Thursday, November 17, 2011

Better Biochemistry: The Problem with Glycerol Phosphate and Citrate and What This Has to Do with Archaebacterial Membranes

Now that you've learned about Fischer Projections [Better Biochemistry: Fischer Projections] you're deady to tackle a more challenging problem. But first some background.

Glycerol phosphate is a major precursor in the synthesis of triacylglycerides and related compounds. These are the major lipid components of membranes. Here's a simplified pathway to show the importance of the glycerol backbone. ("R" stands for long-chain fatty acids.) I've deliberately avoided naming the glycerol-phosphate precursor because it requires a bit of thought.

Look at that glycerol phosphate molecule. It's drawn as a Fischer projection so it's unambiguous with respect to the other stereoisomer. However, there's still the possibility of ambiguity with respect to the number of the carbon atoms. I can illustrate this by showing you the four possible configurations and conformations (left).

The top two molecules are identical—one is simply the upside-down version of the other. But they have completely different names depending on how you draw them. They even differ in their "L-" and "D-" designations! The other stereoisomer (bottom) also has two different versions depending on how you draw it.

This can be quite confusing when you have to describe the reactions of lipid metabolism and name the various intermediates. Are they going to be 3-phosphate intermediates or 1-phosphate intermediates? We need a new rule to establish the proper numbering for the carbon atoms so everyone is on the same page.

You start with a Fischer projection where the hydroxyl group on C2 is to the left. The new stereochemical numbering (sn) system specifies that the "top" carbon atom becomes C1 and the bottom one is carbon atom number 3. Thus, L-glycerol 3-phosphate becomes sn-glycerol 3-phosphate to indicate that you are using the stereochemical numbering system. (The nomenclature for glycerol is specific for that molecule. The stereospecific nomenclature for other compounds is based on the RS rules of naming stereospecific compounds and it's much more complicated.)

Why is this important? Because we need unambiguous and definitive names for the various derivatives or else the scientific literature would become very confusing. Phosphatidylcholine is an example (left). Although most of us can survive quite nicely with the name "phosphatidylcholine" there has to be a universally agreed upon nomenclature for more sophisticated work. That's why the official name incoporates the stereochemical numbering system designated "sn-glycero" in the official name. It tells us that we're using the stereochemical numbering system.

Is this important for students in an introductory biochemistry course? No. On a scale of 1 to 10, where 1 is the lowest, I'd rate this at -3. Students do not need to know the precise nomenclature of lipid molecules and they do not need to know stereospecific nomenclature for that reason (but see below). This also applies to other molecules, particularly citrate, which also is numbered according to the stereochemical numbering system.

Not everyone agrees. Vasel Mezl wrote an article on the stereochemical numbering system for Biochemical Education back in 1996.1 He said,
The stereospecific use of the prochiral ends of glycerol and of citrate is a key concept that is presented in most biochemical texts, yet a nomenclature to designate those ends is usually not given. In fact, few textbooks present structures in a manner that is consistent with stereochemical priorities; among 30 basic biochemistry textbooks that were examined (including7-12), only three textbooks7-9 consistently orient the structure of the key prochiral intermediate, citrate, going from pro-R to pro-S in keeping with the Hirschmann and Hansen proposal6 and only one textbook7 correctly explain the sn system.
Reference 7 is Rawn (1989), the first version of the books I've been involved with. Here's an example similar to how we depicted citrate in that book (right). We included this in the legend: "The carbon atoms in the citrate molecule are numbered according to the proposal of S. Englard and K.R. Hanson .... The numbering begins at the carboxyl carbon of the pro-R carboxymethylene group of the citrate."

I didn't write that part of the textbook back in 1989 but I'm proud of the fact that we were the only book to correctly explain the nomenclature. However, by the time that Mezl wrote his article in 1996, we had already published the second edition of the big book (Moran, Scrimgeour et al. (1994)) and the first edition of the smaller Principles of Biochemistry book (Horton et al. (1993)). There was no mention of the numbering conventions for glycerol phosphate and citrate in those books. It was information that introductory biochemistry students did not need to know.

Undergraduates will be delighted to learn that the complicated nomenclature rules for citrate have been kept out of the most recent edition of Principles of Biochemistry and most (all?) other introductory biochemistry textbooks. However, I've restored an explanation of sn-glycerol and why that numbering system is important. There's a good reason for this; it's because of all the talk about the different kinds of lipids in archaebacteria (Archaea) and what that tells us about the origin of life.

Most bacteria, and all eukaryotes, have triglycerides that use sn-glycerol 3-phosphate as the backbone molecule. In archaebacteria, this precursor is sn-glycerol 1-phosphate. In order to appreciate that these are very different kinds of molecules, you need to understand the differences between the various configurations and conformations of glycerol phosphate and that's why it's back in the books.

You may be wondering why anyone should care about the triglycerides in archaebacteria. Well, you certainly won't care if your biochemistry course is all about human physiology and rat liver biochemistry! But if your course is based on an evolutionary/comparative approach to biochemistry then the difference is important because it suggests a fundamental distinction between two classes of bacteria. It means that you can't really tell which kinds of triglycerides were present in the last universal common ancestor (LUCA). It might even suggest that membranes and their lipids arose independently in the two lineages. To some, this means that lipids and membranes were late-comers in the evolution of life (e.g. Koonin, 2012).


1. In the interest of full disclosure, the journal Biochemical Education morphed into Biochemistry and Molecular Biology Education (BAMBED). I am a member of the editorial board of that journal.

Englard, S. and Hansen, K.R. (1969) Stereospecifically labelled citric acid cycle intermediates, Methd. Enzymol. 13:567-598.

Koonin, E.V. (2012) The logic of Chance: The nature and Origin of Biological Evolution. FT Press Science, Pearson Education Inc., Upper Saddle River, New Jersey, USA.

Mezl, V.A. (1996) Straightening out the stereochemical numbering sustem. Biochemical Ediucation 21:29-30. [Straightening out the stereochemical numbering sustem] [doi: 10.1016/0307-4412(95)00159-X]

6 comments :

  1. It might even suggest that membranes and their lipids arose independently in the two lineages. To some, this means that lipids and membranes were late-comers in the evolution of life (e.g. Koonin, 2012).

    Given that our cells mostly derive from archaea, but our membranes from bacteria (presumably from the mitochondrion), I'd say that it's more likely that one membrane architecture can simply supplant another. If (for example) the archaeal membrane were the more ancient, and a descendant lineage started producing a few molecules of the bacterial lipid arrangement, one could envisage a growing 'patch' of bacterial membrane that became the sole resident. When, on endosymbiotic union, those two systems again encountered each other, again the bacterial system won. Pure speculation, but I think the close involvement of membranes with energetics and other gradient processes argues against late arrival. Glycolysis is all very well, but...

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  2. Derive from archaea? For many traits we share a common ancestor with archaea but that doesn't make that common ancestor an archaeon.

    Why assume archaea have the more ancestral form? They are modern organisms like humans, E. coli, etc.

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  3. Derive from archaea? For many traits we share a common ancestor with archaea but that doesn't make that common ancestor an archaeon.

    Why assume archaea have the more ancestral form? They are modern organisms like humans, E. coli, etc.


    My point was that it is well established that we derive from an endosymbiotic event between an archaeon and a bacterium. The bacterium became our mitochondria, and the archaeon gave us much of the rest of the cell. Except the membranes. Forget ancestry; if it was an archaeon, it had archaeal membranes, and we don't.

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  4. My point was that it is well established that we derive from an endosymbiotic event between an archaeon and a bacterium.
    **********************
    My point is that you are incorrect. It is not a well established. Eukaryotes do share a common ancestor with archaea in many regards. That ancestral population was not an archaeon. Part of that population evolved and gave rise to archaea. Another portion of the population evolved and gave rise to eukaryotes, a population that evolved a symbiotic relationship with a certain set of bacteria. The common ancestor of humans and chimps was most likely not a chimp nor a human.

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  5. The common ancestor of humans and chimps was most likely not a chimp nor a human.

    But it was clearly a primate.

    True - we do not know if the ancestor would have been placed within the modern taxonomic grouping of "archaeon" organisms. But there are some who hold that eukaryotes group within achaeon (not sister to). Others do not. Calling the other camp "wrong" at this point is a bit premature.

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  6. @Anon

    I think you are splitting taxonomic hairs. There is so much gene transfer involved in these groups in any case ... I was initially referring to the membrane system only, and following the common convention of calling the one "archaeal" and the other "bacterial". Yes, the common ancestor of bacteria and archaea was neither bacterium nor archaeon. And we can't call it an archaebacterium either; that's taken. Call it what the heck you like. As far as its membranes are concerned:

    1) It had none
    2) It had the "archaeal" arrangement.
    3) It had the "bacterial" (and now eukaryote) arrangement
    4) It had some other membrane architecture.

    My original point was to reject 1).

    As to whether the bacterial or archaeal arrangement is more plausibly ancestral out of 2) and 3), I would still plump for 2) on the grounds that this is more stable in high-temperature environments. If life did not originate in such environments, then I'm wrong. But selection would favour a move to 3) as 'true' bacteria and archaea split. Endosymbiosis involved a fusion either of systems 2) and 3), or 3) and 3). In the former case. sole retention of 3) would be favoured during the cementing of the endosymbiotic union, since we are low-temperature organisms.

    Another portion of the population evolved and gave rise to eukaryotes, a population that evolved a symbiotic relationship with a certain set of bacteria.

    Myself, I favour the view that eukaryotes only arose on endosymbiosis.

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