Biology’s machines

Progression to Biology s Machines from Model Protein Machines... 

Biology s machines are different from man s machines, primarily because they evolved to function efficiently in water. Many of man s machines commonly operate at high temperatures, above the boiling temperature for water. Such conditions are incompatible with life. Other manmade machines, electric motors, and generators and the many energy conversions of the electronic world do not function in water. As shown in Rgure 2.16, even the chemically driven polymeric machines that do function in... 

ATPase, Biology s Workhorse Protein-based Machine... 

The following set of axioms provides the basis for the engineering of diverse protein-based machines and of the design of molecular machines from amphiphilic polymers in general, as considered in Chapter 9. They also open the door to new insights into the function of biology s protein-based machines, as discussed in Chapters 7 and 8. 

Changing the second base of two of the four triplet codons for Val, namely, GUA and GUG to GAA and GAG, respectively, are two ways to convert Val to Glu. Changing the second base of the other two triplet codons for Val, for example, GUU to GAU and GUC to GAC, converts Val to Asp. Thus, the Val triplet codons are such that a single base change of the second base from U to A results in amino acid residues with carboxylate side chains. A single mutation converts a thermally driven (and also a poor chemically driven) protein-based machine into a more efficient chemically driven protein-based machine. How trivial and likely the diversification of biology s molecular machines, especially because it costs no more energy (of biosynthesis) to produce the new or improved protein-based machine. 

More to the point, we now see biology s access to energy by means of the consilient mechanism of energy conversion, combined with readily available mutations to improve protein-based machines, as the source of increased structural order and functional diversity. 

On the Relevance of Hydrophobic and Elastic Consilient Mechanisms to Biology s Protein-based Machines... 

Accordingly, the perspectives in Chapter 5, developed on elastic-contractile protein-based polymers, introduce new concepts into the functional description of biology s protein-based machines. As with the introductory comments in Chapter 7, the footnote relevant to reactions toward new concepts in science is repeated here in footnote form. ... 

This chapter discusses key protein-based machines of biology to demonstrate the relevance of the hydrophobic and elastic consilient mechanisms. The objective in this chapter, therefore, is to investigate selected examples of biology s protein-based machines and to look at the molecular level for a coherence of phenomena with the designed elastic model... 

In terms of the molecular process whereby ATP forms and functions as biology s energy coin, there are two aspects—the protonation/ deprotonation of carboxylates due to a proton concentration gradient that drives a rotor to form ATP from ADP and Pi, as in the ATP synthase, and the molecular process whereby the breakdown of ATP to ADP with release of Pj drives the protein-based machines of biology, as in the myosin II motor of muscle contraction. 

Insights into Biology s Vital Protein-based Machine ATP Synthase... 

The above three discussed protein-based machines—Complex III of the electron transport chain, ATP synthase/Fj-ATPase, and the myosin II motor of muscle contraction—represent the three major classes of energy conversion that sustain Life. Therefore, the facility with which the consilient mechanisms explain their function indeed support the thesis that biology s vital force arises from the coupled hydrophobic and elastic consilient mechanisms. 

Biology s reversal of the much-noted arrow of time and equivalently biological evolution derive simply from fundamental reality of biosynthesis within the context of inverse temperature transitions as expressed in the hydrophobic consilient mechanism. The production of a new and improved protein-based machine occurs by chance, but most significantly it occurs at a cost in energy no greater than that required to produce the initial less useful protein-based machine. This is the nature of the biosynthesis of protein and of the other great macromolecules (the nucleic acids, DNA and RNA) of biology. 

---