7.6.1 Metabolic pathways.
7.6.2 Induced-fit model.
7.6.3 Activation energies.
7.6.4 Competitive and non-competitive inhibition.
7.6.5 End product inhibition of enzyme pathways.
Chemical changes in living things often occurring with a number of intermediate stages.
Each stage has its own enzyme.
Catabolic pathways breakdown molecules
Anabolic pathways build up molecules
Linear Chain Pathways:
Enzyme (1) is specific to substrate 1. This is changed to product 1.
Enzyme (2) is specific to product1 which becomes the substrate and converted to product 2.
Enzyme (3) is specific to products which becomes the substrate and converted t o product 3.
Product 3 is called the 'End product'.
e.g. Glycolysis
Cyclic Pathways:
The initial substrate is fed into the cycle.
Enzyme (1) combines the regenerated 'intermediate 4' with the initial substrate to catalyses the production of intermediate 1.
Enzyme (2) is specific to intermediate 1 and converts intermediate 1 to intermediate 2
Enzyme (3) is specific to intermediate 2 and catalyses it conversion to product and intermediate 3.
Enzyme (4) is specific to intermediate 3 and catalyses its conversion to intermediate 4.
The difference is the regeneration of the intermediate, in this case intermediate 4.
Examples Krebs cycle and Calvin cycle.
The lock and Key hypothesis does not explain the broad specificity of some enzymes. Also the molecular shape of active sites is not always complementary to that of the substrate. The induced fit attempts to over come these difficulties.
a) Note the active site is not complementary to the substrate
b) At the complexing of the enzyme and substrate the active site changes to accommodate the substrate. The structure of the enzyme allows a certain amount of adaptation to the substrate. hence the broad specificity of some enzymes.
States (c), (d) and (e) happen in the same way as the lock and key hypothesis.
Exergonic reactions:
Enzymes lower the activation energy of the chemical reaction that they catalyse.
In the activated complex or transition state energy is put into the substrate to weaken the structure. This allow the reaction to occur with a minimal amount of additional energy required.
Normal activation energy would cause damage to the proteins of the cell. Thus reduced activation energy make these reactions possible in a cell.
After the product is formed energy is released.
Exergonic reactions release more energy than the activation energy. .
Inhibitors are substances that reduce or completely stop the action of an enzyme
Inhibition can act on the active site (competitive) or on another region of the enzyme molecule(non-competitive). The competition in the former being for the active site of the enzyme.
Competitive inhibition:
The substrate and inhibitor are chemically very similar in molecular shape.
The inhibitor can bind to the active site
Enzyme-inhibitor complexing blocks substrate from entering the active site.
This blockage reduces the rate of reaction.
However..
If the substrate concentration is increased it occupies more active sites than the inhibitor. Therefore the substrate out-competes the inhibitor for the active site.
The rate of reaction will increase again.
Example:Succinate is converted to Fumerate by Succinate dehydrogenase(SDase)
SDase can be inhibited by a later intermediate in the cycle called malonate
The presence of a competitive inhibitor reduces the rate of reaction.
Increasing the concentration of the substrate reduces the effect of the inhibitor
At high concentrations the substrate out-competes the inhibitory molecules for the active site. The rate of reaction therefore increases.
Non-competitive Inhibition:
The substrate and the inhibitor are chemically different in molecular structure.
The inhibitor cannot bind to the active site.
The inhibitor can bind to another region of the enzyme molecule.
The bonding of the inhibitor with the enzyme causes structural changes in the enzyme molecule.
The active site changes shape.
The substrate cannot bind therefore the rate of reaction decreases.
Example: Inhibition by metal ions (Ag+)
Silver ions inhibiting the formation of sulphide bridges at the amino acid cysteine.
This changes the protein bonding and in turn the active site changes excluding the substrate
The presence of an non-competitive inhibitor always significantly reduces the rate of reaction.
Increasing the concentration of the enzyme increases the chance of a collision between the substrate and an enzyme that is not inhibited already. Therefore the rate can increase.
The rate of reaction is always lower when the inhibitor is present.
Enzyme pathways can be controlled by concentration of products from the end of the pathway.
The principle is illustrated by the transamination (change R group) of the amino acid threonine to isoleucine
Isoleucine the end product, this molecule can inhibit the enzyme Threonine Deaminase
The inhibition occurs at an inhibition site on the enzyme but not the active site
An excess of end product (Isoleucine) switches off any more production of that product, isoleucine.
At high concentrations, Isoleucine attaches to the inhibition site of Threonine deaminase.
This attachment causes the active site of the enzyme to change blocking any further reaction.
Isoleucine is used up in cellular processes that require this particular amino acid.
The isoleucine concentration in the cell falls and so the Isoleucine that is attached to the enzyme detaches. This amino acid is also used up in the various cellular processes.
With the inhibitor removed the the active site then becomes active again and the pathway switches back on.
The isoleucine is again in production but once high concentrations are reached the pathways is once more inhibited. The process then cycles on in alternating stages of production and inhibition
Notice the similarity with non-competitive inhibition.
This mechanism makes the pathway self-regulating in terms of product manufacture.