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I know the first law is energy can only be converted from one form to the other, therefore in the breakdown of glucose 40% potential energy is converted to ATP and 60% is converted to thermal and unusable.

Does the second law adhere to the breakdown of glucose? Isn't it just the same as the first?

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I'm not sure what you're asking. The first law states that total energy in a closed system is constant, whereas the second law states that systems tend toward an increase in entropy. I don't understand how your question relates to these topics, but the laws of thermodynamics have yet to be violated, even in biology. – Amory Oct 31 '13 at 2:00
Second law adheres to all spontaneous natural processes, including all biochemical transformations occurring spontaneously. – Satwik Pasani Oct 31 '13 at 2:13
The second law may be states in a number of ways, but to quote Gordon M Barrow "all [statements of the second law] generalize our knowledge that processes tend to go to a state of equilibrium. The second law sums up our experience with equilibria just as the first sums up our experience with energy". The breakdown of glucose is used to drive the ATP = ADP + Pi reaction away from equilibrium in the direction of ATP synthesis, mainly through oxidative phosphorylation. – TomD Oct 31 '13 at 9:26
You may wish to research the famous maxim of Clausius: The energy of the universe is constant. The entropy of the universe tends towards a maximum – TomD Oct 31 '13 at 9:31

The Second Law of Thermodynamics is intimately linked to the thermodynamics of the breakdown of glucose. By "the thermodynamics of the breakdown of glucose," I mean: is the breakdown of glucose spontaneous, is it thermodynamically favorable?

You may have seen the criteria for the thermodynamic favorability of a reaction in terms of Gibbs Free Energy:

$$\Delta G = \Delta H - T\Delta S\leq0$$ That is, for a reaction to be favorable, the change in Gibbs free energy from the initial state (glucose) to the final state (carbon dioxide, water, and energy) must be negative. This equation is valid for systems at constant temperature and pressure, which is assumed to be satisfied in biological systems. According to Wikipedia, $\Delta G$ for the breakdown of glucose is negative, $\Delta G = -2880$ kJ/mol.

However, there is a nice derivation on Wikipedia that the above equation is nothing more than a statement of the second law of thermodynamics, applied to the case of constant temperature and pressure. So in sum, the second law of thermodynamics is the reason that glucose can be broken down in such a way that useful energy is released in the form of ATP, i.e. that the reaction is spontaneous or thermodynamically favorable. Saying that the Gibbs Free Energy of the breakdown products is lower than that of glucose itself is the same as saying that the breakdown of glucose does not decrease the total entropy of the reaction and its environment.

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