User:Aconch/sandbox

Introduction
Within this section, I will be summarizing Wikipedia's Five Pillars and editing my entry. I hope to include several functions, including bold and italic texts, as well as, the incorporation of headings and subheadings. I am also incorporating a summary of the characteristics of a target article for my Molecular Biology course and citing sources for two pubmed articles.

UNIT 1-2 Assignment: Wikipedia's Five Pillars
Wikipedia abides by the five distinct principles listed below :

1. Wikipedia is an encyclopedia: It is an online resource that contains generalized information regarding several topics.

2. Wikipedia has a neutral point of view: It states facts, not opinions.

3. Wikipedia is free: All of its content is accessible for free and open to the general public. Furthermore, anyone can edit entries.

4. Wikipedians should respectful: All Wikipedians should act in good faith, be welcoming, and refrain from "Edit Wars"

5. Finally, Wikipedia does not have firm rules: Its policies and guidelines are constantly changing and evolving. The interpretation is flexible, so don't be afraid to be bold.

UNIT 3-4 Assignment: Summary of Characteristics of Target Article
For our Molecular Biology course this semester, the target quality level for our Wikipedia article should be between B-class and Good article. Nevertheless, before elaborating on the target quality level, I want to discuss our article's initial quality.

Initially, our article will belong in the stub-class. A stub article is a short article. This type of article consists of only a few sentences and contains useful, verifiable information; however, it needs further expansion.

As the semester progresses, my partner and I will expand a stub article, contributing enough information so that it falls somewhere between a B-class and Good article by the end of the course. B-articles are mostly complete articles. They are fairly well-written and referenced. However, additional information and further expert knowledge is still needed. Because our aim is to improve an article as much as possible, I will further focus and highlight the characteristics of an article within the "Good article" level.

Good articles are well written, "contain factually accurate and verifiable information, are broad in coverage, neutral in point of view, stable, and illustrated, where possible, by relevant images with suitable copyright licenses." In essence, the article is referenced appropriately and contains quality information that is presented unbiasedly.

Below is a list of characteristics that a Good article possesses:

1. It is well-written. 2. It contains verifiable information and appropriate citations.

3. It stays on-topic and has broad coverage.

4. It is unbiased.

5. It is stable; it refrains from edit warring.

6. It contains relevant images and captions.

UNIT 5 Assignment: Practicing Citations
Dracunculus, whose name means ‘little dragons,’ are parasitic nematode roundworms. These parasites, also commonly known as guinea worms, cause infection when a person consumes water containing their parasitic larvae. These roundworms cause very painful skin blisters, and when a blister bursts, the head of the parasite emerges while the rest of its body remains inside the host. Currently, “there is no drug that kills guinea worm, no vaccine and no protective immunity after infection.” The traditional way to remove the parasite is to wrap its head around a stick and slowly rotate the stick until the parasite exits the host’s body; this process is may last anywhere from “hours to months." Nevertheless, eradication of the disease may be possible by employing preventative methods that include: drinking clean water, preventing infected individuals from contaminating the water supply, and controlling the flea population that harbors the parasitic larvae . These methods have resulted in “99 percent reduction in infections,” and this disease is “poised to become the second human disease after smallpox to be eradicated.”

Note : My initial article assessments can be found on Girum's and my group page.

UNIT 7 Assignment: Initial Work on Biosynthesis Article
List of references from UNIT 5:

Mann, John (1995). Chemical Aspects of Biosynthesis. New York: Oxford University Press. ISBN 978-0198556763 Note:   For now, I've removed this source from the list because it is no longer in my possession. Aconch (talk) 23:12, 20 October 2013 (UTC)

1) Nelson, David L et al (2012). Lehninger Principles of Biochemistry. New York: W.H. Freeman. ISBN 978-1429234146

2) Jones, PJ. (1997). "Regulation of cholesterol biosynthesis by diet in humans." Am J Clin Nutr 66(2):438-446. Link: http://ajcn.nutrition.org/content/66/2/438.abstract

 Additional References : Bullet points will explain possible uses for these references

3) Stoddart, R. W. (1984). The biosynthesis of polysaccharides. New York: Macmillan Pub. Co. ISBN: 0029487501
 * I can get this book from the library. We can use it to develop the synthesis of polysaccharides.

4) Watson, J. D. (2008). Molecular biology of the gene. 6th ed. San Francisco: Pearson/Benjamin Cummings. ISBN:9780805395921
 * Our textbook can be used to give a general overview of polysaccharide, DNA, lipid, and protein biosynthesis.

5) Weissbach, H., & Pestka, S. (1977). Molecular mechanisms of protein biosynthesis. New York: Academic Press. ISBN:0127442502
 * I have also requested this book from the library for our protein synthesis section.

6) Meister, A. (1965). Biochemistry of the amino acids: [Volume II]. S.l.: Academic Press. ISBN:9780123955234
 * This book contains a chapter that summarizes the biosynthesis of the 20 amino acids

7) Umbarger, HE (1978). "Amino acid biosynthesis and its regulation.". Annual review of biochemistry 47: 532–606.
 * Amino acid summery article.

8) Abrams, R. I. C. H. A. R. D. "Nucleic acid metabolism and biosynthesis." Annual Review of Biochemistry 30.1 (1961): 165-188.
 * This article is a review on nucleic acid metabolism.

9) Moldave, K. "Nucleic acids and protein biosynthesis." Annual Review of Biochemistry 34.1 (1965): 419-448.
 * This is a great summery of protein biosynthesis in addition to additional summery on Nucleic acid biosynthesis.

 List of Suitable Images :

1) https://commons.wikimedia.org/wiki/File:Progesterone_Biosynthesis.png
 * This image from wikimedia shows the pathway of progesterone synthesis. This may be one of our specific examples of lipid biosynthesis.

2) https://commons.wikimedia.org/wiki/File:Protein_synthesis.svg
 * This image from wikimedia shows the process of translation or protein synthesis.

3) https://commons.wikimedia.org/wiki/File:DNA_replication_en.svg
 * This image from wikimedia shows the process of DNA replication or DNA synthesis.

4) https://commons.wikimedia.org/wiki/File%3AMetabolism_790px.png
 * This image shows summary of the major biosynthetic pathways within a cell

UNIT 7 Assignment: Preliminary Outline for Biosynthesis Article

 * Introduction: We'll include a brief definition of "biosynthesis" and add links to key words within our first paragraph. We'll also give an overview of key aspects that will be discussed in the article.


 * Body Paragraphs: We hope to include all of the examples below, but because of the time constraint, this section is the most fluid/flexible. Within these examples, we'll talk about pathways, organelles and key factors/proteins that lead to the anabolism of monomers to macromolecules. I'm hoping that we can give a general overview of the biosynthesis of each of these macromolecules and follow that up with a specific example from a manuscript. This will be dependent on the resources at our disposal.
 * Biosynthesis of lipids
 * Biosynthesis of proteins
 * Biosynthesis of polysaccharides
 * Biosynthesis of DNA
 * Biosynthesis of other Amino acids
 * Biosynthesis of Cofactors and Vitamins


 * Final Section: Examines the effects or problems that arise from biosynthesis pathway inhibition.

UNIT 8 Assignment: First Contribution "Scratch Pad Area"
For convenience, here is a link for the Biosynthesis article.

Modified Introduction:

Biosynthesis (also called biogenesis or "anabolism") is an enzyme-catalyzed process by which substrates are converted to more complex products.[1] In biosynthesis, the monomers join together to form macromolecules. These monomers are commonly linked via covalent bonds that form from dehydration reactions [4]. Proteins are made up of monomers called amino acids; these monomers are joined via peptide bonds. Another macromolecule, polysaccharides, is made up of sugars that are joined by glycosidic bonds, and nucleic acids, whose monomers are nucleotides, are joined by phosphodiester bonds.[4] This pattern of simple, similar structures is repeated in the formation of larger complexes. For more intricate structures, noncovalent interactions also occur. For example, phospholipids interact noncovalently to synthesize the lipid bilayer (4). The prerequisite elements for biosynthesis include precursor compounds, chemical energy (such as in the form ATP), and catalytic enzymes, which may require coenzymes (e.g., in the form of NADH, NADPH).[2]

The biosynthesis process often consists of metabolic pathways. Examples of these multi-step biosynthetic pathways include the production of blood clots, amino acids, fatty acids and natural products.[3] Other commonly known complex products of biosynthesis include proteins, polysaccharides, and nucleic acids. [4]

Biosynthesis plays a major role in all cells. Some of the biosynthetic pathways are located within a single cellular organelle. While other pathways, involve enzymes that are located within multiple cellular organelles. Some of the organelles involved in biosynthesis include: Ribosomes, Chloroplast, smooth and rough ER, Mitochondrion, Plastids [6], and Golgi bodies. Additionally some biosynthetic pathway enzymes are located in the Cytosol and Nuclear matrix.[5]

References :

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

2) Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2008). Ch. 20. Carbohydrate Biosynthesis in Plants and Bacteria. In Lehninger Principles of biochemistry (p. 773). New York: W. H. Freeman. ISBN 9780716771081.

3) Jones, Russell Celyn; Buchanan, Bob B.; Gruissem, Wilhelm (2000). Biochemistry & molecular biology of plants. Rockville, Md: American Society of Plant Physiologists. pp. 371–2. ISBN 0-943088-39-9.

3) I removed the original third source because it was biased/not neutral.

4) Lodish, H., Berk, A., Matsudaira, P., Kaiser, C.A., Krieger, M., Scott, M.P., Zipursky, S.L. & Darnell, J. (2004). Molecular Cell Biology. New York: W.H. Freeman and Company. pp. 9. ISBN: 978-0716743668.

5) Srere, P. A. (1987). Complexes of sequential metabolic enzymes. Annual review of biochemistry, 56(1), 89-124.

6) Neuhaus, H. E., and M. J. Emes. "Nonphotosynthetic metabolism in plastids." Annual review of plant biology 51.1 (2000): 111-140.

UNIT 10 Assignment: Contributions: list of things accomplished/message for Girum
For this unit contribution I've: Thanks and talk to you soon!
 * Finished the lipid section
 * Created a DNA section
 * Formatted the page and rearranged your images, so that they fit in the text that you wrote
 * I'm also going to play around with the introduction, so that it's more generalized. The OA wants us to phase out the citations, since the information from the introduction is supposed to be more detailed and cited in the body. So, I'll try to phase those out. Nevertheless, the introduction section will remain "fluid," since we'll be changing the body section of our article with our contributions. I expect that the introduction itself won't be finalized until we're done with the body of the article. Updated
 * I've also gone through and re-read/edited the article. Feel free to look it over as well.

UNIT 12 Assignment: Contributions (Note from Aconch)
For this unit contribution:
 * I'm planning to start a new section utilizing a new source and will include appropriate images. Section TBA: I'm debating on starting the protein synthesis section. It makes sense to, especially since Girum mentioned starting amino acid synthesis for this contribution. Otherwise, the other section that I was considering was polysaccharides. Update: I've decided to do protein synthesis. Depending on how involved this section becomes, this along with the synthesis of amino acids, might be the last macromolecule synthesis sections for our article. Final Update: I finished the protein synthesis section.
 * I will update the introduction so that it mentions the new sections that we're incorporating. Updated
 * I added a chemical properties section
 * I added a see also section.
 * For the final contribution, I think we should concentrate on problems that may occur in the aforementioned macromolecules' biosynthesis, as well as, the effects that arise from these problems.

"Working Area"

Equations that I made for tRNA charging:

1) $$ Amino~acid + ATP \rightleftharpoons {} aminoacyl~AMP + PP_i$$

2) $$ Aminoacyl~AMP + tRNA \rightleftharpoons {} aminoacyl~tRNA + AMP$$

3) $$ Amino~acid + ATP + tRNA \rightleftharpoons {} aminoacyl~tRNA + AMP+ PP_i$$

Table that I constructed of key players in Translation:

UNIT 14 Assignment: Contribution and finishing up (Note from Aconch)
As previously mentioned, I plan to create the final section called: "Diseases associated with macromolecule deficiency and faulty pathways," where I discuss different diseases.

I will also read the article, and do a final check on grammar, spelling, and formatting.

Additionally, I'll try to go ahead and update some of our sources with more recent versions of the textbooks that we've cited.