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Enzymes are proteins:
-Enzymes are globular (spherical/ball-shaped) proteins with a specific tertiary structure built to accelerate biochemical reactions.
-Primary sequence of amino acids leads to secondary structure of alpha helices and beta sheets. This folds in 3D, forming ionic bonds, disulphide bridges, hydrogen bonds and salt bridges to bring about the tertiary structure.
-Often more than one polypeptide chain comes together to form a quaternary structure (associations of multiple chains).
Enzymes have an active site:
-The active site of the enzyme has a shape specific to its substrate.
-This specific shape is brought about due to the specific sequence of amino acids in the enzymes structure.
-The substrate forms chemical bonds with the active site, and the enzyme then undergoes a conformational change to better fit to the substrate.
-The enzyme-substrate complex has now been formed thanks to the complementary nature of the enzyme and substrate.
-The enzyme will now carry out its catalysis dependent on what enzyme it is (some break things down, other build things up) often through hydrolysis.
Competitive Inhibition:
-The inhibitor has a similar, complementary shape to the active site of the enzyme in question. It can therefore compete with the substrate for the availability of the active site. If the inhibitor is bound, the substrate cannot bind with the active site as it is occupied. The substrate cannot therefore be broken down as quickly, so the rate of reaction decreases.
Increasing the concentration of substrate could help increase the rate in the presence of a competitive inhibitor. This is because a higher concentration will mean a higher likelihood of substrate reaching the active site.
Enzyme
Substrate
Competitive Inhibitor
Non- competitive Inhibition:
-The inhibitor does not have a complementary shape to the active site, but binds to the enzyme all the same. This time it binds at an allosteric site and through interactions with the enzymes tertiary structure, it causes deformation of the active site. This means that the enzymes active site is no longer complementary to the substrate, so less substrate can be broken down. The rate therefore decreases.
Non-competitive inhibitors typically cause an irreversible effect owing to the fact that they distort the shape of the active site. Nonetheless, increasing [substrate] right at the start of the inhibition could rescue some rate.
Enzyme
Substrate
Non-Competitive Inhibitor
How enzymes denature is explained in GCSE enzymes. This has detailed explanations for why temperature and pH changes cause the active site to lose its specificity.
Allosteric site: A site on the enzyme that is NOT the active site.
Factors affecting enzyme rates: Temperature
A very low temperature will mean that both the enzyme and the substrate molecules will have a low KE (kinetic energy) and therefore will be less likely to successfully collide to form an ES-complex (enzyme-substrate).
As temperature is therefore increased, the enzyme and substrate molecules will begin to gain more kinetic energy. There will be an increased level of vibration as well as increased frequent successful collisions between enzyme and substrate.
As temperature is increased beyond the optimum, the bond vibrations become so kinetic that they begin to break. This begins to lower the rate of the enzyme, as its active site denatures, losing its shape and therefore specificity to its substrate. This is known as loss of complementarity.
Taq Pol: A polymerase taken from hydrothermal vents and hot springs. It can withstand high temperatures of above 90 degrees Celsius without denaturing. It is therefore used in PCR, which couples a high temperature and free-floating nucleotides and primers to exponential; DNA amplification, with applications in CSI and paternity testing
Factors affecting enzyme rates: pH
Enzymes are highly pH sensitive. Since pH is a measure of the hydrogen ion [H+] concentration, pH is calculated using the equation: pH = -log[H+]
A acidic solution will therefore have a high H+ concentration, whereas an alkaline solution will have a high OH- concentration. As either of these two ions is introduced to a proteins tertiary structure, they begin to interfere with specific bonds. These include ionic bonds/salt bridges as well as hydrogen bonds.
Enzymes have a very narrow pH range, and therefore if their rate is plotted against pH on a graph, a bell-shaped curve will appear. This means that even discrete changes to the pH can cause the active site of the enzyme to denature and lose complementarity, therefore decreasing the rate.
Bell-Shaped: Narrow optimum with denaturation
Rate
pH
Factors affecting enzyme rates: [Enzyme]/[Substrate]
If the concentration of substrate does not change, then increasing the [enzyme] will cause the rate of reaction to increase. This is because there are more active sites available for the substrates to bind to and release the product.
Increasing the [enzyme] beyond a certain point will not cause the rate to increase. This is because now there exist more enzymes (and therefore more active sites) than substrate molecules. The [substrate] therefore becomes the limiting factor at this stage, where increasing the [substrate] will have an effect on ROR.
The same can be said for [substrate], whereby increasing its concentration will saturate enzymes active sites with substrate molecules. The [enzyme] will therefore become the limiting factor.
Limiting factor: Something which constrains the rate of something, or how quickly something happens. Usually it is the variable that must be changed in order to see a change in the rate.
Examples in nature of limiting factors include light, [CO2] and temperature in photosynthesis. Limiting factors can be biotic (living) or abiotic (non-living).
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