o°o figure 3-9 Directional properties of hydrogen bonds, (a) The vector along the covalent O - H bond points directly at the acceptor oxygen, thereby forming a strong bond (b) The vector points away from the oxygen atom, resulting in a much weaker bond.

Weak Bonds between Molecules in Aqueous Solutions

The average energy of a secondary bond, though small compared to that of a cnvalent hnnd, is nonetheless strong enough compared tn heat energy to ensure that most molecules in aqueous solution will form secondary bonds to other molecules. The proportion of bonded

FIGURE 3-10 Diagram of a lattice farmed by water molecules. The energy gained by forming specific hydrogen bonds between water molecules favors the arrangement of the molecules in adjacent tetrahedrons. Oxygen atoms are indicated by large cirdes, hydrogen atoms by small circles. Although the rigidity of the arrangement depends on the temperature of the molecules, the pictured structure is nevertheless predominant in water as well as in ice (Source: Adapted from Pauling L. 1960. The nature of the. cticm/ccl bond and the structure of molecules and crystals: An introduction to modern structural chemistry, 3rd edition, p. 262. Copyright © I960 Cornell University. Used by permission of the publisher.)

to nonbonded arrangements is given by Equation 3-4, corrected to take into account the high concentration of molecules in a liquid, {( tells us that interaction energies as low as 2 to 3 kcal/mol are sufficient at physiological temperatures to force most molecules to form the maximum number of strong secondary bonds.

The specific structure of a solution at a given instant is markedly influenced by which solute molecules are present, not only because molecules have specific shapes, but also because molecules differ in which types of secondary bonds they can form- Thus, a molecule will tend to move until it is next to a molecule with which it can form the strongest possible bond.

Solutions, of course, are not static. Because of the disruptive influence of heat, the specific configuration of a solution is constantly

Box 3-1 The Uniqueness of Molecular Shapes and the Concept of Selective Stickiness

Even though most cellular molecules are built up from only a small number of chemical groups, such as OH, NHa, and CH^, there is great specificity as to whtch molecules tend to lie next to each other. This is because each molecule has unique bonding properties. One very dear demonstration comes from the specificity of stereoisomers. For example, proteins are always constructed from i-amino acids, never from their mirror images, the i>srmno acids (Box 3-1 Figure 1). Although the i> and L-amiro acids have identical covalent bonds, their binding properties to asymmetric molecules ate often very different. Thus, most eniymes ate specific for t-amino acids. If an t-amino acid ts able to attach to a specific enzyme, the d amino aod is unable to bind-

Most molecules in cells can make good "weak" bonds with only a small number of other molecules, partly because most molecules in biological systems exist in an aqueous environment. Tlte formation of a bond in a cell therefore depends not only on whether two molecules bind well to each other, but also on whether bond formation is overall more favorable than the alternative bonds that can form with solvent water molecules.


BOX 3-1 FIGURE 1 The two stereoisomers of the amino acid alanine, {Source: Adapted from Pauling L I960. The nature of the chemical bond and the structure of molecules and crystals: An introduction to modem structural chemistry, 3 rd Edition, p. 465. Copyright © 1960 Cornell University. Used by permission of the publisher. And from Pauling L. 1953. General chemistry, 2nd edition, p. 498. Copyright 1953 by W. H. Freeman. Used with permission,)

changing from one arrangement to another of approximately the same energy content. Equally important in biological systems is the fact that metabolism is continually transforming one molecule into another and so automatically changing the nature of the secondary bonds that can be formed. The solution structure of cells is thus constantly disrupted not only by heat motion, but also by the metabolic transformations of the cell's solute molecules.

Organic Molecules That Tend to Form Hydrogen Bonds Are Water Soluble

The energy of hydrogen bonds per atomic group is much greater than that of van der Waals contacts; thus, molecules will form hydrogen bonds in preference to van der Waals contacts. For example, if we try to mix water with a compound that cannot form hydrogen bonds, such as benzene, the water and benzene molecules rapidly separate From each other, the water molecules forming hydrogen bonds among themselves while the benzene molecules attach to one another by van der Waals bonds. It is therefore impossible to insert a nonhydrogen-bondtng organic molecule into water.

On the other hand, polar molecules such as glucose and pyruvate, which contain a large number of groups that form excellent hydrogen bonds (such as =0 or OH], are soluble in water (that is, they are hydrophilic as opposed to hydrophobic). While the insertion of such groups into a water lattice breaks water-water hydrogen bonds, it results simultaneously in the formation of hydrogen bonds hetween the polar organic molecule and water. These alternative arrangements, however, are not usually as energetically satisfactory as the water-water arrangements, so that even the most polar molecules ordinarily have only limited solubility.

Thus, almost all the molecules that cells acquire, either through food intake or through biosynthesis, are somewhat insoluble in water. These molecules, by their thermal movements, randomly collide with other molecules until they find complementary molecular surfaces on which to attach and thereby release water molecules for water-water interactions.

Hydrophobic "Bonds" Stabilize Macromolecutes

The strong tendency of water to exclude nonpolar groups is frequently referred to as hydrophobic bonding. Some chemists like to call all the bonds between nonpolar groups in a ivoter solution hydrophobic bonds (Figure 3-11). In a sense this term is a misnomer, for the phenomenon that it seeks to emphasize is the absence, not the presence, of bonds. (The bonds that tend to form between the nonpolar groups are due to van der Waals attractive forces.) On the other hand, the term hydrophobic bond is often useful, since it emphasizes the fact that nonpolar groups will try to arrange themselves so that they are not in contact with water molecules. Hydrophobic bonds are important both in the stabilization of proteins and complexes of proteins with other molecules and in the partitioning of proteins into membranes. They may account for as much as one-half the total free energy of protein folding.

Consider, for example, the different amounts of energy generated when the amino acids alanine and glycine are bound, in water, to a

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