Miniature Molecular Power Plant: ATP Synthase (Video)

_{Denyse O'Leary

January 22, 2013

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So I have a request for the next video. :) The proton gradient. How and why it works. How it's maintained. I love concentrating on two aspects of cellular activity (forget DNA->RNA->Protein): 1. Energy 2. Building Blocks Without those two things you don't get anything else. RNA has to be constructed, as do proteins. The molecules they are built from have to be constructed. But to build those molecules, you need... you guess it, DNA and RNA and proteins, and energy. What a cycle!Mung_{January 27, 2013
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A faux ID argument goes something like this: Wow, look at all this magnificent engineering and complexity. Therefore, ID.
Exactly.Eric Anderson_{January 24, 2013
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Luke 19:40 “I tell you,” he replied, “if they keep quiet, the stones will cry out.”bornagain77_{January 24, 2013
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I think Eric Anderson has a point. I made a comment questioning rodent to bat evolution at a website called "Debunking Christianity", and, even though I didn't mention anything about religion, I got an eleven paragraph response denouncing religion: http://tinyurl.com/arsqgxxDavem_{January 24, 2013
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p.s. to add a bit more to Eric's suggestion, perhaps more videos could be produced in collaboration with others who might not normally be inclined to get involved with ID.Mung_{January 24, 2013
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Don't get me wrong, as I said in #1, I love these videos. :)Mung_{January 24, 2013
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Those are some excellent points Eric. Especially if the video is meant to be used in conjunction with an ID textbook. Make the connection to ID in the book. Really, now that you mention it and I watch it again, this video is an example of what I consider faux ID. A faux ID argument goes something like this: Wow, look at all this magnificent engineering and complexity. Therefore, ID. I was just reading something yesterday about how the culture has gone from making arguments to making advertizements. Are we trying to advertise ID, or argue for the merits of ID?Mung_{January 24, 2013
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I might be stirring up a hornet's nest with this comment, but here goes . . . These kinds of animations are good, but if they were less ID-specific they might have a broader impact (think, for example, of some of the Harvard animations). Case in point: while I was watching the video I thought, "This is a great animation that I could share with person x." Then came the closing paragraph with the narrator making an explicit statement of intelligent design. And I said to myself, "Well, shoot." Here's the thing. Those who are sensitive to the idea of intelligent design don't need it spelled out for them. Those who are hostile will immediately dismiss anything that mentions the word. Those who are in the middle might be willing to consider design, but I've found it is often more powerful when a person comes to the conclusion themselves or when I can introduce it in the appropriate way for that person, rather than having it stated in black and white without the appropriate background, etc. Further, having that explicit statement in there really limits how and where the video will be used. If I'm a teacher, for example, I might want to show the video to teach about incredible processes in the cell, but I might not be willing to risk a bunch of problems with the kids, parents, and administrators due to the explicit intelligent design paragraph at the end. If I'm doing a professional talk or presentation (which is another way I thought of using the video) I'm probably going to cut the last part or pick someone else's animation in order to avoid bringing up a design discussion that may or may not be germane to the presentation (regardless of how much I might support intelligent design.) My recommendation (I don't know if you're reading this thread, Casey), would be to do first-class animations like these and let the evidence speak for itself. (Those who have ears to hear . . .) Show the facts, but don't then go on to draw an explicit conclusion of design. Then the videos will be more accessible to a wider audience, will be more likely to be shared among people of all persuasions, and can potentially lead to a situation where the Discovery Institute is known for putting out some great molecular animations. Let's suppose DI does several dozen of these animations in the coming months/years. How great would it be for people to think, "Discovery Institute. Oh yeah, those are the guys who do those really great molecular animations." Rather than, "Discovery Institute. Oh year, those are the guys who do those animations pushing intelligent design theory." Just show the facts and let the audience draw the conclusion. /soapboxEric Anderson_{January 23, 2013
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Amazing. Makes me want to stand up and give God a round of applause.sagebrush gardener_{January 22, 2013
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Mung, Prokaryotes lack mitochandria and still use ATP- the ATPase and the electron transport chain are located inside the cytoplasmic membraneJoe_{January 22, 2013
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An enormous gap exists between prokaryote cells and eukaryote cells. A crucial difference between prokaryotes and eukaryotes is the means they use to produce ATP (energy). http://www.trueorigin.org/atp.asp The ATP Synthase Enzyme - exquisite motor necessary for first life - video http://www.youtube.com/watch?v=W3KxU63gcF4 Mitochondria - Molecular Machine - Powerhouse Of The Cell - video http://www.metacafe.com/watch/5510941/ On The Non-Evidence For The Endosymbiotic Origin Of The Mitochondria - March 2011 https://uncommondescent.com/intelligent-design/on-the-non-evidence-for-the-endosymbiotic-origin-of-the-mitochondria/ On the Origin of Mitochondria: Reasons for Skepticism on the Endosymbiotic Story Jonathan M. - January 10, 2012 Excerpt: While we find examples of similarity between eukaryotic mitochondria and bacterial cells, other cases also reveal stark differences. In addition, the sheer lack of a mechanistic basis for mitochondrial endosymbiotic assimilation ought to -- at the very least -- give us reason for caution and the expectation of some fairly spectacular evidence for the claim being made. At present, however, such evidence does not exist -- and justifiably gives one cause for skepticism. http://www.evolutionnews.org/2012/01/on_the_origin_o054891.html Bacteria Too Complex To Be Primitive Eukaryote Ancestors - July 2010 Excerpt: “Bacteria have long been considered simple relatives of eukaryotes,” wrote Alan Wolfe for his colleagues at Loyola. “Obviously, this misperception must be modified.... There is a whole process going on that we have been blind to.”,,, For one thing, Forterre and Gribaldo revealed serious shortcomings with the popular “endosymbiosis” model – the idea that a prokaryote engulfed an archaea and gave rise to a symbiotic relationship that produced a eukaryote. http://www.creationsafaris.com/crev201007.htm#20100712b Bacterial Protein Acetylation: The Dawning of a New Age - July 2012 Excerpt: Bacteria have long been considered simple relatives of eukaryotes. Obviously, this misperception must be modified. From the presence of a cytoskeleton to the packaging of DNA to the existence of multiple post-translational modifications, bacteria clearly implement highly sophisticated mechanisms to regulate diverse cellular processes precisely. http://darwins-god.blogspot.com/2012/07/bacterial-protein-acetylation-dawning.html Materialism simply has no credible answer for how this extreme level of complexity 'accidentally' arose in the first living cell, nor how this extreme integrated complexity found in life randomly evolved to the next 'simple' step of life. ,,,Consider the following paradox of photosynthesis,,, Plants perform photosynthesis. Plants use massively complex machinery within their cells to capture the light from the Sun and produce sugars (food). The benefit of this is, of course, that they eventually provide food for animals and humans. But plants also then break down the very food that they make by using another set of extremely complex machinery to get ATP (the 'energy currency' molecule of the cell) from the sugars that they initially built. Yet, this makes no sense from an evolutionary perspective because the plants should have only formed the complex machinery (if evolution had any power to create complex machinery in the first place) to take the power of light and convert it directly to ATP so that they could use it themselves instead of producing more 'food' than is necessary...that would be more energetically feasible. But, lo, that's not what happens,,, Moreover photosynthesis is found to be widespread among different bacteria phyla with no clear evolutionary relationships between them: The Elaborate Nanoscale Machine Called Photosynthesis: No Vestige of a Beginning - Cornelius Hunter - July 2012 Excerpt: "The ability to do photosynthesis is widely distributed throughout the bacterial domain in six different phyla, with no apparent pattern of evolution. Photosynthetic phyla include the cyanobacteria, proteobacteria (purple bacteria), green sulfur bacteria (GSB), firmicutes (heliobacteria), filamentous anoxygenic phototrophs (FAPs, also often called the green nonsulfur bacteria), and acidobacteria (Raymond, 2008)." http://darwins-god.blogspot.com/2012/07/elaborate-nanoscale-machine-called.html?showComment=1341739083709#c1202402748048253561 "Despite its complexity, C4 photosynthesis is one of the best examples of 'convergent evolution', having evolved more than 50 times in at least 18 plant families (Sage 2004; Conway Morris 2006)." http://mbe.oxfordjournals.org/content/26/8/1909.full.pdf etc.. etc...bornagain77_{January 22, 2013
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Is it the case that some cells do not have mitochondria? Do those cells which lack mitochondria not use ATP?Mung_{January 22, 2013
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Powering the Cell: Mitochondria - YouTubeMung_{January 22, 2013
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Astonishing Molecular Machines – Drew Berry http://www.metacafe.com/w/6861283 Powering the Cell: Mitochondria - video http://www.youtube.com/watch?v=RrS2uROUjK4 Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video http://www.metacafe.com/watch/3994630 Molecular Machine - Nuclear Pore Complex - Stephen C. Meyer - video http://www.metacafe.com/watch/4261990 Kinesin Linear Motor - Video http://www.youtube.com/watch?v=kOeJwQ0OXc4 Ribosome Translation High Quality - video http://pubs.acs.org/cen/multimedia/85/ribosome/translation_bacterial.html Myosin - video http://www.youtube.com/watch?v=j8F5GGPACkQ The Virus - Assembly Of A Molecular "Lunar Landing" Machine - video http://www.metacafe.com/watch/4023122 The following article has a list of 40 (yes, 40) irreducibly complex molecular machines in the cell: Molecular Machines in the Cell - http://www.discovery.org/a/14791bornagain77_{January 22, 2013
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Related notes: Fine-Tuning Found in Life’s Rotary Engine - August 2010 Excerpt: ATP synthases are among the most abundant and important proteins in living cells. These rotating nano-machines produce the central chemical form of cellular energy currency, ATP (adenosine triphosphate), which is used to meet the energy needs of cells. For example, human adults synthesize up to 75 kg (165 lbs.) of ATP each day under resting conditions and need a lot more to keep pace with energy needs during strenuous exercise or work. The turbine of the ATP synthase is the rotor element, called the c-ring. This ring is 63 A [Angstroms] in diameter (6.3 nm, or 6.3 millionths of a millimeter) and completes over 500 rotations per second during ATP production. http://www.creationsafaris.com/crev201008.htm#20100804a 500 rotations per second amounts to, in the terminology of more familiar motors, some 30,000 RPM. Since three ATP molecules are synthesized for each rotation, one of these motors can generate just short of 100,000 ATP per minute – and your body has quadrillions of them working all your life, even in your sleep. Nanomachines in the Powerhouse of the Cell: Architecture of the Largest Protein Complex of Cellular Respiration Elucidated - July 2010 Excerpt: In biological oxidation, the energy will be released by the membrane bound protein complexes of the respiratory chain in a controlled manner in small packages. Comparable to a fuel cell, this process generates an electrical membrane potential, which is the driving force of ATP synthesis. The total surface of all mitochondrial membranes in a human body covers about 14,000 square meter. This accounts for a daily production of about 65 kg of ATP. (A little over 143 pounds). The now presented structural model provides important and unexpected insights for the function of complex I. A special type of “transmission element,” which is not known from any other protein, appears to be responsible for the energy transduction within the complex by mechanical nanoscale coupling. Transferred to the technical world, this could be described as a power transmission by a coupling rod, which connects for instance the wheels of a steam train. This new nano-mechanical principle will now be analysed by additional functional studies and a refined structural analysis. http://www.sciencedaily.com/releases/2010/07/100702100414.htm World’s Smallest Rotary Engine Highlighted Excerpt: The match implies 100% efficiency for the conversion of the Gibbs free energy of ATP hydrolysis into mechanical work performed on the elastically strained filament. This is not surprising given the approximate thermodynamic equilibrium of the enzyme (long)-filament construct. It is more informative to say that there is no slip between ATP hydrolysis in F1 and rotation in FO under the given conditions. http://www.creationsafaris.com/crev200905.htm#20090525a Your Motor/Generators Are 100% Efficient - October 2011 Excerpt: ATP synthase astounds again. The molecular machine that generates almost all the ATP (molecular “energy pellets”) for all life was examined by Japanese scientists for its thermodynamic efficiency. By applying and measuring load on the top part that synthesizes ATP, they were able to determine that one cannot do better at getting work out of a motor,,, The article was edited by noted Harvard expert on the bacterial flagellum, Howard Berg. http://crev.info/content/111014-your_motor_generators “Torque generation and elastic power transmission in the rotary FOF1-ATPase, Nature 459, 364-370 (21 May 2009) “The coupled operation of two rotary motors, one electrical (FO and one chemical (F1), is unique". “In FOF1-ATPase there is no fine-tuning of the two stepping motors; instead, their coupled operation is smoothed and speeded by elastic power transmission, which accounts for its high kinetic efficiency and robust function. http://www.nature.com/nature/journal/v459/n7245/full/nature08145.html#a1 ATP Synthase Ratchets Up the Case for Intelligent Design - Fazale Rana - April 2011 Excerpt: The bottom line: there is a motor within a motor architecture for the F0-F1 ATP synthase. http://www.reasons.org/atp-synthase-ratchets-case-intelligent-design ATP: The Perfect Energy Currency for the Cell - Jerry Bergman, Ph.D. Excerpt: In manufacturing terms, the ATP (Synthase) molecule is a machine with a level of organization on the order of a research microscope or a standard television (Darnell, Lodish, and Baltimore, 1996). http://www.trueorigin.org/atp.asp Your Rotary Engines Are Arranged in Factories - August 2011 Excerpt: As if ATP synthase was not amazing enough, a team of scientists in Germany now tells us they are arranged in rows with other equipment to optimize performance. From electron micrographs of intact mitochondria, they were able to detect the rotary engines of ATP synthase and other parts of the respiratory chain. Their diagram in an open-source paper in PNAS looks for all the world like a factory.,,, “We propose that the supramolecular organization of respiratory chain complexes as proton sources and ATP synthase rows as proton sinks in the mitochondrial cristae ensures optimal conditions for efficient ATP synthesis.” The authors had virtually nothing to say about how this might have evolved, noting only that the structure is “conserved during evolution” in every sample they examined (3 species of fungi including yeast, potato, and mammal). What this means is a lack of evolution over nearly two billion years, in the standard evolutionary timeline. http://crev.info/content/110817-your_rotary_engines_are_arranged_in_factories Machine Revolution: More Details Emerge on ATP Synthase and Its Exquisite Design (4 New Papers On The Molecular Machine ATP Synthase Are Highlighted - One paper has micro-photographs) - July 2012 http://www.evolutionnews.org/2012/07/the_other_rotar061761.htmlbornagain77_{January 22, 2013
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I love these animations. What would be rally cool, I think, would be to find some way to integrate them. I don't mean by having them connected into one long video or anything like that, I mean indicating the inter-dependence in some way. For example, if there's an upcoming video on kinesin, how is kinesin powered? Is it powered by ATP? Drop in a mention of the ATP video. Is kenesin required in any way to construct the ATP synthases? IOW try not to let each molecular machine be treated in too much isolation, as if it could do what it does all on it's lonesome. my .02cMung_{January 22, 2013
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