User:Snowflake04/sandbox

Week3 Tasks - Info for Methyl oleate

Properties of Methyl oleate

• Molecular formula: C₁₉H₃₆O₂
• Molar mass: 296.49 g/mol
• Melting point: -19.9°C
• Boiling point: 217°C at 16 Torr
• Solubility in water: Insoluble

Methyl oleate

Methyl oleate

Internal Wikipedia Link: Methyl group

External Wikipedia Link: PubChem - Methyl oleate

Analysis of autoxidized fats by gas chromatography-mass spectrometry: I. Methyl oleate

Ethenolysis of Methyl Oleate in Room-Temperature Ionic Liquids

Synthesis and characterization of monomers and polymers for adhesives from methyl oleate

Practice Uploading a PDB Structure Image

Critiques of Carbonic Anhydrase Mechanism Figure

In terms of the figure marking guidelines, the following are errors made throughout the cyclic mechanism for the carbonic anhydrase image.

The carboxylic acid is inconsistent in molecular structure in terms of angle, and their VSEPR shape is incorrect.

The carboxylic acid in the second structure and in the third step where it is being eliminated, the double bonded oxygen is not correctly centred with the carbon.

The arrows indicating the next reaction steps are too big, and are not appropriately sized compared to the overall reaction.

The bond angle of the water molecule being added is not correctly drawn.

There is no sufficient detail (no arrows to indicate the exact mechanism) in terms of the water molecule being added and later on eliminated.

Practice Making a Table

Properties	Data
Molecular Formula	C19H36O2
Molar Mass	296.49 g/mol
Solubility in Water	Insoluble

Practice Entering a Formula

$a_{2}=({\frac {2}{3}})+3^{2}$

Practice Making a Chemical Information Box

Methyl oleate

Names
IUPAC name methyl (Z)-octadec-9-enoate
Properties
Chemical formula	C19H36O2
Molar mass	296.49 g/mol
Melting point	-19.9°C
Boiling point	217°C at 16 Torr
Solubility in water	Insoluble
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa). Infobox references

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

Smokefoot had made these two edits in order to simplify and display the information as facts, rather than the way it was previously laid out, which resembled an essay form (which was previously edited by Ninja Recs).

The comment made by Smokefoot was that Wikipedia is not a school essay, and that it is a compilation of facts. The negative numbers (-3,296) and (-1,805) indicate the change and decrease in bytes, which occurred when words were being removed by Smokefoot while being edited.

These two edits were definitely necessary because as Smokefoot indicated, the facts must be presented in a simplified manner on Wikipedia, rather than an "essay-like" approach.

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

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)

Smokefoot made three edits, aiming towards simplifying and reducing the redundancies in the article. The statistics (-642), (-607), and (-140) represents the overall decrease in bytes that Smokefoot had made when getting rid of information.

The edit made on line 26 by Smokefoot was definitely a good improvement to the introduction compared to the previous version made by Bilal.bhatti96, because it got rid of the additional background information that wasn't focused on the carbonic anhydrase itself, but rather the biological aspect and where it can be found. He also gets rid of small additional words that aren't as important when stating the facts.

In terms of the Nov 28, 2019 edit made by Bilal.bhatti96, it was definitely much more informative, but more so towards the Bohr effect and less about carbonic anhydrase. This definitely could've been included as a topic towards the Bohr theory and should not have been included when discussing the main topic, carbonic anhydrase. The paragraph added by Bilal.bhatti96 is still there in the current version.

There definitely seems to be enough information in the talk page, especially with the editors challenging each other with their information (and references) in the talk page. In terms of the information the editors have discussed, there is definitely enough useful discussion in determining what needs to be done to improve the carbonic anhydrase article.

C - This article has been rated as C-Class on the project's quality scale

Low - This article has been rated as Low-importance on the project's importance scale.

First 250 Words

Subtopics:

• Uptake: Discussing how bacteria competes with each other for Fe³⁺ with its higher binding constant and by having better siderophore.
• Uptake: Discussing about the mechanism (how it's transported across the bacterial membrane and how Fe³⁺ is removed from the siderophore for usage/ storage).
• Introduction: Additional detail about Ferrichrome from Ken Raymond YouTube lecture video.
• Adding citations

Types of Contributions:

• Adding new content
  • Adding to uptake section by discussing how bacteria competes with each other for Fe³⁺, and how it is transported across the bacterial membrane. (Uptake)
  • Adding additional detail about Ferrichrome from Ken Raymond YouTube lecture video. (Introduction)
• Adding citations

Introduction

Ferrichrome was discovered by Joe Neilands in 1952. However, at the time there was no understanding regarding its involvement with iron transport. It was not until 1957, when its proposed iron transport role was determined.

Uptake

Iron uptake is mediated across the intestinal epithelium and requires a passage through both the basolateral and apical membrane. The Fe³⁺ siderophore complexes are taken up into the bacterial membrane, because of the microbes on the outer membranes binding proteins and specific receptors. This would then be able to recognize different characteristics of siderophore structures and transport the Fe³⁺ complexes into the periplasm. The removal of Fe³⁺ occurs through the degradation of Fe³⁺ to Fe²⁺. Fe²⁺ has a lower affinity towards the siderophore ligand and this removal is necessary for use and storage.

AAP (Aerobic anoxygenic phototrophs) is one of the physiological groups that use photosynthesis in oxic conditions. This is used as an additional energy source for respiration and is a large part of bacterial communities, which requires significant iron uptake. Iron is in charge of protecting these cells from the oxidative stress caused by singlet oxygen formation. Although iron is important for the metabolism aspect, it is normally limited because it has a low solubility level at both water surfaces and soil. Due to this limitation, bacteria will begin to compete with each other for Fe³⁺ by developing siderophores for the available iron. These low weighted molecules have a high affinity for iron, and are synthesized and secreted under specific iron deplete growth conditions . Once these siderophores are bound to iron, they are able to be taken up in a substrate specific process.

Revised First 250 Words - Introduction

However, at the time there was no understanding regarding its involvement and contribution to iron transport. It was not until 1957 because of Joe Neilands work, where he first noted that Ferrichrome was able to act as an iron transport agent.

Revised First 250 Words - Uptake

Iron uptake is mediated across the intestinal epithelium and requires a passage through both the basolateral and apical membrane. The Fe³⁺ siderophore complexes are taken up into the bacterial membrane by active transport mechanisms. This uptake process is able to recognize different structural features of the siderophores and transport the Fe³⁺ complexes into the periplasm. The removal of Fe³⁺ occurs through the reduction of Fe³⁺ to Fe²⁺. The reduction strategy helps in making the iron more aqueous soluble, and allows the iron to become more bioavailable in order for uptake to occur. This is because the Fe²⁺ product is not able to mineralize like the Fe³⁺, as it does not bind significantly to the chelate ligand that is designed to bind Fe³⁺. In addition to this, the Fe³⁺ product can also release Fe²⁺ from the chelate ligands that was designed to bind Fe³⁺. Fe²⁺ has little to no affinity towards the siderophore ligand and this removal is necessary for use and storage. This is because Fe²⁺ is an intermediate acid, therefore it is not able to bind significantly to the siderophore chelate ligands and can only bind with a much lower affinity. Whereas, Fe³⁺ is a hard base and can bind to the siderophore chelate ligands with a much higher affinity.

Second 250 Words + Figures

Subtopics:

• New section: "Types of Siderophores"
  • Discussing the different types of siderophores, the HSAB of the donors and the Fe³⁺ binding constants.
  • (Figure) The structures of the different types of siderophores.

Changes to be made in the live Ferrichrome Wikipedia article: The following sentences of the receptor section will be removed, and discussed in the new “Types of Siderophores” section. “Ferrichrome is a unique siderophore, that is of the hydroxamate class (tris(hydroxamate)). It has an exceptionally high binding affinity of log_β110 = 29.07 to ferric iron compared to [Fe(edta)]⁻ that is log_β110 = 25.1 respectively. This indicates that it has an extremely high Fe³⁺ specificity and does not bind other metals in high concentration.”

• Renamed section: From "Receptor" to "FhuA Uptake Mechanism"
  • (Figures) FhuA from E.coli in complex with bound Ferrichrome-Iron PDB structure, and will be labelled accordingly in terms of the information in the existing "Receptor" section.

Changes to be made in the live Ferrichrome Wikipedia article: The details describing the colours of the β-barrel wall and the cork will be adjusted to match the colours of the figure that will be added.

Types of Contribution:

• Adding new content (Types of Siderophores section)
• Edit existing content (Uptake and Renamed: FhuA Uptake Mechanism section)
• Adding new figures (Types of Siderophores and Renamed: FhuA Uptake Mechanism section)
• Adding citations

Types of Siderophores

The main types of siderophores are catecholate, hydroxamate, and carboxylate. An example of catecholate siderophore include enterobactin. Examples of hydroxamate siderophores include desferrioxamine, ferrichrome, aerobactin, rhodotorullic acid, and alcaligin. Aerobactin is a carboxylate siderophore as well. The triscatecholate siderophore, enterobactin, has a higher binding affinity of logβ₁₁₀ = 49 to ferric iron compared to Fe(edta)^-, which has a binding affinity of logβ₁₁₀ = 25.1. This indicates that it would outcompete with the other siderophore and bind more of the available environmental Fe³⁺. It does not bind other metals in high concentration because of its high Fe³⁺ specificity. The trishydroxamate siderophores, desferrioxamine and ferrichrome have a binding affinity of logβ₁₁₀ = 30.6 and 29.07, and both have a higher binding affinity compared to Fe(edta)^-. This also implies that both siderophores can also outcompete and bind more of the available environmental Fe³⁺. However, the bishydroxamate siderophores aerobactin, rhodotorullic acid, and alcaligin have a binding affinity of logβ₁₁₀ = 22.5, 21.55, and 23.5, which indicates a lower binding affinity to ferric iron compared to Fe(edta)^-. These siderophores will not be able to outcompete with the other siderophores, since they do not have high Fe³⁺ specificity. Therefore, they are not able to bind more of the available environmental Fe³⁺.

In terms of the HSAB principle, iron in its trivalent state has an electron configuration of d⁵, therefore, its complexes are preferentially hexacoordinate, quasi octahedral. Ferric siderophores have donor atoms that are mainly oxygen and rarely heterocyclic nitrogen. This is because of the ferric ion being the hard lewis acid and the hard anionic oxygen as the lewis base donor ligand. Ferric iron will therefore seek similar coordination partners. Hence, the ligand field being weak and the ferric siderophore complexes being high spin complexes.

FhuA Uptake Mechanism

Revised Second 250 Words - Siderophore Binding

The main types of siderophores have catecholate, hydroxamate, and carboxylate coordinating ligands. An example of a catecholate siderophore includes enterobactin. Examples of hydroxamate siderophores include desferrioxamine, ferrichrome, aerobactin, rhodotorullic acid, and alcaligin. Aerobactin is a carboxylate siderophore as well. The triscatecholate siderophore, enterobactin, has a higher binding affinity of logβ₁₁₀ = 49 to ferric iron compared to Ferrichrome, which has a binding affinity of logβ₁₁₀ = 29.07. Therefore, it would outcompete with the other siderophore and bind more of the available environmental Fe³⁺. It does not bind other metals in high concentration because of its high Fe³⁺ specificity. The trishydroxamate siderophore, desferrioxamine, has a binding affinity of logβ₁₁₀ = 30.6 and has a lower binding affinity compared to Ferrichrome. Therefore, the desferrioxamine siderophore can also outcompete Ferrichrome, and bind more of the available environmental Fe³⁺. However, the bishydroxamate siderophores aerobactin (logβ₁₁₀ = 22.5), rhodotorullic acid (logβ₁₁₀ =21.55), and alcaligin (logβ₁₁₀ = 23.5) will not be able to outcompete with the triscatecholate and trishydroxamate siderophores, since they do not have high Fe³⁺ specificity. Therefore, they are not able to bind more of the available environmental Fe³⁺.

Iron in its trivalent state has an electron configuration of d⁵, therefore, its complexes are preferentially hexacoordinate, quasi octahedral. In terms of the HSAB principle, ferric siderophores have donor atoms that are mainly oxygen and rarely heterocyclic nitrogen. This is because of the ferric ion being a hard Lewis acid, and the ferric iron therefore binds more strongly with a hard anionic oxygen donor.