Tuesday, July 17, 2007

The Calvin Cycle: Regeneration

 
Nobody took me up on the offer to become an intelligent designer. The goal was to figure out a way of converting the five products of the Rubisco reaction into three new substrate molecules [The Calvin Cycle]. The five products are three carbon (3C) compounds and the three new substrate molecules are five carbon (5C) compounds. Here's how it's done ...

Two 3C molecules are joined to make one six carbon (6C) compound (fructose). Then two of the carbon atoms from fructose are transferred to another 3C molecule to make the first of the five carbon products (red, ribulose). This leaves a 4C molecule that is joined to another one of the 3C molecules to produce a seven carbon (7C) sugar called sedoheptulose. Two carbon are transferred from sedoheptulose to the last 3C molecule to produce a second 5C molecule. This leaves the third and last 5C molecule.

Of course there's a lot of fiddling in the pathway to get the molecules into the right form for these reactions. Here's the complete Calvin Cycle in all its glory. Click on it to see a bigger picture.



You can simplify the pathway a great deal by writing it like this ...

This shows you that, in spite of the complexity, the overall pathway takes three molecules of carbon dioxide and converts it to one molecule of glyceraldehyde 3-phosphate. That's the purpose of the Calvin Cycle, it fixes carbon.

The pathway is expensive. It uses two types of energy currency, ATP and NADPH, but these are produced in abundance by photosynthesis. It's a fair bet that this particular reaction is the ultimate source of 99% of the carbon atoms in your food.

There's a neat trick we can do with this reaction. We can use it to estimate the cost of synthesizing acetyl CoA—the substrate for the citric acid cycle and the product of the pyruvate dehydrogenase reaction. The pathway from glyceraldehyde 3- phosphate to acetyl CoA is coupled to the synthesis of two molecules of NADH and two molecules of ATP. If we subtract these from the cost of making glyceraldehyde 3-phosphate then the total cost of synthesizing acetyl CoA from CO2 is 7 ATP + 4 NAD(P)H. This can be expressed as 17 ATP equivalents since each NADH is equivalent to 2.5 ATP.

Since the net gain from complete oxidation of acetyl CoA by the citric acid cycle is 10 ATP equivalents, the biosynthesis pathway is more expensive than the energy gained from catabolism. In this case, the "efficiency" of acetyl CoA oxidation is only about 60% (10/17 = 59%) but this value is misleading since it is actually the biosynthesis pathway (costing 17 ATP equivalents) that is complex and inefficient.

11 comments :

  1. I might just be getting tired and thus not thinking clearly, but I wondered about your comment "...it is actually the biosynthesis pathway (costing 17 ATP equivalents) that is complex and inefficient." I see that it's pretty complex, but I don't understand why it's inefficient. I guess it's possible in some way to reduce the ATP equivalents in making acetyl-CoA to something less than 17, but would you mind explaining in what way this can be done? You've explained earlier about the low efficiency of rubisco, so I guess you're not referring to that now.

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  2. It's not too difficult to imagine carbon fixation pathways that would be more efficient. The enzyme pyruvate carboxylase, for example, fixes carbon in the form of bicarbonate (dissolved CO2) by attaching it to pyruvate to make oxaloacetate. You could design a cycle that could fix carbon using this enzyme.

    The Calvin Cycle evolved from a pre-existing cycle that's found in all cells. It's called the pentose phosphate pathway and it's used to make ribose. I suspect that the inefficiency of the Calvin Cycle is due to tinkering with a pathway that wasn't originally designed for the purpose of fixing carbon.

    This fits nicely with my view of life as a sort of Rube Goldberg machine but it doesn't fit with the idea of design and optimization. Perhaps the adaptationists can explain why natural selection hasn't done a better job. :-)

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  3. Um, okay, but aside from a number of seemingly unused conditions (which now are revealed to be conflated) that was an obvious solution I think. (I.e. the one that immediately appeared for me. :-P)

    So while evolution doesn't have to stumble on the obvious answer, when it does (again disregarding those conditions), perhaps because it is more probable, it isn't a disproof of ID. The disproof is that ID has no way to predict an answer, obvious or not.

    The IDiots are rambling enough, no need to draw implications that isn't there. Let them figure out if the designer "must" pick the obvious or efficient or whatever mechanism and then call back with the answer.

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  4. Torbjörn Larsson

    So while evolution doesn't have to stumble on the obvious answer, when it does (again disregarding those conditions), perhaps because it is more probable, it isn't a disproof of ID.

    I don't claim that it's a disproof of Intelligent Design Creationism. But it does cause one to question just how intelligent the designer has to be. Not very, as it turns out.

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  5. Perhaps the adaptationists can explain why natural selection hasn't done a better job. :-)

    Well, is there a way to improve the Calvin cycle? Natural selection always takes the best available improvement on the current situation. It can't simply look around the adaptive landscape, see that "there's a better way over there," and leap sideways into an entirely new method.

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  6. wolfwalker,

    Well, is there a way to improve the Calvin cycle? Natural selection always takes the best available improvement on the current situation. It can't simply look around the adaptive landscape, see that "there's a better way over there," and leap sideways into an entirely new method.

    Right. But the Intelligent Designer can do that if He wants to.

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  7. But it does cause one to question just how intelligent the designer has to be. Not very, as it turns out.

    Well, when you put it that way... :-P

    I must agree, a nonoptimal system wouldn't be expected of normal intelligences. (IDiots retreats into "detecting design" at this point. And fail even that.)

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  8. This fits nicely with my view of life as a sort of Rube Goldberg machine but it doesn't fit with the idea of design and optimization. Perhaps the adaptationists can explain why natural selection hasn't done a better job. :-)

    Who are these "adaptationists" who don't know that evolution often tinkers with pre-existing structures and pathways rather than "designing" optimal ones from scratch? This straw man is getting old and moldy.

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  9. Right. But the Intelligent Designer can do that if He wants to.

    Can "He"? The capital 'H' indicates to me that you make precisely the same error the ID crowd themselves are fond of, that of conflating a proposed designer and the pre-scientific Christian idea of "God". Why would you assume that a designer, if one existed, would have this ability (or any other)? You use this as a rebuttal in an on-going meta-conversation, obviously.

    But even so. It's not even illogical; it's utterly alogical. And the only possible reason for it I can imagine is that the ID crowd themselves make this conflation their whole raison d'etre - even tho such a thing is obviously not any part of their actual "theory" (such as it is).

    The reason clear-headed scientists like yourself have so long been unable to fully discredit ID is that you persist in being drawn into a silly argument entirely on their terms. This particular statement argues nothing, indeed, it says nothing. It is purely emotional rhetoric, and I was, frankly, shocked to come across it after such a concise and brilliant exposition of biochemistry.

    Larry, I've never seen your page before, and likely never will again, but I will tell you this much: such snidery should be beneath a man of your intellect.

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  10. After having some microbiology this semester I wonder if the revers Krebs cycle might be superior to the Calvin cycle: http://en.wikipedia.org/wiki/Reverse_Krebs_cycle
    There's no account of how much energy that's used for fixing CO2 in that cycle, but at least the enzymes are more specific for CO2 than rubisco I hope. The CAC is a pretty common cycle, so I wonder why there's not more organisms that use the reverse one than the Calvin. I need to do some reading about this I guess, unless someone else know something about this.

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  11. Wow I am in A.P. Biology in the 11 th grade and our teacher just said to know that it makes what it started out with, but that was not good enough for me. I looked everywhere for what happens and this was the first one that showed me what I wanted to know. Thank you.

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