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Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2013/Group 82E

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Final Progress Report

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WeberOwl

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When this project began, the Dephosphorylation wiki article was classified as a stub, and contained only a few sentences of uncited information. Since then the article has grown to include multiple sections, covering material from the history of discovering dephosphorylation through the critical role that it plays in physiological functions both in health and disease.

Finding primary material, especially open-use images, was difficult for this topic. Phosphorylation is commonly discussed and studies, but specific investigations of dephosphorylation are much more rare. Nevertheless I was able to find some great resources, and even a couple images that highlight the importance of dephosphorylation in signaling pathways. While these pictures are sourced form elsewhere, I created the table summarizing the changes in energy associated with dephosphorylation in different reactions.

I was fortunate to have some fantastic reviewers from within our class. Input ranged from suggestions about content to points about formatting, and on the whole, the dephosphorylation article is much stronger as a result. Sometimes I disagreed with suggestions from the reviewers, but by continuing a discussion, consensus was generally reached. Sometimes I held my ground (for example by not adding pictures of Krebs to the history section) and other times had my mind changed (realized the importance of a disease section).

MonopterusAlbus

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The following changes were made to the wikipedia article, as recommended by reviewers and OAs:

LEAD

  • image depicting schematic of phosphatases and proteases (including ATP)
  • better description of the process of phosphorylation within the introduction/lead
  • basic explanation of phosphorylation/dephosphorylation and the enzymes used
  • explanation of the importance of phosphorylation/dephosphorylation in every physiological process
  • explanation of how the disease can develop from deregulation of reversible phosphorylation

HISTORY

  • provide more information from seminal papers on dephosphorylation

FUNCTION

  • image depicting catalytic domains of phosphatase

LABORATORY APPS

  • section changed to "Research Apps"

DEPHOSPHORYLATION IN DISEASE

  • subsections on pathology and treatment included
  • in pathology, mutations in phosphatases and the diseases that result
  • in treatments, protein targets for drugs and the treatments of the diseases above that target dephosphorylation

The following suggestions were not followed based on precedence in other articles:

  • inclusion of in-line citations in lead section
  • movement of "History" section to the end of the article
  • subsection on protein phosphatase families was not included, as enough background on the enzyme class appears in the lead.

The minor changes below were made for proper categorization of the article and aesthetic appeal:

  • centering of wikitable in "Function" section
  • removal of irrelevant images from article
  • protein primary structure and posttranslational modifications template added (see bottom of article)

Group 82E

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This is the Wikipedia page for 410.602 Molecular Biology, Spring, 2013, group 82E. This group will be working on the dephosphorylation article.

Use the talk page here to collaborate as a group, when learning to use and navigate Wikipedia, assessing articles, or for any other topic.

Use this page (not the talk page) for article assessments; rationale for selecting an article; etc.

Please create a new section here for each of those assignments.

Unit 9 Progress Report

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As of 4/3, I've added some text to the introduction section, as well as the history and laboratory sections. I've created headers for the additional sections we've planned. WeberOwl (talk) 01:21, 4 April 2013 (UTC)[reply]

On 4/5 I added information on the dephosphorylation of ATP. I think that a chemical formula and a figure would add to this section. I'm going to work something up to add in. I also added another reference for the history section. WeberOwl (talk) 04:02, 5 April 2013 (UTC)[reply]

On 4/12 I made some changes to the intro so that it reads more clearly and contains a bit more information. I also added two sections to the Function section, including a formula and a table. I added phosphorylation to the see also section. WeberOwl (talk) 04:17, 12 April 2013 (UTC)[reply]

On 4/24 I rewrote the Lead section of the article. It now discusses the phosphorylation-dephosphorylation reversible reaction, explains the mechanism of the enzyme phosphatase, and alludes to later sections which delve into the role of the process in disease and molecular biology techniques. MonopterusAlbus (talk) 03:35, 11 May 2013 (UTC)[reply]

Initial Article Assessments from MonopterusAlbus

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Dephosphorylation

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This article would not qualify as a Good Article by Wikipedia standards for the following reasons. First, while it contains no original research, it lacks external sources and verifiable information outside of Wikipedia. The article is concise, but hardly broad in its coverage of dephosphorylation. This article would qualify as a definition on Wiktionary. The discussion surrounding the dephosphorylation article includes nothing aside from its classification as a stub, but it is of high importance to the WikiProject Molecular and Cellular Biology. The useful references below include a seminal paper from Dr. Edwin Krebs, the necessity of dephosphorylation in the cell cycle, and calcium-dependent dephosphorylation of CREB in the brain.

Useful References

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  • Krebs, E G; Beavo, J A (1979). "Phosphorylation-Dephosphorylation of Enzymes". Annual Review of Biochemistry. 48: 923–59. doi:10.1146/annurev.bi.48.070179.004423. PMID 38740.
  • Strausfeld, U; Labbé, J. C.; Fesquet, D; Cavadore, J. C.; Picard, A; Sadhu, K; Russell, P; Dorée, M (1991). "Dephosphorylation and activation of a p34cdc2/cyclin B complex in vitro by human CDC25 protein". Nature. 351 (6323): 242–5. Bibcode:1991Natur.351..242S. doi:10.1038/351242a0. PMID 1828290. S2CID 4372756.
  • Bito, H; Deisseroth, K; Tsien, R. W. (1996). "CREB phosphorylation and dephosphorylation: A Ca(2+)- and stimulus duration-dependent switch for hippocampal gene expression" (PDF). Cell. 87 (7): 1203–14. CiteSeerX 10.1.1.368.1299. doi:10.1016/s0092-8674(00)81816-4. PMID 8980227. S2CID 14032887.

FsrA

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While the current article for FsrA is only two sentences long, it at least includes two external citations, making it verifiable according to Wikipedia's criteria for a good article. No talk page exists for this article, but it has already been identified as a stub. The useful references include an article that identifies the genes encoded by the fsr locus (2006) and another defining the kinase-response regulator pair (2000).

Useful References

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Initial Article Assessments from WeberOwl

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Frameshift Mutation

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This is a "good" article by wikipedia standards, though it is lacking in detail and broadness. The formatting is generally correct and the talk page is civil (if somewhat inactive). Adding more detail and general information would help to make this more of a complete article and less of a stub.

It may be interesting to touch on how frameshift mutation rates can vary based on positioning within the genome. A good paper on this can be found here. Also, while the article currently touches on how frameshift mutations are involved in Tay-Sachs, adding information about the role of these mutations in Smith-Magenis syndrome would nicely expand the clinical aspect of the article. A disease/clinical section could probably be created and would be a useful resource.

Within the talk section there is some discussion about how impactful frameshift mutations are concerning the structure of proteins resulting from gene expression. The author makes a good point but does not include references backing up their statement.

Useful References

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DNAx

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This article is severely lacking detail, and contains no references. It has broken links and contains tables which are out of context and likely not necessary. There also hasn't been any activity on the talk page.

A good source to get more info on DNAx is the NCBI library page. Additionally, this article discusses the role of DNAx in forming initiation complexes.

Useful References

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Article Selection Rationale

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Our joint decision to improve the Wikipedia page for dephosphorylation stems from a number of reasons. Firstly, dephosphorylation is required to remove the ubiquitous molecular tag, phosphate, from DNA to regulate gene expression. For this reason, the topic is vital to our understanding of molecular biology. Knowing the importance of dephosphorylation to molecular biology, it is imperative that the most trusted online collaborative encyclopedia contain accurate, verifiable information on the topic.

Importance of Dephosphorylation in Molecular Biology

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In biochemistry and molecular biology, reversible covalent modification by phosphatases and kinases is central to regulation of enzyme activity and gene expression. The enzyme phosphatase works by removing a phosphate group through the hydrolytic process of dephosphorylation. And, while other reversible covalent protein modifications exist (acetylation-deacetylation, adenylylation-deadenylylation, uridylylation-deuridylylation, and methyl­ation-demethylation), the phosphorylation-dephosphorylation pair is the only one that catalyzes and synthesizes high-energy molecules for use elsewhere in the cell. Dephosphorylation is necessary for the proper function of most molecular switches and enzymes. Thus, the process of dephosphorylation is arguably the most important mechanism in molecular biology.

State of the Current Dephosphorylation Article

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The dephosphorylation article is currently classified as a stub within the biochemistry category. The article provides a very brief (three sentence) explanation of dephosphorylation, but none of the information is linked to citations or references. Additionally, there is no activity on the talk page, indicating that there has not been productive interaction of Wikipedia editors prior to our group taking on the goal of improving the dephosphorylation page. To improve the quality of this article to good article status, we will need to expand the broadness of information provided about dephosphorylation, provide ample citations for that information, and add suitable images that add to the overall usefulness of the article.

References

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