Talk:Ribonucleotide

message: We are currently working on this article for our Molecular Cell Biology class and we have some ideas as to how we can improve this article. Some information that we want to include are the history and discovery of ribonucleotides, how ribonucleotides differ from deoxyribonucleotides, the roles that ribonucleotides play in RNA and how they are involved in transcription as well as how ribonucleotides are precursors to deoxyribonucleotides. Let us know if there are any suggestions as to how we can further improve on this article and if there are any additional information we should add along the way. Jessicalau90 (talk) 20:12, 13 March 2013 (UTC)
thread_title:  Ideas on improving the article 

message: Should we include non-standard ribonucleotides, like AIR, AICAR etc? --kupirijo (talk) 22:37, 10 April 2011 (UTC)
thread_title:  Other ribonucleotides 

message: Hi guys, I will be doing a peer review for this article as a participant in the JHU Ambassador program.
*Coverage and Scope: I see that most of the essential information is present and I can not think of any blatantly obvious sections that I would be able to add. The sections seem to be organized logically as well so as to flow. If possible, I would like to see a section detailing perhaps the cutting edge of ribonucleotide research either in a biochemistry setting or in a clinical setting. Interactions with enzymes might be a good to talk about if you really want to go into detail. Another section that I think this article could use would be about ribonucleotide analogs and perhaps their structures, relevance and interactions with enzymes and such. 
*Research and References: All of the references that I was able to double check appeared to be suitably and appropriately represented. I was not able to find any instance of unacceptably close paraphrasing or misrepresentation of the reference material. However, I do feel that this article should have a lot more references considering how much attention ribonucleotides have gotten over the years. In fact, I noticed that most paragraphs have only a single reference at the end. I think this would be improved if we could include a reference at the end of almost every sentence or every other sentence. That way, readers can more easily verify the origin of the information used in each section. Furthermore, I think it would be helpful if more than one reference was used for each paragraph or even single sentences, since multiple corroborating sources lend greater credibility.
*Writing Quality: I have no problems with the writing quality, as it is appropriate in all sections. Language is clear and straightforward with little or no fluff. I still think that there are minor issues  that can be corrected though. The second and third paragraphs in the Discovery section start with “It was...” and “It wasn’t...” respectively. I’m not sure if using the passive voice would be the most prudent choice here. I would personally prefer an active because I think that sounds more straightforward but you might want to check with somebody else since I could be wrong about this. This article in general seems to consistently follow the Wikipedia manual of style and I haven’t found any major abnormal deviations. I do not see any problems with too much jargon.
*Visuals: The images are clear, very straightforward, and represent the subject matter accurately. It might be useful to have one or more images pointing out the different components of the ribonucleotide such as the exactly where the D-ribose makes up the pentose component or exactly where the base is. Perhaps different colors could be used to differentiate between the different components of the various ribonucleotides. Later when you add more images, it might be good to put all four of the ribonucleotides in one image to save space and show them all at once. Also if possible, I would considering a types of ribonucleotide models such as ball and stick or space filling models to give a better idea of the bond angles among the different components and atoms. As I see it now, the first image used in the lead section is at 450 pixels, which I think is too big. It takes up around half of my screen.
*Stability: The subject and writing appears to be stable for all practical purposes. The ribonucleotide is a fairly straightforward topic. It has been the subject of many studies and much has already been deduced since it is such a fundamental part of many important biological mechanisms. I believe it is unlikely that this writing will become significantly obsolete or outdated anytime in the near future.
*Neutrality: The writing appears neutral for the most part. Much of what we know seems to be well established already so there seems to be little controversy and few opposing views to consider. Thanks for reading! Bcheon1 (talk) 20:09, 10 April 2013 (UTC)
replies: text:  Thanks for your thorough input Bcheon1. We will definitely take what you have mentioned into consideration for our upcoming edit. You did a great job of breaking it down into different scopes and kept it real organized. Feel free to provide any more input as this article progresses. Binhtruong (talk) 00:38, 24 April 2013 (UTC)
replies: text: No problem! Don't hesitate to let me know if I can clarify anything I said. Though the parts that I checked seemed okay, it seems like I should have done a more thorough job looking for close paraphrasing. If you want to split up the double checking, I'd be happy to help out with that. Bcheon1 (talk) 04:55, 25 April 2013 (UTC)
replies: text: I just want to echo Binh's reply. Thank you for your review and comments/feedback. We have definitely taken some of your feedback and made some changes in our article. I am looking into adding a section on ribonucleotide analogs and will get to it in the next few days. I am also looking to add more images, perhaps different views on the ribonucleotides (ball and stick model, like you mentioned). I'm not sure about the image in the lead section being too big-it looks fine on my screen. (Binh-how does it appear on yours?) We might have to change it/resize it if it's a problem too. As for the paraphrasing, it'd be great if you could do a quick check for us as well. Thanks a lot for your help! Jessicalau90 (talk) 11:35, 25 April 2013 (UTC)
replies: text: That sounds good, and I'm glad that you guys are making great progress. I'll check back later to see if I can offer further assistance. Bcheon1 (talk) 13:32, 25 April 2013 (UTC)
thread_title:  Comments from Bcheon1 

message: At a glance the page looks great. The sections appear well organized and the paragraphs are good sizes for a Wikipedia article (not too long or too short). The figures are helpful in visualizing the descriptions of the ribonucleotides and the table is also a great summary of information. 
 
I am confused about one thing though. Our textbook (on pg 103) defines a nucleotide as a nucleoside that has one or more phosphate groups added to it. But in your lead section you define it as only having one phosphate group attached. Maybe you could clarify this? I think it is important for readers to understand that ribonucleotides can occur in the cell with one, two, or three phosphate groups. 
The lead section also defines a ribonucleotide as a nucleotide with ribose as its sugar. I think it would be helpful if you briefly described the structure of a nucleotide here as well since many people who just want a quick answer of what a ribonucleotide is might only read that section and not the rest of the article.
 
The lead section also includes the sentence “It is considered the molecular precursor to the building blocks of nucleic acids.” Isn’t the ribonucleotide a building block itself (at least for RNA), not a precursor to a building block? I’m guessing this is supposed to account for the fact that the ribonucleotide is reduced to form a deoxyribonucleotide, the building block of DNA. So in that case it is a precursor to a building block. I just think this sentence is a little confusing. Maybe you could first say that ribonucleotides are the building blocks of one kind of nucleic acid – RNA, and then separately explain that they are also the precursor of the building block of DNA. 
 
The second paragraph and last sentence of the lead section do not have citations and so it is unclear where that information came from.
 
In the section “phosphodiester bonds link successive nucleotides in nucleic acids”, in the first sentence I think it would be more clear if you specify that the phosphate group is joined to the 3’-hydroxyl group of the pentose of the next nucleotide. In the same section, in the sentence that talks about how unlikely mononucleotides are to combine, you may want to specify that this is without the assistance of an enzyme. Otherwise it may be confusing to the readers what you mean.
  
There are several sentences in this article that are copied word for word from Lehninger. They have citations, but you should probably review the policies and guidelines covered in unit 4, specifically the handout called “Understanding and avoiding plagerism.” It is good information, but I think I read somewhere that plagiarized writing can be deleted from Wikipedia so that is something to be careful of. 
 
Overall I think you have a lot of good and well organized information and it is a great start! I hope my suggestions have been helpful. Aluquette (talk) 02:53, 11 April 2013 (UTC)
replies: text:  Thanks for your input and pointing out key areas we can improve on, Aluquette. As for the areas that need clarification, we will definitely look into it on our upcoming edit. Feel free to provide anymore suggestions as this article progresses. Thanks again. Binhtruong (talk) 00:38, 24 April 2013 (UTC)
replies: text: Hi Aluquette, thanks a lot for your suggestions! They were very helpful. Also, thanks for the warning on the citations. We have made quite a few changes rewriting and making sure our information is more clear and less confusing. The page is definitely still a work in progress so please feel free to provide more feedback as time goes, as Binh mentioned. Jessicalau90 (talk) 11:38, 25 April 2013 (UTC)
replies: text:  Glad my suggestions were helpful! Looks like you guys are making a lot of progress. One other suggestion is to add more links. I know this is something I've been putting off somewhat myself :). I wasn't sure how often to link words so I asked Klortho and here's what he told me... "See Wikipedia:Linking#Overlinking_and_underlinking. The quote specific to your question is, "A term should be linked, generally, at most once in an article's lead, perhaps once again in the main article body, and perhaps once at first occurrence in each infobox, table, caption, and footnote." Hope that helps! Aluquette (talk) 01:40, 30 April 2013 (UTC)
thread_title:  Comments from Aluquette 

message: I started to review your article, but I quickly discovered that there were major sections that were copied verbatim from Lehninger.  I will quote my fellow OA:
I would like to make that even stronger:  plagiarism is very much an issue of academic integrity, and could not only get you a zero for this group assignment, it could get you kicked out of the graduate program.  Plus, it is a waste of my, Keilana, and Dr. Ogg's time.
I removed the sections that I found, but I haven't gone through the whole article looking for all instances of plagiarism -- I will leave that up to you two.  Please remove and rewrite any plagiarized material, and then let us know when this is done, so we can continue to review it.
Klortho (talk) 23:31, 21 April 2013 (UTC)
replies: text: Thanks for catching that Klortho. I'm sure it was either unintentional or just a misinterpretation of the Wiki Rules. We'll be more diligent and careful in regards to our next entries and will re-evaluate our past submissions for plagiarism. Binhtruong (talk) 23:49, 23 April 2013 (UTC)
replies: text:  Great, thanks!  Klortho (talk) 01:39, 24 April 2013 (UTC)
replies: text:  Hi Klortho, thank you for the warning on the issue of plagiarism- it definitely was not our intention to plagiarize. We have re-written everything and included more references throughout the article. Please provide us with any more feedback/comments. We are still working on adding more information within the next few days. Thank you. Jessicalau90 (talk) 11:46, 25 April 2013 (UTC)
replies: text:  Okay, thanks again for attending to this.  I'll review it this evening! Klortho (talk) 00:15, 26 April 2013 (UTC)
thread_title:  Comments from Klortho 

message: * Keep in mind that my comments are just suggestions -- don't feel compelled to take my advice if you disagree with it.
* The opening of the lead could be in a little bit less intimidating language, in my opinion.  For example, you say that it "is a nucleotide containing ...", which basically assumes that the reader knows what a nucleotide is.  I would suggest starting with "is a molecule that contains the parts ...", and then later mention that it is a type of nucleotide.
* You could link nucleic acid, and maybe even precursor.
* Similarly, you mention reduction just assuming the reader knows what that is, but a lot of readers will not have a chemistry background.  Could you reword it?
* You could link more stuff in the lead, like cell regulation, cell signalling.
* In the sentence starting "Ribonucleotides can also", the words "as well" are redundant with "also".
* I don't think this sentence is technically accurate, "The nitrogenous bases are derivatives of two parent compounds, purine and pyrimidine.".  Rather, I think that purines and pyrimidines are two categories of nitrogenous bases.
* I'm not sure that the table belongs in the lead.  Maybe it could be moved to a later section that talks about RNA.
* Should the "Discovery" section be named "History"?  (It's a real question -- I'm not sure.)
* Why does that section start out with Watson and Crick?  They show up very late in the story -- why don't you move the first mention of them to later in this section?
* The whole article needs more wikilinks.  But be careful not to overdo them -- you might glance at WP:Link for guidance.
* Section headings are too long -- try to shorten them if you can.  They shouldn't be complete sentences.
* In the section that starts out, "Phosphodiester bonds ...", you begin by mentioning "Ribonucleotide residues", but you hadn't mentioned the term "residues" previously.  Terms like this should be introduced before they are used.  Or, if they are superfluous (this usage might be, in this case) then you could just remove them.
* I didn't read the whole article -- just the lead and then a quick scan through the rest.  So, please try to apply some of this kind of scrutiny to the other sections of the main article body.
* On the whole, though, I think this article is really pointed in the right direction, and has had a lot of good improvements!  Just make sure you get rid of any hint of plagiarism -- keep in mind that "close paraphrasing" is also not acceptable -- you might want to review some of the class materials on that.  Good luck!
Klortho (talk) 02:34, 26 April 2013 (UTC)
replies: text: Hi Klortho, Thank you for taking the time to provide us with the great feedback. We will continue to work on the article in the next few days. Yes, I believe it would definitely help the readers if we use simpler terminology especially at the beginning. That's a really helpful tip! We will also add more wikilinks and rephrase the section headings. Will definitely use these tips while editing and reading through the other sections. 99.43.44.44 (talk) 09:08, 1 May 2013 (UTC)
replies: text: If we include a wiki link for nucleotide, for example, do we still need to define it in the paragraph or is linking it sufficient? Jessicalau90 (talk) 10:11, 9 May 2013 (UTC)
replies: text:  Hi Klortho, here's a little update of what we have done so far to improve on the article. We have added more links to the article and have rewritten some of the sentences. We also moved the table to the section on general structure. Please let us know if that makes more sense. We renamed the discovery section, history. Also, it would be great if you could perhaps suggest where would be the best place to mention the history-beginning or end of the article? We also shortened the section headings. Jessicalau90 (talk) 11:37, 9 May 2013 (UTC)
thread_title:  More comments from Klortho 

message: Hey guys, I’m pleased to see that many of my suggestions have been implemented included the additional references and additional images and changing some sentences to be in the active voice. Also, it looks like the image in the lead section has been fixed to be an appropriate size.  I’ve also recently checked some random snippets of the article for paraphrasing issues and I didn’t see anything that might be a problem. One suggested change that I still don’t see implemented is including images of ribonucleotides that show more accurate representations of the ribonucleotide atoms in three dimensional space (e.g. ball and stick models). If it is difficult to find such images, it might be possible to make them yourselves using the appropriate software. I’m sure there are some that are open source. Bcheon1 (talk) 22:25, 30 April 2013 (UTC)
replies: text:  Hey Bcheon1, Thanks for the follow up! Really appreciate it. We are continuing to use the feedback given from you as well as others to improve the article. I will be looking for more images in regards to the ribonucleotides structures. Thank you for that suggestion. 99.43.44.44 (talk) 09:03, 1 May 2013 (UTC)
replies: text: Sounds good, I'll let you guys know if I come across any images that you can use. Bcheon1 (talk) 13:06, 1 May 2013 (UTC)
thread_title:  Follow-up from Bcheon1 

message: Here are my thoughts after an initial read through of your article. The lead section is written well and gives a good overview of ribonucleotides. The article is structured in a way that flows nicely from one section to the next. The body of the article is also written well, from a neutral point of view, and uses relevant images to compliment the article’s information.
I have just a few, relatively minor suggestions to improving your article:
*Internal wiki Link purine, pyrimidine, monomer, nucleic acid in the lead section
*some lower level information for the lead section. What is a Ribose? A pentose? A monomer? 
*Addition of more Internal wiki links within the body of the article, there are almost none. Examples; phosphate, methylate, hydrolysis, enzyme, etc. 
*In the Synthesis section there are two sources back to back and it’s unclear which source is being sited. Maybe check the wiki tutorial for citing sources to be sure this isn’t against policy of some kind? It would also be beneficial to include an additional source or two for this material as the three-paragraph section is cited from only one source. 
I like the inclusion of the bottom nucleic acid constituents chart. My group contributed to the adenosine diphosphate article, and it would go nicely included on our page.  Overall the article has good information, and it seems all that’s needed is some minor polishing. Well done!  — Preceding unsigned comment added by Jengel11 (talk • contribs) 14:38, 2 May 2013 (UTC)
replies: text: Thanks for the feedback as they were quite helpful. I made a few adjustments according to what you have mentioned. As for the back to back citation, I don't think there is any issue with it as it is commonly done on Wiki's featured front page articles. Again, thumbs up for you input. Binhtruong (talk) 07:37, 9 May 2013 (UTC)
thread_title:  Comments from Jengel11 

message: I agree with many of the comments above -- especially the recent ones from Klortho and jengle.  However, rather than reiterate many of these comments, I'll list some new ones (and I'll keep my list short since we're near the end of the semester):
• The opening paragraph should be revised -- and expanded slighted -- to provide a better and more complete overview for the "lead paragraph".  One idea would be to merge your third paragraph (about the bases) into the first paragraph.
• I think the article could be somewhat longer.  One idea would be to provide more detail to the synthesis section.
• Could you add more information regarding mutations and diseases? 
• I think the "Discovery" section should be moved to the end (or near the end) of the article; and I agree with Klortho that it might be better to call it the "History" section.  In addition, the size of the portrait should be reduced significantly.
• I agree with the others that the references should be rechecked and perhaps reconfigured (maybe adding some).
Best of luck in finishing the article!  Jgould1400 (talk) 03:47, 3 May 2013 (UTC)
replies: text: Thank you for your feedback! I made some changes you and Klortho had mentioned and I am still trying to expand on the lead section. Let me know if you have anymore input. Binhtruong (talk) 07:37, 9 May 2013 (UTC)
replies: text:  I look forward to seeing your revision.  Jgould1400 (talk) 08:57, 9 May 2013 (UTC)
replies: text: Hi Jgould1400, Thank you for your suggestion on moving the "History" section to the end of the article, however, I'm not sure if that is ideal. I have seen most Wikipedia articles and their History section tends to be at the beginning. I think that would make more sense? Binh, what do you think about that? Jessicalau90 (talk) 10:45, 9 May 2013 (UTC)
replies: text:  Hi Jessica.  The small (limited) advice I got was that having the History section towards the end might be preferable, but I'm sure either way is fine (and, in fact, depends on the subject matter and the writer's preference).  Best of luck. Jgould1400 (talk) 05:28, 10 May 2013 (UTC)
thread_title:  Comments from Jgould1400 

message: There has been quite an improvement on this article considering the state of the article before had only a single line description for Ribonucleotide. Here is a list of improvement that were made to the article.
* Expansion on the lead section to give a more clear and precise description of a ribonucleotide and its role in nucleic acids.
* Addition of  structure section to give a better description of the many different ribonucleotides
* Added section on the differences between deoxyribonucleotide and ribonucleotide.
* Added section for the linking of nucleotides.
* Added Function section to describe its role in cellular metabolism and DNA synthesis.
* Added a synthesis section to describe the biosynthesis of purines and pyrimidines via de novo pathway.
* Added a History/Discovery section to provide background information of ribonucleotides.
* Added several tables, images, and illustrations (some self contributed) depicting structure, synthesis pathway, and historic figures.
I would also like to acknowledge several individuals that contributed tremendously on the improvement of the article. 
* Bcheon1 for pointing out several key improvements in terms of the tone of voice the article was exhibiting, in addition to assisting in configuring some of the images.
* Aluquette for catching several errors that would have grossly affected the article in hand.
* Klortho for helping us clean up the minor edits that were necessary.
* Jengel1 and Jgould1400 for encouraging us to expand on some of the key topics worth mentioning.
Thanks again! Binhtruong (talk) 04:01, 10 May 2013 (UTC)
replies: text:  Best of luck! Jgould1400 (talk) 05:29, 10 May 2013 (UTC)
thread_title: Final Progress Report