BIOCHEMISTRY - L. Stryer - 1984

VOLUME 1

CHAPTER 1. MOLECULES AND LIFE

1.2. Space, Time, and Energy

When examining molecular Structure, it is essential to have a clear sense of scale (Fig. 1.5). Lengths at the atomic level are usually measured in angstroms; one angstrom (A) equals 10^-10 meters (m) or 0.1 nanometers (nm). For example, the length of a C — C bond is 1.54 A. Small Biomolecules, such as sugars or Amino Acids, typically measure a few angstroms across. Biological macromolecules, such as Proteins, are at least ten times larger. Hemoglobin, the oxygen-carrying protein of red Blood Cells, has a diameter of 65 A. Supramolecular complexes are larger by another order of magnitude; for instance, Ribosomes—the protein-synthesizing Organelles of The Cell—have a diameter of approximately 300 A. Most Viruses fall within the range of 100 A (10 nm) to 1000 A (100 nm). Cells, by contrast, are typically hundreds of times larger and are measured in micrometers (μm). For example, the maximum length of a red blood cell is 7 μm (7 •10⁴ A). It is worth noting that the resolving limit of a Light Microscope is about 0.2 μm (2000 A), which corresponds to the size of many cellular organelles. Thus, Mitochondria—the primary ATP producers in aerobic cells—are visible under a light microscope. Most of our knowledge regarding biological structures ranging from 1 A (0.1 nm) to 10⁴ A (1 μm) has been gained through Electron Microscopy and X-Ray Diffraction.

Class="center">Fig. 1.5. Sizes of various biomolecules, supramolecular complexes, and cells

The molecules that constitute living matter undergo continuous transformation. In biological systems, Chemical Reactions are catalyzed by Enzymes capable of converting a substrate into a product within a timeframe typically measured in milliseconds (ms, 10^-3 s). Some enzymes work even faster, completing a reaction in a few microseconds (μs, 10^-6 s). Conformational Changes in biological macromolecules also occur extremely rapidly; for instance, the unwinding of the DNA double helix required for Replication and expression takes only microseconds. The rotation of one protein domain relative to another takes nanoseconds (ns, 10^-9 s). Many noncovalent bonds in macromolecules form and break within just a few nanoseconds. Processes that occur even faster can only be assessed using ultra-short laser light pulses. Remarkably, the primary event in Vision—a structural change in light-absorbing groups—takes place within a few picoseconds (ps, 10^-12 s) after photon absorption. All of this demonstrates that the rates of biological processes span a very wide range (Fig. 1.6). It is also crucial to appreciate the scale of evolutionary time. Life on Earth arose 3.5 • 10⁹ years ago, which corresponds to 1.1 • 10¹⁷ s.

Fig. 1.6. Typical reaction rates in biological systems

Let us also consider the energy changes involved in various molecular transformations (Fig. 1.7). The ultimate source of energy required for life is the Sun. The absorption of visible light, such as green light photons, yields 57 kilocalories per mole (kcal/mol). The energy stored in molecules of ATP—the universal energy currency of biological systems—amounts to 12 kcal/mol. By comparison, the average thermal energy per vibrational degree of freedom of a molecule is small: 0.6 kcal/mol at 25°C, which is far below the threshold required to dissociate covalent bonds (83 kcal/mol for a C — C bond, for example). Consequently, the covalent backbone of biomolecules remains stable in the absence of enzymes or an energy input. On the other hand, this same thermal energy is sufficient to form or disrupt noncovalent bonds in biological systems, as their bond energy typically amounts to only a few kilocalories per mole. Processes of ENERGY GENERATION AND storage are discussed in detail in Part II of the book.

Fig. 1.7. Selected biologically important energy values.