MIT Department of Biology 7.013: Introductory Biology - Spring 2005 Instructors: Professor Hazel Sive, Professor Tyler Jacks, Dr. Claudette Gardel 7.013 Solutions to Enzymes/Protein Structure a) i) leu-thr-phe-ala-ser (unchanged) ii) trp-tyr-lys + ala-phe iii) 2 lys + 2 arg GENERIC ENZYME: Schematics of enzymes: (side chains shown in black) ACTIVE SITE - peptide bond cleavage gly asp valilegly phe gly gly -gly protease A protease B protease C RECOGNITION POCKET -specific substrate regognition Schematics of substrates: lysine, arginine phenylalanine, glycine, alanine tryptophan, tyrosine peptide backbone + smalllong & + charged large & hydrophobic b) 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 means that protease A must cut after Phe/Trp/Tyr protease 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 not be enough room because glu is longer than asp. e) The others are required to hold the essential ones in place. The also provide the correct folding to bring these amino acids in close proximity and orientation. G A V M MET C CYS S S P PRO Y TYR F PHE W TRP H HIS R ARG KQ GLN E GLU NDT THR S SER I ILE L LEUALA LYS ASN ASP VAL GLY Figure by MIT OCW. AA sidechains, 7.013 CG 2004, 1AA 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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