Molecular Mind in Cellular Motors 2: Water, The Universal, Dynamic, Non-covalent, Weak Bonds for all of Life’s Activity

Water is the medium that makes life possible. Water is so ordinary that we rarely think of it as doing anything. But inside a living cell, water is not a passive background—it is an active participant in nearly every molecular event

and every cellular structure.

The water molecule has a peculiar geometry. One oxygen atom pulls so strongly on two hydrogen atoms that it ends up slightly negative, while the two hydrogens are left slightly positive, which results in four partial charges pointing outward in four directions, forming a tetrahedron.  These partial charges make water molecules attract each other into specific shapes—positive to negative, again and again—forming and breaking billions of bonds every second.  These attractions can produce a perfect tetrahedron

lattice—the shape of water when it is not moving at all, such as in ice.

These attractions of two water molecules are called hydrogen bonds. When liquid, the shape of water’s bonding fluctuates between various structures. These same positive and negative attractions also bond with every other nearby molecule.

Liquid water, even in the crowded cell interior, flows—but it flows with purpose. Water molecules immediately wrap around proteins, RNA strands, lipids, sugars, and single atoms in layered sheets called hydration layers, sometimes twenty molecules deep. These layers are neither liquid nor ice—they are something in between, structured enough to influence the behavior of every large molecule they touch. They become part of the dynamic molecular clusters that form throughout the cell.

Water that is not in a hydration layer is called bulk water and is made up of two rapidly alternating states (timescales of about one picosecond): one is the tetrahedron structure and the other a constantly fluctuating mixture of many variations of a broken lattice. The network of the shifting bonds is so pervasive that it behaves as though permanently structured with a combination of strength, flexibility, and omnipresence, making it the only known matrix capable of supporting biological life.

These fluctuating bonding structures account for seventy extraordinary anomalous physical properties of water that set it apart from every other substance. The tetrahedral geometry allows each water molecule to form up to four hydrogen bonds simultaneously in four directions—two as a donor and two as an acceptor—creating a cooperative, self-reinforcing network unlike anything found in other common liquids.

Molecules that repel water in hydration layers (those molecules without a charge and unable to form hydrogen bonds) cluster their water-avoiding regions together, forcing a shape change that becomes part of a 3D functional structure, such as in proteins. This is a primary force forming the highly sought shape of proteins, which were long believed to determine all of life and have been the holy grail of bioscience. Parts of molecules that attract water spread their charged regions to the outside of large molecules, seeking connection with water. Those parts of the molecule with no charge are then pushed inward to form the inside of large protein molecules, such as the middle portion of a large protein receptor that spans a membrane. The regions of the protein outside of the lipid membranes on either side are attracting water and that part of the protein inside the lipid is stable, away from water. 

The push and pull between water and everything else is the invisible choreographer of molecular shape—and molecular shape, as we will see, is almost everything. But, this molecular shape can be enduring, such as for the entire life of a neuron or it can be instantaneous in the middle of a chemical reaction, where a transient hydrogen bond in one region of the molecule, shifts the entire structure of the large molecule just a little, enough for action to occur far away on the other side of the large molecule.

The first one or two hydration layers are the most ordered: hydration shells are not merely passive envelopes—they actively stabilize protein and nucleic acid shapes, mediate the recognition of one molecule by another, determine whether two surfaces will bind or repel each other, and create the energetic context within which every molecular interaction in the cell occurs.

Another underappreciated role of water is as a structural architect of solid materials, biological scaffolds, and mineral frameworks. In collagen, water molecules surround the triple helix in a precisely organized hydrogen-bonded cylinder called a hydration shell. Rows of water molecules fill crevices in all of life’s vital large enzymes.  These aligned water molecules can form effective wires where protons can uniquely and rapidly be transferred.  This is the essence of mitochondrial energy production and photosynthesis (discussed in future post).

There are protein molecules that do not form one shape, but rather constantly change their form, as if flapping in the wind, or dancing. These changes are almost instantaneous, and just as fast, water coalesces hydration layers around the moving molecular strands. These hydration layers change rapidly in complex ways, which can produce an extended effect, creating sweeping electrostatic fields that influence the orientation of water molecules over long distances in the cell. In these swirling water structures, water wires can be briefly produced where protons are transferred, as if transmitting information or energy in a global communication grid.

Water is not a passive solvent in which life happens to take place. It is an active, responsive, informationally rich medium that participates directly in every process of the living cell. The accumulated evidence from molecular biology, biophysics, materials science, and structural chemistry now supports a view of water as something closer to a distributed molecular intelligence than a simple chemical background. Molecular clusters perform all cellular actions, and individual water molecules become an integral, functional chemical member of every molecular cluster in the cell.

The cell is not a bag of chemicals in water. It is water, thinking through chemistry. How can these infinitely complex behaviors of water, along with non-covalent bonds, not be part of the actions of mind in nature?

After this series on molecular motors, I will be doing a series devoted to the multifaceted, complex nature of water in life. The next posts in this series will advance the description of living, moving, interacting, communicating molecular creatures called cellular motors.