The biological world is magnificently diverse. The animal kingdom is rich with species ranging from nearly microscopic insects to elephants and whales. The plant kingdom includes species as small and relatively simple as algae and as large and complex as giant sequoias. This diversity extends further when we descend into the microscopic world. Organisms such as protozoa, yeast, and bacteria are present with great diversity in water, in soil, and on or within larger organisms. Some organisms can survive and even thrive in seemingly hostile environments such as hot springs and glaciers.

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The development of the microscope revealed a key unifying feature that underlies this diversity. Large organisms are built up of cells, resembling, to some extent, single-celled microscopic organisms. The construction of animals, plants, and microorganisms from cells suggested that these diverse organisms might have more in common than is apparent from their outward appearance. With the development of biochemistry, this suggestion has been tremendously supported and expanded. At the biochemical level, all organisms have many common features (Figure 1.1).

As mentioned earlier, biochemistry is the study of the chemistry of life processes. These processes entail the interplay of two different classes of molecules: large molecules such as proteins and nucleic acids, referred to as biological macromolecules, and low-molecular-weight molecules such as glucose and glycerol, referred to as metabolites, that are chemically transformed in biological processes.

Members of both these classes of molecules are common, with minor variations, to all living things. For example, deoxyribonucleic acid (DNA) stores genetic information in all cellular organisms. Proteins, the macromolecules that are key participants in most biological processes, are built from the same set of 20 building blocks in all organisms. Furthermore, proteins that play similar roles in different organisms often have very similar three-dimensional structures (Figure 1.1).

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Key metabolic processes also are common to many organisms. For example, the set of chemical transformations that converts glucose and oxygen into carbon dioxide and water is essentially identical in simple bacteria such as Escherichia coli (E. coli) and human beings. Even processes that appear to be quite distinct often have common features at the biochemical level. Remarkably, the biochemical processes by which plants capture light energy and convert it into more-useful forms are strikingly similar to steps used in animals to capture energy released from the breakdown of glucose.

These observations overwhelmingly suggest that all living things on Earth have a common ancestor and that modern organisms have evolved from this ancestor into their present forms. Geological and biochemical findings support a time line for this evolutionary path (Figure 1.2). On the basis of their biochemical characteristics, the diverse organisms of the modern world can be divided into three fundamental groups called domains: Eukarya (eukaryotes), Bacteria, and Archaea. Domain Eukarya comprises all multicellular organisms, including human beings as well as many microscopic unicellular organisms such as yeast. The defining characteristic of eukaryotes is the presence of a well-defined nucleus within each cell. Unicellular organisms such as bacteria, which lack a nucleus, are referred to as prokaryotes. The prokaryotes were reclassified as two separate domains in response to Carl Woese’s discovery in 1977 that certain bacteria-like organisms are biochemically quite distinct from other previously characterized bacterial species. These organisms, now recognized as having diverged from bacteria early in evolution, are the archaea. Evolutionary paths from a common ancestor to modern organisms can be deduced on the basis of biochemical information. One such path is shown in Figure 1.3.

Much of this book will explore the chemical reactions and the associated biological macromolecules and metabolites that are found in biological processes common to all organisms. The unity of life at the biochemical level makes this approach possible. At the same time, different organisms have specific needs, depending on the particular biological niche in which they evolved and live. By comparing and contrasting details of particular biochemical pathways in different organisms, we can learn how biological challenges are solved at the biochemical level. In most cases, these challenges are addressed by the adaptation of existing macromolecules to new roles rather than by the evolution of entirely new ones.

Biochemistry has been greatly enriched by our ability to examine the three-dimensional structures of biological macromolecules in great detail. Some of these structures are simple and elegant, whereas others are incredibly complicated. In any case, these structures provide an essential framework for understanding function. We begin our exploration of the interplay between structure and function with the genetic material, DNA.

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