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lec 11 - BL/CH401 Lecture 11 Introduction to Enzymes Part I...

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BL/CH401 Lecture 11 -- Introduction to Enzymes Part I. Background: What do enzymes really look like? Floating in space in front of the screen at eye level was a computer-generated visual model of the receptor site within the human protein (enzyme) dihydrofolate reductase. The protein looked like a lumpy, airy, sculpture made of clouds of blue and red points aggregated into the shape of beach balls and tennis balls melded together...The colored sphere-clouds were clumped, folded and twisted into a geometrically complex pocket -- the docking site (the active site of the enzyme). Think of it as similar to the kind of 3-D puzzle found inside a lock: a proper key opens a door by solving the lock. Quotation from Virtual Reality by Howard Reinhold, 1991, p. 26-27 (copyright ©1991 Howard Reinhold). How are computers changing the way we see enzymes? Clearly, this is illustrated by the quote above from Reinhold's Virtual Reality. Reinhold is describing what he saw when shown the structure of an enzyme in a virtual reality machine at the Univ. of North Carolina. His description of the active site of the enzyme is much more dynamic and colorful than anything I have been able to show you even with the computer programs showing the 3-D shape of proteins. The future prospect is that virtual reality machines will bring a better picture of what proteins really look and how they interact with the small molecules they bind like their substrates. To give another perspective on enzyme structure, here are some 3-D drawings of several proteins presented at the same scale. These drawings show the proteins at 5 million times their real size. The drawings emphasize the irregular surface of proteins. This may help you to understand what enzymes really look like. Figure 1. Cytochrome c (A) compared to an antibody (B). Figure 2. Two dehydrogenases: A) alcohol dehydrogenase; and B) GAP dehydrogenase. These
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figures are from American Scientist 80: 460-1, 1992. Part II. Enzyme Types Enzymes are biological catalysts. Like all catalysts, enzymes lower the energy needed to get a reaction started. Enzymes are much generally better at accelerating the rates of reactions than non-biological catalysts. Figure 3. Diagram showing that less energy is required to get an enzyme catalyzed reaction started as compared to a non-catalyzed reaction. Figure from Zubay et al., Principles of Biochemsitry copyright 1995 Brown Comm. Enzymes have been divided into 6 classes by the International Commission on Enzyme Nomenclature. All enzymes are assigned a number (called an EC number) which defines exactly the reaction catalyzed by the enzyme. For example, trypsin is EC since it is in class 3 (hydrolases) which work on peptide bonds (3.4) in the middle of proteins (3.4.21 are serine endopeptidases) - trypsin is the 4th entry in this subclass. Enzyme EC numbers can be looked up on the Web at http://expasy.hcuge.ch/sprot/enzyme.ht
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