Chapter 2 – Orientation for the Bio-Curious  25

The general field of study of carbon compounds is known as “organic chemistry,” to dif­

ferentiate it from inorganic chemistry that involves noncarbon compounds, but also confus­

ingly can include the study of the chemistry of pure carbon itself such as found in graphite,

graphene, and diamond. Biochemistry is largely a subset or organic chemistry concerned

primarily with carbon compounds occurring in biological matter (barring some inorganic

exceptions of certain metal ions). An important characteristic of biochemical compounds is

that although the catenated carbon chemistry confers stability, the bonds are still sufficiently

labile to be modified in the living organism to generate different chemical compounds during

the general process of metabolism (defined as the collection of all biochemical transform­

ations in living organisms). This dynamic flexibility of chemistry is just as important as the

relative chemical stability of catenated carbon for biology; in other words, this stability occu­

pies an optimum regime for life.

The chemicals of life, which not only permit efficient functioning of living matter during

the normal course of an organism’s life but also facilitate its own ultimate replication into

future generations of organisms through processes such as cellular growth, replication,

and division can be subdivided usefully into types mainly along the lines of their chemical

properties.

2.3.2  LIPIDS AND FATTY ACIDS

By chemically linking a small alcohol-​type molecule called “glycerol” with a type of carbon-​

based acid that contain typically 20 carbon atoms, called “fatty acids,” fats, also known as

lipids, are formed, with each glycerol molecule in principle having up to three sites for

available fatty acids to bind. In the cell, however, one or sometimes two of these three

available binding sites are often occupied by an electrically polar molecule such as cho­

line or similar and/​or to charged phosphate groups, to form phospholipids (Figure 2.3a).

These impart a key physical feature of being amphiphilic, which means possessing both

hydrophobic, or water-​repelling properties (through the fatty acid “tail”), and hydrophilic,

or water-​attracting properties (through the polar “head” groups of the choline and/​or

charged phosphate).

This property confers an ability for stable structures to form via self-​assembly in which

the head groups orientate to form electrostatic links to surrounding electrically polar water

molecules, while the corresponding tail groups form a buried hydrophobic core. Such

stable structures include at their simplest globular micelles, but more important biological

structures can be formed if the phospholipids orient to form a bilayer, that is, where two

layers of phospholipids form in effect as a mirror image sandwich in which the tails are at

the sandwich center and the polar head groups on the outside above and below (Figure 2.3b).

Phospholipid bilayers constitute the primary boundary structure to cells in that they confer

an ability to stably compartmentalize biological matter within a liquid water phase, for

example, to form spherical vesicles or liposomes (Figure 2.4a) inside cells. Importantly, they

form smaller organelles inside the cells such as the cell nucleus, for exporting molecular

components generated inside the cell to the outside world, and, most importantly, for forming

the primary boundary structure around the outside of all known cells, of the cell membrane,

which arguably is a larger length scale version of a liposome but including several additional

nonphospholipid components (Figure 2.4b).

A phospholipid bilayer constitutes a large free energy barrier to the passage of a single

molecule of water. Modeling the bilayer as a dielectric indicates that the electrical permit­

tivity of the hydrophobic core is 5–​10 times that of air, indicating that the free energy

change, ΔG, per water molecule required to spontaneously translocate across the bilayer

is equivalent to ~65 kBT, one to two orders of magnitude above the characteristic thermal

energy scale of the surrounding water solvent reservoir. This suggests a likelihood for the

process to occur given by the Boltzmann factor of exp(−ΔG/​kBT), or ~10⁻²⁸. Although gases

such as oxygen, carbon dioxide, and nitrogen can diffuse in the phospholipid bilayer, it can

be thought of as being practically impermeable to water. Water, and molecules solvated in