Enzymes Are Protein Based Structures Biology Essay

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The surface of enzymes active sites are lined with group of amino acid residues, that have substituent groups which can bind the substrate and lead to the beginning of the catalyzed reaction. Enzymes are astonishing catalysts, they been shown to speed up the rate of a reaction by 5 to 17 orders of magnitude.

Where E is the Enzyme, S is the substrate and P is the product. Firstly the enzyme cons into contact with the substrate, this then forms the Enzyme Substrate complex. Then the enzymatic reaction takes place forming a product or products and the enzyme is free to bind to another substrate.

Enzymes catalyze reactions due to their ability to lower the activation energy for the reaction to take place. there is a energy barrier in the way of substrates turning into products, this energy is

By lowering the activation energy the time it takes and energy needed to turn a substrate into its relative products is decreased dramatically. While enzymes catalyze chemical reactions they do not disturb the equilibrium of the reaction.

Chymotrypsin is a enzyme that acts on and hydrolyses proteins into smaller molecules. It's is produced in the pancreas in the form of an inactive precursor called chymotrypsinogen. As the chymotrypsinogen is secreted in to digestive system, proteases change chymotrypsinogen into it active form of chymotrypsin. Two forms of Chymotrypsin exist, A and B, which both have the same affinity to specific proteins and they selectively cleave peptide bonds that are formed in tryptophan, phenylalanine and tyrosine.

Chymotrypsin belongs to a particular category of enzymes known as serine proteases or serine endopeptidases, this is on the basis that a reagent such as diisopropylfluorophophate can modify a serine side chain on the molecule which in then leads to inactivation of the enzyme. Chymotrypson has a reactive serine site called Ser195.

The structure of chymotrysin is made up of three polypeptide chains which are interconnected by disulphide bonds. Comparing to other enzymes, chymotripsin has an abnormal structure which comes to fruition because of the change it undergoes when being converted to a protease (protease is a group of enzymes that catalyze the reactions that break down peptide bonds in protein molecules).

The construction of a-chymotrypsin is made up of a primary structure of two folded areas of amino acids, in which the secondary structure sits, within the secondary structure there are six strands of anti-parrallel b-sheet. This formation creates a distorted hydrogen connected cylinder. The active site of chymotrypsin has a shallow depression which is between the two domains mentioned above, added to this structure are also distinct pockets that have an important role in binding specific substrates. The active site also has certain charged groups; for example the a-amino group of Ile 16 and the carboxylate side-chains of Asp 102 and Asp 194 are buried in the interior of the molecule. These charged groups also help the enzymes with binding substrates to the active site.

Chymotrypsinogen is the zymogen for chymotrypsin, this zymogen is inactive due to the active site isnt properly formed, and therefore the substrate cannot be precisely postioned to take advantage of the reactive serine side chain. The substrates that chymotrypsin attach to are those with large hydrophobic side-chains, mostly those of tyrosine, tryptophan, or phenylalanine, and to a lesser degree those of leucine and methionine. Specificity of chymotrypsin is shown for the nature of the R group attached to the carbon atom on the amino side of the amide bond.

All the serine proteases have very similar structures, yet display quite different specificities to their substrates. Chymotrypsin has a specific attraction for amides with aromatic or other large hydrophobic side chains. But on the other hand trypsin has a specific attraction for amides with positively charged side chains: for example Lysine and Arginine. These differences in attraction to certain substrates can be derived from the major differences in the active sites of the enzymes. Chymotrypsin, which has a specific attraction for amides with aromatic or other large hydrophobic side chains, contains non polar side chains in the active site, this creates a complimentary site to come in contact with the hydrophobic side chains of the protein. Trypsin, which has a specific attraction for amides with positively charged side chains, conversely has an active site where the serine is substituted by aspartic acid and the negatively charged side chain is attached to the positively charged side chain of the substrate.

The cleavage of peptide bonds performed by Chymotrypsin are described in the following steps.

1. The substrate or polypeptide binds to the active site, the side chain of the residue neighboring the peptide bond places itself into the hydrophobic area of the enzyme allowing the peptide bond to be aligned for the following steps. This forms the Enzyme Substrate complex.

2.The formation of a Nucleophilic Alkoxide ion on Ser195 is created from the interaction between Ser195 and His57. This ion attacks the peptides carbonyl group, which then creates tetrahedral acyl-enzyme (tetrahedral intermediate).

3. The instability of the substrates carbonyl oxygen leads to the re-formation of the double bonding with carbon, which then displaces the bond between the carbon and amino group of the peptide link, therefore cleaving the peptide bond. This results in the first product being released from the enzyme substrate complex.

4. After the first product is released, a water molecule is released into the reaction, creating another Nucleophilic Alkoxide ion, this creates the second tetrahedral intermediate.

5. The second tetrahedral intermediate collapses and forms the second product which is a carboxulate anion, which displaces Ser195.

6. The second product is released and the active site on the enzyme is ready for another substrate to be bonded.

The chymotrypsin catalyzed reaction is pH dependent. The rate at which chymotrypsin cleaves peptide bonds is at its greatest with a pH of 8. This is very close to the pH of the small intestine, where chymotrypsin is in its active form.

Proteases such as chymotrypsin and trypsin degrade protein molecules into smaller peptides, this is an essential mechanism for the digestion of amino acids. These proteases are necessary for digestion, but uncontrolled they can be dangerous to cellular proteins. Because of this problem the body has created a set of controls, to activate and inactivate the proteases when needed.

Firstly chymotrypsin is produced in the pancreas in an inactive form, called chymotrypsinogen. This inactive form is then secreted into the small intestine where it is transformed into the A and B active forms by trypsin.

Protease inhibitors are also used to control chymotrypsin and other proteases while they are in their active form. In mammals glycoprotein's can act as protease inhibitors, they use the reactive site peptide bond, which binds to the enzyme, forming a stable complex in which the inhibitor peptide bond is hydrolyzed very slowly and this renders the enzyme inactive. Without the presence of inhibitors and the fact that chymotrypsin is produced in its inactive form, they could begin degrading intra and extra cellular proteins that they are not intended for.