Sandbox 32: Difference between revisions

=Catalytic Mechanism=

The function of Trypsin is to break down peptides using a hydrolysis reaction into amino acid building blocks. This mechanism is a general catalytic mechanism that all Serine proteases use.  The active site where this mechanism occurs in Trypsin is composed of three amino acids and called a <scene name='Sandbox_45/Ctriadd102h57s195/4'>catalytic triad</scene>. The three catalytic residues are Serine 195, Histidine 57, and Aspartate 102 <ref>Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008.</ref>. The structure of the catalytic triad and the mechanism are shown in the figures to the right. In the mechanism, serine is bonded to the imidazole ring of the histidine. When histidine accepts a proton from serine an alkoxide nucleophile is formed. This nucleophile attacks the substrate when the substrate is present. The role of the aspartate residue is hold histidine in the proper position to make it a good proton acceptor. What makes this mechanism works is that a pocket if formed from the three residues and the three residues function to hold each other in proper position for nucleophilic attack.  

The steps of the mechanism involve two tetrahedral intermediates and an Acyl-enzyme intermediate <ref>Structural Biochemistry. 10 June 2010. 30 October 2010.<http://en.wikibooks.org/wiki/Structural_Biochemistry/Enzyme/Catalytic_Triad>.</ref>. The mechanism can be followed in more detail in the figure on the right <ref>Image From: http://www.bmolchem.wisc.edu/courses/spring503/503-sec1/DRAWINGS/503-3a-2serineprotease.jpg</ref>.

<applet scene='Sandbox_32/Chymotrypsin/1' size='275' frame='true' align='true' align='left' caption='Structure of Chymotrypsin and Elastase.'/>  

Trypsin, chymotrypsin, and elastase are all digestive enzymes that are produced in the pancreas and catalyze the hydrolysis of peptide bonds. Each of these enzymes has different specificities in regards to the side chains next to the peptide bond. Chymotrypsin prefers a large hydrophobic residue, trypsin is specific for a positively charged residue, and elastase prefers a small neutral residue. Chymotrypsin, trypsin and elastase are all proteins that contain a catalytic mechanism and hydrolyze peptides using the serine protease mechanism. Chymotrypsin and elastase are both homologs of Trypsin since they are 40% alike in structure and composition <ref> Pratt, C.W., Voet, D., Voet, J.G. Fundamentals of Biochemistry - Life at the Molecular Level - Third Edition. Voet, Voet and Pratt, 2008. </ref>. In the <scene name='Sandbox_32/Chymotrypsin/2'>Chymotrypsin</scene> structure shown the alpha helices are blue, the beta sheets are green, and the remainder of the protein is red. In the <scene name='Sandbox_32/Elastase/2'>Elastase</scene> structure shown the alpha helices are in red, the beta sheets are yellow, and the remainder of the protein is orange.

==References==