Enzymes oh enzymes !

Enzymes what would we do without them? Im guessing we probably die because we need them to sustain life!

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Ok we all know what an enzyme is, they are biological catalyst, which speed up a chemical reaction by providing an alternate pathway with a lower activation energy. The enzyme itself however is not used up, so it can be used again.

What is the activation energy?

It is the minimum amount of energy required for the reaction to take place.

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Transition state

During any reaction there would be a point where bonds would be broken and bonds would be formed. The transition state is the highest – energy arrangement of atoms that is intermediate in structure between the structure of the reactants and structure of the products.

Most enzymes are made up of proteins, some are even RNA molecules. Catalytic RNA’s or ribozymes satisfy the following criteria

  • Being substrate specific
  • Enhancing the reaction rate
  • Emerging from the reaction unchanged

An organisms metabolism consists of thousands of reactions linked together, where the product of one reaction is the substrate for the next. This is know as the metabolic pathway, and each step is catalysed by a different enzyme. Because of this enzymes must be specific.

Now don’t get confused ok, even though the enzymes speed up the reaction they do not change the free energies of the reactants or products and therefore, does not change the equilibrium of the reaction.

All it does is accelerate the rate at which equilibrium is reached.

An enzyme has three distinctive features

  • catalytic power
  • specificity
  • regulation

It is the catalytic power of enzymes that make them so special, imagine they can increase reactions from 10^3 to 10^8 times faster than uncatayzed reactions.

It the number of moelcules of substrate that is converted into product per enzyme molecule per second is called the turnover number or  Kcat, if you would kindly explore my blog you would see that i have an interesting post about the turnover number, it is titled Enzymology so you can check it out.

When naming enzymes there are different ways !

  • based on substrate 
  • based on the action they perform
  • Sometimes they just end in ase
  • And at times they don’t end in ase, and we don’t know what they do, but they are enzymes :/

Classification of enzymes

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I used this picture from my teacher’s youtube video, as I find it explains the different classes of enzymes well.

Sometimes an enzyme needs a little help and this help is known as a cofactor.

Apoenzyme : Inactive protein part

Cofactor : Non protein part

Apoenzyme + Cofactor = Holoenzyme

Holoenzyme : Active enzyme.

What we already know!

  • Enzymes are very specific
  • The substance upon which it acts is know as its substrate
  • Because an enzyme is so specific, in its reaction there is no nonproductive side reaction, no wasteful products
  • Even the products are very specify
  • Basis of specificity is due to the intimate interaction between an enzyme and its substrate through molecular recognition, this is based on structural complementarity.
  • The site at which the enzyme binds to its substrate is know as the enzyme’s active site
  • This is a small cleft or pocket in the surface of the enzyme where certain amino acid residues are exposed.
  • The substrate molecule fits into the active site and interacts with these amino acids by ionic and hydrogen bonding, forming an enzyme – substrate complex.
  • After the reaction occurs the products that are formed leave the active site.
  • The active site not only bind substrates, they also provide catalytic groups to facilitate the chemistry and provide specific interactions that stabilize the formation of the transition state for the chemical reaction.

There are different hypothesis to explain the specificity and catalysis of enzymes.

The lock and key hypothesis

Koshland’s Induced fit hypothesis

The Lock and Key hypothesis

This is kind of straight forward. When the substrate enters the enzyme’s active site the fit is exact, just like a key fitting into a lock.

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Substrate analogous to the key.

Enzyme’s active site analogous to the lock.

Even though the substrate fits exact into the active site the products however are a different shape, and once release they cant enter into the active site again.

This is a great way to show the specificity of  an enzyme

The induced fit hypothesis

In this model the fit isn’t exact like the lock and key model, but thank God for the structural pliancy of these enzymes, because they are highly flexible, when the substrate binds to the enzyme, it will induce change in the enzyme’s conformation.

The active site is now moulded into a precise conformation which makes the chemical environment suitable for the reaction to take place.

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There are many factors that affect the reaction velocity of an enzyme – catalysed reaction

Such as [S], [E] , temp and pH.

Substrate Concentration [S]

Maximum velocity : The rate or velocity of a reaction is the number of substrate molecules converted to products per unit time.

When the rate of the reaction would increase with increasing [S] until maximal velocity is reached.

When maximal velocity is reach , the leveling off of the [S] reflects the saturation of the reaction, this just means that all the enzyme’s active sites are occupied at the same time.

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At high [S] the velocity of the reaction is zero order , it means that it is constant and independent of [S]. At low [S] the velocity of the reaction is first order and is proportional to [S].

Enzyme concentration [E] is the same as [S]

Temperature

The reaction velocity increase with temperature until a peak velocity is reached, this increase is a result of the number of molecules having sufficient energy to pass over the energy barrier and form the products of the reaction, there will be increased collision frequency. Decrease of velocity with a higher temperature results in temperature- induced denaturation of the enzyme. This is a cooperative process.

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pH

Most enzymes have an optimum pH at which they function best at. Changing the pH would mean a change in the concentration of hydrogen ions (H+) in the surroundings of the enzyme, this affects the ionization of the R-groups in the amino acid residues of the protein molecule. This in turn would affect the shape of the active site and binding with the substrate. At the optimum pH, the shape of the active site is best suited to the formation of an enzyme- substrate complex.

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We have now reached the end of my enzyme reflection! I hope you enjoyed it 🙂

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