Biochemistry For Dummies. John T. Moore

that arise from the nucleus of one atom attracting the electron cloud of another atom. These forces are normally only significant when other intermolecular forces are not present, as in nonpolar molecules.

      Dipole-dipole forces

      Dipole-dipole forces exist between polar regions of different molecules. The presence of a dipole means that the molecule has a partially positive end and a partially negative end. Oppositely charged partial charges attract each other, whereas like partial charges repel. In most cases, biological systems utilize a special type of dipole-dipole force known as hydrogen bonding (see the following section). (We said, “hydrogen bond,” not “hydrogen bomb” — there’s a big difference!)

      Hydrogen bonding

      Hydrogen bonding, as the name implies, involves hydrogen. The hydrogen atom must be bonded to either an oxygen atom or a nitrogen atom. (In nonbiological situations, hydrogen bonding also occurs when a hydrogen atom bonds to a fluorine atom or sometimes a chlorine atom.) Hydrogen bonding is significantly stronger than a normal dipole-dipole force and is much stronger than London dispersion forces (discussed in the preceding sections). The hydrogen that bonds to either a nitrogen or an oxygen atom is strongly attracted to a different nitrogen or oxygen atom. Hydrogen bonding may be either intramolecular or intermolecular.

      Ionic interactions

      In biological systems, ionic interactions, in which oppositely charged ions attract each other strongly, may serve as intermolecular or intramolecular forces. In some cases, these may involve metal cations, such as , or anions, such as . In many cases, the cation is an ammonium ion from an amino group, such as ; the anion may be from a carboxylic acid, such as .

In nonbiological systems, such interactions are commonly referred to as ionic bonding.

      Water-related interactions: Both the lovers and the haters

      The predominant factor leading to hydrophobic interactions is the presence of portions of a molecule containing only carbon and hydrogen. Hydrocarbon regions are nonpolar and are attracted to other nonpolar regions by London dispersion forces.

      

In general, the presence of any atom other than carbon and hydrogen makes a region polar. Oxygen and nitrogen are the most effective elements in biochemistry for making a region of a molecule polar. Sulfur is the least effective of the common biologically important elements at imparting polar character. Dipole-dipole, hydrogen bonding, and ionic interactions are all hydrophilic interactions. London dispersion forces are hydrophobic interactions. (See the section “Everybody has ‘em: Intermolecular forces,” earlier in this chapter, for the lowdown on these types of interactions.)

      

The more carbon and hydrogen atoms that are present without other atoms, the more important the hydrophobic nature of a region becomes in defining the molecule’s properties. A molecule may have both a hydrophilic and a hydrophobic region, and both regions are important to the molecule’s behavior. The formation of a micelle (see Chapter 2) is an example of using molecules with both hydrophilic and hydrophobic regions. Think of these micelles every time you wash dishes. The soap or detergent dissolves the grease or oil and forms a micelle, keeping the grease in solution so that it can go down the drain.

      How bond strengths affect physical properties of substances

      The physical properties of biological substances depend on the intermolecular forces present. The general order of strength is:

      A few exceptions occur in borderline cases (molecules that are not simple molecular species) and for very large molecules (called macromolecules).

The strongest types of intermolecular forces involve ions. Next strongest is hydrogen bonding. Polar substances interact through dipole-dipole forces, which are weaker than hydrogen bonds. All biological substances containing oxygen, nitrogen, sulfur, or phosphorus are polar. London forces, the weakest intermolecular forces, are important in nonpolar situations. The hydrocarbon portion of biological molecules is nonpolar.

      Melting points, boiling points, and solubility

      As the strength of forces decreases, so do the melting points, boiling points, and solubility in water. In addition, the vapor pressure and the solubility in nonpolar solvents increase.

      

Substances that have a high solubility in water are hydrophilic, and substances that have a low solubility in water are hydrophobic. You can get the scoop on solubility in the section.

      A molecule may have both hydrophilic and hydrophobic regions. The region that represents a greater portion of the molecule predominates. For this reason, for example,

      is more hydrophilic than

      because the hydrophilic end (-COOH) is a much more significant portion of the entire molecule in the first case than in the second case.

      In addition,

      is more hydrophilic than

      because of the presence of the second hydrophilic region .

      Odors

      

Many functional groups have distinctive odors. Small carboxylic acids smell like acetic acid (vinegar), while larger ones have unpleasant odors. Most esters, if volatile, have pleasant odors, which is why esters are used extensively in the food and perfume industry. Most sulfur-containing compounds have strong, unpleasant odors. Small amines have an ammonia odor, whereas larger amines have a fishy odor or worse. That’s why people squeeze lemon juice on fish — the acidic lemon juice reacts with the basic amines to form an ammonium salt that doesn’t have an odor. (Believe us, there are odors worse than fish — putrescine is one!)

Getting a Reaction out of a Molecule: Functional Groups

      Most carbon compounds have one or more reactive sites composed of a specific grouping of atoms in their structure. These sites are where chemical reactions occur. These specific groupings of atoms