Among the many events that occur in the life of a cell are a multitude of specific chemical transformations, which provide the cell with usable energy and the molecules needed to form its structure and coordinate its activities. These biochemical reactions and other cellular processes are governed by basic principles of chemistry reviewed in Chapter 2. Here we briefly describe the functions of the main types of chemicals that compose cells. Throughout many later chapters we will focus on the interactions and transformations of these molecules.
Water, inorganic ions, and a large array of relatively small organic molecules (e.g., sugars, vitamins, fatty acids) account for 75 - 80 percent of living matter by weight. Of these small molecules, water is by far the most abundant. The remainder of living matter consists of macromolecules, including proteins, polysaccharides, and DNA (Figure 1-2). Cells acquire and use these two size classes of molecules in fundamentally different ways. Ions, water, and many small organic molecules are imported into the cell. Cells also make and alter many small organic molecules by a series of different chemical reactions. In contrast, cells can obtain macromolecules only by making them. Their synthesis entails linking together a specific set of small molecules (monomers) to form polymers through repetition of a single type of chemical-linkage reaction.
Some small molecules function as precursors for synthesis of macromolecules, and the cell is careful to provide the appropriate mix of small molecules needed. Small molecules also store and distribute the energy for all cellular processes; they are broken down to extract this chemical energy, as when sugar is degraded to carbon dioxide and water with the release of the energy bound up in the molecule (Chapter 16). Other small molecules (e.g., hormones and growth factors) act as signals that direct the activities of cells (Chapter 20), and nerve cells communicate with one another by releasing and sensing certain small signaling molecules (Chapter 21). The powerful effect on our body of a frightening event comes from the instantaneous flooding of the body with a small-molecule hormone that mobilizes the “fight or flight” response.
Macromolecules, though, are the most interesting and characteristic molecules of living systems; in a true sense the evolution of life as we know it is the evolution of macromolecular structures. Proteins, the workhorses of the cell, are the most abundant and functionally versatile of the cellular macromolecules. To appreciate the abundance of protein within a cell, we can estimate the number of protein molecules in a typical eukaryotic cell, such as a hepatocyte in the liver. This cell, roughly a cube 15 μm (0.0015 cm) on a side, has a volume of 3.4 × 10-9 cm3 (or milliliters). Assuming a cell density of 1.03 g/ml, the cell would weigh 3.5 × 10-9 g. Since protein accounts for approximately 20 percent of a cell’s weight, the total weight of cellular protein is 7 × 10-10 g. The average yeast protein has a molecular weight of 52,700 (g/mol), as noted in Chapter 3. Assuming this value is typical of eukaryotic proteins, we can calculate the total number of protein molecules per liver cell as about 7.9 × 109 from the total protein weight and the number of molecules per mole, which is a constant (Avogadro’s number). To carry this calculation one step further, consider that a liver cell contains about 10,000 different proteins; thus, a cell contains close to a million molecules of each protein on average. In actuality, however, the abundance of different proteins varies widely, from the quite rare cell-surface protein that binds the hormone insulin (20,000 molecules) to the abundant structural protein actin (5 × 108 molecules).
Many of the proteins within cells are enzymes, which accelerate (catalyze) reactions involving small molecules. Other proteins allow cells to move and do work, maintain internal cell rigidity, and transport molecules across membranes. Proteins even direct their own synthesis and that of other macromolecules. Reflecting their numerous functions, proteins come in many shapes and sizes (Figure 1-3). The elucidation of the structure of proteins and the relation of protein structure to function remain active areas of scientific investigation (Chapter 3). Proteins are formed from only 20 different monomers, the amino acids. That such a limited set of building blocks can do so much is a continuous marvel, even to researchers who work with proteins every day. They are the true glory of the biological world.
The macromolecule that garners the most public attention is not protein but deoxyribonucleic acid (DNA), whose functional properties make it the cell’s master molecule. The three-dimensional structure of DNA, first proposed by James D. Watson and Francis H. C. Crick about 50 years ago, consists of two long helical strands that are coiled around a common axis forming a double helix (Figure 1-4). The double-helical structure of DNA, one of nature’s most magnificent constructions, is critical to the phenomenon of heredity, the transfer of genetically determined characteristics from one generation to the next.
Each strand of DNA is composed of just four different types of monomers called nucleotides. Genes are simply coded representations of the structures of individual proteins, a code written in four chemical “letters” - the nucleotides - and displayed as a continually varying sequence in DNA. Since cells use proteins (enzymes) to make other molecules like sugars or fats, DNA indirectly directs the synthesis of many small molecules as well as proteins. DNA also contains a coded set of instructions about when various proteins are to be made and in what quantities.
In the common view, DNA is the storage form of genetic information, which protein “machines” read out for use by the cell. But a third macromolecule, ribonucleic acid (RNA), is necessary in the process. The central dogma of biology states that the coded genetic information hard-wired into DNA is transcribed into individual transportable cassettes, composed of messenger RNA (mRNA); each mRNA cassette contains the program for synthesis of a particular protein (or small number of proteins). This critical trio of macromolecules - DNA, RNA, and proteins - is present in all cells. The mechanism whereby the information encoded in DNA is deciphered into proteins is now understood quite well and explained in Chapter 4. How this process of gene expression is regulated - that is, how cells “know” to make the right proteins at the right time in the right amounts - is a major focus of current research in molecular cell biology and a recurring theme throughout this book