Enzymes - Principles and Kinetics Quiz

Answer: Something which alters the rate of a reaction without being consumed or permanently changed in the process

Catalysts are commonly utilised in industry. Iron catalysts help us manufacture ammonia, vanadium catalysts give us sulphuric acid, and platinum catalysts help keep harmful gases from our cars being released into the atmosphere. These catalysts all speed up the rate of reaction and are not consumed in the process. Even among industrial catalysts, enzymes are on another level.

The efficiency with which enzymes speed up reactions remains unmatched in the technological world and they are examples of evolution (at a molecular level) at its best.

Answer: The transition state

The idea that enzymes reduce the activation energy by having a high affinity for the transition state is called the transition state stabilisation theory. This theory contradicts Fischer's Lock and Key hypothesis, which states that the enzyme has the highest affinity for the starting substrate.

It was proven experimentally that lysozyme (an enzyme) has a higher affinity for the transition state than for its starting substrate. In non-enzyme assisted reactions, the transition state is often too unstable and so the reaction cannot progress.

Answer: The ability to form permanent covalent bonds with the substrate

Enzymes do not tend to interact covalently with substrate molecules. Interactions tend to be non-covalent and (most importantly) transient, since the enzyme must be regenerated to its original form at the end of the chemical reaction. In between the start and the end of the reaction, residues in the active site may donate and accept protons, therefore acting as both acids and bases.

This acid/base catalysis is common (though not universal) and utilises histidine residues at the active site. Residues such as arginine and asparagine are also common in active sites, since these are capable of forming hydrogen bonds with the substrate molecule.

Answer: Transferases

Transferases catalyse the transfer of chemical groups onto and off of proteins and other biomolecules. Methane is just one example of a group which may be transferred. One of the most commonly transferred groups in biology is the phosphate group, which is added to molecules by kinases and is removed by phosphatases.

Oxidoreductases catalyse oxidation/reduction reactions. Lyases catalyse the breakage of chemical bonds using methods other than hydrolysis or oxidation. Isomerases catalyse isomerisation (e.g. converting fructose into glucose). Ligases catalyse the formation of chemical bonds. These groups form the basis of the numerical classification system of enzymes. For example, an enzyme which has a numerical code starting with 1 tells you it is an oxidoreductase. Subsequent digits reveal more specific information about the enzyme's properties.

Answer: Water adds negative charge to the enzyme

Rather than being rigid entities, enzymes are dynamic and this improves the chances of firstly colliding with substrate molecules and secondly facilitating a chemical reaction. The surrounding solvent is in continuous motion, and these motions are transmitted through the protein as vibrations which assist the chemical reaction.

Answer: The active sites are saturated

At low substrate concentration, enzyme-based catalysis is said to be a first order reaction. This means that the rate of reaction is directly proportional to the concentration of substrate. However, if the enzyme concentration is fixed, there is a limited number of active sites which are themselves limited in how fast they can convert substrate into product.

After this saturation point, the rate of reaction is independent of substrate concentration and is thus said to be a zero order reaction.

Answer: The lysosomes of cells

Lysosomes are membrane-bound organelles in the cell where proteins and other biomolecules are taken to be degraded. Proteins known as V-type hydrogen pumps acidify the lysosome, and the hydrolytic enzymes kept there function most efficiently at around pH4. Enzymes found in the small intestine lumen and bile are more likely to function at alkaline pHs, whilst enzymes in the saliva are likely to function at neutral pHs.

As well as pH, enzymes function only at optimal temperatures. When the temperature is too high, bonds are broken and the enzyme denatures. When the temperature is too low, enzyme dynamics become so minuscule that it is unable to carry out its catalytic function.

Answer: Km is a measure of an enzyme's affinity for its substrate

If Km is low, this means that only a low concentration of substrate is needed to reach half the maximum rate of reaction, and so the enzyme has a high affinity for its substrate. If Km is high, this means that lots of substrate is needed to reach half the maximum rate of reaction, meaning the enzyme has a low affinity for the substrate. Therefore, the lower the value for Km, the higher the affinity of the enzyme for the substrate.

Another value used in enzyme kinetics is Kcat. Kcat is a measure of the amount of substrate converted into product per mole of enzyme per second. Therefore, the higher the Kcat, the higher the turnover rate of substrate. By dividing an enzyme's Kcat by its Km, you obtain a value for the enzyme's efficiency.

Answer: The Burge-Dazzler plot

The Michaelis-Menten equation can be linearized (y = mx + c) so that experimental data can be plotted on a graph, allowing us to deduce values for Vmax and Km. The most commonly used straight line equation here is the Lineweaver-Burk equation (1/v = (Km/Vmax) x (1/[S]) + 1/Vmax).

Therefore, if 1/v is plotted on the y-axis and 1/[S] on the x-axis, Vmax can be deduced by taking the reciprocal of the y-intercept. Km may then be calculated by multiplying the gradient of the line by the value obtained for Vmax.

Answer: Pacific inhibition

The extent of regulation of enzymes is testament to their importance in our well-being. For example, glutamine synthase can be regulated by the binding of specific amino acids, the attachment of adenylate groups, phosphate groups, and several other modifications.

The effect of the different types of inhibition is neatly demonstrated on the Lineweaver-Burk plot. Competitive inhibitors increase Km (and therefore decrease enzyme affinity), but leaves Vmax unchanged. Non-competitive inhibitors do not affect Km, but do reduce Vmax. Uncompetitive inhibitors actually decrease Km, but also decrease Vmax. In our bodies, enzymes are often inhibited by the products they make, thus preventing overproduction. This is an example of feedback inhibition.