FIGURE 2.3 The oxygen atom is more electronegative than either carbon or hydrogen. Therefore,the bonds between oxygen and these atoms are polarized to place a fractional negative charge (indicated by δ−) on the oxygen atom and a fractional positive charge (indicated by δ+) on the carbon or hydrogen atoms.

carbon and another carbon, is determined. For example, it can be predicted that glucose, whose molecular structure (Figure 2.4) is easily seen to have many carbon-oxygen and oxygen-hydrogen polar bonds, is polar and easily dissolved in water, even though it is not an ion. Such molecules are called hydrophilic (water loving).

Conversely, the molecule octane, a component of gasoline, has only carbon and hydrogen atoms, 8 and 18, respectively, and thus only nonpolar carbon-carbon and carbon-hydrogen bonds. Octane is therefore predicted to be nonpolar and insoluble in water, but soluble in other oils. Such molecules are called hydrophobic (averse to water).


Molecules that contain only carbon-carbon and carbon-hydrogen covalent bonds are relatively unreactive at standard temperatures.b Even terran life does not generally break unactivated carbon-carbon bonds directly and requires highly reactive species when it does so. The issue is slightly complicated because bonds can break in different ways.A bond strength is usually reported as a homolytic disassociation, in which one of the two electrons forming the bond remains on each of the atoms. Bond dissociation energies describe a bond’s strength after the bond has been broken and no new bonds are being formed. Reactivity is a different concept not unrelated to bond strength but often dependent on environment, because atoms that are no longer bonded can form bonds elsewhere.

The key to chemical reactions, including terran biochemical reactions,at standard temperatures and pressures is the reactivity of carbon-carbon and carbon-hydrogen bonds in molecules that also contain carbon-heteroatom (any atom other than carbon or hydrogen) bonds. Bonds to heteroatoms are often said to activate carbon-carbon and carbon-hydrogen bonds. In terran metabolism, the most important heteroatoms are oxygen and nitrogen, although sulfur is also important, and other heteroatoms such as phosphorus occasionally play a role.

The influence of these heteroatoms on the reactivity of carbon-scaffolded molecules is briefly reviewed in Section 2.4.1. As one unifying principle,hydrogen-heteroatom bonds break and re-form dynamically in water. In contrast, carbon-heteroatom bonds are rarely broken at standard temperatures unless another bond is formed at the same time. In general, for a chemical reaction to proceed under standard conditions at a rate metabolically useful for terran organisms, new bonds must be formed as old bonds are broken, or soon thereafter.

FIGURE 2.4 Structures of glucose (left) a and octane (right). Given the large number of dipolar C-O bonds and the large number of nonbonding electrons (the dots in the structure), one expects glucose to be a hydrophilic molecule that dissolves well in water.In contrast, octane can be seen, by its structure, to contain only nondipolar C-C and C-H bonds, and no unshared electron pairs. Therefore, octane is expected to be a hydrophobic compound insoluble in water.


Standard temperatures are temperatures where water is liquid at 1 atmosphere Earth pressure.

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