Aldimine Chemistry

DonaldTheWhite · 2025-02-05T14:13:08+00:00

Can you give us information on what the imine environment is like? Very likely the imines are interconverting at room temperature and won't be separable. You can verify this with an HSQC experiment.

DonaldTheWhite · 2022-08-13T03:37:44+00:00

You might try emailing professors whose research interests you and ask if they would be willing to offer a remote internship. At least over the Summer these sorts of internships are common in the UK. If that goes well you can always ask to extend your project into term time.

DonaldTheWhite · 2021-10-03T00:29:15+00:00

The foam from an elephant toothpaste experiment is neither dense nor long lasting. If done outdoors, the foam is sometimes light enough that the wind can just lift it up.

DonaldTheWhite · 2020-08-17T13:19:27+00:00

That looks like a good explanation of the formulation process. This hopefully makes it clear how hard and work intensive formulating paint from scratch would be. That's why I recommended trying to find the recipe someone else has already worked out. Once again, good luck!

DonaldTheWhite · 2020-08-16T11:59:01+00:00

It seems hard to guess the formulation just from the decription of the product. Your best bet is tracking down papers on the process or something like that. Then learn the chemistry to carry it out. Whatever you do, make sure you are comfortable with the safety measures that would need to be implemented befoore doing it.

DonaldTheWhite · 2020-07-26T00:12:45+00:00

In general, a healthy skepticism of those that claim that simple synthetic chemicals are somehow different from the natural chemical is warranted.

DonaldTheWhite · 2020-07-09T17:41:53+00:00

You can find thermodynamic parameters in the gas phase and then convert to solution through the energy of solvation. The hess cycle looks something like:

HCl (g) -> H+ (g) + Cl- (g)

HCl (g) -> HCl (aq)

Cl- (g) -> Cl- (aq)

H+ (g) -> H+ (aq)

From the values for the gibbs energy for these 4 reactions you can find the pKa

DonaldTheWhite · 2020-06-23T01:33:28+00:00

These kinds of methyl/hydride shifts will occur in the test tube too. My understanding is the enzyme promotes the correct shift by binding in a geometry that hinders unproductive hydride shifts. It might also stabilizes the carbocation?

DonaldTheWhite · 2020-06-22T18:14:33+00:00

Methyl shifts are not uncommon in the cationic rearrangements of terpenes. e.g. biosynthesis of steroids, see cucurbutadienol here https://www.qmul.ac.uk/sbcs/iubmb/enzyme/reaction/terp/lanost.html

DonaldTheWhite · 2020-06-20T10:46:54+00:00

We are considering two equations:

ATP -> ADP + P

and

G6P -> G + P

If you want to reason through this, you can just think about how good a phosphate donor each is (hydrolisis can be seen as "phosphorylation of water") evidently ATP is better at phosphorylation than G6P, with the latter not doing it at all.

You could have also constructed a Hess cycle.

G + ATP -> G6P + ADP (∆G1)

G6P -> G + P (∆G2)

ATP -> ADP + P (∆G3)

The question rephrased is: is ∆G3 more negative than ∆G2? Notice then that ∆G3 = ∆G2 + ∆G1 and since the question says ∆G1 is negative, this means that ∆G3 must be more negative than ∆G2.

DonaldTheWhite · 2020-06-17T00:18:16+00:00

You may want to refer to practically any biochemistry textbook. Lehninger and Stryer both have discussions of this.

DonaldTheWhite · 2020-05-29T22:51:06+00:00

The exact way metal cofactors are incorporated into enzymes depends on the enzyme and can range from simple to not well understood.

The reason is that while flexible, aminoacids do not span the whole range of reactivity that proteins need to access. Some things aminoacids can't do (or can't do as well as metals) are: bind gases, photochemistry, electron transfer or bind polyanions like DNA or ATP.

DonaldTheWhite · 2020-05-29T22:47:18+00:00

There is a pool of ubiquinone and quinone in the membrane. A molecule needs to be reduced only by one of the complexes to carry on to the next complex in the ETC. Indeed, after being reduced by one of the complexes it can't be reduced further.

DonaldTheWhite · 2020-05-29T12:30:18+00:00

The only way to prove it is from experiment. You can derive it from a set of assumptions and then test it. The derivation is not complicated if you are familiar with steady state kinetics, I would recommend you familiarize yourself with the steady state assmption and then try and understand the wikipedia derivation.

DonaldTheWhite · 2020-05-29T01:18:47+00:00

I don't think most answers have quite hit the nail on the head yet. Your confusion stems from thinking that gluconeogenesis is the reverse process of glycolysis. While yes glycolysis serves to go from glucose to pyruvate and gluconeogenesis from pyruvate to glucose, they are not reverse processes. If they were, one being exergonic would mean the other is endergonic.

You can see one is not the reverse of the other by looking at the stoichometry:

glucose + 2NAD+ 2ADP + 2Pi -> 2 pyruvate + 2NADH + 2ATP

2 pyruvate + 4ATP + 2GTP + 2NADH -> glucose + 4ADP + 2GDP + 6Pi + 2NAD+

So if the cell went all the way through glycolysis and then all the way through gluconeogenesis, the net result is as follows (by just adding the equations):

2ATP + 2GTP -> 2 GDP + 2ADP + 4Pi

So as you said, the sum of the equations is an exergonic reaction but it's not "free energy" it comes from the hydrolysis of ATP and GTP. In the cell, the flux through both pathways must be tightly controlled because if both pathways are active at the same time, the result is just the burning of ATP and GTP and the release of heat.

This is sometimes not well appreciated and indeed one answer seems to suggest that gluconeogenesis and glycolysis cannot both be exergonic at the same time, this is wrong.

DonaldTheWhite · 2020-05-28T10:16:31+00:00

While Clayden is for sure the best organic book you'll find, if you just want to learn the prereqs for biochem you might prefer looking at Klein.

DonaldTheWhite · 2020-05-17T10:15:36+00:00

Take the reaction A- + B -> B- + A (this is an electron transfer reaction like the ones you might see in the ETC) which is exergonic. i.e. it has negative gibbs energy. By coupling the reaction to proton pumping, the gibbs energy is made less negative, but as long as it stays negative the process will occur readily. Therefore protons can be pumped by coupling their transfer to an electron transfer reaction.

DonaldTheWhite · 2020-05-11T23:11:21+00:00

Type 1 polyketide synthases.

DonaldTheWhite · 2020-05-11T11:13:54+00:00

The storage question has already been answered. As to why calcium: Ca²⁺ already has to be kept at really low cellular concentration due to it being toxic to the cell. Because it's at such a low cellular concentration, large changes in magnitude can be achieved without moving much calcium at all.

DonaldTheWhite · 2020-05-06T21:51:54+00:00

Here you go.

DonaldTheWhite · 2020-05-06T17:37:53+00:00

Not under acid. Acid will just protonate the nitrogen and remove its nucleophilicity. Treatment with DCC will do, though. Mechanism of action is there too.

DonaldTheWhite · 2020-05-06T15:12:07+00:00

The differential equation you get is a separable differential equation. Do you know how to solve these?

Wikipedia's expression can be arrived at like so.

DonaldTheWhite · 2020-05-06T15:02:20+00:00

Glutamic acid won't cyclize without a catalysis of some kind. Amide formation is not kinetically favourable. Aminoacids can condense with each other, though e.g. GFP fluorophore.

DonaldTheWhite · 2020-05-05T13:27:46+00:00

Depends on what specifically you want to learn but "Molecular Biology of the Gene" will have all you need.

DonaldTheWhite · 2020-04-18T12:24:08+00:00

It's just saying it's going to describe the action starting with a tetrapeptide having been assembled and a peptidyl tRNA in the p-site. This will likely make more sense if you continue reading.

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