1.1 The Molecules of Life
While large polymers are the focus of molecular cell biology, small molecules are the stage on which all cellular processes are set. Water, inorganic ions, and a wide array of relatively small organic molecules (Figure 1-5) account for 75 to 80 percent of living matter by weight, and water accounts for about 75 percent of a cell’s volume. These small molecules, including water, serve as substrates for many of the reactions that take place inside the cell, including energy metabolism and cell signaling. Cells acquire these small molecules in different ways. Ions, water, and many small organic molecules are imported into the cell (see Chapter 11); other small molecules are synthesized within the cell, often by a series of chemical reactions (see Chapter 12).
FIGURE 1-5 Some of the many small molecules found in cells. Only the L-forms of amino acids such as serine are incorporated into proteins, not their D-mirror images; only the D-form of glucose, not its L-mirror image, can be metabolized to carbon dioxide and water.
Even in the structures of many small molecules, such as sugars, vitamins, and amino acids, we see the footprint of evolution. For example, all amino acids save glycine have an asymmetric carbon atom, yet only the L-stereoisomer, never the D-stereoisomer, is incorporated into proteins. Similarly, only the D-stereoisomer of glucose is invariably found in cells, never the mirror-image L-stereoisomer (see Figure 1-5). At an early stage of biological evolution, our common cellular ancestor evolved the ability to catalyze reactions with one stereoisomer instead of the other. How these selections happened is unknown, but now these choices are locked in place.
An important and universally conserved small molecule is adenosine triphosphate (ATP), which stores readily available chemical energy in two of its chemical bonds (Figure 1-6). When one of these energy-rich bonds in ATP is broken, forming ADP (adenosine diphosphate), the released energy can be harnessed to power energy-requiring processes such as muscle contraction or protein biosynthesis. To obtain energy for making ATP, all cells break down food molecules. For instance, when sugar is degraded to carbon dioxide and water, the energy stored in the sugar molecule’s chemical bonds is released, and much of it can be “captured” in the energy-rich bonds in ATP. Bacterial, plant, and animal cells can all make ATP by this process. In addition, plants and a few other organisms can harvest energy from sunlight to form ATP in photosynthesis.
FIGURE 1-6 Adenosine triphosphate (ATP) is the most common molecule used by cells to capture, store, and transfer energy. ATP is formed from adenosine diphosphate (ADP) and inorganic phosphate (Pi) by photosynthesis in plants and by the breakdown of sugars and fats in most cells. The energy released by the splitting (hydrolysis) of Pi from ATP drives many cellular processes.
Other small molecules (e.g., certain hormones and growth factors) act as signals that direct the activities of cells (see Chapters 15 and 16), and neurons (nerve cells) communicate with one another by releasing and sensing certain small signaling molecules (see Chapter 22). The powerful physiological effects of a frightening event, for example, come from the instantaneous flooding of the body with the small-molecule hormone adrenaline, which mobilizes the “fight or flight” response.
Certain small molecules (monomers) can be joined to form polymers (also called macromolecules) through repetition of a single type of covalent chemical-linkage reaction. Cells produce three types of large macromolecules: polysaccharides, proteins, and nucleic acids. Sugars, for example, are the monomers used to form polysaccharides. Different polymers of D-glucose form cellulose, an important component of plant cell walls, and glycogen, a storage form of glucose found in liver and muscle. The cell is careful to provide the appropriate mix of small molecules needed as precursors for synthesis of macromolecules.