Reading Enzyme Graphs

Analyse means identify the components and the relationships between them. For a graph question that means describing the shape in sections — where it rises, where it turns, where it falls or levels — and giving the molecular reason for each section.

6 marks, three graphs. Two marks each: describe the shape in its sections, then explain each section. Never describe all three and then explain all three.

The temperature graph rises steadily to a peak at the optimum, approximately 37 degrees Celsius for a human enzyme, then falls steeply to zero over a much narrower range of temperature than it took to rise. The curve is therefore asymmetric, with a gradual rise and an abrupt fall.

Below the optimum, raising the temperature increases the kinetic energy of enzyme and substrate molecules, so they collide more frequently and with more energy, and a greater proportion of collisions are successful, raising the rate. Above the optimum, the additional thermal energy begins to break the hydrogen bonds and other weak interactions that hold the enzyme in its three-dimensional shape; the active site is progressively distorted, substrate can no longer bind, and the enzyme is denatured. Because denaturation is permanent, the rate falls to zero and does not recover on cooling.

The pH graph is a roughly symmetrical bell curve, peaking sharply at the enzyme’s optimum pH and falling away on both sides. The peak occurs where the charges on the amino acid residues in the active site give it the shape and charge distribution that best bind the substrate. Moving away from the optimum in either direction alters the ionisation of those residues and of the substrate, disrupting the ionic and hydrogen bonds maintaining the active site’s shape, so binding becomes less effective and the rate falls; at extremes of pH the enzyme denatures.

The substrate concentration graph rises steeply and approximately linearly at low concentrations, then curves and levels off at a plateau, after which further increases in substrate produce no increase in rate. At low concentrations substrate availability limits the rate, because many active sites are unoccupied at any moment, so adding substrate increases the frequency of successful collisions proportionally. At the plateau every active site is occupied as soon as it becomes free, so the enzyme is saturated, and the rate is now limited by the number of enzyme molecules and by how quickly each completes its catalytic cycle rather than by substrate supply.

The three graphs differ because the limiting factor differs. Temperature and pH act on the enzyme’s structure, so their curves have a genuine optimum and activity is lost beyond it, permanently in the case of denaturation. Substrate concentration acts on the frequency of collision alone and never damages the enzyme, so its curve has no optimum and no downturn — only a ceiling imposed by the amount of enzyme present.

This is a single explain question about two shapes, so the answer must give a cause for each and then a reason they differ. Describing the shapes is the premise of the question, not the answer to it.

5 marks. Two for why temperature is asymmetric, two for why pH is symmetrical, one for the underlying difference between the two factors.

The two sides of the temperature curve are produced by two different mechanisms acting in the same direction of change. The rise reflects increasing kinetic energy, which raises the frequency and energy of enzyme-substrate collisions gradually and steadily as temperature increases. The fall reflects denaturation, which is not gradual: the weak bonds maintaining the enzyme’s tertiary structure fail over a narrow range of temperature, so once that threshold is passed activity collapses quickly.

Denaturation is also irreversible, because the enzyme cannot refold into its original tertiary structure once the bonds maintaining it have broken. Every enzyme molecule that denatures is permanently removed from the population, so the loss of activity accumulates rather than fluctuating, which makes the fall both steep and final.

The pH curve is symmetrical because a single mechanism operates on both sides of the optimum, and it operates in the same way in each direction. Activity depends on the ionisation state of the charged amino acid residues in and around the active site; at the optimum pH these carry the charges that give the site its correct shape and allow the substrate to bind. Moving to a more acidic pH adds hydrogen ions and moving to a more alkaline pH removes them, but both changes disturb the same ionic and hydrogen bonds, and a comparable departure in either direction disturbs them to a comparable degree.

The shapes differ, therefore, because temperature changes two things at once — the energy available for collisions and the stability of the enzyme’s structure — with the second taking effect abruptly and permanently past a threshold, whereas pH changes only one thing, the ionisation of the active site, whose effect is gradual and, over the moderate range near the optimum, reversible. Where a curve is produced by one reversible mechanism it is symmetrical; where it is produced by a gradual mechanism on one side and an abrupt irreversible one on the other, it is not.