thermodynamics

Metabolism is the sum of all anabolic and catabolic reactions in a cell, connected in a network of reaction pathways.

Anabolic reactions synthesize or 'build' molecules with more bonds, making higher free energy products; they also use or store energy (endergonic), reduce entropy, and are non-spontaneous.

Catabolic reactions degrade or 'break' molecules to make lower free energy products with fewer bonds; they also increase entropy and release energy (exergonic), and are spontaneous.

The First and Second Laws of Thermodynamics state that energy is transformed in many ways, but always at cost of energy lost through entropy that is not available to do work. Free energy (G) is chemical energy available to do work and is expressed as the difference between enthalpy (total energy) and entropy.

Any reaction involves a change in free energy, $\Delta G$, between reactants and products. The direction of change in free energy tells if it is positive or negative $\Delta G$ (anabolic or catabolic).

Enzymes are proteins that reduce the activation energy of a reaction.

Enzyme specificity and function are the result of the structure (shape) of the protein.

Substrates interact with enzymes at the active site, forming an enzyme-substrate complex with a close interaction through induced fit.

Anabolic reactions use or store energy (endergonic), while catabolic reactions release energy (exergonic).

Anabolic reactions reduce entropy and are non-spontaneous, while catabolic reactions increase entropy and are spontaneous.

Allosteric effectors bind to a site other than the active site (called the allosteric site) and alter the shape of the enzyme protein to either inhibit or activate its function.

Metabolic pathways can be regulated at different steps depending on the demands of the cell, allowing the cell to fine-tune its metabolism.

Negative feedback loops use the product of a metabolic pathway to inhibit an enzyme at the beginning of the pathway, providing a way to regulate pathway activity in response to the cell's needs.

Positive $\Delta$G reactions are accomplished through reaction coupling, which combines a positive $\Delta$G reaction with a negative $\Delta$G reaction (such as ATP hydrolysis) to give a new net negative $\Delta$G for the combined reactions. This allows the cell to harness the energy released from the negative $\Delta$G reaction to drive the positive $\Delta$G reaction.

The hydrolysis of ATP, yielding a $\Delta$G = -7.3 kcal/mole, is commonly used to generate phosphorylated intermediate molecules of higher energy. ATP is continuously used and regenerated from ADP + P$_i$ in the cell's metabolism.

Redox reactions transfer electrons between molecules, with oxidation being the loss of electrons and reduction being the gain of electrons. NADH (or NADPH) is a commonly used high-energy electron carrier in metabolism that captures high-energy electrons from organic molecules and holds them for later use when the energy from those electrons can be extracted through an electron transport chain.

The first law of thermodynamics states that energy can be transformed but not created or destroyed. The second law states that the entropy (disorder) of an isolated system not in equilibrium will tend to increase over time, approaching a maximum value at equilibrium. These laws govern the energy transformations and changes in entropy that occur in cellular processes.

The free energy ($\Delta$G) of a reaction is determined by the changes in enthalpy ($\Delta$H) and entropy ($\Delta$S) according to the equation $\Delta$G = $\Delta$H - T$\Delta$S. Reactions with a negative $\Delta$G are spontaneous, while those with a positive $\Delta$G are non-spontaneous. Enzymes help drive positive $\Delta$G reactions by lowering the activation energy barrier.

Anabolic reactions are biosynthetic, building larger molecules from smaller ones, and have a positive $\Delta$G, decreasing entropy, are non-spontaneous, and are endergonic. Catabolic reactions are degradative, breaking down larger molecules into smaller ones, and have a negative $\Delta$G, increasing entropy, are spontaneous, and are exergonic.

Enzymes lower the activation energy barrier of reactions, allowing negative $\Delta$G reactions to occur more readily. Enzyme structure, with an active site that binds substrates, is key to their catalytic function. Enzymes can be regulated allosterically, where effector molecules bind to sites other than the active site and alter the enzyme's shape to inhibit or activate it, or through covalent modification like phosphorylation.