Hydrogen, oxygen, carbon, nitrogen, phosphorus, and sulfur are the most abundant elements found in biological molecules. These atoms, which rarely exist as isolated entities, readily form covalent bonds with other atoms, using electrons that reside in the outermost electron orbitals surrounding their nuclei. As a rule, each type of atom forms a k k characteristic number of covalent bonds with other atoms, with a well-defined geometry determined by the atom's size and by both the distribution of electrons around the nucleus and the number of electrons that it can share. In some cases (e.g., carbon), the number of stable covalent bonds formed is fixed; in other cases (e.g., sulfur), different numbers of stable covalent bonds are possible.
All the biological building blocks are organized around the carbon atom, which normally forms four covalent bonds with two to four other atoms. As illustrated by the methane (CH4) molecule, when carbon is bonded to four other atoms, the angle between any two bonds is 109.5° and the positions of bonded atoms define the four points of a tetrahedron (Figure 2-2a). This geometry helps define the structures of many biomolecules. A carbon (or any other) atom bonded to four dissimilar atoms or groups in a nonplanar configuration is said to be asymmetric. The tetrahedral orientation of bonds formed by an asymmetric carbon atom can be arranged in three-dimensional space in two different ways, producing molecules that are mirror images of each other, a property called chirality. Such molecules are called optical isomers, or
▲ FIGURE 2-2 Geometry of bonds when carbon is covalently linked to four or three other atoms. (a) If a carbon atom forms four single bonds, as in methane (CH4), the bonded atoms (all H in this case) are oriented in space in the form of a tetrahedron. The letter representation on the left clearly indicates the atomic composition of the molecule and the bonding pattern. The ball-and-stick model in the center illustrates the geometric arrangement of the atoms and bonds, but the diameters of the balls representing the atoms and their nonbonding electrons are unrealistically small compared with the bond lengths. The sizes of the electron clouds in the space-filling model on the right more accurately represent the structure in three dimensions. (b) A carbon atom also can be bonded to three, rather than four, other atoms, as in formaldehyde (CH2O). In this case, the carbon bonding electrons participate in two single bonds and one double bond, which all lie in the same plane. Unlike atoms connected by a single bond, which usually can rotate freely about the bond axis, those connected by a double bond cannot.
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