MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel 7.012 Chemistry Review ANSWERS C C C C C C C OO H H H H N H H H CC O O C H H N H H C C O CH H C C CH HH H H H H C S CH H C H Protein Solution Substrate 1 2 3 4 This is the simplest correct bonding arrangement of the atoms and charges. 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-polar 13) Analog 1 (does not bind) C O O C O O (-) charge repels (-) charge of side group (1). Analog 2 (binds) H3N C OH3C Can still H-bond with side group (4). N H3N C O O H Polar group interacts unfavorably with hydrophobic environment.* Analog 3 (does not bind) * 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+ P S-P complex (dissolved (dissolved (dissolved in water) in water) 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 P.
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