AA sidechains, 7.013 CG 2004, 17.012 Solutions to Enzymes/Protein Structurea) i) leu-thr-phe-ala-ser (unchanged) ii) trp-tyr-lys + ala-phe iii) 2 lys + 2 argACTIVE SITE -peptide bond cleavageRECOGNITION POCKET -specific substrate regognitionGENERIC ENZYME:glyaspvalileprotease Aprotease Cprotease Bglyphegly gly-peptide backbonelysine, argininephenylalanine, tryptophan, tyrosineglycine, alanineSchematics of substrates:Schematics of enzymes: (side chains shown in black)+long & + chargedlarge & hydrophobicsmallglyb) Matching them up:protease A - large open pocket. Could be Lys/Arg or Phe/Trp/Tyr.protease B - large open pocket with (-) charge at bottom. Therefore, Lys/Arg, which meansthat protease A must cut after Phe/Trp/Tyrprotease C - small pocket. Gly, Ala.c) Change the asp in the bottom of the pocket in protease B to a lys or arg.d) It might still bind lys or arg, but if the space in the pocket were constrained, there might notbe enough room because glu is longer than asp.e) The others are required to hold the essential ones in place. The also provide the correctfolding to bring these amino acids in close proximity and orientation.GA VMMETCCYSSSPPROYTYRFPHEWTRPHHISRARGKLYSQGLNEGLUNASNDASPTTHRSSERIILELLEUVALALAGLYFigure by MIT OCW.MIT Biology Department7.012: Introductory Biology - Fall 2004Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette GardelAA sidechains, 7.013 CG 2004, 2f) Protease A is a protein, therefore other protease A molecules can cleave it and therebyinactivate it. Having casein around decreases the chance that a protease A molecule will cleavea protease A molecule, because it will be more likely to cleave the more numerous caseinmolecules.g) The protease enzyme must be able to bind to the target amino acids. If they are buriedinside the target protein, the protease can't "see" them and therefore can't cut at them.Eventually, the structure of the target protein gets so broken down that the inside amino acidsare exposed to the protease.h) To protect protease A from degradation by other protease A molecules, bury all thephe/trp/tyr inside the protein so that they cannot be recognized and cleaved.i) The graph should show an exponential rise – the more enzyme, the faster enzyme will beproduced. Eventually, the enzyme will be degraded as in part (e). This is sketched
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