Talk:Transferase

Possible Revisions

Addition of a longer introductory section, with more information and sources might be nice. Have also discussed the addition of a section expanding explanation of the various types of transferases. Other sections we have discussed as possible targets for expansion include: structural considerations, cofactors/coenzymes, regulation/inhibition, kinetics, disease importance, and applications to biotechnology/medicine. Also, a good diagram is likely necessary to better illustrate the action of a transferase. --WillPugarth (talk) 23:49, 22 October 2013 (UTC)

Unit 8 Article Revsions

I have been working on the diseases section from the outline. Covered three so far, galactosemia, SCOT deficiency, and carnitine palmitoyltransferase II deficiency, with references.Adimart1 (talk) 06:09, 29 October 2013 (UTC)

Excellent! If you don't mind, I thought I might start work on the introduction section (that you already found citations for).--WillPugarth (talk) 22:56, 29 October 2013 (UTC)

I have adjusted some of the sub headings and added a section on the history of transferases, crosslinking to other wikipedia sites is necessary in history section.--WillPugarth (talk) 01:26, 30 October 2013 (UTC)

I have added some in text links to other Wikipedia articles by keyword--WillPugarth (talk) 02:15, 30 October 2013 (UTC)

Review by Neelix

Hi all,

You have been doing some great work on this article. Below are some suggestions for how to proceed from here:

• Paragraphs should consist of several lines of text.
• All statements in the article should be sourced.
• There should be no bare urls; all citations should provide the relevant citation information.
• I recommend finding additional sources.
• Be sure to use commas appropriately.
• The article should be expanded beyond the limitations of a stub.
• The first sentence of the lead should be reworded to start with the title of the article rather than its definition; for example, "In biochemistry, a transferase is a..."

I hope you are having good experiences on Wikipedia thus far. I would be glad to answer any questions you might have about editing if you would like to contact me. Neelix (talk) 01:58, 4 November 2013 (UTC)

Thank you very much for the assistance! I have tried a revision of the introductory paragraph as per your suggestion. I also am trying to add more citations to verify the text. Again, thanks for the revision outline you provided above! --WillPugarth (talk) 23:28, 4 November 2013 (UTC)

Hi all,

I appreciate you taking my suggestions to heart; you've implemented them well. Here are some additional suggestions:

• The capitalization of section headings should follow the rules for body paragraph sentences. For example, "Group Transfer" should read "Group transfer".
• In the naming of section headings, the article title can be assumed. For example, "Transferase deficiencies" can be simplified to "Deficiencies".
• Avoid duplicate wikilinks.
• Categories should not be linked in the body of the article.
• Captions should be used to explain the contents of images such as diagrams.

Thank you for contributing to Wikipedia and thereby making information more accessible to the world. I hope you decide to continue contributing to the project once the semester is over, whether that be in the field of biochemistry or some other field that interests you. Neelix (talk) 06:24, 26 November 2013 (UTC)

Hello Neelix!

Thank you very much for your suggestions, they have been immeasurably effective in updating the article!

I have already begun trying to integrate these suggestions, but have not yet begun the process of actually going through and revising the wikilinks (although I have gone back and reviewed the Wikipedia article on Headlines and the one on wikilinking just to make sure I know how it is supposed to be done). I wasn't sure about the captions on photos, so I need to go and look that up as well. Either way, I am hoping to have all of these suggestions taken care of in short order. Again, thanks for the assistance!--WillPugarth (talk) 01:59, 2 December 2013 (UTC)

Peer-review by Agulati4

Great job getting started on the article! The outline of the article looks very good. I particularly like that you included the history of the enzyme so that readers can get some additional information as to how transferases were discovered. I would also suggest adding information on the scientists involved in the discovery of transferases, if available, and the techniques that they used to discover them. This would allow the reader to read more on the scientists if they are interested; hopefully, there are wiki links for them as well!

Overall, the writing flows very well and the sections that have been edited are well cited. However, the “Nomenclature” section is still in need of citations. Also, the in-line citations should generally be located after the period. So, for the “Transferase reactions” section, the citations should be moved to after the period. In addition, the last sentence in the “Transferase reactions” section is missing a period.

Also, I would suggest reorganizing the structure of the article just a bit and discussing the transferase reactions before transferase deficiencies. This would allow readers to get a complete background on transferases prior to learning about how transferase deficiencies are involved in disorders. Let me know what you guys think! Great start on the article. I am very excited to see how it turns out! -Agulati4 (talk) 23:58, 4 November 2013 (UTC)

Thank you very much for the informative feedback! I will definitely look into these issues as soon as I can. I actually was in the process of revising the "Nomenclature" section when you posted, so hopefully I added some appropriate citations. Additionally, I just added some information on a Nobel Prize related to a specific transferase. Again, thanks for the feedback! --WillPugarth (talk) 00:05, 5 November 2013 (UTC)

Hi Will! The article is looking great! You all have made some great progress. I really like how the history is split up according to dates. This makes it a lot easier to read and understand what discoveries happened when. The biotechnology applications involving transferase section is also a very good section to add as most people will want to know not only what transferase is, but how it is used and applied. Great job! - Agulati4 (talk) 23:38, 15 November 2013 (UTC)

Hello again Agulati4! Thanks for the continued feedback. We are hoping to add much, much more, but it has been difficult to find very much information. The goal is to add more to the biotechnology section, as that seems to be very interesting. Additionally, I am currently not sure what else to add as far as new sections are concerned. If you have any ideas, feel free to add them here! Again, thank you for all the correspondence

--WillPugarth (talk) 06:51, 18 November 2013 (UTC)

Hey, Agulati4, Thanks so much for the advice. I have expanded the reactions section, combined the two we accidentally had and moved it to the beginning-ish of the page. Much appreciated. Adimart1 (talk) 06:21, 21 November 2013 (UTC)

Hi WillPugarth and Adimart1, I was thinking about new sections or information you could add to the article. I am always very interested in reading about how certain molecules or enzymes affect the development of diseases in humans. So, I was thinking you could add a new section on the involvement of transferases in diseases or just add to the transferase deficiencies section. Here are some articles I found that may help: 1) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1379001/pdf/gut00588-0109.pdf, 2) http://www.ncbi.nlm.nih.gov/pubmed/9802272, and 3) http://www.ncbi.nlm.nih.gov/pubmed/16020876. The first and second articles are about Gluthathione transferase and its involvement in diseases and Parkinson's disease, respectively. The last article is about Gamma-glutamyl transferase and its link to cardiovascular disease. I hope that helps! - Agulati4 (talk) 05:53, 26 November 2013 (UTC)

Thanks for the additions! I definitely like where you are going with this. I also looked into the Glutathionine transferases and found them interesting. I definitely would like to add some information on this to article, but previously I wasn't sure how I would word it. Now with a little more Wikipedia editing experience, I feel I might be able to make this addition. Again, thanks for all the help, as well as the sources!--WillPugarth (talk) 01:53, 2 December 2013 (UTC)

I'm glad the suggestions were helpful! I really like how you have expanded on the diseases affected by transferase deficiencies under the "Deficiencies" section. It's really looking great! - Agulati4 (talk) 19:10, 5 December 2013 (UTC)

Thanks! It was definitely a group effort! I think this article still needs some clean up time, but otherwise it is looking better and better! Everyone has helped immensely with their suggestions, and for that I am quite appreciative. --WillPugarth (talk) 19:29, 7 December 2013 (UTC)

Hi everyone! The article is looking absolutely amazing! Great work! - Agulati4 (talk) 00:31, 13 December 2013 (UTC)

Thanks again! We definitely put a lot of time into it. Hopefully we will be able to improve it some more! --WillPugarth (talk) 03:34, 14 December 2013 (UTC)

Comments from Galemu2

This is a great article. I enjoyed reading It. You guys are in the right direction. I suggest the following improvements for this article.

• The first thing I noticed is that the references are not in proper format. Wikipedia has a cite function that makes it easy for citing books and journals. I’ve actually changed one of the references within the reaction section. I used Pub med ID and wiki generated the format. In most cases it is possible to find a Pub Med ID for an article.

• In the lead section the word “Biochemistry ..” could be omitted. I think it is obvious from the definition of the word that the topic falls under this subject. According to Wikipedia lead guideline there is no need to add inline citation in the lead section.

• You were editing the article when I was reviewing it. I think the reaction example should stay in the lead section. It shows what transferases do. However, you have to clearly explain the part that transferases play in your example.

• I think the organization is great for the article. It would improve to place the reaction section under nomenclature. This way the reader knows the function of these groups of enzymes. Afterward it would make sense to read the deficiencies.

• In the History section the reference you cite are about the actual discoveries. I think it would be better to cite a historic source. It would be better Wikipedia article when you cite conclusions made by others.

• The Nomenclature section needs additional citation. I think it would also improve article to add example for the formal names and the common names.

• I like the list of classifications, and the wikilinks for each classifications. It may improve article if you clarify what EC stands for.

• The transferase reaction section is very important for this article. You have started mentioning some key enzymes. I think you should include at least one example from each classification. It would make a better article to explain reaction mechanism.

• The article also needs images.

Happy editing. Galemu2 (talk) 03:36, 5 November 2013 (UTC)

Thanks Galemu! I actually had thought I had responded to your post, but I must have forgotten, or accidently cancelled my response. Either way, I am working on the citations right now and I just found a historical type source to use for the history section. I am also planning on adding examples to the nomenclature section as suggested. Thanks for all the feedback!--WillPugarth (talk) 02:13, 13 November 2013 (UTC)

Hello again Galemu! We have tried to incorporate as many of your suggestions as possible. Sadly, I haven't been able to find historical source (like a textbook) for the history section other than the sources I have found. The oldest source so far is from 1941, but it references transferases as if they are commonly known. I'd ideally like to have a source that says what the first transferase discovered was, or how they came up with the name (like when the EC system was created), but that information seems to be difficult to obtain. Additionally, I am still updating the reactions section to include examples, as per your suggestion.--WillPugarth (talk) 06:56, 18 November 2013 (UTC)

Hello WillPugarth. Keep up the good work. The article is improving very well. I understand you are still updating the recommended improvements. I just wanted to throw this out. We just finished class discussed on translation. We learned that the enzyme amino aceyl tRNA synthetase charges tRNAs with their corresponding amino acids. I mention this because I think this enzyme is a well-noted transferase enzyme and might be a great image for lead section. Good luck with the edits. Galemu2 (talk) 05:38, 19 November 2013 (UTC)

Hey Galemu, you clearly put a lot into your review. We have been reworking and expanding several sections. Our plan is to try to have one at least from each classification and our text is actually a huge help here. Thanks, Adimart1 (talk) 06:24, 21 November 2013 (UTC)

Helo Adimart1 and WillPugarth. Great job on improving this article. I can see you guys have really put in some time into this article. You have used lots of references. I really like that you put in examples for each category of transferase enzymes. Keep up the good work. Galemu2 (talk) 06:18, 7 December 2013 (UTC)

Hello again Galemu! Thank you for all your support and recommendations so far! We are still working on quite a bit of the suggestions that we have been given, trying to figure out what works and what doesn't. We are hoping to still add some more information as well as clean up quite a bit of the syntax, as well. Again, thank you or all your help!--WillPugarth (talk) 20:33, 7 December 2013 (UTC)

Hello WillPugarth. Hope all is well. Great job on improving this article. I like seeing the reaction images. Its a great way of showing what the enzymes are doing. One small subbestion i have is that the navigation box should be placed below the “see also” section and above the references. Other than that great job. Galemu2 (talk) 04:18, 14 December 2013 (UTC)

Hi again! Thanks for the support throughout the term. I double checked what you were saying about the navbox. It seems there are some conflicting ideas about where it is supposed to be located. I followed the link you included, but didn't find any information on where navboxes were supposed to be. So I went over to navboxes and that said that navboxes go under the article's appendix. But then I read somewhere else that it goes under the "See also" section, as well. So I think I will leave it for now, pending clarification. Thanks for noticing that, until now I didn't even realize that there was a set place for it (although someone else came through a couple of weeks ago and moved the navbox to where it is now)! --WillPugarth (talk) 20:24, 14 December 2013 (UTC)

Comments from Jim892

Great start on this topic and what a big improvement over where it was when we started this semester! I’m going to toss out some suggestions in this review. Please view them as true “suggestions” and take them or leave them as you see fit for the look-and-feel that you want for your article.

I like the lead section. It is “just right” length-wise and definitely makes me interested to read more!

I have a suggestion for the “Reactions” sections. This would be a great opportunity to make an illustration (perhaps with powerpoint or word or even excel if you don’t have a graphical software package) to show really great looking reaction-style equations. And, a nice illustration could add a “wow” factor to the article. The current symbols kind of confuse me because the “X-Y” (which is meant to mean X bonded to Y) looks kind of like X minus Y. You might use “Donor” and “Acceptor” and “G” for functional group…such as….. DonorG + Acceptor + Transferase ----> AcceptorG + Donor + Transferase Or, if you get a graphics package, you could put “transferase” under the arrow. There might be “freebee” chemical equation writer software on the net.

History section – Would it make sense to turn this into a sort of a timeline? I think just indented “bullets” would work with the year after the bullet. Maybe bullets for “Early Beliefs”, “1950’s”, “1970” ( for Nobel Prize Recognition). Also, the long chemical names kind of make my eyes glaze over and I’m wondering if this could also be a place to create reaction-style equations (even if you used just the words in the reaction equation, it would help visual understanding I think). This might also be a place for using a table.

Nomenclature – I love this topic and a lot of examples here would be very helpful. You might be able to get an example from several (or all) of the classification subclasses. A table format might work great for this and you could show off your wiki skills. See this link for how to make a simple table: Help:Table#Using_the_toolbar

Considering we are just at the first contribution stage, your content is looking pretty good. I took a look at the “possible outline” in your sandbox (User:WillPugarth/sandbox) and that outline looks really nice. I like the wording of the topics in that outline. In the current article, all the topics are just one word. It might be just a style choice, but I like the more conversational topic headers such as you have in the outline. Items like “General Structure of Transferases” and “How transferases work”. Of course there will be others who want one-word headers probably :-)

The wikilinking looks great and is plentiful. Referencing is also good. I think the overall flow will be great when you add the other outline topics in as the contributions continue in coming weeks.

Overall – great job and keep up the good work! -- Jim Perry (Jim892) (talk) 23:15, 5 November 2013 (UTC)

Hello again. I was looking at the wikipedia article on isoelectric point and noticed an equation that looked really nice. I went into edit mode to see how they did it. It is a math function that is part of wikipedia. See below for an idea.

$DonorX+Acceptor{\xrightarrow[{transferase}]{}}AcceptorX+Donor$        (where "X" is a functional group)

Here is the code:

 <math> DonorX + Acceptor \xrightarrow[transferase]{} AcceptorX + Donor </math>

-- Jim Perry (Jim892) (talk) 22:51, 7 November 2013 (UTC)

Thanks for the formula equation. I added it in as soon as I saw your post here. I have also changed the conventions of how "donor" and "acceptor" are included in the Transferase Reactions section (I read back through it and you were totally right, it was confusing!). I will definitely be looking into changing the section headings as well. And I am looking into several of your other suggestions (graphics and equations). Thanks for all the help!--WillPugarth (talk) 02:07, 13 November 2013 (UTC)

Hi Will, the article is really taking shape. The equation done with the math function looks really good and I especially like the change you made in the history section by making "1950's" and "1960's" different sub-sections. Looks very nice and much more fun to read. Good luck with the second set of contributions! --Jim Perry (Jim892) (talk) 04:39, 13 November 2013 (UTC)

Hello again! I think I will be using the formula equation you gave us to expand the classification section, hopefully improving the understandability of each type of transferase. --WillPugarth (talk) 23:06, 13 November 2013 (UTC)

Hi Folks! I was checking back on your article and it is really looking good. I got to it this time by going to Google and searching on "transferase" and Google also lists two subtopics. You already mention one of them and so you might want to include something on the other which is "Peptydyl transferase". This would also give you a second item under the header of "Uses in Biotechnology". There is already a wiki article on "Peptydyl" topic just like for "Glutathione", so you would need only a short discussion like you have for "Glutathione". --Jim Perry (Jim892) (talk) 17:28, 18 November 2013 (UTC)

Hello again Jim! Thanks again for the immensely helpful suggestions! I really appreciate how much assistance you have been giving throughout the term. I will be definitely adding something about Peptidyl Transferase, in that case. I am always looking for more topics that should be included (to add density to the article). If you think of any others, feel free to send them our way!--WillPugarth (talk) 21:13, 18 November 2013 (UTC)

Hi Jim, the reaction code you sent us is much better than the one we had before. It is more pleasing to the eye and more understandable. Thanks so much for that! Adimart1 (talk) 06:27, 21 November 2013 (UTC)

Progress Report from 10/29/2013

• We have added two new sections to the article: "Transferase Deficiencies" and "History."
• Added new Wikipedia cross reference links to other articles
• Added prose
• Added/Revised "See also" heading
• Added/Revised "References" heading

--WillPugarth (talk) 00:49, 14 November 2013 (UTC)

Progress report for 11/13/2013

Completed:

• Added new section on biotechnology applications
• Combined and eliminated a section, put into Transferase reactions section
• Improved wikilinking, improved syntax, content edits, new citations
• Changed History section to be per decade
• Added equation to Donor/Acceptor in Transferase reactions section (Thanks Jim892!)

Next:

• Need to add images
• Add equations for each of the EC system transferases listed
• Add nomenclature example for systematic naming
• Tables? (add table for EC examples)
• Improve headings to be more informative
• Add Terminal transferases to Biotech section
• Find diagrams for some of the reactions listed (or make them)

--WillPugarth (talk) 00:59, 14 November 2013 (UTC)

• Add Discovery of RNAP (RNA Polymerase) to history section?
• Add Kinetics Section . . . Found sources for Kinetics Section (as per outline in sandbox). Will need to add section on CoA Transferase in E.coli. (this is as per suggestions from several reviewers! Thanks everybody!)--WillPugarth (talk) 19:43, 15 November 2013 (UTC)

Unit 11.

James, is there something in particular you would like me to work on next? — Preceding unsigned comment added by Adimart1 (talk • contribs) 20:10, 15 November 2013 (UTC)

Sure! If you want you could work on writing up the Kinetics section. I added some references for in my sand box. It mainly has to do with E.coli CoA-Transferase, I think. Or you could add some information on Terminal transferases and what they do. Or any historically significant transferases you find could be added to that section. Also, anything on the list above works as well.

I'm pretty much just adding depth to whatever is already there, or trying to add everything that people suggested in their reviews. I think the most important part is adding lots of sections with large amounts of content. Thanks! (here are the links for the CoA transferase info: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC232864/ --> article on kinematics of CoA Transferase; http://www.sciencedirect.com/science/article/pii/000398617590003X --> another on the same enzyme) --WillPugarth (talk) 01:41, 16 November 2013 (UTC)

Progress Report for 11/15/2013 (Unit 10)

Completed (since last report):

• Added new sections with new content
• Improved wikilinking, improved syntax, content edits, new citations
• Added images and equations
• Expanded EC terminology section into short descriptions of each class

In progress (before next report):

• Add section on Terminal transferase
• Add section on Medicines/therapies that use transferases — Preceding unsigned comment added by WillPugarth (talk • contribs) 07:08, 18 November 2013 (UTC)
• Expand History Section
• Add section on Kinetics of CoA transferase in E. coli
• More images and charts/tables and equations/reactions
• Improve headings
• More citations for EC section (and any future additions)

--WillPugarth (talk) 05:57, 16 November 2013 (UTC)

Comments from Pdholak1

Hi! Congratulations on the progress on your article - it looks great! I like your use of the table and the pictures. They really pull the article together. Here are some suggestions I have based on what you have now:

1. In the history section, I don't think you need the subsections of "1950" and "1960". It is helpful to see that the history spans over 2 decades but I think since each section is limited, plus the 1960 section mentions the 1970 award, it would be ok to make that one big paragraph.
2. Each section is a little wordy - there are a lot of run-on sentences. Shortening the phrasing may make the article easier and faster to read (as people tend to do on Wiki!)
3. In the nomenclature section, the specific polymerases you mention may be able to be wikilinks? Just something to check if you havent already!
4. Under the section "Transferase deficiencies", it is a little confusing why you mention SCOT deficiency in the intro and Galactosemia has its own heading. Same under "Uses in biotechnology." I'd either add the headings or scrap all of them. A formatting suggestion!

Overall I think if you keep going at the speed you are, this article will be good to go in no time. Thank you and I hope some of these suggestions help. I look forward to seeing your progress! Pdholak1 (talk) 02:33, 19 November 2013 (UTC)

Hello Pdholak1! Thank you for your feedback. I agree with you that dates for the history section is probably not necessary. However, I wasn't quite sure how to keep the different time periods from mixing within a single paragraph (maybe as a list?).

As per your suggestions, I have gone through and added some more wikilinks. I did not see the polymerases you mentioned, however, but was able to add in some links for the equation reactants and products. I wasn't sure about run-on sentences, but I am planning on toning down the style aspects of the writing to some extent.

I see what you are saying about the transferase deficiencies section. I have (just now) attempted to fix the problem by adding more subheadings. I am not sure my fix will be entirely successful, so I may end up changing it back to a single paragraph like you mentioned.

Thank you again for your feedback! Please feel free to continue to add suggestions and to continue to help --WillPugarth (talk) 06:21, 19 November 2013 (UTC)

Hello! Thanks, I am glad my suggestions were helpful! I think for the history section a list may be effective -- a good way to show progression while being concise. What I meant by run-on sentences was that your writing is like reading a book rather than what you usually see on Wiki, but that was just my opinion! Content wise, you are great! I like the subheadings -- it seems like you could go either way with that one so whatever you prefer style wise. Good luck with the next unit!! Pdholak1 (talk) 04:12, 20 November 2013 (UTC)

Phodlak1, thanks so much. I am working on expanding the deficiencies section as it does not meet my own standards of writing (I wrote the original section). I forgot when it went in that people can see it right away and I should put "drafts" in my sandbox. I just haven't gotten back to it. Thanks again. Adimart1 (talk) 06:32, 21 November 2013 (UTC)

Hi! The deficiencies section looks great, as well as the rest of the article. Good luck with the finishing touches, you seem to be close to done! Pdholak1 (talk) 18:38, 8 December 2013 (UTC)

Hi again! Thanks for the support! Hopefully we will be able to get everything done. Good luck to you too!--WillPugarth (talk) 03:36, 14 December 2013 (UTC)

Comments from hnagy2

The general flow of the article is easy to follow and it makes sense. It can be difficult to write on such a broad topic but it went in interesting directions. The lead was kept appropriately general and broad while introducing transferase reactions. The first subsection was succinct and contained good examples without getting bogged down in particulars. I like the idea of touching on the discovery of transferases in general and some of the history behind highlighted breakthroughs. That section is short and simple but it makes the overall concept of this category of enzymes less abstract and more relevant to real life applications. The nomenclature section was straightforward as well with good examples. Highlighting RNA polymerase as an example is a good idea, since so many people probably do not think of them as transferases.

The organization of the categorization section is clean and streamlined. Using a chart for each category with linked examples is very easy on the eyes. Including sections on uses of transferases in biotechnology and cases of transferase deficiencies is very useful. Expanding a bit on these two subsections would really balance the article and make for an interesting read. Adding subheadings to these sections consistently or not using them at all would be best. The images used were appropriate and strengthen the text. A wide variety of third-party published references were used. They appear to link to the proper papers and are properly formatted. The text in general reads well and seems like a good summary of the included references without overuse of quotes or heavy paraphrasing. The overall structure and compartmentalizing of sub-topics are spot-on. Adding more content to the last few sections will make for a very strong article.Hnagy2 (talk) 05:04, 19 November 2013 (UTC)

Hello hnagy2! Thank you for all your feedback. I agree with your idea of expanding the section on uses of transferase, as well as the biotechnology coverage. This type of addition will definitely help to improve the interest in transferase. As far as the subheadings are concerned, it is definitely hard to decide whether to use them or not at this point. If the sections remain so short, it might be best to remove them. However, if the length of each part becomes rather expansive, then those divisions might be necessary. We are definitely looking into adding more content to the end sections. Again, thank you for your review!--WillPugarth (talk) 02:00, 20 November 2013 (UTC)

hnagy2, thanks for the review. Several sections do need expansion and we are certainly working on them. The transferase deficiencies sections definitely needs improvement. I hope you'll see more there soon. Adimart1 (talk) 06:35, 21 November 2013 (UTC)

Unit 12 Progress report

1. expanded glutathione section
2. expanded SCOT deficiency section
3. expanded CPT-II deficiency section
4. expanded Galactosemia section
5. added new section: rubber transferases

Adimart1 (talk) 05:55, 23 November 2013 (UTC)

11/26/2013 Progress Update

Completed:

1. Further expanded Reactions section

2. Condensed unnecessary section into introduction

3. Updated section headings/removed some subheadings

Next:

1. Finish adding EC divisions to Reactions section

2. Edit style, grammar, Wikilink corrections, etc.

3. Add reaction images for Reactions section (or make new diagrams)

4. Add more academic citations

5. Kinetics section

--WillPugarth (talk) 01:08, 27 November 2013 (UTC)

Comment on Intro Equation

Wow! This article has come a long way! Really looking nice and very extensive! I do have a comment/suggestion for the equation in the introduction that concerns X-Group + Y -> X + Y-Group.   No problem with this equation at all. The larger equation, however, is totally different and so having two different equations is confusing. My suggestion is to have just one by removing the "small one" (done in normal text) and changing the large equation to be:

$Xgroup+Y{\xrightarrow[{transferase}]{}}X+Ygroup$

With this change, the description you have will still work fine. Once again, nice job on this article!
--Jim Perry (Jim892) (talk) 21:33, 4 December 2013 (UTC)

Hi Jim. We will definitely consider this suggestion. I don't want to change it without his opinion, but i certainly appreciate the observation. Adimart1 (talk) 04:43, 5 December 2013 (UTC)

Hey Jim! I totally didn't catch that discrepancy before. I will look into changing it as soon as I can. I will likely use your exampel above, as it looks good. Thanks again for the assistance throughout the term!--WillPugarth (talk) 20:35, 7 December 2013 (UTC)

Comments from Madscientist2007

Hi WillPugarth and Adimart1,

Awesome job! You have put together a superb article. I can’t get over how much this article has changed since I first read it earlier this week, let alone how much it has improved since the beginning of the semester. You have both obviously put a great deal of time and energy into this article as evidenced by the quality of your work. The outline that you have listed in WillPugarth’s sandbox has clearly provided you a wonderful foundation upon which to build. From this starting point, you have constructed a very well-research, well-written article which has a logical flow to it. You have taken a rather large topic and formatted it in such a way as to make it quite understandable and accessible.

After reading through the article again this evening, I am finding it difficult to make any major recommendations. However, I do have two minor suggestions that I will leave for your consideration:

1) This first suggestion is actually based on a suggestion that Jim892 made for my group’s article:

“Here is the idea: When the article opens up, most of what I see is a super long "contents box" that kind of overwhelms me. And, as I scroll through the article, I hit the major sections, sub-sections, and sub-sub-sections and I can't really tell what is a "sub-section" and what is a "sub-sub-section". (If I look real close, I can see that the font size is very slightly smaller, but it is hard to tell.) So, one idea is the make the sub-sub-sections just "indented bullets". This will help to visually separate sub-sections from sub-sub-sections and also will take the sub-sub-sections out of the contents box (making it much shorter). To illustrate this, I did a copy/paste of part of your article into my "sandbox3". Click this link to get to it: Jim892/sandbox3 Good luck thinking through this. Note that I replaced the sub-sub-sections (that have 4 equal signs on each side) with a "*" at the beginning of the line and then bolded the sub-sub-section text. Then, I added two ":" at the beginning of each block of text below the sub-sub-section. The editing required to do the indenting is a little tedious, but might be worth it for the visual effect.”

As to the “content’s box,” my group’s is a little bit longer than what you have for your page. However, in terms of your overall article, this formatting change might be something that you want to take a look at. I looked at the example in Jim’s sandbox and found this type of formatting to be easier on the eyes. Just something to think about.

2) This suggestion is in regards to the classifications table that you constructed. While you have many of the terms wikilinked, you might want to consider adding inline citations where applicable. I will admit that I found this process slightly cumbersome when dealing with the table I put together for my group’s article and my table is not as involved as yours. Should you go in this direction I would suggest using the named references option. This makes looking at the table in the editing box easier as you do not have the whole reference stream listed in the midst of your table text and formatting. Again, just something to consider.

I wish you both the best of luck and I greatly look forward to reading the finished product come mid-December. Madscientist2007 (talk) 03:48, 6 December 2013 (UTC)

Hi again,

I wanted to provide you with the following information. Earlier today Jim892 contacted me about a concern that he had with the formatting suggestion he had given my group (and I, in turn, gave to you (see suggestion #1 in my review above)):

From Jim892: "You are correct. The "TOC limit" just changes what displays in the Contents Box. You can do the "TOC limit" and the indenting/bulleting together or do just one and not the other. They won't interfere with each other. Now, one concern I have about my own suggestion on the indenting and bulleting...You might want to check with an Online Volunteer concerning my approach to be sure it doesn't violate Wikipedia's style guidelines or something. I got a comment on my own article about "bolding" items in a list, so I'd hate for you to do all that work and then find out it isn't "legal" to do it that way."

I took his advice and contacted two of the OAs (Klortho and Neelix) about this concern in the hopes of getting some guidance from them. Neelix wrote back with the following advice:

"I'm glad that you are experimenting with formatting on Wikipedia. I would recommend against bolding and bulleting sub-subsection headings, both because words should not be bolded for this reason and also because it requires all of the text in each sub-subsection to be indented in a way that is contrary to established practice. Nonetheless, I understand your desire to distinguish between the subsections and the sub-subsections. Having taken a look at the Molecular-weight size marker article, I have two recommendations. One option is to simply remove the sub-subection headings. The sub-subsections are so short that they probably don't need to be sectioned off; most sections on well-developed articles consist of several paragraphs. If you really want to retain the headings, a second option is to create a table with one column being the sub-subsection headings and the second column being the paragraphical text currently in those sub-subsections. What do you think?"

I hope that Neelix's suggestions help. Please feel free to contact me with any questions.Madscientist2007 (talk) 04:01, 7 December 2013 (UTC)

Thank you so much for your two posts here! I actually was wondering about the whole formatting thing as well. Thanks for the heads-up, as I can now try to integrate these changes, especially the sub-subheadings and subheadings part. I already began decreasing the number of subheadings and I think I will try rewriting the sections with multiple sub-subheadings (with short descriptions) into related paragraphs. Ideally an image or two will further clarify the content of the revised, sub-subheading-less paragraphs. Thanks again for this excellent and very useful post!--WillPugarth (talk) 20:40, 7 December 2013 (UTC)

I am glad that these posts were helpful! Good luck with your article!Madscientist2007 (talk) 20:51, 7 December 2013 (UTC)

Here are comments that Klortho made regarding formatting:

"Hi, I have mixed feelings about Jim's suggestions. On the one hand, I can see his concern about the structure of the article being difficult to discern when you are reading through it. On the other, I'm not crazy about his proposed solution, and also, I think that you are using the heading levels in the way that they were intended.

I also agree with Neelix, for the most part. But in my opinion, some of the subsections should stay as they are, and for others, I agree that you could just remove the subsection headings. I don't like his idea about making them into a table -- I don't think a table is appropriate. So, specifically:

• I think you could do away with the subsection headings under the Effects of gel conditions sections (both of them).
• On the other hand, under Choosing the correct protein marker, I think the subsection headings are good and helpful, albeit I agree that the difference in the style isn't very good -- but that's Wikipedia's fault.
• Under Protein markers, it might be marginally helpful if you were to put Choosing the correct protein marker after Effects of Gel Conditions.
• For the level-3 subsections underneath 4.2, 4.3, and 4.4, you might consider using description lists. These are similar to Jim's suggestions, but I think more "standard", and more appropriate in this case. For the wiki-syntax, see here."

I hope this helps! Madscientist2007 (talk) 22:39, 8 December 2013 (UTC)

Hey Madscientist, thanks for the suggestions and for following up on whether the formatting would be appropriate or not. Personally, I don't mind the giant contents section at the beginning of articles. I think it makes it easier to "jump" directly to the piece of information you are looking for. That being said, I might eliminate the subsections from the histoblood group area. I meant to expand them, but it might be better to just consolidate into one section.Adimart1 (talk) 20:20, 9 December 2013 (UTC)

Brief suggestion

Impressive work on the article. A couple of small suggestions:

• some evolutionary history cold be included (e.g. relatedness of some transferuses to hydrolases)
• a white background on protein structures is more in line with wikipedia's aesthetic.

Good luck, T. Shafee (Evo&Evo) (talk) 13:34, 7 December 2013 (UTC)

Thanks for the post! Honestly, I hadn't even made that connection between transferases and hydrolases myself. From a preliminary search just now, I can see that they are linked mechanistically, so therefore could have a sort of evolutionary past. I definitely will look into this as it could be included in a future section on kinetics and mechanisms of action for transferases. I have added two links to my sandbox page to get the process of creating a section on this started. I agree on the image suggestion as well, but at the time had only found that one enzyme. Now that I have spent more time working with Wikimedia Commons, I believe I can probably find a better representative molecule. I will look into it. Again, thank you for your suggestions!--WillPugarth (talk) 20:50, 7 December 2013 (UTC)

Brief suggestion

Impressive work on the article. A couple of small suggestions:

• some evolutionary history cold be included (e.g. relatedness of some transferuses to hydrolases)
• a white background on protein structures is more in line with wikipedia's aesthetic.

Good luck, T. Shafee (Evo&Evo) (talk) 13:34, 7 December 2013 (UTC)

Comments from jirwin1097

Hey guys, I am assigned to review your article this week. Overall this is a great article. I couldn’t find anything major that needs to be fixed. I just have a few suggestions. I will be using the rubric to critique in this peer review:

Content coverage

The article is composed of a lead paragraph and six main sections: History, nomenclature, classification, reactions, role in histo-blood group, deficiencies, and uses in biotechnology. The lead paragraph is very well done. It includes the function of tranferase, its involvement in reactions and pathways, and an example of a reaction is provided. This introduction is great in that it is succinct without going into too much detail. My only suggestion is to include a little about transferase deficiencies and how transferases are used in biotechnology. To be in accordance Wikipedia guidelines the lead paragraph should “summarize the body of the article” in equal weight. I think the best way to do this is to include at least one sentence on the main sections of the article.

Wikilinking

You guys did a great job adding wikilinks to your article. I only added “translation,” which is location in the lead paragraph. I think it’s relevant enough to be wikilinked.

References

Lots of references are used in the article. They appear to be properly formatted, and the ones I looked at are from research papers and other reliable sources. No suggestions here.

Writing/spelling/grammar/typos

No suggestions here either.

Illustrations

I really like the use of illustrations in the article especially in the “reactions” section. I also like the chart that you guys used for the classification of tranferases. 76.111.110.6 (talk) 22:52, 7 December 2013 (UTC)

Thanks jirwin! We appreciate your review of the article. We will definitely see about adding a little bit to the intro to bring it into line with the wikipedia guidelines. I can't take any credit for the pictures and charts, James is totally responsible for those!!Adimart1 (talk) 20:14, 9 December 2013 (UTC)

Thanks for the review! Additionally, thank you for the suggestion about deficiencies needing to be in the intro section, I didn't even think about it at the time! Also thanks for the Wikilink assist, as well. We've been working fairly intensely on the article, so its nice to know that we are on the right path!--WillPugarth (talk) 07:13, 11 December 2013 (UTC)

Comments from Juanquina Thomas

Hi guys. I wasn't assigned your article for peer review, I was just checking out the structure for ideas for my article (Isomerase). I do like the way you guys put the classifications of transferases in a table. I also noted that guys have several citations! This is great. 76.100.202.179 (talk) 04:58, 9 December 2013 (UTC)

thanks, Juanquina, good luck with your article!!Adimart1 (talk) 20:15, 9 December 2013 (UTC)

No worries! Thanks for checking out our article! Feel free to use anything you think is useful, and don't hesitate to send any suggestions you have our way, we can use all the feedback we can get!--WillPugarth (talk) 07:13, 11 December 2013 (UTC)

Hello all, I was just giving your article a final read. I really enjoyed it and think you guys did an awesome job in revamping it. Thanks for your suggestions to our page, it made a world of difference. Good luck to you guys! Juanquina Thomas (talk) 02:52, 15 December 2013 (UTC)

Comments from Wenwatata

Hi All, You article on transferases is very comprehensive and I must commend you for such an effort. However, please take a look at the introduction and examine the need for the sentence involving PDH and phosphatase. I can under the involvement of a transferase in the PDH complex, but a phosphatase I guess does not belong there. Once the phosphate or phosphoryl group is cleaved, for instance inorganic phosphate, it does not transfer within that reaction to another group. In all, congratulations for your excellent work. Godwin Ifere 04:41, 12 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Thanks for the assistance! I checked what you said, and you were right. I can't believe I didn't catch the error there with PDH. I changed the way it was written to remove the phosphate part. Thank you again!--WillPugarth (talk) 03:29, 13 December 2013 (UTC)

Hi All, Doing my last visiting rounds to see to the progress of the article. Thanks for doing the little correction. Congratulations to the group for a job well done. Take care Godwin Ifere 04:45, 15 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

12/14/2013 Progress Update

Completed since last update:

• Added EC Reactions, Deficiencies, and Histo blood group sections; expanded history section
• Added diagrams and images, equations for each reaction type
• Improved citations
• Made all changes (as far as I can tell) suggested by Neelix in previous review (includes removing duplicate wikilinks, heading fixes, removal of category links, captions added)
• Attempted to address all changes suggested by others

Next/In progress:

• Add section on mechanisms, regulation, and thermodynamics
• Describe cofactors/add cofactors section
• Structure: similarities between Transferases and Hydrolases — Preceding unsigned comment added by WillPugarth (talk • contribs) 22:56, 14 December 2013 (UTC)

Final Progress Report

Overall changes to Transferase Article:

• Extensive content additions
• Improvements to references
• Improved wikilinking
• Addition of images and diagrams.
• Created table for EC classification
• Overall Wikipedia guideline fixes

Special thanks to (in no particular order): Neelix (main Wikipedia editor), Adimart1 (group partner), Agulati4, Galemu2, Jim892, Pdholak1, Hnagy2, Madscientist2007, T.Shafee (Evo&Evo), jirwin1097, Juanquina Thomas, Wenwatata, and countless others who did quick fixes here and there throughout the project. Thanks everybody!--WillPugarth (talk) 23:02, 14 December 2013 (UTC)