6H12O6 + [ADP  +P + NADP+ + H+]
or                    (ATP - ADP) + (NADPH - NADP+) + CO2 => C6H12O6
or                     6 ATP + 6 NADPH +6 CO2 => C6H12O6 +6 [ADP + PO3] + 6 [NADP+]  + 3O2
Looks like it may work. (ATP -ADP) bring in 6H and (NADPH - NADP+) bring in 6 H which make up the 12 H needed for glucose. This reaction however means that 3 O2 come out of the dark reaction!!!, which most high level charts do not show!! (can't make the charges work!)

        -- ATP and ADP are in chemical equilibrium in water, so almost all the ATP will be converted to ADP. Any system that is far from equilibrium contains potential energy, and is capable of doing work. Living cells maintain the ratio of ATP to ADP at a point ten orders of magnitude from equilibrium, with ATP concentrations a thousandfold higher than the concentration of ADP. This displacement from equilibrium means that the hydrolysis of ATP in the cell releases a great amount of energy.

        --  ATP does not contain "high-energy bonds". Energy is not released directly from the breaking of phosphate bonds. In fact, the bond breaking in ATP requires energy input, as with all bond-breaking in chemistry. When the new "hydration" bonds form between the products (ADP + phosphate) and water, energy is released, as with all bond formation in chemistry.

ATP + H2O => ADP(hydrated) + Pi(hydrated) + H+(hydrated)  = -30.54 kj/mol
not cosistent with above. Here H is added to ATP to get ADP (opposite of above)
-------------------------------------------------
Bond 'pictures'
        A picture is worth a thousand words. Below three so-called bond types (bonds actually span a continuum) are illustrated with high and low electronegative elements fluorine (4.0), oxygen (3.5), and lithium (1.0). Left two identical atoms (F, F) cause shared electron to split evenly, a (pure) covalent bond. Middle is oxygen  and fluorine with a small electronegativity difference of 0.5, so here the shared electron spend more time around fluorine on right. This bond can also be considered covalent, but the asymmetry makes it polar, so its called polar covalent. Right are lithium and fluorine two atoms with about as big a difference in electronegativety as possible (3.0). Here the shared electron spend nearly all the time around fluorine, so (crudely speaking) lithium has 'lost' its electron to fluorine making this an ionic bond. A more common substance with an ionic bond is sodium cloride  [Na (0.9), Cl (3.0)] table salt.

Chloroplasts
        -- chloroplasts are typically 5 to 10 micron in dia
        -- stroma surrounds thylakoid membranes
        -- PHII and its antenna molecules are located in the stacked regions of the grana thylakoids
**        -- PHI, its antenna molecules and ATP synthase are located (almost exclusively) in the stroma lamallae (membrane) and at the edges of the grana thylakoids
        -- thylakoid lumen is the space enclosed by the thylakoid membrane
        -- thylakoid means 'sac-like'
        -- thylakoid membranes are about 7 to 8 nm thick and space between them is about the same dimension (another ref said 10 nm between them)
        -- potential at oxygen 'electrode' = +0.8eV and NAD+/NADH = -.4eV
        -- Jap paper directly measure ATP synthase rotation of 320 rev/sec
*        -- a photon is absorbed by a chlorophyll pigment (without antenna) about every tenth of a second on a good day
*      -- an electron transfers into a (given) P700 reaction center about 1,000 times a sec (in other words the antenna complex has gathered in x100 more photons than chloroplyll alone)

        --- many plants have an efficiency in terms of oxygen of 0.106 +/- .001 mol of O2 for mol of photons
                      very close to theoretical max of 0.125 = 6 O2/48 photons
                        http://www.pnas.org/content/87/19/7502.full.pdf
        --- tested with growth lights
                        red 580-740 nm PSI                75 micromol of photons per meter squared per sec
                    cool white PSII 520-695 nm      95 micromol of photons per meter squared per sec
                me
                    bright sun   1,000 watts/m^2 mean 2.3 ev @ 550 nm
                                # of photons       10^3/(2.3 ev x[ 1.6 x 10^-19 j/1 ev] =
                                                                        2.7 x 10^21 photons per meter squared per sec
                                        6 x 10^23 = 1 mol, so 6 x 10^17 is micromol
                      sunlight       2.7 x 10^21/6 x 10^17 =4.5 x 10^3 = 4,500 micromol per meter squared per sec
                                so grow lights provide about 1.8% the # of phtons as bright sunlight
check
                       find for sun 2,000 micromol of photons per meter squared per sec,  or 2,000 microEinstein

                            Def: Einstein  = mole of photons per meter squared per sec

            quantum efficiency begins to roll off before full sunlight.
            Bean plant (high sun plant) the light sat point is perhaps 1,000 micromol (1/2  sunlight)
        -- photosynthesis efficiency curves are S shaped
                       response falls off at low amplitude if photons are seconds apart because energized
                        states decay (like in water oxidizing complex)
        -- efficiency of isolated chloroplasts measured at 2/3 of theoretical (12 quantum per CO2  vs 8 on block diagram)
        -- Hard data (tropical plant leaf)!

Partial efficiencies --book (good)
                                O2 output/photon                              .125 theroetical =  6/48
                                CO2 fixation/photon                         .125 theroetical =  6/48
                               PHII electron chain                              .85 to .95 actual
                                PSI electon  chain                                    > .95

                   measured in lab for leaves, white light of limiting intensty (low light?) CO2 adjusted  for low photorespiration
                                    CO2                                                     0.073 to 0.098
                                    O2                                                        0.083 to 0.115
                                                                                                       0.106   for wide range of plants

                in air (photorespiration, which is oxygen competing with CO2 at RuBisCo, is now higher
                                    CO2                                                    0.07 or less

    in non-limiting light (more light) quantum efficiencies fall
            higher light levels lead to saturation of "photosynthetic electron transport"
            PSII limits first? on its acceptor side

            one model is thinking of   'fluxes' of energy and materials' like ohms law (potential drives a flux acosss a resistance0
        -- "close to equilibrium the driving potential can be usefull modeled as a chemical potential difference, but far from equilibrium flows are not linear with voltage, so its not so useful.
        -- the resistance to the flux is inversely proportional to the 'rate constant' of a reaction
        -- key limitiation appears to be 'P700 reduction'
                         It is characterized by a half time (constant)
             'Linear electron transport' rate constant of 59 sec^-1 (59 per sec) translates to a half time (constant) of
                                                        (1/2) x (1/59) sec = 8.5 msec
                                (in other words if a reaction takes 2 x 8.5 mec, throughput is 59 times in a second)
          Plot shows P700 rate constant at 60 per sec and PSI potential at 0.7 V?. Does this mean PSI can only run 60 times a second
                        if so then each reaction center can only produce about 2.5 glucose (= 60/24)per sec!
                    Wait 59 per sec rate this may be the rate driven by one volt, because 1/rate is a resistance,
                                so maybe the reaction rate of PSI is 0.7 x 59 = 41 or 1.7 glucose
                Qa to P700 redox potential drives the electron transport chain

            One the proton potential is reached to start ATP synthase making ATP, a further increase of one PH (59 mv) saturates the proton flow through ATP synthase (hence ATP making is at max)

        translate above into rate for one reaction center.

** could this be one of the keys --- plants are only efficient at low light levels. Some plants do best at 1,000, but their response is likely rolling way off.
 

** possible place to send my block diagram. Yale on photosynthesis. Very creative. Above is high school teaching aid showing how a thylakoid membrane can fold into stacks of grana. (high school teacher on the difficulty of teaching photosynthesis to high school students.)

Working some numbers
        How much glucose and ATP does a chloroplast make and ATP synthase machines does it have? Most references have no numbers. But starting with estimated leaf efficiency (see figure elewhere) of 5% and an estimated chloroplast size of 5um we can work some numbers. (5 um is small compared to an average cells size, which from C elegans worm is [(1/2) mm/cube root{500}] = 63 um. Confirming this is Wiki which gives a range of 10-30 um for animal cells and 10-100 um for plant cells)

        chloroplast area (5 x 5 um)                    25 x 10^-12 m^2
        photon energy @ 1000 w/m^2              1,000 watt/m^2 x 25 x 10^-12 m^2 =
                                                                                   25 x 10^-9 joule/sec

        # of 1.8 ev (av) photons/sec arriving     25 x 10^-9 joule/ [1.8 x 1.6 x 10^-19 joule] =
                                                                                  8.7 x 10^10 photon/sec
        Total arriving photon energy converted
           to glucose @ 5% leaf efficiency      0.05 x [1.8 ev/photon x  8.7 x 10^10 photon/sec] =
                                                                                   8.0 x 10^9 ev/sec
        # glucose molecules/sec
            @ 29.7 ev per glucose                        8.0 x 10^9 ev/sec/29.7 ev per glucose =
                                                                                    2.7 x 10^8 glucose molecules/sec
---------------
new
            4 glucose/sec per reaction center
                    @ 10 nm centers + ATP synthase
                            5 microns size                             (5,000 nm/10 nm) x 4/sec =
                                                                                       25 x 10^4 x 4 = 10^6  one layer
                                                                                            10^7 ten layers
                         reduction in efficiency since light levels are too high and too low in many grana
                                       penalty maybe 3-5  => 2 to 3 million glucose

ATP density not a problem
           One ATP synthase easily keeps up with one reaction center. At four glucose/sec this is 4 x18/3ATP/rev = 24 rotations. At 200 rev/sec this is 24/200 = 120 msec. Thus one ATP synthase can make the ATP needed for  8 reaction centers! (four at 100 rev/sec)
---------------
        # of ATP molecules/sec
             @ 18 ATP per glucose                    18 x 2.7 x 10^8 glucose molecules/sec =
                                                                                    4.9 x 10^9 ATP/sec

        #  ATP synthase needed  @ 6,000 to 12,000 RPM (100 to 200 rev/sec) and three ATP/rev
                      equiv to [300 to 600 ATP per sec]
                                          4.9 x 10^9 ATP/sec/[300 to 600 ATP per sec per ATP synthase] =
                                                         (8.2 to 16.4) x 10^6 ATP synthase

Summarizing, at an assumed leaf/chloroplast efficiency of 5% one five micron chloroplast:

            * 87 billion photon/sec arrive carrying about 157 billion ev energy
            * 8 billion ev/sec of light energy is captured
            * 270 million glucose molecules/sec are made
            * 4.9 billion ATP and 3.2 billion NADPH molecules are made
            * 8 to 16 million ATP synthase rotary machines are needed to make 4.9 billion ATP/sec

        spacing of ATP synthase                        5 um/sqrt{(8.2 to 16.4) x 10^6}  = (1.7 to 1.2) nm
                                                                                Whoops! (dia of ATP synthase is 9 nm)

Whoops -- ATP synthase don't fit?
        Assuming the ATP synthase rotary machine are spread evenly in a single layer grid across the area of the five micron square chloroplast, we find they don't fit. And they don't fit by a huge margin. Most of the thylakoid membrane area has to be devoted to molecules that capture photons, the rest of the membrane machinery, like ATP synthase, must be a minority of the area. What goes on here?

        The number of ATP synthase rotary machines that must fit into the chloroplast is pretty solid The amount of light energy coming in and being converted glucose is pretty well known, the number of ATP needed to make the glucose is known exactly, and the (maximum) rate of ATP production per ATP synthase is known (within a factor of two), a lot of ATP synthase machines being needed because being mechanical they are slow. Not one reference I have ever seen comments on this problem.

Solution?
        After struggling with this a few day, maybe I found the solution. A minor part of the solution may be indicated in the first figure below, which shows folds in the membrane with ATP lining it. But look at the 2nd figure, this is the 3d view of a chloroplast, confirmed with the scanning electron microscope below, which even has a dimension scale.

Stacked up thylakoid membranes
        Notice the thylakoid membranes stacked up in bundles called grana (granum singular). Not one photosynthesis reference I have ever comments on this. On its face it looks very strange. Why would light collecting membranes be stacked up in huge stacks (the electron photos shows a dozen or more) rather than spread out?  Are thylakoid membranes translucent? No one ever mentions this. The electron photo shows each grannum to be only about 50 nm thick, so they might very well let a lot of light through. If so, then a stack of them, while costly for the plant to build, might be viewed as a strategy to raise the photon capture efficiency of the plant. With a big stack the probability of a photon getting captured somewhere in the stack is improved.

        Now there's a lot more membrane area to fit all the required ATP synthase machines. But the numbers still look dodegy. If with x9 or x16 times more area than a single layer, the center-center spacing still comes out to be less than the dia of the rotary machine. It doesn't go. Maybe the stack depth is still higher and there wrinkling or folding to increase the area more. Unclear.

        Also a stack illuminated from the top means a light gradient down through the stack, very bright at top and likely dim at bottom. Unless ATP and NADPH can migrate through the whole stack, this doesn't seem like an efficient arrangement.

Rods and cones really stack!
        I gained some perspective of the stacking issued from a great book on vision I am now reading -- 'First Steps in Seeing' by Rodieck. The vision system is optimized  to work at much lower light levels than plant leaves which get direct sunlight. Being able to see (or sense) dimmer light than competing animals provides a huge evolutionary edge. At the retina level this means, one, maximizing the probability of photon capture (technically photoisomerization), and, two, it's important that photocells are able to respond to a single photon. The latter is much more important  than it might (at first) because, as Rodieck explains, if two photons have to arrive in 100 msec shutter time (rather than one) the light needs to be orders of magnitude higher. (I think the example he gives is that at low light threshold each rod may only catch a photon every 85 min, so that's a light ratio of 85 x 60/0.1 = 50,000!  (The implications for Z photosynthesis where two photons are needed is clear!)  For details on how single photons are sensed at the cellular and molecular level see my essay on Vision.

        The (active) capture of photons is maximized in rods and cones is by having the light pass into a stack of 1,000 membranes layers all packed with photosensitive proteins! Seems to be the purpose of membrane stacking in eyes is a somewhat different than in photosynthesis. I have not seen a comparison, but here is my speculation:

         At very low light levels the time between photons entering a photocell can be minutes, so it's important for seeing in dim light to capture a photon if it enters a photocell. According to Rodieck rods and cones do a good job at this (actively) capturing about 68% of entering photons. The stack must be thick enough so that it looks opaque to the photons. My guess is that it's biologically profitable to have many 'extra' membrane layers even if they contribute little to the capture rate, hence the 1,000 layers. Curiously the light must pass through four cell layers and the whole of the long narrow rod and cone cells to get to the 1,000 stacked layers on the outside of the retina.

        In contrast photosynthesis is optimized for much higher light levels. It appears that there are often more photons than can be used. Fewer layers can be used, photons can be allowed to pass through. If appears that photosynthesis efficiencies often fall off at light levels above 1/10th bright sunlight. No reference that I have seen has a good handle on photosynthesis efficiency (there my be too much variation), but it would make sense to allow photons to be wasted if something else is limiting. One biological limit may be the high level of supporting molecular machinery needed to make photosynthesis work.
---------------------
** BOOK @ 2000 uEienstein (full sunlight) one chlorohyll molecule will absorb
                            10 photon/sec
        Antenna complexes are 100 to 300 molecules, so by extrapolation
                            1,000 to 3000 photons full sunlight per reaction center
                            50 to 150 at 100 uEinstein
scaling
            2000 uEinstein - 2 x 10^3 x [10^-6 x 6 x 10^23] = 12 x 10^20
            for 11 nm square         11^2 x 10^-18 x 12 x 10^20 = 1,500 x 10^2
                                                                                                    = 150,000 photons/sec in bright sun

Antenna complex level
        One reference says (spinchace choroplasts)
        -- scanning electron microscope PHI reaction center (not antenna complex)  7 x12 nm
                antenna complex had 40 cholorphyll
                PSI had a measured diode like band gap of 1.8 ev
        -- 11.2 nm dia
        -- 50 to 100 nm wide, 100 to 300 nm long (book) green bacteria
                        membrane 4 nm thick
        -- electron micrope picture shows dia of thlaloid disks 0.5 um (500 nm)
       -- reaction center sizes
                    300 - 800 molecules _ 47 choloroplyll cynobacteria
                    1,000 molecules (big one) green sulfer bacteria
                    35 molecules (small one)
                    20-200 purple bacteria
        -- adaption to high light
                        cynobacteria on surface have sunscreens
         -- 5 of 36 bacteria 'lineagages' do photosynthesis

scaling glucose to 11.2 nm rect antenna
 # glucose molecules/sec
            @ 29.7 ev per glucose               (11.2 x 10^-9/5 x 10^-6)^2 x 2.7 x 10^8 glucose molecules/sec
                                                                    5 x 10^-6  x 2.7 x 10^8 =13 x 10^2 = 1,320 glucose/sec
Much more reasonable numbers
                         in other words at full sunlight with full efficiency the Z cycle does 24 turns in about 1 msec
but curve shows 10 uEinstein this 10/2000 or 200 times less light of 6.6 glucose full 24 turns (or 158 electrons). 6 msec per electron. This agrees pretty well with 80 P700 reduction (with in factor of 2) or 12 msec per electron
Other references show a light limiting begins at about 50 uEeinstein whichis x5 higher, so each electon takes about 1 msec and glucose output is 30 per sec.

Reason for folding?
        Whoops, just assuming a flat chloroplast membrane we find there is not enough room on the thylakoid membrane to hold all the ATP synthase rotating machine (plus of course all the other stuff a cell needs). The dia of ATP synthase rotating machines is about 9 to 10 mm in dia, which sets their minimum spacing. But the thylakoid membrane in the figure (all those tiny cylinders) looks to be very folded, which the calculation in the last step ignored. If we guess the folding increases surface area of the thylakoid membrane by x 50 to x100, it changes the spacing between centers to 12 nm to 17 nm, so it just fits but the membrane has a very high concentration of ATP synthase machines!

Bottom line --- The molecular numbers are truly huge (mind boggling) for a tiny 5 um (square) chloroplast. One tiny chloroplast is capturing about 13 billion photons/sec in bright sunlight and making about 270 million glucose molecules per sec! With all its ATP synthase spinning at top speed (12,000 RPM) making 600 ATP/sec we find that even with a folded membrane increasing surface area x100 that 28% [(9 nm/17nm)^2] of the membrane must be occupied by ATP synthase machines.
 

Efficiency
Basic respiration summary equation
        The reaction for aerobic respiration is essentially the reverse of photosynthesis and is simplified as:

                        C6H12O6 + 6O2 => 6CO2 + 6H2O + 2,880 kj/mol (29.8 ev)                (Wikipedia)

Theoretical efficiency
        A simple ratio of the energy recoverable from one molecule of glucose when oxidized (29.8 ev) to the energy in the light photons needed to generate that glucose (24 turns of Z cycle is 48 photons x 1.8 ev/photon = 86.4 ev) gives us a maximum theoretical efficiency. Note this assumes the following idealized conditions, obviously real efficiencies are going to be lower than this calculated 34% value.

                    a) every photon is collected
                    b) all the intermediate steps are 100% efficient
                    c) everything in the electron chain and back reactions can keep up
                                    with the photons coming in.(Rubisco is slow and some of it does
                                    contribute because it takes in oxyen.)

                  29.8 ev (oxidation of one glucose molecule)/48 x 1.8 ev photons
                            = 29.8/86.4
                            = 34.4%                                        (maximum theoretical efficiency)

        -- The ultimate rate-limiting factor of the Calvin cycle is slowness of RuBisCO that cannot be ameliorated in short time by any other factor

         -- (1990 paper abstract)  Within the ideal assumptions: (1) two Photosystems for photosynthetic fixation of CO2, (2) all solar photons with wavelength  of 700 nm are absorbed, (3) the photon requirement is 8 for each CO2 molecule fixed and O2 molecule evolved (OK) and (4) the principal stable product of photosynthesis is d-glucose, the theoretical maximum efficiency of conversion of light to stored chemical energy in green-plant type (oxygen-evolving) photosynthesis in bright sunlight is calculated to be 13.0%.

        -- Since RuBisCO is often rate-limiting for photosynthesis in plants, it may be possible to improve photosynthetic efficiency by modifying RuBisCO genes in plants to increase its catalytic activity and/or decrease the rate of the oxygenation activity.

        -- Since photosynthesis is the single most effective natural regulator of carbon dioxide in the earth's atmosphere, a biochemical model of RuBisCO reaction is used as the core module of climate change models.
-------------------------------------
Photon rates and antenna complex
        Paper says reaction center of purple non- sulfur bacterium is 115 angstrum in dia (11.5 nm)

Photons in bright sunlight 1,000 w/m^2
Visible light is 400 nm to 700 nm, so I will use 550 nm
                    wavelength x freq = c
                        freq = c/wavelength
                                = [3 x 10^8 m/sec]/5.50 x 10^-7 m
                                = 0.545 x 10^15 hz
                        E (550 nm photon) = h x freq
                                                        = 6.63 x 10^-34 x 0.545 x 10^15
                                                        = 3.62 x 10^-19 joule
                                                       = 3.62 x 10^-19 joule x [1 ev/1.60 x 10^-19 joule]
                                                        = 2.26 ev

Photon/sec in a meter squared (assuming all 550 nm and 1,000 wattt/m^2).
                                               [10^3 joule/sec]/3.62 x 10^-19 joule =
                                                        2.76 x 10^21 photons/m^2
photons/sec in a box the size of wavelength (550 nm)
                                     2.76 x 10^21 photons/m^2 x [5.5 x 10^-7m]^2 =
                                                      0.83 x 10^9 photons/sec (in 550 nm box)
                                                                  1.20 nsec spacing (in air photons are about a foot apart)

Useful rule of thumb
        In bright sunlight photons come hit a rectangular area defined by their wavelenght (550 nm nom) about once every nsec.

                                            [550 nm/11.5 nm]^2 = 2,287

# photons/sec in 11.5 nm rect area
                           0.83 x 10^9/2,287  = 0.362 x 10^6 photons/sec (in 11.5 nm box)
so photons come in every
                                    1/0.83 nsec x 2,287 = 2.75 usec

It takes 48 photons to run the Z cycle, so if capture efficiency is 100% (every photon hitting reaction center antenna complex is captured), the time to run the Z cycle once would be

                                        2.76 usec x 48 = 132 usec  (or 7,575 Z cycles/sec)

Another mystery --- ATP synthase way two orders of magnitude slower than photon set rate
        Something is really strange here. Both the reaction centers and the ATP synthase rotating machines are in the thykaloid membrane. The ATP synthase at 9 nm dia is about the same size as the antenna complex (11.5 nm dia), yet it takes 30 msec (maybe 60 msec) to run one Z cycle (6 rev to make 18 ATP). To keep up with the photons coming in in bright sunlight it would take 227 rotating machines!

                                        30 msec/0.132 usec for 48 photons = 227 !!

The membrance comes out to be 99% ATP synthase rotating machines and only 1% light gathers. This is ridiculous. It should be the other way around. Whats wrong here? Even full out capacity at 1/2 or 1/4 strength sunlight does not solve this problem!!

---------------------------------
                        H2O oxidize (one electron)                      0.82V
                        PHxxx receiver (one electron)                  0.32V
                        # of electrons per NADPH                            2
                        Energy stored per NADPH       2 x 1.14V = 2.28 ev
                        Light energy per NADPH          4 x 1.772 ev = 7.09ev
                        Effficiency (NADPH)                 2.28 ev/7.09ev = 32.2%

But this ignores the energy stored in ATP coming from the same electrons in the transport chain
                                                  1/12 x 18 ATP x 0.48 ev = 0.72 ev
                        Effficiency (NADPH + 1.5 ATP)       (2.28 ev + 0.72 ev)/7.09ev = 42.3%
--------------------------------
ATP efficiency
    -  Making ATP from glucose
                C6H12O6 + 6O2 + 36Phosphate + 36ADP --> 6CO2 + 6H2O + 36ATP
you get 13 ATP from one glucose
                efficiency          36 x 0.48 ev (ATP in cells) est/ 29.7 ev = 58 % with balance lost as heat
    - Making ATP with 'Oxidative phosphorylation', process used in mitochondria (see figure)
                coupled reaction -- electron energy from oxication of NADH are coupled to ATP synthase
                * Wiki models this as a circuit. Proton current flow through pumps x proton motive force (sume of membrane voltage  and proton gradient) Proton pumps called 'batteries' and the ATP synthase a motor.
                efficiency         "somewhere between 30–36 ATPs are produced by the oxidative phosphorylation of the 10 NADH and 2 succinate molecules made by converting one molecule of glucose to carbon dioxide and water." misleading?? from figure it looks like the energy of glucose was used to make the NADH as an intermedate step
            If NADH separte input (terrible)    (30 - 36) x 0.48/(29.7 + 10 x 2.21) = 27.5% to 33%
            if NADH not separate                     (30 - 36) x 0.48/(29.7) = 48 to 58%
               anaerobic fermentation in contrast produes on 2 ATP from same raw materials (minus oxygen)
                                of 1/18th as much

        -- PSI    To transfer an electron from a donor to an acceptor with 90% efficiency requires the redox potential of the donor be lower by 110 mv than that of the acceptor based on thermodynamic consierations.
------------------------------
Efficiency of leaf photosynthesis
        A photosynthesis book (ref in figure) estimates the efficiency of photosynthesis at the leaf level at 5% as shown below.  Efficiency is defined as the ratio of increased chemical energy (glucose oxidation) to the energy of all solar photons (bright sunlight, 1,000 w/m^2) hitting the leaf. Obviously the overall efficiency is lower because not all photons hit a leaf. In cultivated fields maybe only 10-20% of photon hit a leaf reducing overall photosynthesis efficiency to 1/2% to 1%, but in a dense forest the ratio I can believe that overall efficiency might be 4% or more because in dense canopies most photons probably hit leaves.

make baseline H+ for ATP = 4
Est is 5% of sunlight is abosorbed by chlorophyll and other antenna pigments (seems to be a sea & land av)
somehow they end up with 1% of energy absorbed by photosynthetic elements ends up in plant tissue
experimentally for low levels of red light efficiency = 34% (my theoretical value!)
Best with sunlight is 10% because only half  the sunlight spectrum can be absorbed (giving 17%, but some sunlight is reflected and some absorbed by non-photosyntehic pigment in plant cells reducing the final best efficiency to 10%. field measurments with sunlight give a mx of 7%. In upper leaves the cycle saturates some much photon energy is wasted as heat.
---------------
book ref 1 (endergonic reaction, four turns, 8 photons)
PHII        2 NADP+ + 4H+ + 4e- => 2 NADPH + 2H+            E = -0.32V
PHI         2 H2O => O2 + 4H+  +4e-                                          E = -0.82V
            --------------------------------------------------------
combined    2 NADP+  + 2H2O => 2 NADPH + O2 + 2H+

               delta E = - 1.14 V  (just the sum of E's above)
                delta G = +220 kj/mol  (2.28 ev)

       Note 2.28 ev is exactly double 1.14V (looks the energy comes from a flow 2e through 1.14V drop)
        (figure appears to show 1.2V as the redox drop in the PHII electron transport and 1.0V for PHI electron transport) text says electron drop of PHII (to PHI) is 1.2V per 2e- transferred. "because the drop is transversed twice by 2e- in each pass the total potential is 2.4V" ???
            " 220 kj/mol is the energy expendure for the synthesis of a mole of NADPH, or 440 kj/mol for 2 moles. The 8 photon energy is 1,368 kj (8 x 1.77 ev)
           "Therefore the efficiency of NADP+ to NADPH synthesis [440kj/1368kj =32%]" (looks weird to me because some of the light energy is going into making ATP, OK they next include this. But this book has 4 ATP being generataed for each 12H+ whereas I have 3, which seems to be the baseline number.)

             ATP hydrolysis has delta G = - 30.5 kj/mol (0.316 ev), wrong this is for 'standard conditions'

book ref 2
        "to remove electron from water (+0.8V potential) to ferredoxin (-0.43V) requires two photons in series"
        PHI redox drop makes ATP, PHII redox drop makes NADPH
        PHII redox energy +0.8 to -0.2 (delta 1.0V) and PHI from +0.4 to -0.8 (delta 1.2V) for a total of 2.2V
                "of the 1V lost part is recovered in ATP" ??
            photon energy exceeeding the transport chain deltat V must be dissipated (loose translation) energy is dissipated in the antenna complex of PHII
--------------
        ATP (transport) energy
                    ATP + H2O => ADP + Pi + 7.3 kcal/mol (0.316 ev)   at equal concentration,
but typ in plants there is about 1/10th as much ADP as ATP and Pi, increases energy required to make
 ATP by about x17.7 to 0.54 ev (52kj/mol) book
        -- A significant amount of photon energy is stored in ATP ???  (I get 15 to 30%)

        NADPH energy         carries high energy electrons
                   energy value depends on what NADPH reduces
* book (photosynthesis)
        NADPH           51 kcal/mol(2.21 ev)   x 12 = 26.52 ev
         ATP                 12 kcal/mol (0.519 ev) x18 = 9.34 ev
         glucose per mol of   CO2         479 mj/mol (4.06 ev) x 6 = 29.8 ev
Calvin efficiency = 29.8 ev/[27.4 + 9.33] =81%       other ref say 90%

dissassociation of water (electroloysis)
Note this equation is just what happens at the Mn complex where water is ripped apart!
                    2H2O => O2 +4H+ (aq) + 4e-                Eox = -1.23V

MIT book
                an electron into redox potential of 1 V yields 23.1 kcal/mol or just 1 ev!
So energy to disassoicate 12 water is (I think) 24 (e-) x 1.23V = 29.52 ev  (this is 34.2% of the light energy)

(text book)
                           kj/mol    In       6 x [440 redox + 3 x 31 ATP]
                                                     6 x [4.56 ev + 3 x 0.321 ev)] = 6 x 5.52 ev = 33.13 ev
                             Out glucose     479.5 x 6  = 2877 kj/mol  (29.8 ev)
                             efficiency         29.8 ev/33.13 ev = 90.0%

                membrane voltage = nom pot - 59 mv x (delta ph)
==========================================================
Key molecules and enzymes

Chlorophyll
        Chlorophylls are greenish pigments built around a chlorin ring (or porphyrin ring), the center of which is a single metal atom of magnesium surrounded by four nitrogen.

Porphyrin Ring
        A multi-ring‚ carbon-based molecule with nitrogens at its central corners‚ found in heme groups and chlorophyll.

        Chlorophyll looks green because it has a doubled humped abosorption profile, absorbing strongly blue and red and hardly at all in the center of the spectrum. Chemical formula is

        Chlorophyll a        C66 H72 O5 N4 Mg
        Chlorophyll a        C66 H70 O6 N4 Mg

        -- Note the system of alternating single and double bonds that run around the porphyrin ring. Although the single and double bonds are drawn in fixed positions, actually the "extra" electrons responsible for the double bonds are not fixed between any particular pair of carbon atoms but instead are free to migrate around the ring. This property enables these molecules to absorb light.

        Almost for sure the light gathering region of chlorophyll is the ring, with the tail serving to anchor it into the thylakoid membrane. So how big it it? Have found no numbers in references, but it looks to be 5 to 6 atoms across and atoms (order of magnitude) are 1 angstrom in dia (0.1 nm). I found two references that say it is estimated that in bring sunlight a chlorophyll molecule absorbs about 10 photon/sec.

Check
        Incoming photons @ 0.5 nm square @ 2000 uEinstein (bright sunlight)

            (0.5  x 10^-9 m)^2 x [12 x 10^20 photons/sec @ 2,000 uEinstein] = 300 photons/sec

OK ballpark, 10 photons/sec would be 3% of incoming 300 photons/sec for each chlorophyll molecule.

--------------------------------------------------
Chlorophyll vs Hemoglobin  structure ---  My high school chemistry teacher, Mrs Holt who I always thought of highly, once told us that chlorophyll and hemoglobin molecules were the same except for a single metal atom in the center, magnesium in chlorophyll and iron in hemoglobin. (To be honest, while I remembered the single metal atom difference, I no longer remembered the metal atoms, I had to look them up.)

        This impressed me --- Wow, this sure indicates something deep about animals and plants, I thought ---  and I always remembered her saying it. It's a good story, but recently when I researched it, I found out it's not completely true, but it's true enough. Chlorophyll and hemoglobin both have similar porphyrin rings with a single metal atom inside, but outside the ring there are some differences (see image below).

 

comparison of chlorophyll (green) and hemoglobin (red) porphyrin rings
(my scan from book Eating the Sun by Oliver Morton, 2007)

        A chemistry book poses this questiion: What is magnesium (element #12) for in chlorophyll?
                        (Ans: reduces flourescence, small molecule, no redox potential) (tells me little)

        -- Bacteriorhodopsin is a photosynthetic pigment used by archaea, most notably halobacteria. It acts as a proton pump, i.e. it captures light energy and uses it to move protons across the membrane out of the cell. The resulting proton gradient is subsequently converted into chemical energy..

        -- It is thus likely that photosynthesis independently evolved at least twice, once in bacteria and once in archaea.

        -- The three-dimensional tertiary structure of bacteriorhodopsin resembles that of vertebrate rhodopsins, the pigments that sense light in the retina. Rhodopsins also contain retinal, however the functions of rhodopsin and bacteriorhodopsin are different and there is no homology of their amino acid sequences.

        -- The electron transfer reactions concentrate protons inside the membrane vesicle and create an electric field across the photosynthetic membrane.

        -- Protons pass through the ATP-Synthase protein complex that transforms electrochemical free energy into a type of chemical free energy known as phosphate group-transfer potential (or a high-energy phosphate bond). The energy stored in ATP can be transferred to another molecule by transferring the phosphate group.

        --  The oxidation- reduction midpoint potential (Em,7) of water is +0.82 V (pH 7). In photosystem II this reaction is driven by the oxidized reaction center, P680+ (the midpoint potential of P680/P680+ is estimated to be +1.2 V at pH 7)

**     -- Compared to the inner membranes of mitochondria, which have a significantly higher membrane potential due to charge separation, thylakoid membranes lack a charge gradient. To compensate for this, the 10,000 fold proton concentration gradient across the thylakoid membrane is much higher compared to a 10 fold gradient across the inner membrane of mitochondria.

**     -- Thylakoid membrane allows passage of  Mg+ and Cl-, which results in elimination of membrane potential. Electrochemical gradient is almost entirely PH (proton) gradient.

        -- Photosynthesis occurs in two stages. In the first phase light-dependent reactions or photosynthetic reactions (also called the Light reactions) capture the energy of light and use it to make high-energy molecules. During the second phase, the light-independent reactions (also called the Calvin-Benson Cycle, and formerly known as the Dark Reactions) use the high-energy molecules to capture carbon dioxide (CO2) and make the precursors of glucose.

        -- The potential energy that an electron has is determined by its distance from the nucleus.  The more energy the electron contains, the further it will be from the nucleus; an electron with low energy will be closer to the nucleus. Electrons can move to a higher energy level by having added to it (sunlight and light energy). When this electron moves back to its original position, the same amount of energy that it took to move the electron is released.

        -- Most carbohydrates have the empirical formula (CH2O)n. Carbohydrates are composed of covalently bonded atoms of carbon, hydrogen, and oxygen.

            -- The basic unit of a carbohydrate is a monosaccharide or simple sugar. Monosaccharides can be burned (oxidized) to yield carbon dioxide, water, and energy. The principle source of energy for organisms is glucose (C6H12O6). Structurally a sugar consists of a carbon backbone of three or more carbon atoms with either an aldehyde or carbonyl group on one carbon and hydroxyl groups on each of the other carbons.

        -- Electron carriers  Some compounds can accept and donate electrons readily, and these are called electron carriers in organisms. NADP is an electron carrier used in photosynthesis. These molecules readily give up 2 electrons (oxidized) and gain two electrons (reduced). Along with the electrons the molecules accept 2 hydrogens to offset the negative charge of the electrons.

        --  Oxydation Losing electrons, hydrongen or the gaining ofoxygen.  An electron loses potential energy when it shifts from a less eletronegative atom towards a more electronegative one.  A redox reaction that relocates electrons closer to oxygen realeases chemical energy which can be put to work.

        -- Changing in Covalent Status  Usually, organic moelcules that have and abundance of hydrogen are excellent fuels because their bonds are a source of electrons with high  potential energy.  They also have the potential to drop the energy when they  move closer to oxygen.  The important point in aerobic respiration is the change in covalent status of electrons as hydrogen is transfered to oxygen.This is what liberates the energy.

        --  At key steps in aerobic respiration, hydrogen atoms are stripped from glucose, but they are not directly tranferred to oxygen.  They are passed to a coenzyme called NAD+ (nicotinamide adenine dinucleotide) which  functions as the oxidizing agent. Enzymes called dehydrogenases remove a pair of hydrogen atoms from the substrate.  These enzymes deliver two electrons along with one proton to NAD+, forming NADH.  The other proton is released as a hydrogen ion into the surrounding solution.

        -- Electrons lose very little potential energy when they are transferred by dehydrogenases from glucose (organic molecules) to NAD+.  Thus, each NADH molecules formed during respiration represents stored energy that can be used to make ATP when the elctrons complete their journey from NADH to oxygen.

        -- Light Antennas gather light energy.  When the light strikes the molecules, it vibrates. Because the molecules are tightly packed together, the excitation of the molecules spreads rapidly from molecule to molecule until it reaches the reaction center.  The reaction center releases electrons into the electron transport chain.

        -- P680 w/out e- becomes powerful oxidizer (it'll rip off electrons)
It'll strip off e- from a Z-protein.
Z-protein w/out that electron becomes a strong oxidizer.
Z-protein catalyzes reactions to strip electrons from water.
Water loses two electrons to form two H+ protons and an oxygen atom, O
The O immediately binds with another O to form O2, which diffuses out of the plant cell (or is consumed for cell-respiration)
The H+ protons help augment the H+ gradient necessary for ETC

        --  A chromophore is a region in a molecule where the energy difference between two different molecular orbitals falls within the range of the visible spectrum. Visible light that hits the chromophore can thus be absorbed by exciting an electron from its ground state into an excited state.

        -- The metal complex chromophores arise from the splitting of d-orbitals by binding of a transition metal to ligands. Chromophores consist of four pyrrole rings. One type forms a ring (porphyrin) with a metal in the center, for example, chlorophyll.

        -- The "visual purple" rhodopsin (opsin-2) of the rod cells in the vertebrate retina absorbs green-blue light. The photopsins of the cone cells of the retina differ in a few amino acids resulting in a shift of their light absorption spectra. The three human photopsins absorb yellowish-green (photopsin I), green (photopsin II), and bluish-violet (photopsin III) light and are the basis of color vision, whereas the more light-sensitive "visual purple" is responsible for the monochromatic vision in the dark
--------------------------------------------------------------------
70$ photosynthesis paperback book at coop (from memory)
            1100 photons/sec  hit a cholorphyll molecule
            only 10 photons/sec are absorbed and processes 1%

        inside of cell has excess of H+ (so memebrane e field points inward)
        electron transport path causes electrons to flow from outer edge of membrane to inner edge
                        (thus there is a positive current pointed out of the cell (in to out)
        electron transport functions to pump H+ into the cell (maintaining the H+ gradient across membrane)
                        (the chain is three?  H+ pumps in cascade, with each taking some energy out of the
                                energetic electron is was passed)
        in another path the H+ flow out of the cell (forced by the H+ gradient) and do work making ATP
                  --  ATP is produced from ADP and Pi when hydrogen ions pass out of the thylakoid through ATP synthase. This method of synthesizing ATP by using a H+ gradient in the thylakoid is called photophosphorylation.  (H+ thus circulate continuously pumped in by the energy of the electron transport and they do work making ATP going out)
        electron flow is electrons pulled from H2O in the cell (leaving oxygen inside cell) and after two up steps flow out of the cell reducing Nxxx (which goes to the dark processing of CO2)???
            -- The acceptor passes it to NADP+, which becomes reduced to NADPH. According to the following equation, NADP+ has the capacity to carry two electrons. NADP+ + 2e- + H+ ® NADPH
            -- In the light reactions, electrons move one way from water to NADPH
                (dark reaction) Calvin Cycle takes ATP and NADPH from the reaction centers and uses them to oxidize CO2 into glucose, outputting    { ADP +P and NADP+ + H+} which circulate back to the reaction center to (re)reduced. (in desert the Calvin cycle may run only at night when the plants open there stomata to let in CO2 -- this may be wrong. other references (see below) CO2 comes in at night and is stored then used as Calvin cycle runs in daytime. daylight is needed to activate some calvin reactions. (it also lets water escape)

Modified photosynthesis -- C4 and CAM
        Most plants use the basic Z-cycle photosynthesis and are known as C3 plants. C3 refers to the immediate output of photosynthesis a three carbon 'half sugar' (C3H6O3 + Pi) two of which in the following step are combined to form a molecule of the sugar glucose (C6H12O6). But about 3% of plants, called C4 plants, have evolved a more complex variation of photosynthesis that can work with fewer inputs, specifically less CO2 and water, because they are able to more efficiently gather in the CO2 they need for carbon.

        References often say that in C4 plants carbon is fixed to a four carbon intermediate, rather than three carbon as in C3 plants, which is why they are called C4 plants. This makes it sound like their calvin cycle is fundamentally different, but that is not the case. What C4 plants have is pre-processing stage preceding the calvin cycle that gathers up CO2 and feeds it directly into the rubisco of the calvin cycle. In C4 plants carbon is fixed twice. The first intermediate that holds the CO2 for feeding into the calvin cycle is one of two simple molecules, malate (C4H6O5) or aspartate (C4H7NO4), both of which have a four carbon backbone.

        There are several advantages to a pre-processing CO2 stage. One is that Z-cycle runs better because oxygen, which rubisco will grab if given a chance (called photorespiration), can be excluded, so more sugar can be produced for a given amount of CO2 and water. Photorespiration is a big problem in the warm tropics where the take up of CO2 can be cut in half. It takes additional energy to run the pre-processing stage. Essentially what is going on in C4 (and CAM plants) is the light reactions need to works harder, capture more light energy and make more ATP, so that the dark reactions work better. In the bright tropics (C4) and in the desert (CAM) the additional light energy is available, so there is a net gain in carbon fixation to the plant from a CO2 pre-processing stage. These plants are also more heat tolerant.

        More than half of grasses, which have a large light collecting area, are C4 plants. This includes the important food crops corn, sugar cane and maize. Crab grass in your lawn is a C4 plants too, as is switch grass a potential biofuel. The early crops domesticated in the Near East, China, Africa, and the Americas were all C3 plants (exception millet). They were grown for their seeds, but the seeds of C4 plants tend to be small and brittle.

        Another variant of photosynthesis is CAM photosynthesis. About 8% of plants use CAM photosynthesis, many are succulents. CAM plants, like C4 plants, have a pre-processing step to gather up CO2, and they too transiently fix CO2 to the molecule malate. These plants usually open their leaf pores (stomata) only at night to gather in CO2, which they then feed into the Z-cycle during the day. This is just the opposite of C3 and C4 plants which open their stomata during the day while both light reactions and dark reactions are operating and close them at night. This strategy is effective at reducing evaporation loss during the heat of the day so many desert plants are CAM plants. The only well known food crop that is a CAM plant is the pineapple.

Pre-CO2 preprocessing
        There exist two biochemical pathways for improving the uptake of CO2 in difficult growing conditions: C4 and CAM. C4 is not the same as CAM. Both concentrate CO2 near RuBisC. RuBisCo will capture oxygen as well as CO2. This is a competing reaction, known as  photorespiration (see Wiki -- photorespiration), and it reduces efficiency of photosynthesis. So plants have various stategies to keep levels of CO2 up and O2 down near RuBisCo.

       CAM concentrates CO2 in time. Taking in CO2 at night and making it available in daytime. C4 plants concentrate CO2 spacially. Most plants, C3 plants, have neither. They take in CO2 in real time (via open pores called stomata).  Only one plant is known to have both CAM and C4 pathways (portulacaria afra, small bonzi tree).

Pre-CO2 processing -- C4 pathway
        -- C4 plants separate rubisco from atmospheric oxygen, fixing carbon in the mesophyll cells and using oxaloacetate and malate to ferry the fixed carbon to rubisco

        -- The product is usually converted to malate, a simple organic compound that is transported to the bundle-sheath cells

        -- C4 plants have developed a mechanism to efficiently deliver CO2 to the RuBisCO enzyme. They utilize their specific leaf anatomy where chloroplasts exist not only in the mesophyll cells in the outer part of their leaves but in the bundle sheath cells as well. Instead of direct fixation in the Calvin cycle, CO2 is converted to a 4-carbon organic acid (hence name C4) which has the ability to regenerate CO2 in the chloroplasts of the bundle sheath cells. Bundle sheath cells can then utilize this CO2 to generate carbohydrates by the conventional C3 pathway.

** C4 needs an extra 12 ATP
        -- Since every CO2 molecule has to be fixed twice, the C4 pathway is more energy-consuming than the C3 pathway.  The C3 (Calvin) pathway requires 18 ATP for the synthesis of one molecule of glucose while the C4 pathway requires 30 ATP. More ATP means more light energy is needed to feed the dark reactions, but the increase in efficiency of the dark reaction carbon fixing pathway due to a big reduction in photorespiration makes for an efficency gain overall, at least for plants in the tropics.

       -- Since otherwise tropical plants lose more than half of photosynthetic carbon in photorespiration, the C4 pathway is an adaptive mechanism for minimizing the loss.

       -- Malate (C4H6O5) is built around a four carbon skeleton, hence the term C4 plants.

        -- C4 plants possess a characteristic leaf anatomy.

        -- C4 plants have a competitive advantage over plants possessing the more common C3 carbon fixation pathway under conditions of drought, high temperatures and nitrogen or carbon dioxide limitation. 97% of the water taken up by C3 plants is lost through transpiration,[1] compared to a much lower[quantify] proportion in C4 plants, demonstrating their advantage in a dry environment.

        -- Plants which use C4 metabolism include sugarcane, maize, sorghum, and switchgrass. They represent about 5% of Earth's plant biomass and 1% of its known plant species. However, they account for around 30% of terrestrial carbon fixation.[2] These species are concentrated in the tropics (below latitudes of 45°) where the high air temperature contributes to higher possible levels of oxygenase activity by RuBisCO, which increases rates of photorespiration in C3 plants.

        -- C4 pathway has thought to have independenly evolved 40 times.

Pre-CO2 preprocessing -- CAM
        (see Wiki -- Crassulacean acid metabolism (CAM processing))
        In some plants (includes 'C4' plants) CO2 does not come in directly from the air.  Instead it has come earlier (at night) and been stored as malic acid in vacuoles in the cell.

        Wikipedia has an interesting aside about CAM CO2 storage in malic acid. Leaves of desert plants can changes from tasting sour at dawn to tasting sweet at sunset. The reason is that the plants loads up on malic acid (in vacuoles) during the night and then use it up during the day.

        Wiki says it takes quite a bit of energy to run the CAM cycle, so it only makes sense for the plant if there are problems, like in the desert, with bringing in CO2 in real time. "CAM can be considered an adaptation to arid conditions. C3 plants lose 97% of the water their roots bring up via transpiration."

        -- The majority of plants possessing Crassulacean Acid Metabolism (CAM) are either epiphytes (e.g. orchids, bromeliads) or succulent xerophytes (e.g. cacti, cactoid). Pineapple, a tropical plant, is a CAM plant.
 

Examples of C3 plants
        -- most small seeded cereal crops such as rice, wheat,  barley, rye, and oat;  soybean, peanut, cotton, sugar beets, tobacco, spinach, potato;

        -- most trees and lawn grasses such as rye, fescue, and Kentucky bluegrass;

        -- includes evergreen trees and shrubs of the tropics, subtropics, and the Mediterranean; temperate evergreen conifers like the Scotch pine; deciduous trees and shrubs of the temperate regions.
====================================================================================

Marine cyanobacteria
        There are lots of different strains of photosynthetic cyanobacteria. Cyanobacteria run the Z-cycle using water as an input and outputting oxygen. They live pretty much everywhere on earth where there is water, but one particular cyanobacteria, prochlorococcus, is special. Not only is it the smallest and simplest photosynthetic cell on earth, but it is also the #1 oxygen producer in the ocean, generating a full 20% of the oxygen that goes into the atmosphere. It is probably the most abundant photosynthetic organism on Earth, says Wikipedia (Prochlorococcus). It is the dominant photosynthetic organism in the surface waters (extending down 150 feet) of the nutrient poor regions of oceans, common from (40S to 40N), which is an 80 degree band around mid-earth oceans. It's small size gives it a high surface area to volume ratio, which is probably an advantage for a photosynthetic cell living free in nutrient poor water.  It is a true bacteria that belongs to a class of photosynthetic picoplankton. It is very tiny, only 0.6 micron across, quite a bit smaller than chroloplasts of eukaryotic cells, which are typically a few microns across.

Sallie Chisholm's tiny prochlorococcus (cyanobacteria)
        Prochlorococcus was only found in 1986 by MIT researcher Sallie Chisholm using a new tool, flow cytometry. Here are notes from a Sallie Chisholm lecture, 'The Invisible Forest, Microbes in the Sea' (below), about the cyanobacteria ('blue' bacteria) prochlorococcus.

           * most abundant photosynthetic cell on planet
           * smallest photosynthetic cell on planet (0.6 um across)
            * smallest number of genes of any photosynthetic cell (1,700 genes)
            * takes in only CO2 from water (air), sunlight, and minerals from sea water and makes
                        life ("no guts of other creatures needed")
            * only discovered in 1986 (Chisholm refers to this as a lesson in humility)
            * more than half of the ocean's photosynthesis is done by prochlorococcus
            * oceans' photoplankton fix as much carbon (from CO2) as all the plants on land!
                            (Chisholm says "almost no one knows this")

        Only discovered about 24 years ago (1985, by a researcher at MIT, Sallie Chisholm) it has been intently studied including having the genome of its two variants fully decoded. It has the smallest genome of the photosynthetic bacteria, only 1.7 million pairs. (NYT article and Wikipedia, prochlorococcus) In spite of it being a bacteria, and its small size, and small genome, it implements the full Z (photosystem II and photosystem I) photosynthesis scheme with water oxidation for electrons and protons and emission of waste oxygen. (There are some bacteria that use just PSII (green sulfur bacteria) or PSI (purple bacteria), but typically these bacteria do not get their electrons from water, hence do not output oxygen.)

        Cyanobacteria have thylakoid membranes and that is where photosynthesis occurs. (Cyanobacteria, like  prochlorococcus, are sometimes called blue-green algae, but they are (true) bacteria, not eukaryotes.) I'm guessing the thylakoid membranes are the five coiled layers seen in the above image, which occupy about half the volume of the cell. Prochlorococcus uses chlorophyll b pigmentation, which Wikipedia (prochlorococcus article) characterizes as unusal. In the Wikipedia chlorophyll article five types of chlorophyll are listed:

                                    chlorophyll a                 (universal)
                                    chlorophyll b                 (land plants)
                                    chlorophyll c1,c2         (algae)
                                    chlorophyll d                 (cyanobacteria)

so maybe what's unusual is that the cyanobacteria prochlorococcus uses b instead of d. Chlorophyll is a 130 (or so) atom molecule built around one magnesium atom (mg), not manganese.

        Prof Chisholm's specialty is prochlorococcus and synechococcus, which is another photosynthetic bacteria living in both the ocean and fresh water. Both of these bacteria have their own Wikipedia entry. There is online from MIT a one hour lecture by Prof Chisholm on the "Invisible forest, microbes in the sea".

         http://mitworld.mit.edu/video/421/

Prochlorococcus worldwide distribution
Percents marked in the dark blue mid latitude oceans, regions of lowest chlorophyll,
are the fraction of chlororphyll in these regions from prochlorococcus
(screen capture from Chisholm's 2006 online MIT talk)

        Its tiny size gives it a large surface area to volume, so it easier to absorb the minerals it needs, which are at very low concentrations in the oceans in which it lives. (Photosynthesis requires a magnesium atom for each chlorophyll molecule, four manganese atoms and a clorine atom for each P680 water 'cracking' reaction center, and a bunch of other elements.) Its large surface area to volume also allow a high percentage of the cell to be thylakoid membranes, where the light is captured and water is 'cracked', yet the membranes can all be near the outside and well illuminated.

        It's photocollection area is made up almost entirely of chlorophyll (b and a), which is quite unusual, they make up the reaction centers and the antenna pigments. There are two common strains of prochlorococcus. The strain that lives near surface, where light is bright, has mostly chlorophyll a, while the strain that lives deeper, where light is dim and more blue, have mostly chlorophyll b, which captures better at the higher end of the spectrum.

Tiny photosynthetic eukaryote, ostreococcus
        In 1994 a tiny (0.8 um) free living photosynthetic eukaryote, a green algae, was discovered. It's a picoplankton, which are less than 2 um. It is only a hair bigger than (0.6 um) prochlorococcus, the smallest known photosynthetic bacteria. As a general rule eukaryotes are x10 larger in linear dimension than bacteria with x1000 higher volume for all the 'stuff' a eukaryotic cell contains, but ostreococcus is only x1.33 larger than prochlorococcus, so its volume is only x2.4 times bigger. Wikipedia says it has one chloroplast and one mitochondrion. (In my summary specs I show the typical size of a chloroplasts as 5 um, but obviously they can be a lot smaller!)

ostreococcus 0.8 um eukaryote
Ostreococcus micrograph, Wenche Eikrem and Jahn Throndsen, University of Oslo.
source -- http://www.jgi.doe.gov/News/news_4_30_07.html

        Its genone indicates it has (for its size) a lot of selenium based proteins, which may be one of the tricks it uses to be so small because selenium based catylists are known to be very efficient. (People have 25 selenium proteins, ostreococcus has 21.)  Ostreococcus has its own virus(!), whose genome has also been sequenced.

        -- one of the smallest and most compact nuclear genomes
        -- 12.6 Mb (million base pairs) nuclear genome has an extremely high gene density (divided into 19 chromosomes)
        -- compaction is usually associated with severe gene loss. By contrast, ostreococcus  has retained a large complement of genes.
        -- phylogenetic analysis and composition do not support alien gene origin
                        (Interesting comment! I think this refers to a proposal by Freeman Dyson that a place to
                        look for alien life (non-earth creatures) is in microbe DNA, possibly from extreme
                         environments. The geneone of ostreococcus is quite unusual. It was found in a brackish
                        lagoon in some French owned pacific island.)
        -- Ostreococcus species display the highest ratio of intragenic to intergenic noncoding DNA detected thus far. (Translation, only a small amount of non-coding DNA outside genes, but a surprising number of introns, which is non-coding DNA inside genes sequences.) Ref

Flow cytometer
        The key to the discovery of tiny prochlorococcus was the flow cytometer, an instrument that counts single cells as they flow in liquid past a sensor. Built around a laser focused on a frail glass capillary tube, the finicky, expensive instruments (in the 1980's) weren't particularly well suited to the rolling, pitching, vibrating environment of a boat at sea. This is now a commercial instrument widely used in medical research as well as microbiology.

        Apparently photoreceptive molecules, like chlorophyll, fluorescence (briefly) when illuminated with an intense laser light and fluoresce at frequencies related to their spectral sensitivity. The laser light frequency is higher than the fluoresce frequencies to provide the needed energy. Displaying the various florescence frequencies combined with amplitude of forward and side scatter in two dimensional plots allows cell size and different photoreceptive molecules to be identified. If the cells being studies are not naturally fluorescent (as are photosynthetic molecules), they can be stained with florescent dies, and in medicine florescent antibodies can be attached. This instrument works particularly well for cell sizes in the micron range.

        When iron is used to fertilize the sea, the blooms are dominated by diatoms (eukaryotic algae), so clearly they use iron and for them it is a limiting mineral. Eleven major iron fertilization experiments have been done and all resulted in 'blooms'. The dominant photospecies in the blooms were diatoms, though after some days cyanobacteria also increased substantially.

Good prochlorococcus reference:
         http://www.genoscope.cns.fr/spip/-Prochlorococcus-marinus-SS120,339-.html

Chisholm's concern with ocean fertilization
        Chisholm is concerned that ocean fertilization (with iron) will lead to unintended consequences. She decribes one worry: Mississippi brings lots of nutrients to the ocean and near the river mouth the photoplankton bloom. Result is dead zones with no oxygen. She is worried same thing will happen at bottom of ocean.

        Ocean fertiliziers will cause large blooms of photoplankton that will sink carrying carbon into deep ocean, hopefully to be sequestered. At bottom the photoplankton bloom will be eaten by bacteria using up all the oxygen (no photosynthesis down there to replenish it). Then anaerobic bacteria will go to work, and they make methane and nitrous oxide which molecule for molecule are far more powerful greenhouse gases than CO2.

        It's somewhat puzzling how the levels up north are so high. The north Atlantic is almost all green, and there are even very high (red) areas in the Artic along the coast of Russia. Maybe this is a seasonal effect, the artic high levels caused by the long summer days?

        Note the map coloration on land is natural, with light yellow indicating deserts, but the ocean coloration seems to me backwards! The dark areas, like the dark blue bands that dominate the mid earth, are ocean deserts, meaning the chlorophyll is low. The high chlorophyll area of the ocean are lighter blue and especially green and yellow, which dominate in the north Pacific and north Atlantic.

        Note the striking fact about photosynthesis in the oceans. Photosynthesis is low over the equator and mid regions of the earth where sunlight is most abundant, and photosynthesis is higher at higher latitude (especially north latitudes), where there is much less sunlight! Often summarized as 'most of the deep ocean is a desert.'
Notice also green trails off some land areas. These trails are thought to be caused (I think) by prevailing winds blowing nutrients, like iron, off the land and fertilizing the ocean.

        This whole pattern indicates strongly that the limit to photosynthesis in the ocean is very likely the concentrations of 'minerals' in the water, meaning the few atoms of N, P, Si, Mn, Mg, Fe, Ca, etc. needed for life that are not obtainable from the 'cracking' of water and CO2 by photosynthesis. The global variation can't be explained by CO2 variations in water, because wave action keeps CO2 in surface waters in equilibrium with the atmospheric CO2 concentration. This pattern, and experiments showing that iron (Fe) is often the limiting element, has led to the idea of fertilizing the ocean with iron to increase plankton and (hopefully) sequester more carbon.

        A really high resolution chlorophyll world map (ocean only) is available here: (It shows the Bearing Sea off Alaska is especially rich.)

        http://oceancolor.gsfc.nasa.gov/FEATURE/IMAGES/S19972442003273.L3m_CU_CHLO.moll70W.png

Diatom gallery
         Diatoms are a family (5,000) of single cell, photosynthetic algae whose distinguishing feature is spectacularly complex cell wall made essentially out of glass (silica, SiO2). Diatoms are are not bacteria, they are protists. Protists are a family of amazingly complex single (eukaryotic) cells, some like little animals and some like little plants (algae). Diatom algae are large eukaryotic cells implementing the full Z photosynthesis with water the source of electrons and oxygen as a byproduct. Compared to submicron size prochlorococcus, these cells are very large (10 - 150 micron).

        One diatom reference says they are the largest contributor to oxygen in the atmosphere. (Wikipedia says basically the same thing, giving an estimate of 40 - 50% of atmospheric oxygen comes from diatoms.) They also claim diatoms are very efficient photosynthesizers with about 55% of the energy they absorb from the sun is converted into energy of carbohydrate chemical bonds, one of most efficient rates known! (There's an interesting story here, or this claim of 55% efficiency is just plain wrong. The Z diagram analysis shows the maxium efficiency for absorbed photons to glucose energy is about 34%.)

        Here from Wikipedia are some images of diatom silica (essentially glass!) cell walls, known as frustule. When the cells die the glass shells remain, sinking to the ocean bottom to form an ooze. (Chisholm in her 'microbe forest' video showed these diatoms, calling them the charismatic microbes.)

        Love the resolution and detail of this electron microscope picture (colored green) of a 10 micron algae: "Coccolithophores are unicellular, eukaryotic phytoplankton (algae)."  The plates on this one cell eukaryotic marine algae are not silicon dioxide (like above) they are calcium carbonate (CaCO3), which is what makes most seashells are made of. "Coccoliths are composed of calcium carbonate as the mineral calcite and are the main constituent of chalk deposits such as the white cliffs of Dover."

        What looks puzzling for a creature dependent on photosynthesis is how the sun gets in. Maybe the answer is simple, the CaCO3 plates are so thin, they may be translucent.  In fact Wikipedia has this to say about calcite: "Calcite is transparent to opaque. ... A transparent variety called Iceland spar is used for optical purposes." Since this is a (single cell) eukaryotic plant, it must have chloroplasts inside.

Winogradsky columns
        Photosynthesis => photosynthetic bacteria => winogradsky columns?

        It's a logical progression I guess. Learning  about photosynthesis leads to learning about photosynthetic bacteria, which leads to the urge to grow some! I had never heard of a winogradsky column, but somewhere while working on photosynthesis I stumbled onto it. I saw a video and some pictures and it looked pretty easy (but messy), Wikipedia has an article on it too. You can use only home built material, or the Carolina Biological Supply sells a kit that's reasonably priced at 12.

Winogradsky column zones
        The idea of a winogradsky column is this. In the foot or so of the column mud, with a little standing water on top slightly open to the air, two gradients appear. The mud is oxygenated at the top, but oxygen falls off as you go deeper, and an opposite sulfur gradient appears (not sure why, maybe due to the action of the bacteria?), high sulfur at the bottom which decreases as you go up the column. This provides a series of horizontal zones where various types of photosynthetic bacteria (& various other microbes) can find the oxygen and sulfur concentrations they like.

        The references say (full Z) cynobacteria grow in the water. In the mud aerobic photosynthetic bacteria grow near the top (ripping apart water and outputting oxygen), while down near the bottom anaerobic photosynthetic bacteria grow, typically green sulfur and purple sulfur bacteria. These bacteria can fix carbon, but they rip apart sulfur compounds instead of water and output sulfur.

        It's sometimes claimed a winogradsky column is like a section of a pond bed, but that cant' be right, because here the outside of the mud column, even a foot down where there is little oxygen and lots of sulfur, is bathed in light. The photosynthetic bacteria respond by growing in the illuminated outside layer of mud.

        In my homemade column (large bottle) with its somewhat weird nutrients, the water region is very opaque showing under the flash dense structured growth (purple non-sulphur bacteria?), and it also grew a very dense mat on top (hard to photo). In contrast the Carolina water turned and remained a uniform green (probably cynobacteria) and also grew a mat on top, but quite a bit thinner than my homemade column. The white stuff near the bottom of the right colum is some of the calcium carbonate & calcium sulfate that I didn't get fully mixed with the mud.

Purple non-sulphur bacteria?
        One source suggests bright red in the water is likely to be purple non-sulphur bacteria. Wikipedia says their colors range from "purple, red, brown, and orange. The only way to know is to look at the cells with a microscope, but I don't own a microscope.

        -- Purple non-sulfur bacteria bacteria grow in anaerobic conditions, gaining their energy from light reactions but using organic acids as their carbon source for cellular synthesis. So they are termed photoheterotrophs. The organic acids that they use are the fermentation products of other anaerobic bacteria, but the purple non-sulphur bacteria are intolerant of high H2S concentrations, so they occur above the zone where the green and purple sulphur bacteria are found.

Winogradsky summary
        -- The Winogradsky column is a classic demonstration of the metabolic diversity of prokaryotes. All life on earth can be categorised in terms of the organism's carbon and energy source: energy can be obtained from light reactions (phototrophs) or from chemical oxidations (of organic or inorganic substances) (chemotrophs); the carbon for cellular synthesis can be obtained from CO2 (autotrophs) or from preformed organic compounds (heterotrophs).

        -- Combining these categories, we get the four basic life strategies: photoautotrophs (e.g. plants), chemoheterotrophs (e.g. animals, fungi),  photoheterotrophs and chemoautotrophs. Only in the bacteria - and among the bacteria within a single Winogradsky column - do we find all four basic life strategies.
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Photosynthesis cells
        Upon photon energy absorption, the reaction center chlorophyll A molecule is raised to an excited state. The excited chlorophyll A (is oxidized) then donates an electron to a primary electron acceptor, which then transfers the electron to another molecule, starting glucose synthese reaction. The oxidized chlorophyll A is regenerated by an reducing molecule and the process starts over.

        Photosynthesis in purple and green bacteria, such as rhodopseudomonas virdis, takes place in chlorosomes, organelles distributed throughout the cell membrane. The bacteria consists of a number of dyes, including a 'special pair' of bacterio-chlorophyll A molecules. Light adsorption excites the special pair chlorophylls which transfer an electron to a pheophytin molecule. The electron is then transferred to two quinine molecules, Qs, and then Qb. The result of this electron shuffle is charge separation across the cell membrane.
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Raw notes

Chemical formulas from Wikipedia
ATP   Adenosine triphosphate    C10 H16 N5 O13 P3
ADP  Adenosine diphosphate     C10 H15 N5 O10 P2  confirm diagrams show phosphate group = P O3
NADPH     Nicotinamide adenine dinucleotide phosphate          C21 H29 N7 O17 P3
NADP+     oxidized form of NADPH = NADPH + H+ - 2e-      C21 H28 N7 O17 P3

front             photons + 12 H2O  + {18 [ADP + PO3] + 12[NADP+]}  => [18 ATP + 12 NADPH] + 12 H+ + 6 O2
end            6 CO2 + [18 ATP + 12 NADPH] +12H+  => C6H12O6 + {18 [ADP + PO3] + 12 [NADP+]}  + 6 H2O
feedback     {18 [ADP + PO3] + 12 [NADP+]}
---------------------------------
The Z cycle needs to run 2 x 12 = 24 times (48 total photons)
(NADP+ & NADPH) is the mobile electron carrier across the membrane

        -- The net reaction is the transfer of electrons from a water molecule to NADP+, producing the reduced form, NADPH. In the photosynthetic process, much of the energy initially provided by light energy is stored as redox free energy (a form of chemical free energy) in NADPH
        -- electrons and protons go on separate paths. Protons are released from water inside and are joinded by protons pumped in from outside, both then flow outside through ATP generating synthase
        -- initially protons get concentrated 'inside' then as they leak out ADP is converted to ATP
        -- The oxidation- reduction midpoint potential (Em,7) of water is +0.82 V (pH 7). In photosystem II this reaction is driven by the oxidized reaction center, P680+ (the midpoint potential of P680/P680+ is estimated to be +1.2 V at pH 7).
        -- In saturating light a single reaction center can have an energy throughput of 600 eV/s (@ 1.8 ev per photon this is about 333 cycles/sec (reaction center absorbs runs every 3.3 msec using energy from one photon)
        -- with outer pH = 8 and inner pH = 6 (high proton concentration), there is 120 mv across membrane. And the free energy from the high density proton concentration is 12kj/mol x [1 ev/ 96.5 kj/mol] = 0.125 ev (pretty low)
        -- damn -- dark block diagram shows no water output (maybe omitted because the whole thing runs in water??)
**   -- Each molecule of CO2 reduced to a sugar [CH2O]n requires 2 molecules of NADPH and 3 molecules of ATP.
(see equations cont, below figures)
----------------------
Feedback
        This figure is better than most in showing the connections between light and dark reactions. Notice separate hydrogens are shown coming out (next to NADPH), and Pi (what is this exactly) is shown feedback so ADP can be converted to ATP. (So where do the extra oxygen in CO2 go, is part of Pi?)

        -- There is a continuous flow of electrons from water to NADPH.

        -- If 8 red quanta are absorbed (8 mol of red photons are equivalent to 1,400 kJ) for each CO2 molecule reduced (480 kJ/mol), the theoretical maximum energy efficiency for carbon reduction is 34%.

        -- Under optimal conditions, plants can achieve energy conversion efficiencies within 90% of the theoretical maximum. However, under normal growing conditions the actual performance of the plant is far below these theoretical values. The factors that conspire to lower the quantum yield of photosynthesis include limitations imposed by biochemical reactions in the plant and environmental conditions that limit photosynthetic performance. One of the most efficient crop plants is sugar cane, which has been shown to store up to 1% of the incident visible radiation over a period of one year. However, most crops are less productive. The annual conversion efficiency of corn, wheat, rice, potatoes, and soybeans typically ranges from 0.1% to 0.4%

        -- Initially, the O2 released by cyanobacteria reacted with ferrous iron in the oceans and was not released into the atmosphere. Geological evidence indicates that the ferrous Fe was depleted around 2 billion years ago, and earth's atmosphere became aerobic. The release of O2 into the atmosphere by cyanobacteria has had a profound affect on the evolution of life.

        -- Calvin was able to show that the product formed in this CO2 fixation reaction is an organic compound known as phosphoglyceric acid. What had formerly been assumed to be a reduction of carbon dioxide was shown to be a reduction of phosphoglyceric acid. For a reduction of phosphoglyceric acid to the carbohydrate level, the plant has to supply both a reducing agent and a so-called energy-rich phosphate. It is for the production of these co-factors that plants utilize light energy.

        -- New Quantum Secrets of Photosynthesis, 2007 Berkley lab news
        Green plants and certain bacteria are able to transfer solar energy almost instantaneously from light-capturing pigment molecules — for plants, the main photosynthetic pigment is chlorophyll — into reaction centers where solar energy is converted into chemical energy. The energy transfer happens so fast and is so efficient that less than five percent is lost as heat. Basiclly they are saying its a quantized coherent (between molecules) electron vibration that carries the energy.

ATP
        -- With ATP energy is released by hydrolysis (essentially by putting ATP in water where water molecules split into hydrogen (H) and hydroxide ions (OH)) of the third phosphate group . After this third phosphate group is released, the resulting ADP (adenosine diphosphate) can absorb energy by regaining the cleaved (PO3H) group, thus regenerating an ATP molecule. This allows ATP to store energy like a rechargeable battery. (Nanotechnologist are looking into using ATP to replace batteries for implant hearts.)

Glucose model
        Here's (C6 H12 C6) glocose model (d_glocose, but I don't what the d flovor means). Five of the twelve hydrogen (white) are bonded to oxygen (red) with the other seven hydrogen bonded to carbon (green). Here's my totally made up story to 'explain' oxidation of glucose by 6 O2. Six oxygen come in. They steal away the seven hydrogen from the carbon. This causes the structure to collapse or flop around (really precise) allowing the five oxygen that already have one hydrogen to replace their carbon with a hydrogen. The remaining oxygen then scoop up the carbon by breaking the carbon-carbon bonds.

Glucose & efficiency
            -- All plants oxidize glucose exactly the same way
                            C6 H12 O6 + 6  O2 => 6 CO2 + 6 H2O + 686 kcal/mol  x [1 ev/23.1 kcal/mol] = 29.7 ev
It says the energy released by the oxidation of glucose is 29.7 ev. Note this equation is exactly the reverse of the photosynthesis (summary) equation.

        At a theortical efficiency of 34% this requires 87.4 ev of light energy. At 48 photons (full Z) for one molecule of glucose this is 87.4 ev/48 = 1.82 ev per photon. Yes!!!. This means the Z cycle runs 24 times with 48 photons coming in.

**        -- Although many texts list a product of photosynthesis as C6H12O6, this is mainly a convenience to counter the equation of respiration, where six-carbon sugars are oxidized in mitochondria. The carbohydrate products of the Calvin Cycle are three-carbon sugar phosphate molecules, or "triose phosphates," specifically, glyceraldehyde-3-phosphate.

Calvin cycle  (water on left!! doesn't balance in O or H???)
6 CO2 + 12 NADPH + 10 H2O + 18 ATP => 2 C3H5O3-PO32- + 4 H+ + 12 NADP+ + 18 ADP + 16 Pi
or
6 CO2 + 12 C21H29N7O17P3 + 10 H2O + 18 C10H16N5O13P3 => 2 C3H5O3-PO32- + 4 H+ + 12 NADP+ + 18 C10H15N5O10P2 + 16 Pi

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OK I increased ATP/ADP from 12 to 18 for 6 CO2, but now the protons don't balance. Are they pumping around separately somehow? Maybe the 6 extra protons now needed for ATP don't come from water, they come from the proton pump that pumps protons inside. This could be right.
front
 48  photons + 24 electrons + 12 H2O  + 6 protons (pump in) {18 [ADP + PO3] + 12 [NADP+]}  => [18 ATP + 12 NADPH] + 6 O2
end
 [18 ATP + 12 NADPH] +6 CO2 => C6 H12 O6 + {18[ADP + PO3] + 12 [NADP+]}  + 6 protons (released outside) + 6 H2O +24 electrons
feedback     {18[ADP + PO3] + 12 [NADP+] +24 electrons + 6 protons pump around}

if Pi = phosphate has an H, then ATP/ ADP +Pi carries no hydrogen (just energy), but I'm back to the problem of dark reaction outputting O2
[18 ATP + 12 NADPH] +6 CO2 => C6 H12 O6 + {18[ADP + PO3H] + 12 [NADP+]}  3 O2 +24 electrons

Arizona problem gives this as equation for dark reaction. Seems to me the hydrogen don't come anywhere near balacing! Idiots, they have the 6 water on the wrong side!
[18 ATP + 12 NADPH] +6 CO2 + 6 H2O => C6 H12 O6 + {18[ADP + PO3] + 12 [NADP+]}
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Mysteries (1/30/09)
        * Where does the extra oxygen in CO2 go?
        CO2 has twice as many oxygen as carbon, but glucose (multiples of CH2O) has the same number, so where does the extra oxygen go? Output as O2, output as H2O, recycled back (perhaps as part of phosphate in ATP/ADP)?  Nobody talks about this basic point. None of the figure I have seen talk about O2 or H2O coming out of the dark reactions.

        Ans?
        Wiki - Calvin Cycle
        -- The immediate product of the Calvin cycle is glyceraldehyde-3-phosphate (G3P) and water.
        -- If the plant does the above paragraph, then it will have a glucose molecule plus those six extra oxygen atoms, these six extra oxygen atoms are combined with additional NADPH's hydrogens forming six water molecules (H2O). In other words it is the job of all 12 NADPH, which bring in one hydrogen each, to remove the six extra oxgyen as 6 H2O.

                    6 CO2 + 12 H2O => C6H12O6 + 6 O2 + 6 H20

Notice those output water from NADPH are not shown below or on virtually any other diagram! I read in other places that showing 6 H2O on the left and 12 H2O on right is the "old view" of photosynthesis!!

                --- RPI lecture seems to say that water comes out (taking away the excess oxygen) in this simple, photosynthesis summary, but this may just result from the simplification. (alternative explanation is that ATP carries no hydrogen, because the extra hydrogen is hidden in phosphate PO3 or PO3H)  "It turns out that the overall reaction of photosynthesis takes place in two steps.  In the first step, the oxygen in water is oxidized by the light energy:"

             CO2 + H2O  =>    (CH2O) +O2  (requires photons, hv)                                 (1)
but in more detail
           2 H2O             =>     O2 + 4 [H.]     (requires photon energy)                             (2)

Here, [H.] represents a reducing agent. In the second step, the [H.] reduces the carbon in CO2:

           4 [H.] + CO2   =>   (CH2O) + H2O                                                                 (3)

        When one adds these two reactions together, the overall reaction (1) results. [H.], the reducing agent, is an "intermediate" in the overall reaction.  It looks like two H2O molecules are needed in reaction (2) but then you get one of them back in reaction (3)

Equation balances
                A lot of equations published don't seem to balance. Specifically they often have H2O on left side of dark reactions.
            Possible Ans
                    - ATP is energy transporter
                    - NADPH is electron/hydrogen carrier molecule
                    -  NADPH essentially  provides  the hydrogen which are part of the glucose molecule.

***            maybe Wiki is wrong?, and ATP & (ADP + Pi) have same hydrogen.  From figure this could be right. Does the extra H in the equation hides in the phosphate group (PO3H).    Check

        * Protons flows
        How are protons to be reprented in equations? Physically some protons enter into the high concentration 'inside' directly from water disassembly while others get pumped in from 'outside'. What's the ratio?. Then both get pumped out through the ATP making syntase complex. And is a fraction of the flow taken up to go into ATP?

        * Local energy balances
        While some references give an energy balance globally, showing it is consistent with light energy, virtually never are local energy balances given, which would show how they can thermodynamically proceed.

        Specifically, what is the energy balance on the thermodynamically difficult step of oxidizing water? The problem here is assigning energy values to the intermediate outputs. More specifically what is the energy balance of the light reactions and the dark reactions? I have never seen it.

        * Dark to light feedback terms
        While it's qualitatively described, there is little on it quantitatively. My best reference does say that for each CO2 processed two NADPH and three ATP are needed, which if accurate is a strong hint.

        * Number of photons
        Specifically, for a molecule of glucose, how many times does the basic cycle run, how many photons are needed and how many electrons transferred. From the rare refenrece that discusses this the most likely candidates seem to be 24 turns of the Z cycle and 48 totol photons.

        * Efficiency
        I would like to see more detail on efficiency, meaning glucose energy out vs light energy in. Most references say nothing. My best reference says it's 34%, but with little supporting detail about the assumptions and conditions.

---------------------------------
Average bond energies
                   kcal/mol                        kj/mol
        O-H         110                           460
        O=O         116 (2 x 58)            485
        H-H         103                            431
        C=O *      187 (2 x 93.5)         782
        C-O         78                              326
        C-H         98                              410
        C=C         145 (2 x 72.5)          607
        C-C         80                             335
        C-N         65                               272
        (* as found in CO2)
------------------------------

*** Progress  whoops the numbers look backward, O2 is higher than water bonds
          The explanation may be that the final state is O2 @ 498 kj/mol. (498 - 459)/1300 x 13.6 ev = 0.41 ev which doubled is the 0.8 V value usually quoted at "mid point". Not sure about the x2, but still this looks like it probably why the energy to oxidize water with O2 as a byproduct does not take that much 'net' energy. Depends on Mn complex being an efficient catalyists (data seems to indicate it stores up the energy of four photons and then pulls apart 2 H2O yielding four protons and one O2. This makes a lot of sense from an energy perspective, because the electrons falling together in O2 reduce the net energy needed to split water by about a factor of 10 (or 5)!

        The energy of a 680 nm (red) photon is 1.8 ev. The potential of P680, the highest oxidizating potential (or high positive redox potential) "in any living organism" is 1.1 ev (confirmed value). (One ref shows ev for change of state in the Mn water breaking complex as 5% to 10% of the 459 kj/mol, or 1/4 to 1/2 ev)

        -- The capture and conversion of solar radiation by photosynthetic organisms directly or indirectly provides energy for almost all life on our planet. About 2.5 billion years ago a remarkable biological “machine” evolved known as photosystem two (PSII). This machine can use the energy of visible light (actually red quanta of 1.8 eV) to split water into dioxygen and “hydrogen”. The latter is made available as reducing equivalents, ultimately destined to convert carbon dioxide to organic molecules.

        In PSII, the “hydrogen” reduces plastoquinone (PQ) to plastoquinol (PQH2). The water splitting process takes place at a catalytic centre composed of 4 Mn atoms and the reactions involved are chemically and thermodynamically challenging. The process is driven by a photooxidised chlorophyll molecule (P680•+) and involves electron/proton transfer reactions aided by a redox active tyrosine residue situated between the 4 Mn cluster and P680. The P680•+ species is generated by light induced rapid electron transfer (a few picoseconds) to a primary acceptor, pheophytin a, before being transferred to PQ acceptors.

        -- Redox potential of P680 must be sufficiently positive in comparison with that of H2O/O2. H2O/O2 reversible potential is given as
                            E = +1.23V  - 59 mv x ph
@ ph = 5.5         E = +1.23 V - (59 mv x 5.5)
                                = +1.23 V - 0.325 V
                                = 0.91 V
authors argue to get the reaction to drive to O2 "overdrive voltage" of about 0.3V is needed, so P680 would need to supply 0.91V + 0.3 V = 1.21V, which they say is problem, because its higher than the know value of 1.1 V. The give an accepted value for "water oxidation" = 0.82 V

        -- mid point oxidizating potential of water = 1.2 ev
        -- 1.2 ev per electron transferred <=> 27.7 kcalmol   x  [436 kj/mol/104 kcal/mol]
                                                                 <=> 116 kj/mol  amazingly this checks
                                                                            [116kj/mol/1,300 kj/mol] x 13.6 ev = 1.21 ev

         -- Efficiency of photosynthesis is calculated. Starts with 1.2 V uphill change through electron transport chaing (no mention here of water oxidation??). And they assume it takes 2 photons of roughly 1.8 ev each. Further they assume that this region of the suns spectrum captured by the chlorophylls is about 47% of its power.
                        Efficiency (max) = [1.2 ev/ (2 x 1.8 ev)] x 47%
                                                      = 15%     (books writes 13% !!)

        -- (summary) Primary electron donor of photosystem II is P680, P680 transfer an electron to pheophytin (Phe). P680 midpoint oxidizing potential is very high at 1.2 ev (other say 1.1 ev), so it can drive the oxidation of water which requires 0.8 ev.

        -- P680+ and Phe- is referred to as "primary radical pair" and has an electrochemical potential of 1.7 ev (OK, red photon as 1.8 ev)

        --                         2 H2O <=> O2 + 4H+ + 4e- @ ph =7
                  has a reversible midpoint potential of +0.8V vs SHE (standard hydrogen electrode)
                    ("in practice the actual effective oxidizing potential is higher than 0.8V")

        -- Photosynthetic water oxidation, where water is oxidized to dioxygen, is a fundamental chemical reaction that sustains the biosphere. This reaction is catalyzed by a Mn4Ca complex in the photosystem II (PS II) oxygen-evolving complex (OEC): a multiprotein assembly embedded in the thylakoid membranes of green plants, cyanobacteria, and algae. The mechanism of photosynthetic water oxidation by the Mn4Ca cluster in photosystem II is the subject of much debate, although lacking structural characterization of the catalytic intermediate. (Our) results show that Ca is not just a spectator atom involved in providing a structural framework, but is actively involved in the mechanism of water oxidation and represents a rare example of a catalytically active Ca cofactor.

** Artificial photosynthesis
       -- (Standford Univ) Direct conversion of solar energy into chemical fuels may solve one of the principal shortcomings of conventional solar technologies – the intermittent nature of solar energy – by providing a medium for energy storage and distribution. The use of sunlight to produce hydrogen from splitting water by mimicking natural photosynthetic processes is an ideal solution to this challenge. However, no water splitting system has yet been demonstrated that produces hydrogen cheaply enough to compete with fossil fuels. Electrolyzer systems that are currently used in combination with photovoltaic cells are too expensive and not scalable to the level needed to make them a significant component of global energy production.

        The concept underlying this project involves using sunlight directly to produce hydrogen and oxygen in a system that absorbs light and produces charges to drive separate water reduction and oxidation half-reactions. The system consists of a conductive photocatalytic membrane composed of two photoactive inorganic electrodes with bandgaps chosen to maximize sunlight absorption (1.1-1.4 eV) and with energy levels generating an overall separation potential exceeding 1.23V to allow water splitting.

        Since O-O bonding is most likely the main barrier to water oxidation (??), compounds that catalyze the oxidation of water to either oxygen or hydrogen peroxide will be the principal targets of this investigation

Glucose vs cellulose
        Carbohrdrates (multiples of C H2 O), like glucose (C6 H12 O6), are food or fuel easily oxidized to yield energy. What is a food, really?  My initial thinking is that 'high energy' food type molecules must be loosely put together, some of the valence bonds must be far from nucleii, easily broken, so when oxygen comes by these electrons can reconfigure and fall into the nice energy well oxygen provides.

        The highest level formula for photosynthesis

            n CO2   +   n H2O   +   energy ==>    Cn H2n On  (carbohydrate) +   n O2

From the formula it might be guessed that the nO2 comes from the CO2, but this is wrong. All the O2 comes from split water at the front end of the process. At the back end of the process the hydrogen freed from water is combined with the carbon and oxygen from CO2 to make carbohydrate (multiple of C H2 O).

Is something seems funny here?
        While the formula above balances, it doesn't seem consistent with (my current) understanding of how the photosynthesis works. For example with n = 2, two water come in, releasing one O2, and four H are now available to migrate across the membrane to combine with two CO2, but now the ratio is wrong for a carbohydrate. We have two carbon, four hydrogen and and four oxygen, we have an extra O2 after the carbohydrate is made. Does this mean that oxygen is coming out of the back end (dark reactions) too, or perhaps some (or all) of this O2 is used for resperiration.

Good reference on carbohrdrates and cellulose.

        http://www.cem.msu.edu/~reusch/VirtualText/carbhyd.htm
 

        -- Over half of the total organic carbon in the earth's biosphere is in cellulose.
        -- Cotton fibres are essentially pure cellulose.

Dark reactions
        This section is early notes where I am trying to decode references to figure out how the dark reactions work and getting very confused. I did later get a good handle on the steps of the dark reactions (see my block diagram), and how the dark reactions are powered.
-----------------------------------
        I've concluded it's basically impossible to really understand the dark reactions, where CO2 is converter to carbohydrates (sugar). Why, because it's horribly complicated! Take a gander at the detail in this nine page dark reactions (calvin cycle) reference from RPI:

        http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/dark.htm

        -- Encyclopedia Britianna photosynthesis intro
        It would be impossible to overestimate the importance of photosynthesis in the maintenance of life on Earth. If photosynthesis ceased, there would soon be little food or other organic matter on Earth. Most organisms would disappear, and in time the Earth’s atmosphere would become nearly devoid of gaseous oxygen. The only organisms able to exist under such conditions would be the chemosynthetic bacteria, which can utilize the chemical energy of certain inorganic compounds and thus are not dependent on the conversion of light energy.

        -- Fluorescence: Light (photons) emitted when an electronically excited molecule decays to a lower state of the same multiplicity.  About 3-6% of the light absorbed by plants is dissipated in this way.

        --- see Brief Review of thermodyamic calculations here. Applies  'reduction potentials' to light reactions. (O2 + 4 e- +4 H+ => 2 H2O) Gets   +.815 V for water oxidizing and -.324 V for NADPH being reduced (NADP+ +H+ + 2e- => NADPH). Combined (-.324 -.815 = -1.139 v that light must supply)
         http://www.rpi.edu/~bellos/photosynthesis.htm
        -- PSII oxidizes water
           PSI reduces NADP+
            electrons flow from low to high reduction potential

        -- key light ratios

        -- There are many other (besides ATP) activated carriers in organisms, such as: NADH, NADPH, FADH2, Acetyl CoA, Carboxylated biotin, S-Adenosylmethionine, and Uridine diphosphate glucose. The high energy groups which they carry are respectively: electrons, hydrogen, electrons, acetyl group, carboxyl group, methyl group, and glucose. (saying NADPH carries hydrogen)

ATP & ADP
        ADP and ATP structures from Wikipedia

Phosphate (wiki)
           Glucose                               C6 H12 O6
            Glucose 6-phosphate         C6 H13 O9 P    = C6 H12 O6 + PO3H
                    This compound is very common in cells as the vast majority of glucose entering a cell will become phosphorylated in this way. The major reason for the immediate phosphorylation of glucose is to prevent diffusion out of the cell. The phosphorylation adds a charged phosphate group so the glucose 6-phosphate cannot easily cross the cell membrane.

    G3P =  Glyceraldehyde 3-phosphate        C3 H7 O6 P    =1/2 [C6 H12 O6] + P03H
                This is the actual output of the Calvin cycle (wiki) G3P is generally considered the prime end-product of photosynthesis
wiki balance
            6 CO2 + 6 RuBP (+ energy from 12 ATP and 12 NADPH) => 12 G3P (3-carbon)
            10 G3P (+ energy from 6 ATP) => 6 RuBP (ie starting material regenerated)
           2 G3P => glucose (6-carbon)

my reduction
            6 CO2 + (+ energy from 12 ATP + 6 ATP for regen and 12 NADPH) => 2 G3P (3-carbon)
           2 G3P => glucose (6-carbon)
                Yikes why are the two P03H not shown as outputs ! It doesn't. Yes the two phosphates takes away the extra six oxygen, but also 2P and 2H. Where do they come from? good grief

        --  Chemists short hand
                        * A phosphoanhydride bond of ATP (~P) is cleaved.

        -- From detailed RPI biomolecular site
        http://rpi.edu/dept/bcbp/molbiochem/MBWeb/mb2/part1/dark.htm

        Summary of Calvin Cycle, omitting compounds that are regenerated (Glyceraldehyde-3-phosphate is the three carbon output of the calvin cycle)

solving for Pi (using Wiki formula and assuming ATP - ADP = Pi)
          3 CO2 + 9 ATP + 6 NADPH => glyceraldehyde-3-phosphate + 9 ADP + 8 Pi + 6 NADP+

         8 Pi = 3 CO2 + 9 ATP + 6 NADPH  -[C3 H7 O6 P + 9 ADP + 6 NADP+]
                 =  + 9 Pi + 6 H  -  H7 P
            Pi = HP   (no oxygen!!)   all the O from CO2 is in the sugar! so even though on a quick look
                                        it seems as if a photphate has been added to the sugar, it doen't have enough sugar to accomodate 3 O from phosphate and 6 O from oxygen, or from other point of view half the O in sugar come from CO2 and where does the the other 3O go!! (there is not the 6H needed for water output, are they possibly picked up from solution?)

        -- The immediate product of the Calvin cycle is glyceraldehyde-3-phosphate (G3P) and water. Wiki pretty clear. Two G3P or F6P. Hexose isomerase converts about half of the F6P molecules in to glucose-6-phosphate.(C6 H12 O6 + PO3H) These are dephosphorylated and the glucose (C6 H12 O6)  Give summary formula as (text says water is output, then show it as input!)
        3 CO2 + 9 ATP +6 NADPH  +  5 H2O => C3 H5 O3-PO3 + 2 H+  + 9 ADP + 8 Pi + 6 NADP+
compare
        3 CO2 + 9 ATP + 6 NADPH => glyceraldehyde-3-phosphate + 9 ADP + 8 Pi + 6 NADP+
                                                                       C3 H7 O6 P Wiki = 1/2 (C6 H12 O6) + PO3H
my fix to above is to add 6 more NADPH/NADP+ to bring in 6 H more then combine with extra O3 into 3 H2O as output

        -- From Principles of Modern Microbiology  by Mark Wheelis - 2007 Amazon (see figure above)
        3 CO2 + 9 ATP +6 NADPH  +  [3 H2O ?? (hidden)] => C3 H4 O3-PO3H + 9 ADP + 6 Pi + 6 NADP+
I balanced this all around the loop it has unbalnces in O, H and Pi (Pi unbalance is particularly blantant, Unforturnately no hint about where the oxygen)

        -- MIT molecular biology text book dark reaction summary. Another different equation and of course, unbalanced. This equation was in terms of glucose and had six water as input!

    -- An excellent photosyntheis ppt slides is below. It compares the different types of photosynthesis. Great graphics, best I have ever seen. The slides (MetabolicDiversity.ppt) appear to have been prepared by 'Pearson Education' (or Pearson Benjamin Cummings) and are being used by various colleges. I found two slightly differnet versions of the same slides.

         Metabolic Diversity: Phototrophy, Autotrophy, Chemolithotrophy ..  (Yonsei Univ in Korea)
                    (Brook Biology of Microorganisms, Chap 20)
                    MatabolicDiversity.ppt     and      CH20 PPT.ppt
================================================================================
Misc photosynthesis topics
Photosynthesis in very dim light (8/10)
        I saw an interesting story on History channel about researchers exploring small shallow lakes in Antarctica that are permanently covered in ice. They melt a three foot dia hole through 15 feet of ice and then go diving in. Researchers on camera said they originally expected to find no life, because the limit on low light photosynthesis was thought to be about 1% of sunlight, and light levels were lower than that.

         But in fact in lake after lake they find thick microbial mates that they believe are photosynthesizing at light levels of about 0.1% of sunlight! There is no other life in the lakes but microbes (no fish, no insects, just bacteria), so the bacteria are not grazed on by animals and have evolved some unique structures.

Photosynthesis at very low CO2 levels (4/16)
        Ice core data shows CO2 levels during ice ages varies between about 180 and 280 ppm. The low end is the 85k years or so of  high ice cover, and the upper end the 15k or so years of interglacials. At 180 ppm a lot of plants do not do well. The reason is that are 'starved' of carbon. One professor thinks a reason farming did not begin until the beginning of the current interglacial is that the CO2 levels would not support it, plants were too spindly to be worth cultivating.

        However, C4 plants are another matter. They have a front end CO2 concentrating mechanism that is very effective. Oliver Morton in his book 'Eating the Sun' says that some C4 plants (and microbes too)can survive down to CO2 levels as low as 10 ppm.

Other ways bacteria fix CO2 into glucose
        Found a Mexican paper that had a nice set of photosynthetic glucose synthesis equations. All these bacteria use light to produce one molecule of glucose. In most cases the 6C being fixed comes from 6CO2, the exceptions being #6 where 2C come from CO2 and 4C from methanol and #9 where its 6CO2 is not an external input.  Various substances can be oxidized ('eaten') by the energy of light to provide the hydrogen and excited electrons to run the electron transport chains. Cyanobacteria (#1) are the only bacteria running classic Z cycle photosyntheis where water is the source of the hydrogen and electrons. It outputs oxygen and has the highest thermodynamic efficiency. In #2 the equation is very similar, but the source of the hydrogen and excited electrons is H2S (hydrogen sulfide) which gets oxidized to sulfur.

1) Cyanobacteria (and plants)
                                    6 CO2 + 12 H2O => C6H12O6 + 6 H2O + 6O2                      2,880 Kj/mole        (680 nm)              (Z cycle)

2) Sulfur purple bacteria and sulfur green bacteria (young bacteria)
       6 CO2 + 12 H2S (hydrogen sulfide) => C6H12O6 + 6 H2O + 12S                       430 Kj/mole        (890 nm)

3) Sulfur purple bacteria (old bacteria)
       6 CO2 + 6 H2O + 3 H2S (hydrogen sulfide) => C6H12O6 + 3 H2SO4                 745 Kj/mole        (890 nm)

4) Sulfur purple bacteria and sulfur green bacteria
    6 CO2 + 15 H2O + 3 Na2S2O3 (sodium thiosulfate) => C6H12O6 + 6 H2O + 6NaHSO4  621 Kj/mole    (870 nm)

5) Non-sulfur purple bacteria and non-sulfur green bacteria
    6 CO2 + 12 CH3CH2OH (ethyl alcohol) => C6H12O6 + 12 CH3CHO (acetaldehyde) + 6H2O       585 Kj/mole    (870 nm)

6) Non-sulfur purple bacteria and non-sulfur green bacteria
          2 CO2 + 4 CH3OH (methanol) => C6H12O6 + 2 H2O                                       71 Kj/mole        (870 nm)

7) Non-sulfur purple bacteria
                   6 CO2 + 12 succinic acid => C6H12O6 + 6 H2O + 12 fumaric acid     1,067 Kj/mole   (870 nm)

8) Non-sulfur purple bacteria
                      6 CO2 + 12 malic acid => C6H12O6 + 6 H2O + 12 oxalacetic acid    609 Kj/mole   (870 nm)

9) Heliobacteria
       3CH3COOH (acetic acid) + 6 H2O => 6 CO2 + 12 H2 (hydrogen gas)
             6 CO2 + 12 H2  (hydrogen gas) => C6H12O6 + 6 H2O                                    321 Kj/mole   (798 nm)

         http://mdpi.org/entropy/papers/e9040152.pdf

Does calvin cycle run at night?
        Maybe not, but have not researched this --
Ans: during day (only) because NADPH needed.

        Some references specifically say that light is needed to activate or catalyze some calvin reactions, implying that the calvin cycle only runs (or only runs well) during daytime. A reference on storage of CO2 as malate says the stored CO2 is used by calvin cycle during daytime. If NADPH and ATP can't be stored, then calvin cycle can only run during day while they are being made.

        -- Carbon dioxide fixation is catalyzed by RuBP carboxylase (rubisco).
        -- Rubisco makes up 20 - 50% of the protein in chloroplasts. It acts very slowly, catalyzing 3 molecules per second. This compares to 1000 per second for typical enzymatic reactions. Large quantities are needed to compensate for its slow speed. It may be the most abundant protein on earth. (This reaction requires energy from ATP and electrons from NADPH.)
        -- For each six CO2 molecules that enter the cycle one glucose molecule is produced.
        -- About 30% of the energy available in ATP and NADPH is finally present in the glucose produced.

        energy levels --- multiple due to electronic (pumped to different orbits)
                                    vibrational (electon moves instantly when photon hits but nucleaus is slow
                                               to move. This causes transient polar (electrostatic forces) and
                                                vibration (there are two other types of energy the electron can have too
                                                        like rotational?)
                                --- there are inefficiencies in the process. For example how far away was the antenna
                                                molecule was hit. Some excess energy can be dumped, with emission or heat
                                --- the measured photoshnthesis response shows some broad peaking
                                --- there are also polarization/directional effects (aligment of the photon e field
                                               with certain axis of the photopigments.
                                    (saw no mention of damping per see)

        -- The entire cycle of events can run at 200-300 times per second, yet even on a bright day, the reaction center electron donor only absorbs a photon of sunlight per second. So the reaction center in plants is surrounded by 200-300 absorber molecules that make up the light harvesting system. If this works with perfect efficiency—and it does—then the photosynthetic system can run optimally.

        -- (P680 pulling four electrons from water) The S state cycle S0 ® S4 is driven by quaternary, light-induced transmembrane electron transfers from P680 to QA. P680+ oxidizes step by step via tyrosine YZ, a manganese dimer up to S3. The oxidized YZ has been hypothesized in Ref. 35 to be the fourth oxidizing equivalent in S4 that triggers the electron transfer from the two oxo-atoms to the four oxidizing equivalents by its electric field.
--------------------------------------------------
Osmosis overview
            Inside a cell there is water with stuff (larger molecules) dissolved in it. The small water molecule is able to diffuse though the cell wall and membrane. If the cell is placed in an water with less stuff dissolved in it (it doesn't matter what the stuff is!) and the pressure inside the cell is the same as outside, what happens is that net water molecules travel into the cell raising the pressure of the cell against its cell wall.

        Water diffuses into the cell, because inside the cell fewer water molecules per sec hit the barrier than on the outside since inside the water molecules are spaced further apart due to the stuff dissolved in it. (From an entropy point of view the water moves to try an equalize the solute concentrations.) As water diffuses in, the pressure inside the cell builds up, eventually stopping the net inflow of water.  (The higher pressure must either increases the speed of the water molecules or the number of water molecules/sec hitting the barrier.)

        Osmotic pressure a very important to cells. For example, it builds up high pressure in the cells of plant leaves giving the leaf structure. If you drink sea water, (apparently) there is more salt in the sea water than solutes in your cells, so water diffuses out of your cells. Reverse osmosis, which is used to desalinate sea water, is simply appling pressure higher than the osmotic pressure to cause water to diffuse from the side with lots of solutes to the side with fewer.

    -- The separation of an electronic charge across the membrane creates an electrical potential — a microscopic cellular battery — that can be used to carry out the chemical work of the cell.

        -- In 1988, Hartmut Michel and his colleagues at the Max Planck Institute in Germany won the Nobel Prize in chemistry for solving the molecular structure of the reaction center from a lake-dwelling bacterium.

        --  When the reaction center is photoexcited, the topmost “special pair” of chlorophyll molecules (red) lose a single electron, which appears on the green molecule (pheophytin) within a few trillionths of a second. The electron is then very rapidly transferred to the yellow molecule labeled Q (quinone), which completes its transit across the photosynthetic membrane.  (Normally electrons are paired so their magnetic moment (due to spin) cancels. Electron magnetic resonance, or EMR, spectroscopy work at Northeastern is being used to track single electrons during photosynthesis.)

        -- Within the leaf, a molecule of chlorophyll absorbs the energy, knocking one of its electrons into an excited state. A ring-shaped molecule called a quinone transfers the excited electron away from the chlorophyll and then shepherds it to a second quinone. The plant has now stored the sunlight energy in the electric field between the negatively charged quinone and the now positively charged chlorophyll -- a tiny battery, in other words.

        --  (Electrons can lower their energy by pairing {cancelling magnetic moment??} This explains a lot of bonding and chemistry) --- Two atoms of hydrogen, each with one proton and one orbiting electron, will join into a dumbbell-shaped hydrogen molecule. With the two electrons now paired, the molecule has a lower energy state than the two separate hydrogen atoms. For this reason molecules with an odd number of electrons are highly unstable, likely to react with the first molecule that passes by.
==========================================================================
Cell membranes (Wikipedia excerpts)
        The cell membrane is a semipermeable lipid bilayer common to all living cells. The movement of substances across the membrane can be either passive, occurring without the input of cellular energy, or active, requiring the cell to expend energy moving it across the membrane. For determination of membrane potentials, the two most important types of membrane ion transport proteins are ion channels and ion pumps.

        Ion channel proteins create paths across cell membranes through which ions can passively diffuse without expenditure of energy. Most cells have potassium-selective ion channel proteins that remain open all the time.

        While most descriptions of the genesis of membrane potential begin with the concentration gradients already in place, as if by magic (therefore ignoring the principle of conservation of energy), these gradients can only be created at the expense of putting energy into the system. This work is done by the ion pumps (ion transporters or exchangers) and generally is powered by ATP.  The resting membrane potential is not an equilibrium potential as it relies on the constant expenditure of energy (for ionic pumps as mentioned above) for its maintenance.???

        One of the key roles of the membrane is to maintain the cell potential. In most cells the resting potential has a negative value, which by convention means that there is excess negative charge inside compared to outside. For most animal cells potassium ions (K+) are the most important for setting the resting potential. Due to the active transport of potassium ions, the concentration of potassium is higher inside cells than outside. (Note, the high concentration of positive potassium ions inside the cell is (initially) charge balanced by immobile?? negative (An-) ions (free electrons?)

        The outward movement of positively-charged potassium ions is due to random molecular motion (diffusion) and continues until enough excess positive charge accumulates outside the cell to form a membrane potential which can balance the difference in concentration of potassium between inside and outside the cell. 'Balance' means that the electrical force (qE) that results from the build-up of ionic charge increases until it is equal in magnitude but opposite in direction to the tendency for outward diffusive movement of potassium.

        The typical membrane potential of a cell arises from the separation of potassium ions from intracellular immobile (meaning unable to move through the ion channels?) anions across the membrane of the cell. If the membrane were to become permeable to a type of ion that is more concentrated on one side of the membrane, then that ion would contribute to membrane voltage because the permeant ions would move across the membrane with net movement of that ion type down the concentration gradient.

        (Wikipedia figure shows) K+ diffusing out of the cell. (initially inside of cell is neutral with as many K+ and An- ions) As positive charge builds up outside the membrane and negative (due to loss of K+) inside the membrane an E field pointed inward develops. This E field pushes K+ ions back toward the inside of the cell. Steady state is reached when the E field is strong enough to bring (net) K+ diffusion across membrane to a halt.  (energy is transferred from the concentration gradient to the electrical energy (voltage) across the membrane capacitance).

What's the purpose of the cell potential?
        While cells expend energy to transport ions and establish a transmembrane potential, they use this potential in turn to transport other ions and metabolites such as sugar. (The cell E field will pull any positive ion from the outside into the cell if the cell provide an open channel for the ion.)
------------------------------------
        -- Chloroplasts are organelles found in plant cells and eukaryotic algae that conduct photosynthesis.
                            (in other words there are no chroroplasts in photosynthetic bacteria)

        -- "Soil microorganism utilize the strongest electron acceptors available in order to obtain the maxium energy from their food." Oxygen (O2) is best, then nitrate (No3), manganese, iron, sulfate, "and in extreme cases reduce water to H2".

        -- Huber won the Nobel prize for chemistry in 1988 for helping to explain how photosynthesis works at the molecular level. Here's the link to his Nobel lecture, 'A structural basis for light energy and electron transfer in biology':
        http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=401142&blobtype=pdf

        -- In 1886 Boltzman wrote the reactions of photosynthesis are a complete mystery to us

        -- The harnessing of light to accomplish the splitting of water was arguably nature's most successful experiment in biological innovation. It enabled global proliferation of oxygenic photosynthesis and created the biogeochemical cycles of oxygen and carbon on earth.
 

Electrochemical gradient
        -- electrochemical potential is the mechanical work done in bringing 1 mole of an ion from a standard state to a specified concentration and electrical potential.

        --  In mitochondria and chloroplasts, proton gradients are used to generate a chemiosmotic potential that is also known as a proton motive force. This potential energy is used for the synthesis of ATP by oxidative phosphorylation

        - An electrochemical gradient has two components. First, the electrical component is caused by a charge difference across the lipid membrane. Second, a chemical component is caused by a differential concentration of ions across the membrane. The combination of these two factors determines the thermodynamically favourable direction for an ions movement across a membrane.

        -- With respect to a cell, organelle, or other subcellular compartments, the inclined tendency of an electrically charged solute, such as a potassium ion, to move across the membrane is decided by the difference in its electrochemical potential on either side of the membrane, which arises from three factors:
                * difference in the concentration of the solute between the two sides of the membrane
               * charge or "valence" of the solute molecule
                * difference in voltage between the two sides of the membrane (i.e. the transmembrane potential)

        -- A solute's electrochemical potential difference is zero at its "reversal potential". The transmembrane voltage to which the solute's net flow across the membrane is also zero. This potential is predicted theoretically either by the Nernst equation (for systems of one permeant ion species)  In physiology the Nernst equation is used for finding the electric potential of a cell membrane with respect to one type of ion.

        -- The potential level across the cell membrane that exactly opposes net diffusion of a particular ion through the membrane is called the Nernst potential for that ion.

        -- Nernst equation for cell membrane voltage. Note 'ln' arises because the ratio of oxidized to reduced molecules, [Ox]/[Red], is equivalent to the probability of being oxidized (giving electrons) over the probability of being reduced (taking electrons). And these are describe with Botzmann statistics  e^-(volt treshold/KT) . Also  -- Dividing by e converts from chemical potentials to electrode potentials, and (kT/e) = (RT/F)

                            E = E0 - (RT/nF) ln (reduced concetration/oxided concetration)
                                        + (59mv/n) log (ion outside of cell/ion inside of cell)

Electrons
       --  Two water molecules are oxidized by four successive charge-separation reactions by photosystem II to yield a molecule of diatomic oxygen and four hydrogen ions; the electron yielded in each step is transferred to a redox-active tyrosine residue that then reduces the photoxidized paired-chlorophyll a species called P680 that serves as the primary (light-driven) electron donor in the photosystem II reaction center.

        -- The oxidation of water is catalyzed in photosystem II by a redox-active structure that contains four manganese ions; this oxygen-evolving complex binds two water molecules and stores the four oxidizing equivalents that are required to drive the water-oxidizing reaction. ( Photosystem II is the only known biological enzyme that carries out this oxidation of water.)

        -- Through photosynthesis, sunlight energy is transferred to molecular reaction centers for conversion into chemical energy with nearly 100-percent efficiency. .. suggests that long-lived wavelike electronic quantum coherence plays an important part in this instantaneous transfer of energy. (This is brand new with reference to an April 07 Nature article)

cell membrane
        http://en.wikipedia.org/wiki/Membrane_potential
=================================================================================
Perspective on ATP energy
        The overview (from below) is that ATP does not look like it's suitable to provide substantial long term storage to help run the Calvin cycle all night. Each ATP carries relatively little energy, and any sustained energy flows using ATP require it to continually be regenerated. The lifetime of a typical ATP molecule in the human body is only about 1.5 min, and it drops to seconds when tissue is rapidly metabolising.

        A detailed UK college biochemistry lecture (extracts below) provides some interesting perspective on the energy ATP provides in cells. In most body cells ATP is continually being regenerated (by mitochondria) using energy extracted from the oxidation of glucose. ATP molecules diffuse around the cell available locally to power a wide variety of cell reactions. Of course, ATP is used in photosynthesis too, the light reactions generating ATP to help power the Calvin cycle make glucose from CO2 and hydrogen freed from water.

        -- ATP is a very common metabolite and is present in high concentration (~6mM) in most cells.

        -- ATP is often described as a 'high energy' compound, but hydrolysis of ATP to ADP or AMP yields only modest amounts of energy. Although small, this additional energy tips the balance and is sufficient to drive many unfavourable processes in the required direction.

        In general, living cells avoid big changes in free energy, because enzymes are only held together by weak hydrogen bonds and hydrophobic interactions, and it is difficult to build them strong enough to withstand the thump from a violent reaction. The energy released from ATP hydrolysis is not much bigger than the peaks of thermal energy that are constantly rattling molecules around at body heat. But for reactions that are already close to equilibrium, the extra input from ATP is still enough to bias the process in the desired direction. Rather than one big heave at infrequent intervals, living cells use ATP to apply an endless series of little nudges at every point where the flow needs a boost.

        Allowing for a few leaks and overheads, complete oxidation of a molecule of glucose would yield about 25 - 30 molecules of ATP and the energy recovery would be about 50%. You may see slightly larger figures in some textbooks, but I think these are a bit optimistic. If glucose is worth a fiver, then each ATP is worth about 10p

        Calculating the lifetime of ATP is a bit misleading. The ratio of ATP:ADP in the cytosol is typically 200:1 or more, and it is the lifetime of ADP rather than ATP which is critical for success. When running for your life, what matters is the maximum possible reaction flux. Diffusion rate is proportional to concentration, so the real bottleneck is returning the "empties" for recycling. The minuscule amount of ADP in working muscle has only milliseconds to get back from the contractile proteins to the mitochondria for reconversion into ATP.

        Units are not standardized --- For energy about half the references use [kcal/mol] and half [kj/mol], whereas I would argue the natural unit (best unit) for work on photosynthesis is the [ev]. You can't read the literature without remembering [1 ev = 23.1 kcal/mol = 96.5 kj/mol] and keeping a calculator handy.

        Names are not standardized  --- Wikipedia in an article on the enzyme that adds [H+ and 2e-] to NADP+ to make NADPH, which is a key biological energy and hydrogen carrying molecule, has this incredible tidbit. After giving the chemical name of the enzyme, it lists other names for it "in common use", and there are 13 more names. That's right, a key enzyme in photosynthesis and respiration may be described in the literature by any of 14 different names! It's hard not to call biologists idiots when you come across something like this.

        One of the handful of pathways by which microbes fix CO2 is called variously: Reverse krebs cycle, or reductive krebs cycle, or reverse TCA cycle (reverse tricarboxylic acid cycle), or reductive carboxylic acid cycle, or reverse citric acid cycle. (For some reason biologist often use 'reductive' for 'reverse'.) Good grief!

        I can only conclude that biologists (apparently) don't have international conferences like electrical engineers and physicists do to standardize things.

        There are still more problems. In introductory materials tables of 'standard' bond energy and redox potentials never seem to agree. Each reference is likely to be different from other references by a few percent. Technically there are probably good reason why values vary (different conditions), but the lack of an agreed upon standard values just makes life difficult for students for no good reason. And equations are sometimes given that are not balanced. (I found out later there apparently is a certain sloppiness in accounting for H2O as it is a common input or output of biological reactions. But I would argue the use of unbalanced equations in introductory material is really dumb.)

        Reaction voltages  -- Another major confusion is reaction voltages. The energy in/out of a redox (pair of) reactions can be estimated by knowing the voltage difference 'seen' by the transferring electrons. There are tables of standard reduction values, but some references us oxidation voltages instead of reduction voltages. This is not too bad and it's just a sign change. Then you find a table of reduction voltages in water and they're all substantially different from the standard voltages! Turns out in water (pH =7) the voltages are all shifted negative by 0.41V (= 59 mv x 7), so the standard ripping apart of water voltage +1.23V (same as water electrolysis voltage) changes: +1.23 V - 0.41V = +0.82 V. Then there electronegativity, which ranks the ability to suck in electrons, and looks like it should be a voltage, but it's not.

Idiot Calvin figures
        I found so many bad photosynthesis figures, some just plain wrong, others simplistic and/or misleading that I have grouped them together in a section (tongue only slightly in cheek) called 'idiot photosynthesis'. Under each figure I list its error(s):

Four Calvin figures --- Can't anyone count?
       Both of the fancy Calvin figures immediately above (from difference sources) have the Pi count wrong. Can't anyone count?  (The source www.wicknet, appears to be a private Greenwich Conn school, but it's unlikely they are the original source of the figure.) The issue is one Pi goes out with each G3P sugar, so of the nine ATP coming into the process (per G3P) only 8 Pi can be shown going out. Both of the above figures agree on the count in the forward path, so the error is probably in the feedback path. The feedback path Pi output count should probably be two, whereas the figures above show three and zero!

Pi count (6/10/10 update)
        Notice above 2 Pi on left coming off followed by 3ATP coming in an (apparently) dropping off 3Pi. This is probably correct. Wikipedia (Calvin cycle) says intermediates in the regeneration part of the cycle release Pi into solution. At the end ATP phosphorylates (adds a Pi) each intermediate BuP, changing it from a phosphate (one Pi) to a biphosphate (two Pi), yielding the final product RuBP.

        The figure above doesn't show Pi in the drawing, but it includes Pi in the equations at bottom. But for some reason it shows one Pi glommed onto the glucose (or fructose) with 17 Pi separate. I have never ever seen the equations written this way. Two G3P 'sugar', each of which have a Pi, are the immediate outputs of the Calvin cycle, so the logical way to show the post processed output is the G3P combined into sugar (glucose, or maybe fructose) with the two stripped Pi and added to the 16 Pi output from the Calvin cycle.

        The figure above highlights some Pi, but not others, weird. It shows # of C and Pi in each molecule, but with no counts there is no way to follow the Pi flow.

What?
        Wikipedia (Photosynthesis) has the equation below (x6) for light reactions. Everyone else seems to think the ratio is 18 ATP for 12 NADPH:

        The overall equation for the light-dependent reactions under the conditions of non-cyclic electron flow in green plants is

        12 H2O + 12 NADP+ + 12 ADP + 12 Pi + light =>12 NADPH + 12 H+ + 12 ATP + 6O2

        I originally thought DNA code and amino acids was exactly the same everywhere, but there are a few minor variants in the coding, but not (as far as I know) in the 20 amino acids, and interestingly one of the variants in the coding is in mitochondria DNA. But even here the change is very small two or three of the 64 codons encodes for a different amino acid (but still one of the 20).

Made of H,O,C, N plus S
        Amino acids are simple molecules with 10 to 20 atoms. All amino acids (says Wikipedia) have a NH3 (amine, a group with nitrogen) & COOH (carboxyl, essentially CO2 with an H connected to one of the oxygen (OH). This is a carbon bonded to one oxygen with a double bond and to another oxygen with a single bond, the remaining oxygen bond taken by a hydrogen). Most amino acids have only one nitrogen (N), but there are a couple have two or three N. Two amino acids include one sulfur (S), but otherwise they are made of only the atoms photosynthesis assembles: carbon, oxygen and hydrogen. To get a handle on amino acids I started looking at the three simplest amino acids: Glycine, Alanine and Cysteine.

Almost every reference draws the structure differently  -- Is there something wrong with chemists?
        Below are alanine and glycine from the first references that pop up in Google include Wikipedia. Why are there so many variations? Isn't there a preferred way to show a simple key biological molecule. The definition of amino acids:

        -- In chemistry, an amino acid is a molecule containing both amine and carboxyl functional groups. General formula is NH2 CHR COOH (see below).

        Other references say an amino acid has NH3 group and a COOH group. Only about half of the 3d figures I found look like the general Wikipedia amino acid formula. The others remove the H from the O and add it to the N. Here's the general structure of an amino acid:

        The right side 3D figures of both alanine and glycine have an H on an O (so COOH group is there) plus two H on N. The right side 3D figures move the H from O to N. Now N has three H bonded (so NH3 is there), but N is also shown bonded to C. N with four bonds, how does this work? N is element seven and has three valance electrons. The five symbols of alanine are all different (this is not rigged)! In the left two the H count is wrong!

        Are chemists just idiots, in the sense that nothing is standardized and/or they have all kinds of hidden conventions, which they don't bother to explain to students at the elementary level?

Glycine structure
        Glycine (C2 H5 N O2), or written to show its structure is CH2 NH2 COOH

Alanine structure
        Alanine (C3 H7 N O2), or  written to show its structure is CH3 CH(NH2) COOH.

        On the two left figures have the general Wikipedia structure. On the two right diagrams N bonds with C and 3H, whereas on the two right diagrams N bonds with C and 2H, the extra H moving to one of the O (red). Since N has three valence electrons, how is it that it can bond to 3H and still be able to make a bond with C? Are the two right diagrams an isomer, or just plain wrong? (maybe chemists know, but it's not clear to a chemcial  novice like me).

Same amino acid and they are all drawn differently!

.  .. 

On left I count 4H, on 2nd left 6H (correct is 7H).

        There's an elaborate 3D model of glycine here

        http://www.umass.edu/molvis/tutorials/hemoglobin/glycine.htm

It shows the white version above (no H on the O). It's a polar molecule with one of the O marked O- and one of the H on N marked H+, so maybe an H moves around.

Cysteine structure
        Another simple amino acid is cysteine (C3 H7 N O2 S). It has a sulfur.

Phenylalanine structure
        A cool one is phenylalanine (C9 H11 N O2). This has the basic amino acid structure with the extension (R) featuring a six carbon ring.

Tryptophan structure
        Another cool one, probably the most complex amino acid is tryptophan (C11 H12 N2 O2). It has the basic amino acid structure with a double ring, the same six carbon ring as in phenylalanine plus a hexagon ring that includes a N.

At least the color coding of stick/ball molecule figures seems to be (pretty well) standardized.

What other elements do photosynthetic cyanobacteria need?
        Photosynthetic organisms are often referred to as 'self feeders' or photoautotrophs, but nothing can live on just C,O, and H, which are the only elements that photosynthesis provides. At a minimum some 'inorganic minerals' are needed, some in the form of nitrates and sulfates. Quite a few elements are available (at low concentrations) disolved in seawater.

         Authoritative show Planet Earth makes the point that most coastal waters in the tropics are crystal clear and nearly lifeless. The show focused on whales coming in from the arctic to calf. The calf gets 130 gallons of milk a day from its mother, but the mother can find nothing to eat. The water is bathed in sun light, so why no photosynthesis? The answer is there is not enough inorganic minerals in the water to support photosynthetic life.

        -- Photoautotrophs must build all their own molecules from water, CO2, nitrates, sulfates and other minerals.

        I've never seen a reference on this (they must exist), so I did a little spade work. It's fairly easy to find the elements needed for proteins and DNA as they are made of repetitive building blocks. Then there's structure (membranes), protoplasm, and the various specialized structures for photosynthesis and respiration. (There's probably a lot more to, but, hey, I'm not a biologist.)

Photosynthesis yields in chemical form elements C,O,H
        Composed of just C,O,H

                * Carbohydrates (multiples of C H2 O) including glucose (generally considered the output of photosynthesis), other sugars, starch (storable form of 'food' energy), fat (mostly C,H with a little O),  alcohols

                * Cellulose (multiples of C6 H10 O5), which make up the cell wall of green algae, and is the "most common organic compound on earth" (Wikipedia).

        Starch, which is essentially linked glucose molecules, has the same general formula as cellulose (multiples of C6 H10 O5), and plants store it up in fruits, seeds and tubers. Wikipedia says starch is most important carbohydrate in the human diet found in rice, wheat, corn, and potatoes. Note from a formula viewpoint, cellulose and starch at multiples of (C6 H10 O5) looks like glucose molecules (C6 H12 O6) minus a water.

Bacterial cell walls elements
        N, Various chemicals mostly C,O, H with a little N. Also these are the elements in chitin, which is the main component in the exoskeleton of insects and lobsters.

Proteins -- amino acids elements
        N,S, Proteins form a large part of the molecular machinery in cells. In writing the section above on the amino acids I checked the formula of all 20 amino acids used in proteins (of every known organism). Amino acids are mostly made of C,O,H, each a little N with a tiny amount of sulfur (2 of 20 amino acids include one S atom).

        Almost all nitrogen in the biosphere (except for action of man) is due to the action of a few 'nitrogen fixing' bacteria, which can make ammonia (NH3) from nitrogen pulled from the atmosphere. (I don't know how nitrogen is taken up by prochlorococcus, but a good guess is some form of dissolved nitrate.)

DNA & RNA elements
        DNA base pairs (rungs) --- C,H,N,O
        DNA backbone --- P, phosphate group (PO4) plus sugars (C,O,H)

        The DNA backbone alternates sugars and a phosphate group, built around one phosphorus atom, for every rung. Phosphorus is also used in RNA.

Photosynthesis machinery elements
        chlorophyll --- Mg (one magnesium) Magnesium is also found in DNA polymerase (reads
                                                and assembles DNA strands)
        ATP & NADPH --- P (three phosphorus) Phosphorus is also included in every molecule of
                                                the calvin cycle
        membrane --- P  Membranes of all cells are made from phospholipids, which as the name
                                                indicates are built around a  phosphate group (PO4)
        water oxidizing complex --- Mn (four manganese), Ca (one calcium), Cl (one chlorine)
        cyctochrome --- Fe (one iron) H+ pump in PhII electron transport chain
        ferredoxin --- Fe (two iron with two S sulfur) part of PhI electron transport chain. Referred to
                                                as a biological capacitor
        plastocyanin --- Cu (one copper) another H+ pump in PhII electron transport chain

Seawater elements

source -- Mineral Resources of the Sea (book)

        In eukaryotic cells sodium Na+ and potassium K+ are the main ions used to control cell membane voltage (they flow in/out to to pulse membrane voltages in nerve cells), but I don't see any references to them in bacterial cells. One reference said protons are usually the main membrane voltage control ion in bacteria, which is consistent with ion control inside thykaloid membranes of photosynthesis.

In plants the following are considered 'macronutrients' (for the whole plant):
         Ca = Calcium, Mg = Magnesium, N = Nitrogen, P = Phosphorus, K = Potassium,  S = Sulfur

        Three of the above are the main ingredients in plant fertilizer, which is characterized by three numbers: nitrogen (N), phosphorus (P), and potassium (K).

and below are plant 'micronutrients' (trace elements):
        Cl = Chlorine, Cu = Copper, Fe = Iron, Mn = Manganese, Mo = Molybdenum,  Ni= Nickel, Na = Sodium,  Zn = Zinc

Running out of phosphorus -- an aside
        An article in June 2009 Scientific American points out that the world's supply of phosphorus, a major component of fertilizer, is getting dangerously low. Of the the three elements in fertilizer, nitrogen is pulled from the air, but potassium and phosphorous are mined. There's lots of potassium around, but not so phosphorous. US is world's 2nd largest producer and 65% of our phosphorous comes from a few mines near Tampa Florida (bone valley). 40% of the known world's supply of phosphorus deposits are in Morocco.

        When human and animal waste were used for fertilizer, phosphorus just circulated around. But now wastes and fertilizer are almost completely decoupled. The result is that phosphorus used for fertilizer all eventually ends up in the sea, some in direct run off and others thorough waste treatment, and eventually it sinks to the sea bottom where it entombed in the seabed.

        We can't produce food without phosphorous. We have maybe 50 to 100 year supply, but 'peak phosphorous' could happen in 30 years. On top of everything else, idiot bifuels are using huge amounts of the stuff. A June 2008 article said phosphate rock had increased in price 700% in the last 14 months. "The risk of a future phosphorus shortage blows a hole in the concept of biofuels as a 'renewable' source of energy. Ethanol is not truly renewable if an essential fundamental element is, in reality, growing more scarce."

Used in some animals, but not humans (as far as is known):
        Arsenic, boron, bromine, cadmium, silicon, tungsten, and vanadium
used in humans??: cobalt, chromium, iodine, selenium
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Five pathways to fix CO2 + H => organic material
        In a 1969 paper I find, "until recently the reductive pentose cycle (calvin cycle) was the only known mechanism of autotrophic carbon dioxide fixation", the "reductive carboxylic acid cycle" having just been proposed as the mechanism used by green sulfur photosynthetic bacteria.

        A 1991 paper begins-- "We know of three routes that organisms have evolved to synthesize complex organic molecules from CO2: calvin cycle. the reverse tricarboxylic acid cycle, and the reductive acetyl-CoA pathway." A 2009 evolution book says there are five known metabolic pathways to combine CO2 and hydrogen to form organic material (material of life).

        The number of CO2 fixing pathways may depend on how you count. For example, some references refer to C4 plants as having a different CO2 fixing pathway than standard C2 plants. C4 plants do first fix carbon into a molecule that's not rubisco, but then CO2 is delivered to rubisco and fixed again as it enters the standard calvin cycle. But from another point of view this is just the standard calvin CO2 fixing pathway with a pre-processing step.

      * Calvin cycle (reductive pentose cycle)
                used by plants, cyanobacteria and purple bacteria
                unique enzymes - ribulose bisphosphate carboxylase (RuBisCo) and phosphoribulokinase
                (2 NADPH, 3 ATP per CO2)

                6 CO2 + 12 NADPH + 18 ATP => glucose + 12 NADP+ + 18 ADP + 18 PO4-3

       * Calvin with C4 pre-processing or (Hatch & Slack C4 pathway)
                 used by some tropical plants
                (2 NADPH, 5 ATP per CO2)

                6 CO2 + 12 NADPH + 30 ATP => glucose + 12 NADP+ + 30 ADP + 30 PO4-3 ?

      * Reverse krebs (reverse TCA cycle) or (reverse tricarboxylic acid cycle) or (reverse citric acid cycle)
                used by green sulfur bacteria
                unique enzyme is citrate lyase
                (4 NADPH, 1.66 ATP per CO2)

                3 CO2 + 12 NADPH + 5 ATP  => triose phosphate + 12 NADP+ + 5 ADP + 5 PO4-3

      * Hydroxypropionate pathway or (3-hydroxypropionate cycle)
                used by green nonsulfur bacteria, oxidative lithotrophic archaea
               (2 NADPH, 1.5 ATP per CO2)

                2 CO2 + 4 NADPH + 3 ATP  => glyoxylate + 8 NADP+ + 3 ADP + 3 PO4-3

      * Reductive (reverse) acetyl-CoA pathway or (Wood Ljungdahl Pathway)
               used by some bacteria and archaea (in Lost City hydrothermal vents?)
               (does not use NADPH or ATP)?

                CO2 + H2 => acetyl Coenzyme A

Oxidative pathways run in reverse
        Turns the many (all?) of the metabolic pathways that fix CO2 into organic material are respiration (oxidative) pathways run backwards. In classic respiration you take in organic material and oxidize it yielding energy in the form of ATP and NAD(?) with outputs CO2 and H2O.

        I read that biologist were surprised when it was found the classic krebs (respiration) cycle (or reverse TCA cycle) could be run backwards. You feed in ATP and NADPH to supply energy and the cycle transforms CO2 into organic material. In Wikipedia comments I see that some biologist quibbling about whether this cycle should be called the 'TCA cycle in reverse', because while basically it's the same a few of the enzymes are different.

        -- Before glucose (the product of photosynthesis) can be converted into ATP it has to be broken down into two pyruvate molecules (the ionized form of pyruvic acid). This process is known as glycolysis. Glycolysis takes place in the cytoplasm and can occur without the presence of oxygen and is the primary energy source for most organisms. This process consumes two ATP molecules, and produces four ATP molecules and two NADH2+ molecules. After the glucose molecule has been converted into pyruvate, it is then sent to the Kreb Cycle to be converted into more usable forms of energy.

        -- The pyruvate molecules produced during glycolysis contain a lot of energy in the bonds between their molecules. In order to use that energy, the cell must convert it into the form of ATP. To do so, pyruvate molecules are processed through the Kreb Cycle, also known as the citric acid cycle. Because glycolysis produces two pyruvate molecules from one glucose, each glucose is processed through the kreb cycle twice. For each molecule of glucose, six NADH2+, two FADH2, and two ATP are produced.

        -- What happens to the NADH2+ and FADH2 produced during the Krebs cycle? The molecules have been reduced, receiving high energy electrons from the pyruvic acid molecules that were dismantled in the Krebs Cycle. These carrier molecules transport the high-energy electrons and their accompanying hydrogen protons from the Krebs Cycle to the electron transport chain in the inner mitochondrial membrane.

        -- In a number of steps utilizing enzymes on the membrane, NADH2+ is oxidized to NAD+, and FADH2 to FAD. The electrons are then passed from molecule to molecule in the inner membrane of the mitochondron, losing some of their energy at each step. These electrons provide energy to "pump" hydrogen protons across the inner mitochondrial membrane to the outer compartment. This high concentration of hydrogen protons produces a free energy potential that can do work. That is, the hydrogen protons tend to move down the concentration gradient from the outer compartment to the inner compartment. The free energy of the hydrogen protons is used to form ATP by phosphorylation, bonding phosphate to ADP in an enzymatically-mediated reaction. Since an electrochemical osmotic gradient supplies the energy, the entire process is referred to as chemiosmotic phosphorylation.

        -- Once the electrons (originally from the Krebs Cycle) have yielded their energy, they combine with oxygen to form water. If the oxygen supply is cut off, the electrons and hydrogen protons cease to flow through the electron transport system. If this happens, the proton concentration gradient will not be sufficient to power the synthesis of ATP. We're not used to thinking of plants needing oxygen, but this is why they, and most living organisms, are not able to survive for long without it!
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        (update) I found it very difficult to dig out the details of the half 'Z' photosynthesis in various bacteria. The question I tried to answer is, Can both PHI and PHII half 'Z' bacteria swich their one photosystem back and forth making ATP and NADPH? It takes more energy to make NADPH than ATP, so I suspect that PHI bacteria. like green sulfur bacteria, may have this ability, able to switch their NADPH cycle to making the 'easier' ATP cycle. But can PHII bacteria, say purple bacteria, which normally make only ATP, switch PSII to make NADPH?  I suspect not, but found this very difficult to confirm.

        I did find these tantlizing tidbits below.

        -- All (PSII) have quinone acceptors and CAN NOT reduce NAD(P)+ directly--requires reverse electron flow. (What's reverse electron flow?)

        --  Reaction center used primarily to produce a proton gradient for ATP synthesis and to provide driving force for reverse electron flow. Light-driven electron transport is CYCLIC, and no net oxidation/reduction can take place. Reductant for CO2 fixation comes from organic compounds ("non-sulfur" bacteria) or from inorganic sources ("sulfur" bacteria).

        -- CYCLIC elctron transport can also occur around PS I, producing only a proton gradient for ATP synthesis.

        Above seems to indicate that PSI can be switched to cyclic and make a proton gradient for ATP, but that PSII organisms use something other than NADPH for CO2 fixation. (but the details are fuzzy)

        --  In heliobacteria, Green sulfur, and Green non-sulfur bacteria, NADH is formed using the protein ferredoxin, an energetically favorable reaction. In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center. In all cases, however, a proton motive force is generated and used to drive ATP production via an ATPase. (Wikipedia -- Microbial metabolism (lots of good info)

        -- The third type of iron-oxidizing microbes are anaerobic photosynthetic bacteria such as Chlorobium (green sulfur), which use ferrous iron to produce NADH for autotrophic carbon dioxide fixation. Biochemically, aerobic iron reduction is a very energetically poor process which therefore requires large amounts of iron to be oxidized by the enzyme rusticyanin to facilitate the formation of proton motive force. Like sulfur oxidation, reverse electron flow must be used to form the NADH used for carbon dioxide fixation via the Calvin cycle.

        -- Either light or ATP can provide the energy for reverse electron transport

        -- All of these examples of photoassimilation (in purple bacteria) require a light driven cyclic electron transport chain supplemented by a reverse electron flow pathway, which can be driven by cyclic electron flow.

        -- In purple sulfur bacteria the picture changes when CO2 fixation is carried out with reduced sulfur compounds as electron donors. In addition to cyclic electron flow for ATP production linear electron flow from reduced sulfur compounds to NAD+ vai the UQ pool requires a light driven step through the RC as shown in Fig 3.  (inorganic material can supply the electrons to the UQ pool, which are subsequently used to reduce NAD+)

   **    -- In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center. In all cases, however, a proton motive force is generated and used to drive ATP production via an ATPase. (Wikipedia)

        -- Sulfur-oxidizing organisms generate reducing power for carbon dioxide fixation via the Calvin cycle using reverse electron flow, an energy-requiring process that pushes the electrons against their thermodynamic gradient to produce NADH.

        -- (Nitrification is the process by which ammonia (NH3) is converted to nitrate (NO3-).) As in sulfur and iron oxidation, NADH for carbon dioxide fixation using the Calvin cycle is generated by reverse electron flow, thereby placing a further metabolic burden on an already energy-poor process.

** -- In anoxygenic photosynthetic bacteria, electron flow is cyclic, with all electrons used in photosynthesis eventually being transferred back to the single reaction center. A proton motive force is generated using only the quinone pool. (Wikipedia)

** -- In heliobacteria, Green sulfur, and Green non-sulfur bacteria, NADH is formed using the protein ferredoxin, an energetically favorable reaction. In purple bacteria, NADH is formed by reverse electron flow due to the lower chemical potential of this reaction center. the lower chemical potential of this reaction center. In all cases, however, a proton motive force is generated and used to drive ATP production via an ATPase. (Wikipedia)

        -- Some photosynthetic bacteria (e.g. Chloroflexus) are photoheterotrophs, meaning that they use organic carbon compounds as a carbon source for growth. (I think this conflicts with table far above )(Wikipedia)

        -- Many aspects of energy storage in green bacteria, especially photophosphorylation and the role of cytochrome b/c complexes in electron transport, remain poorly understood.

Finally in a book, Bacteria in Biology, Biotechnology and Medicine by Paul Singleton, I found a clear statement as to how purple and green bacteria make NADPH.

        -- Bacteria need reducing power to make NADPH (or NADH) for biosynthesis
        -- 'green' photosynthetic bacteria (& cyanobacteria) obtain these reduced molecules by direct reduction using non-cyclic electron flow.  (He adds obtaining these molecules in never a problem for bacteria using fermentation )
        -- 'purple' photosynthetic bacteria cannot do this, because electrons ejected from their reaction centers do not have enough energy to reduce NAD (or supposedly NADP).
        -- Instead these organisms (meaning 'purple' photosynthetic bacteria) use reverse electron transport. In this process 'proton motive force' is used to drive electrons 'uphill' to a membrane bound enzyme, NAD dehydrogenase, where NAD is reduced to NADH. This requires electrons from an external electron donar. Purple bacteria typically use organic electron donars, but some can use inorganic donars like (hydrogen) sulfide. (Reverse electron transport is also used by nitrifying bacteria and chemolithotrophs.)

whoops --- A ref & a figure show the energy to run the reverse electron transport coming from oxidation of an inorganic input (in fig Fe2+ ferrous to Fe3+ ferric). This energy both runs the reverse electron transport making NADPH and pumps protons to make ATP. Both then used to run calvin cycle fixing CO2 in a non-photosynthentic bacteria

Metal complexies
        Cytochromes            --- contains iron & sulfur

lithotrophs ("rock-eaters") ---  Inorganic electron donors include hydrogen, carbon monoxide, ammonia, nitrite, sulfur, sulfide, and ferrous iron. Lithotrophs have been found growing in rock formations thousands of meters below the surface of Earth.

Lithotrophy - mode of life in which organisms utilize chemical bond energy in inorganic compounds to generate ATP and NAD(P)H (reducing power), then use them to reduce carbon dioxide to form organic compounds