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FROM WATER TO DNA: THE CHEMISTRY OF LIFE

Organisms are made up of a lot of different chemicals. These vary in size, from small molecules like water to large molecules like DNA, and interact and associate in many different ways to generate the processes of life. In this chapter we will introduce some basic concepts of how these chemicals are made and interact. We will then describe the most important of these chemicals: water, carbohydrates, nucleotides, amino acids, and lipids.

H THE CHEMICAL BOND: SHARING ELECTRONS

Water is the most abundant substance in organisms. Cells are rich in water. Cytoplasm consists of organelles floating in a watery medium called cytosol that also contains proteins. The situation is not so different outside our cells. Although we are land animals living in air, most of our cells are bathed in a watery fluid called extracellular medium. We will therefore start by considering water itself.

Figure 2.1a shows a molecule of water, consisting of one atom of oxygen and two hydrogen atoms, joined to form an open V shape. The lines represent covalent bonds formed when atoms share electrons, each seeking the most stable structure. Oxygen has a greater affinity for electrons than does hydrogen so the electrons are not distributed equally. The oxygen grabs a greater share of the available negative charge than do the hydrogen atoms. The molecule of water is polarized, with partial negative charge on the oxygen and partial positive charges on the two hydrogens. We write the charge on each hydrogen as 5+

Cell Biology: A Short Course, Second Edition, by Stephen R. Bolsover, Jeremy S. Hyams, Elizabeth A. Shephard, Hugh A. White, Claudia G. Wiedemann ISBN 0-471-26393-1 Copyright © 2004 by John Wiley & Sons, Inc.

Figure 2.1. Water is a polar molecule while the chlorine molecule is nonpolar.

Figure 2.1. Water is a polar molecule while the chlorine molecule is nonpolar.

to indicate that it is smaller than the charge on a single hydrogen nucleus. The oxygen atom has the small net negative charge 25-. Molecules that, like water, have positive regions sticking out one side and negative regions sticking out the other are called polar.

Figure 2.1b shows a molecule of chlorine gas. It consists of two chlorine atoms, each of which consists of a positively charged nucleus surrounded by negatively charged electrons. Like oxygen, chlorine atoms tend to accept electrons when they become available, but the battle is equal in the chlorine molecule: The two atoms share their electrons equally and the molecule is nonpolar.

Figure 2.2. Formation of sodium chloride, an ionic compound.

Figure 2.2a shows what happens when a chlorine molecule is allowed to react with the metal sodium. Each atom of chlorine takes over one electron from a sodium atom. This leaves the sodium atoms with a single positive charge because there is now one more positive charge on the sodium nucleus than negatively charged surrounding electrons. Similarly, each chlorine atom now has a single negative charge because it now has one more electron than there are positive charges in its nucleus. Chemical species that have either gained or lost electrons, and that therefore bear an overall charge, are called ions. The reaction of chlorine and sodium has produced sodium ions and chloride ions. Positively charged ions like sodium are called cations while negatively charged ones like chloride are called anions. The positively charged sodium ions and the negatively charged chloride ions now attract each other strongly. If there are no other chemicals around, the ions will arrange themselves to minimize the distance between sodium and chloride, and the resulting well-packed array of ions is a crystal of sodium chloride, shown in Figure 2.2b.

INTERACTIONS WITH WATER: SOLUTIONS

Ionic Compounds Will Dissolve Only in Polar Solvents

Figure 2.3a shows one molecule of octane, the main constituent of gasoline. Octane is an example of a nonpolar solvent. Electrons are shared equally between carbon and hydrogen, and the component atoms do not bear a net charge.

Figure 2.3b shows a small crystal of sodium chloride immersed in octane. At the edge of the crystal, positively charged sodium ions are being pulled in toward the center of the crystal by the negative charge on chloride ions, and negatively charged chloride ions are being pulled in toward the center of the crystal by the positive charge on sodium ions. The sodium and chloride ions will not leave the crystal. Sodium chloride is insoluble in octane. However, sodium chloride will dissolve in water, and Figure 2.4a shows why. The chloride ion at the top left is being pulled into the crystal by the positive charge on its sodium ion neighbors, but at the same time it is being pulled out of the crystal by the positive charge on the hydrogen atoms of nearby water molecules. Similarly, the sodium ion at the bottom left is being pulled into the crystal by the negative charge on its chloride ion neighbors, but at the same time it is being pulled out of the crystal by the negative charge on the oxygen atoms of nearby water molecules. The ions are not held in the crystal so tightly and can leave. Once the ions have left the crystal, they become surrounded by a hydration shell of water molecules, all oriented in the appropriate direction (Fig. 2.4b)—oxygen inward for a positive ion like sodium, hydrogen inward for a negative ion like chloride. A chemical species in solution, whether in water or in any other solvent, is called a solute. Liquids whose main constituent is water are called aqueous.

Acids Are Molecules That Give H+ to Water

When we exercise, our muscle cells can become acid, and this is what creates the pain of cramping muscles and the heart pain of angina. Acidity is important in all areas of biology, from the acidity gradient that drives our mitochondria (page 261) to the ecological consequences of acid rain.

Acid solutions contain a high concentration of hydrogen ions. The hydrogen atom is unusual in that it only has one electron while, in its most common isotope, its nucleus

(a)

sodium chloride octane

Figure 2.3. (a) Structure of the nonpolar compound octane. (b) Ionic compounds are insoluble in nonpolar solvents.

comprises a single proton. In gasses at very low pressure it is possible for bare protons to exist alone and be manipulated, for example, in linear accelerators. However, in water protons never exist alone but always associate with another molecule, for example, with water to create the H3O+ ion. Acid solutions are those with an H3O+ concentration higher than 100 nmol liter-1.

Sour cream contains lactic acid. Pure lactic acid has the structure shown at the left of Figure 2.5a. The —COOH part in the box is called a carboxyl group. Both oxygens have a tendency to pull electrons away from the hydrogen and, in aqueous solution, the hydrogen is donated with a full positive charge to a molecule of water. The electron is left behind on the now negatively charged lactate ion.

Figure 2.4. Ionic compounds dissolve readily in water.

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