ATP synthases: molecular nano power plants

Science and Technology
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ATP synthases: molecular nano power plants

From Marcos Eberlin’s excellent book : Life and the Universe by Intelligent Design
https://www.widbook.com/ebook/life-and-the-universe-by-intelligent-design
ATP synthase motor. The smallest and most efficient power plant on this planet powering the production of energy of Life. One of the essential requirements for Life is energy. Living organisms require large amounts of energy, and the molecule that stores and releases energy of life is adenosine triphosphate represented by the acronym ATP (Figure 2). And then there is a need for a huge amount of this molecule. And to synthesize it with efficiency and optimization, Life requires adenosine - a heterocyclic nitrogenous base, a ribose sugar molecule (one sugar) and three phosphates. Note the difficulty here for any unguided process you “want to imagine” to form such a molecule. Sugars are formed by formaldehyde - essentially - a highly reactive molecule. Sugars are reactive and unstable, and reaction media that allow synthesis of sugars are incompatible with the means of synthesis of nitrogenous bases. Anions phosphate precipitate in the presence of metal ions such as Ca2 +, for example. And links between phosphate anions involve slow reactions, and need to be catalyzed by enzymes. Therefore, this molecule synthesis routes give a hell lot of work that only the machinery of life can perform. And to make matters worse for the task, the ATP molecule is unstable and hydrolyzes easily in water, and is exothermical (gives off heat).

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And then to establish the third phosphate connection, which requires most energy, life must go against the kinetics and enthalpy and so uses the only way to overcome such cumber thermodynamic: a machine, and an incredible nanomachine: ATP synthase
The ATP molecule - a chemical masterpiece- to generate the energy of Life.
The ATP synthase is the name given to a true nanomolecular “power plant” made by turbines and protein reactors, that in a spectacular and artfully crafted way, synthesizes - and reverse the synthesis - the molecule of ATP (adenosine triphosphate) from ADP (adenosine bifosfate) and anions of inorganic phosphate in the cells (Figure 1). A nanomolecular marvel of technology, chemistry and mechanical engineering mega intelligent.
Carved like a work of chemical art , beautiful and awe-inspiring - it appears to challenge failed theories - ATP synthase has the smallest engine known in this universe. And this engine, professional thing, it performs like a perfect and finely tuned ballet, a synchronized set of thousands and thousands of inter- and intramolecular interactions. This plant also has input channels and output protons also artfully constructed with extreme skill and sophistication and astonishing precision, and nanometrical distances and forces set and finely calculated for the purpose of building a nanomolecular plant maximized to produce chemical energy.
With a nanomolecular turbine powered by protons and which transmits its movement through a molecular rotor, and channels that direct the movement of these protons - kind of molecular slides to the water parks, the ATP synthase has fascinated many electrical and chemical engineers primarily - for its perfection in performing reactions and producing energy. In it, we also have “molecular pins” that attach the rotor to the chemical reactor (F1 unit) catalyst, which accommodates within itself the reagents and literally confines them and “Squeezes”, so as to accelerate the desired chemical reaction. And that tightens and loosens are all promoted by a synchronized spin - one opens and closes nanometrically set - governed by a molecular piece of oval shape crankshaft type in camshafts, those that man added to their combustion engines
A fantastic chemical reaction then occurs in the ATP synthase: ADP + ATP → PO4-. And the whole machinery of ATP synthase is there fitted perfectly in the cell wall of the inner mitochondrial membrane , that hyper mega high tech " cell ship" . And all with homochiral molecules, AA type lefthanded only.

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The ATP synthase is therefore a show of sophistication, specification and aperiodicity, and hyper mega irreducible complexity . Disconnect one of its components, disturb one of its forms, replace some of your AA position, and there are thousands and thousands of them, and the system loses function altogether. Try to build it slowly, step by step, by mindless unguided processes, will it be possible? Viable at the molecular level? Where would the energy come from to build it, if it is the energy provider of life? Remember though that the energy that produces ATP synthase is essential to life, virtually for all forms of life. And it is power required at the right time at the right flow! The structure of ATP synthase is so ingenious that its elucidation earned a Nobel Prize in 1997, as the enormity and significance of the feat. Our cells contain thousands of these nanomotors embedded in their mitochondria, and installed in their membranes. And these nanomotors - nano power plants - are about 200,000 times smaller than a pinhead. And that nanomotor is there for the sole purpose of forcing the occurrence of a single reaction: the third phosphate bond in ADP “crushing it” along with phosphate to form ATP
The ATP molecules are used in key processes in the cell which require energy, which is released , then regenerating ADP and a free phosphate. The energy produced is directed, for example in humans, for contraction of muscles, beating of the heart and processes in the brain, whereas the reaction products are economically and wisely recycled . In the center of the ATP synthase is a small rotor which rotates around 100 revolutions per second, synthesizing 3 ATP molecules per revolution, or 300 molecules of ATP per second! Only for our thinking and walking, we recycle proportional to our body weight (80 kg) of ATP every day. Each enzyme in the ATP synthase is composed of 31 other proteins that, in turn, are made of thousands of amino acids precisely arranged. Remove any of the 31 proteins and the motor becomes simply useless.
The ATP synthase, along with the Scourge, is one of the most “striking” examples of mega irreducible complexity we see around the corner in life. And there’s more: all the immense set of genetic information and RNA, plus dozens of proteins needed to build the ATP synthase, are in total even more irreducibly complex than the ATP synthase itself. The car factory is -by principle - more irreducibly complex than the car it manufactures.

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Described in more details chemical and biochemical (insane task), the ATP synthase is a protein complex consisting of several proteins that fit perfectly synchronously, and - in a synchronized chemical ballet - in the form of a “mushroom”. This nano mill is in thousands “installed” on the inner membrane of the mitochondria (Figure 6). There are two main components: (1) head - a spherical area comprised by the catalytic portion of the enzyme known as Factor connection 1, or simply F1, which measures about 90 Å in diameter; and (2) basic - called F0 - fixing the whole to the inner membrane of mitochondria. High resolution SEM micrographs revealed that the head (1) and the bottom part (2) are joined by a central rod - formed by subunits F1 and F0 - relatively narrow (45) which is connected to a peripheral button 90-100 Å in diameter. A mitochondria located in human liver cells has about 15,000 copies of ATP synthase
The most efficient way to conduct a chemical reaction known in this universe, “the hard way”! In the ATP synthase, a protein complex jointly embraces a ADP difosfate molecule and one anion phosphate (Pi) providing energy and forcing them “mechanically” by reacting . Reaction occurred “by force”, the engine spins at 8,500 RPM and the protein complex “opens” then its arms, by the action of the crankshaft driven by an engine and rotor, and releases the product, the tri-phosphate ATP molecule. The ATP synthase is the smallest rotary engine known today. To give you an idea of its tiny size, in a millimeter, can be grouped, side by side, approximately about 100 000 ATP synthases. This engine is driven not by power, but by “proton energy”; that is, by a countercurrent flow of protons.
The ATP synthase would then be the headless product of evolution, not guided or inexcusable evidence of intelligent design? Remember that without energy there is no life, and in life there is no power without ATP, and in life there is no ATP without ATP synthase. The ATP synthase is thus more one of the great “chicken-egg” dilemmas of Life! For all biochemical processes that coordinate the functioning and structure need to be supplied ATP synthase molecule itself produces: ATP. About 14 trillion body cells at this point are conducting this biochemical reaction via ATP synthase, in about a million times per minute through mitochondria.

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To give you even more ingenius details of this fabulous machine, note that the F1 region of ATP synthase (F1-ATPase) is made up of six protein units, and divided into three pairs of active sites. These units form regions which provide “chemical hugs” through a docking site for ADP and phosphate. An anchoring (or stator) is curved on the outside of the structure in order to fix the base (F0) to the head (F1). Three molecules of ATP are formed for each complete shaft rotation. Chemical engineering of ATP synthase is shown - there’s no denying - intelligent and mega efficient . The complex has a spiral shaft, called “Y”, which is the circumference between F0 and F1 and allows the connection of one region to the other, like a pen within a cardboard tube. The intelligent design of this nanomolecular machine causes the flow of protons, across the membrane, turn the shaft and the base. So it’s not turning the base and the axis “attracts” the protons, as originally thought, but it is the flow of protons turning the engine. The turning occurs when the central axis (y) puts pressure on the inner walls of the six proteins in the F1 region thus result in a smooth structural deformation with consequent reformation alternately. My vote here for the “pinnacle” of chemical engineering in the nanomolecular this universe. Heck, what a genius mind that knew Chemistry as anyone else, to come up with something like that!
Note further that the F0 subunit, which is fixed on the membrane of mitochondria, rotates clockwise. Laterally annexed the F0, is another input channel subunit which serves as the channel where the protons will be directed to the engine. The rotation is synchronized around its own axis and provides that individually protons enter and exit, respectively. Since the protons are attracted to the input channel, they connect to F0, and follow nearly a complete rotation, they then are conveyed to an output channel present on the same side frame attached to where F0 enters. The subunit F1 (F1 ATPase) is that attracts molecules adenosine diphosphate (ADP) and phosphate (Pi), which are released together with ATP.
3D view at the molecular level of ATP synthase: nano power plant vital to life on this planet.

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But there is even more wonder in the ATP synthase: the rotational mechanism used for F0 is performed routinely when there is a high concentration of protons in the cytosol and a low concentration of ATP inside the mitochondria. But when these concentrations are reversed, the enzyme " understands biochemically" that its function was successful, and if it continues, will promote serious imbalance in the cell. Control is everything! In this situation, the ATP synthase “thinks and reacts,” and and makes its F0 turn now in the opposite direction, and the mechanism is reversed, and the proton exit channel now becomes the input channel, and the protons inside the organelle return to the cytosol. ATP molecules are now converted to ADP and phosphate free, in a chemical “retro-reaction” . A chemical balance nano-mechanically directed and controlled! Since you know this fantastic nanomachine a little better at the molecular level, , what do you think: chance or design?

Referências e notas

  1. “ATP synthase — a marvellous rotary engine of the cell” M. Yoshida, E. Muneyuki, T. Hisabori, Nature Reviews Molecular Cell Biology 2001, 2, 669.
  2. Paul D. Boyer. The ATP Synthase - a splendid molecular machine. Annual Review of Biochemistry, Vol. 66: 717-749 (July 1997)
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Neither. Evolution.

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I guess you talk about yourself ? agreed.

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I guess you talk about yourself ? agreed.
I'm talking about all of us.
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Well , i think i am perfectly rational. All evidence points to the fact that ATP synthase is IC.

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Well , i think i am perfectly rational. All evidence points to the fact that ATP synthase is IC.
If you were perfectly rational you wouldn't post a long thread on biology and end it with a false dichotomy. Evolution is not chance and Intelligent Design is a fairy tale.
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Well , i think i am perfectly rational. All evidence points to the fact that ATP synthase is IC.
If you were perfectly rational you wouldn't post a long thread on biology and end it with a false dichotomy. Evolution is not chance and Intelligent Design is a fairy tale. What does my op have to do with evolution ?
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Well , i think i am perfectly rational. All evidence points to the fact that ATP synthase is IC.
If you were perfectly rational you wouldn't post a long thread on biology and end it with a false dichotomy. Evolution is not chance and Intelligent Design is a fairy tale. What does my op have to do with evolution ? What does your op have to do with anything? I'll admit I only skimmed your rapid fire cut and pastes, but it seems mainly a description of an incredibly complex molecular machine. Your links take us to Intelligent Design faux science blogs, but that's all we got to work with. What is the point you are trying to make?
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It looks so much more amazing than it reads.

Molecular animation of ATP synthase Aditya Chopra https://www.youtube.com/watch?v=GM9buhWJjlA Published on Oct 14, 2013 John Walker shared his Nobel Prize with the Paul Boyer for their elucidation of the enzymatic mechanism underlying the synthesis of adenosine triphosphate (ATP). Here is an animation showing the architecture and catalytic function of ATP synthase. It sits in the inner membranes of the organelle, where it uses the trans-membrane proton motive force (pmf) generated by the oxidation of nutrients as a source of energy for making ATP. The pmf across the inner membrane of the organelle is coupled to the chemical synthesis of ATP from ADP and phosphate by a rotary mechanism. During ATP synthesis, the central rotor turns in the direction shown about 150 times every second. In order to provide energy to sustain our lives, every day, each one us produces a quantity of ATP by this mechanism that is approximately equal to our body weights.
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The Evolution of Electron-Transport Chains Molecular Biology of the Cell. 4th edition. http://www.ncbi.nlm.nih.gov/books/NBK26849/ Much of the structure, function, and evolution of cells and organisms can be related to their need for energy. We have seen that the fundamental mechanisms for harnessing energy from such disparate sources as light and the oxidation of glucose are the same. Apparently, an effective method for synthesizing ATP arose early in evolution and has since been conserved with only small variations. How did the crucial individual components—ATP synthase, redox-driven H+ pumps, and photosystems—first arise? Hypotheses about events occurring on an evolutionary time scale are difficult to test. But clues abound, both in the many different primitive electron-transport chains that survive in some present-day bacteria, and in geological evidence about the environment of the Earth billions of years ago. Go to: The Earliest Cells Probably Produced ATP by Fermentation ... ~~~ Electron-transport Chains Enabled Anaerobic Bacteria to Use Nonfermentable Molecules as Their Major Source of Energy ... ~~~ By Providing an Inexhaustible Source of Reducing Power, Photosynthetic Bacteria Overcame a Major Evolutionary Obstacle ... ~~~ The Photosynthetic Electron-transport Chains of Cyanobacteria Produced Atmospheric Oxygen and Permitted New Life-Forms ... ~~~ Summary Early cells are believed to have been bacteriumlike organisms living in an environment rich in highly reduced organic molecules that had been formed by geochemical processes over the course of hundreds of millions of years. They may have derived most of their ATP by converting these reduced organic molecules to a variety of organic acids, which were then released as waste products. By acidifying the environment, these fermentations may have led to the evolution of the first membrane-bound H+ pumps, which could maintain a neutral pH in the cell interior by pumping out H+. The properties of present-day bacteria suggest that an electron-transport-driven H+ pump and an ATP-driven H+ pump first arose in this anaerobic environment. Reversal of the ATP-driven pump would have allowed it to function as an ATP synthase. As more effective electron-transport chains developed, the energy released by redox reactions between inorganic molecules and/or accumulated nonfermentable compounds produced a large electrochemical proton gradient, which could be harnessed by the ATP-driven pump for ATP production. Because preformed organic molecules were replenished only very slowly by geochemical processes, the proliferation of bacteria that used them as the source of both carbon and reducing power could not go on forever. The depletion of fermentable organic nutrients presumably led to the evolution of bacteria that could use CO2to make carbohydrates. By combining parts of the electron-transport chains that had developed earlier, light energy was harvested by a single photosystem in photosynthetic bacteria to generate the NADPH required for carbon fixation. The subsequent appearance of the more complex photosynthetic electron-transport chains of the cyanobacteria allowed H2O to be used as the electron donor for NADPH formation, rather than the much less abundant electron donors required by other photosynthetic bacteria. Life could then proliferate over large areas of the Earth, so that reduced organic molecules accumulated again. About 2×109 years ago, the O2released by photosynthesis in cyanobacteria began to accumulate in the atmosphere. Once both organic molecules and O2had become abundant, electron-transport chains became adapted for the transport of electrons from NADH to O2, and efficient aerobic metabolism developed in many bacteria. Exactly the same aerobic mechanisms operate today in the mitochondria of eucaryotes, and there is increasing evidence that both mitochondria and chloroplasts evolved from aerobic bacteria that were endocytosed by primitive eucaryotic cells.
Copyright © 2002, Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter; Copyright © 1983, 1989, 1994, Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson . Bookshelf ID: NBK26849
My point is that serious smart students and scientists have dedicated life times into studying, learning about and understanding these matters. They have done an excellent job of describing the evolution, nothing certain, questions and gaps are openly discussed and approached, the scientific process don't you know. Looks beautiful and eminently believable to me. So Adonai888, can you explain what your point is?
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You know I just watched that video again. It is pretty unfathomable, but damn there you go, it’s happening all the time.
A folks understand it, much more than ID types could ever admit.
The whole ID thing is built on willfully deluding oneself about the available evidence, information and understanding.
I’ve been listening to an amazing book, this one over and over not just 2,3 times, but over a half dozen and counting,
it simply that amazing of narrative.
First Life
by David Deamer
another real scientist, in fact he’s collaborated with Robert Hazen
another origins author who I can listen to repeatedly, got to if I’m going to absorb any of that amazing information.

http://news.ucsc.edu/2011/06/first-life.html Biochemist David Deamer explores how life began in new book, 'First Life' New findings support author's view of membranes as key to the origin of life June 02, 2011 By Tim Stephens
It's worth reading or listening, much more refreshing and inclusive than that ID fairytales and such machinations.
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Well , i think i am perfectly rational. All evidence points to the fact that ATP synthase is IC.
If you were perfectly rational you wouldn't post a long thread on biology and end it with a false dichotomy. Evolution is not chance and Intelligent Design is a fairy tale. What does my op have to do with evolution ? Nothing, and that is my point.
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You know I just watched that video again. It is pretty unfathomable, but damn there you go, it's happening all the time. A folks understand it, much more than ID types could ever admit. The whole ID thing is built on willfully deluding oneself about the available evidence, information and understanding. I've been listening to an amazing book, this one over and over not just 2,3 times, but over a half dozen and counting, it simply that amazing of narrative. First Life by David Deamer another real scientist, in fact he's collaborated with Robert Hazen another origins author who I can listen to repeatedly, got to if I'm going to absorb any of that amazing information.
http://news.ucsc.edu/2011/06/first-life.html Biochemist David Deamer explores how life began in new book, 'First Life' New findings support author's view of membranes as key to the origin of life June 02, 2011 By Tim Stephens
It's worth reading or listening, much more refreshing and inclusive than that ID fairytales and such machinations.
abiogenesis is impossible. Deal with it. http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible
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abiogenesis is impossible. Deal with it. http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible
We know that intelligence is able to create high-information containing codes, like books, computer codes, and complex machines and factories. We observe in the natural world organisms made by the same principles, namely codified specified information, and irreducible and interdependent molecular machines and cell factories, while the only possible natural mechanisms, namely chance or random chemical reactions, do not have this broad range of intelligence-like capabilities. Its safe therefore to conclude, that the origin of life is best explained through a intelligent creator, and not well explained through natural mechanisms. ... Your arguments only works when you are allowed to misrepresent what your 'opponents' are actually saying! That's what makes all that "reasonandscience" so f'n dishonest. If you would take the time to become familiar with the work of Hazen and Deamer and what they have learned you'd realize that "chance" and "random" has nothing to do with these atomic and chemical reactions. Atoms and molecules have specific electron-magnetic properties, interactions are limited, in a sense directed, at least to the point that we should agree that "chance" and "random" don't belong in this discussion. By deliberately over-simplying and misrepresenting what the experts are saying you are merely justifying your own lack of curiosity to yourself. I think that's beyond sad, it's tragic because I know the real world out there, the one that serious scientists are learning about, is way more fascinating, as much for the remaining mysteries, as for all we've learned. than all that stale rehashing of contrived children's tales, that are actually meant to make dumb and docile. PS. An orchestra-leader God is impossible. It's been billions of years of step by step evolution from something like a big bang moment, the flash of creation, to matter and stars and planets and Earth and our biosphere and us. Folds within folds of harmonic cumulative complexity, cascading down the stream of time, one day at a time. (even if that doesn't mean anything beyond our little wonderful once in a creation world.) Once there was nothing and now there is this and the steps from there to here are ever better understood. Deal with it. … and enjoy your one moment to experience it. Here check this out http://whatsupwiththatwatts.blogspot.com/2016/01/2-coevolution-of-minerals-and-life.html It's a lecture by Hazen and I've added time signature notes for easy reference, fascinating stuff, give it a try.
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abiogenesis is impossible. Deal with it. http://reasonandscience.heavenforum.org/t1279-abiogenesis-is-impossible
We know that intelligence is able to create high-information containing codes, like books, computer codes, and complex machines and factories. We observe in the natural world organisms made by the same principles, namely codified specified information, and irreducible and interdependent molecular machines and cell factories, while the only possible natural mechanisms, namely chance or random chemical reactions, do not have this broad range of intelligence-like capabilities. Its safe therefore to conclude, that the origin of life is best explained through a intelligent creator, and not well explained through natural mechanisms. ... Your arguments only works when you are allowed to misrepresent what your 'opponents' are actually saying! That's what makes all that "reasonandscience" so f'n dishonest. If you would take the time to become familiar with the work of Hazen and Deamer and what they have learned you'd realize that "chance" and "random" has nothing to do with these atomic and chemical reactions. Atoms and molecules have specific electron-magnetic properties, interactions are limited, in a sense directed, at least to the point that we should agree that "chance" and "random" don't belong in this discussion. By deliberately over-simplying and misrepresenting what the experts are saying you are merely justifying your own lack of curiosity to yourself. I think that's beyond sad, it's tragic because I know the real world out there, the one that serious scientists are learning about, is way more fascinating, as much for the remaining mysteries, as for all we've learned. than all that stale rehashing of contrived children's tales, that are actually meant to make dumb and docile. PS. An orchestra-leader God is impossible. It's been billions of years of step by step evolution from something like a big bang moment, the flash of creation, to matter and stars and planets and Earth and our biosphere and us. Folds within folds of harmonic cumulative complexity, cascading down the stream of time, one day at a time. (even if that doesn't mean anything beyond our little wonderful once in a creation world.) Once there was nothing and now there is this and the steps from there to here are ever better understood. Deal with it. … and enjoy your one moment to experience it. Here check this out http://whatsupwiththatwatts.blogspot.com/2016/01/2-coevolution-of-minerals-and-life.html It's a lecture by Hazen and I've added time signature notes for easy reference, fascinating stuff, give it a try. In order to make proteins, you need coded, specified, complex information. To make the minimal gene set and proteins for the first cell, , the alternative to design is chance, since evolution only starts with replication.