Chapter 15

The Molecules of Life

15.1

Molecules and Supramolecular Structure

Table 15.1 gives some approximate values for the atomic composition of a cell.

The atomic composition represents a highly reductionist view, somewhat akin to

asserting that the informational content of Macbeth is minus sigma summation Underscript alphabet Endscripts p Subscript i Baseline log Subscript 2 Baseline p Subscript i−^Σ

alphabet ^{pi log}2 ^{pi, where}

p Subscript ipi is the normalized frequency of occurrence of the iith letter of the alphabet. The

next stage of complexity is to consider molecules (Table 15.2) and macromolecules

(Table 15.3). This is still highly reductionist, however, it corresponds to calculating

Shannon entropy from the vocabulary of Macbeth. Words are, however, grouped

into sentences, which, in turn, are arranged into paragraphs. The cell is analogously

highly structured—molecules are grouped into supramolecular complexes, which,

in turn, are assembled into organelles. This structure, some of which is visible in

the optical microscope, but which mostly needs the higher resolution of the electron

microscope, is often called ultrastructure. It is difficult to quantify—that is, assign

numerical parameters to it, with which different sets of observations can be compared.

The human eye can readily perceive drastic changes in ultrastructure when a cell is

subjected to external stress, but generally these changes have to be described in

words.

The most prominent intracellular structural feature is the system of lipid bilayer

membranes, such as the endoplasmic reticulum. Also prominent are the proteins such

as actin, which form large filamentous structures constituting a kind of skeleton (the

cytoskeleton). There are also many more or less compact (globular), large multi-

protein complexes (e.g., the proteasome). Furthermore, proteins may be associated

with lipid membranes or with the DNA. These structures are rather dynamic; that is,

there is ceaseless assembly and disassembly, depending on the exigencies of survival.

Some of them are described in more detail under the descriptions of the individual

classes of molecules.

© Springer Nature Switzerland AG 2023

J. Ramsden, Bioinformatics, Computational Biology,

https://doi.org/10.1007/978-3-030-45607-8_15

217