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User:Samuew/sandbox

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Article Evaluation

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Article to Evaluate: DNA Origami

  • Is everything in the article relevant to the article topic? Is there anything that distracted you?

Nearly everything in the article is relevant to the concept and application of DNA origami. However, the final section, similar approaches, was not directly related to DNA origami. I appreciated this section because it allowed me, at the end of the article, to find more about similar fields that could give me more answers, or at least direct my research.

  • Is the article neutral? Are there any claims, or frames, that appear heavily biased toward a particular position?

The article is very well balanced. It maintains a nice balance between technical jargon and easy reading. I enjoy that without a technical background, i could understand a majority of the article.

  • Are there viewpoints that are overrepresented, or underrepresented?

I almost feel that the applications is more overrrepresented. There could perhaps be another section, or at least more detail, on how the scaffold and origami is made. However, then the approachable nature of the article could be changed dramatically.

  • Check a few citations. Do the links work? Does the source support the claims in the article?

Yes, the links I check do work. The articles I checked were all primary sources that were significant papers in the respective field.

  • Is each fact referenced with an appropriate, reliable reference? Where does the information come from? Are these neutral sources? If biased, is that bias noted?

Most of the sources appear to be primary papers that delve deep into the technical side of DNA origami. The sources appear neutral and appropriate. It does appear that most facts are citated correctly. However, sometimes the citation does not occur until the end of the paragraph, as long as the full thing is from that paper.

  • Is any information out of date? Is anything missing that could be added?

It is up to date as far as I understand the field. The only thing missing would be a more technical section that someone not in the field would not have to read to get the overarching idea of the article.

  • Check out the Talk page of the article. What kinds of conversations, if any, are going on behind the scenes about how to represent this topic?

The conversation has very few talking points. There was one quick discussion about who originally dreamed up this idea. The only other conversation was discussing how in depth to take the article. They seem to have agreed to keep the article at a more surface level, rather than delve into the topic in depth.

  • How is the article rated? Is it a part of any WikiProjects?

The article is rated C-class, low importance in 3 projects: Genetics, Molecular and Cell Biology, and Biology.

  • How does the way Wikipedia discusses this topic differ from the way we've talked about it in class?

The main difference is how in depth. This article also has great section of current applications, which we have not discussed in class. I look forward to the opportunity at looking at the papers mentioned in order to further explore this topic.

Article

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Prokaryotic Small Ribosomal Subunit

30S is the smaller subunit of the 70S ribosome found in prokaryotes. It is a complex of the 16S ribosomal RNA and 19 proteins[1]. This complex is implicated in the binding of Transfer RNA onto the messenger RNA (mRNA)[2]. The small subunit is responsible for the binding and the reading of the mRNA during translation. The whole subunit, both the rRNA and the 22 proteins, complexes with the larger 50S subunit to form the 70S prokaryotic ribosome in the cell. This 70S ribosome is then used to translate [[mRNA]] into proteins.

Translation

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The 30S subunit is an integral part of mRNA translation. It binds three Prokaryotic initiation factors: IF-1, IF-2, and IF-3[3].

A portion of the 30S subunit (the 16S rRNA) guides the initiating (5')-AUG-(3') codon of the mRNA into by a complementary binding to the Shine-Dalgarno sequence on the mRNA[4]. This ensures the ribosome starts translation at the correct location. The tightness of the bonding between the SD sequence on the mRNA and the 16S rRNA determines how efficiently translation proceeds[4]. Once the 16S rRNA recognizes the mRNA start codon, a special tRNA, F-Met-tRNA binds and protein translation begins[5]. The binding site of the f-Met-tRNA on the 30S ribosomal subunit is referred to as the "D-site"[6] This step is required in order for protein synthesis to occur and once it has, then the large ribosomal subunit will bind and protein synthesis will continue[7]. The binding of the large subunit causes a conformational change in the 30S subunit, allowing for another binding site in the subunit[6].

In order to form the translation complex with the 50S subunit, the 30S subunit must bind: IF-1, IF-2, IF-3, mRNA, and f-met-tRNA. Next, the 50S subunit binds and a GTP is cleaved to GDP and inorganic phosphate, thus dissociating the initiation factors and resulting in protein translation[8][5]. This process is referred to as "Initiation" and is the slowest process of translation[5].

Structure

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The small ribosomal subunit is made up of 16S rRNA and 19 full proteins[9]. There is also one polypeptide chain that measures in at 26 amino acids[10]. Conventionally, the rRNA is labeled with "H#" to indicate the helix number in high resolution images. Proteins are labelled "S#" to indicate the different peptides involved in rRNA stablization. S11 and H45 are located near the Shine-Delgarno binding site, which is also near the IF3 binding site. Proteins S3, S4, S5, and S12, along with H18, are located near the channel where mRNA is present in the 30s[1].

Inhibition

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The 30S subunit is the site of inhibition for the tetracycline and aminoglycoside antibiotics[11]. Tetracycline (Tc) is shown to interact with H27 in the small subunit as well as binding to the A-site in the large subunit[11]. Puromycin is a common inhibitor of ribosomal translation[6]. Pactamycin interrupts the binding in the Shine-Dalgarno binding region in the small subunit, thus disrupting activity. Finally, Hygromycin B also interacts with H44 and inhibits the translocation movement that is necessary during protein synthesis[11]. These antibiotics are known to target the prokaryotic ribosome specifically, hence their robust use in treating bacterial infections in eukaryotes.

See also

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References

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  1. ^ a b Schluenzen, Frank; Tocilj, Ante; Zarivach, Raz; Harms, Joerg; Gluehmann, Marco; Janell, Daniela; Bashan, Anat; Bartels, Heike; Agmon, Ilana (2000-09-01). "Structure of Functionally Activated Small Ribosomal Subunit at 3.3 Å Resolution". Cell. 102 (5): 615–623. doi:10.1016/S0092-8674(00)00084-2.
  2. ^ Thompson, John F.; Hearst. "Structure-Function Relations in E. coli 16s RNA" (PDF). Cell. 33: 19–24.
  3. ^ L Gold; D Pribnow; T Schneider; S Shinedling; B S Singer; Stormo, and G. (1981). "Translational Initiation in Prokaryotes". Annual Review of Microbiology. 35 (1): 365–403. doi:10.1146/annurev.mi.35.100181.002053. PMID 6170248.
  4. ^ a b Malys, Naglis (2012-01-01). "Shine-Dalgarno sequence of bacteriophage T4: GAGG prevails in early genes". Molecular Biology Reports. 39 (1): 33–39. doi:10.1007/s11033-011-0707-4. ISSN 0301-4851.
  5. ^ a b c Gualerzi, Claudio O.; Pon, Cynthia L. "Initiation of mRNA translation in prokaryotes". Biochemistry. 29 (25): 5881–5889. doi:10.1021/bi00477a001.
  6. ^ a b c Igarashi, Kazuei; Tanaka, Shigeaki; Kaji, Akira (1971-02-11). "On the aminoacyl-tRNA binding site of the 30-S ribosomal subunit and its relation to the chain initiation site of the ribosome". Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis. 228 (3): 728–731. doi:10.1016/0005-2787(71)90737-4.
  7. ^ Slobin, Lawrence I (December 1972). "Structural and Functional Properties of Ribosomes Crosslinked with Dimethylsuberimidate" (PDF). PNAS. 69: 3769–3773.
  8. ^ Milon, Pohl; et al. (2010). "The Ribosome-bound initiation factor 2 recruits initiator tRNA to the 30s initiation complex" (PDF). EMBO Reports. 11: 3112–3116. {{cite journal}}: Explicit use of et al. in: |first= (help)
  9. ^ Tsiboli, Paraskevi; Herfurth, Elke; Choli, Theodora (1994-11-01). "Purification and Characterization of the 30S Ribosomal Proteins from the Bacterium Thermus thermophilus". European Journal of Biochemistry. 226 (1): 169–177. doi:10.1111/j.1432-1033.1994.0t169.x. ISSN 1432-1033.
  10. ^ Choli, Theodora; et al. (June 1993). "Isolation and Characterization of a New Ribosomal Protein from the Thermophilic Eubacteria, Thermus thermophilus, T. aquaticus, and T. flavus" (PDF). Biological Chemistry. 374: 377–383. {{cite journal}}: Explicit use of et al. in: |first= (help)
  11. ^ a b c Brodersen, Ditlev E.; Clemons, William M.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, V. (2000-12-22). "The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit". Cell. 103 (7): 1143–1154. doi:10.1016/S0092-8674(00)00216-6.
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