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0 60 120 180 240 300 360 Torsion angle (degrees)

FIGURE 1-21 Conformations. Many conformations of ethane are possible because of freedom of rotation around the C—C bond. In the ball-and-stick model, when the front carbon atom (as viewed by the reader) with its three attached hydrogens is rotated relative to the rear carbon atom, the potential energy of the molecule rises to a maximum in the fully eclipsed conformation (torsion angle 0°, 120°, etc.), then falls to a minimum in the fully staggered conformation (torsion angle 60°, 180°, etc.). Because the energy differences are small enough to allow rapid interconversion of the two forms (millions of times per second), the eclipsed and staggered forms cannot be separately isolated.

0 60 120 180 240 300 360 Torsion angle (degrees)

FIGURE 1-21 Conformations. Many conformations of ethane are possible because of freedom of rotation around the C—C bond. In the ball-and-stick model, when the front carbon atom (as viewed by the reader) with its three attached hydrogens is rotated relative to the rear carbon atom, the potential energy of the molecule rises to a maximum in the fully eclipsed conformation (torsion angle 0°, 120°, etc.), then falls to a minimum in the fully staggered conformation (torsion angle 60°, 180°, etc.). Because the energy differences are small enough to allow rapid interconversion of the two forms (millions of times per second), the eclipsed and staggered forms cannot be separately isolated.

FIGURE 1-22 Complementary fit between a macromolecule and a small molecule. A segment of RNA from the regulatory region TAR of the human immunodeficiency virus genome (gray) with a bound argin-inamide molecule (colored), representing one residue of a protein that binds to this region. The argininamide fits into a pocket on the RNA surface and is held in this orientation by several noncovalent interactions with the RNA. This representation of the RNA molecule is produced with the computer program GRASP, which can calculate the shape of the outer surface of a macromolecule, defined either by the van der Waals radii of all the atoms in the molecule or by the "solvent exclusion volume," into which a water molecule cannot penetrate.

FIGURE 1-22 Complementary fit between a macromolecule and a small molecule. A segment of RNA from the regulatory region TAR of the human immunodeficiency virus genome (gray) with a bound argin-inamide molecule (colored), representing one residue of a protein that binds to this region. The argininamide fits into a pocket on the RNA surface and is held in this orientation by several noncovalent interactions with the RNA. This representation of the RNA molecule is produced with the computer program GRASP, which can calculate the shape of the outer surface of a macromolecule, defined either by the van der Waals radii of all the atoms in the molecule or by the "solvent exclusion volume," into which a water molecule cannot penetrate.

they are freely interconvertible. However, when one or more of the hydrogen atoms on each carbon is replaced by a functional group that is either very large or electrically charged, freedom of rotation around the C—C bond is hindered. This limits the number of stable conformations of the ethane derivative.

Interactions between Biomolecules Are Stereospecific

Biological interactions between molecules are stereo-specific: the "fit" in such interactions must be stereo-chemically correct. The three-dimensional structure of biomolecules large and small—the combination of configuration and conformation—is of the utmost importance in their biological interactions: reactant with enzyme, hormone with its receptor on a cell surface, antigen with its specific antibody, for example (Fig. 1-22). The study of biomolecular stereochemistry with precise physical methods is an important part of modern research on cell structure and biochemical function.

In living organisms, chiral molecules are usually present in only one of their chiral forms. For example, the amino acids in proteins occur only as their l isomers; glucose occurs only as its d isomer. (The conventions for naming stereoisomers of the amino acids are described in Chapter 3; those for sugars, in Chapter 7; the RS system, described above, is the most useful for some biomolecules.) In contrast, when a compound with an asymmetric carbon atom is chemically synthesized in the laboratory, the reaction usually pro duces all possible chiral forms: a mixture of the d and l forms, for example. Living cells produce only one chiral form of biomolecules because the enzymes that synthesize them are also chiral.

Stereospecificity, the ability to distinguish between stereoisomers, is a property of enzymes and other proteins and a characteristic feature of the molecular logic of living cells. If the binding site on a protein is complementary to one isomer of a chiral compound, it will not be complementary to the other isomer, for the same reason that a left glove does not fit a right hand. Two striking examples of the ability of biological systems to distinguish stereoisomers are shown in Figure 1-23.

SUMMARY 1.2 Chemical Foundations

■ Because of its bonding versatility, carbon can produce a broad array of carbon-carbon skeletons with a variety of functional groups; these groups give biomolecules their biological and chemical personalities.

■ A nearly universal set of several hundred small molecules is found in living cells; the interconversions of these molecules in the central metabolic pathways have been conserved in evolution.

■ Proteins and nucleic acids are linear polymers of simple monomeric subunits; their sequences contain the information that gives each molecule its three-dimensional structure and its biological functions.

FIGURE 1-23 Stereoisomers distinguishable by smell and taste in humans. (a) Two stereoisomers of carvone: (R)-carvone (isolated from spearmint oil) has the characteristic fragrance of spearmint; (5)-carvone (from caraway seed oil) smells like caraway. (b) Aspartame, the artificial sweetener sold under the trade name NutraSweet, is easily distinguishable by taste receptors from its bitter-tasting stereoisomer, although the two differ only in the configuration at one of the two chiral carbon atoms.

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