CCCCCCCOOH HHHNHHHC COOCHHNHHCCOCHHCCCHH HHHHHCSCHHCHProteinSolutionSubstrate1234This is the simplest correct bonding arrangement of the atoms and charges.MIT Department of Biology 7.013: Introductory Biology - Spring 2005 Instructors: Professor Hazel Sive, Professor Tyler Jacks, Dr. Claudette Gardel 7.013 Sp 05 Chemistry Review Answers 1) 2) Non-covalent Interactions a)Group Interaction(s) of Group with Substrate Classification of Group (1) ionic (hydrogen also possible) hydrophilic-charged (2) VDW (neither C nor S is electronegative enough to cause a H-bond to form) hydrophobic (3) VDW (all non-polar bonds) hydrophobic (4) H-bond (VDW also possible) hydrophilic-polar7.013 Sp 05 Chemistry Review Answers 3) Substrate Analogues Analog 1(does not bind)CO OCOO(-) charge repels (-) charge of side group (1).Analog 2(binds)H3NCOH3CCan still H-bondwith side group (4).Analog 3(does not bind)NH3NCO OHPolar group interacts unfavorably with hydrophobic environment.** Note: a more complete way to look at these cases is:!! Binding of substrate (S) and protein (P) to form complex (S-P) is an equilibrium: S(dissolved in water)+ P(dissolved in water)S-P complex(dissolved in water)• Compared to the normal substrate, the extra COO- group in analog 1 destabilizes (raises the free energy of) the S-P complex because of the charge repulsion, shifting the equilibrium to favor free S and P.• Compared to the normal substrate, the addition of the polar N-H group (whichcan H-bond with water) in analog 3 stabilizes (lowers the free energy of) free S in solution, shifting the equilibrium to favor free S and
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