Correspondence Between Coding and Coded Units Enables the World of Unconstrained Biological Complexity

This system is built up of modular units at all levels and depends on that fact to make it open ended and flexible.A mutation that replaces one nucleotide by another in a codon may change the amino acid that is specified: for example, GCA specifies the amino acid alanine; an A^C mutation, resulting in GCC, will have no effect on the protein because the latter is also a codon for alanine; this is known as a synonymous mutation. However, if the G mutates to A, the resulting ACA codon specifies threonine, and hence is a nonsynonymous mutation because it changes the amino acid that is coded by this piece of DNA.

Modularity does not imply independence among the constituent parts, however. A change in one can have dramatic effect on the others. An insertion or deletion of a nucleotide will alter the reading frame, throwing all subsequent amino acids out of order. Thus, removing the second letter (h) of the following sentence, while preserving the number of letters in each word, destroys its meaning completely: "The fish swam well" becomes "Tef ishs wamw ell." The following single-letter substitu tions make relatively little change: "The fish swim well" and "Thy fish swam well." The following change also makes sense—but with quite a difference: "The dish swam well."

With a modular amino acid coding mechanism, matched by the modularity in tRNA, a system evolved by which a sequence of amino acids could be assembled and "remembered" across replication, cell division, or organism reproduction. The number of ways a polypeptide can be put together via different amino acid sequences is essentially limitless, and life evolved to build structures and catalyze reactions around the kinds of interactions that depend on the chemical properties of folded, modified polypeptides. This constrains, but also enables, the huge diversity of life and form on Earth.

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