Oxidative phosphorylation?

Oxygen is used to oxidize NADH and FADH2 to run proton pumps to create an H+ gradient. The H+ gradient then creates a proton flow through the ATP synthase, almost like a water wheel turning a mill grindstone.

The ATP synthase catalysis subunit runs through some conformational changes, as a result of the H+ flow rotating a shaft, to put ADP and P(i) together so that they can bond.

Is just being in proximity sufficient to bring about that phosphorylation reaction?

I don't know but I suppose proximity may or may not be sufficient depending on the affinity of the substrates for the synthase. I think one would need a sufficient concentration of ADP to drive it onto the synthase as well as the Pi donor in sufficient concentration as well. My biochemistry is a bit rusty though.

Any reason you are asking? :-)

I was just reading on it. I had expected oxygen to have a more direct role with the ATP synthesis reaction. I am still left with how the synthesis occurs in the synthase.

ADP and Pi are bound to the enzyme active site, but there still needs to be an addition of energy to phosphorylate the ADP, or at least I thought.

It did not seem enough to have the ADP and Pi at the active site. I guess I think there is something I have missed.

The text books and most of Google talk more about the electron transport chain and chemiosmosis. They describe the actual synthesis with a sentence, and nothing about the energy required.

The only thing I can come up with is that the kinetic energy of the conformational change in the enzyme imparts enough energy to cause the reaction to occur.

"ADP and Pi are bound to the enzyme active site, but there still needs to be an addition of energy to phosphorylate the ADP, or at least I thought."

My biochemistry is quite rusty as well, but I think that no additional energy is required -- the energy, as you indicate -- comes from the H+ gradient. The transmembrane electrochemical proton potential difference drives rotation of the ATP synthase component. The analogy to a water mill works well, where the potential energy difference between the water levels before and after a dam turns a water wheel; the rotation performs work. The work in the case of this nanomachine is mechanically driving the conformation changes in the second synthase component.

As I understand it (and I'm not sure that the full atomic anatomy of this has been resolved but this seems to be the working theory), the conformation changes sequentially alter the strength of binding of ADP and P to catalytic sites in the enzyme. In one of these sequential binding states ADP and P are tightly bound, and in this configuration the energetics favor ADP + P --> ATP.

Or have I misunderstood the question?

Stellar,

Thanks.

You have perfectly understood the question. And you may be correct about the status of the hypothesis, not fully worked out yet. My text book is 12 years old, and that age was apparent when it reached this section. I think many details are being worked out.

I would like to track the energetics. It does not seem sufficient that the conformational changes in the 3 step sequence supplies sufficient energy to phosphorylate the ADP.

Perhaps kinetic energy is supplied?, perhaps there is sufficient pressure from the enzyme to push the phosphate group to bind?

I thought also that perhaps there are some positive charges, Mg++, lysine or arginine, present in the enzyme that might reduce the binding energy requirements.

Every source I can find simply puts the ADP and the phosphate together and they bind. A simple sentence. I keep thinking surely I have missed something? If additional details remain to be worked out, then that would satisfy me.

But if the turning H+ wheel is all there is, then I have missed something. The free energy of the reaction remains regardless of how close the enzyme brings them together, or at least I think that is the case.

Again thank you for your explanation. It has helped.

ETA
The process of proton motive force driving ATP synthase rotation is more common than I realized. It is in anaerobic respiration and in photosynthesis. Not sure how I missed picking up on the difference between this mechanism for ATP synthesis and pathway synthesis. I still don't understand the energetics, but the mechanism is apparently ancient and responsible for the high efficiency of respiration, compared to the lower efficiency of processes like fermentation.

This may not explain the mechanism, but it does seem to answer the question experimentally that, yes, the energy from the proton gradient is sufficient to drive the reaction:

http://biowiki.ucdavis.edu/Biochemistry/Oxidation_and_Phosphorylation/ATP_and_Ox...

The following two posts give an account of the energetics:

"Thermodynamics of the ATP synthesis/hydrolysis

Traditionally the thermodynamics of ATP synthesis/hydrolysis is described for the hydrolysis reaction:

ATP4- + H2O ADP3- + Pi2- + H+ ( pH > 7.2 )

"Physical Chemistry" (P.W.Atkins, 2nd edition) gives a value of -30 kJ mol-1 (-7.16 kcal/mol) at 37oC as a "biological" standard Gibbs free energy change (Delta Go´) for this reaction. This is a reasonable estimate, for figures from -28 to -36 kJ mol-1 can be found in literature, the most popular being -30.6 kJ mol-1 (-7.3 kcal/mol).
The standard Gibbs free energy change, Delta Go, is the total amount of energy which is either used up or released during a chemical reaction under standard conditions when the chemical activities of all the reactants is equal to 1. In case of reactions in aqueous solutions the activities are usually substituted by concentrations (i.e. 1 M); the activity of water itself is taken as 1. "Biological" standard Gibbs free energy change, Delta Go´, is a similar parameter, but is defined at pH 7, i.e. the concentration of H+ is not 1 M, but 10-7M. It is more practical and convenient, for most biological reactions take place at physiological pH.

A very important, and sometimes ignored point, is that Delta Go´ is not the amount of energy available to drive other, endothermic reactions in the cell, because the conditions in the cell are not standard (see the definition above). The actual Gibbs energy change is

Delta G = Delta Go' + 2.3 RT log CADP CPi (CH+ / 10-7) / CATP ,

where CADP, CPi, CH+, and CATP are the actual concentrations of the corresponding reactants, R is the molar gas constant (8.314 J mol-1K-1), and T is the temperature in Kelvins. To make this point clear, let us consider the following example with the arbitrary values that are close to the real intracellular concentrations:

CATP 2 x 10-3 M-1
CADP 2 x 10-4 M-1
CPi 10-2 M-1
CH+ 5 x 10-8 M-1(pH approx. 7.3)

The Gibbs energy change under such conditions (temperature 310oK, or 37oC) will be

Delta G = Delta Go' + 2.3 RT log ( CADP CPi CH+ / CATP ) = -30 - 19.6 = - 49.6 kJ mol-1

This figure, calculated from the actual concentrations of the reaction components, reflects the energy available as a driving force for any other process coupled to ATP hydrolysis under given conditions.
It follows that the same 49.6 kJ mol-1 must be provided by the proton transport across the membrane down the electrochemical gradient to maintain such a high ATP/ADP ratio. If we assume that 3 protons are transported per each ATP molecule synthesized, a transmembrane H+ electrochemical gradient of 49.6 / 3 = 16.5 kJ mol-1 (i.e., protonmotive force of 171 mV) is necessary.
The conclusion from the example above is:
The energy provided by ATP hydrolysis is not fixed (as well as the energy necessary to synthesize ATP). In first approximation it depends on the concentrations of ADP, ATP, Pi and on the pH. This energy increases logarithmically upon decrease in ADP and Pi concentration and upon increase in ATP or H+ concentration (= decreases linearly with increase in pH). The graphs below illustrate this point, showing change in the upon the change in the concentration of one reactant (x axis), assuming that the concentrations of other reactants are kept constant at values used in the example above (red dots indicate the calculated in this example).

Graphs of Delta G dependence on C(ATP), C(ADP) and pH.

To close up this section, I would like to note that although the thermodynamics of the ATP synthesis described here might seem rather complex, it is actually much more complex. One point neglected here was the different ADP and ATP protonation states (see above), the other is that the actual substrates in the reaction catalyzed by ATP synthase are not pure nucleotides, but their magnesium complexes. However, as the magnesium concentration in the living cell is relatively high and the pH is usually above 7.2, so the description given is still applicable for thermodynamic estimates."

And:

"ATP synthesis catalyzed by ATP synthase is powered by the transmembrane electrochemical proton potential difference, Delta mu H+ composed of two components: the chemical and the electrical one....

Quantitatively Delta mu H+ is measured in Joules per mole (J mol-1) and is defined as:

Delta mu H+ = -F DeltaPsi + 2.3 RT (pHP - pHN),

where the "P" and "N" indices denote the positively and the negatively charged sides of the coupling membrane; F is Faraday constant (96 485 C mol-1); R is the molar gas constant (8.314 J mol-1K-1), T is the temperature in Kelvins, and is the transmembrane electrical potential difference in volts. The value of Delta mu H+ tells, how much energy is required (or is released, depending on the direction of the transmembrane proton flow) to move 1 mol of protons across the membrane.
It is often more convenient to use not Delta mu H+, but protonmotive force (pmf):

pmf = - Delta mu H+ / F = DeltaPsi - 2.3 RT/F (pHP - pHN)

At room temperature (25oC) the protonmotive force (in millivolts, as well as Delta Psi) is:

pmf = DeltaPsi - 59 (pHP - pHN)

In the absence of transmembrane pH difference pmf equals the transmembrane electrical potential difference and can be directly measured by several experimental techniques (i.e. permeate ion distribution, potential-sensitive dyes, electrochromic carotenoid bandshift, etc.). Each pH unit of the transmembrane pH gradient corresponds to 59 mV of pmf.
For most biological membranes engaged in ATP synthesis the pmf value lies between 120 and 200 mV (Delta mu H+ between 11.6 and 19.3 kJ mol-1)."

You can read the whole thing here:

http://www.atpsynthase.info/FAQ.html#Sec6

Hope that helps! Thanks for posing this question - I enjoyed looking into it and learning more about it!

Not good enough! Nothing short of quantum mechanical analysis of ADP phosphorylation will do! ;)

ATP synthesis is indeed complex and there are various unknowns, but I wonder if perhaps something more elementary might not be missing from your picture, Richard? Judging by, for example,

I would like to track the energetics. It does not seem sufficient that the conformational changes in the 3 step sequence supplies sufficient energy to phosphorylate the ADP. Perhaps kinetic energy is supplied?, perhaps there is sufficient pressure from the enzyme to push the phosphate group to bind?

and

Every source I can find simply puts the ADP and the phosphate together and they bind. A simple sentence. I keep thinking surely I have missed something?

perhaps something explaining the formation of chemical bonds and chemical thermodynamics in general would be more helpful.

And yes, it is the kinetic energy of the free protons that is made available to the ATP synthase in the mitochondria. They flow, they move, they vibrate, they bop and boogie!

>9 LolaWalser: "Not good enough! Nothing short of quantum mechanical analysis of ADP phosphorylation will do! ;)"

LOL. I was afraid of that!

Quantum mechanics is apparently required for photosynthesis.

Stellar, thanks for the links. They definitely help with the energetics.

LW, I fairly well understand the formation of bonds. And I am slowly accepting that for oxidative phosphorylation the energy is supplied by the mechanical conformational changes - I guess just pushing the molecules together.

I was expecting I suppose a more direct chemical interaction, a reaction coupling, more similar to glycolysis. A more use of oxygen more directly oxidizing the reaction.

Thank you both.

I was expecting I suppose a more direct chemical interaction, a reaction coupling, more similar to glycolysis. A more use of oxygen more directly oxidizing the reaction.

Oy vey. This is extremely confusing, but I guess the most important thing is that you seem to feel you know what it's about, so...

Good luck in your quest!

My apologies for confusing you.

Definitely not my intention.

Thank you for your effort. Probably best to leave the next question unasked?

Um... I don't know why you're asking, or if you're asking me, but I'll hazard it and say go ahead and ask.

Thanks.

Stellar and you have fully answered my question. You have been very helpful. : )

Actually, you've got me hooked. I started describing the structure of the enzyme to my son, a college freshman, and he recognized it and pointed me to some YouTube videos on the topic that he liked. Watching them now. Will report back if they are contributory...

The structure of ATP synthase was not understood when I took my last biochem course in 1983. It's sobering to realize how oblivious we can be to what we don't know until we do.

One of the text books I am reading is 12 years old and just hinted at some ideas about it. It was clear that this was newly discovered. The text just had the barest outline of the hypothesis.

The enzyme seems to me to be ancient. Or perhaps there was a more ancient precursor.

All of the electron transport chain respiration reactions seem to be based on the proton motive force across the membrane gradient, using this water wheel like mechanism.

Basically I have two questions. Still how does the conformation change produce by the rotation of a shaft, provide the energy for the reaction. I understand there is enough energy in the proton flow, but how does it overcome the chemical energy requirements of phosphorylation.

It still bothers me that the enzyme just puts the two molecules together, and they bind. Perhaps there is sufficient KE to overcome the positive free energy of the reaction. Or perhaps there is something in the molecular structure that reduces the energy requirements.

The second question is whether this rotational shaft mechanism is involved with all forms of respiration that use the electron transport chain and proton motive force. That would make this mechanism very ancient I think, and perhaps as significant an evolutionary step as photosynthesis.

It is not just oxidative phosphorylation, it is the mechanism to convert energy for all forms of respiration, aerobic and anaerobic. Anything except substrate level phosphorylation. And it seems to me to be a very complex enzyme and enzymatic process overall which evolved very early.

I am fairly astounded.

Anyway, please post your videos. I went to google myself as soon as I realized that my text was so out of date on this subject.

Here is one series that I found helpful.

I like this guy. A mathematician I think.

https://www.youtube.com/watch?v=kI9rD9bO6wU

Watched a few. As to the specific question at hand, the best explanation I got supported the above, with the additional comment that the catalyzing mechanism of the ATP synthase F1 unit is to bind the ADP and P tightly and hold them in close proximity. The notion is that bringing them into close proximity combined with the energetics are the decisive features in facilitating conversion to ATP.

This may still fall short of a complete and fundamental account however.

Just saw your last comment. After watching several videos I too concluded that the guy you found was the most effective lecturer.

Or it may be all that is known at this time, the enzyme simply hold the ADP and Pi together until they bind. And it may be the full answer. It just seems to me not to be the full story.

Enzymes speed reaction times, but they are not supposed to change the energy differentials.

The basics of this process seem to be present in all forms of cellular respiration. So that H+ wheel must work, even without the full reducing potential of oxygen.

Another question, perhaps is why is this process so much more efficient than the other more directly chemical pathways.

I appreciate your help. Trying to learn about this respiration process has been eye opening. I thought I have a vague idea that oxygen oxidized glucose more completely, when in actuality oxygen just is the bottom of the reduction well, and sets up the H+ wheel.

And the wheel mechanically puts the ADP and the Pi together, until they bond. : )

As to your follow up question, this is way beyond my knowledge base, but I did encounter a discussion that pointed to this article, "Inventing the dynamo machine: the evolution of the F-type and V-type ATPases":

http://www.nature.com/nrmicro/journal/v5/n11/abs/nrmicro1767.html

From the abstract:

"The rotary proton- and sodium-translocating ATPases are reversible molecular machines present in all cellular life forms that couple ion movement across membranes with ATP hydrolysis or synthesis. Sequence and structural comparisons of F- and V-type ATPases have revealed homology between their catalytic and membrane subunits, but not between the subunits of the central stalk that connects the catalytic and membrane components. Based on this pattern of homology, we propose that these ATPases originated from membrane protein translocases, which, themselves, evolved from RNA translocases. We suggest that in these ancestral translocases, the position of the central stalk was occupied by the translocated polymer."

I offer that not because it answers your question directly, but because it bears on the question of the history and antiquity of the rotory proton-driven mechanism in energy pathways.

I really like that AK fellow. He repeats everything, intentionally and helpfully for slow people like me.

So this mechanism reaches to the RNA world?

Apparently at least in origin.

Stellar,
For some reason that idea just astounds me. And that mechanical process has been conserved and improved since the earliest times.

It was there to be adapted for photosynthesis.

It was there to be adapted for free oxygen.

Anyway, thanks, for the help.

BTW, the story of this hypothesis and the development of the chemiosmotic theory is very interesting. The discovery earned a Nobel prize in 1978.

>17 richardbsmith: "Basically I have two questions. Still how does the conformation change produce by the rotation of a shaft, provide the energy for the reaction. I understand there is enough energy in the proton flow, but how does it overcome the chemical energy requirements of phosphorylation.

It still bothers me that the enzyme just puts the two molecules together, and they bind. Perhaps there is sufficient KE to overcome the positive free energy of the reaction. Or perhaps there is something in the molecular structure that reduces the energy requirements."

While I can't offer any definitive solution to this, I did find a paper that addresses the underlying problem. It's from 2003 and expresses the need to resolve the very question you pose. I haven't seen anything more recent that changes the formulation of the question; I have to imagine we still lack complete answers.

"Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase"
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC299816/

From the article (and I have culled a few passages to make the point that your question, rbs, is a topic of active study by people at the forefront of biochemical research):

"Understanding the nature of energy transduction in biology in general and molecular machines in particular is one of the central problems in bioenergetics. The pioneering work of Boyer and .... Walker... have established that the action of molecular machines involves conversion of external energy to conformational changes."

"One of the major difficulties in developing such an analysis is the evaluation of the free energy of large conformational changes in proteins as a response to changes in the charges of bound ligands."

"Significant progress has been achieved in recent years in providing a mechanical picture of the action of ATP synthase. However, the current description is based on a macroscopic description, and the actual molecular details are not fully understood."

It seems to me, and this is my sense of the state of scientific understanding -- I could be wrong -- that the problem you pose is a general one, one that scientists are still trying to nail down with greater specificity. Namely, how to we understand the energetics of enzyme action on a molecular level?

Couldn't resist adding one more thing from another article on the general problem:

"Since the discovery of enzymes as biological catalysts, study of their enormous catalytic power and exquisite specificity has been central to biochemistry. Nevertheless, there is no universally accepted comprehensive description. Rather, numerous proposals have been presented over the past half century. The difficulty in developing a comprehensive description for the catalytic power of enzymes derives from the highly cooperative nature of their energetics, which renders impossible a simple division of mechanistic features and an absolute partitioning of catalytic contributions into independent and energetically additive components."

CHALLENGES IN ENZYME MECHANISM AND ENERGETICS

http://cmgm.stanford.edu/herschlag/publications%20(PDF)/Kraut_et_al2003.pdf

Thanks Stellar.

I am of course OK with an answer of we don't know yet. I wish that the text books would just add those words to the description. : )

I wonder if there is a crystallograph of the structure, or perhaps even of the conformational changes. My guess is that there are some charged aminos positioned with the conformational changes - K and/or R, or perhaps a Mg2+. Something like that would change the energetics.

Anyway, perhaps it will be soon resolved.

The other question, more intriguing for me, is the roll this mechanism has played in the history of life. This mechanism seems to be ancient, at the very beginnings of life.

Anyway, thanks for helping work through this.

We thought the discovery of DNA, the double helix, and the sequencing of genomes was exciting.

It may be that we have even more excitement around the corner.

Not to mention the real possibility soon of the discovery of life outside Earth. : )

We all wait with bated breath. The news will arrive someday, maybe soon.

Great thread, reminds me of when I subscribed to Scientific American many years ago and was only impressed when half the article was over my head {I was impressed by all the articles ;-) }.

I think you guys might like a book I wandered through recently, Nick Lane's Why is Life the Way it Is.

It took me long time to read it and I really just skimmed the last chapter but his manner of writing reminded me of watching one of those sci fi movies where everyone is shrunken down to molecular size. He described the "mechanical process" part of H+ and other ion pumps across membranes very well and actually theorizes the evolution of the processes with the energy requirements etc.

Of particular interest to me is his theory of cells/life evolving from alkaline hydrothermal vents as mentioned in the link below:

"Chemiosmosis refers to the movement of ions down an electrochemical gradient and across a selectively permeable membrane. This process was there at the begining in what is now widely held to be life's most diffuse state, the alkaline hydrothermal vent."

A good synopsis of the book is at: http://phys.org/news/2015-04-vital-life.html#jCp

and his home page: http://www.nick-lane.net/

Thanks -- just ordered that -- looks terrific!

Will report back after checking it out

>30 DugsBooks: He also covers it in Power, sex, suicide : mitochondria and the meaning of life but The Vital Question is 10 years further on, I'll have to try to get a hold of it.

I'm reading it now. I have to say, I'm enjoying it tremendously. He's clear, but without talking down to the reader.

It seems obvious now that I'm looking into it. Naturally-occurring biological processes such as the action of ATP synthase are being used as one means of driving progress in nanotech engineering. See this account (11 years old now):

"It is interesting to consider some of the applications of self-assembled protein arrays. Soong et al. (2000) demonstrated that the ATP synthase protein complex could be used to power the rotation of an inorganic nickel “nanopropeller.” ATP synthase is a multisubunit protein complex with a domain that rotates about its membrane-bound axis during the natural hydrolysis of ATP within a cell. Soong et al. attached a nanoscale inorganic “propeller” to the rotary stalk of ATP synthase, creating a “rotary biomolecular motor.” It is intriguing to consider the construction of an ordered array of ATP synthase driven nanomachines, each positioned precisely along a DNA scaffold, similar to that described by Yan et al. Such an assembly, combined with proposed “nanogears” (Han et al. 1997), may one day enable the construction of nanoscale variations of the traditional “gear-train” and “rack-and-pinion” gearing systems. Construction of such systems may facilitate the design of machines that can transmit and transform rotary motion at the nanoscale.

In addition to rotary biomolecular motors, proteins that undergo substantial conformational changes in response to external stimuli might also find some interesting uses in nanoarrays. Dubey et al. (2003) are working on methods to exploit the pH dependent conformational changes of the hemagglutinin (HA) viral protein to construct what they term viral protein linear (VPL) motors. Proteins that undergo substantial conformational changes in response to environmental stimuli may facilitate the design of nanoscale machines that produce linear motion (Drexler 1981), as opposed to rotary motion. At neutral pH, the HA2 polypeptide forms a compact structure composed of two α-helices folded back onto each other. At low pH, HA2 undergoes a substantial conformational change, which results in a single “extended” helix. This conformational change results in a linear mechanical motion, with a linear movement of approximately 10 nm (Dubey et al. 2003). It would be interesting to investigate the applications of ordered arrays of dynamic VPL motors, since an array of such “hinge” structures may enable the coordinated linear movement of hundreds of tethered macromolecules in a synchronous manner."

http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0020073

Of course!

>34 stellarexplorer: Yep, I had a flight of fancy thinking about nano sized machines while reading the book and how they might be engineered into single cell "factories". I always have tardigrades/water bears spring to mind when considering that even though they don't fit into the "nano" category and I wonder if anyone has tried to genetically engineer them.

I searched to see if their genome had been processed yet and serendipitously found an article published only a few days ago where a school I went to for a while many years ago has just published a genomic study of the critters which is being questioned by a university in England.

The dispute is over the volume of genes in the tardigrade which appear to be the product of " horizontal gene transfer", a process that Mr. Lane gives a good bit of time to in his book if I remember correctly.

https://www.washingtonpost.com/news/speaking-of-science/wp/2015/12/07/when-labs-...

>35 DugsBooks: Thanks for the article! Very interesting. I think with larger animals if you want to be totally clean you can artificially fertilize and grow the embryos under sterile conditions, but I don't know anything about tardigrades.

I don't know much about tardigrades either, except they're really cute. Highly magnified, that is.

Here's one meeting a paramecium :

https://www.youtube.com/watch?v=iLj4tBp00wo

Found this to be a nicely filmed intro:

http://youtu.be/o9kPQ0GY_W8

>37 stellarexplorer: Very interesting! Thanks! I wonder what that is inside the tardigrade. Do you think that is a previously met paramecium or the innards of the tardigrade? Any expert opinions?

I think they eat algae. They're mostly vegetarians. The central colored blob does resemble an ex-paramecium, but I dont think that's what it is. The second video shows them eating, and from that you'd have a hard time envisioning that paramecium is on the menu!

>38 stellarexplorer: What a wonderful video. I loved the music that went with it too! Their feet are so adorable! Thank you for posting.

I'm about halfway through Nick Lane's The Vital Question. It is a terrific book. But I wanted to mention two things from my reading so far. First, I think he answers the motivating question behind this thread. He mentions a number of gaps in our understanding of the functioning of ATP synthase (which he always refers to as the ATP synthase), saying "we still don't know exactly how it works." Among these are "how the clefts that open and close in {the catalytic}* head clasp ADP and P and force them together in mechanical union, to press an new ATP." One mystery solved. Or unsolved :)

Secondly, his account is convincing on another point, probably among the ones about which he is most passionate:

"I mentioned that ATP is called the universal energy 'currency' of life. The ATP synthase and the proton-motive force are also conserved universally across life. And I mean universally. The ATP synthase is found in basically all bacteria, all archaea, and all eukaryotes ...barring a handful of bugs that rely on fermentation instead. It is as universal as the genetic code itself. In my book, the ATP synthase should be as symbolic of life as the double helix of DNA. Now that you mention it, this is my book, and it is."

*Aside: apparently you can't use the convention of brackets to insert explanatory unstated words in a quote, due to their use in html on sites like this one. Instead I used braces.

Stellar,

I have that book and a couple others pertaining to this general topic. I hope to get to them soon.

The points you mentioned are the sense of awe that came over me, even as this thread developed, when I started to realize how pervasive this mechanism is. It is mechanism is right there with other major leaps in the development of life - one of the great steps, and perhaps the first great step.

And it happened so early.

I may have to drop some other reading I am doing and get back to this.

One of my first questions was how this complex process just showed up when oxygen reached 1% PAL. Then I realized this process was there almost from the beginning. As you said, right there with DNA, or even in the RNA world. Early.

I am still grasping and a little shy on understanding the source of energy to phosphorylate the ADP. For some reason a mechanical compression type force just does not seem adequate.

He does mention that electron flows from redox center to redox center in respiratory complexes/chains suggests quantum tunneling effects may be operating. The door may be open to other than plain mechanical and chemical effects. That may or may not apply to ATP synthesis. I can't really offer anything more on that point than we've said previously.

As far as the early formation of life and of the crucial enzymes, I'm reading about Lane's ideas on that now. I'll say something when it's a little clearer in my head.

I am also curious about the different membrane structures between archaea and bacteria. With eukaryotes taking the bacteria membrane and ingesting an archaea cell for the nucleus. Whether, for instance, the bacterial membrane is especially suitable to enlarge or perhaps to incorporate varied proteins for transport, more so than the ether linkage used in archaea. And I think there is evidence that the eukaryotic cells were nearly as early as bacterial and archaea.

Perhaps Lane might have some thought there. I hope to start on Vital Dust in a couple weeks. Maybe that will better inform my questions.

This has been just about the greatest thread ever.

As a modest contribution to some of the ideas here, let me put in a word for Eating the Sun, which gave me a much better sense of the current understanding of photosynthesis.

Thanks Bob. I will definitely give that one a try!

Cell respiration and related issues have a part in this work--thought you might find it interesting.

http://www.ncbi.nlm.nih.gov/pubmed/9236778

See also KUPIEC ; stochastic gene expression; ontophylogenesis. At this cellular level the processes are all very simple and related in character, aren't they?

>45 richardbsmith: as far as the early origin of the complexities of access to energy and the ATP synthase enzyme, early is a relative term.

Lane goes through the necessary elements for the origin of protocells and ultimately for LUCA, the cell that is the last universal common ancestor to all life on earth.

His account has early carbon and energy metabolism driven by proton gradients and fluxes in carbon and energy in alkaline hydrothermal vents. These (and he wants to emphasize) force the production of organic material. While he acknowledges the details of the formation of complex molecules like ATP synthase and the genetic code are not settled and are problems actively being researched, his purpose is to get at the driving forces behind the origin of life on earth. He describes plausible means by which deterministic chemistry might have gotten cells to the point where more ordinary selective processes could operate, as long as the earlier chemistry -- the primary object of his concern -- can generate a rich supply of reactive organic precursors.

>45 richardbsmith: "I am also curious about the different membrane structures between archaea and bacteria. With eukaryotes taking the bacteria membrane and ingesting an archaea cell for the nucleus. Whether, for instance, the bacterial membrane is especially suitable to enlarge or perhaps to incorporate varied proteins for transport, more so than the ether linkage used in archaea. And I think there is evidence that the eukaryotic cells were nearly as early as bacterial and archaea."

A few points. While the moment of the earliest eukaryotes cannot be proved, they didn't begin to thrive until ~2 billion years ago. Before then it was a prokaryotic world.

The endosymbiosis theory -- with plenty of supporting evidence -- has it the other way around. An archaea was the host cell, and a bacterial cell the endosymbiont.

As far as membrane properties, and reading Lane, it doesn't appear that the bacterial membrane had advantages over the archaean cell membrane. In fact if it were so, one wonders why - as lateral gene transfer is so prevalent among prokaryotes - bacteria and archaea which lived and live in close proximity to each other didn't exchange membrane properties and adopt the most advantageous version. Their cell membranes have been conserved, and each is effective while different. Lane has it that choices were made at the very beginning, some due to chance, and that it would have required an unreasonable magnitude of change (and thus an astonishing degree of advantage) to scrapping something so basic and beginning again. Each membrane has its own transport proteins, slightly different chemical components, but function effectively. Interestingly, both use glycerol in their phospholipid cell membrane heads, but use mirror image glycerol stereoisomers requiring the use of entirely different enzyme packages to control - surely an early choice.

As an aside, my friends and family are not necessarily grateful, richardbsmith.

I am so hyped up about this stuff that I won't shut up about it to everyone I see. This is not necessarily what everyone else wants to be discussing at holiday parties, though I clearly don't understand why not!

I will get to the book soon I hope. (I am taking some online courses that might derail that plan.)

Does Lane think the proton motive force was before more basic chemical reactions. That seems to be a large step in the processes of the orgins of life.

And let's put some absolute dates in the discussion about relative earliness, maybe 3.5 BYA for bacteria, archaea and eukaryotes. And 3.8 BYA for the earliest of the prokaryotes.

>51 stellarexplorer: "my friends and family are not necessarily grateful"

It is good though that you have others to discuss with. My wife just thinks I am nuts.

>51 stellarexplorer: "An archaea was the host cell, and a bacterial cell the endosymbiont."

I thought archaea ingested a bacteria also. Until I saw that eukaryotes have a bacterial type cell membrane. I cannot explain that if archaea was the host cell.

It seems more likely that a bacteria engulfed an archaea, which became the nucleus. (Also explaining the double membrane around the nucleus.)

https://figures.boundless.com/19094/large/figure-22-02-07f.jpe

I have come close over the last few days to post a question comparing carbon and silicon. Carbon the versatile backbone of life. Silicon the versatile backbone of minerals. I was led to that question by reading on the Bowen's Reactive Series trying to understand more about magma differentiation.

Your thoughts as to whether this is an appropriate topic. I think I have settled on the electronegativity difference as being the essential difference. And there is some issue over pi bonds between silicon and oxygen that I have not yet understood.

There are bunches of questions. Thanks for your help on this one.

>52 richardbsmith: can we call it ~4 billion years ago for bacteria and archaea, and 2 billion before eukaryotes got going?

>53 richardbsmith: The opinion of the listener hadn't occurred to me :)

>56 stellarexplorer: "can we call it ~4 billion years ago for bacteria and archaea, and 2 billion before eukaryotes got going?"

Certainly we can. The dates may be less interesting than the evolutionary relationship. To that question this may be a good summary.

http://sitn.hms.harvard.edu/flash/2014/origins-of-eukaryotes-who-are-our-closest...

Ideas on eukaryotic origins are many. Fossils exist at the 1.5 BYA time frame. Some sources I have read suggest an earlier date for eukaryotic origins.

"The question is the subject of an ongoing and lively controversy. The best guesses for the time when eukaryotes evolved range from just below 2.0 billion years to around 3.5 billion years before the present.

"One of the less ambiguous sources of information is the fossil record. Work by Gonzalo Vidal of the University of Uppsala in Sweden indicates that single-celled planktonic eukaryotes certainly date back to 1.7 billion years B.P. and very likely to at least 2.2 billion years B.P. The early fossil record is very sparse, however, and small eukaryotic cells present in the fossil record would not necessarily have been positively identified. "

http://www.scientificamerican.com/article/when-did-eukaryotic-cells/
This above article may be too dated, 1999.

"The eukaryotes developed at least 2.7 billion years ago, following some 1 to 1.5 billion years of prokaryotic evolution."

http://www.ncbi.nlm.nih.gov/books/NBK9841/

I read some other suggestions about very early eukaryotic life. But I have not been able quickly to fine the sources. I am too haphazard in my notes.

Definitely though no need to get caught up on those dating questions.

> 54 I'll have to come back to the question in >52 richardbsmith: ("Does Lane think the proton motive force was before more basic chemical reactions") when I have a moment.

But as to the issue of archaean vs eukaryotic cell membrane differences, yes, true. The membrane lipids vary, and eukaryotic cell membranes have bacterial lipid elements rather than archaeal.

The thinking on this as I understand it is that most of the DNA from the bacterial endosymbiont became transferred to the cytosol of the combined archaeal host/bacterial endosymbiont cell. Only a small minority of the original endosymbiont DNA remained in the proto-mitochondrion as (what we now term) mitochondrial DNA. That transfer of bacterial DNA to the host cell must have included genes for bacterial lipid synthesis.

>52 richardbsmith: "Does Lane think the proton motive force was before more basic chemical reactions. That seems to be a large step in the processes of the orgins of life."

Speaking for Lane, and of course I would not post on his behalf without consulting him ;), he believes the formation of the earliest protocells was driven by a proton gradient. He suggests that inorganic iron-sulfur barriers were common in microporous alkaline hydrothermal vents. Such barriers separate the more acidic ocean water (higher proton concentration) from the flow from the vents (lower proton concentration). The Fe-S barrier serves as a weak inorganic catalyst for the flow of protons across the barrier, setting up a primitive version of the acetyl CoA pathway (by directly reducing CO2 with H2). As Lane describes it, this generates organic molecules directly, providing the source of reactive organics necessary for the next step in the formation of life.

In the next step, simple organic protocells assemble as a "natural outcome of the physical interactions between organics -- simple dissipative cell-like structures, formed by the self-organization of matter, but as yet without any genetic basis or real complexity". A major difference in the second step is that while the proton gradient is still used to drive formation of organics, the process occurs across the protocells' own cell membranes rather than across the inorganic walls of the vents.

Of course there's much more, but it is in the third step where the cells develop significant chemical complexity.

I just read an article about a child with "mitochondrial disease" and picked up a few facts that reinforced what I learned from Nick Lane's book and some stuff that I didn't know that most may be familiar with.

"Mitochondrial DNA mutations occur frequently, due to the lack of the error checking capability that mtDNA has (see Mutation rate). This means that mitochondrial DNA disorders may occur spontaneously and relatively often. Defects in enzymes that control mitochondrial DNA replication (all of which are encoded for by genes in the nuclear DNA) may also cause mitochondrial DNA mutations.

Most mitochondrial function and biogenesis is controlled by nuclear DNA. Human mitochondrial DNA encodes only 13 proteins of the respiratory chain, while most of the estimated 1,500 proteins and components targeted to mitochondria are nuclear-encoded. Defects in nuclear-encoded mitochondrial genes are associated with hundreds of clinical disease phenotypes including anemia, dementia, hypertension, lymphoma, retinopathy, seizures, and neurodevelopmental disorders."

Both quotes from wiki

>60 stellarexplorer: & others. I came across this Space.com article entitled Life's Building Blocks Form In Replicated Deep Sea Vents, wherein they discuss and have a link to a lab reproduction of alkaline hydrothermal vents experiment. {July 22 issue of the journal Astrobiology}

Thanks for that. An irresistible topic!

>35 DugsBooks: >36 krazy4katz: >37 stellarexplorer:

Spinning the topic even more here is a recent article on genomic research done in Japan on tardigrades. It mentions the Chapel Hill horizontal gene transfer estimates & that Japan {albeit a different species} came in with a lower percentage {similar to the European group}. Here is a quote of one of the more interesting aspects of the Japan study:

"This is where it gets a little weird.
When the team treated human cells in culture with extract of tardigrade, the GFP-tagged proteins stuck to human DNA just like they stick to tardigrade DNA, and cheerfully started doing what they do best: tamping down oxidative stress. When X-rays hit human cells, they do two kinds of damage. X-rays can cause direct DNA strand breaks, which are mostly single-strand. When they strike water molecules, they can also excite them into producing reactive oxygen species, which also cause single-strand breaks. High enough doses of X-rays can cause double-strand breaks. The damage-suppressing protein Dsup went immediately to work on the culture of human cells, suppressing or repairing single-strand and double-strand breaks by about 40%."

http://www.extremetech.com/extreme/236180-tardigrade-dna-inserted-into-human-cel...

I came back to this thread while working on a YouTube video about Nick Lane's book. This was a terrific thread. And a resource because I don't have to redo all the mental work. The thread is of necessity much more technical than the video. Different audiences.

>61 DugsBooks: Still flailing about off topic here is an interesting article on Mitochondrial disease:

https://www.vox.com/2018/7/24/17596354/mitochondrial-replacement-therapy-three-p...

A good layman's explanation I guess, since I can understand some of it.

Finished the video:

https://youtu.be/p3wldsGqgeI