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3. The table on the last page compares for each of four different proteolytic enzymes the chemical bonding structure of a classical substrate with the structures of two competitive inhibitors. For each substrate structure an arrow indicates the position of the scissile bond, i.e., the bond that is cleaved through catalytic action. For each enzyme, one of the inhibitors is a classical competitive inhibitor while the other is a transition-state inhibitor analog. While ordinary competitive inhibitors are associated with (dissociation) inhibitor equilibrium con- stants of ~10-³ to 10-6 M, transition-state analogs exhibit inhibitor constants ≤ 10-⁹ M. (a) For each enzyme draw a circle around those parts of the substrate that account for specificity of substrate recognition. (b) For each enzyme identify the transition-state inhibitor analog by drawing a circle around it and give a brief explanation of why it mimics the structure of the transition-state species. (c) Draw a "generic" Lineweaver-Burk plot that would apply to each enzyme in which there are only three straight lines that separately represent (1) initial velocity data in the absence of an inhibitor, (2) initial velocity data in the presence of the classical competitive inhibitor, and (3) initial velocity data in the presence of the transition-state inhibitor analog.

3. The table on the last page compares for each of four different proteolytic enzymes the chemical bonding structure of a classical substrate with the structures of two competitive inhibitors. For each substrate structure an arrow indicates the position of the scissile bond, i.e., the bond that is cleaved through catalytic action. For each enzyme, one of the inhibitors is a classical competitive inhibitor while the other is a transition-state inhibitor analog. While ordinary competitive inhibitors are associated with (dissociation) inhibitor equilibrium con- stants of ~10-³ to 10-6 M, transition-state analogs exhibit inhibitor constants ≤ 10-⁹ M. (a) For each enzyme draw a circle around those parts of the substrate that account for specificity of substrate recognition. (b) For each enzyme identify the transition-state inhibitor analog by drawing a circle around it and give a brief explanation of why it mimics the structure of the transition-state species. (c) Draw a "generic" Lineweaver-Burk plot that would apply to each enzyme in which there are only three straight lines that separately represent (1) initial velocity data in the absence of an inhibitor, (2) initial velocity data in the presence of the classical competitive inhibitor, and (3) initial velocity data in the presence of the transition-state inhibitor analog.

Biochemistry
Biochemistry
9th Edition
ISBN:9781319114671
Author:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Publisher:Lubert Stryer, Jeremy M. Berg, John L. Tymoczko, Gregory J. Gatto Jr.
Chapter1: Biochemistry: An Evolving Science
Section: Chapter Questions
Problem 1P
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3. The table on the last page compares for each of four different proteolytic enzymes the chemical bonding structure of a classical substrate with the structures of two competitive inhibitors. For each substrate structure an arrow indicates the position of the scissile bond, i.e., the bond that is cleaved through catalytic action. For each enzyme, one of the inhibitors is a classical competitive inhibitor while the other is a transition-state inhibitor analog. While ordinary competitive inhibitors are associated with (dissociation) inhibitor equilibrium con- stants of ~10-3 to 10-6 M, transition-state analogs exhibit inhibitor constants ≤ 10-⁹ M. (a) For each enzyme draw a circle around those parts of the substrate that account for specificity of substrate recognition. (b) For each enzyme identify the transition-state inhibitor analog by drawing a circle around it and give a brief explanation of why it mimics the structure of the transition-state species. (c) Draw a "generic" Lineweaver-Burk plot that would apply to each enzyme in which there are only three straight lines that separately represent (1) initial velocity data in the absence of an inhibitor, (2) initial velocity data in the presence of the classical competitive inhibitor, and (3) initial velocity data in the presence of the transition-state inhibitor analog.
Transcribed Image Text:3. The table on the last page compares for each of four different proteolytic enzymes the chemical bonding structure of a classical substrate with the structures of two competitive inhibitors. For each substrate structure an arrow indicates the position of the scissile bond, i.e., the bond that is cleaved through catalytic action. For each enzyme, one of the inhibitors is a classical competitive inhibitor while the other is a transition-state inhibitor analog. While ordinary competitive inhibitors are associated with (dissociation) inhibitor equilibrium con- stants of ~10-3 to 10-6 M, transition-state analogs exhibit inhibitor constants ≤ 10-⁹ M. (a) For each enzyme draw a circle around those parts of the substrate that account for specificity of substrate recognition. (b) For each enzyme identify the transition-state inhibitor analog by drawing a circle around it and give a brief explanation of why it mimics the structure of the transition-state species. (c) Draw a "generic" Lineweaver-Burk plot that would apply to each enzyme in which there are only three straight lines that separately represent (1) initial velocity data in the absence of an inhibitor, (2) initial velocity data in the presence of the classical competitive inhibitor, and (3) initial velocity data in the presence of the transition-state inhibitor analog.
Enzyme Carboxypeptidase A Papain α-chymotrypsin HIV protease Substrate CBZ-NH-CH,-C--NH-CH-COOH N-CBZ-glycyl-L-phenylalanine CH₂ T C6H5 i CBZ-NH-CH--C-NH-CH, CẠNH NHI NH CH₂ C6 Hz N-CBZ-L-phenylalanyl-glycyl- CH₂- p-nitroanilide i CH,-C-NH-CH-C-NH-CH2-COOH 1 CH2 C6 H5 NO2 N-acetyl-L-phenylalanyl-glycine CHO LINH CHÍNH CH -NH-- 1 CH CH₂ CH3 CH3 C6H5 NH-CH-C-NH-CH-COOH I CH3 N-acetyl-L-valyl-L-phenylalanyl-L-alanine Inhibitor I CBZ-NH-CH-C-NH-CH-COOH CH3 N-CBZ-D-alanyl-L-phenylalanine CH3-C i CBZ-NH-CH-C--NH-CH,CH 1-C₁₂-1 T CH₂ C Hs T CH₂ C6H5 N-CBZ-L-phenylalanyl-glycinal ů NH--CH--C--OH CH₂ C6H5 N-acetyl-L-phenylalanine CH,--C--NH-CH-C-NH-CH-C-CH2-CH-COOH CH CH2 CH3 CH3 C6H5 CH 3 N-(N-(acetyl)-valyl)-5-amino-5-benzyl-4-keto- 2-methyl-pentanoic acid CBZ--NH-CH₂--P--NH-CH--COOH O Inhibitor II N-(CBZ-aminomethyl-oxyhydroxyphos- phinyl)-L-phenylalanine i CBZ--NH--CH--C--NH-CH2-COOH 8 1 CH2 C6H5 CH 2 C6H5 N-CBZ-L-phenylalanyl-glycine 요 CH3--C--NH--CH--CH(OH)CH₂CH₂COOH CH2 C6H5 N-acetyl-5-amino-5-benzyl-4-hydroxy- pentanoic acid 요 CH,--C--NH--CH--C-NH--CH--C--OH CH CH 11E0 CH₂ CH3 CH3 C6H5 N-acetyl-L-valyl-L-phenylalanine
Transcribed Image Text:Enzyme Carboxypeptidase A Papain α-chymotrypsin HIV protease Substrate CBZ-NH-CH,-C--NH-CH-COOH N-CBZ-glycyl-L-phenylalanine CH₂ T C6H5 i CBZ-NH-CH--C-NH-CH, CẠNH NHI NH CH₂ C6 Hz N-CBZ-L-phenylalanyl-glycyl- CH₂- p-nitroanilide i CH,-C-NH-CH-C-NH-CH2-COOH 1 CH2 C6 H5 NO2 N-acetyl-L-phenylalanyl-glycine CHO LINH CHÍNH CH -NH-- 1 CH CH₂ CH3 CH3 C6H5 NH-CH-C-NH-CH-COOH I CH3 N-acetyl-L-valyl-L-phenylalanyl-L-alanine Inhibitor I CBZ-NH-CH-C-NH-CH-COOH CH3 N-CBZ-D-alanyl-L-phenylalanine CH3-C i CBZ-NH-CH-C--NH-CH,CH 1-C₁₂-1 T CH₂ C Hs T CH₂ C6H5 N-CBZ-L-phenylalanyl-glycinal ů NH--CH--C--OH CH₂ C6H5 N-acetyl-L-phenylalanine CH,--C--NH-CH-C-NH-CH-C-CH2-CH-COOH CH CH2 CH3 CH3 C6H5 CH 3 N-(N-(acetyl)-valyl)-5-amino-5-benzyl-4-keto- 2-methyl-pentanoic acid CBZ--NH-CH₂--P--NH-CH--COOH O Inhibitor II N-(CBZ-aminomethyl-oxyhydroxyphos- phinyl)-L-phenylalanine i CBZ--NH--CH--C--NH-CH2-COOH 8 1 CH2 C6H5 CH 2 C6H5 N-CBZ-L-phenylalanyl-glycine 요 CH3--C--NH--CH--CH(OH)CH₂CH₂COOH CH2 C6H5 N-acetyl-5-amino-5-benzyl-4-hydroxy- pentanoic acid 요 CH,--C--NH--CH--C-NH--CH--C--OH CH CH 11E0 CH₂ CH3 CH3 C6H5 N-acetyl-L-valyl-L-phenylalanine
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For answer (a) regarding the last row of compounds, why is the -CH-(CH3)2 not also responsible for the substrate specificity given it is also identical across the substrate and the inhibitors?

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