Enzyme Structure

Dr Ruqaya Jabeen

Enzyme StructureEnzymes are globular proteins. Their folded conformation creates an area known as the active site. The nature and arrangement of amino acids in the active site make it specific for only one type of substrate.

Cofactor

Many enzymes require an additional small molecule, known as a cofactor to aid with catalytic activity. A cofactor is a non-protein molecule that carries out chemical reactions that cannot be performed by the standard 20 amino acids. Cofactors can be either inorganic molecules (metals) or small organic molecules (coenzymes).

Cofactors, mostly metal ions (such as Fe2+, Mg2+, Cu2+) or coenzyme, are inorganic and organic chemicals that function in reactions of enzymes.

Coenzymes are organic molecules that are non-proteins and mostly derivatives of vitamins soluble in water by phosphorylation; they binds apoenzyme protein molecule to produce active holoenzyme.

Apoenzyme- An enzyme that requires a cofactor but does not have it bound. An apoenzyme is an inactive enzyme, activation of the enzyme occurs upon binding of an organic or inorganic cofactor.

Holoenzyme- An apoenzyme together with its cofactor is called as holoenzyme. A holoenzyme is complete and catalytically active. Most cofactors are not covalently bound but instead are tightly bound. However, organic prosthetic groups such as an iron ion or a vitamin can be covalently bound.

Examples of holoenzymes include DNA polymerase and RNA polymerase which contain multiple protein subunits.

RNA polymerase is a holoenzyme that catalyzes RNA. RNA polymerase is needed for constructing RNA chains from DNA genes as templates, a process known as transcription.

Specificity of Enzymes

One of the properties of enzymes that makes them so important is the specificity they exhibit in the reactions they catalyze. In general, there are four distinct types of specificity:

Absolute specificity - the enzyme will catalyze only one reaction.

Group specificity - the enzyme will act only on molecules that have specific functional groups, such as amino, phosphate and methyl groups.

Linkage specificity - the enzyme will act on a particular type of chemical bond regardless of the rest of the molecular structure.

Stereochemical specificity - the enzyme will act on a particular steric or optical isomer.

Mechanism of Enzyme ActionThe basic mechanism by which enzymes catalyze chemical reactions begins with the binding of the substrate(or substrates) to the active site on the enzyme.

The active site is the specific region of the enzyme which combines with the substrate. The binding of the substrate to the enzyme causes changes in the distribution of electrons in the chemical bonds of the substrate and ultimately causes the reactions that lead to the formation of products. The products are released from the enzyme surface to regenerate the enzyme for another reaction cycle.

The active site has a unique geometric shape that is complementary to the geometric shape of a substrate molecule, similar to the fit of puzzle pieces. This means that enzymes specifically react with only one or a very few similar compounds.

Lock and Key Theory:

The specific action of an enzyme with a single substrate can be explained using a Lock and Key analogy first postulated in 1894 by Emil Fischer. In this analogy, the lock is the enzyme and the key is the substrate. Only the correctly sized key (substrate) fits into the key hole (active site) of the lock (enzyme).

Smaller keys, larger keys, or incorrectly positioned teeth on keys (incorrectly shaped or sized substrate molecules) do not fit into the lock (enzyme). Only the correctly shaped key opens a particular lock.

Induced Fit Theory:

The induced-fit theory assumes that the substrate plays a role in determining the final shape of the enzyme and that the enzyme is partially flexible.

It is said that as the substrate gets closer to the enzyme’s active site it induces slight change in shape of the enzyme and thus allowing the active site to become totally complimentary. 

In the figure, the substrate is represented by the magenta molecule, the enzyme protein is represented by the green and cyan colors. The cyan colored protein is used to more sharply define the active site. The protein chains are flexible and fit around the substrate.

Factors that Affect the Rate of Enzyme Reactions

1. Temperature: Enzymes have an optimum temperature at which they work fastest. For mammalian enzymes this is about 40°C, but there are enzymes that work best at very different temperatures, e.g. enzymes from the arctic snow flea work at -10°C, and enzymes from thermophilic bacteria work at 90°C.

Up to the optimum temperature the rate increases geometrically with temperature (i.e. it's a curve, not a straight line). The rate increases because the enzyme and substrate molecules both have more kinetic energy and so collide more often, and also because more molecules have sufficient energy to overcome the activation energy.

Above the optimum temperature the rate decreases as more of the enzyme molecules denature. The thermal energy breaks the hydrogen bonds holding the secondary and tertiary structure of the enzyme together, so the enzyme loses its shape and becomes a random coil - and the substrate can no longer fit into the active site. .

2. pH

Enzymes have an optimum pH at which they work fastest. For most enzymes this is about pH 7-8 (normal body pH), but a few enzymes can work at extreme pH, such as gastric protease (pepsin) in our stomach, which has an optimum of pH 1.

The pH affects the charge of the amino acids at the active site, so the properties of the active site change and the substrate can no longer bind. For example a carboxyl acid R groups will be uncharged a low pH (COOH), but charged at high pH (COO-).

3. Enzyme concentration As the enzyme concentration increases the rate of the reaction also increases, because there are more enzyme molecules (and so more active sites), available to catalyse the reaction therefore more enzyme-substrate complexes form. In cells, the substrate is always in excess, so the graph does not level out.

4. Substrate concentration The rate of an enzyme-catalysed reaction is also affected by substrate concentration. As the substrate concentration increases, the rate increases because more substrate molecules can collide with active sites, so more enzyme-substrate complexes form.

At higher concentrations the enzyme molecules become saturated with substrate, and there are few free active sites, so adding more substrate doesn't make much difference (though it will increase the rate of E-S collisions).

5. Covalent modification The activity of some enzymes is controlled by other enzymes, which modify the protein chain by cutting it, or adding a phosphate or methyl group. This modification can turn an inactive enzyme into an active enzyme (or vice versa), and this is used to control many metabolic enzymes and to switch on enzymes in the gut e.g. HCl in stomach → activates pepsin → activates rennin. 6. Inhibitors Inhibitors inhibit the activity of enzymes, reducing the rate of their reactions. They are found naturally, but are also used artificially as drugs, pesticides and research tools. There are two kinds of inhibitors

(a) A competitive inhibitor molecule, so has a similar structure to the substrate molecule, and so it can fit into the active site of the enzyme. It therefore competes with the substrate for the active site, so the reaction is slower. Increasing the concentration of substrate restores the reaction rate and the inhibition is usually temporary and reversible.

(b) A non-competitive inhibitor molecule is quite different in structure from the substrate and does not fit into the active site. It binds to another part of the enzyme molecule, changing the shape of the whole enzyme, including the active site, so that it can no longer bind substrate molecules.

Non-competitive inhibitors therefore simply reduce the amount of active enzyme. This kind of inhibitor tends to bind tightly and irreversibly – such as the poisons cyanide and heavy metal ions. Many nerve poisons (insecticides) work in this way too.

7. Feedback Inhibition (Allosteric Effectors) The activity of some enzymes is controlled by certain molecules binding to a specific regulatory (or allosteric) site on the enzyme, distinct from the active site. Different molecules can either inhibit or activate the enzyme, allowing sophisticated control of the rate. They are generally activated by the substrate of the pathway and inhibited by the product of the pathway, thus only turning the pathway on when it is needed. This process is known as feedback inhibition.