Monday, March 29, 2010

Thermodynamics Take I: The Basics, Free Energy, Entropy, Enthalpy

Today’s post will be a slight departure from cell biology and genetics and will focus, instead, of some of the basics of biochemistry.  It is true that I disliked biochemistry, and that’s putting it lightly, but it’s still something that is important (how important is another question) to understand.  I took a few days off from updating but I return with more review fun.  This set of posts will include a number of equations that I will summarize after all of the thermodynamics notes have been posted.  Also, the illustrations for these posts will be simplistic, but if you have some better ideas of how to illustrate thermodynamics, I'd like to know because I'm coming up with nothing...
Thermodynamics is the study of the relationships between energy and chemical processes.  This energy can come in two distinct forms, namely potential and kinetic energy.  Most of use probably learned in high school physics class that potential energy is stored energy, as in a ball that you hold above the ground  has the potential to fall to the ground and therefore has stored / potential energy.  Kinetic energy is the energy of motion, which you probably learned as the energy of a moving ball during that same physics lesson.  In terms of biology, however, potential energy has deeper meaning (it’s more than balls), such as stored energy in chemical bonds (ATP), concentration gradients, and electrical potential via ion gradients.  Kinetic energy in terms of biology can come in the form of heat energy due to atomic motion (just as we learned in physics) or in radiant energy, including electromagnetic radiation (light).

The First Law of Thermodynamics: energy is conserved
Sure, there are about a billion ways of rephrasing the first law of thermodynamics, but, put simply, energy is conserved.  In terms of chemical reactions, there is what is called the free energy (Gibbs free energy), or G.  Gibbs free energy is the work that is available to do work.  In a reaction or process, the change in free energy is calculated as:

ΔG = ΣGproducts - ΣGreactants

When ΔG is negative (ΔG < 0), the reaction or physical process is spontaneous, though that is not to say that it will happen quickly.  A negative ΔG value simply means that energy need not be added to the system for it to react.  A negative ΔG value is considered exergonic, while a positive ΔG value is endergonic.  A positive value for ΔG means that energy must be added to the system for the process.  At equilibrium in a reaction, ΔG is zero, meaning that neither the amount of products or reactants is changing: no energy is consumed or released.

Free energy, G, can be further broken down into enthalpic, H, and entropic, S, components. 

Enthalpy is a measure of the internal energy of a system in kcal/mol (or kJ/mol).  At constant temperature and pressure, enthalpy is equivalent to the heat absorbed or released and

 ΔH = ΣHproducts - ΣHreactants

Endothermic reactions are those that absorb heat (ΔH > 0); exothermic reactions release heat energy (ΔH < 0).  Adding heat will affect the equilibrium of the reaction (whether it favors products or reactants).  Because endothermic reactions require energy for the reaction to occur, raising the temperature favors the reactants forming products.  Conversely, adding heat to an exothermic reaction will favor the formation of reactants from products because, in fact, heat is a product of the reaction.

Entropy is a measure of the randomness of a system.  While many would dispute this definition, for our purposes it works (and this write-up is not about semantics).  Entropy is measured in cal/mol K (J/mol K).  As you would expect,

ΔS = ΣSproducts - ΣSreactants

The second law of thermodynamics states that entropy of a system and its surroundings always increases in a reaction.  The disorder will tend to a maximum and ΔS > 0.  Therefore, if we want a more ordered system (such as in the polymerization of DNA from dNTPs), we have to add energy.  This may seem counterintuitive to some degree, but one must remember that we are considering the entropy of both the system and its surroundings:

ΔSuniverse = ΔSsystem + ΔSsurroundings > 0


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