chapter  2
Mechanics of Single Molecules and Single Proteins
Pages 30

We begin this chapter by first classifying objects as either macroscopic or microscopic to determine how to best analyze their behavior. This distinction is not trivial. In fact, it has launched the field of nanoscale biomechanics, which bridges the scale between molecules, the vast majority of which have a linear dimension of less than 100 nm, and cells, which typically have a linear dimension of more than 1 μm. Examples of small molecules include water (H2O), benzene (C6H6), acetic acid (CH3COOH), and adenosine triphosphate (ATP) (C10H16N5O13P3). Usually we consider the behavior of these on purely chemical terms

(thermodynamics, formation and breaking bonds). And typically, the thermochemical behavior of these molecules is measured in samples containing molar quantities of these molecules, i.e., >1023 molecules in solution. Consider hydrogen and oxygen reacting to produce water and heat:

2H2 + O2  2H2O + heat. (2.1) 2.1.1 Macroscale vs. Microscale

Likewise, when we examine the behavior of large mechanical structures such as automobile engines we examine the behavior of such systems by considering thermal expansions, mechanics of gears and levers. These systems, which might contain tens to hundreds of times the mass used in a benchtop experiment, are also governed by the same laws that govern the reaction of equation (2.1). The overall mechanics of any combustion engine may be outlined as follows:

combustion  work by expanding gases  levers move, gears turn, wheels turn  car moves

So essentially, the vast majority of our technologies are chemotrophic rather than phototropic: we convert paleopetrochemical photosynthetic energy into kinetic and ultimately thermal energy at a rate ten million times greater than the rate at which it was stored. That said, all species that do not employ technology, i.e., every species but one, extract energy from the environment that has only been recently stored. It is thus of primary importance that the biotechnologist understands the fundamentals of the molecules that allow for this conversion in the absence of technology.