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Enzyme Kinetics Notes

Pharmacology Notes > BIOL10212 Biochemistry Notes

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Biochemistry - Lecture 9 (26/03/2018)

Enzyme Kinetics
Biological Catalysts


At the end of the nineteenth century, agriculture had become extremely dependent on an ever-dwindling supply of saltpeter from South America.
Nitrogen is a limiting factor for crop productivity in many soils, and the nitrate from guano and saltpeter was for a long time the only source of nitrogen fertilizer.
Chemists around the world were looking for a way to turn atmospheric nitrogen into nitrate, or ammonia that can later be oxidised to nitrate. Just before the first world war, Fritz Haber succeeded in developing a process where nitrogen and hydrogen gas were brought together at high temperature and, crucially, with a catalyst, to produce ammonia.
A version of this process is still the main way in which nitrogen fertiliser is produced and it has boosted agricultural productivity immensely.

The reaction is chemically extremely slow, so catalysts are crucial to allow it to occur at a useful rate. In the industrial setting, that catalyst is a form of specially treated iron.

Interestingly, many free living and symbiotic bacteria can achieve the same thing without high temperature and without high pressure, although it still costs a lot of energy.

Biological nitrogen fixation happens with one of nature's own catalysts- an enzyme called
Nitrogenase.

Properties of Enzymes


Enzymes are mostly proteins.
Their 3D structure provides an active site for the binding of substrates and the catalytic conversion to products.
Enzymes may be single proteins, or may contain 2 or more subunits (ie: polypeptide chains).

The 3D structure of enzymes has evolved to provide an active site, which acts as a docking surface to bind one or several substrates to, and then to catalytically convert those substrates to products.

Many enzymes are made from a single polypeptide chain, whilst others have two or more subunits.

This is sometimes because the reaction is complicated and several substrates need to be held in place; or it can be because having more than one subunit allows for more precise control of enzyme activity. 

Catalysts speed up the attainment of the reaction equilibrium, but do not affect the equilibrium itself (i.e., final ratio of products to reactants), and the enzyme itself is unchanged.

Enzymatic reactions are 103 to 1017 faster than the corresponding uncatalyzed reactions.

Enzymes are catalysts as they bring a chemical reaction to its equilibrium much faster, but they don't change where the equilibrium lies.

Also, we only call something a catalyst, or enzyme for that matter, if it is itself unchanged in the reaction. As an example, hydrogen peroxide spontaneously dissociates into water and oxygen, but this is a slow process. If a catalyst is added then we don't need to change where that equilibrium lies, but we can get there much faster as the rate of reaction is sped up.

Substrates


Substrates are highly specific reactants for enzymes.
Substrates are stereospecific and the enzymes will usually act upon only one stereoisomer of the substrate.
Substrates have reaction specificity, and the enzyme product yields are essentially 100%,
with no formation of wasteful by-products.

The Gibbs Free Energy
Enzymes lower the activation energy of the reaction.
 G‡ is affected by enzymes.
 G‡ determines the reaction rate.
 The enzyme reduces the energy barrier, resulting in a faster reaction.
 G'º is not affected by enzymes.
This reflects the ratio of Substrate to Product.
(Here, G'º is negative, so it favours the product.)

This diagram is an energy diagram where the x axis represents the reaction coordinate,
(the progress from substrates [S] to products [P], and the y axis represents the overall energy, and more specifically: the Gibbs free energy of the molecules at any one time.

Enzymes do not affect the Net free energy change of a reaction. ΔG reflects the ratio of the substrate to product at equilibrium, and if it is negative, then the formation of product is energetically favoured. 

A high activation energy means that the reaction will naturally progress to equilibrium much more slowly than one with a low activation energy. Enzymes can reduce that energy barrier,
and so speed up the reaction, by providing an alternative reaction pathway with a lower activation energy.

In summary, the energy barrier between enzyme-bound substrates and enzyme-bound product (ES to EP) is much lower than in the original uncatalyzed reaction. This is the essence of catalysis. By providing an alternative reaction pathway with lower activation energy, the rate of the reaction (its kinetics) is sped up considerably.

Factors affecting Substrate conversion to Product

Substrate binding is specific but not completely complementary (not 'lock and key') as in actual fact, the active site fits much better to the substrate after binding to it, through the
'induced fit' model.

The active site is most complementary in shape to (has highest binding energy for) the transition state and in turn the transition state stabilisation lowers the energy barrier.

The reaction of the substrates is also favoured by a proximity effect, as a reaction on an enzyme increases the effective concentration of reacting groups.

Active Site Functional groups

To help with the binding and conversion of substrate molecules, the amino acid residues of the active site of enzymes contribute to binding by noncovalent interactions, as well as catalysis.

The role of enzyme active site residues includes:

 Increasing the binding energy, through non-covalent interactions.
 Contains catalytic functional groups.

The Catalytic functional groups include proton donors/acceptors, which act as ionisable side chains, as well as groups that can form covalent bonds to the substrate (nucleophiles,
electrophiles).

Some active site residues can transiently form covalent bonds with the substrate. And finally,
many enzymes have metal ions in their active site, such as Mg. These are held in place,
depending on the metal, with active site glutamate and aspartate residues, or for heavy metals, cysteine and histidine.

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