Monday, March 2, 2015

How much energy do you need for ATP synthesis? part I

The other day I was trying to write my thesis when I started to divagate about something I’ll probably talk later in another post. Anyway, a paper took me to others papers and I ended up reading two papers about bioenergetics in archaea and bacteria that are really interesting if you are interested in such things. Also they help you to understand certain things about biodigesters!

So, I’m sharing some things I learned from them with you because I think it is important for us to know at least the basics of bioenergetics and also because I’m lonely here and I don’t have anyone to discuss about bioenergetics in anaerobes.

Ok, let’s start!

The paper I liked the most was “Adaptations of anaerobic archaea to life under extreme energy limitation” from Florian Mayer and Volker Müller, which explains about mechanisms for energy conservation in 4 different anaerobic archaea, and of course they discuss about methanogens. It has been about three years since it was confirmed that hydrogenotrophic pathways is actually cyclic but new things have been discovered and actually hydrogenotrophic methanogens are more versatile than we thought. But the reason of why I liked this review is not because of methanogens.

The interesting part is the introduction of some basic concepts of bioenergetics and also the description of the structure and functioning of the ATP synthase from archaea, which allows you to understand how this enzyme translocates H+ or Na+ and also how many of these are needed for the synthesis of ATP.

Anyway, what do you have to know to understand?

First, how much energy do you need for the synthesis of ATP from ADP and Pi?
According to Thauer et al. (1977) (Another review you should read):

So, for phosphorylation of ADP at standard conditions you need approximately +32 kJ/mol of energy. Now, where do you get such energy?

For that, two mechanisms of ATP synthesis are known: substrate level phosphorylation and che­miosmotic ion gradient-driven phosphorylation.

In the case of substrate level phosphorylation, there must be a highly exergonic reaction, which liberates enough energy to drive phosphorylation. In other words, the free energy (AG) of such reaction must be higher than -32 kJ/mol. The number of reactions that are that exergonic is limited, and some of them are listed in the review. The first three are the ones that are usually employed by fermentative organisms and they are reactions mediated by the enzymes acetate kinase, phosphoglycerate kinase and pyruvate kinase.

If you pay attention to those reactions, you will notice that there is something else they share besides their high free energies at standard conditions.

Anyway, for an anaerobic chemoorganotrophic organism fermenting hexoses to acetate, the maximum ATP gain is:

Yes, just 4 ATP. But the important thing you have to know from this is that for the gain of that number of ATP, the fermentative organism needs to produce hydrogen in order to recycle the reducing equivalents produced during fermentation (NADH, NADPH or ferredoxin). What would happen if, by any reason, they don’t get to produce the 4 molecules of hydrogen? I leave that question to you.

Now that it is clear that there are reactions whose free energies are high enough to drive ADP phosphorylation, let’s move on in to the second mechanism for ATP production: che­miosmotic ion gradient-driven phosphorylation.

We know that in this mechanism, ADP is phosphorylated by the activity of the ATP synthase and this reaction is driven by the ion gradient across the membrane (more outside, few inside). To maintain the ion gradient, the cell, mitochondria and chloroplasts must translocate ions across the membrane. And this, of course, requires energy. So, an exergonic reaction, which involves integral enzymes, is needed to couple ion translocation.

Electron transfer along integral enzymes/cytochromes (aka. the respiratory chain) is the classic example of exergonic reactions coupled to ion translocation. But of course, not all living organisms have respiratory chains. For this matter, such organisms must employ another type of reactions in order to obtain energy for ion translocation and a principal requisite is that those reactions must take place in the membrane.

The reaction of the CH3-H4M(S)PT:CH3-CoM Methyl-tranferase in the methanogenic pathways along with hydrogen production by reduced ferredoxin are examples of reactions that couple ion translocation in organisms that don’t have cytochromes.

Now, this leads us to one of the most important questions: how much energy is needed in order to translocate one ion across the membrane?

This section is full of equations that explain how are you supposed to calculate the minimum amount of energy for the translocation of one ion across the membrane. Personally, I think that when you have to lead with equations, you are supposed to understand what those equations mean instead of memorizing them. So I’m not going to write any more equations (for that you can read the paper), instead, I’m going to try explaining them so that at least you can understand how the minimum energy for ion translocation is calculated.

In order to avoid any confusion, by using the word “ion” I’m referring to either H+ or Na+. Although H+ translocation is more common, organisms living under energy limitation use Na+. You’ll discover later in the paper why this information is important (specially you, Isco!).

Let’s start this long explanation by reminding you (again) that there must be an electrochemical ion gradient across the membrane and that this is possible thanks to exergonic reactions that keep pumping ions in order to maintain such gradient.

The electrochemical ion gradient is the one that defines the minimum of energy required.

Why? It’s really simple. Every system tries to reach the equilibrium. Since maintaining high concentrations of ions outside the membrane is going against such equilibrium, it obviously involves the input of energy. So imagine that you start with an “x” quantity of ions outside the membrane, which is higher than the one you find inside the membrane. For that quantity, you have to invest some “y” amount of energy in order keep translocating ions. After some time (and assuming ions are not returning to the inside of the membrane), you will have a greater amount of ions than the “x” initial quantity, which means you are far from reaching the equilibrium, so the energy required from ion translocation must be higher than the initial “y”. So the electrochemical ion gradient is just the difference of ion concentration across the membrane.

What I wrote above it’s what first equation of the article tries to explain with the appropriate concepts of thermodynamics. What do you need to know in order to calculate the electrochemical ion gradient? Well, first, the membrane potential. You can measure it directly or calculate its theoric value. Second, you need to know the concentrations of the ion outside and inside of the cell. Having at least that information will help you to determine the ion gradient.

As the article points it out, this value has been determined in just a few organisms and is about -180 to -200 mV. Now, you can calculate the minimum amount of energy required for translocation of only one ion, using the equation from the review:

In which:
, Represents the electrochemical ion gradient (-180 to -200 mV)
F, the Faraday constant (96. 485 KJ V-1mol-1)
n, the number of ions translocated (just 1)

If you substitute the values from above in the equation you’ll see that you need about -17 to -21 KJ/mol of energy in order to translocate just one ion across the membrane. However, the minimum energy could be lower if the electrochemical ion gradient is lower too. This is important because microorganisms that live under extreme energy limitations might use such strategy for their survival.

Now that we know the energy for the translocation of one ion across the membrane, the next question we have to answer is… how many ions do the cell need for the synthesis of ATP?

I’ll leave that question to you for now, because if I keep going with this post, it will be getting longer and longer and you will lose the interest.

I’ll try to write part two this week but meanwhile you can read the whole paper and try to answer that question. If you want to discuss something, you can ask me here or you can send me an email.

So, see you soon!

1 comment:

prof prem raj pushpakaran said...

prof premraj pushpakaran writes -- 2018 marks the 100th birth year of Paul Delos Boyer!!!