Wikipedia:United States Education Program/Courses/JHU MolBio Ogg 2012/Section 81/Group 81A

Group 81A

This is the Wikipedia page for 410.602 Molecular Biology, 2012, group 81A. This group will be editing the Endonuclease 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 (optional, see Unit 5); rationale for selecting an article (Unit 6); progress reports (Units 9 and 12); and the final report (Unit 14). Please create a new section here for each of those assignments.

Unit 6 article selection rationale

Our group has chosen Endonuclease as the article of interest. We would like to work on this article because it’s listed as a stub article with mid-importance which needs additional citations and information. We think we can find additional information and contribute by adding value to the article's development in the process. Endonucleases are significant enzymes that cleave the phosphodiester bond within a polynucleotide chain. These enzymes play important roles in DNA recombination and many biological processes. The areas we would like to change and/or contribute to the article’s development are,

1. We would like to improve the various functionalities of the different types and categories of endonucleases by adding more text, related examples, and providing clarity for the reader. Something that is extremely lacking in the article is use of pictures. Having images incorporated into the article allows for words to come alive and can help the reader grasp a better understanding.
2. We would like to add value to the restriction aspect of the enzyme and outline possible mechanisms which allow such behavior.
3. We would also like to underscore the enzyme’s importance across multiple organisms. We also need to look at how these enzymes function similarly or differently across organism. We can provide depth to the article by adding information regarding how endonucleases are affected by mutations in different cell types.
4. We would like to highlight its overall significance with regards to molecular biology from reader’s perspective.
5. Another aspect we would like to highlight is the role endonucleases play in recombinant DNA technology. This is important to allow the reader to see how endonucleases are playing a key role in DNA manipulation.
6. Another area the article fails to mention is the role endonucleases play in DNA repair.
7. Finally, at the end of the article it briefly mentions and lists a few of common endonucleases. We think this area can definitely be expanded upon and include more common examples.

While we have 7 areas that we would like to improve upon, we think the main focus behind all these improvements is to provide reliable sources for all areas to make this a reliable and useful article.

Unit 9 progress report

Functions of the three different categories of endonucleases – Type I, II, and III.

In general, many cells contain nucleases that behave differently. There are two classes namely- exonucleases and endonucleases. On one hand, most of the exonucleases work in only the 5’ → 3’ or 3’ → 5’ direction to degrade nucleic acids. The endonuleases, on the other hand, are capable of degrading nucleic acid at specific internal sites of the strand or molecule and essentially shrink it to pieces. Those endonucleases that have this capability do belong to a class called restriction endonucleases which tend to be really significant in biotechnology. Ultimately, there are three types of restriction endonucleases that are grouped as I, II, and III. The types I and III are large multisubunit complexes that include both the endonuclease and methylase activities. Type I can cleave at random sites of about 1000 bp or more from the recognition sequence and it requires ATP as source of energy. The type II behaves slightly different, it was first isolated by Hamilton Smith in 1970, they are simpler versions of the endonucleases and requires no ATP in its degradation processes. Some examples of the type II restriction endonucleases include BamHI, EcoRI, EcoRV, and Haelll. The type III, however, cleaves the DNA at about 25 bp from the recognition sequence and also requires ATP in the process.

DNA Repair

Endonucleases play a role in DNA repair. AP Endonuclease, specifically, catalyze the incision of DNA exclusively at AP sites, and therefore prepare DNA for subsequent excision, repair synthesis and DNA ligation (1). For example, when depurination occurs, this lesion leaves a deoxyribose sugar with a missing base. The AP enodnuclease recognizes this sugar and essentially cuts the DNA at this site and then allows for DNA repair to continue (2). E. coli cells contain two AP endonucleases: endonuclease IV (endoIV) and exonuclease III (exoIII). While in Eukaryotes, there is only one AP enodnuclease (3).

Future Plan: As previously seen in the rationale for choosing our topic, we have come up with seven areas of improvement. The plan for the remainder of the semester is to split up the 7 points between the two of us. Derrick will be focusing on points 1-3 and I (Brittany) will be focusing on 4, 5 & 7. We wanted to have one of the points completed by Monday and then that would allow for each of us to work on two more points for the remainder of the semester. We both would like to contribute to the picture aspect of our topic. This is something we can work on towards the end, once major contributions have been made and will allow us to add applicable pictures.

Brittany’s Struggles: I have come up with a few struggles. The main struggle I have is honestly getting use to the Wikipedia and all of the rules. I am honestly kind of scared to do something that is considered a “big no no”. I guess the only way to learn is to try and learn from my mistakes. Another struggle was I had to go back and review the correct way to cite references. I am still actually figuring this out. I am glad we have come up with a schedule because now we can make adjustments every week and not get behind.

Derrick’s Struggles: I also had to go back and review how to cite references properly. I am slowly getting use to all the rules in Wikipedia but it's a constant struggle to make sure I do not violate anything major. Please kindly bring to my attention if something is not done correctly.

Unit 12 progress report

I have checked into Group 81D's article nucleic acid structure as a reviewer. I think the organization and flow of information of their article looks good. I also think it transitions nicely from primary structure through quaternary structure in addition to the images that allow the contents "come alive". I will continue to review the article and provide feedback where applicable. I received some feedback from our reviewers (Group 81F) with regards to the initial contents that I added on the actual article. As per our reviewers feedback comments, I have added a new section called "Categories of Endonucleases" and have edited the contents that were added under that section. This includes properly citing the reference to reflect on the contents added. With respect to the restrictive behavior under my point #2. I have gone ahead and added the following contents - The restriction enzymes used in molecular biology usually recognize short target sequences of about 4 – 8 base pairs. For instance, the EcoRI enzyme recognizes and cleaves the sequence 5' – GAATTC – 3'. I will continue to edit by adding more contents to the article as we go along.

New material I added to our article.

Xeroderma pigmentosa is a rare, autosomal recessive disease caused by a defective UV-specific endonuclease. Patients with mutations are unable to repair DNA damage caused by sunlight.

Sickle Cell anemia is a disease caused by a point mutation. The sequence altered by the mutation eliminates the recognition site for the restriction endonuclease MstII that recognizes the nucleotide sequence.

tRNA splicing endonuclease mutations cause pontocerebellar hypoplasia. Pontocerebellar hypoplasias (PCH) represent a group of neurodegenerative autosomal recessive disorders that is caused by mutations in three of the four different subunits of the tRNA-splicing endonuclease complex .BCoss1 (talk) 21:13, 1 December 2012 (UTC)

Besides adding this new material to the article, I also added the DNA repair material from our previous week to the actual article. Therefore, I have added two new sections, a DNA repair section and a Mutation section. Over the remainder of the semester I will be working on adding information about endonuleases overall significance toward molecular biology for readers. I will also be looking for images we can add to our article because I believe that the lack of images in our article is a huge downfall. Derrick has been a great help with figuring things out and I will say I am learning a lot!! I think honestly the hardest part was figuring out to correctly reference my citations. Now that I have figured it out, it is actually pretty easy. BCoss1 (talk) 21:41, 1 December 2012 (UTC)

I also had a chance to look over Group 81D's article nucleic acid structure, I provided feedback on their talk page. I really like the flow of their article but I really liked all the images they incorporated into it as well. I gave them another topic they might want to include in their article and mentioned that the only issue I saw was the lack of references. I will also continue to review their article over the remainder of the semester. BCoss1 (talk) 21:53, 1 December 2012 (UTC)

Final progress report

I have added my final contributions to our article. Initially I was going to add another section (the role in recombinant DNA technology) to the article however I took a look at both Klortho’s suggestions and also the suggestions by our peer review and wanted to improve upon those areas instead of just adding another section. (The role in recombinant DNA technology is also briefly mentioned in the first section.) I first added what a restriction site is that way it is introduced before we reference it. I also explained the difference between an endonuclease and a restriction endonuclease is because I agree with the comments, it was somewhat confusing. I also removed what was previously under the section Common Endonucleases and created two tables containing information about common eukaryotic and prokaryotic endonucleases. I think putting the information in a table makes it much easier to understand instead of writing about them in a paragraph or bullet point form. I had to research how to insert a table in Wikipedia. Once I figured it out, it was actually very easy! I also added two pictures and a 3-D image/cartoon. I think the pictures really helped improve our article. The 3-D image I think is really neat and helps make the section of DNA repair, where I discuss AP endonucleases, come alive. I found Wikimedia Commons a great tool!!! I have definitely spent a lot of time doing research on our topic and also just as much time learning how to correctly use Wikipedia. I think what we have done really improved the article and I also learned a ton about Wikipedia. I look forward to Derrick’s final contributions and what the article will look like in the end! I also added my final suggestions to the nucleic acid structure talk page. BCoss1 (talk) 18:10, 14 December 2012 (UTC)

Here are my final contributions as per suggestions from our reviewers:

1. Introduced restriction endonucleases as being the most important nucleases in biotechnology with the following statement: There are a small amount of significant classes of endonucleases that cleave only at the specific nucleotide sequences (such as the restriction endonucleases which are so vital in biotechnology).
2. Removed ambiguous statement that may have been inserted by previous editors of the article: “A given sample of DNA is likely to contain a recognition sequence for any restriction endonuclease”.
3. Inserted a brief definition of Recombinant DNA with the following statement: DNA formed by the joining of genes into new combinations.
4. Refined the introductory sentence under the categories section.
5. Linked DNA ligase and Recombinant DNA
6. Inserted the heading for Notations and Further discussions: This was done to separate some pertinent contents from the categories section.

I also added my final suggestions to the nucleic acid structure article. Dgambrah (talk) 02:40, 15 December 2012 (UTC)

References

Functions of the three different categories of endonucleases – Type I, II, and III. 1. Nelson, David L.; Cox, Michael M. (2005). Principles of Biochemistry. New York: W.H. Freeman and Company. ISBN 0-7167-4339-6.

DNA Repair 1. Tom Ellenberger; Friedberg, Errol C.; Walker, Graham S.; Wolfram Siede; Wood, Richard J.; Schultz, Roger (2006). DNA repair and mutagenesis. Washington, D.C: ASM Press. ISBN 1-55581-319-4.

2. Alberts, Bruce (2002). Molecular biology of the cell. New York: Garland Science. ISBN 0-8153-3218-1.

3. "Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors".