Chapter 15: Epologue

Chapter 15: Epilogue

We began with an extremely brief history of how science reached its present point. Over the next 13 chapters, we reviewed the physics and chemistry of water in its interactions with proteins, nucleic acids, and lipids. Water turns out to be ubiquitous in any biological system, validating, at least in part, the comment from the Star Trek alien with which we began, calling humans “ugly bags of mostly water.” Animals and plants and fungi and bacteria all have internal surfaces that are in contact with water; prokaryotes also have external surfaces that are in contact with water. The functions of proteins are now known to include water as a part of their structure, or, if structure is defined differently, part of the immediate environment of the molecules, which helps determine the function of the protein; proteins that transport protons are critical for several functions, and proton transport almost always requires water as a part of the path.

We have gone through some of the physics of hydration of ions, as well as hydration of the larger species of biomolecules. We discussed some common themes in the way water interacts with hydrophilic and hydrophobic solutes. In the Conclusions, we summarized the ways in which it was possible to understand these interactions, as of 2023. However, we made it clear that this could not be the end of the story. The Conclusions not only tried to pull together the strands of the story as it stands now, but made it clear that the story is but half told—if that.

The questions we will be able to answer as we make further advances in both experimental and theoretical/computational techniques will show how the water participates in essentially all biological functions. Sometimes this involves actual chemical bonds, or their formation. Often, considering hydrogen bonds, it may be more like partial bonds. The hydrogen bond networks formed by water are a fairly unique property. Although water is not the only substance with hydrogen bonds, water appears to be alone in being able to both donate and accept two hydrogen bonds, leading to networks that other substances cannot produce. This has profound effects on the actions of biomolecules. Right now, we can make a rather good estimate of the strength and other properties of hydrogen bonds; however, we see that hydrogen bonds vary considerably, and that in turn makes the properties of the proteins that are responsible for most biological functions, as well as the properties of nucleic acids, difficult to compute or simulate very accurately. Networks of hydrogen bonds are only beginning to be investigated at a serious level.