Sunday, February 19, 2006

Just add water...

Water molecules - Image from the NSF Special Feature on Water.  Click to view Flash Animation.
"Enzymes and ribosomes can only work in water, and therefore cannot build anything that is chemically unstable in water. Biology is wonderous in the vast diversity of what it can build, but it can't make a crystal of silicon, or steel, or copper, or aluminum, or titanium, or virtually any of the key materials on which modern technology is built. ... I can only guess that you imagine it is possible to make a molecular entity that has the superb, selective chemical-construction ability of an enzyme without the necessity of liquid water. If so, it would be helpful to all of us who take the nanobot assembler idea of "Engines of Creation" seriously if you would tell us more about this nonaqueous enzymelike chemistry. What liquid medium will you use? How are you going to replace the loss of the hydrophobic/hydrophilic, ion-solvating, hydrogen-bonding genius of water in orchestrating precise three-dimensional structures and membranes? "
-- Richard Smalley, in a letter to Eric Drexler.

Apparently, water is the 'key ingredient' that makes all of the complex cellular mechanics of life possible. It has some very unique 3D characteristics that make it possible for cells to manipulate molecules to construct a wide variety of different compounds out of a small number of building blocks - e.g. to make a huge variety of different protein molecules out of a set of about 20 amino acids.

The following has been pulled together from Raymond Kurzweil's site - it's the best written discourse I've found on this topic:
Nature shows that molecules can serve as machines because living things work by means of such machinery. Enzymes are molecular machines that make, break, and rearrange the bonds holding other molecules together. Muscles are driven by molecular machines that haul fibers past one another. DNA serves as a data-storage system, transmitting digital instructions to molecular machines, the ribosomes, that manufacture protein molecules. And these protein molecules, in turn, make up most of the molecular machinery.
-- Eric Drexler
Life's local data storage is, of course, the DNA strands, broken into specific genes on the chromosomes. The task of instruction-masking (blocking genes that do not contribute to a particular cell type) is controlled by the short RNA molecules and peptides that govern gene expression. The internal environment the ribosome is able to function in is the particular chemical environment maintained inside the cell, which includes a particular acid-alkaline equilibrium (pH between 6.8 and 7.1 in human cells) and other chemical balances needed for the delicate operations of the ribosome. The cell wall is responsible for protecting this internal cellular environment from disturbance by the outside world.

In a liquid state, the two hydrogen atoms make a 104.5° angle with the oxygen atom, which increases to 109.5° when water freezes. This is why water molecules are more spread out in the form of ice, providing it with a lower density than liquid water. This is why ice floats.

Although the overall water molecule is electrically neutral, the placement of the electrons creates polarization effects. The side with the hydrogen atoms is relatively positive in electrical charge, whereas the oxygen side is slightly negative. So water molecules do not exist in isolation, rather they combine with one another in small groups to assume, typically, pentagonal or hexagonal networks. The partially positive hydrogen atom on one molecule is attracted to the partially negative oxygen on a neighboring molecule (hydrogen bonding). Three-dimensional hexamers involving 6 molecules are thought to be particularly stable, though none of these clusters lasts longer than a few picoseconds; they can change back and forth between hexagonal and pentagonal configurations 100 billion times a second. At room temperature, only about 3 percent of the clusters are hexagonal, but this increases to 100 percent as the water gets colder. This is why snowflakes are hexagonal.

These three-dimensional electrical properties of water are quite powerful and can break apart the strong chemical bonds of other compounds. Consider what happens when you put salt into water. Salt is quite stable when dry, but is quickly torn apart into its ionic components when placed in water. The negatively charged oxygen side of the water molecules attracts positively charged sodium ions (Na+), while the positively charged hydrogen side of the water molecules attracts the negatively charged chlorine ions (Cl-). In the dry form of salt, the sodium and chlorine atoms are tightly bound together, but these bonds are easily broken by the electrical charge of the water molecules. Water is considered "the universal solvent" and is involved in most of the biochemical pathways in our bodies. So we can regard the chemistry of life on our planet primarily as water chemistry.

Excellent flash animation that illustrates the chemistry of water molecules in action (by John Kyrk)
NSF Special Report - the Chemistry of Water
From the University of Arizona: Chemistry Tutorial: The Chemistry of Water

(I've been putting together some notes on bio-chemistry basics - they're available here.)

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