Macromolecular assembly

Transcription

Let me summarize the bioorganic phosphorus chemistry that we've studied up till now. First we began by looking at phosphoric acid and we saw that it was suitable to buffer the cell at a pH near 7. Second, we looked at the phosphomonoesters; in fact, throughout the semester we've seen examples of transforming hydroxyl groups through phosphorylation into phosphomonoesters. These are good leaving groups, then, for substitution and elimination chemistry. Third, we've looked at the phosphodiester linkage, and its resistance to hydrolysis makes it suitable for storing information through nucleic acids like DNA and RNA. And fourth, we want to look at the phosphoanhydride group, which is shown here, and we'll see that it's quite suitable for chemical potential or energy storage in the cell. Okay, let's take a look at the phosphoanhydride, which is formed by a dehydration condensation reaction from phosphoric acid. So at high temperatures, the loss of water generates the functional entity which joins two phosphorus groups through an oxygen. It has a structure that's quite analogous to the carboxylic anhydride that we've already encountered in which carbonyl is linked to another carbonyl through the oxygen group. It's also formed by a dehydration condensation reaction from carboxylic acids. We encountered carboxylic anhydrides when we talked about bock groups and putting them on amino acids, if you want to remember where you, ah, where you heard that. Alright, what are some of the properties of the phosphoanhydride? Well, for one thing it forms an excellent leaving group in substitution chemistry. For example, this bond between this carbon and oxygen group is broken to generate inorganic pyrophosphate, whose structure is shown here. It's often abbreviated as PPi; it's a structure you probably want to memorize, you'll see it a lot in biochemistry. It's accelerated; it's a reaction that is accelerated by chelation to divalent metal ions such as magnesium and zinc that really causes electron density to be polarized in this bond and facilitates this reaction. What else besides, ah, the substitution chemistry are the phosphoanhydrides capable of doing? Well, this is where they come in and play their role in energy storage. It's the reaction that's known as phosphoryl transfer, and so for example for the molecule of ATP, adenosine triphosphate whose structure is shown here, the energy storage part of the molecule is this portion, the triphosphate portion, the other part really is there to serve as a recognition element that can dock in enzyme active sites. Phosphoryl transfer takes place at either of the three phosphorous positions shown here. So for example, with an alcohol functional group, ROH, ROH could come in and in fact it would attack the γ phosphorous, breaking the indicated bond there to make ADP, adenosine diphosphate, and this phosphomonoester from the alcohol. That's one phosphoryl transfer reaction. A second type of phosphoryl transfer reaction also would involve an alcohol, ROH, but it would, ah, attack at the β phosphorous, breaking the indicated bond there. That would leave adenosine monophosphate, and attached to the alcohol would be the pyrophosphate functional group that's shown here. That's the second type of phosphoryl transfer. The third type of phosphoryl transfer involves a different kind of reaction. It actually takes place by attacking the α phosphorous here, breaking pyrophosphate, so PPi is lost, and what we have, then, is the organic residue or organic constituent R bound to the adenosine group and so we call this an acyl adenylate or adenylate derivative, acyl adenylate if the R group is actually a carboxylic acid. So rather than an alcohol, we would have the important O attached to this phosphorous, the α phosphorous, and we'll actually see an example of acyl adenylate, which is what nature uses to activate carboxylic acids in the synthesis of proteins. We'll see that in the next series of webcasts. So, these are three modes of phosphorylation, and what makes this phosphorylation transfer reaction so important for energy storage is this concept that this is a metastable functional group. It has a very large negative free energy. We'll actually look at some of the free energy values for phosphoryl transfer. However, kinetically, it's quite stable, meaning that this reaction doesn't take place very easily; in fact, it's that chelation through a divalent metal that triggers this reaction that lowers its activation barrier and turns it on to be kinetically labile. So in general, this cell can allow ATP to run around and not be hydrolyzed by water, it's resistant to hydrolysis much like phosphodiesters are resistant to hydrolysis, but it can be turned on and become quite reactive by the chelation to a divalent metal. So the combination of having a large driving force but being kinetically stable makes it what we call metastable, and that really is an ideal, ah, functional ability for energy storage. Let's look at some of the thermodynamics behind these phosphoryl transfer reactions. In the case of hydrolysis of a molecule we've already encountered before, phosphoenolpyruvate, where we end up breaking the phosphomonoester group, the resulting enol is transformed into a carbonyl. So, this carbon used to be this CH2, but there was a tautomerization along the way. And if you remember back when we talked about bond energies, that carbonyl group had a huge number of, ah, k, kilocalories associated with it and so this reaction does two things. Not only does it break the phosphomonoester group, but it also does this, ah, tautomerization which generates a large amount of energy. There's a huge thermodynamic driving force in phosphoenolpyruvate hydrolysis. Here's an example of a phosphoanhydride that's called a mixed anhydride. It's a mixed anhydride because it contains a carboxylic acid on the one half and on the other half it contains the phosphoric acid. The hydrolysis of this mixed anhydride gives a relatively large amount of energy in comparison to the other energies that we'll see, that's a pretty significant number; not quite as large as phosphoenolpyruvate, but it's definitely up there. Pyrophosphate itself, it's hydrolysis into two phosphate groups is about, ah, half of that or about 7.9 kilocalories per mol. ATP, if you wanna know its various modes of, ah, phosphorylation hydrolysis either by the hydrolysis at the ah, γ position or between the α and the β positions, you can see that it has similar amounts of energies associated with it and, ah, that are comparable to the last reaction that we looked at. And finally if we look at a typical phosphorylation hydrolysis with a monophosphate like an AMP, we see that it carries still with it a fairly large thermodynamic driving force, about half of that where we hydrolyze the phosphoanhydride, ah, type bond. So phosphomonoester hydrolysis versus the phosphoanhydride hydrolysis has a factor of two difference in kilocalories per mol of energy currency associated with it.