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VIDEO: A look at the ATP Synthase in action, courtesy Discovery Institute (and Wikipedia)

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DI has just released a video on the ATP Synthase in action (HT: ENV):

[youtube XI8m6o0gXDY]

The blurb at Youtube reads:

ATP Synthase is a molecular machine found in all living organisms. It serves as a miniature power-generator, producing an energy-carrying molecule, adenosine triphosphate, or ATP. The ATP synthase machine has many parts we recognize from human-designed technology, including a rotor, a stator, a camshaft or driveshaft, and other basic components of a rotary engine. This machine is just the final step in a long and complex metabolic pathway involving numerous enzymes and other molecules—all so the cell can produce ATP to power biochemical reactions, and provide energy for other molecular machines in the cell.

{Added, courtesy commenters below, here is another useful animation:}

[youtube H7P4xOUPYVw]

Wiki’s somewhat more schematic GIF animation, will help us see what is going on in each cycle of rotation, a little more closely:

Here, we have an enzyme made of a protein complex of subunits, constituting a rotary machine in the mitochondria of the living cell

A typical animal cell

 

. . . and responsible for providing the molecular energy batteries without which life would collapse.  And, it is recognisably a motor with a working head on its shaft.

What is the empirically grounded explanation for motors, again?

And, the spontaneous, chance and necessity model for its origin is ________, based on _______ as observational evidence?

Any takers? END

Comments
Bioenergetic Processes of Cyanobacteria Check out Chapter 10. ATP Synthase: Structure, Function and Regulation of a Complex Machine An entire chapter. :) ATP Synthase heaven!Mung
January 30, 2013
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CR: The key issues are in the C1 - 5 factors. Adapting things from one purpose to another is not a simple business, especially in a context of automated self assembly. KFkairosfocus
January 29, 2013
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And there is more:
Rotary Motors Evolution has generated not only an exquisite variety of translational motors, but also motors whose motions are rotational. Two of the most widely studied examples of rotary motors are the bacterial flagellar motor and ATP synthase... ATP synthase is one of the central powerhouses of living cells, found in the inner membrane of bacterial cells and also in the mitochondria of eukaryotic cells. It is an amazing molecular machine that is constructed of two different rotary motors connected to a common drive shaft. The F0 motor of the ATP synthase is similar to the flagellar rotary motor, in that it uses the energy stored in the transmembrane gradient of hydrogen ions to rotate. The F1 motor uses ATP hydrolysis to rotate in the opposite direction. Under normal circumstances, when the transmembrane electrochemical gradient is strong, the F0 motor generates more torque than the F1 motor, and so the F0 motor forces the F1 motor to rotate in reverse, and thereby synthesize ATP from ADP plus inorganic phosphate. However, if the transmembrane electrochemical gradient is weak, the balance can tilt in the other direction, and the F1 motor will generate more torque than the F0. Under these circumstances, the coupled motor uses ATP hydrolysis to pump hydrogen ions out of the cell. - Physical Biology of the Cell, 2e (p. 634)
They forget to mention how evolutiondidit. =PMung
January 28, 2013
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"And the science that backs up this wild speculation is…?"
We find similar parts in other machines.
I can no longer say evolutionists believe in magic. Even magic has a magician.
That would make a good tagline.Chance Ratcliff
January 28, 2013
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Yup. If we just take this subunit here, and this one here, and this one here, and jostle them about vigorously, voila! ATP Synthase! And the science that backs up this wild speculation is...? So we have this motor part here, and it was managing quite fine without this stator, and we have this cell here, and it was managing just fine without the ATP generated by an as yet non-existence ATP Synthase, and we have this membrane here, and this proton gradient... I can no longer say evolutionists believe in magic. Even magic has a magician.Mung
January 28, 2013
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Folks: There is the usual just so first there was something else then there was a cobbling together story:
[Q:] ATP Synthase is ubiquitous throughout life on earth and so most probably evolved within the last universal common ancestor (LUCA) before that lineage diversified into the various kingdoms of life. It is suggested that the functional domains comprising the ATP Synthase complex were cobbled together from pre-existing sub-units, each with with a related activity (e.g. the union of a proton motor with a DNA Helicase with ATPase activity), which seems reasonable, although a bit vague in the details [--> unwitting shades of Behe's observation on evolutionary stories on origin of IC systems!]. The fact that a primitive ATP Synthase [--> What's primitive about it? But of course, that word suggests, crude, simple, lashed together etc . . . ] arose in the first place suggests that ATP already had a central role in cellular metabolism and so begs the question, what preceded ATP Synthase in the role of generating ATP in the LUCA cell? . . . . [A:] There are metabolic processes in which ATP is synthesised without the involvement of ATP synthase. The best examples are, in fact, two steps in the glycolytic pathway, catalysed by phosphoglycerate kinase and pyruvate kinase. This is why, in the absence of any aerobic metabolism [--> and how did such a complex system vital tot he life of aerobic organisms come about?], many organisms (like yeast for example) can grow quite happily, producing two molecules of ATP for each molecule of glucose that is metabolised. Presumably this process is what enabled ATP to gain its central role in energy metabolism without any need for an ATP synthase.
What is going on yet again, is the imposition of the a priori evolutionary materialist framework. On that f/w, the gaps are filled with vague just so narratives and promissory notes, "good enough" to keep going on the presumed credit in the system as a whole. Lewontinian a priori materialism, anyone? To which I say, a system based on a towering pile of IOU's leading a boom is building up to a bust! Let's not forget Menuge's challenges C1 - 5 for origin of any IC system (presented for the flagellum but applicable far more broadly) and what this implies about such lash-up narratives:
For a working [bacterial] flagellum to be built by exaptation, the five following conditions would all have to be met: C1: Availability. Among the parts available for recruitment to form the flagellum, there would need to be ones capable of performing the highly specialized tasks of paddle, rotor, and motor, even though all of these items serve some other function or no function. C2: Synchronization. The availability of these parts would have to be synchronized so that at some point, either individually or in combination, they are all available at the same time. C3: Localization. The selected parts must all be made available at the same ‘construction site,’ perhaps not simultaneously but certainly at the time they are needed. C4: Coordination. The parts must be coordinated in just the right way: even if all of the parts of a flagellum are available at the right time, it is clear that the majority of ways of assembling them will be non-functional or irrelevant. C5: Interface compatibility. The parts must be mutually compatible, that is, ‘well-matched’ and capable of properly ‘interacting’: even if a paddle, rotor, and motor are put together in the right order, they also need to interface correctly. (Agents Under Fire: Materialism and the Rationality of Science, pgs. 104-105 (Rowman & Littlefield, 2004). HT: ENV.)
Until we see these five criteria addressed on empirical evidence, we should not take the credit of such IOU's at all, as in rubbery documents tend to bounce. KFkairosfocus
January 28, 2013
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So many AAA ATPases
Protein degradation within a cell is essential for protein turnover, for regulatory control, and for quality control to remove incorrectly folded or damaged proteins. However, a cell must be able to tightly regulate which proteins are degraded to avoid removing proteins vital to cellular function, and to cope with the ever-changing protein requirements within cells. The proteasome is responsible for selective protein degradation within cells, degrading only those proteins that are marked for destruction. The proteins targeted are often short-lived molecules, such as regulatory proteins that are controlled in part through rapid synthesis and degradation. Proteins are selected for degradation by the proteasome through an ubiquitin-tagging system, a highly regulated process whereby a chain of small ubiquitin proteins are covalently attached to a condemned protein. However, some proteins can be degraded by proteasomes without the ubiquitin tag. The breakdown of proteins by proteasomes is an ATP-dependent process. Proteasomes make use of a specialised family of ATPases known as AAA ATPases (ATPases Associated with various cellular Activities).
Will it never end!?!?Mung
January 27, 2013
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Ah yes, the unguided miracle! Now if that doesn't require a leap of wishful thinking I don't know what does.
The database details a comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, except that it incorporates both functional and phylogenetic information. Descriptions, TC numbers, and examples of over 600 families of transport proteins are provided. Functional and Phylogenetic Classification of Membrane Transport Proteins
Mung
January 27, 2013
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"There is an entire family of the things!"
But doesn't that demonstrate that they are all related in evolutionary history, hence evolution is true? What other unguided options exist???Chance Ratcliff
January 27, 2013
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"ATP Synthase – RCSB PDB-101"
What a great read. More quotes:
ATP synthesis is composed of two rotary motors, each powered by a different fuel. The motor at the top, termed F0, an electric motor. It is embedded in a membrane (shown schematically as a gray stripe here), and is powered by the flow of hydrogen ions across the membrane. As the protons flow through the motor, they turn a circular rotor (shown in blue). This rotor is connected to the second motor, termed F1. The F1 motor is a chemical motor, powered by ATP. The two motors are connected together by a stator, shown on the right, so that when F0 turns, F1 turns too.
Each motor is also a generator, and so each part plays its role depending upon the context: generating ATP or pumping ions back across the membrane.
So why have two motors connected together? The trick is that one motor can force the other motor to turn, and in this way, change the motor into a generator. This is what happens in our cells: the F0 motor uses the power from a proton gradient to force the F1 motor to generate ATP. In our cells, food is broken down and used to pump hydrogen ions across the mitochondrial membrane. The F0 portion of ATP synthase allows these ions to flow back, turning the rotor in the process. As the rotor turns, it turns the axle and the F1 motor becomes a generator, creating ATP as it turns.
If ATP and thus ATP synthase is required for all major cellular processes to run, hence replication, then by necessity, this enzyme antedates Darwinian evolution. This means we need a non-Darwinian process capable of building such motors to explain this in a materialistic framework. However we're told that it's the very power of Darwinian evolution which explains the building such structures. If non-Darwinian processes can build them, then Darwinian processes are superfluous, are they not? Shouldn't Occam's razor apply here? This seems fundamentally perplexing. We find, if naturalism is true, that there is a non-Darwinian process for generating biological nanotechnology. Why is Darwinian evolution required in order to do the same? Are there indeed twin forces, unrelated, neither elucidated, which perform the same or similar tasks of protein engineering? Can someone disabuse me of my confusion?Chance Ratcliff
January 27, 2013
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And of course, this gets us back to the subject of Hydrogen and thence to Fine-Tuning of the Cosmos for Life. A teleological idea. :)Mung
January 27, 2013
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ATP synthase is one of the wonders of the molecular world. ATP synthase is an enzyme, a molecular motor, an ion pump, and another molecular motor all wrapped together in one amazing nanoscale machine.
ATP Synthase - RCSB PDB-101
The energy currency used by all cells from bacteria to man is adenosine triphosphate (ATP). Every process within an organism – DNA and protein synthesis, muscle contraction, active transport of nutrients and ions, neural activity, maintenance of osmosis, carbon fixation – requires a source of ATP.
ATP Synthase There is an entire family of the things!
ATPases are membrane-bound ion channels (actually transporters, as they are not true ion channels) that couple ion movement through a membrane with the synthesis or hydrolysis of a nucleotide, usually ATP. Different forms of membrane-associated ATPases have evolved over time to meet specific demands of cells. These ATPases have been classified as F-, V-, A-, P- and E-ATPases based on functional differences. They all catalyse the reaction of ATP synthesis and/or hydrolysis.
The ATPase FamilyMung
January 27, 2013
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ATP Synthase Gradient: The MovieMung
January 27, 2013
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KF, thanks much. Understood.Chance Ratcliff
January 27, 2013
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CR: Pardon, note adjustment. The problem is not merely sensibilities, if we leave known broken windows lying around here at UD -- on track record -- it invites vandals who hardly need an excuse to carry on in ways that have to be seen to be believed then demand to know why you object to their behaviour when you tolerate XXXXXXXXX when s/he falls off the wagon. KFkairosfocus
January 27, 2013
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KF, with regard to my comment at #27, I will try to be more aware to your sensitivities when I post on your threads in the future. It was not my intention to be disrespectful. Might I ask however that you revise your edit to the contents in such a way as to avoid doing violence to the meaning of it? Allow me to make the following suggestion:
Lol. Especially not. Not when the real story is so $#%& utterly remarkable.
Chance Ratcliff
January 27, 2013
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Mung,
"I think it depends on the pump."
On further reflection this makes perfect sense. It couldn't be the case that every mechanism for charging the gradient uses ATP. However I'm reminded that ATP synthase is itself a proton pump that runs on ATP (it's dual purposed). Isn't evolution grand?Chance Ratcliff
January 27, 2013
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Chance:
So the proton pumps push the protons back across the membrane, to maintain the gradient. I’m not yet sure what powers the pumps. I wonder if it’s ATP.
I think it depends on the pump. Wikipedia:
In this process, the complex translocates four protons across the inner membrane per molecule of oxidized NADH, helping to build the electrochemical potential used to produce ATP.
Oh, and lest we forget. The membrane is also impermeable to ATP. So if we're talking mitochondria, there has to be a channel to get the ATP out of the mitochondrion.Mung
January 27, 2013
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Chance Ratcliff posted this:
There is simply no reason to ascribe creative power to a putative “selective” force when that which needs to be explained, a massively complex system capable of replication with variation, must by necessity precede it.
What is your explanation for the "massively complex system"?timothya
January 27, 2013
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KF, yes, well worth adding that one. Of course, Darwin, et al, could not have imagined the technological sophistication of this protoplasm. There is simply no reason to ascribe creative power to a putative "selective" force when that which needs to be explained, a massively complex system capable of replication with variation, must by necessity precede it.Chance Ratcliff
January 27, 2013
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The second animation has been added to the OP, thanks. KFkairosfocus
January 26, 2013
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Folks: Interesting onward comments and a useful vid. I wonder what Darwin et al would have made of the discovery of a rechargeable battery molecule in the heart of a lot of cell based life manufactured using an enzyme that is to all intents and purposes a complex reversible, electric motor driven rotary process unit. KFkairosfocus
January 26, 2013
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Thanks for those links Mung: Proton Pump, Permeability Barrier, and Solute Movement. Permeability Barrier:
There are four types of carrier-mediated transport systems in procaryotes. The carrier is a protein (or group of proteins) that functions in the passage of a small molecule from one side of a membrane to the other side. A transport system may be a single transmembranous protein that forms a channel that admits passage of a specific solute, or it may be a coordinated system of proteins that binds and sequentially passes a small molecule through the membrane. Transport systems have the property of specificity for the solute transported. Some transport systems transport a single solute with the same specificity and kinetics as an enzyme. Some transport systems will transport (structurally) related molecules, although at reduced efficiency compared to their primary substrate. Most transport systems transport specific sugars, amino acids, anions or cations that are of nutritional value to the bacterium.
The transport proteins use the energy from ATP hydrolysis to power their activity. From Proton Pump:
Proton pumps are protein complexes that move the protons generated during oxidation reactions across the cell membrane. As the protons move through the proton pump, they begin to build up on the outside of the membrane. The protons accumulate on the outside of the membrane creating a concentration gradient. The membrane is not permeable to the charged hydrogen ions, and they cannot diffuse back across the membrane. Instead they must pass through a special channel. The protons move through this special channel which is the enzyme, ATP synthase. This enzyme uses the energy derived from the movement of these protons to convert ADP into ATP. The movement of protons down a concentration gradient provides the energy for ATP synthase to form ATP. This mechanism of producing ATP is called chemiosmosis.
So the proton pumps push the protons back across the membrane, to maintain the gradient. I'm not yet sure what powers the pumps. I wonder if it's ATP.Chance Ratcliff
January 26, 2013
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Lol. Especially not. Not when the real story is so xxxx utterly remarkable. Truth is stranger than ... evolution.Chance Ratcliff
January 26, 2013
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Imagining some simple membrane enclosing some RNAs doesn’t even qualify as good imaginative fiction.
Not even good imaginative science fiction?Mung
January 26, 2013
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Heh. Solute Movement:
The presence of membrane proteins make biological membranes much more permeable to certain solutes than are simple artificial phosophlipid bilayers.
Chance Ratcliff
January 26, 2013
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Cells that had a membrane that could allow for a proton gradient were more likely to replicate than those that didn’t?
That's evolution. It's synonymous with magic. Of course, one must be able to imagine that there existed simpler structures which could also replicate, right on down to some enigmatic and indiscernible self-organization principle. In other words, we know evolution occurred, so we just need to discover the way in which it was brought about through unguided processes. Science is working on it. Much research is being done. :p
So it all comes back to the cell membrane, my favorite topic, haha. Imagine that.
If permease is any indication, the function of the membrane to regulate materials transport is highly dependent on enzymes which perform the task. This would also implicate signalling mechanisms for gene expression. Imagining some simple membrane enclosing some RNAs doesn't even qualify as good imaginative fiction.Chance Ratcliff
January 26, 2013
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Thanks for that. I was just looking at the NDSU channel on Youtube. Particularly, the video for the lac operon in E. coli, which codes for three proteins, one of which, permease, is specifically purposed for binding to the membrane and aiding the importation of lactose. It's really quite remarkable. The expression of the lac operon is inducible by the presence of lactose, which can, in small quantities, enter the cell and bind to a repressor protein on the lac operon, triggering gene expression and the production of the proteins responsible for processing lactose, including the permease, which imports the lactose into the membrane. It's a signalling mechanism, in which the substance to be processed becomes a chemical trigger for the expression of genes which code for the proteins that import and process the lactose.Chance Ratcliff
January 26, 2013
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NDSU Virtual Cell Animation Collection HT: ba77Mung
January 26, 2013
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Yes, my grandfather repaired antique clocks of which I still have a couple that are weight driven. Much the same concepts I think. We're not talking about energy in the matter that makes up the weight as being what provides the energy needed by the clock. It's not "metal energy" or even "stone energy." Once the weight reaches the base of the clock it has to be wound to bring the weight back up. I would think that in order for there to be a proton gradient the protons can't be allowed to just diffuse through the membrane. So at a minimum we need the conditions for a proton gradient and then the means to make use of it. Cells just got lucky in the makeup of their membranes? Cells that had a membrane that could allow for a proton gradient were more likely to replicate than those that didn't? Assuming they could replicate at all without ATP. I guess it's possible that there is diffusion but that it's finely tuned in some way to allow for a gradient. But what are the odds of that? ;) Proton Pump So it all comes back to the cell membrane, my favorite topic, haha. Imagine that.
The cell membrane is the most dynamic structure in the cell. Its main function is as a permeability barrier that regulates the passage of substances into and out of the cell. The plasma membrane is the definitive structure of a cell since it sequesters the molecules of life in the cytoplasm, separating it from the outside environment. The bacterial membrane freely allows passage of water and a few small uncharged molecules (less than molecular weight of 100 daltons), but it does not allow passage of larger molecules or any charged substances except when monitored by proteins in the membrane called transport systems. - Permeability Barrier
Solute MovementMung
January 26, 2013
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