6
$\begingroup$

On the Wikipedia article about pyrophosphate, it states that:

The group (pyrophosphate) is also called diphosphate or dipolyphosphate.

But for example, why is ADP apparently called adenosine diphosphate but not adenosine pyrophosphate? The same for geranyl pyrophosphate (GPP) instead of geranyl diphosphate? In which context the terms diphosphate and pyrophosphate are used?

$\endgroup$
4
$\begingroup$

Great question, but unfortunately without a great answer. Chemistry is very inconsistent in its naming of phosphates. In addition to the terms diphosphate and pyrophosphate, the term bisphosphate is also used.

Someone will probably put in an answer that cites "official" IUPAC or IUBMB rules. In many cases (but not all) these rules are more sensical and well thought-out than the terms in common usage in the field, but unfortunately, they are not in universal (or even wide) use.

Here is a rough breakdown of my sense of how these three terms are used:

Inorganic chemistry

  • Pyrophosphate indicates a phosphate anhydride.
  • Diphosphate indicates a salt that contains more than one (ortho)-phosphate anion.
  • Bisphosphate is not widely used.

Biochemistry

  • Pyrophosphate: used inconsistently to name an organic derivative of a phosphate anhydride. This is what you see in geranyl pyrophosphate (GPP). It is also used to refer to "inorganic" pyrophosphate anion, often abbreviated as PPi.
  • Diphosphate: an unfortunate term that is ambiguous, although usage is shifting towards synonymity with pyrophosphate. It is often used to mean "pyrophosphate" and but sometimes still used to mean "bisphosphate". Biochemically, the most important phosphate anhydrides are undoubtedly ATP, ADP, etc. These are never referred to as pyrophosphates even though that term would be more accurate. History has chosen "triphosphate" and "diphosphate" as the terms to use for adenosine-substituted phosphate anhydrides, icky though the term may be.
    Older literature will also use "diphosphate" to mean "bisphosphate". The name "fructose diphosphate was formerly in wide usage for what is now known as "fructose-1,6-bisphosphate", for example. That compound contains no phosphate anhydrides.
    Geranyl diphosphate is still a fairly widely used synonym for geranyl pyrophosphate. You see abbreviations for this molecule of both GPP and GDP. I prefer the name GPP, but unfortunately not everyone uses it.
  • bisphosphate: Now in wide usage as the preferred term for an organic molecule with multiple ortho-phosphate esters, such as fructose 1,6-bisphosphate. Biochemists have done a relatively good job of adopting this usage in modern times.

A common confusion that stems from this nomenclature concerns the stability of organophosphate compounds. Phosphate esters, e.g. glucose-1-phosphate or glucose-6-phosphate or adenosine monophosphate, are much more stable and less reactive than phosphate anhydrides such as acetyl phosphate (a mixed anhydride of acetic acid and phosphoric acid) or the phosphoanhydride bonds in adenosine triphosphate (ATP).

$\endgroup$
2
$\begingroup$

Pyrophosphate came about from heating inorganic phosphates, with the loss of water to create new compounds. Since ADP and GDP are organic compounds, diphosphate is used.

See the Dictionary definition:

Chemistry. a combining form used in the names of inorganic acids, indicating that the acid's water content is intermediate between that of the corresponding ortho- (more water) and meta- (least water) acids ...

$\endgroup$
  • 2
    $\begingroup$ But geranyl pyrophosphate is also an organic compound, and is not generated by heat. My guess is that the researchers studying terpenoid chemistry were different from those working on nucleotides and the different nomenclatures just stuck. $\endgroup$ – user137 Nov 30 '14 at 12:04
  • $\begingroup$ @user137 It's possible that when it was synthesized for confirmation, that they used pyrophosphate and a terpenoid to create geranyl pyrophosphate. The structure of ADP was probably determined later, and confirmed by a different team, so the diphosphate name was used. Unfortunately, a quick search finds a lot of information about geranyl pyrophosphate synthase. $\endgroup$ – LDC3 Nov 30 '14 at 13:50
  • $\begingroup$ Yeah, but if geranyl pyrophosphate was discovered and named before the enzyme, they would have named the enzyme after the molecule, so that's reasonable. $\endgroup$ – user137 Nov 30 '14 at 19:40
-3
$\begingroup$

Pyro- is for when both phosphate are together, di- means the phosphates can occur anywhere in the molecule.

$\endgroup$
  • 1
    $\begingroup$ This does not provide an answer to the question. To critique or request clarification from an author, leave a comment below their post - you can always comment on your own posts, and once you have sufficient reputation you will be able to comment on any post. $\endgroup$ – M.A.R. Jul 2 '15 at 15:54
  • 3
    $\begingroup$ @M.A.Ramezani I think it does provide an answer to the question, it just needs fleshing out a bit. Perhaps if you could expand on what you mean by 'both phosphate are together' then this could form the basis of a good answer. $\endgroup$ – bon Jul 2 '15 at 16:44

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.