Energy, Thermodynamics and ATP

• Energy is the capacity to do work. Kinetic energy is energy of motion (moving molecules, flowing ions, heat); potential energy is stored energy, including the chemical energy held in the arrangement of atoms and electrons in molecules such as glucose.
• First law of thermodynamics — energy cannot be created or destroyed, only transferred or transformed. A plant does not make energy; it converts light energy into chemical energy. You do not make energy either; you convert the chemical energy of food into ATP, motion and heat.
• Second law of thermodynamics — every energy transfer or transformation increases the entropy (disorder, or spread-out-ness of energy) of the universe. In practice, some energy is always lost as heat, a form too dispersed to do useful work in a cell. No transformation is 100% efficient.
• Open system — a cell exchanges energy and matter with its surroundings. That is how it can stay highly ordered without breaking the second law.
• Metabolism — the sum of all chemical reactions in an organism, organized into metabolic pathways in which the product of one enzyme-catalyzed step is the substrate of the next. Catabolic pathways break complex molecules down and release energy (respiration breaks glucose into ${\text{CO}}_2$ and water). Anabolic pathways build complex molecules and consume energy (making proteins from amino acids, or glucose from ${\text{CO}}_2$). Catabolism pays for anabolism, and ATP is the go-between.

Free energy: will a reaction happen on its own? Chemists combine enthalpy (heat content, $H$) and entropy ($S$) into one quantity, Gibbs free energy ($G$): the portion of a system's energy that is available to do work at constant temperature and pressure. What matters for a reaction is the change in free energy, $\Delta G$. If $\Delta G$ is negative, the products have less free energy than the reactants and the reaction is spontaneous: it can proceed without a continuous energy input. If $\Delta G$ is positive, the reaction is non-spontaneous and will happen only if energy is supplied. Note that spontaneous does not mean fast. Glucose in a sugar bowl sits unchanged for years even though its oxidation has $\Delta G\approx -2870\text{ kJ/mol}$, because the reaction must first get over its activation energy. In cells, enzymes lower the activation energy so that spontaneous reactions happen at useful rates.

Adenosine triphosphate (ATP) is a nucleotide made of three parts: the nitrogenous base adenine, the five-carbon sugar ribose (adenine plus ribose is called adenosine) and a chain of three phosphate groups. The three phosphates each carry negative charge and sit close together, so they repel one another; the molecule is like a compressed spring. When the terminal phosphate is removed by hydrolysis, the products, ADP (adenosine diphosphate) and inorganic phosphate (${\text{P}}_{\text{i}}$), are more stable than ATP: there is less charge repulsion, and free phosphate is stabilized by resonance and by water molecules around it. The energy released comes from that overall gain in stability, not from the bond itself; breaking any bond always requires energy.

Energy coupling is the use of an exergonic reaction to drive an endergonic one. Cells rarely just hydrolyze ATP and let the energy escape as heat. Instead an enzyme transfers ATP's terminal phosphate to a reactant (phosphorylation), producing a phosphorylated intermediate that is less stable and more reactive than the original molecule. For example, joining glutamic acid and ammonia to make the amino acid glutamine has $\Delta G=+14.2\text{ kJ/mol}$, so it will not happen by itself. The enzyme first phosphorylates glutamic acid using ATP; the intermediate then reacts with ammonia. The overall change is $+14.2+(-30.5)=-16.3\text{ kJ/mol}\text{,}$ so the coupled process is spontaneous. Because ATP is used and remade so quickly, a resting human holds only about 250 g of ATP at any moment yet recycles roughly their own body mass of ATP every day.

Most of the energy in food is harvested by moving electrons. In a redox (reduction–oxidation) reaction, oxidation is loss of electrons and reduction is gain of electrons: OIL RIG. The two always happen together: one substance (the reducing agent) is oxidized as another (the oxidizing agent) is reduced. In biology, electrons usually travel with protons as whole hydrogen atoms, so a useful shortcut is: losing H atoms = oxidation; gaining H atoms = reduction. In ${\text{C}}_6{\text{H}}_{12}{\text{O}}_6+6{\text{O}}_2\to 6{\text{CO}}_2+6{\text{H}}_2\text{O}\text{,}$ glucose loses its hydrogens (it is oxidized) and oxygen gains them (it is reduced to water). Electrons moving toward very electronegative oxygen release energy, just as a ball releases energy rolling downhill. Enzymes called dehydrogenases remove hydrogen atoms from food molecules and hand them to carrier molecules, which ferry the electrons (and their energy) to where they are needed.