Metabolic reactions often involve the attack by lone pairs of electrons residing on electron-rich molecules termed nucleophiles upon electron-poor atoms calledelectrophiles. Nucleophiles and electrophiles do not necessarily possess a formal negative or positive charge. Water, whose two lone pairs of sp3 electrons bear a partial negative charge, is an excellent nucleophile. Other nucleophiles of biologic importance include the oxygen atoms of phosphates, alcohols, and carboxylic acids; the sulfur of thiols; and the nitrogen atoms of amines and of the imidazole ring of histidine. Common electrophiles include the carbonyl carbons in amides, esters, aldehydes, and ketones and the phosphorus atoms of phosphoesters.
Nucleophilic attack by water typically results in the cleavage of the amide, glycoside, or ester bonds that hold biopolymers together. This process is termed hydrolysis. Conversely, when monomer units such as amino acids or monosaccharides are joined or condensed together to form biopolymers, such as proteins or starch, water is a product.
Hydrolysis typically is a thermodynamically favored reaction. Yet, the amide and phosphoester bonds of polypeptides and oligonucleotides are stable in the aqueous environment of the cell. This seemingly paradoxical behavior reflects the fact that the thermodynamics that govern the equilibrium point of a reaction do not determine the rate at which it will proceed toward its equilibrium point. In the cell, macromolecular catalysts called enzymes accelerate the rate of hydrolytic and other chemical reactions when needed. Proteases catalyze the hydrolysis of proteins into their component amino acids, while nucleases catalyze the hydrolysis of the phosphoester bonds in DNA and RNA. Precise and differential control of enzyme activity, including the sequestration of enzymes in specific organelles, enables cells to determine the physiologic circumstances under which a given biopolymer will be synthesized or degraded.
Many Metabolic Reactions Involve Group Transfer
Many of the enzymic reactions responsible for synthesis and breakdown of biomolecules involve the transfer of a chemical group G from a donor D to an acceptor A to form an acceptor group complex, A—G:
The hydrolysis and phosphorolysis of glycogen, for example, involve the transfer of glucosyl groups to water or to ortho phosphate. Since the equilibrium constants for these hydro lysis reactions strongly favor the formation of split products, it follows that many of the group transfer reactions responsible for the biosynthesis of macromolecules are, in and of themselves, thermodynamically unfavored. Enzyme catalysts play a critical role in surmounting these barriers by virtue of their capacity to directly link two normally separate reactions together. For example, by linking an energetically unfavorable group transfer reaction to a thermodynamically favorable one such as the hydrolysis of ATP, a new enzyme-catalyzed reaction can be generated. The free energy change of this coupled reaction will be the sum of the individual values for the two that were linked, one whose net overall change in free energy favors the formation of the covalent bonds required for bio polymer synthesis.
Water Molecules Exhibit a Slight but Important Tendency to Dissociate
The ability of water to ionize, while slight, is of central importance for life. Since water can act both as an acid and as a base, its ionization may be represented as an intermolecular proton transfer that forms a hydronium ion (H3O+) and a hydroxide ion (OH−):
The transferred proton is actually associated with a cluster of water molecules. Protons exist in solution not only as H3O+ but also as multimers such as H5O2 + and H7O3 +. The proton is nevertheless routinely represented as H+, even though it is in fact highly hydrated.
Since hydronium and hydroxide ions continuously recombine to form water molecules, anindividualhydrogen or oxy gen cannot be stated to be present as an ion or as part of a water molecule. At one instant it is an ion; an instant later it is part of a water molecule. Individual ions or molecules are therefore not considered. We refer instead to the probability that at any instant in time, a given hydrogen will be present as an ion or as part of a water molecule. Since 1 g of water contains 3.35 × 1022molecules, the ionization of water can be described statistically. To state that the probability that a hydrogen exists as an ion is 0.01 means that at any given moment in time, a hydro gen atom has 1 chance in 100 of being an ion and 99 chances out of 100 of being part of a water molecule. The actual prob ability of a hydrogen atom in pure water existing as a hydrogen ion is approximately 1.8 × 10−9. The probability of its being part of a water molecule thus is almost unity. Stated another way, for every hydrogen ion or hydroxide ion in pure water, there are 0.56 billion or 0.56 × 109water molecules. Hydrogen ions and hydroxide ions nevertheless contribute significantly to the properties of water.
For dissociation of water,
where the brackets represent molar concentrations (strictly speaking, molar activities) and K is the dissociation constant. Since 1 mole (mol) of water weighs 18 g, 1 liter (L) (1000 g) of water contains 1000 ÷ 18 = 55.56 mol. Pure water thus is 55.56 molar. Since the probability that a hydrogen in pure water will exist as a hydrogen ion is 1.8 × 10−9, the molar con centration of H+ ions (or of OH− ions) in pure water is the product of the probability, 1.8 × 10−9, times the molar concentration of water, 55.56 mol/L. The result is 1.0 × 10−7mol/L.
We can now calculate the dissociation constant K for pure water:
The molar concentration of water, 55.56 mol/L, is too great to be significantly affected by dissociation. It is therefore considered to be essentially constant. The concentration of pure water may therefore be incorporated into the dissociation constant K to provide a useful new constant Kw termed the ion product for water:
Note that the dimensions of K are moles per liter and those of Kw are moles2 per liter2. As its name suggests, the ion product Kw is numerically equal to the product of the molar concentrations of H+ and OH−:
At 25°C,Kw = (10−7)2, or 10−14(mol/L)2. At temperatures below 25°C,Kw is somewhat less than 10−14, and at temperatures above 25°C it is somewhat greater than 10−14. Within the stated limitations of temperature ,Kw equals 10−14(mol/L)2 for all aqueous solutions, even solutions containing acids or bases. We can therefore use Kw to calculate the pH of any aqueous solution.
