Talk:Nucleotide

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Images

I uploaded two images in the "Synthesis" section and i made them as thumbs as i thought that having them in full size would take too much space. Well if anyone feels that they have to be full size then go ahead and do it. BorisTM 12:20, 4 November 2005 (UTC)

Introduction

There was some redundancy like - heterocyclic nucleobase (nucleobases by definition are heterocyclic), pentose sugar (pentose by definition is a sugar). Nucleotides are class of molecules and not all of them have purine or pyrimidine derivative as their base or pentose as their sugar. Boris 03:45, 16 December 2005 (UTC)

Genetic nucleotides information needed

There should be some distinction between nucleotides in nucleic acids (DNA, meaning Deoxyribonucleic acid and RNA,meaning Ribonucleic acid) and those used in other ways, most prominently ATP. Maybe there should be a few separate articles discussing these different types rather than making people have to read the articles on adenine, guanine, thymine, cytosine, and uracil and have to find the similarities for themselves.

Typo in picture

There is a typo in the first picture, but I'm not able to edit it easily.

Change 'Deoxyribose' to 'Deoxyribose'

Thanks. --64.251.84.43 03:14, 24 February 2006 (UTC)

There is another typo where is says triphoshpate

There is another typo in the first figure: "Pyramidine" should be "Pyrimidine". I cannot edit it easily. Rbcody (talk) 21:27, 17 November 2007 (UTC)

person above me, you just said to change deoxyribose to deoxyribose. how can you change one word to the same word....

Nucleoside vs Nucleotide

Resolved

 – also, the article has been updated in the intervening time to reflect consensus Shanata (talk) 15:50, 11 March 2009 (UTC)

I am not a biochemist by training, but all my references list the various Nucleotides as Nucleoside monophosphate, Nucleoside diphosphate, and Nucleoside triphosphate. Which is correct, or are they both correct? Ted 15:26, 28 February 2006 (UTC)

They are both correct. -- Boris 23:20, 6 March 2006 (UTC)

No. nucleoside monophosphate, or nuclelotide. saying "nucleotide monophosphate" is redundant, as "nucleotide" = "nucleoside phosphate" and "nucleoside phosphate monophosphate" sounds a little silly.

As far as my understanding, if a phosphate group attached it is a necleotide otherwies it is a necleoside.

Yes, I agree. There's no such things as nucleotide phosphates. It's either nucleoside phosphates, or nucleotides. 130.243.248.239 14:35, 19 November 2006 (UTC)

Yes, I also agree.

Nucleoside vs Nucleotide: How many phosphates?

The first sentence of the section Nucleotide structure reads: "A nucleotide is composed of a nucleobase (nitrogenous base), a five-carbon sugar (either ribose or 2-deoxyribose), and one phosphate group." Yet the illustration in the upper right corner indicates that nucleosides with ONE OR MORE phosphate group are nucleotides. Similarly, the entry for ATP (Adenosine_triphosphate#Physical_and_chemical_properties) describes ATP as being a nucleotide. Unless I am given a reason to do otherwise, I intend to alter the first sentence of the "Nucleotide structure" section to read: "A nucleotide is composed of a nucleobase (nitrogenous base), a five-carbon sugar (either ribose or 2-deoxyribose), and one or more phosphate groups." --Ben Best 17:51, 27 September 2012 (UTC)

The figure caption and the ATP article are incorrect. The ACS Style Guide clearly states that a nucleotide has one phosphate. I will make the necessary corrections. Antony–22 (^talk⁄_contribs) 06:41, 28 September 2012 (UTC)

Thanks for your input, Anthony. --Ben Best 14:36, 28 September 2012 (UTC)

Although there is nothing incorrect in the very nice figure, it's a little uninformative to not actually define nucleotide graphically. Would it be useful to add another dashed bar below nucleoside triphosphate indicating that anything spanning the base/ribose and phosphates is a nucleotide? Ggggt (talk) 12:38, 30 December 2012 (UTC)

Regarding the figure "Structural elements of three nucleotides": All of my resources say "nucleoside" for ribose + base, and a distinct term of "nucleotide" for ribose + base + phosphate(s). I motion to change the graphic please, it is inconsistent with biochemistry textbooks. — Preceding unsigned comment added by Dlucibello (talk • contribs) 20:38, 28 March 2019 (UTC)

Nucleosides OR Nucleotides

In the same vein as the above topic... Why do the introduction figures of this article focus on nucleosides? The explanation of the difference between nucleosides and nucleotides should be more emphasized, so as not to confuse readers.
A nucleotide is a PHOSPHATE + pentose + base
A nucleoside does NOT include the PHOSPHATE.
--159.178.76.107 (talk) 19:25, 6 November 2009 (UTC)

Re-write

The page was kinda confusing, and had lots of pictures but little text. I tried to improve things, but biochem isn't my strong suit and I may have just messed things up. Further, the section bases at the bottom is very messed up because of the mixture of diagrams. The pyrimidine section could definitely use a lot more text, right now it's just a single sentence that says 'look at the diagram'. WLU (talk) 14:59, 4 January 2008 (UTC)

I don't know if this is related to you or not - I found the following rather confusing:

"Nucleotide synthesis and structure A nucleotide is composed of a ring of nitrogen, carbon and oxygen atoms, a one carbon sugar (together referred to as a nucleoside) and one phosphate group."

Where it says one carbon sugar, it links to 5 carbon sugars. I believe it should say five carbon sugar. Have I misunderstood or is there an error? —Preceding unsigned comment added by 131.111.213.45 (talk) 21:34, 1 June 2008 (UTC)

You're right, should have been five carbon. Fixed now, thanks! Schu1321 (talk) 21:54, 1 June 2008 (UTC)

The same sentence has been used twice in two different sections "Nucleotides can be synthesized through a variety of methods both in vitro and in vivo." I think that section should be divided clearly. First should talk about strucutre and chemical properties, 2nd about biosynthisis, then 3rd about in vitro synthesis.

Also the diagrams referse to intermediates in biosynthesis by their abbrevations. These should be expanded upon and referred to in the text. --Strathallen (talk) 20:15, 6 December 2008 (UTC)

In the Synthesis section it states "The first step in nucleotide synthesis is the formation of a nucleoside, the nitrogenous base joined to a sugar." This is not correct. Purine and pyrimidines are biosynthesised in quite different manners.--Strathallen (talk) 21:12, 19 December 2008 (UTC)

Types of bases section. "(Thymine is uracil with an additional methyl group.)" is a redundant non-sequiter and should be removed. In fact I will do this now. --Strathallen (talk) 21:20, 19 December 2008 (UTC)

I have moved much of the structure sentences which had been spread in diverse section into the same paragraph. Also removed erroneous information about synthesis. I have expanded a little on pyrimidine synthesis. How do others feel about changing the purine synthesis detail. It seems to me that it contain too much information about enzymes--Strathallen (talk) 22:07, 19 December 2008 (UTC)

Un-merge kilobase

When a user looks up kilobase, he wants to find its definition quickly. Currently, kilobase just redirects to the TOP of the base pair article, which much less useful and requires manually searching through that article to find the definition of kilobase.76.85.197.151 (talk) 08:57, 11 May 2008 (UTC)

Nucleotide structural diagrams

Does anybody else feel that this schematic is an eyesore and vastly obtrusive? Surely we don't need the chemical structure of each with tri di and mono phosphates. Wisdom89 _{(T / ^C)} 03:23, 20 May 2008 (UTC)

I would agree that they seem to be a bit much for a general article. Is there somewhere else more appropriate for them? Schu1321 (talk) 03:31, 20 May 2008 (UTC)

Well, if they were removed from the article they wouldn't be orphaned. I say that each one could stay within its own article. Wisdom89 _{(T / ^C)} 03:39, 20 May 2008 (UTC)

Ok, I've gone ahead and removed them. I think the article will breathe easier now. If anyone has an earnest objection to this, feel free to discuss it here. Wisdom89 _{(T / ^C)} 04:21, 20 May 2008 (UTC)

I would think that that a complete overhaul of all the strutures in this page is appropriate. They are a bit garish and probably contain more detail than is required to illustrate the point. Also the text is not clear about synthesis and the diagram should illustrate the text, not act as a substitute. --Strathallen (talk) 21:18, 19 December 2008 (UTC)

Is a structure of ribose appropriate here? I feel it is redundant since the structure is present on the ribose page as is the deoxyribose on its respective page. What is important as far as structures go is the relevant bases and the the relationship between base, sugar and phosphates. The other central theme should be biosynthesis of nucleotides, since nucleobabses and nucleosides are derived from nucleotides.--Strathallen (talk) 06:55, 22 December 2008 (UTC)

Moles in human body?

How many moles of nucleotide in the human body? --Una Smith (talk) 00:44, 1 January 2009 (UTC)

I could probably calculate a very rough estimate for you, but it wouldn't really be a very informative number. Why is it that you want to know? Tim Vickers (talk) 17:05, 2 January 2009 (UTC)

Synthetic nucleotides

As per Dr. Steven A. Benner's spearheading research, I think a new section mentioning the new synthetic nucleotides needs to be added, especially what they are and diagrams of them. There are 8 in all named: Z, P, V, J, Iso-C, Iso-G, X and K, which are permutations of the constituents of those molecules found in non-synthetic DNA. 204.56.7.2 (talk) 22:40, 23 March 2009 (UTC)

Figure is wrong.

Fig1 looks incorrect to me. The general label should be nucleoside monophosphate, nucleoside diphosphate and nucleoside triphosphate. Any chemists here to confirm the nomenclature? David D. (Talk) 07:15, 17 December 2009 (UTC)

Activated nucleotide

The article never defines what it means for a nucleotide to be activated/inactivated. Other wiki article w/ the term link here, assuming it's defined.

Foggg (talk) 20:34, 15 February 2010 (UTC)

In what context? The only links using that phrase I can find refer to activated nucleotide sugars, so aren't referring to nucleotides. Tim Vickers (talk) 23:14, 15 February 2010 (UTC)

Pyridine nucleotides

Unless this article is intended to focus solely on nucleotides' role in nucleic acids, it would be worth including a paragraph on pyridine nucleotides, e.g. nicotinamide mononucleotide, NMN, and flavin nucleotides, e.g. flavin mononucleotide, FMN. Although never found in nucleic acids, these play an important role in metabolism, and the nomenclature makes it clear that they are nucleotides in their own right, not merely coenzymes with a nucleotide component like CoA. 96.54.32.44 (talk) 01:07, 4 December 2010 (UTC)

Purine ribonucleotides - Reaction 1

In the text it says "This reaction is also shared with the pathways for the synthesis of the pyrimidine nucleotides, Trp, and His. " Which links to Tryptophan and Histadine, but they are amino acids, not nucleotides. Perhaps this should be ". . . synthesis of the pyrimidine nucleotides, Thymine and Cytosine"

Also, the next sentence "As a result of being on (a) such (a) major metabolic crossroad and the use of energy, this reaction is highly regulated." doesn't make sense.

Unfortunately I don't know enough biochemistry to make the correction, is someone more knowledgeable able to assist? —Preceding unsigned comment added by 220.233.16.16 (talk) 11:35, 26 April 2011 (UTC)

Figure for UMP synthesis

The last part of the figure for UMP synthesis is incorrect (part 6). The Carboxylic group that was lost as CO2 in the step before is not removed. — Preceding unsigned comment added by Jeffpkamp (talk • contribs) 22:22, 27 September 2011 (UTC)

Radionucleotides?

Would someone be familiar with the term radionucleotide? Is this term actually used with a meaning such as radiotracer-labelled (³²P?) nucleotide. Wikipedia now has a redirect at radionucleotide which points instead to the article on Radionuclide, suggesting that the term is just an error by people who mean radionuclide, or else that some Wikipedia editor thought it is such an error. There has been discussion at Talk:Radionuclide#nuclide vs. nucleotide about changing the redirect to point here instead, but since this article now contains nothing about radionucleotides, it seems best to ask here first if the term is really used to mean radiotracer-labelled nucleotide. If so the redirect can be changed, and also perhaps a short section about radionucleotides can be added to this article. Dirac66 (talk) 01:17, 25 October 2012 (UTC)

I've never heard or seen anyone in the business say "radionucleotide"; it's always "hot ATP", or "alpha-P32-dTTP" or some such. Seems most likely that someone just confounded nuclide and nucleotide. --John Mackenzie Burke (talk) 21:08, 16 November 2012 (UTC)

Definition of nucleotide

Well, geez, the ACS Style Guide says that nucleotides have only one phosphate, but Alberts says they can contain multiple phosphates. I was afraid of something like that. How shall we resolve this? Antony–22 (^talk⁄_contribs) 20:10, 16 November 2012 (UTC)

I'm quite sure the ACS is wrong in this case. And it's a common error; for example the NIH genome center has the same mistake on one its educational pages. Nucleotides containing one or more phosphates has been standard biochemical parlance for a long time. I just checked three Biochemistry textbooks (Lehninger 1975, Stryer 1988, and Garrett/Grisham 2007) and they all say clearly that things like ATP and ppGpp are nucleotides. But I must confess to some, er, skepticism regarding ACS as an authority on nucleic acids chemistry--in the galleys of the first paper on ribozymes that we published in Biochemistry, they changed each and every one of our G's, A's and C's to gly, ala, and cys! --John Mackenzie Burke (talk) 21:02, 16 November 2012 (UTC)

I always thought that calling ATP and so on nucleotides was the common error; the ACS Style Guide, IUPAC Gold Book, and Bloomfield/Crothers/Tinoco 2000 back me up here. ACS and IUPAC are definitely reliable sources. It might just be that the chemistry and molecular biology communities have different usages of the term, so both usages should be discussed. (For example, as a chemist I cringe every time I see the word catalysis sloppily used to describe a self-cleaving ribozyme: it is not a catalytic reaction because the reactant is not regenerated!) Antony–22 (^talk⁄_contribs) 22:34, 30 June 2014 (UTC)

Why does "thionucleotides" redirect here?

Not mentioned or defined in article. 109.157.79.50 (talk) 07:06, 9 January 2015 (UTC)

Error in Synthesis for UMP picture??

In the Synthesis picture on the left the step from Orotate to OMP to UMP - isn't that wrong?? UMP is shown with a -COO Group. Thats still OMP not UMP isn't it? — Preceding unsigned comment added by 46.59.141.109 (talk) 15:27, 6 July 2015 (UTC)

Nice work for being the first to notice that after 9.5 years.  Fixed, thanks. Adrian J. Hunter^{(talk•contribs)} 12:19, 11 July 2015 (UTC)

picture at top is ribose ring?

The nucleotide shown has an OH instead of just an H but it is still called deoxyribose? Or am I being stupid because the OH is on the left side instead of the right? 195.195.168.33 (talk) 14:48, 14 October 2019 (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)