Biochemistry For Dummies. John T. Moore

functional groups. Functional groups contain atoms other than carbon and hydrogen and/or double or triple bonds, and they define the reactivity of the organic molecule.

      Hydrocarbons

Alkanes are hydrocarbons — compounds containing only carbon and hydrogen, with no traditional functional groups. For this reason, they aren’t very reactive. Alkenes and alkynes are also hydrocarbons. They contain carbon-carbon double and triple bonds, respectively. The presence of more than one type of bond makes them more reactive. Aromatic hydrocarbons, normally ring structures with alternating single and double carbon-to-carbon bonds, contain one or more aromatic systems, which are much less reactive than other systems containing double bonds. Alkynes aren’t very common in biological systems. Figure 3-2 shows the structure of these compounds.

      FIGURE 3-2: Examples of alkanes, alkenes, alkynes, and aromatic hydrocarbons.

      Functional groups with oxygen and sulfur

      Many functional groups contain oxygen, including alcohols, ethers, aldehydes, and ketones. You encounter many of these oxygen-containing functional groups when you study carbohydrates (one of our favorite things). In carbohydrates, many times the ether groups are referred to as glycoside linkages (more on carbohydrates in Chapter 7). In addition, carboxylic acids and esters are important functional groups that appear as fatty acids and in fats and oils.

Alcohols and ethers contain only singly bonded oxygen atoms. An alcohol group attached to an aromatic ring is a phenol. Aldehyde and ketone functional groups contain only doubly bonded oxygen atoms. Carboxylic acids and esters contain both singly and doubly bonded oxygen atoms. The combination of a carbon atom connected to an oxygen atom by a double bond is a carbonyl group.

Sulfur, the element immediately below oxygen on the periodic table, may replace oxygen in both alcohols and ethers to give thiols (mercaptans) and thioethers. Many of these sulfur-containing compounds really stink! Sulfur may also form a disulfide, which has a bond between two sulfur atoms. Figure 3-3 illustrates these compounds.

      FIGURE 3-3: Oxygen- and sulfur-containing functional groups.

      Functional groups containing nitrogen

      Amines and amides are two important functional groups containing nitrogen. Amines are present in amino acids and alkaloids. Amides are present in proteins, in which they’re known as peptide bonds.

The difference between amines and amides is that amides have a carbonyl group adjacent to the nitrogen atom. Amines are derivatives of ammonia (NH₃) where one or more organic groups replace hydrogen atoms. In a primary amine, an organic group replaces one hydrogen atom. In secondary and tertiary amines, two or three organic groups, respectively, replace two or three hydrogen atoms. Figure 3-4 shows these compounds, as well as aniline and ammonia.

      FIGURE 3-4: Some nitrogen-containing functional groups.

      

Alkaloids are basic compounds produced by plants. Examples include nicotine, caffeine, and morphine.

      Functional groups containing phosphorus

      Phosphorus is an important element in biological systems and is normally present as part of a phosphate group. Phosphate groups come from phosphoric acid (H₃PO₄). The phosphate groups may be alone, part of a diphosphate, part of a triphosphate, or part of a phosphate ester.

Phosphates are in teeth and bone, and are a part of the energy transport molecules ATP and ADP (see Chapter 12 for more on these molecules). Figure 3-5 illustrates phosphorous-containing functional groups.

FIGURE 3-5: Phosphorous-containing functional groups.

      Reactions of functional groups

      As you study the different biochemical molecules and their functions within the living organism, you see that the way a certain molecule reacts is primarily determined by the functional groups in the molecule’s structure. Take a few minutes with the following sections and refresh your organic chemistry knowledge of the typical reactions of the various functional groups.

      Alcohols

      Alcohols are subject to oxidation (loss of electrons, gain of oxygen, or loss of hydrogen). Mild oxidation of a primary alcohol (where the is attached to the carbon atom at the end of a chain (called a terminal carbon) produces an aldehyde, which may undergo further oxidation to a carboxylic acid. Under similar conditions, a secondary alcohol ( is attached to a carbon bonded to two other carbons) yields a ketone, and a tertiary alcohol ( is attached to a carbon bonded to three other carbons) doesn’t react. This behavior is important in the chemistry of many carbohydrates.

Under extreme oxidizing conditions, alcohols and all other organic compounds will undergo combustion. Under controlled conditions this combustion is really useful (campfires, barbeque grills, and so on), but uncontrolled combustion can lead to a fiery mess.

      

The presence of the leads people mistakenly to assume that alcohols are bases. Nothing could be further from the truth! Alcohols, under biological conditions, are neutral compounds. Phenols, in which the is attached to an aromatic ring, though, are weak acids.

      Aldehydes and ketones

      Aldehydes easily undergo oxidation to carboxylic acids, but ketones don’t undergo mild oxidation. With difficulty (unless you use enzymes, biological catalysts), it’s possible to reduce aldehydes and ketones back to the appropriate alcohols.

      Reducing sugars behave as such because of mild oxidation of the carbonyl groups present. Tollens’ test uses silver nitrate, which reacts with a reducing sugar to generate a silver mirror on the inside walls of the container. Both Benedict’s