I really like this book! So this is what P-Chem is about? Nice. I had no idea what it might be like.
The first chapters read like my Statistical Mechanics book, Pathria and Beale, which is good because I need to review, review, review. I was impressed that Partition functions were mentioned so early on. Wow!
This was nice quote I stumbled on:
The Molecular Logic of Biology Is Encoded in Coupled-Binding Actions Biological machines are varied and powerful, like computers. The power of computers comes from the multiplicity of useful ways that you can link together a few elementary logic units, such as and gates, or gates, and bistable flip-flops. In a simple logic device, you have two inputs x and y. Each input is given to be in one of two states, call them 0 or 1. A truth table (Figure 29.7) describes the outputs for the different possible inputs. Biology uses this principle too. Biomolecules can act as logic elements.
Dill, Ken. Molecular Driving Forces (p. 595). CRC Press. Kindle Edition.
I’m thinking of starting a separate thread on P-Chem just to deposit some of my thoughts, but this is exactly how I see the modern view of biology, with lots of computer-like processing. I see it with a lot of the binding and releasing and chemical modification. I’m glad my perspective isn’t idiosyncratic, though I’ve been criticized by some of my detractors for saying there is massive information processing in biological systems. I see it a lot in the post-translational modifications in Eukarytic proteins. The sophisticatoin boggles the mind!
But, back to the topic, when we talk about creating proteins with our mind, one of the issues is not really the fold, but in some cases like histones, one of it’s roles is like an information repository that is managed by bio-logic processes. Visually the bits and bytes that are read/written/erased can be visualized this way:
When I saw this, I had a different view of what it meant to design a protein in a complex eukaryotic creature. It requires thinking of the protein not merely as a catalytic molecule, but rather an information storing molecule!