8.1 Principles of bioenergetics and enzyme kinetics

Thermodynamics and Bioenergetics

Every cellular process requires energy, and thermodynamics provides the rules governing how that energy moves and transforms. Understanding these principles is essential because they explain why reactions happen spontaneously, why cells need ATP, and why metabolism is organized the way it is.

Laws of thermodynamics in biology

The First Law of Thermodynamics states that energy cannot be created or destroyed, only converted from one form to another. In living systems, energy transformations happen constantly: chemical bond energy becomes mechanical work during muscle contraction, or gets released as heat during metabolic reactions. The total energy in the system plus surroundings stays the same.

The Second Law of Thermodynamics states that the total entropy (disorder) of the universe always increases over time.

• Spontaneous processes naturally increase entropy (e.g., diffusion of molecules from high to low concentration, heat flowing from hot to cold).
• Living organisms appear to violate this law because they maintain highly ordered internal states. They don't actually break it, though. Cells consume energy and increase entropy in their surroundings by expelling heat and waste products. The net entropy of the universe still goes up.

Gibbs Free Energy ($\Delta G$) ties these laws together and tells you whether a reaction will proceed spontaneously:

$\Delta G = \Delta H - T\Delta S$

where $\Delta H$ is the change in enthalpy (heat content), $T$ is temperature in Kelvin, and $\Delta S$ is the change in entropy.

• Negative $\Delta G$ → exergonic reaction, spontaneous, releases free energy (e.g., ATP hydrolysis: $\Delta G \approx -30.5 \text{ kJ/mol}$)
• Positive $\Delta G$ → endergonic reaction, non-spontaneous, requires energy input (e.g., ATP synthesis, building macromolecules)

A common point of confusion: "spontaneous" doesn't mean "fast." It just means the reaction is thermodynamically favorable. Many spontaneous reactions are extremely slow without a catalyst.

Role of ATP in cellular energy

Adenosine triphosphate (ATP) is the primary energy currency of the cell. Structurally, it consists of an adenine base, a ribose sugar, and three phosphate groups linked by phosphoanhydride bonds.

ATP hydrolysis is the exergonic reaction that releases usable energy:

$\text{ATP} + \text{H}_2\text{O} \rightarrow \text{ADP} + \text{P}_i \quad (\Delta G \approx -30.5 \text{ kJ/mol})$

The bond between the second and third phosphate groups is broken, producing ADP (adenosine diphosphate) and inorganic phosphate ($\text{P}_i$). This released energy drives endergonic cellular processes like biosynthesis, active transport, and muscle contraction.

ATP synthesis is the reverse: an endergonic reaction that regenerates ATP from ADP and $\text{P}_i$. The energy to drive this comes from substrate-level phosphorylation (in glycolysis and the citric acid cycle) or oxidative phosphorylation (at the electron transport chain).

The key concept here is energy coupling. ATP acts as an intermediary that links energy-releasing catabolic reactions to energy-requiring anabolic reactions. Catabolic pathways break down fuel molecules and capture some of that energy as ATP. Then ATP hydrolysis provides the energy to power endergonic processes. Without this coupling mechanism, most biosynthetic reactions in the cell simply wouldn't proceed.

Enzyme Kinetics

Enzymes are biological catalysts, mostly proteins, that accelerate reactions by lowering the activation energy (the energy barrier that must be overcome for a reaction to proceed). They don't change the $\Delta G$ of a reaction or shift its equilibrium. They just make it reach equilibrium faster.

Factors affecting enzyme activity

Substrate concentration is described by the Michaelis-Menten equation:

$v = \frac{V_{max}[S]}{K_m + [S]}$

where $v$ is the reaction velocity, $[S]$ is substrate concentration, $V_{max}$ is the maximum velocity, and $K_m$ is the Michaelis constant.

Two things to understand about this equation:

1. At low $[S]$, the reaction rate increases nearly linearly as you add more substrate. At high $[S]$, the enzyme becomes saturated and the rate plateaus at $V_{max}$.
2. $K_m$ is the substrate concentration at which $v = \frac{1}{2}V_{max}$. A low $K_m$ means the enzyme reaches half-max velocity at a low substrate concentration, indicating high affinity for its substrate. A high $K_m$ means lower affinity.

Temperature generally increases reaction rate (molecules move faster, collisions increase) up to an optimal temperature. Beyond that optimum, the enzyme denatures: its protein structure unfolds, the active site loses its shape, and catalytic function drops sharply. For most human enzymes, the optimum is around 37°C.

pH affects the ionization state of amino acid residues in and around the active site. Each enzyme has an optimal pH range. For example, pepsin in the stomach works best near pH 2, while trypsin in the small intestine functions optimally near pH 8. Moving away from the optimum disrupts charge distribution and active site geometry, reducing activity.

Enzyme concentration determines the reaction rate when substrate is abundant (not limiting). More enzyme molecules mean more active sites available, so the reaction proceeds faster.

Competitive vs. noncompetitive enzyme inhibition

Competitive inhibition occurs when an inhibitor molecule resembles the substrate and binds directly to the enzyme's active site, blocking substrate access.

• The effect on kinetics: apparent $K_m$ increases (the enzyme appears to have lower affinity for its substrate), but $V_{max}$ stays the same. Why? If you add enough substrate, it will eventually outcompete the inhibitor for active site binding.
• Classic example: malonate inhibits succinate dehydrogenase because malonate's structure closely resembles the normal substrate, succinate. Malonate occupies the active site but can't be converted to product.

Noncompetitive inhibition occurs when an inhibitor binds to an allosteric site (a location distinct from the active site), changing the enzyme's shape and reducing its catalytic ability.

• The effect on kinetics: $V_{max}$ decreases because some fraction of enzyme molecules are rendered inactive, but $K_m$ remains unchanged. The inhibitor doesn't interfere with substrate binding, so the enzyme's affinity for substrate is unaffected.
• Increasing substrate concentration cannot overcome noncompetitive inhibition, which is a major distinction from competitive inhibition.

Noncompetitive inhibition actually has two subtypes:

1. Pure noncompetitive: the inhibitor binds with equal affinity to the free enzyme and the enzyme-substrate complex. Only $V_{max}$ changes. Examples include heavy metal ions (like mercury or lead) and cyanide, which binds to cytochrome c oxidase.
2. Mixed inhibition: the inhibitor binds to both the free enzyme and the enzyme-substrate complex, but with different affinities. This changes both $V_{max}$ and $K_m$. Some drugs and pesticides act as mixed inhibitors.