Three Dimensional Structure Is Described by Configuration and Conformation

The covalent bonds and functional groups of a biomol-ecule are, of course, central to its function, but so also is the arrangement of the molecule's constituent atoms in three-dimensional space—its stereochemistry. A carbon-containing compound commonly exists as stereoisomers, molecules with the same chemical bonds but different stereochemistry—that is, different configuration, the fixed spatial arrangement of atoms. Interactions between biomolecules are invariably stereo-specific, requiring specific stereochemistry in the interacting molecules.

Figure 1-17 shows three ways to illustrate the stereo-chemical structures of simple molecules. The perspective diagram specifies stereochemistry unambiguously, but bond angles and center-to-center bond lengths are better represented with ball-and-stick models. In space-

FIGURE 1-17 Representations of molecules. Three ways to represent the structure of the amino acid alanine. (a) Structural formula in perspective form: a solid wedge (! represents a bond in which the atom at the wide end projects out of the plane of the paper, toward the reader; a dashed wedge ( ) represents a bond extending behind the plane of the paper. (b) Ball-and-stick model, showing relative bond lengths and the bond angles. (c) Space-filling model, in which each atom is shown with its correct relative van der Waals radius.

FIGURE 1-17 Representations of molecules. Three ways to represent the structure of the amino acid alanine. (a) Structural formula in perspective form: a solid wedge (! represents a bond in which the atom at the wide end projects out of the plane of the paper, toward the reader; a dashed wedge ( ) represents a bond extending behind the plane of the paper. (b) Ball-and-stick model, showing relative bond lengths and the bond angles. (c) Space-filling model, in which each atom is shown with its correct relative van der Waals radius.

gc=cd hoocd gcooh

Maleic acid (cis)

HOOC H

GC=CD

hd gcooh

Fumaric acid (trans)

FIGURE 1-18 Configurations of geometric isomers. (a) Isomers such as maleic acid and fumaric acid cannot be interconverted without breaking covalent bonds, which requires the input of much energy. (b) In the vertebrate retina, the initial event in light detection is the absorption of visible light by 11-c/s-retinal. The energy of the absorbed light (about 250 kJ/mol) converts 11-c/s-retinal to all-trans-retinal, triggering electrical changes in the retinal cell that lead to a nerve impulse. (Note that the hydrogen atoms are omitted from the ball-and-stick models for the retinals.)

FIGURE 1-18 Configurations of geometric isomers. (a) Isomers such as maleic acid and fumaric acid cannot be interconverted without breaking covalent bonds, which requires the input of much energy. (b) In the vertebrate retina, the initial event in light detection is the absorption of visible light by 11-c/s-retinal. The energy of the absorbed light (about 250 kJ/mol) converts 11-c/s-retinal to all-trans-retinal, triggering electrical changes in the retinal cell that lead to a nerve impulse. (Note that the hydrogen atoms are omitted from the ball-and-stick models for the retinals.)

13 CH3

13 CH3

11-cis-Retinal light

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