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8885dc02_47-747/25/0310:05 AM Page54mac76mac76:385 Part I Structure and Catalysis Ordered water other Random variations in the positions of the electrons interacting with around one nucleus may create a transient electric di pole, which induces a transient, opposite electric dipole in the nearby atom. The two dipoles weakly attract each other, bringing the two nuclei closer. These weak at- tractions are called van der waals interactions. As Substrate the two nuclei draw closer together, their electron clouds begin to repel each other. At the point where the van der Waals attraction exactly balances this repulsive force. the nuclei are said to be in van der waals contact Each atom has a characteristic van der waals radius a measure of how close that atom will allow another to approach (Table 2-4). In the"space-filling"molecular models shown throughout this book, the atoms are de- picted in sizes proportional to their van der Waals radii. Weak Interactions Are crucial to macromolecular Structure and function The noncovalent interactions we have described (hy drogen bonds and ionic, hydrophobic, and van der Waals interactions)(Table 2-5) are much weaker than cova- Disordered water lent bonds. An input of about 350 kJ of energy is re- quired to break a mole of (6 X 102)C-C single bonds enzyme-substrate interaction nd about 410 k to break a mole of c-h bonds but little as 4 k is sufficient to disrupt a mole of typical van der Waals interactions. Hydrophobic interactions are also much weaker than covalent bonds, althoug they are substantially strengthened by a highly polar sol- vent (a concentrated salt solution, for example). Ionic interactions and hydrogen bonds are variable in strength, depending on the polarity of the solvent and stabilized gen-bonding ionic and obic interactions TABLE 2-4 van der Waals Radii and Covalent FIGURE 2-8 Release of ordered water favors formation of ar (Single-Bond)Radii of Some Elements enzyme-substrate complex. While separate, both enzyme and sub- Covalent radius for strate force neighboring water molecules into an ordered shell. Bind- Element radius(nm) single bond (nm) ing of substrate to enzyme releases some of the ordered water, and the resulting increase in entropy provides a thermodynamic push to- H 0.11 0.030 ward formation of the enzyme-substrate complex N 0.15 0.070 0.18 P 0.19 0.110 of the driving force for binding of a polar substrate (re 0.133 actant) to the complementary polar surface of an en- zyme is the entropy increase as the enzyme displaces ordered water from the substrate(Fig. 2-8) Sources: For van der Waals radii, Chauvin, R.( 1992)Explicit periodic trend of van der Waals radil. J Phys. Chem. 96, 9194-9197 For covalent radi, Pauling, L(1960)Nature of van der waals Interactions Are weak lote: van der waals radii describe the space filling dimensions of atoms. when two atoms Interatomic Attractions re joined covalently, the atomic radii at the point of bonding are less than the van der Waals radii, because the joined atoms are pulled together by the shared electron pair. The When two uncharged atoms are brought very close to- an der Waals interaction or a covalent bond is about equal he van der Waals or covalent radil, respectively, for the two atoms. Thus the gether, their surrounding electron clouds influence each length of a carbon-carbon single bond is about 0.077 nm +0.077 nm=0.154 nmof the driving force for binding of a polar substrate (reactant) to the complementary polar surface of an enzyme is the entropy increase as the enzyme displaces ordered water from the substrate (Fig. 2–8). van der Waals Interactions Are Weak Interatomic Attractions When two uncharged atoms are brought very close together, their surrounding electron clouds influence each other. Random variations in the positions of the electrons around one nucleus may create a transient electric dipole, which induces a transient, opposite electric dipole in the nearby atom. The two dipoles weakly attract each other, bringing the two nuclei closer. These weak attractions are called van der Waals interactions. As the two nuclei draw closer together, their electron clouds begin to repel each other. At the point where the van der Waals attraction exactly balances this repulsive force, the nuclei are said to be in van der Waals contact. Each atom has a characteristic van der Waals radius, a measure of how close that atom will allow another to approach (Table 2–4). In the “space-filling” molecular models shown throughout this book, the atoms are depicted in sizes proportional to their van der Waals radii. Weak Interactions Are Crucial to Macromolecular Structure and Function The noncovalent interactions we have described (hydrogen bonds and ionic, hydrophobic, and van der Waals interactions) (Table 2–5) are much weaker than covalent bonds. An input of about 350 kJ of energy is required to break a mole of (6 1023) COC single bonds, and about 410 kJ to break a mole of COH bonds, but as little as 4 kJ is sufficient to disrupt a mole of typical van der Waals interactions. Hydrophobic interactions are also much weaker than covalent bonds, although they are substantially strengthened by a highly polar solvent (a concentrated salt solution, for example). Ionic interactions and hydrogen bonds are variable in strength, depending on the polarity of the solvent and 54 Part I Structure and Catalysis Substrate Enzyme Disordered water displaced by enzyme-substrate interaction Enzyme-substrate interaction stabilized by hydrogen-bonding, ionic, and hydrophobic interactions Ordered water interacting with substrate and enzyme FIGURE 2–8 Release of ordered water favors formation of an enzyme-substrate complex. While separate, both enzyme and substrate force neighboring water molecules into an ordered shell. Binding of substrate to enzyme releases some of the ordered water, and the resulting increase in entropy provides a thermodynamic push toward formation of the enzyme-substrate complex. Sources: For van der Waals radii, Chauvin, R. (1992) Explicit periodic trend of van der Waals radii. J. Phys. Chem. 96, 9194–9197. For covalent radii, Pauling, L. (1960) Nature of the Chemical Bond, 3rd edn, Cornell University Press, Ithaca, NY. Note: van der Waals radii describe the space-filling dimensions of atoms. When two atoms are joined covalently, the atomic radii at the point of bonding are less than the van der Waals radii, because the joined atoms are pulled together by the shared electron pair. The distance between nuclei in a van der Waals interaction or a covalent bond is about equal to the sum of the van der Waals or covalent radii, respectively, for the two atoms. Thus the length of a carbon-carbon single bond is about 0.077 nm 0.077 nm 0.154 nm. van der Waals Covalent radius for Element radius (nm) single bond (nm) H 0.11 0.030 O 0.15 0.066 N 0.15 0.070 C 0.17 0.077 S 0.18 0.104 P 0.19 0.110 I 0.21 0.133 van der Waals Radii and Covalent (Single-Bond) Radii of Some Elements TABLE 2–4 8885d_c02_47-74 7/25/03 10:05 AM Page 54 mac76 mac76:385_reb: