User:Swiftie1999/sandbox

Week 3 tasks - "info for Methyl Oleate"

Properties of Methyl Oleate

Molecular formula -${\ce {C19H36O2}}$

Molar mass - 296.49 g/mol

Melting point - N/A

Boiling point - 218 °C

Solubility in water - insoluble in water

Practice Uploading a PDB Structure Image

Zoomed image of the oxygen ligand binding to the Iron metal of the Heme group.

Critique of Carbonic Anhydrase Mechanism Figure

The text size is small in the mechanism figure. The arrows can be zoomed to show the flow of electrons more clearly. Overall, each part of the mechanism should be spaced out to be seen more clearly.

1.7 - making a table

The H NMR values for methyl benzoate

Carbon	ppm value
A	3.886
B	7.26 -7.65
C	8.028

1.8 - Practice entering a formula

Arrhenius equation

$k_{1}=Ae^{\left({\frac {-E_{a}}{RT}}\right)}$

1.9 - Practice making a chemical information box

Methyl Oleate

Names
IUPAC name methyl (Z)-octadec-9-enoate
Systematic IUPAC name Methyl (9Z)-9-octadecenoate
Other names methyl-cis-oleate\methyl cis-9-octadecenoate\methyl (Z)-9-octadecenoate\(Z)-9-octadecenoic acid, methyl ester
Properties
Chemical formula	C19H36O2
Molar mass	296.495 g·mol−1
Density	0.874 g/mL
Melting point	−19.9 °C (−3.8 °F; 253.2 K)
Boiling point	218.5 °C (425.3 °F; 491.6 K)
Refractive index (nD)	1.452
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Infobox references

Tracking categories (test):

• PairSizeSet

2.0.  Practice Using History Pages, Talk pages, Article ratings and Watchlists

what was the main purpose of these two edits by Smokefoot?  

The main purpose of the edits were to omit unnecessary details and only include factual information. The comments made by Smokefoot indicates that a Wikipedia article cannot be written as if it was a school essay, it should only be compiled of facts. I believe the two edits were necessary, the articles were far more concise after making the changes. The information was presented in a more professional manner and the writing style was far more suited for a Wikipedia article.

what do the negative signs mean?

The statistic numbers refer to the amount of bytes of data added or removed, in these edits , data were removed therefore, It means that the article got shorter.

Wikipedia “Iron–sulfur cluster” article: Talk page discussion of Dec 4th / 5th 2018 edits

I propose to merge this article with the one on Iron-sulfur protein. Adding to the confusion, we also have an article on ferredoxin, which I propose to leave alone. --Smokefoot (talk) 22:42, 30 December 2007 (UTC)[reply]

I don't think it should be totally merged since organometallic iron sulfur clusters are not biological and should not be mentioned in the iron-sulfur protein article. But the synthetic iron sulfur clusters (like those from Richard Holm at Harvard) should be moved to the iron-sulfur protein article since they are meant to be biomimetic analogs of the biological clusters. Conversely, there should be very little, almost no, discussion of the biological iron sulfur clusters in this article since that is redundant with the iron-sulfur proteins article, so the two sections should be merged and have only one or two sentences with an internal link to the iron-sulfur proteins article. I also don't think this article is very worthwhile since I don't think there are enough non-biological iron sulfur clusters, Im surprised this article was started in the first place.

Proposal[edit]

"Hello,

I hoping to contribute, my knowledge to this article by discussing the strength, covalency and electron transfer effects." Ninja Recs (talk) 01:00, 12 October 2018 (UTC)

"You are writing at a level that indicates that your teacher is needed. Please ask your teacher to read some Wikipedia articles first." --Smokefoot (talk) 01:20, 5 December 2018 (UTC)

"Ninja Recs's Instructor gave 58 revisions to make to this contribution before moving to the live article however, regrettably, none of them were made" --Kcsunshine999 (talk) 22:46, 5 September 2021 (UTC)

Carbonic Anhydrase Edits

What was the main purpose of the edits?

The main purpose of the edit was to filter out the unnecessary details and make the information more concise. The information was edited so that the article was more direct. For example, the main function of this enzyme is to transport carbon dioxide, this information was rewritten and other minor details were edited out.

why in the history page summary of these edits the statistics say (-642), (-607), (-140), ie. what do the negative signs mean?  

The statistics are (-642), (-607), (-140), because of the amount of data that was taken out of the article. The negative signs indicate the amount of bytes of data that was edited out. If more information was added, this number would be positive.

 In your sandbox give your opinion (and explanation of your opinion) as to whether or not the line 26 edit makes a good improvement to the Introduction compared to the previous version.

I believe this edit makes a good improvement compared to the previous version. The new edit highlights the most important information further reinforcing the purpose of Wikipedia articles. The previous version uses phrases such as "most important functions of this enzyme..", this does not seem appropriate, it was better to mention the enzyme's function more directly.

Edits made by (the A2-25 edit Nov 15 2019) and Bilal.bhatti96

I believe that the new edit included more important information on the topic. It is relevant to the points discussed before and the author has related the Bohr effect to the functions of the carbonic anhydrase enzyme. The previous editor mentions that carbonic anhydrase helps regulate pH and fluid balance by converting carbon dioxide and water to bicarbonate and hydrogen protons. The Bohr effect is also affected by increased levels of carbon dioxide which would affect hemoglobin's oxygen binding affinity.

There wasn't much useful discussion on improvement of the article. There are some facts presented on the reaction of carbon dioxide converting to bi carbonate ions. Overall, only minor questions were discussed.

Article rating on Carbonic Anhydrase

There was a C-class rating for this article and it is not rated on an important scale.

Week 4 tasks - First 250 word text contribution

Topic - Formate Dehydrogenase

Sub Topics:

• Showing a figure of the MO-SH transfer mechanism.
• discussing details of the mechanism as shown in the figure.

Types of contributions:

• Adding a new section titled "mechanism of Formate Dehydrogenase"
• Including a figure of the mechanism.

First 250 word contribution

Mechanism of Formate Dehydrogenase

Proposed mechanism of Formate Dehydrogenase.(A) Oxidation of the FDH catalytic site (B) carbon dioxide reduction

Formate oxidation is initiated by the formate ion binding to the sulfo ligand of the FDH catalytic active site. The electrophilic hydrogen present in the formate ion forms a bond with the sulpho ligand. The conserved arginine harbored by the formate binding site facilitates the process of driving the C$\alpha$ hydrogen of formate toward the sulfo ligand. This leads to the formation of ${\ce {Mo^{+4}}}$ attached to SH with a single bond and carbon dioxide. In the last step, The molybdenum center is oxidized to +6 by an electron transfer. The oxidation decreases the pKa of the sulfo ligand which leads to deprotonation. The Sulphur atoms forms a double bond with the molybdenum center and the initial FDH catalytic site is regenerated.

Carbon dioxide reduction is the reverse mechanism of formate oxidation. In this process, carbon dioxide binds to the reduced active site with an oxidation state of 4+ at the protonated sulfo group. It has been determined that carbon dioxide binds to the same site as formate with the conserved arginine. Next step is a hydride transfer from the protonated sulfo group in the reduced site which leads to the formation of a formate moiety. The molybdenum center would gain an oxidation state of 6+, restoring a double bond between the center atom and the sulfo group. In the last step of the catalytic cycle, the molybdenum center is reduced from ${\ce {Mo^{+6}}}$ to ${\ce {Mo^{+4}}}$ through intramolecular electron transfer as shown in the reaction mechanism. After the release of the formate ion, the initial reduced active center is regenerated.

250 word text contribution (revised)

Formate Dehydrogenase catalyzed formate oxidation and carbon dioxide reduction.

Figure 1.Proposed reaction mechanism for Formate dehydrogenase catalyzed (A) formate oxidation(purple arrows) and (B) carbon dioxide reduction (red arrows).

Close up of the molybdenum active site of formate dehydrogenase from E. coli, showing a Secystine residue, four sulphur atoms of molybdopterin guanosine dinucleotide and an aquo ligand coordinating (dashed lines) the molybdenum ion at the center. From PDB: 1KQF

Formate oxidation (Figure 1A) is initiated by the formate ion strongly binding to the Arg446 side chain and weakly forming Hydrogen bonds with the backbone of His448. This allows the ion to position itself so that the C-H bond is close to the sulfide ligand of the FDH catalytic active site. The molybdenum metal ion has an oxidation state of 6+ in this first step. The active site positions the side chain of arginine and asparagine residue to facilitate driving the C α hydrogen of formate toward the sulfide ligand. There is a hydride transfer over to the sulfido ligand with a consequent transfer of two electrons from the sulfido ligand to the Mo 6+ producing Mo+4 and -SH ligand (Figure 1A). In the last step, the molybdenum center is oxidized to +6 by an electron transfer. The oxidation decreases the pKa of the sulfide ligand which leads to deprotonation and the sulphur atoms forms a double bond with the molybdenum center and the initial FDH catalytic site with 6+ oxidation state is regenerated.  

Carbon dioxide reduction is the reverse mechanism of formate oxidation (Figure 1B). In this process, the conserved arginine binds carbon dioxide to the reduced Mo4+ in the active site. In the next step, there is a hydride transfer from the sulfide ligand (Mo4+-SH) to the carbon of the carbon dioxide producing a formate moiety, the molybdenum center gains an oxidation state of 6+ in the process. In the last step of the catalytic cycle, the molybdenum center is reduced from Mo⁺⁶ to Mo⁺⁴ through intramolecular electron transfer as shown in the last step of reaction mechanism(figure 1B). After the release of the formate ion, the initial Mo6+ is regenerated.

References

1. Energetics for CO2 reduction by molybdenum-containing formate [1]
2. Reduction of Carbon Dioxide by a Molybdenum-Containing Formate Dehydrogenase: A Kinetic and Mechanistic Study [2]