As we will see, biological systems are extremely complex; both their overall structural elements and many of their molecular components (including DNA) are the products of thermodynamically unfavorable processes and reactions. How do these reactions take place in living systems? The answer comes from the coupling of thermodynamically favorable reactions to a thermodynamically unfavorable reactions. This is a type of work, although not in the standard macroscopic physics model of work (w) = force x distance. In the case of (chemical) reaction coupling, the work involved drives thermodynamically unfavorable reactions, typically the synthesis of large and complex molecules and macromolecules (that is, very large molecules). Here we will consider the thermodynamics of these processes.
Thinking about energy: Thermodynamics is at its core about energy and changes in energy. This leads to the non-trivial question, what is energy? Energy comes in many forms. There is energy associated with the movement and vibrations of objects with mass. At the atomic and molecular level there is energy associated with the (quantum) state of electrons. There is energy associated with fields that depends upon an object’s nature (for example its mass or electrical charge) and its position within the field. There is the energy associated with electromagnetic radiation, the most familiar form is visible light, but electromagnetic radiation extends from microwaves to X-rays. Finally, there is the energy that is present in the very nature of matter, such energy is described by the equation:
e (energy) = m (mass) x c2 (c = speed of light)
To illustrate this principle, we can call on our day-to-day experiences. Energy can be used to make something move. Imagine a system of a box sitting on a rough floor. You shove the box so that it moves and then you stop pushing – the box travels a short distance and then stops. The first law of thermodynamics is that the total energy in a system is constant. So the question is where has the energy gone? One answer might be that the energy was destroyed. This is wrong. Careful observations lead us to deduce that the energy still exists but that it has been transformed. One obvious change is the transformation of energy from a mechanical force to some other form, so what are those other forms? It is unlikely that the mass of the box has increased, so we have to look at more subtle forms – the most likely is heat. The friction generated by moving the box represents an increase in the movements of the molecules of the box and the floor over which the box moved. Through collisions and vibrations, this energy will, over time, be distributed throughout the system. This thermal motion can be seen in what is known as Brownian motion. In 1905, Albert Einstein explained Brownian motion in terms of the existence, size, and movements of molecules148.
In the system we have been considering, the concentrated energy used to move the box has been spread out throughout the system. While one could use the push to move something (to work), the diffuse thermoenergy cannot be used to do work. While the total amount of energy is conserved, its ability to do things has been decrease (almost abolished). This involves the concept of entropy, which we will turn to next.
148 Albert Einstein: The Size and Existence of Atoms http://youtu.be/nrUBPO6zZ40