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Name: Rozalia
Status: Student
Grade:  Other
Location: N/A
Country: Australia
Date: Summer 2009


Question:
May I ask a question, regarding the statement: "...Note that nucleotides have only one phosphate group, whereas ATP has three, so ATP is not strictly speaking a nucleotide..." Sarina Kopinsky, MSc, CGC, HED, on the subject of 'Nucleic Acid vs Nucleotide 2002066', please?

My question is: Since the forming of a phosphodiester bond is a catalyzed reaction, is it not necessary for the nucleotides to have more than one phosphate groups, in order to use the released energy from the breaking of their phosphate bonds, to fuel the catalyzed reaction?



Replies:
All nucleotides are in fact nucleotide triphosphates. The diphosphate groups are clipped off during DNA or RNA synthesis.

Ron Baker, Ph.D.


It's strictly a matter of the definition you use.

A nucleotide is a nucleoside bonded to a phosphate group. Should it be bonded to exactly one phosphate group, or is the definition more flexible, so that it may contain two, three, or even more? That's probably the issue addressed in the quote you cite.

Richard E. Barrans Jr., Ph.D., M.Ed.
Department of Physics and Astronomy
University of Wyoming


Thank you for your question. It’s exciting to learn that someone reads the archives.

First I’ll try to clarify what I said before, and then I’ll tell you what I think now.

I said originally that a nucleoside = a sugar + a nitrogenous base. A nucleotide = a sugar + a base + a phosphate = a nucleoside monophosphate. If so, ATP (and also GTP, CTP, TTP) would not strictly be defined as a nucleotide, since they have three phosphate groups and not one.

The only question was about the language, whether to use the word nucleotide for the triphosphate form. The actual biochemistry of energy supply is well understood.

Whether you call ATP a nucleotide or not, your point is correct, that energy is made available when a phosphate group breaks off from ATP. Yes, ATP needs more than one phosphate. (After the first phosphate group is gone, it is no longer ATP, of course; it is ADP, with two phosphates.)

The wording of the original question 2002066 was a bit ambiguous. The questioner asked why ATP is called a nucleotide and not a nucleic acid, but then defined a nucleotide as a sugar + base + phosphate, whereas ATP has a sugar + base + three phosphates.

It’s quite confusing because a nucleic acid is a long chain of nucleotides strung together into a chain of DNA or RNA. In the chain, each nucleotide has a sugar + base + one phosphate. But the separate nucleotides floating around in the cell may have one, two or three phosphate groups attached. The question is whether these versions are all called nucleotides.

Today I consulted a biochemist who checked his favorite biochem textbook, and I also Googled the definition of nucleotide. I found both definitions being widely used. Perhaps both were widely used before, and I was simply wrong. I apologize for any confusion.

Many websites say: a nucleotide is a sugar + base + phosphate. Many other websites say: a nucleotide is a sugar + base + one, two or three phosphate groups.

I don’t know if one definition is more strictly accurate than the other. (I am a genetic counselor, not a biochemist, though I majored in biochemistry many years ago.)

Languages evolve and words may grow new layers of meaning as they become more widely used. If people communicate well enough to understand each other, are these new usages wrong, or are they acceptable? That is a philosophical question about linguistics.

There may also be regional differences, e.g., between Australia and elsewhere, as to how people tend to understand a word.

Now that DNA is so famous, thanks to the Human Genome Project and other amazing research, the public are better educated about science (yay!), and often say words that used to be spoken mostly by scientists.

Since both definitions are widely used, you can take your pick. Why not use the definition your teacher prefers?

Sarina Kopinsky, MS, CGC
July 2009; Denver, Colorado



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