Codons are triplets of nucleotides that together specify an amino acid residue in a polypeptide chain. Most organisms use 20 or 21 amino acids to make their polypeptides, which are proteins or protein precursors. A triplet is a set of three items, and includes in particular: one of three babies in a multiple birth a preparation of opal as a gemstone, with a thin layer of opal backed with a dark material and covered with cap of clear quartz in poetry, a tercet (three... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ... Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ... In biology and ecology, an organism (in Greek organon = instrument) is a complex adaptive system of organs that influence each other in such a way that they function as a more or less stable whole and have properties of life. ... A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... First Impressions Precursors is an upcoming science fiction/first person shooter game made by Deep Shadows studio, based in Ukraine. ...

Because there are four possible nucleotides, adenine (A), guanine (G), cytosine (C) and thymine (T) in DNA, there are 64 possible triplets to recognize only 20 aminoacids plus the STOP signal. Due to this redundancy, most amino acids are coded by more than one triplet. Different organisms often show particular preferences for one of the several codons that encode the same given amino acid. How these preferences arise is a much debated area of molecular evolution. Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids DNA and RNA. In DNA, adenine (A) binds to thymine (T) via two hydrogen bonds to assist in stabilizing the nucleic acid structures. ... Guanine is one of the five main nucleobases found in nucleic acids (, DNA and RNA). ... Cytosine is one of the 5 main nucleobases used in storing and transporting genetic information within a cell in the nucleic acids DNA and RNA. It is a pyrimidine derivative, with a heterocyclic aromatic ring and two substituents attached (an amine group at position 4 and a keto group at... Thymine, also known as 5-methyluracil, is a pyrimidine nucleobase. ... The general structure of a section of DNA Deoxyribonucleic acid (DNA) is a nucleic acid —usually in the form of a double helix— that contains the genetic instructions specifying the biological development of all cellular forms of life (and most viruses). ...

It is generally acknowledged that codon preferences reflect a balance between mutational biases and natural selection for translational optimization. Optimal codons in fast growing microorganisms like Escherichia coli or Saccharomyces cerevisiae (the baker's yeast), reflect the compostion of their respective genomic tRNA pool. It is thought that optimal codons help to achieve faster translation rates and high accuracy. Due to these factors, translational selection is expected to be stronger in highly expressed genes, and this is indeed the case for the above mentioned organisms. In other organisms that do not show high growing rates, or that present small genomes, codon usage optimization is normally absent, and codon preferences are determined by the characteristic mutational biases seen in that particular genome. Examples of this are Homo sapiens (human) and Helicobacter pylori. Organisms that show an intermediate level of codon usage optimization include Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode worm) or Arabidopsis thaliana (wall cress). Binomial name Escherichia coli T. Escherich, 1885 E. coli at 10,000x magnification Escherichia coli (usually abbreviated to E. coli) is one of the main species of bacteria that live in the lower intestines of warm-blooded animals (including birds and mammals) and are necessary for the proper digestion of... Binomial name Saccharomyces cerevisiae Meyen ex E.C. Hansen Saccharomyces cerevisiae is a species of budding yeast. ... Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... Human beings are defined variously in biological, spiritual, and cultural terms, or in combinations thereof. ... Binomial name Helicobacter pylori ((Marshall 1985) Goodwin 1989) Helicobacter pylori is a bacterium that infects the mucus lining of the human stomach. ... Binomial name Drosophila melanogaster Meigen, 1830 Drosophila melanogaster Meigen , 1830 (Black-bellied Dew-lover) a dipteran (two-winged) insect, is the species of fruit fly that is commonly used in genetic experiments; it is among the most important model organisms. ... Binomial name Caenorhabditis elegans Maupas, 1900 Caenorhabditis elegans (pronounced see-no-rab-DYE-tis) is a free-living nematode (a roundworm), about 1 mm in length, which lives in a temperate soil environment. ... A worm is an elongated soft-bodied invertebrate animal. ... Binomial name Arabidopsis thaliana (L.) Heynh. ... Cress can refer to several edible members of the family Brassicaceae used as leaf vegetables including watercress, rock cress, winter cress and garden cress. ...

The nature of the codon usage-tRNA optimization has been very debated. It is not clear whether codon usage drives tRNA evolution or the opposite. At least one mathematical model has been developed where both, codon usage and tRNA expression coevolve in feedback fashion (i.e. codons already present in high frequencies drive up the expression of their corresponding tRNAs, and tRNAs normally expressed at high levels drive up the frequency of their corresponding codons!), however this model does not seem to have experimental confirmation yet. Another problem is that the evolution of tRNA genes has been a very inactive area of research.

External links

• Codon Usage Database
• Graphical Codon Usage Analyser
• JCat - Java Codon Usage Adaptation Tool