ATP Synthesis
Another place where physicists get chemical energy wrong is in the study of ATP synthesis. Since ATP is about energy, it is studied by biophysicists. If they studied any biology with the physics, they couldn't have gotten it so wrong. They have kinetic energy restoring the chemical energy of ATP. A truism is that kinetic energy can never be converted to biochemical energy.
Biochemical energy is in covalent bonds, which means electrons orbiting the bonded nuclei. The energy is in the motion of electrons. Kinetic energy is in the motion of nuclei. Nothing can be done to nuclei short of a nuclear reaction which will add energy to electrons.
The ionic bonds of inorganic chemistry are different from the covalent bonds of organic chemistry. Ionic bonds are not understood, but they are weak and do not involve electrons orbiting nuclei in a close and strict manner. They are subject to electrochemical influences which organic molecules are not.
The linear motion of electrons (such as copper wires) is a totally different question. Yet the childish rationalizing on this subject includes a lot of reference to batteries claiming that the chemical energy of batteries is derived from the mechanical motion of the generator (or alternator). Batteries are not a form of chemical energy; they are electrical energy. The difference is that chemical energy is in electrons which orbit nuclei, while electrical energy is linearized for flowing through wires, not around nuclei.
Only the radiation of photosynthesis can increase chemical energy in biological systems. All other reactions reduce the amount of chemical energy, as heat is a byproduct of energy transfers.
ATP is the universal energy carrier in biology. It donates chemical energy to biochemical reactions. It gives up its energy by splitting into ADP and inorganic phosphate (Pi). To become reenergized, another source of chemical energy is needed. During respiration, the primary carrier of the energy is hydrogen attached to NAD, which is at a higher energy state than ATP. In fact, three ATPs are usually reenergized from each NADH.
What biologists know about the process is this: NADH feeds a high energy electron into the cytochrome system. An electron flow through three cytochromes energizes three ATP molecules. Biologists do not know exactly what cytochromes do. Biophysicists virtually ignore the cytochromes and concoct an absurd alternative.
The structure of cytochromes provides much evidence of their function. Cytochromes are somewhat circular structures containing a large number of double bonds creating properties much like aromatics, and they have a metal in the center, usually iron and sometimes copper. These characteristics point to a quasi linearization or free motion of electrons (with no mechanical energy involved). Copper and iron seem to linearize or free-up the motion of electrons.
An important thing about cytochromes is that you can give or take a few electrons, at least one. This is what creates the extremely high efficiency of energy transfer. Almost no energy is lost in generating three ATPs. Electrons can be traded in this system. A high energy electron can be fed in, and one of just the right amount of energy can be taken out for energizing an ATP molecule. Biophysicists have a totally unrecognizable method of getting ATP energized.
During respiration, hydrogen ions (protons) are pumped across a membrane into an area where they form an osmotic pressure. They then use that force to turn rotating proteins which control the reactions. The rotating proteins move reactants into place and remove the finished product as ATP.
Biophysicists claim that the high energy electrons are used to create the osmotic pressure of the protons. No such mechanism exists. As protons turn proteins, ATP is said to be energized by "binding force" from the rotating proteins. This says kinetic energy is converted into chemical energy, an impossibility. It also uses as much energy as it transfers, so there can be no increased energy in the resulting ATP.
ATP is commonly used to transport hydrogen ions (protons) across membranes. This is called the hydrogen ion pump. It is used to control pH inside of cells by excreting excess acid (hydrogen ions). It would also be the way in which the osmotic pressure of protons is created for ATP synthesis. It means some ATP is used up creating the concentrated mass of protons called an osmotic gradient.
Therefore, according to the theory of biophysicists, the same amount of energy would be required to create the osmotic gradient as gained in the resulting ATP, and there would be no net gain in the process. It takes the energy equivalent of an ATP molecule to move a proton into place and the energy of the proton to synthesize an ATP molecule.
What really happens would be that an ATP molecule would be used to pump a proton into its gradient, but the proton is then used only to turn the rotating proteins. One proton would turn the proteins through numerous revolution, as very little energy would be lost in keeping the proteins rotating.
The purpose of the rotating proteins is to move reactants into place and out of the way again. Every biochemical reaction would benefit from rotating proteins for moving reactants around. Otherwise, simple diffusion is required for moving reactants, and it would be much slower.
Using rotating proteins is way too demanding for most biochemical reactions, as there are a large number of proteins involved. But it's a mechanism worth the trouble for respiration, because the rate of respiration determines the amount of activity animals can produce and the speed that they can move. When muscles are heavily used, they switch from respiration to fermentation and produce ATP, because respiration cannot keep up. This means respiration is pushed to its limits in animal activity, and rotating proteins are needed to maximize the rate of respiration.
Biologists could not have butchered the subject the way biophysicists did. Biologists (or at least biochemists) account for the amount of energy involved in each reaction. Biophysicists didn't bother. Not only did biophysics have kinetic energy converting into chemical energy, they contrived a new method of transferring energy, which they called "binding force." Such a degree of arrogance and wanton disregard for established scientific knowledge only comes out of physics. It's a mentality that has been nurtured in physics for three hundred years.
Even if the energy of a battery is said to be chemical energy (arbitrary terminology), the energy is not defined by electron orbits around nuclei, as it is with ATP. With ions, the relevant electrons are mobile, where the energy is not determined by defined orbits around nuclei, as it is in biochemistry. With batteries, it is only after these mobile electrons are traveling through wires in a linearized form that the mechanical motion of the generator increases their energy. To then say this represents how energy is added to ATP is absurd. This means mechanical motion cannot increase biochemical energy, even if the linearized motion of electrons in a battery is increased by mechanical motion.
The battery analogy is not the only problem with the ATP analysis of biophysicists. They left out cytochromes. They have binding force of rotating proteins doing what cytochromes do—transferring high energy electrons to ATP. And they have no net gain in ATP—using one molecule of ATP to create the proton gradient for each molecule of ATP energized by the rotating proteins.
Even if biophysicists say the electrons pass through the cytochromes on their way to the rotating proteins (Frauds in science go to great effort to obfuscate rather than explain.), they leave no relevant function for the cytochromes. The source of energy in NADH energizes three ATP molecules. But if all it does is create the proton gradient, it can only energize one ATP molecule.
Respiration only distributes the energy which it gets from NADH. Getting energy out of binding force is not a redistribution process but a transformation process. Transformation means one form of energy is converted into another form. In this case, biophysicists have transformation from biochemical energy (ATP) into mechanical motion (kinetic energy) to turn the rotating proteins, and then the kinetic energy is transformed back into biochemical energy, as binding force supposedly energizes ATP.
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There are two hydrogen atoms and an oxygen atom attached most of the carbon atoms. The greater oxidation of carbohydrates means they are in a lower energy state than hydrocarbons. Heat and pressure cannot increase the energy state of carbohydrates to that of hydrocarbons.