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Topic: Confused about missing H in glycolysis  (Read 11758 times)

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Offline gonzo

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Re: Confused about missing H in glycolysis
« Reply #15 on: March 08, 2013, 12:55:38 PM »
Sorry, but I don't get it :(

I thought I was supposed to count the oxidation numbers for carbon (I was looking at the Bentley paper and how it described that all the interesting stuff in NAD+ reduction really took place on the carbons and not the charged nitrogen atom). If I'm also counting for oxygen I get confused because then I don't know how to pick out one from the other - as you say in a carboxyl group the electrons 'belong' to the oxygen. But that's sorted by giving them away as per the formula.

I know that it's the oxygen atom that has the charge, but I still have to include that charge somehow. You're right that it says in table III that carbon has an oxidation number of +3, but shouldn't that be something that can be shown from the formula without having to look it up?

So I don't know if I'm supposed to count for both oxygen and carbon now (and if so, also any other atom in the molecule I suppose). I understood the trick as simply seeing whether carbon 'owned' or didn't own the electrons and then adding charges for each group.

Maybe it's just because I don't really get what I'm counting. From I understand redox reactions the whole point is not just the transfer of electrons but the energy level of said electrons (thereby transfering energy with them), and that depends on the bonds.. thus I'm confused about how one can keep score simply by tallying in this way.

But then again, I can't figure that out anyway.

Ignoring that, isocitrate would then be:

     COO-
     CH2
    HC-COO-
HO-CH
     COO-

+3; -2; -1; +3; +0; +3; making the oxidation number 6

doing the same with alpha-ketoglutarate:

COO-
CH2
CH2
C=O
COO-

+3; -2; -2; +2; +3; making the oxidation number 4, so it still doesn't add up, does it? Considering we also have a CO2 to account for. Ugh, chemistry.

(edited)

Offline Babcock_Hall

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Re: Confused about missing H in glycolysis
« Reply #16 on: March 08, 2013, 01:44:05 PM »
The reason I brought up acetate in Table III was to show that the calculation I presented was correct.  With respect to isocitrate, It looks as if you have done the calculation correctly.  So the sum of the oxidation numbers of carbon atoms on the reactant side is +6, and the sum of oxidation numbers of carbon atoms on the product side is +4 + +4 = +8.  Thus, isocitrate is 2 electrons more reduced than alpha-ketoglutarate plus carbon dioxide.  Those are the two electrons picked up when NAD becomes NADH.  Does this help?

Offline gonzo

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Re: Confused about missing H in glycolysis
« Reply #17 on: March 08, 2013, 03:00:41 PM »
Yes, it helps sort of, but I'm confused about how to properly calculate charged segments like COO- if I can't find them in a table.. I understand that it works out to +3 for the carbon atom, but what about the charge? Even though it's oxygen that's charged, the charge still matters, doesn't it?

I wasn't implying that your calculation was wrong, I'm just confused about chemistry. And I still don't understand the deeper concept here because just tabulating electrons can't be the whole story given that their energy level varies depending on the bond..

I also have another question about an oxygen popping up in the citric acid cycle, so it's along the same lines, can I use the same thread?

Offline Babcock_Hall

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Re: Confused about missing H in glycolysis
« Reply #18 on: March 08, 2013, 04:41:04 PM »
With respect to the carboxylate group, I think you should treat each atom individually, not as a segment.  Also, if you do the calculation by the method of the 2000 paper or the 2002 paper, the oxidation number of the carbon atom comes out the same, which should be reassuring.

I think tabulating oxidation numbers can be helpful in biochemical processes for a number of reasons.  It can allow one to check whether any proposed anaerobic catabolism can actually happen.  For example, glucose can be catabolized to two molecules of lactic acid, and one can check the oxidation numbers to see that they add up to the same value on reactant and product side.  Aerobic catabolism does allow for the sum of the redox numbers of the carbon atoms of metabolites to be different, but the oxidation numbers of the carbon atoms in NAD or FAD should change accordingly.

Another thing is that some reactions may not look like redox processes, until you check the oxidation numbers.  Aminotransferases are a good example; glutamate synthase and thymidylate synthase are two more.  It is difficult to say whether or not your question belongs in this thread, but I see no reason not to post it here.

Offline gonzo

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Re: Confused about missing H in glycolysis
« Reply #19 on: March 09, 2013, 02:28:15 PM »
Hmm, if I treat each atom individually does it go like this?

COO- is +3 for carbon, -2 for double bound oxygen and -2 for negatively charged oxygen (1 +n = -1 so n = -2) giving a combined oxidation number of -1 for the caroboxylate group?

if I do that for all oxygens in isocitrate I get -14 and for hydrogen +5, combined with the +6 for carbon that's n=-3

doing the same for alpha-ketoglutarate I get -10 for oxygen, +4 for hydrogen and the +4 for carbon makes n=-2

for the CO2 molecule it cancels out to 0.

So that didn't work or I made mistakes (likely).

I couldn't read the 2000 paper that you linked to, I have to be a member or pay for it, that's why I've been using the Bentley method since it was free.

I do understand that oxidation numbers can be useful for the reasons you give, I just don't really understand how they work because there must be more to it, energy levels depend on electron orbits and here the only deciding factor for electrons being counted one way or the other seems to be which atom is more electronegative. I can't see how that's the whole picture, but if it works it works I guess.

Also, thanks for all the help, even if I am confused about a lot of stuff it helps to juggle it around a bit.

Offline Babcock_Hall

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Re: Confused about missing H in glycolysis
« Reply #20 on: March 11, 2013, 09:46:05 AM »
I do understand that oxidation numbers can be useful for the reasons you give, I just don't really understand how they work because there must be more to it, energy levels depend on electron orbits and here the only deciding factor for electrons being counted one way or the other seems to be which atom is more electronegative. I can't see how that's the whole picture, but if it works it works I guess.

Also, thanks for all the help, even if I am confused about a lot of stuff it helps to juggle it around a bit.
The question of energy in biochemical redox reactions is a separate matter, but I can give you a thumbnail sketch.  The oxidation of NADH to NAD by molecular oxygen is thermodynamically quite favorable.  The electron transport chain carries out this oxidation in many small steps, with the creation of a protonmotive force (basically protons are moved uphill in an electrochemical sense).  When these protons move back downhill, this movement is coupled to the synthesis of ATP.  I will have to leave the rest of your post for later.

Offline gonzo

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Re: Confused about missing H in glycolysis
« Reply #21 on: March 11, 2013, 11:36:42 AM »
Yes I understand this part fine, it's more about the concept of oxidation numbers as simple integers that can be tabulated in this way, it seems to me it must be a whole lot more complicated than that :)

Offline Babcock_Hall

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Re: Confused about missing H in glycolysis
« Reply #22 on: March 11, 2013, 06:46:59 PM »
I have gotten busy at work and may not be able to write a lengthy response for a day or two.  Can you obtain the 2000 paper from your library via interlibrary loan?  It is simpler, but perhaps less general, than the 2002 paper.  With respect to your question, the integer nature of oxidation numbers seems inevitable when one assigns ownership to one or to the other atom completely.

Offline gonzo

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Re: Confused about missing H in glycolysis
« Reply #23 on: March 12, 2013, 04:39:37 PM »
First of all, thanks again for all the help. I don't think I can get that paper from the library at the moment, but I'm ok with using the other method.

I understand why they have to be integers the way oxidation counting works, my question is more in terms of why it works on the physics level. I'd think that, say, hydrogen electrons bonded with oxygen would have a different energy level than carbon electrons. But that doesn't seem to be reflected when counting oxidation numbers (oxygen 'owns' them in both cases), so I'm just not sure how the true energy changes are accounted for. Not sure I'm explaining myself very well, but even from a simple electron shell perspective it seems weird to me. I'm not saying it's wrong (I remember it from chemistry classes), I'm just not really clear on why it works.

Offline Babcock_Hall

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Re: Confused about missing H in glycolysis
« Reply #24 on: March 15, 2013, 09:24:57 AM »
The sum of all of the oxidation numbers of each atom in a chemical species is equal to its charge, and that is what you have shown above.  If you want to balance charges in this reaction you have to include the conversion of NAD to NADH.  If I were going to do that as an exercis, I would replace the large adenosine diphosphoribosyl (ADPR) group with something smaller, like a methyl group.  Those atoms don't change oxidation number, so a little bit of simplification is justified in my opinion.

If you just look at the sum of oxidation numbers on carbon atoms, you will see that for isocitrate they sum to +6; for alpha-KG, they sum to +4; and for carbon dioxide, it is +4.  Looking at it just from the point of view of carbon atoms allows one to see that the carbons have become oxidized by two electrons, which is balanced by the reduction of NAD by two electrons.

Offline gonzo

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Re: Confused about missing H in glycolysis
« Reply #25 on: March 19, 2013, 10:19:32 AM »
I thought that NAD+ simply obtained two charges, so I didn't think it would be necessary to count them if the difference was already known to be two..

About the added oxygen in the citric acid cycle I wanted to ask earlier; the diagram in my book doesn't show how it's added when acetyl CoA reacts with oxaloacetate, but in this wiki a hydration reaction is shown http://en.wikipedia.org/wiki/File:Citric_acid_cycle_with_aconitate_2.svg - I still can't see from that either how the oxygen is added between succinyl CoA and succinate though. I see the substrate level phosphorylation taking place, but where does the oxygen come from, is that just a hydration reaction not shown?

Offline Babcock_Hall

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Re: Confused about missing H in glycolysis
« Reply #26 on: March 19, 2013, 10:57:24 AM »
I just have time for a quick response today.  We have to account for the two electrons lost by carbons in the isocitrate-to-alphaKG+CO2 conversion.  Those two electrons reduce (change the oxidation number of) two carbons in the nicotinamide ring of NAD.  I think that the 2002 paper does a nice job going through NAD versus NADH in this regard.

Molecular oxygen is not part of the citric acid cycle, but I think that there is one molecule of water in the citrate synthase reaction.  One has to convert citryl CoA to citrate.  When one makes GTP from GDP and inorganic phosphate, one molecule of water is produced.  I believe that this accounts for the oxygen you are thinking of in comparing succinyl CoA to succinate.  This reaction trades one "high energy" bond for another. 
« Last Edit: March 19, 2013, 11:08:04 AM by Babcock_Hall »

Offline gonzo

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Re: Confused about missing H in glycolysis
« Reply #27 on: March 20, 2013, 04:43:35 PM »
Yes that would account for the extra oxygen between succinyl CoA and succinate if there's a water produced from the reaction (I can't seem to find details of this anywhere, but I'm curious about it).

Offline Babcock_Hall

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Re: Confused about missing H in glycolysis
« Reply #28 on: March 20, 2013, 04:51:06 PM »
The combination of phosphate and GDP is basically the reaction of two acids forming an anhydride bond.  That produces water.  Conversely, if we hydrolyzed GTP, our products would be GDP and phosphate.

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