Enzymes

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CHAPTER 4:
ENZYMES
Enzymes are biological catalysts. There are about 40,000 different enzymes in human cells, each controlling a different chemical reaction. They increase the rate of reactions by a factor of between 106 to 1012 times, allowing the chemical reactions that make life possible to take place at normal temperatures. They were discovered in fermenting yeast in 1900 by Buchner, and the name enzyme means "in yeast". As well as catalysing all the metabolic reactions of cells (such as respiration, photosynthesis and digestion), they may also act as motors, membrane pumps and receptors. The active site of RUBISCO, the key enzyme in photosynthesis, contains just 6 amino-acids.

Substrate in active site

Enzyme Structure
Enzymes are proteins, and their function is determined by their complex structure. The reaction takes place in a small part of the enzyme called the active site, while the rest of the protein acts as "scaffolding". This is shown in this diagram of a molecule of the enzyme trypsin, with a short length of protein being digested in its active site. The amino acids around the active site attach to the substrate molecule and hold it in position while the reaction takes place. This makes the enzyme specific for one reaction only, as other molecules won't fit into the active site – their shape is wrong.

Many enzymes need cofactors (or coenzymes) to work properly. These can be metal ions (such as Fe2+, Mg2+, Cu2+) or organic molecules (such as haem, biotin, FAD, NAD or coenzyme A). Many of these are derived from dietary vitamins, which is why they are so important. The complete active enzyme with its cofactor is called a holoenzyme, while just the protein part without its cofactor is called the apoenzyme.

How do enzymes work?
There are three parts to our thinking about enzyme catalysis. They each describe different aspects of the same process, and you should know about each of them.

1.

Reaction Mechanism
In any chemical reaction, a substrate (S) is converted into a product (P):

S

P

(There may be more than one substrate and more than one product, but that doesn't matter here.) In an enzyme-catalysed reaction, the substrate first binds to the active site of the enzyme to form an enzyme-substrate (ES) complex, then the substrate is converted into product whilst attached to the enzyme, and finally the product is released, thus allowing the enzyme to start all over again (see right)

An example is the action of the enzyme sucrase hydrolysing sucrose into glucose and fructose (see left)

2.

Molecular Geometry
The substrate molecule is complementary in shape to that of the active site. It was thought that the substrate exactly fitted into the active site of the enzyme molecule like a key fitting into a lock (the now discredited ‘lock and key’ theory). This explained why an enzyme would only work on one substrate (specificity), but failed to explain why the reaction happened. It is now known that the substrate and the active site both change shape when the enzyme-substrate complex is formed, bending (and thus weakening) the target bonds. For example, if a substrate is to be split, a bond might be stretched by the enzyme, making it more likely to break. Alternatively the enzyme can make the local conditions inside the active site quite different from those outside (such as pH, water concentration, charge), so that the reaction is more likely to happen. Although enzymes can change the speed of a chemical reaction, they cannot change its direction, otherwise they could make "impossible" reactions happen and break the laws of thermodynamics. So an enzyme can just as easily turn a product into a substrate as turn a substrate into a product, depending on the local concentrations. The transition state is the name given to the distorted shape of the active site and substrate.

This diagram shows another enzyme with its 5 disuphide bridges in yellow and regions of α –helix in blue. The...
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