Biomaterial Database

A mechanism for the association of amino acids with their codons and the origin of the genetic code. 2005

Shelley D Copley, and Eric Smith, and Harold J Morowitz

Cooperative Institute for Research in Environmental Sciences, Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA. shelley@cires.colorado.au

The genetic code has certain regularities that have resisted mechanistic interpretation. These include strong correlations between the first base of codons and the precursor from which the encoded amino acid is synthesized and between the second base of codons and the hydrophobicity of the encoded amino acid. These regularities are even more striking in a projection of the modern code onto a simpler code consisting of doublet codons encoding a set of simple amino acids. These regularities can be explained if, before the emergence of macromolecules, simple amino acids were synthesized in covalent complexes of dinucleotides with alpha-keto acids originating from the reductive tricarboxylic acid cycle or reductive acetate pathway. The bases and phosphates of the dinucleotide are proposed to have enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.

UI	MeSH Term	Description	Entries
D007651	Keto Acids	Carboxylic acids that contain a KETONE group.	Oxo Acids,Oxoacids,Acids, Keto,Acids, Oxo
D008954	Models, Biological	Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.	Biological Model,Biological Models,Model, Biological,Models, Biologic,Biologic Model,Biologic Models,Model, Biologic
D008957	Models, Genetic	Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.	Genetic Models,Genetic Model,Model, Genetic
D010766	Phosphorylation	The introduction of a phosphoryl group into a compound through the formation of an ester bond between the compound and a phosphorus moiety.	Phosphorylations
D003062	Codon	A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).	Codon, Sense,Sense Codon,Codons,Codons, Sense,Sense Codons
D003653	Decarboxylation	The removal of a carboxyl group, usually in the form of carbon dioxide, from a chemical compound.	Decarboxylations
D003663	Decision Trees	A graphic device used in decision analysis, series of decision options are represented as branches (hierarchical).	Decision Tree,Tree, Decision,Trees, Decision
D005815	Genetic Code	The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).	Code, Genetic,Codes, Genetic,Genetic Codes
D000596	Amino Acids	Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.	Amino Acid,Acid, Amino,Acids, Amino
D019143	Evolution, Molecular	The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations.	Molecular Evolution,Genetic Evolution,Evolution, Genetic