The Machinery of Life

The Machinery of Life

David S. Goodsell

Language: English

Pages: 168

ISBN: 0387849246

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.

Biohistory: Decline and Fall of the West

Biomedical Signal Analysis: Contemporary Methods and Applications

Peacemaking among Primates

Darwin

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

protect our bodies from the surrounding environment, but at the same time, we need to sense and respond to changing conditions. Modern organisms have developed a bewildering variety of molecular machines to balance these two opposing needs. This is where the full diversity of life is expressed. The basic methods of molecular construction and energy production, discussed in the previous sections, are very similar in all living cells. But organisms have evolved many different and unique ways of

detoxify reactive forms of oxygen. Superoxide dismutase detoxifies superoxide molecules, and catalase and peroxiredoxin destroy hydrogen peroxide. Each of these enzymes uses a special chemical tool in the reaction. Superoxide dismutase uses copper and zinc atoms (one is seen in the active site here, in bright blue), catalase uses iron ions trapped in heme molecules, and peroxiredoxin uses a particularly reactive sulfur atom in a cysteine amino acid (colored bright yellow here) (5,000,000 X)

15 minutes to cross the room! In this time, you may be pushed all over the room, perhaps even back to your starting point a few times. This is similar (although molecules do not have a goal in mind) to the contorted path molecules take in the cell. You might ask how anything ever gets done in this chaotic world. It is true that the motion is random, but it is also true that the motion is very fast compared to the motion in our familiar world. Random, diffusive motion is fast enough to perform

entirely different targets, so the population of viruses is faced with the impossible task of mutating several molecular machines at the same time to evade all of the drugs. Antibiotic Drugs 153 Fig. 9.9 Drug resistance in HIV In order for HIV drugs to be effective, they must bind tightly to HIV enzymes and block their action. HIV protease becomes resistant to drugs by mutating important amino acids in the active site. In this picture, the drug ritonavir is shown in green, and the amino acids

155 (see Fig. 6.10). These poisons act by blocking the binding of acetylcholine to the receptor, so the muscle never gets the signal to contract. If you have ever had your eyes examined at the ophthalmologist, you have probably been poisoned by atropine. A small drop of the poison in each eye temporarily paralyzes the muscles that close the iris, dilating the pupils and allowing the doctor to see inside. Strychnine acts in the opposite way. It blocks inhibitory receptors in nerve synapses that

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