Figure 1–8 Life as an autocatalytic process. (A) The cell as a self-replicating collection of catalysts. (B) Polynucleotides (the nucleic acids dnA and RnA, which are nucleotide polymers) provide the sequence information, while proteins (amino acid polymers) provide most of the catalytic functions that serve—through a complex set of chemical reactions—to bring about the synthesis of more polynucleotides and proteins of the same types.
A living cell is a dynamic chemical system, operating far from chemical equilibrium. For a cell to grow or to make a new cell in its own image, it must take in free energy from the environment, as well as raw materials, to drive the necessary synthetic reactions. This consumption of free energy is fundamental to life. When it stops, a cell decays toward chemical equilibrium and soon dies.
Genetic information is also fundamental to life, and free energy is required for the propagation of this information. For example, to specify one bit of information—that is, one yes/no choice between two equally probable alternatives— costs a defined amount of free energy that can be calculated. The quantitative relationship involves some deep reasoning and depends on a precise definition of the term “free energy,” as explained in Chapter 2. The basic idea, however, is not difficult to understand intuitively.
Picture the molecules in a cell as a swarm of objects endowed with thermal energy, moving around violently at random, buffeted by collisions with one another. To specify genetic information—in the form of a DNA sequence, for example—molecules from this wild crowd must be captured, arranged in a specific order defined by some preexisting template, and linked together in a fixed relationship. The bonds that hold the molecules in their proper places on the template and join them together must be strong enough to resist the disordering effect of thermal motion. The process is driven forward by consumption of free energy, which is needed to ensure that the correct bonds are made, and made robustly. In the simplest case, the molecules can be compared with spring-loaded traps, ready to snap into a more stable, lower-energy attached state when they meet their proper partners; as they snap together into the bonded arrangement, their available stored energy—their free energy—like the energy of the spring in the trap, is released and dissipated as heat. In a cell, the chemical processes underlying information transfer are more complex, but the same basic principle applies: free energy has to be spent on the creation of order.
To replicate its genetic information faithfully, and indeed to make all its complex molecules according to the correct specifications, the cell therefore requires free energy, which has to be imported somehow from the surroundings. As we shall see in Chapter 2, the free energy required by animal cells is derived from chemical bonds in food molecules that the animals eat, while plants get their free energy from sunlight.
All cells Function as Biochemical Factories dealing with the same Basic molecular Building Blocks
Because all cells make DNA, RNA, and protein, all cells have to contain and manipulate a similar collection of small molecules, including simple sugars, nucleotides, and amino acids, as well as other substances that are universally required. All cells, for example, require the phosphorylated nucleotide ATP (adenosine triphosphate), not only as a building block for the synthesis of DNA and RNA, but also as a carrier of the free energy that is needed to drive a huge number of chemical reactions in the cell.
Although all cells function as biochemical factories of a broadly similar type, many of the details of their small-molecule transactions differ. Some organisms, such as plants, require only the simplest of nutrients and harness the energy of sunlight to make all their own small organic molecules. Other organisms, such as animals, feed on living things and must obtain many of their organic molecules ready-made. We return to this point later.
Another universal feature is that each cell is enclosed by a membrane—the plasma membrane. This container acts as a selective barrier that enables the cell to concentrate nutrients gathered from its environment and retain the products it