When some substances dissolve in water, they release hydrogen ions (H+) which are actually single, positively charged protons. These tiny bits of charged matter can attach to other molecules, and in doing so, change their properties. For example, the protons in acid rain can damage plants, and you are probably familiar with excess stomach acidity that affects digestion. In this section, will be examined the properties of substances that release H+ (called acids) and substances that attach to H+ (called bases). We will distinguish strong and weak acids and bases and provide a quantitative means for stating the concentration of H+ in solutions: the pH scale.
Acids donate H+, bases accept H+
If hydrochloric acid (HCl) is added to water, it dissolves and ionizes, releasing the ions H+ and Cl–: HCl → H+ + Cl–.
Because its H+ concentration has increased, such a solution is acidic. Just like the combustion reaction of propane and oxygen the dissolution of HCl to form its ions is a complete reaction. HCl is therefore called a strong acid.
Acids release H+ ions in solution. HCl is an acid, as is H2SO4 (sulfuric acid). One molecule of sulfuric acid may ionize to yield two H+ and one SO42–. Biological compounds that contain —COOH (the carboxyl group; are also acids (such as acetic acid and pyruvic acid), because —COOH → —COO– + H+ not all acids dissolve fully in water. For example, if acetic acid is added to water, at the end of the reaction, there are not just the two ions but some of the original acid as well. Because the reaction is not complete, acetic acid is a weak acid. Bases accept H+ in solution. Just as with acids, there are strong and weak bases. If NaOH (sodium hydroxide) is added to water, it dissolves and ionizes, releasing OH– and Na+ ions: NaOH →Na+ + OH–. Because the concentration of OH– increases and OH– absorbs H+ to form water, such a solution is basic. Because this reaction is complete, NaOH is a strong base. Weak bases include the bicarbonate ion (HCO3–), which can accept a H+ ion and become carbonic acid (H2CO3), and ammonia (NH3), which can accept a H+ and become an ammonium ion (NH4+). Amino groups (—NH2) in biological molecules can also accept protons, thus, acting as bases: —NH2 + H+ →—NH3+.
The reactions between acids and bases may be reversible
When acetic acid is dissolved in water, two reactions happen. First, the acetic acid forms its ions: CH3COOH → CH3COO– + H+. Then, once ions are formed, they re-form acetic acid:
CH3COO– + H+ → CH3COOH
This pair of reactions is reversible. A reversible reaction can proceed in either direction—left to right or right to left—depending on the relative starting concentrations of the reactants and products. The formula for a reversible reaction can be written, using a double arrow: CH3COOH ~ CH3COO– + H+. In principle, all chemical reactions are reversible. In terms of acids and bases, there are two types of reactions, depending on the extent of reversibility:
– Ionization of strong acids and bases is virtually irreversible.
– Ionization of weak acids and bases is somewhat reversible. Many of the acid and base groups on large molecules in biological systems are weak.
Water is a weak acid
The water molecule has a slight but significant tendency to ionize into a hydroxide ion (OH–) and a hydrogen ion (H+). Two water molecules participate in this ionization. One of the two molecules “captures” a hydrogen ion from the other, forming a hydroxide ion and a hydronium ion: The hydronium ion is in effect a hydrogen ion bound to a water molecule. For simplicity, biochemists tend to use a modified representation of the ionization of water:
H2O →H+ + OH–. The ionization of water is important to all living creatures. This fact may seem surprising, since only about one water molecule in 500 million is ionized at any given time. But there will be less surprise when the attention is focused on the abundance of water in living systems and the reactive nature of the H+ produced by ionization.
pH is the measure of hydrogen ion concentration
The terms “acidic” and “basic” refer only to solutions. How acidic or basic a solution is depends on the relative concentrations of H+ and OH– ions in it. The terms “acid” and “base” refer to compounds and ions. A compound or ion that is an acid can donate H+; one that is a base can accept H+. A solution with a pH of less than 7 is acidic — it contains more H+ ions than OH– ions. A solution with a pH of 7 is neutral and a solution with a pH value greater than 7 is basic.
Buffers minimize pH change
Some organisms, probably including the earliest forms of life, live in and have adapted to solutions with extremes of pH. Most organisms control the pH of the separate compartments within their cells. The normal pH of human red blood cells, for example, is 7.4, and deviations of even a few tenths of a pH unit can be fatal. The control of pH is made possible in part by buffers: chemical mixtures that maintain a relatively constant pH even when substantial amounts of an acid or base are added. Abuffer is a mixture of a weak acid and its corresponding base—for example, carbonic acid (H2CO3) and bicarbonate ions (HCO3–). If an acid is added to a solution containing this buffer, not all the H+ ions from that acid stay in solution. Instead, many of them combine with the bicarbonate ions to produce more carbonic acid. This reaction uses up some of the H+ ions in the solution and decreases the acidifying effect of the added acid: HCO3– + H+~ H2CO3. If a base is added, the reaction essentially reverses. Some of the carbonic acid ionizes to produce bicarbonate ions and more H+, which counteracts some of the added base. In this way, the buffer minimizes the effects of an added acid or base on pH. This is what happens in the blood where this buffering system is important in preventing significant changes in pH that could disrupt the ability of the blood to function in carrying vital O2 to tissues. A given amount of acid or base causes a smaller change in pH in a buffered solution than in an unbuffered one. Buffers illustrate an important chemical principle in reversible reactions called the law of mass action. Addition of a reactant on one side of a reversible system drives the reaction in the direction that uses up that compound. In this case, addition of an acid drives the reaction in one direction; addition of a base drives it in other direction.
Properties of Molecules
So far, this section has discussed many properties of molecules, including size, polarity, solubility and acid/base properties. Two other important properties that influence the behavior of molecules in a chemical reaction are the presence of recognizable functional groups and existence of different isomers of molecules with the same chemical formula.
Functional groups give specific properties to molecules
Certain small groups of atoms called functional groups are consistently found together in a variety of different molecules, a fact that simplifies our understanding of the reactions that molecules undergo in living cells. Each functional group has specific properties that, when attached to a larger molecule, in turn, give the larger molecules specific properties. An important category of biological molecules containing functional groups is the amino acids which have both a carboxyl group and an amino group attached to the same carbon atom. Different side chains have different chemical compositions, structures and properties. Each of the 20 amino acids found in proteins has a different side chain that gives it its distinctive chemical properties. Because they possess both carboxyl and amino groups, amino acids are simultaneously acids and bases. At the pH values commonly found in cells, both the carboxyl and the amino group are ionized: the carboxyl group has lost a proton and the amino group has gained one.
Isomers have different arrangements of the same atoms
Isomers are molecules that have the same chemical formula but different arrangements of the atoms. (The prefix iso- ,meaning “same,” is encountered in many biological terms.) Of the different kinds of isomers, will be considered two: structural isomers and optical isomers.
Structural isomers differ in how their atoms are joined together.
Consider two simple molecules, each composed of 4 carbon and 10 hydrogen atoms bonded covalently, both with the formula C4H10. These atoms can be linked in two different ways, resulting in two forms of the molecule: The different bonding relationships of butane and isobutene are distinguished in their structural formulas and the two compounds have different chemical properties.
Optical isomers occur whenever a carbon atom has four different atoms or groups attached to it
This pattern allows two different ways of making the attachments, each the mirror image of the other. Such a carbon atom is an asymmetrical carbon and the pair of compounds are optical isomers of each other. You can imagine your right and left hands as optical isomers. Just as a glove is specific for a particular hand, some biochemical molecules can interact with one optical isomer of a compound but are unable to “fit” the other. Therefore, amino acids exist in two isomeric forms called D-amino acids and L-amino acids. D and L are abbreviations for the Latin terms for right (dextro) and left (levo), respectively. Only L-amino acids are commonly found in most organisms, and their presence is an important chemical “signature” for life. Now after having covered the major properties of all molecules, let’s review them in preparation for the next chapter which focuses on the major molecules of biological systems.
Molecules vary in size
Some are small, such as H2 and CH4, others are larger, such as a molecule of table sugar (sucrose, C12H22O11) which has 45 atoms. Still other molecules, especially proteins, such as haemoglobin (the oxygen carrier in red blood cells), are gigantic, sometimes containing tens of thousands of atoms. The formation of large molecules from simpler ones in the environment was a key precursor to the emergence of life during the Archean.
All molecules have a specific three-dimensional shape
For example, the orientation of the bonding orbitals around the carbon atom gives the methane molecule (CH4) the shape of a regular tetrahedron (see Figure 2.10c). In carbon dioxide (CO2), three atoms are in line. Larger molecules have complex shapes that result from the numbers and kinds of atoms present and the ways in which they are linked together. Some large molecules, such as haemoglobin, have compact, ball-like shapes. Others, such as the protein, called keratin that makes up your hair, are long, thin, ropelike structures. Their shapes relate to the roles these molecules play in living cells.
Molecules are characterized by certain chemical properties
These properties determine the biological roles of molecules: the characteristics of composition, structure (three-dimensional shape), reactivity and solubility to distinguish a pure sample of one molecule from a sample of a different molecule. The presence of functional groups can impart distinctive chemical properties to a molecules, as does the physical arrangement of atoms into isomers.