The Machinery of Life
David S. Goodsell
Format: PDF / Kindle (mobi) / ePub
Imagine that we had some way to look directly at the molecules in a living organism. An x-ray microscope would do the trick, or since we’re dreaming, perhaps an Asimov-style nanosubmarine (unfortunately, neither is currently feasible). Think of the wonders we could witness firsthand: antibodies atta- ing a virus, electrical signals racing down nerve fibers, proteins building new strands of DNA. Many of the questions puzzling the current cadre of sci- tists would be answered at a glance. But the nanoscale world of molecules is separated from our everyday world of experience by a daunting million-fold difference in size, so the world of molecules is completely invisible. I created the illustrations in this book to help bridge this gulf and allow us to see the molecular structure of cells, if not directly, then in an artistic rendition. I have included two types of illustrations with this goal in mind: watercolor paintings which magnify a small portion of a living cell by one million times, showing the arrangement of molecules inside, and comput- generated pictures, which show the atomic details of individual molecules. In this second edition of The Machinery of Life, these illustrations are presented in full color, and they incorporate many of the exciting scientific advances of the 15 years since the first edition.
for the past 8 years. I also thank the Fondation Scientifique Fourmentin-Guilbert for their kind support of this project. The computer-generated illustrations were produced with methods that I developed under the auspices of the Daymon Runyon-Walter Winchell Cancer Research Fund, the National Institutes of Health, and the National Science Foundation. Finally, I would like to thank Bill Grimm for his support and confidence. La Jolla, CA D.S. Goodsell Contents Preface . . . . . . . . . . . . .
into the nervous system, keeping us up-to-date on the state of our surrounding environment. Each of the senses has a different molecular machine that probes an environmental variable. The eyes have lightsensitive rhodopsin proteins that initiate nerve signals when they absorb photons. Taste buds in our tongue have receptors that sense the level of ions or acid, and send signals that are interpreted as ‘‘salty’’ or ‘‘sour.’’ Receptor proteins in our ears sense the motion of small, hair-like
Cell Death Cells that are gravely injured make a mess when they die. They swell and burst, and the contents of the cell spill out and get into inconvenient places. Lysosomes (small compartments that perform digestion inside cells) may be damaged, releasing their destructive enzymes. Programmed Cell Death 117 The body responds by inflaming the area with immune cells that struggle to clean up the mess without damaging the surrounding healthy tissue too much. To avoid this messy problem, our
acid carbohydrate attached to proteins on the cell surface. The viral capsid has a network of pockets that recognize these cellular receptors, attaching the virus to the surface of the cell. This triggers a change in the structure of the viral coat, causing it to inject the RNA through the membrane and into the cell. Once the RNA is inside, the cell’s own ribosomes translate the RNA into a long polyprotein. This polyprotein is composed of all the viral proteins, strung together like a string of
exotic atoms only when needed for special tasks. These atoms may be connected in only very limited ways, defined by the underlying chemistry of the atoms. Molecular machines must be constructed within these significant limitations. It is much like trying to build machines with Tinkertoys or Lego blocks: you may build a wide variety of different objects, but the final form is shaped and limited by the shapes and connections of the underlying units. We will see that molecular machines take