Talk:Nucleotide

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Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT (talk) 05:29, 17 January 2022 (UTC)

Phosphates vs phosphate groups

The issue of 'how many phosphates' has been raised here multiple times, and the resolution reached has been unsatisfactory, in part because the issue is a quagmire. There really are conflicting definitions of a nucleotide, but part of this seeming conflict is due to generalization, part due to simple semantics, and part actual differing definitions. Generalization: most definitions of a nucleotide are really definitions of a 'typical' nucleotide, thus they describe it as having a phosphate group on the 5'-C of the sugar. That is the most common configuration, but not the only one. There are nucleotides with a phosphate group on the 3'-C, or even compounds like Guanosine pentaphosphate (pppGpp), which is a nucleotide that has separate phosphate groups on both the 5' and 3' carbons, but compounds of this type are extremely rare, and so not generally included in the standard definition. Semantics: often as well, the definition is given in the context of describing a nucleic acid component, in which case a nucleotide, the individual unit of that polymer, has one phosphate only. Separately, part of the issue is not how one defines a nucleotide at all, but how one defines a phosphate group. It is tricky because a 'phosphate group' in everyday molecular biology parlance is just used synonymously with a 'phosphate' moiety. However, in defining a nucleotide as having one phosphate, some are using a more precise definition. See for example, T A Brown, Genomes 3, 2007, describing the components of a nucleotide: "a phosphate group, comprising one, two or three linked phosphate units attached to the 5'-carbon of the sugar." In this sense, the distinction between ACS and biochemistry text definitions is not really a difference at all, as one is referring to a phosphate group and the other to 1, 2, or 3 phosphates. The Oxford Dictionary of Molecular Biology actually gives three definitions: 1) specifies a single [ortho]phosphate on either the 5'- or 3'-C, representing a single subunit of a nucleic acid, 2) says a nucleoside with a 'phosphate or oligo-phosphate' (i.e. Brown's definition of a phosphate group); and 3) any chemical compound containing a nucleotide (defs. 1 or 2). This one is too vague to be useful as directly expressed (it would seemingly include adenylated proteins), but it then gives examples that include nucleotides that have extra phosphates attached at other carbons (e.g. pppGpp), or two nucleotides linked together (NAD, FAD, etc.). Thus we need to be a bit careful in how we define this, and the excursion we take contrasting ACS with biochemistry sources seems misplaced. I have taken a whack at clarifying these issues, primarily by distinguishing phosphates from phosphate groups, but others may want to deal with the issue differently than I have. Agricolae (talk) 07:44, 18 April 2020 (UTC)

There are two definitions of nucleotide in scientific literature. Both definitions should be explained in the article, saying "the IUPAC says that ..." and "other reliable books say that...", with references.--Miguelferig (talk) 11:53, 3 October 2021 (UTC)

And a 'nucleotide sugar' would be an additional problem. For example, UDP-galactose.--Miguelferig (talk) 17:55, 13 August 2022 (UTC)

5-nucleotide term used and not defined

The introduction mentions 5-nucleotides but nowhere is the term defined. We are left to infer that a 5-nucleotide, if it is a well defined thing at all, is defined by some particular combination of the consistituents previously mentioned, e.g., the sugar. Being left to infer this has no place in this kind of article. 2601:600:877F:4660:58DB:7E6B:FE39:B762 (talk) 08:39, 14 July 2025 (UTC)

Pentose sugar

I don't dispute that the convention is to pretend that deoxy ribose is a pentose and a sugar. It surely is a gross distortion of the definition to claim C5-H9-O3-N(R,R') is "a pentose", let alone its diphosphate ester. It's probably too deeply embedded in the terminology for the distortion to be corrected, but surely it's noteworthy that it does not meet the classical definition of what a sugar is. It is, in fact, a sugar derivative (or better said, a derivative of the sugar ribose). But not all derivatives of X maintain their membership in the set of Xs. Methoxy ethanol is (still an alcohol) but ethyl methoxylate is not (or is it methyl ethoxylate?).) ~2026-92463-4 (talk) 22:26, 23 March 2026 (UTC)

Structure

The figure (currently the 2nd figure showing a double helix stub, as well as some other very poorly described entities) fails and the body of the article fails, miserably, to discuss the actual structure of the so-called sugar. IF the stick figure in that image's bottom half is taken seriously (there are good reasons why it shouldn't be taken seriously), then the 1' N-bond is "straight up" from the plane of the furanose sugar (deoxy ribose). Is it really? citation please. As a flawed Haworth projection, I believe the drawing gets the C-O bonds right (citation please!). The reader would have to go somewhere else to discover that the 5 membered ring is roughly planar, that the 1', 3' and 4' ring carbons are chiral (or should I say could be chiral, as far as know the stereo-isomer doesn't vary). Nor does it mention (as I've harped on before) that the reason that "unit" is claimed to be a sugar is because it is (from what I've read) a metabolic product with ribose as an earlier 'starting material' rather than it actually qualifying as a sugar based on its composition. (i.e. it is a sugar derivative, at best). The caption makes the ludicrous claim that it is showing "At the upper right four nucleotides form two base-pairs:..." but that drawing shows two molecules, each composed of two nucleotides which have been joined (that is, the two of the 3' -OH groups have been replaced by an O-P linkage). These fail to be captured by the definition of nucleotide, given. A naive reader might think "Oh! this is a tetraphospate nucleotide!" Yeah, totally clear, right? Also it's pretty pathetic that this article avoids the use of the term 'nucleoside', as if it has no relationship to the nucleotide. There's not even a mention of it in the See Also section! I disagree with the editors lumping together various DIFFERENT definitions of what a nucleotide is. I sympathize with them in that it's not easy to articulate that in some contexts the nucleotide is strictly a monophosphate, in others a mono or polyphosphate and in some other contexts (maybe most?) the term refers to a structural group, not a chemical compound. But that's why they're paid the big bucks, right?~2026-92463-4 (talk) 23:19, 23 March 2026 (UTC)