Life Science 7A - Enzymes & Energy (Week 2b)

What is kinetic energy versus potential energy?

Kinetic energy is energy of motion. Potential energy is stored energy due to position, arrangement, or chemical structure.

State the first law of thermodynamics and apply it to a cell.

Energy is conserved: it is transferred or transformed, not created or destroyed. Cells transform energy from food or light into chemical energy and other forms.

State the second law of thermodynamics.

Every energy transfer increases the total entropy of the universe; usable energy becomes more dispersed. A cell can maintain internal order only by taking in energy and releasing heat/waste.

Define free-energy change (ΔG).

ΔG indicates whether a process is thermodynamically favorable under the specified conditions. ΔG < 0 is exergonic; ΔG > 0 is endergonic; ΔG = 0 is equilibrium.

What are enthalpy (H) and entropy (S)?

Enthalpy relates to heat content at constant pressure; entropy describes how energy/matter is dispersed and the number of accessible microscopic arrangements. Their changes help determine ΔG.

How are ΔG, ΔH, ΔS, and temperature related?

ΔG = ΔH − TΔS, where T is absolute temperature in kelvin. Use consistent energy units. The signs of ΔH and ΔS and the temperature determine the sign of ΔG.

A reaction has ΔH < 0 and ΔS > 0. Is it exergonic or endergonic?

ΔG = ΔH − TΔS is negative at all positive temperatures under the simplified assumptions, so it is exergonic.

A reaction has ΔH > 0 and ΔS < 0. Is it exergonic or endergonic?

Both terms make ΔG positive, so it is endergonic at all positive temperatures under the simplified assumptions.

A reaction has ΔH < 0 and ΔS < 0. How does temperature affect favorability?

It is favored at lower temperatures when the negative ΔH dominates; at high temperatures, subtracting TΔS adds a positive term and may make ΔG positive.

A reaction has ΔH > 0 and ΔS > 0. How does temperature affect favorability?

It may be unfavorable at low temperatures but favorable at high temperatures because the −TΔS term becomes more negative as temperature rises.

What does exergonic mean? Does it mean the reaction happens quickly?

Exergonic means ΔG is negative and the reaction is thermodynamically favorable. It does not mean fast; kinetics and activation energy determine rate.

What does endergonic mean?

Endergonic means ΔG is positive for the reaction as written, so it requires an energy input or coupling to a sufficiently favorable process.

How can an endergonic reaction be coupled to an exergonic reaction?

The reactions are linked so they proceed together, and their ΔG values add. The combined process is favorable when the total ΔG is negative.

Reaction A has ΔG = +8 kJ/mol and reaction B has ΔG = −12 kJ/mol. Can they drive a coupled process?

Yes, if they are genuinely coupled: total ΔG = +8 + (−12) = −4 kJ/mol, so the combined process is exergonic.

Reaction A has ΔG = +10 kJ/mol and reaction B has ΔG = −6 kJ/mol. Is their coupled total favorable?

No. Total ΔG = +4 kJ/mol, so the combined process remains endergonic as written.

What is the difference between thermodynamics and kinetics?

Thermodynamics asks whether a process is favorable and where equilibrium lies. Kinetics asks how fast it proceeds and depends strongly on the activation-energy barrier.

What is activation energy?

The energy barrier reactants must overcome to reach the transition state. A large activation energy generally corresponds to a slower reaction at a given temperature.

What is a transition state?

A brief, high-energy arrangement of atoms near the top of the reaction pathway, where bonds are partly broken and/or formed.

What are a substrate and an active site?

A substrate is the reactant an enzyme acts on. The active site is the enzyme region that binds substrate and facilitates the reaction.

How do enzymes speed up reactions?

They lower activation energy by stabilizing the transition state and orienting substrates or providing a favorable chemical environment. They do not change the reaction's ΔG or equilibrium position.

Can an enzyme make an endergonic reaction exergonic?

No. An enzyme changes reaction rate by lowering activation energy, not the ΔG. An endergonic reaction still needs coupling or another change in conditions to be favorable.

How would an enzyme change a free-energy-versus-reaction-progress graph?

It lowers the activation-energy peak for the catalyzed pathway but leaves the reactant and product free-energy levels, and therefore ΔG, unchanged.

What is the difference between enzyme activation and inhibition?

An activator increases enzyme activity; an inhibitor decreases it. Either may change substrate binding, catalytic steps, or enzyme shape.

How can a competitive inhibitor affect enzyme kinetics?

It competes with substrate for the active site. Its effect can often be reduced by increasing substrate concentration; in a simple model, apparent Km increases while Vmax remains unchanged.

How can a noncompetitive inhibitor affect enzyme kinetics in the simplified pure case?

It reduces the amount of functional enzyme without preventing substrate binding; Vmax decreases while Km remains unchanged in the ideal pure noncompetitive model. Real allosteric inhibitors can have more complex effects.

What is allosteric regulation?

A regulatory molecule binds at a site other than the active site and changes enzyme shape or dynamics, increasing or decreasing activity.

What is feedback inhibition in a metabolic pathway?

A pathway's end product inhibits an enzyme earlier in the pathway, preventing unnecessary production and conserving resources.

How can an inhibitor's effect be inferred from activity-versus-substrate data?

Compare curves: a lower plateau suggests reduced Vmax; a right-shift with the same plateau suggests increased apparent Km, as in simple competitive inhibition. Interpret using the experimental model and conditions.

How do temperature changes affect enzyme activity?

Activity often rises with temperature up to an optimum because molecular collisions increase. Above the optimum, structure may destabilize or denature, causing activity to fall.

How do pH changes affect enzyme activity?

pH changes the protonation and charge of amino-acid side chains and sometimes the substrate, altering active-site interactions and protein structure. Each enzyme has a suitable pH range.

What does pH measure, and how does it relate to H+ concentration?

pH = −log10[H+]. Lower pH means higher hydrogen-ion concentration; a one-unit decrease in pH means 10 times more H+.

A solution changes from pH 7 to pH 5. How does [H+] change?

It increases by 100-fold because a two-unit decrease in pH corresponds to 10² times more H+.

What does a reversible reaction's ΔG depend on in a cell?

It depends on the standard free-energy change and the actual concentrations of reactants and products: ΔG = ΔG°′ + RT ln Q. Changing concentrations can change ΔG and even reverse net direction.

Why might a reaction that is unfavorable under standard conditions proceed in a cell?

Actual cellular concentrations may make ΔG negative, or the reaction may be coupled to an exergonic reaction such as ATP hydrolysis.

How do anabolic and catabolic pathways relate to free energy?

Anabolism generally requires energy input and builds complex molecules; catabolism often releases free energy by breaking down molecules. Cells couple catabolic energy release to ATP production and anabolic work.

How do you read a free-energy diagram to find ΔG?

Compare product and reactant free-energy levels: ΔG = Gproducts − Greactants. Products lower than reactants means ΔG < 0; products higher means ΔG > 0.

On a free-energy diagram, what does a taller peak mean?

A larger activation-energy barrier, which generally means a slower reaction under the same conditions—not necessarily a different ΔG.

Two reactions have the same ΔG but different activation-energy barriers. Which is faster?

Usually the one with the lower activation-energy barrier, assuming comparable conditions and mechanisms.

How can a drug alter an enzyme's activity?

It may bind the active site, bind an allosteric site, change enzyme conformation, or alter the enzyme's environment. Predict its effect from binding location, substrate concentration, and activity data rather than assuming every drug is an inhibitor.

A metabolic pathway's final product accumulates. What might happen if it acts as a feedback inhibitor?

It can inhibit an early pathway enzyme, decreasing pathway flux and preventing further overproduction. When product levels fall, inhibition may be relieved.

In an enzyme activity graph, rate rises with substrate concentration and then levels off. What does this mean?

At low substrate concentration, adding substrate increases rate. At high concentration, most active sites are occupied and the enzyme approaches Vmax.

What is Vmax, and what is Km in a simple Michaelis–Menten model?

Vmax is the maximum rate when enzyme is saturated with substrate. Km is the substrate concentration at half Vmax; a lower Km often indicates higher apparent substrate affinity in the simple model, but it is not always a direct binding-affinity measure.

A drug lowers the maximum rate even when substrate is abundant. What is a reasonable interpretation?

The drug may reduce the amount of active enzyme or impair catalytic function, consistent with a decrease in Vmax. More data are needed to identify the exact mechanism.

A graph shows the same product and reactant energy levels with and without enzyme, but a lower peak with enzyme. What conclusion follows?

The enzyme lowers activation energy and speeds the reaction without changing ΔG or the equilibrium position.

A reaction has ΔG = 0. What does that imply about net direction?

The system is at equilibrium under those conditions: forward and reverse rates are equal, so there is no net change, although both directions continue.

How should you approach an unfamiliar biological model on an exam?

Identify the parts and what each represents; note the direction of arrows and any gradients; identify what is held constant versus changed; apply the relevant rule; then predict the outcome and explain the mechanism. Do not assume the drawing is to scale or includes every detail.