The Machinery of Life

Robert is reading The Machinery of Life, by David S. Goodsell, which is thus far a remarkable book.  It describes the workings of cells at the nano (molecular) level, which is where all the scientific research action is these days, or so Robert is told .  When looked at at this level, everything begins to look very mechanical.  Thus, new medical research is all about creating mechanical “bots” that interact with cellular molecules.

Here is a brief summary of what he is learning in each chapter.

1.  Introduction. The principles that guide objects in everyday life– gravity, friction, temperature– are different at the molecular scale.  Molecules are so small that gravity is completely negligible. The motions and interactions of biological molecules are dominated by surrounding water molecules. At room temperature a medium-sized protein travels at 5 meters per second.  If placed alone in space, this protein would travel its own length in a nanosecond (billionth of a second).  Inside the cell is is battered from all sides by water molecules, bouncing back and forth, taking a “long time” to get anywhere. Imagine a person not being able to walk through a crowded room to get to the bar on the other side. The inside of the cell is similar, but molecules do not a goal in mind.  But motion is the cell, while slow compared to the potential speed of a protein, still occurs quickly compared to our world. Each molecule within a cell may encounter EVERY OTHER molecule within the cell in a matter of seconds. Each molecule keeps bumping around until it finds the right place (i.e., attachment with another molecule). This is molecular diffusion.

2. Molecular Machines. Almost everything in the human body happens at the atomic level. Molecules are captured, sorted, shuffled, packaged, transported. All within cells of a size of a few nanometers. Tiny molecular machines orchestrate all life. But molecular machines must be made of atoms, and atoms come in only a few shapes and sizes. Most cells are made with six types of atoms. Carbon, oxygen, nitrogen, sulfur, phosphoruous, and hydrogen. Atoms may be connected in only limited ways. But the molecules uses lots of tricks to get to the end shape and result. So making molecular machines is like building machines with Tinkertoys or Legos. Molecular machines are made of (A) proteins, (B) nucleic acids, (C) lipids, and (D) polysaccharides. Each has a different personality (like wood, metal, plastic and ceramic). The basic personalities are manifested in (i) chemical complementarity and (ii) hydrophobicity. Complementery molecules bind tightly to each other. Complementarity results from (a) fitting together of molecules of complementary shapes, (b) hydrogen bonding between hydrogen atoms and oxygen or nitrogen atoms, (c) salt bridges that carry different electrical charges. These all act like fasteners. Hydrophobicity is the amount by which molecules interact strongly with water (hydrophillic) or do not interact (hydrophobic).

a. Nucleic Acids (Encoders). Nucleic acids play an essential role in the process of life. They encode information. They are composed of long chains of nucleotides. Each nucleotide has a specific arrangement of hydrogen-bond-forming atom that causes it to match with other nucleotides. For example, in DNA, the Adenine-Thymine and Cytosine-Guanine matchings.

b. Proteins (Workers). Proteins do work.  Some are motors, others are rods, nets, hollow spheres, and tubes. Many are catalysts. Like nucleic acids, they are chains.  But they are built with 20 types of amino acids (not merely, for example, 4 nucleotides, as is DNA). Some amino acids carry a charge, other are strongly hydrophobic. Some a big, some are small and can fit into tight corners. Some are rigid.  Some are flexible. By using these diverse amino acids, the proteins can be even more diverse.

c. Lipids. Lipids are tiny molecules that group together to make the largest structures of the cell. These are the fats and oils that aggregate to create huge sheets that are used to enclose cells, forming the primary boundary between the cell and the outside world.

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