lec 15 b - BL/CH 401 Lecture#15B Enzyme Mechanisms Serine...

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BL/CH 401 Lecture #15B Enzyme Mechanisms - Serine Proteases Part I. Introduction - Concept of an Enzyme's Mechanism of Catalysis. The concept of a mechanism of a reaction as used in organic chemistry was explained in the last lecture as an introduction for its use in biochemistry. In biochemistry the same thing is done to explain how an enzyme catalyzes a reaction. But the process is more complicated. Here the question raised at the end of the last lecture will be answered. These questions were: How do the amino acid side chains of an enzyme assist is bond rearrangements? Can a plausible mechanism of action for enzyme catalyzed reactions be formulated by the biochemist in a manner similar to that done by the organic chemist? First, one must discover what amino acid (AA) side chains in the enzyme (protein) are involved in catalysis - so try to identify the active site of the enzyme. We know that only a few AAs will be at the active site, since most of the AAs are involved in forming the framework of the enzyme (protein). OK - so you determine the AA sequence of the enzyme. Assuming that there are similar enzymes catalyzing the same type of reaction, then determine the AA sequences of enzymes that catalyze the same type of reaction. Then compare those sequences to identify identical residues (AAs). These AA residues will have important side chains involved in the active site and in forming the framework. Let's approach this subject using proteases like trypsin, chymotrypsin etc., which are enzymes that you are already a bit familiar with. The mechanism of catalysis for these enzymes, which are called serine proteases since serine plays a key role in catalysis, is very well understood. Part II. Serine Proteases - Comparison of Amino Acid Sequences. To understand this process let's look at an example. Trypsin is a member of a family of enzymes known as the serine-proteases. Chymotrypsin and Elastase are also members of this family of enzymes. Trypsin, Chymotrypsin, and Elastase are synthesized in the pancreas and excreted into the intestine. They are made as pre-enzymes and activated in the intestine by partial proteolytic degradation. The AA sequences are very similar with 62 AA the same out of 257. Their 3-D structures are very similar - little alpha-helix - and a central beta sheet.
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elastase. Figure from Principles of Biochemistry Zubay et al. copyright ©1995 by Wm. C. Brown Communications, Inc. The amino acids in common and their positions in the sequence are shown by colored highlighting. Three key amino acids (His-57, Asp-102 and Ser-195) involved in the mechanism of catalysis of these enzymes are emphasized by the large circles over them. The thin lines in each sequence represent disulfide bonds which cross-link the polypeptide backbone of each enzyme. In trypsin and chymotrypsin, the sections of the amino acid sequences removed by proteolytic degradation during activation in the intestine are shown by '+++'. Thus, part of the
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This note was uploaded on 09/02/2009 for the course BIO BL 401 taught by Professor Wilbur during the Spring '07 term at Michigan Technological University.

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lec 15 b - BL/CH 401 Lecture#15B Enzyme Mechanisms Serine...

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