Notes

Chapter 8: Implications for Everyday Systems

Section 5: Fundamental Issues in Biology


Proteins

At a molecular level much of any living cell is made up of proteins formed from chains of tens to thousands of amino acids. Of the thousands of proteins now known some (like keratin and collagen) are fibrous, and have a simple repetitive underlying structure. But many are globular, and have at least a core in which the 3D packing of amino acids seems quite random. Usually there are some sections that consist of simple α helices, β sheets, or combinations of these. But other parts—often including sites important for function—seem more like random walks. At some level the 3D shapes of proteins (tertiary structure) are presumably determined by energy minimization. But in practice very different shapes can probably have almost identical energies, so that in as much as a given protein always takes on the same shape this must be associated with the dynamics of the process by which the protein folds when it is assembled. (Compare page 988.) One might expect that biological evolution would have had obvious effects on proteins. But as mentioned on page 1184 the actual sequences of amino acids in proteins typically appear quite random. And at some level this is presumably why there seems to be so much randomness in their shapes. (Biological evolution may conceivably have selected for proteins that fold reliably or are more robust with respect to changes in single amino acids, but there is currently no clear evidence for this.)

From Stephen Wolfram: A New Kind of Science [citation]