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Chapter: Biochemistry: Biochemistry and the Organization of Cells

Chemical Foundations of Biochemistry

Can a chemist make the molecules of life in a laboratory? What makes biomolecules special?

Chemical Foundations of Biochemistry

Organic chemistry is the study of compounds of carbon and hydrogen andtheir derivatives. Because the cellular apparatus of living organisms is made up of carbon compounds, biomolecules are part of the subject matter of organic chemistry. Additionally, many carbon compounds are not found in any organ-ism, and many topics of importance to organic chemistry have little connection with living things. We are going to concentrate on the aspects of organic chem-istry that we need to understand what goes on in living cells.

Can a chemist make the molecules of life in a laboratory?

Until the early part of the 19th century, there was a widely held belief in “vital forces,” forces presumably unique to living things. This belief included the idea that the compounds found in living organisms could not be produced in the laboratory. German chemist Friedrich Wöhler performed the critical experi-ment that disproved this belief in 1828. Wöhler synthesized urea, a well-known waste product of animal metabolism, from ammonium cyanate, a compound obtained from mineral (i.e., nonliving) sources.

It has subsequently been shown that any compound that occurs in a living organism can be synthesized in the laboratory, although in many cases the synthesis represents a considerable challenge to even the most skilled organic chemist.

The reactions of biomolecules can be described by the methods of organic chemistry, which requires the classification of compounds according to their functional groups. The reactions of molecules are based on the reactions of their respec-tive functional groups.

What makes biomolecules special?

Table 1.1 lists some biologically important functional groups. Note that most of these functional groups contain oxygen and nitrogen, which are among the most electronegative elements. As a result, many of these functional groups are polar, and their polar nature plays a crucial role in their reactivity. Some groups that are vitally important to organic chemists are missing from the table because molecules containing these groups, such as alkyl halides and acyl chlorides, do not have any particular applicability in biochemistry. 

Conversely, carbon-containing derivatives of phosphoric acid are mentioned infrequently in beginning courses on organic chemistry, but esters and anhydrides of phos-phoric acid (Figure 1.2) are of vital importance in biochemistry. Adenosine triphosphate (ATP), a molecule that is the energy currency of the cell, contains both ester and anhydride linkages involving phosphoric acid.

Important classes of biomolecules have characteristic functional groups that determine their reactions. We shall discuss the reactions of the functional groups when we consider the compounds in which they occur.


Life is based on compounds of carbon. This is the subject matter of organic chemistry.

The reactions of organic compounds are those of their functional groups, which are specifically linked atoms that react in similar ways under many different conditions.

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