Often in a chemical process, the transformation leads to charged particles assuming different positions with regard to one another. A transformation might have occurred so that in the final state an electron has been removed from an atom, or maybe a set of electrons in the substance are occupying a new set of molecular orbitals and now they are very tightly held by a powerfully electronegative atom. To judge the internal energy change in a chemical process, try to get a sense of how the arrangement of charges has changed between the initial and the final state. Has the new arrangement allowed opposite charge to move closer together or like charge to spread out? Either of these particular cases corresponds to an internal energy decrease. Internal energy decrease occurs, for example, when a powerful oxidizing agent gains electron control in a redox reaction. Its powerfully positive nucleus draws the new electrons in tightly. The large electrostatic potential energy decrease for the charges contained in the matter means an internal energy decrease for the system. A central road to understanding chemistry is learning to apply this kind of basic analysis to changes occurring at the atomic, molecular, or intermolecular level.
We hope you have really begun to notice how often we are repeating these basic concepts week by week, changing the context and slowly adding ideas as we proceed through our MCAT course. This is a major theme within the spiraling curriculum. Where is it going? To help you have a sense of where we are heading over the next few months, imagine a mitochondrion, the powerhouse of eukaryotic cells, laid out on your desk. In other words, imagine what a mitochondrion would look like if it were as big as the top of your desk. A mitochondrion is a few thousand or tens of thousands of angstroms long, so the mitochondrion can be only a few thousand chemical bonds long. If it were laid out on your desk, you would just be able to make out the individual atoms of the mitochondrion like grains of sand.
Think about what goes on in a mitochondrion. Picture the plasma membranes of its outer and inner membranes. Picture the cytochrome system on the inner membrane. Imagine you can see the contents of the matrix (water, ATP, NADH, the intermediates of the citric acid cycle), and imagine the proton gradient between the inner and outer compartment. What you see within the aqueous solution environment is a very complex system of electric charges with chemical structure.
Imagine step by step, pulling the atoms apart of the molecules of glycolysis or the citric acid cycle and letting them fall together into subsequent forms in the pathways of oxidative metabolism. What is happening to energy? Imagine watching chemiosmosis across the inner membrane as if you were watching water fall through the hydroelectric power station, but instead of gravitational potential energy doing the work of pumping protons, within the mitochondrion, the potential energy decrease is not gravitational but electrostatic. Picture oxygen down at the end of the electron transport chain, electron greedy, with its thin electron cloud barely shielding its powerful nucleus, pulling the electrons towards itself, driving the proton pumps.