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 groupsare 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

Isomersare 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 isomersdiffer 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.