A-level Biology/Biology Foundation/enzymes

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Overview[edit]

Induced fit diagram.svg

Enzymes are protein molecules that act as biological catalysts on reactions. This means that they speed up said reactions, but remain unchanged at the end. A vast majority of metabolic reactions are catalysed by enzymes. Enzymes are globular molecules just as we learnt about in the previous chapter, and so have their hydrophilic r R groups on the outside, making them soluble, but enzymes also have a speciality in that they possess an 'active site'. This active site allows other molecules to bind to the enzyme, and these molecules are known as the 'substrate', and the shape of the active site allows them to fit perfectly. Temporary bonds form between the substrate and the R groups on the enzymes amino acids, forming the enzyme-substrate complex. The substrate then unbinds in the form of its product.

Enzymes are said to be specific in their nature, as the shape of the active site will only allow one molecule to fit. It may either catalyse the breaking up or joining of molecules, forming one or more products. When the reaction is complete, these products leave the active site, and as said before - the enzyme is unchanged and can thus receive another substrate molecule. Most enzymes end in 'ase', for example lipase, amylase

Activation Energy[edit]

All reactions require energy - and the threshold of the reaction happening is known as the activation energy - the point at which the reaction begins to occur. Enzymes lower this activation energy, and sometimes this not only speeds up the process, but makes it happen in the first place as most of the reactions in living cells would be so slow that they would (for practical purposes), not happen at all.

One way of providing energy to reactions is to heat them, since this gives kinetic energy to the molecules and increases the rate of collisions between enzymes and substrates (more in the temperature section). Humans do this, maintaining a constant 37c within the body, but this is not enough for the activation energy required for many reactions - and thus enzymes solve this problem by reducing the activation energy. Enzyme-catalysed reactions take place faster and at a much lower temperature than standard reactions.

A reaction's path[edit]

We have said that when an enzyme catalyses a reaction, substrates combine with enzymes to form enzyme-substrate complexes, and a product is created. Take a look at this graph. Time is along the bottom, amount of product produced on the y-axis. It is a generic enzyme catalysed reaction - as you can see there is a large amount (the majority) of product collected quickly, but then the line levels off.

This is because when there is a large amount of both enzyme and substrate, all enzyme molecules have a substrate in its active site, and collisions are constantly occurring, but as the reaction goes on and more substrate is used up, the longer it takes for a substrate to hit an enzyme (as the substrate becomes more scarce), and thus the more time enzymes are simply waiting. This initial period is known as the initial rate of reaction.

Reaction Rate[edit]

Rate of reaction can be measured in a couple of ways - the amount of product produced, the amount of substrate left (as subtracted from the initial total). For example, the rate at which amylase breaks down starch - both the product and substrate remain colourless in the mixture. Last chapter, the food test section showed that we test for the presence of starch with iodine - so to see the rate of reaction we can take a sample from the reaction mixture, mix it with iodine and test the intensity of the change with a colourimeter. This will give us results that can be plotted into a graph - the amount of starch remaining against time.

Various things affect a reaction rate, enzyme concentration, substrate concentration, temperature, pH and presence of enzyme inhibitors. These are discussed next.

Enzyme Concentration[edit]

Take a look at this graph. It shows how increasing enzyme concentration increases the rate of the reaction, and this is in line with enzyme theory as so long as there is sufficient substrate, there is more enzyme-substrate complexes being formed per second and thus, more product being formed every second - faster rate of reaction. However, something to note is that left to their own devices, these reactions would all eventually produce the same amount of product (assuming each has the same amount of substrate). The rate of reaction increases linearly with enzyme concentration.

Substrate Concentration[edit]

This graph shows how increasing the substrate concentration increases the rate of reaction, to a certain point. This is because, as substrate concentration increases, more enzyme-substrate complexes can be formed per second, but point x on the graph is known as the saturation point, which is where every enzymes active site is working continuously, and the enzymes cannot work faster so substrate simply ends up 'queuing up' and waiting for an active site.

Temperature[edit]

The speed at which molecules move around freely is determined by the temperature giving them more or less energy to do so - at high temperatures the molecules, the enzymes and the substrates, move around fastest, and thus there are the most collisions per second, causing enzyme-substrate complexes to be formed more frequently. So why does the graph show the rate of reaction peak at 40c? After 40c, the bonds in the enzyme molecule begin to shake so violently that they begin to break, which causes the enzyme to lose it's shape, which changes the shape of the active site (so the substrate will no longer fit) and the enzyme is said to be denatured. The reason the rate of reaction does not immediately drop to 0 is that the enzyme slowly loses shape as the temperature increases, and so the substrate fits less well and eventually not at all, and so the catalysis does not occur. The process of denaturing is usually irreversible.

In humans 40c is the optimum temperature for enzyme reactions- the temperature at which an enzyme catalyses a reaction at the maximum rate. We keep our bodies at 37c to make sure we never go above 40c as enzymes would start to denature at even the slightest upward variation - which would be extremely dangerous as nearly all reactions within the body rely on enzymes.

Effects of pH[edit]

This graph shows the effect of pH on enzyme activity. pH is a measure of hydrogen ions in a solution (think: percentage Hydrogen), and these affect enzyme activity since the hydrogen ions can react with the enzyme and change the enzymes shape, deforming the active site. As with temperature, too high or low pH for the enzyme will denature the enzyme. The graph is just an example, since different enzymes have different optimum pH

Inhibition[edit]

There are two types of enzyme inhibition - that is, things that inhibit the enzymes function. They can be harmful in that they can stop a reaction happening, or helpful in stopping a reaction from running wild - perhaps the end-product of a chain of reactions will be an enzyme inhibitor to prevent the reaction continuing indefinitely.

Competitive[edit]

Example

Competitive enzyme inhibitors are named as such because they compete with the substrate for the enzyme molecule's active site's. They achieve this by being a similar shape and fitting into the active site, temporarily blocking substrate from entering. This makes the reaction slower, since there is less chance that genuine substrate will collide with an enzyme and form product. Competitive inhibitors affect on the enzyme is always reversible. They can be overcome by increasing the substrate concentration. This then increases the chances of for substrate to bond with the enzyme active site, and decreases the chances for the inhibitor.


Non-Competitive[edit]

Competitive inhibition.svg

Non-competitive inhibitors are ones that do not compete for the active site. Instead they bind indirectly to either another active site on the enzyme or just to any position on the enzyme. This is turn causes the enzymes active site to change shape and denature because the inhibitor that has bind to the enzyme changes the tertiary structure of the enzyme and thus also the active site stopping any substrate from bonding. This is usually permanent. This can also be overcome by increasing the substrate concentration as it has the same effect as with a competitive inhibitor.