Structure of an enzyme
Structure of ShPatB (Apo) enzyme

Biology toolbox: An introduction to enzymes

All biology requires enzymes. From basic cellular functions such as respiration, to intricate brain activities such as learning and memory, enzymes are crucial for life. This is because enzymes act as catalysts to speed up biological reactions that would otherwise take too long to complete. For example, pyrimidine synthesis (a nucleic acid base) requires conversion of orotidine monophosphate to uridine monophosphate; a reaction that would take over 70 million years without a catalyst. In the presence of an enzyme OMP decarboxylase, this reaction is completed in a matter of milliseconds! This is impressive efficiency.

Note: Enzymes increase the rate of a chemical reaction, but cannot cause impossible reactions to occur

Chemical reactions involve making and breaking bonds. The business of changing chemical bonds involves energy. In many cases, bond formation releases energy, whereas breaking bonds requires energy. You can visualise the energy state of a chemical reaction using a graph.

free energy of uncatalysed reaction. It highlights that the peak of the graph to be the transition state and that the difference between the free energy of reactants and the transition state is called activation energy.

All molecules start with a certain amount of free energy (G) [the y-axis]. The progression of the reaction is plotted on the x-axis as the Reaction coordinate which represents what happens to the free energy as the reaction progresses. The graph shows that the product has lower free energy than the reactant (this makes sense as some energy is used up in the reaction). The lower energy state is favoured because it is more thermodynamically stable.

Before product is formed, you need to invest energy to reach a transition state. The transition state is the highest energy state of the reaction and occurs when the reactant is transitioning to product. This is because the reactant is a thermodynamically stable molecule, breaking the first bond/making a new one is therefore very unfavourable and a lot of energy is required to do so. This extra energy cost is known as activation energy. Activation energy is the energy needed to reach transition state. The rate of the reaction (how quickly it happens) depends on how many of the reacting molecules acquire enough activation energy to reach and pass through the transition state in a particular time. Reactions that need a lot of energy to reach the transition state are slower than those with lower activation energies. An enzyme lowers the activation energy to convert substrate (S) to product (P) (note the term reactant is changed to substrate in enzymatic reactions).

Free energy of catalysed reaction: This graph compares the free energy landscape of uncatalysed and catalysed reactions. The graph changes to show that under catalysis, energy requirement is reduced i.e. the activation energy os reduced. It also highlights that the peak of the graph to be the transition state and is reduced under catalysed conditions

To use an analogy, enzymes shave off the top of a mountain and turn it into a much smaller hill making it easier and faster to climb.

Note: Heat is another good catalyst. But in the context of biology it is pretty useless. Reaction rate is only doubled by every 10°C rise in temperature. Imagine having to run a fever every time your cells need to process a reaction (which is all the time)! A 3°C fever is fatal! And this is merely to double the rate.

Rate of Reaction

Rate of reaction can be measured by the amount of substrate consumed or the amount of product formed. In the absence of an enzyme, reaction rate (v) is proportional to the amount of reactant (A) available in the reaction, so the relationship between rate and concentration of reactants can be represented by a straight line on a graph.

In the presence of an enzyme, initially the reaction rate is proportional to concentration of substrate [S], but slowly plateaus as the concentration of substrate increase and the rate of reaction approaches the maximum rate (Vmax) as enzyme becomes saturated.

This graph shows the reaction rate as a function of substrate concentration: In the presence of an enzyme, initially the reaction rate is proportional to concentration of substrate **[S]**, but slowly plateaus as the concentration of substrate increase and the rate of reaction approaches the **maximum rate** (**Vmax**) as enzyme becomes saturated.

Question: Why do you think there is a maximum rate?

Answer: When the concentration of enzyme remains the same in a reaction, as substrate concentration increases, fewer enzyme active sites will be free and you reach a maximum rate because the enzyme becomes limiting. This means that no matter how much more substrate you add to the reaction, the rate at which the product is formed will not get any faster as there is no free enzyme for more substrate to bind to.

How do enzymes lower the activation energy?

The business end of an enzyme is its active site where it interacts with its substrate(s). In some cases part of the role of an enzyme is to act as a molecular match-maker, bringing together two components that might struggle to quickly find each other in a complex mixture. The nature of the enzyme-substrate interaction determines how an enzyme lowers activation energy. For example, non-covalent bonds form between enzyme and substrate, which gives the enzyme its specificity. During the transition state, enzyme and substrate(s) form a complex before product(s) formation.

This animation is a gif enzyme-substrate interaction, where selectivity is achieved because molecules that are not substrates do not interact with the enzyme active sites and but substrate does")

Animation of enzyme substrate interaction showing selectivity

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