Friday, November 28, 2008

Biochemistry on the Web: The Citric Acid Cycle

Here are some websites that discuss the Citric Acid Cycle [Krebs animation][Wikipedia].

This is one of the fundamental biochemical pathways yet both of these sites contain errors. This is the time of the year when I challenge the students in my introductory biochemistry class to find one single website that correctly shows the reactions of the citric acid cycle with all the correct substrates and products (including water and protons). There are two sites that don't count: ones with images from my book (Horton et al.) and ones that are direct copies of the International Biochemistry and Molecular Biology (IUBMB) website. In five years my students have not succeeded. Can any Sandwalk reader find one?

Here are the links to the IUBMB reactions. They all have the correct reaction at some location. You may have to follow one or more of the links to the reaction to see the complete, correct version.

Enzymes of the Citric Acid Cycle

citrate synthase [EC 2.3.3.1]
aconitase [EC 4.2.1.3]
isocitrate dehydrogenase [EC 1.1.1.41][EC 1.1.1.42]
α-ketoglutarate dehydrogenase [EC 1.2.4.2]
succinyl-CoA synthetase [EC 6.2.1.4][EC 6.2.1.5]
succinate dehydrogenase [EC 1.3.5.1]
fumarase [EC 4.2.1.2]
malate dehydrogenase [1.1.1.37]


12 comments:

  1. find one single website that correctly shows the reactions of the citric acid cycle with all the correct substrates and products (including water and protons)

    This one seems correct to me:
    http://www.xumuk.ru/biologhim/bio/img774.jpg
    (The pic is from Russian chemistry education site)

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  2. I hope you're joking!!!

    That Russian site makes every single one of the most common errors.

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  3. What might you suggest be done? I'm thinking in addition to just this pathway, too. There's a whole lot of misinformation out there, is there any particular strategy to see if it can get corrected?

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  4. This comment has been removed by the author.

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  5. There's a website called Wikipathways, which was highlighted a few months ago in Nature Reviews Molecular Cell Biology.
    "Each pathway has a dedicated page with a description and visual representation, relevant references, component lists and version history. Crucially, a custom-designed graphical tool allows scientists to amend and annotate all the pathways online".

    So, if you find any mistakes, you can correct them :)

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  6. No, I really thought it's correct :( Reminds me why I hated metabolism back in school!

    OK, so contrary to what shown in most illustrations, there is no net proton release in ketoglutarate and succinyl-CoA synthesis steps - right?

    I suppose purists might insist on phosphate ion instead of phosphoric shown but that's just a matter of what protonated state one assigns to GTP.

    And if your beef is with FADH2 shown as a product of succinate dehydrogenase then I'd suggest it's just a matter of taste. Subsequent FADH2 oxidation is just a coupled reaction that only happened to be catalyzed by the same multienzyme complex. (I am sure the two can be taken apart and suspect the two activities are physically separate in at some ogranisms). Stryer also shows FADH2 and I wouldn't consider it an error.

    Anything else? Care to enlighten?

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  7. DK says,

    OK, so contrary to what shown in most illustrations, there is no net proton release in ketoglutarate and succinyl-CoA synthesis steps - right?

    Right. Those are two of the proton errors on that website.

    I suppose purists might insist on phosphate ion instead of phosphoric shown but that's just a matter of what protonated state one assigns to GTP.

    We could quibble about that one but the correct ionic states of these molecules under physiological conditions are known. Why not show them?

    And if your beef is with FADH2 shown as a product of succinate dehydrogenase then I'd suggest it's just a matter of taste. Subsequent FADH2 oxidation is just a coupled reaction that only happened to be catalyzed by the same multienzyme complex. (I am sure the two can be taken apart and suspect the two activities are physically separate in at some ogranisms). Stryer also shows FADH2 and I wouldn't consider it an error.

    It's an error. Succinate dehydrogenase is a flavoprotein. FAD is not a substrate in the reaction and FADH2 is never released as a product. Showing FAD+ as a substrate and FADH2 as a product makes about as much sense as showing the various reduced and oxidized forms of the iron-sulphur clusters as reactants and products.

    They are all part of an internal electron transfer chain and should never be considered as substrates and products.

    There's one other important reason why it is wrong to show FADH2 as a product. It hides the real substrate and product of the reaction. When you look at an incorrect version of the reaction with FADH2 as the "product" you have no idea what the real product is (it's QH2). What's the point of that?

    Here's a short article by Simon Brown that might help you understand the issue [Does succinate oxidation yield FADH2 or ubiquinol?].

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  8. Here's a short article by Simon Brown that might help you understand the issue

    I understand the issue. IMO, it's a non-issue. Like a said, a matter of taste. I can see your point and I agree it's a reasonable position. But I can also see another point and I agree that it is also reasonable. As far as CAC is concerned, exactly how FAD is recycled does not matter. It does not have to be ubiquinone. FADH2 might as well go out, be be oxidized somewhere else and rebind - such a mechanism would not alter CAC per se.

    In a similar example, you'll write for pyruvate carboxylase:
    ATP+pyruvate+HCO3 = ADP+Pi+oxaloacetate

    But this same reaction is catalysed by two completely separate enzymes in many organisms.
    Biotin carboxylase:
    P-biotin+HC03+ATP = P-biotin-CO2+ADP+Pi

    Pyruvate carboxyltransferase:
    P-biotin-CO2+pyruvate = P-biotin+oxaloacetate.

    If I am only concerned about biotin carrier protein (P-biotin above) and, say, fatty acid metabolism (as in Ac-CoA carboxylation), why must I necessarily learn about its role in oxaloacetate production???

    The supposed great importance of the distinction between single enzyme having many activities and many enzymes having single activity escapes me. It reminds me of discussions with an enzymologist friend of mine: 1. Are chaperones that don't use cofactors enzymes? 2. Is transposase (say, Tn5 or Mu) that does not have a turnover an enzyme? Myself, I am not stuck with definitions and happily consider both as enzymes.
    But when others disagree, I don't have a problem - no classification is perfect and the distinction is a non-issue in real world.

    DK

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  9. DK-

    But, I think that it is more than a matter of taste and that Larry is correct with respect to succinate dehydrogenase. It is clear that you understand the reaction--I don't question that.

    Enzymes are catalysts, and the covalent binding of FAD to the protein makes it a part of the enzyme. The reaction sequence is not complete until the enzyme is able to catalyze another reaction, and that only occurs when the FADH2 returns to FAD.

    BTW, when Larry issued his challenge previously I looked at quite a few sites with the TCA cycle using Google Images and did not come up with any that used UQ as part of the reaction pathway as Larry suggests.

    I will make sure I mention this point to our Med students when I give the metabolism lecture on the TCA cycle this week, but my handout has it the "wrong" way.

    Bill Chaney

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  10. DK says,

    I understand the issue. IMO, it's a non-issue. Like a said, a matter of taste. I can see your point and I agree it's a reasonable position. But I can also see another point and I agree that it is also reasonable. As far as CAC is concerned, exactly how FAD is recycled does not matter. It does not have to be ubiquinone. FADH2 might as well go out, be be oxidized somewhere else and rebind - such a mechanism would not alter CAC per se.

    I don't think you understand how the enzyme works. FADH2 cannot "go out" and reduce anything other than quinone. FAD is an integral part of the enzyme. In the direction of the citric acid cycle the electrons are passed from succinate to FAD+ to three Fe-S clusters and then to quinone. The electron acceptor for FADH2 is the closest Fe-S cluster and that's the only thing that can normally be reduced by enzyme-bound FADH2.

    Bill's comment is important. If enzyme-FADH2 were the correct product of the reaction then the enzyme would not be a catalyst.

    The depiction of FADH2 as the product of this reaction is wrong on so many levels that I use it as a way of evaluating textbooks and biochemistry course websites. Anyone who shows FADH2 as the product of this reaction is probably making lots of other mistakes as well.

    Note that one of the earlier reactions—the one catalyzed by α-ketoglutarate dehydrogenase—also has FAD+ as an intermediate electron carrier in an electron transfer chain. The terminal electron acceptor is NAD+ and the product of the reaction is always shown as NADH.

    Why is the product never shown as FADH2?

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  11. To Larry:
    I don't think you understand how the enzyme works. FADH2 cannot "go out" and reduce anything other than quinone.

    I do. I don't think you understood me. Let me repeat: I meant that as far as CAC is concerned, it does not matter just how FAD is recycled. IF FADH2 were to go out and IF the ultimate acceptor were not quinone but anything else, nothing would change in the cycle.

    α-ketoglutarate dehydrogenase—also has FAD+ as an intermediate ... and the product of the reaction is always shown as NADH. Why is the product never shown as FADH2?

    You got me here. I don't know why! If I understand mechanism correctly, it's a ping pong and by the time FADH2 and NAD+ are involved, both CO2 and succinyl-CoA are synthesised. So, to be logically consistent, I must say that as far as CAC is concerned, it does not matter whether one shows FAD2 or NADH - both are just part of recycling lypoic acid. I imagine you will sneer at this suggestion as utterly ridiculous - but I maintain that it is logical and not inherently wrong. (Although, of course, it is wrong if one's narrow purpose is to describe one particular complex enzyme's activities).

    If enzyme-FADH2 were the correct product of the reaction then the enzyme would not be a catalyst

    So you would deny Tn5 trasposase an enzyme status?

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  12. Larry, why don't you edit the Wikipedia article to correct its mistake?

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