Energy in chemical reactions
Chemical reactions involve a redistribution of energy within the reacting chemicals and with their environment. So, like it or not, we need to develop some models that can help us to describe where energy is in a system (perhaps how it is "stored"/distributed) and how it can be moved around in a reaction. The models we develop will not be overly detailed in the sense that they would satisfy a hard-core chemist or physicist with their level of technical detail, but we expect that they should still be technically correct and not form incorrect mental models that will make it difficult to understand the "refinements" later.
In this respect, one of the key concepts to understand is that we are going to think about energy being transferred between parts of a system rather than referring thinking too much about it as being transformed. The distinction between "transfer" and "transform" is important because the latter gives the impression that energy is a property that exists in different forms, that it gets reshaped somehow. The common use of the term "transform" in relation to energy is understandable as different phenomena associated with the concept of energy physically "look" different to us. However, one potential problem with using the "transform" language is that it is sometimes difficult to reconcile with the idea that energy is being conserved (according to the first law of thermodynamics) if it is constantly changing form. How can the entity of energy be conserved if after a transformation it is no longer the same thing (e.g. transformed)? Moreover, the second law of thermodynamics tells us that no transformation conserves all energy in a system. If energy is getting "transformed," how can it be conserved and still be consistent with the second law of thermodynamics?
So, instead, we are going to approach this issue by transferring and storing energy between different parts of a system and thus think about energy as a property that can get redistributed. That'll hopefully make the accounting of energy easier. Not that the energy "transfer" idea is, of course, completely consistent and compatible with terms like "potential energy" and "kinetic energy", as these are useful for describing how the energy is distributed between the motion of matter and the various fields (e.g. electric, gravational, etc.) in a system.
If we are going to think about transferring energy from one part of a system to another, we also need to be careful about NOT treating energy like a substance that moves like a fluid or "thing." Rather, we need to appreciate energy simply as a property of a system that can be measured and reorganized but that is neither a "thing" nor something that is at one time in one form then later in another.
Since we will often be dealing with transformations of biomolecules, we can start by thinking about where energy can be found/stored in these systems. We'll start with a couple of ideas and add more to them later.
Let us propose that one place that energy can be stored is in the motion of matter. For brevity, we'll give the energy stored in motion a name: kinetic energy. Molecules in biology are in constant motion and therefore have a certain amount of kinetic energy (energy stored in motion) associated with them.
Let us also propose that there is a certain amount of energy stored in the biomolecules themselves and that the amount of energy stored in those molecules is associated with the types and numbers of atoms in the molecules and their organization (the number and types of bonds between them). The discussion of exactly where the energy is stored in the molecules is beyond the scope of this class, but we can approximate it by suggesting that a good proxy is in the bonds. Different types of bonds may be associated with storing different amounts of energy. In some contexts, this type of energy storage could be labeled potential energy or chemical energy. With this view, one of the things that happens during the making and breaking of bonds in a chemical reaction is that the energy is transferred about the system into different types of bonds. In the context of an Energy Story, one could theoretically count the amount of energy stored in the bonds and motion of the reactants and the energy stored in the bonds and energy of the products.
In some cases, you might find that when you add up the energy stored in the products and the energy stored in the reactants that these sums are not equal. If the energy in the reactants is greater than that in the products, where did this energy go? It had to get transferred to something else. Some will certainly have moved into other parts of the system, stored in the motion of other molecules (warming the environment) or perhaps in the energy associated with photons of light. One good, real-life example is the chemical reaction between wood and oxygen (reactants) and it's conversion to carbon dioxide and water (products). At the beginning, the energy in the system is largely in the molecular bonds of oxygen and the wood (reactants). There is still energy left in the carbon dioxide and water (products) but less than at the beginning. We all appreciate that some of that energy was transferred to the energy in light and heat. This reaction where energy is transferred to the environment is termed exothermic. By contrast, in some reactions, energy will transfer in from the environment. These reactions are endothermic.
The transfer of energy in or out of the reaction from the environment is NOT the only thing that determines whether a reaction will be spontaneous or not. We'll discuss that soon. For the moment, it is important to get comfortable with the idea that energy can be transferred among different components of a system during a reaction and that you should be able to envision tracking it.