Enzymes

The majority of the reactions that occur in living organisms are enzyme-controlled. Without them, the rate of the reactions would be so slow as to cause serious, if not fatal, damage. Without enzymes toxins would soon build up and the supply of respiratory substrate would decrease.

Enzymes are proteins and thus have a specific shape. They are therefore specific in the reactions that they catalyse - one enzyme will react with molecules of one substrate.

The site of the reaction occurs in an area on the surface of the protein called the active site. Since the active site for all molecules of one enzyme will be made up of the same arrangement of amino acids, it has a highly specific shape.

Generally, there is only one active site on each enzyme molecule and only one type of substrate molecule will fit into it.

Chymotrypsin and trypsin both catalyse the hydrolysis of peptide bonds but due to their shapes, the active site of chymotrypsin only splits bonds after an aromatic amino acid (one containing a ring of atoms) whereas trypsin only splits bonds after a basic or straight chain amino acid.

This specificity leads to the lock and key hypothesis.

However, it has been discovered that competitors for an active site (similar in shape to the substrate) could fit even though they are larger than the substrate. This means that the substrate and active site are a little flexible.

This has lead to the induced fit model...

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When the enzyme and substrate form a complex, structural changes occur so that the active site fits precisely around the substrate (the substrate induces the active site to change shape).

The reaction will take place and the product, being a different shape to the substrate, moves away from the active site. The active site then returns to its original shape.

Reactions proceed because the products have less energy than the substrates.

However, most substrates require an input of energy to get the reaction going, (the reaction is not spontaneous).

The energy required to initiate the reaction is called the activation energy.

When the substrate(s) react, they need to form a complex called the transition state before the reaction actually occurs. This transition state has a higher energy level than either the substrates or the product.

Outside the body, high temperatures often supply the energy required for a reaction. This clearly would be hazardous inside the body though! Fortunately we have enzymes that provide an alternative way with a different transition state and lower activation energy.

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The rate of the reaction without any external means of providing the activation energy continues at a much faster rate with an appropriate enzyme than without it. The maximum rate that any reaction can proceed at will depend, among other things, upon the number of enzyme molecules and therefore the number of active sits available.

  1. Temperature: enzymes work best at an optimum temperature.

    Below this, an increase in temperature provides more kinetic energy to the molecules involved. The numbers of collisions between enzyme and substrate will increase so the rate will too.

    Above the optimum temperature, and the enzymes are denatured. Bonds holding the structure together will be broken and the active site loses its shape and will no longer work.

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  2. pH: as with temperature, enzymes have an optimum pH. If the pH changes much from the optimum, the chemical nature of the amino acids can change.

    This may result in a change in the bonds and so the tertiary structure may break down. The active site will be disrupted and the enzyme will be denatured.

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  3. Enzyme concentration:at low enzyme concentration there is great competition for the active sites and the rate of reaction is low. As the enzyme concentration increases, there are more active sites and the reaction can proceed at a faster rate.

    Eventually, increasing the enzyme concentration beyond a certain point has no effect because the substrate concentration becomes the limiting factor.

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  4. Substrate concentration: at a low substrate concentration there are many active sites that are not occupied. This means that the reaction rate is low.

    When more substrate molecules are added, more enzyme-substrate complexes can be formed. As there are more active sites, and the rate of reaction increases.

    Eventually, increasing the substrate concentration yet further will have no effect. The active sites will be saturated so no more enzyme-substrate complexes can be formed.

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Most enzymes require additional help from cofactors, of which there are 2 main types:

  1. Coenzymes - these are organic compounds, often containing a vitamin molecule as part of their structure.

    Coenzymes are not permanently bound to the enzyme but may be temporarily and loosely bound for the duration of the reaction and then move away once it is completed. For example NAD, which transfers hydrogen away from one molecule in a dehydrogenase reaction and takes it to another molecule (see the Respiration Learn-it).

  2. Metal ions - most speed up the formation of the enzyme-substrate complex by altering the charge in the active site e.g. amylase requires chloride ions, catalase requires iron.

Inhibitors slow down the rate of a reaction. Sometimes this is a necessary way of making sure that the reaction does not proceed too fast, at other times, it is undesirable.

Reversible inhibitors:

Competitive reversible inhibitors: these molecules have a similar structure to the actual substrate and so will bind temporarily with the active site. The rate of reaction will be closer to the maximum when there is more 'real' substrate, (e.g. arabinose competes with glucose for the active sites on glucose oxidase enzyme).

Non-competitive reversible inhibitors: these molecules are not necessarily anything like the substrate in shape. They bind with the enzyme, but not at the active site. This binding does change the shape of the enzyme though, so the reaction rate decreases.

Irreversible inhibitors:

These molecules bind permanently with the enzyme molecule and so effectively reduce the enzyme concentration, thus limiting the rate of reaction, for example, cyanide irreversibly inhibits the enzyme cytochrome oxidase found in the electron transport chain used in respiration. If this cannot be used, death will occur.

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