Talk:Isomerase

A preliminary outline

Overview

Subcategories

Epimerases

Racemases

Allylic isomerases

Mechanisms of isomerases

-isoparaffins

-ring openings

-transalkylation

-hydrogenation

-hydrocarbon cracking

-cis-trans isomerism

-roles of keto-enol tautomers

Roles in human disease — Preceding unsigned comment added by Hnagy2 (talk • contribs) 01:02, 23 October 2013 (UTC)

I think the first this article could use is organization. We can accomplish this with our outline. Juanquina Thomas (talk) 02:27, 23 October 2013 (UTC)

We can also add several types of isomerases and their basic functions, where they can be found, etc. Juanquina Thomas (talk) 02:27, 23 October 2013 (UTC)

Adding pictures would be great! Juanquina Thomas (talk) 02:27, 23 October 2013 (UTC)

Maybe we should discuss the basic structure of isomerases as well. Juanquina Thomas (talk) 02:27, 23 October 2013 (UTC)

Review by Neelix

Hi all,

I like what you've done with this article thus far. Here are some observations that might help with future development:

• Citations should go after punctuation rather than before.
• All statements in the article should be sourced.
• Make sure that all relevant terms are wikilinked.
• Categories should not be wikilinked in the body text of the article.
• The lead should summarize the body text; the citations should follow the statements in the body text rather than in the lead.
• The title of the article should be bolded in the first sentence of the lead.
• There should not be multiple hard spaces between sections, because that lengthens the whitespace unnecessarily.

I'm glad you are all contributing to Wikipedia. Feel free to leave a message on my talk page if you ever have any questions about editing. Neelix (talk) 01:51, 4 November 2013 (UTC)

Thank you! The formatting issues were things we weren't entirely sure about so we appreciate the guidelines. We will clean it up. We also need to work on fleshing out the information instead of jamming it all into the lead.Hnagy2 (talk) 01:57, 6 November 2013 (UTC)

Hi all,

Thank you for going through and implementing my suggestions above; you're doing a great job with the article. Here are some more recommendations:

• The "Nomenclature" section should be the first section so that the terminology in subsequent sections can be understood.
• The shortest sections should be expanded; three sentences is barely enough to justify a section.
• When deciding how to name sections, one does not need to recapitulate the article title. For example, "The Role of Isomerase in Human Disease" can be simplified to "Role in human disease" or simply "Human disease".
• All references should be listed in the "References" section; including "(yahoo health)" after a sentence does not direct readers to the source text.
• Be careful to avoid duplicate links, while also linking all terms readers are likely to want to read more about.

Your hard work on Wikipedia is of benefit to the world. I hope you continue to contribute on articles that interest you once your coursework is complete. Neelix (talk) 06:15, 26 November 2013 (UTC)

Comments from klortho

Here are just a few comments -- I haven't read the whole article.

• The lead could use more wikilinks, for example, enzymes, constitutional isomers, etc.
• The lead has a misspelling: 'isomerses". Also, is it "cis-trans isomers" or "cis-trans isomerases"?
• Nomenclature: citation needed.
• In my opinion, "EC" should be glossed, for those who are unfamiliar with this classification scheme. Remember who your audience is: non-biologists.
• You should not have links inside headings. In my opinion, it would be better to take out all of the "EC x.x" prefixes from the headings, and put them into the text. Also, they should like to the relevant Wikipedia article/section, not the Wikipedia category. For example, "This is category EC 5.3."

Klortho (talk) 14:47, 4 November 2013 (UTC)

Thank you for the review! We had some back and forth but I should have caught the typos, thank you for catching them. The classification scheme and how to link to each one tripped us up. That would be a much more elegant solution.Hnagy2 (talk) 01:54, 6 November 2013 (UTC)

Thanks for the review. We definitely have a lack of wikilinks that we will be adding to the article. Thanks for the suggestion concerning our classification set-up. I think that's a great idea. Juanquina Thomas (talk) 03:48, 6 November 2013 (UTC)

Comments from Aconch

Hi all,

I wanted to provide some feedback for your article. Overall, I think it's a fantastic start! I found the article to be very well organized, neutral, and on-topic. I particularly like how the subclasses of isomerases have their own sections, and how all of your sections progress nicely; ending your article with the consequences of isomerase deficiencies works really well. Additionally, the sources used in your article are neutral and reflect the article's content appropriately. Below are some minor changes/suggestions that might improve the article; a couple of these were mentioned by Neelix and klortho as well:

• In the first sentence of your lead section, "Isomerases" should be bolded, since it is the article's title.
• If possible, incorporate a reference for the second sentence in your lead section, the second paragraph in the introduction, as well as, the sentence under the "Nomenclature" section.
• In general, the article is clear and well written, but I had trouble understanding the third sentence in your lead section and the second sentence of the second paragraph in the introduction. Perhaps, these can be reworded.
• Structurally, it might also read better if the discussion about isomers in the second paragraph is moved/inserted after the first sentence.
• Additionally, wikilink relevant terms in the article. For example, within the lead section, you could wikilink "constitutional isomers." The subclasses of isomerases listed in the lead section can also be wikilinked, and additional wikilinks under the "subclasses" sections may include terms like "chiral carbon" and "stereocenters."
• For the disease section, in addition to listing what protein is affected, consider expanding the bodily/physical effects that result from the isomerase deficiency. For example, for the Krone et al paper that talks about phosphohexose isomerase (PHI) deficiency, you could mention that the deficiency causes nonspherocytic hemolytic anemia in humans. On a related note, you can wikilink the disease and list some of the signs and symptoms that result from the enzyme deficiency.
• As you develop the article, also consider including images that illustrate the isomerases' mechanisms. This would make a great accompaniment for the text.

The article looks quite promising so far. Keep up the good work! Aconch (talk) 02:25, 5 November 2013 (UTC)

Thank you! The parts you pointed out were a bit awkward on the eyes, we will definitely work on the wording. I appreciate the suggestion on moving the bit about isomers to make the article flow better. We had trouble making the flow work, it's such a general topic. That would read better. I missed prime places to add wikilinks for ease of reference, that was a big mistake. I like the particular example you gave about bodily effects from deficiencies! Images would be great, I will probably have to work on some from scratch. Thanks!Hnagy2 (talk) 02:03, 6 November 2013 (UTC)

Thanks for your suggestions. The structural fixes are something will definitely iron out throughout the course. Pictures will also be added for a visual effect. All of your suggestions have helped greatly. Thanks for your review. Juanquina Thomas (talk) 03:51, 6 November 2013 (UTC)

Hi guys! I'm glad that I could help :) I also just wanted to make a quick amendment to my statement regarding citations in the lead section. In his review of the "Biosynthesis" article, Neelix pointed out that the lead section does not require citations. It appears that unless it's a direct quote, no citations should be in the introduction, as that is supposed to be a general overview for the details that will be cited later in the body. Aconch (talk) 17:47, 13 November 2013 (UTC)

Hi all, I just wanted to congratulate you on the progress of your article. It reads well, and it's clear and concise. It was very smart to split your introduction in order to make it more general and then incorporate the more detailed sentences (that need citations) in the "overall function." Furthermore, the sentences that introduce each respective EC category were a great addition. Great job! Aconch (talk) 17:19, 15 November 2013 (UTC)

Thank you! We were a bit confused about the lead and references but it's nice to have it cleared up. The first draft was very rough, we very happily took the suggestion to cut the lead and add more to the following subsections, especially for individual categories.Hnagy2 (talk) 05:10, 19 November 2013 (UTC)

Hi all, I just wanted to stop in and let you know how impressed I am with the progress of your article! The images were an excellent addition, and you did a wonderful job expanding the roles of isomerase in disease. I also wanted to make a very quick note. Per the OA, I recently learned that headings and subheadings of an article follow the structure of a sentence. Therefore, for any headings and subheadings that consist of more than one word, only the first word is capitalized. For example, "Triosephosphate Isomerase Deficiency" should read "Triosephosphate isomerase deficiency." Best of luck with the article! Aconch (talk) 01:16, 5 December 2013 (UTC)

Hi! I just looked over your article again, and it looks great! It has a very polished look, and I think that the images of mechanisms that you included were a wonderful addition. Great job! Aconch (talk) 23:16, 11 December 2013 (UTC)

Comments from Apoptosis81

Hi Group 84C! I was assigned your article to review for Unit 11. I took a look at your article from back in October before you started working on it and can really see you have made substantial progress. The article is looking really great so far and I had some feedback after reading through it:

• It looks like there are many places where additional wikilinking could be done throughout the article. For example some general terms like "intramolecular", "electrons" and "ultraviolet radiation" would be good to wikilink for those without extensive scientific knowledge.
• I wonder if "Overall Function" is the best title for your first section. While you do discuss the function of some of the classes isomerases, it also covers a lot on the topic of isomers and serves an introduction to what an isomer is.
• An image at the top of your article may be a nice touch and adds much to the overall look of an article in my opinion. I noticed that your images are a little blurry (especially the 3rd) although this could just be my laptop I'm working on. I wonder if you have looked on Wikicommons? I did a search and found a number of potentially high quality images of isomers and isomerases (http://commons.wikimedia.org/w/index.php?title=Special%3ASearch&profile=default&search=isomer&fulltext=Search&uselang=en) and (http://commons.wikimedia.org/w/index.php?title=Special%3ASearch&profile=default&search=isomerase&fulltext=Search&uselang=en) There may not be the images for the specific examples you provide in the article but maybe one of these would make a good header image.
• I like how you have shown the different classes of isomerases, but wonder if you are going to provide examples for Cis-trans and Intramolecular lyases as you did for other classes.
• There appears to be a broken citation to "yahoo health" in the third to last paragraph.
• Your citations appear to be mostly from peer reviewed journals and textbooks, so that is great. I noticed your most cited reference (#12 to Orphanet) is cited 10 times. I wonder if it might be good to get another supporting reference to supplement this section instead of citing this one reference so many times, especially as it is to another website.

Hello! Thank you for your feedback. We definitely need to add another image. Thank you for the examples you provided! I'm sure my partner and I will come to a consensus on the image to add. We added some wikilinks from suggestions from the first review, but we will definitely add more in there! We will take all of your suggestions into consideration as we progress. Thank you again! Juanquina Thomas (talk) 02:27, 23 November 2013 (UTC)

You have added a lot of great content and I look forward to seeing your final additions to the article over the next couple weeks. Apoptosis81 (talk) 04:33, 21 November 2013 (UTC)

Thank you for the review! We need to add more wikilinks. I'm not sure what to call the first section to be honest. We had a lot of that information in the introduction but moved it into its own section under suggestion. Maybe just calling it Isomerization or Isomers or Background information would be a better sub-title? The three images under mechanisms look fine on my browser so I hope it is not just on my end... The third image was taken with credit from a journal article. Do the images look proportional when you click on them? In the article itself they are smaller in size but they are rather large and detailed.I would like to add an image showing an example of isomers at least. I wasn't sure what would be appropriate for the main image since so many pictures I found were of isomerization reactions but without any reference to the isomerase itself. Looking for "isomerase" itself in the commons is a great idea! The sub-classes for cis/trans isomerases and lyases don't have further sub-categories so that section does look unbalanced. I was thinking of adding specific examples to each sub-section. That might help.Hnagy2 (talk) 01:43, 26 November 2013 (UTC)

I went back and implemented your suggestions. The one mechanism thumbnail is weird, though. I run Firefox on Linux and it looks fine but apparently on some other systems it looks very blurred. I'm not sure why since the other images look fine. I'm not really sure how to fix that but I went back and added some more images where it really needed them!Hnagy2 (talk) 03:18, 27 November 2013 (UTC)

Hi Heather, your images look great and the new additions are very good. The only image that still looks blurry to me is: Chorismate mutase mechanism.gif. You asked if the images look proportional...I think they look good overall, but a few are a bit small. I actually have been working on resizing the images in my article and found some helpful Wikipedia code that allows you to resize images. This code is: "File:Organelles of the Secretory Pathway.png|thumb|upright=1.5|Organelles of the Secretory Pathway Involved in the Secretion of Exoenzymes". In this example the section "upright=1.5" defines the size...by default wikipedia does all thumbnails to 0.75 so in this example I doubled the size of the image (Note the above code should be within [[ ]] not " ", but I didn't want the image to show up here). Sorry if you already know all about this! I like the new title of your first section "Isomerization" as well. You have really added a ton of great content and I look forward to seeing the final changes in the next couple weeks. Apoptosis81 (talk) 04:15, 28 November 2013 (UTC)

Comments from Adimart1

Hey guys, You have done a LOT of work on this article and it looks great. I think maybe a nice boldly colored illustration of a typical isomerase might add some "pop" at the start of the article. Also, in the classification section you have a subsection titled "miscellaneous". I don't know, for some reason it sticks out to me. I would probably consider titling it "other isomerases" or something like that. Naming a section "miscellaneous" feels to me like the person writing it got bored or side tracked or something....NOTHING wrong with it, that is merely a personal opinion on my part. Do with it as you will. You have several references, which is great, but I think you rely really heavily on one in particular and I think a little expansion on that would be great. I like all the diagrams you included. Overall the page looks great! Keep up the good work.Adimart1 (talk) 06:46, 21 November 2013 (UTC)

Hello! Thank you for your review! We will definitely need to add another image, as this has been suggested a few times. As for the references, I am in the process of looking for a different source that has substantial information that can be used for this topic. My partner and I will definitely take your suggestions in consideration as we progress. Thank you again! Juanquina Thomas (talk) 02:31, 23 November 2013 (UTC)

Thanks for the review! I am hesitant to change the name of the miscellaneous subcategory since that is the official category title from Enzyme Nomenclature 1992, which is the recognized set of guidelines for enzyme classification. I added text to each category to give some context but all titles and sub-titles are taken directly from those guidelines (it does seem like a lazy title to me, but I didn't want to make any changes to the categories). We need to pick an image for the beginning of the article. Before, I found tons of images for isomerization reactions in general but nothing with the actual isomerases involved. I have found better images so we'll pick one, the beginning looks very plain and sparse without one. Thanks!Hnagy2 (talk) 01:59, 26 November 2013 (UTC)

suggestions

Well done on your edits over the last few months, two suggestions:

• a section on the evolution of isomerases
• mention of the diffusion limit achieved by some isomerases.

Nice work, T. Shafee (Evo&Evo) (talk) 13:50, 7 December 2013 (UTC)

Thanks for the suggestions! Do you think it is alright to go back and add new sections? I know we should have had all of the content integrated by now so I am not sure. On the other hand, these don't seem like huge additions so maybe I can squeeze them in. I considered a subsection of the evolution of isomerases but much of what I found focused on sugar isomerases. Perhaps I could add it in. I honestly did not even think about diffusion limits. I will search for that and see if I can integrate it without it getting unwieldy.50.27.76.206 (talk) 00:49, 8 December 2013 (UTC)

Your suggestions are appreciated. Hnagy, we can add new sections, however I wonder if it is too late in the game to do that? We're on our third (and final) peer review now. I'm not sure if we should just enhance information/sections or actually try adding new sections? What do you think? Juanquina Thomas (talk) 04:43, 9 December 2013 (UTC)

Maybe we could add a little bit to the intro or to the first section... I agree that it is a bit late at this point to add substantially. They are good ideas for additional content but I am not sure how well we could do entire new sections so close to the due date.Hnagy2 (talk) 02:41, 14 December 2013 (UTC)

Comments from WillPugarth

Hi all! I have been checking out your article for ideas since we first started the project, and I have to say your improvements have definitely made Isomerase much, much better. I like the diagrams and images you have included, as well as your explanation of Isomerization. As far as changes go, however, I still will make a few reccomendations:

1. You could definitely use a few more citations, so as to prevent later removal of text. I read somewhere that the goal is to have a citation every 1-2 sentences for science articles on Wikipedia (not sure how true this is though).

2. Another group mentioned that they were told that bullet points and sub-subheadings were not standard format for Wikipedia articles, and that the correct format included using tables or writing everything in paragraphs.

3. On the Transferase article, we avoided bulleting by adding tables to explain the EC classifications. Here is a copy of our table, converted to match your article (just go into edit mode and you can copy this and expand it, etc.):

Classification of isomerases into subclasses:

EC number	Examples	Description
EC 5.1	alanine racemase, lactate racemase, ribulose-phosphate 3-epimerase	Acts on molecules with a single chiral carbon
EC 5.2	Maleate isomerase, Linoleate isomerase	Changes the isomerization state of substrates from cis to to trans.
EC 5.3	Triose-phosphate isomerase	Catalyze transfer of electrons throughout the substrate

4. The format for headings and subheadings in Wikipedia is usually capitalize the first word, then all words in the heading after are lower case. So, "The Role of Isomerase in Human Disease" would be "The role of isomerase in human disease." If you don't mind, I might go through and change your headings to match this format?

Other than those suggestions, I'd say your article is really good. Your content and examples are pretty well expanded and you have plenty of diagrams and images. Good luck on the rest of your article!--WillPugarth (talk) 21:57, 7 December 2013 (UTC)

Thank you for the review! I actually waffled a bit on organizing the categorization section into a table. I noticed that many of the enzyme class articles used them and they look so clean. I have some bulky paragraphs within that section to give background for the classes. I am not sure if I should just leave them there or integrate them into the tables. I was leaning towards keeping the paragraphs and just putting the bullet point categories and examples into tables.

For citations (at least in the sections I wrote), much of the content is organized so that each paragraph summarizes information from one source. I had some doubts about that since it looks like much of it may be uncited but I also did not want to cite the same source many sentences in a row, especially for some of the broad background information on isomers and isomerization (much of the information is simply from the IUPAC gold book). The category section is also awkward since most of that came from the Enzyme Nomenclature book, aside from some cited background information. I'm not sure how to handle that since so much of the information is broad and I used a handful of authoritative sources, mostly from IUPAC.50.27.76.206 (talk) 01:02, 8 December 2013 (UTC)

Thanks for your suggestions. I think I will check out your Transferase article to get more ideas on organization. Thank you for noting the capitalization of the title, as I did not know this fact. As for the citations in the portion I wrote,I cited after almost every sentence. The problem is, there was not a lot of credible information available on some of our topics, so I found myself citing the same source over and over. We will continue to make improvements with these suggestions. Thank you. Juanquina Thomas (talk) 04:53, 9 December 2013 (UTC)

Thanks for responding! I totally get where your coming from on the sources issue, my apologies! I had a similar issue come up when I was trying to find the history of Transferases. I know I kinda dropped a ton of suggestions during basically the last week, and I know how much time it takes to work on these articles. As far as enzyme classification system stuff goes, I used several different databases to keep diversity in my citation up: BRENDA, ExPASy, and PDB. Just running through their classification info is useful for finding additional information on each subclass of an enzyme group. Hopefully that is helpful information (you probably already tried that though!). Either way, good luck with the rest of the assignment!--WillPugarth (talk) 07:04, 11 December 2013 (UTC)

Hi Will! Thanks for the reference suggestions. I visited your article page just to see how you guys structured everything. I took a few notes. I'm going to look very vigourously for a few more sources so that everything doesn't look as if it came from the same source. And no worries about all the suggestions! That's what the peer review is for. Thank you for helping us to better our article! Juanquina Thomas (talk) 05:51, 13 December 2013 (UTC)

Comments from Wenwatata

Hi All, Your write up on isomerase is excellent and I must commend you covering all the vital areas in this field. on the basis of this thorough work , I have only a few comments to make. I guess it would be appropriate to include a few lines in the article on the reason for the existence of isomerism, especially as it relate to drug or enzyme recognition of specific isomers (Hence its medical implications). I would congratulate you for this fine work. Take care. Godwin Ifere 04:09, 12 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)

Hello! Thank you for your suggestions. I will see if I can add at least a line or two on the existence of isomerism. Juanquina Thomas (talk) 05:53, 13 December 2013 (UTC)

Maybe we could add a little bit of this to the intro or first subsection?Hnagy2 (talk) 02:42, 14 December 2013 (UTC)

I am going to add some more on isomerase kinetics and uses. I will add them in and see if new sections are necessary.72.182.8.91 (talk) 17:17, 14 December 2013 (UTC) PS this was me, my browser had logged me out from Wikipedia.Hnagy2 (talk) 02:07, 15 December 2013 (UTC)

Heather, I added more content and changed a few sentences around in the industrial uses of isomerases. I think that is the only new section we should add. Juanquina Thomas (talk) 01:44, 15 December 2013 (UTC)

That would be best. I didn't want to give kinetics its own section so I kept it in "isomerization" and it seems to work. The applications section is a pretty big addition so I hope it reads well. I couldn't make it work in an existing section.Hnagy2 (talk) 02:06, 15 December 2013 (UTC)

Hi All, This is my last formal round on the article. I found that the quality has greatly improved. Thank you fro all the efforts, as you have done a marvelous job. Take care everybody. Godwin Ifere 04:50, 15 December 2013 (UTC) — Preceding unsigned comment added by Wenwatata (talk • contribs)