Genetic Code: Introduction

Kimitsuna Watanabe, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan
Shin‐ichi Yokobori, Tokyo University of Pharmacy and Life Sciences, Tokyo, Japan

Published online: October 2011

DOI: 10.1002/9780470015902.a0000809.pub2

The genetic code establishes the relationship between all 64 possible arrangements of triplets (codons) of the four nucleotide bases contained in either DNA (A, T, G and C) or RNA (A, U, G and C) and the 20 amino acids that are used to construct proteins via ‘translation’ system as well as signals of translation initiation and termination. The historical events from 1950s to 1960s that contributed to the deciphering of the genetic code led to the development of the field of molecular biology. In 1960s, the genetic code was established to be ‘universal’ for all living organisms. However, from late 1970s, variations of genetic code have been found in various genetic systems. Variations of genetic code promote studies on the origin and evolution of the genetic code.

Key Concepts:

  • Genetic code is the correlation between nucleotide triplet and the corresponding amino acid.
  • Genetic code consists of 64 triplet codons and sometimes ‘degenerate’.
  • Central dogma states that genetic information flows unidirectionally from DNA to protein via RNA as an intermediary.
  • A cell-free protein system contains ribosome, S100 fraction, tRNA, amino acids, ATP, an energy recycling system and a template.
  • Termination codon consists of UAG (amber codon), UAA (ochre codon) and UGA (opal codon), which code for no amino acid but instead cause protein synthesis to terminate.
  • Initiation codon is AUG, which initiates protein synthesis with formyl-methionine in bacteria and phage.
  • Universal genetic code shows the way of assignment of 64 triplet codons to each of 20 amino acids and 3 termination codons, which is common to almost all extant organisms – bacteria, yeasts, viruses, plants and animals.

Keywords: amino acids; DNA; nucleotide; codon; genes; universal genetic code

Figure 1. Gene map of frameshift mutants of T4 phage rIIB cistron caused by proflavin. Modified from Crick et al. (1961).
Figure 2. Frameshift mutants of T4 phage rIIB cistron caused by proflavin. Addition and deletion on the nucleotide sequence. Redrawn from Crick et al. (1961).
Figure 3. Replacement of the amber codon with amino acids in the head protein of T4 phage amber mutant grown in various E. coli Su+ strains.
Figure 4. Nucleotide sequences of the translation initiation sites in the coat protein, replicase and A protein of R17 RNA. The underlined sequences are the Shine–Dalgarno sequences. Redrawn from Steitz (1969).
Figure 5. Comparison between amino acid sequences of lysozyme of wild-type T4 phage and eJ42eJ44 frameshift mutant. Determination of in vivo code. Redrawn from Terzaghi et al. (1966).
Figure 6. The universal genetic code. At the time of the Cold Spring Harbor Symposium (1966) the UGA opal codon was not identified and all the codons were not completely allocated. The initiation codon was uncertain.
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 References
    Anderson S, Bankier AT, Barrell BG et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290: 457–465.
    Anderson S, de Bruijn MHL, Coulson AR et al. (1982) Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. Journal of Molecular Biology 156: 683–717.
    Barrell BG, Anderson S and Bankier AT (1980) Different pattern of codon recognition by mammalian mitochondrial tRNAs. Proceedings of the National Academy of Sciences of the USA 77: 3164–3166.
    Barrell BG, Bankier AT and Drouin J (1979) A different genetic code in human mitochondria. Nature 282: 189–194.
    Beck E, Sommer R, Auerswald EA et al. (1978) Nucleotide sequence of bacteriophage fd DNA. Nucleic Acids Research 5: 4495–4503.
    Brenner S, Stretton AO and Kaplan S (1965) Genetic code: the ‘nonsense’ triplets for chain termination and their suppression. Nature 206: 994–998.
    Capecchi MR and Gussin GN (1965) Suppression in vitro: identification of a serine-sRNA as a ‘nonsense’ suppressor. Science 149: 417–422.
    Castresana J, Feldmaier-Fuchs G, Yokobori S, Satoh N and Pääbo S (1998) The mitochondrial genome of the hemichordate Balanoglossus carnosus and the evolution of deuterostome mitochondria. Genetics 150: 1115–1123.
    Clark BFC and Marcker KA (1966) The role of N-formyl-methyonyl-sRNA in protein synthesis. Journal of Molecular Biology 17: 394–406.
    Clary DO and Wolstenholme DR (1985) The mitochondrial DNA molecule of Drosophila yakuba: nucleotide sequence, gene organization and the genetic code. Proceedings of the National Academy of Sciences of the USA 71: 2777–2781.
    de Crécy-Lagard V, Marck C, Brochier-Armanet C and Grosjean H (2007) Comparative RNomics and modomics in Mollicutes: prediction of gene function and evolutionary implications. IUBMB Life 59: 634–658.
    Crick FHC (1958) On protein synthesis. Symposia of the Society for Experimental Biology 12: 138–163.
    Crick FHC, Barnett L, Brenner S and Watts-Tobin RJ (1961) General nature of the genetic code for protein synthesis. Nature 192: 1227–1232.
    Fiers W, Contreras R, Duerinck F et al. (1976) Complete nucleotide sequence of bacteriophage MS2 RNA: primary and secondary structure of the replicase gene. Nature 260: 500–507.
    Fiers W, Contreras R, Haegeman G et al. (1978) Complete nucleotide sequence of SV40 DNA. Nature 273: 113–120.
    Franklin RE and Gosling RG (1953) Molecular configuration in sodium thymonucleate. Nature 171: 740–741.
    Fraser CM, Gocayne JD, White O et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270: 397–403.
    Gamow G (1954) Possible relation between deoxyribonucleic acid and protein structures. Nature 173: 318.
    Goodman HM, Abelson J, Landy A, Brenner S and Smith J (1968) Amber suppression: a nucleotide change in the anticodon of a tyrosine transfer RNA. Nature 217: 1019–1024.
    Himeno H, Masaki H, Kawai T et al. (1987) Unusual genetic codes and a novel gene structure for tRNASerAGY in starfish mitochondrial DNA. Gene 56: 219–230.
    Horowitz S and Gorovsky M (1985) An unusual genetic code in nuclear genes of Tetrahymena. Proceedings of the National Academy of Sciences of the USA 82: 2452–2455.
    Jacob JEM, Vanholme B, Van Leeuwen T and Gheysen G (2009) A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Research Notes 2: 192.
    Kawaguchi Y, Honda H, Taniguchi-Morimura J and Iwasaki S (1989) The codon CUG is read as serine in an asporogenic yeast Candida cylindracea. Nature 341: 164–166.
    Last JA, Stanley WM Jr, Salas M et al. (1965) Translation of the genetic message, IV. UAA as a chain termination codon. Proceedings of the National Academy of Sciences of the USA 57: 1062–1067.
    Li M and Tzagoloff A (1979) Assembly of the mitochondrial membrane system: sequences of yeast mitochondrial valine and an unusual threonine tRNA gene. Cell 18: 47–53.
    Macino G, Coruzzi G, Nobrega FG, Li M and Tzagoloff A (1979) Use of the UGA terminator as a tryptophan codon in yeast mitochondria. Proceedings of the National Academy of Sciences of the USA 76: 3784–3785.
    Muramatsu T, Nishikawa K, Nemoto F et al. (1988) Codon and amino-acid specificities of a transfer RNA are both converted by a single post-transcriptional modification. Nature 336: 179–181.
    Nakanishi K, Bonnefond L, Kimura S et al. (2009) Structural basis for translational fidelity ensured by transfer RNA lysidine synthetase. Nature 461: 1144–1148.
    Nirenberg MW and Leder P (1964) RNA code words and protein synthesis. The effect of trinucleotides on the binding of sRNA to ribosomes. Science 145: 1399–1407.
    Nirenberg MW and Matthaei JH (1961) The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides. Proceedings of the National Academy of Sciences of the USA 47: 1588–1602.
    Nishimura S, Jones DS and Khorana HG (1965) Studies on polynucleotides XLVIII. The in vitro synthesis of a co-polynucleotides containing two amino acids in alternating sequence dependent upon a DNA-like polymer containing two nucleotides in alternating sequence. Journal of Molecular Biology 13: 302–324.
    Okimoto R, Macfarlane JL, Clary DO and Wolstenholme DR (1992) The mitochondrial genomes of two nematodes, Caenorhabditis elegans and Ascaris suum. Genetics 130: 471–498.
    Osawa S and Jukes TH (1989) Codon reassignment (codon capture) in evolution. Journal of Molecular Evolution 28: 271–278.
    Schultz DW and Yarus M (1994) Transfer RNA mutation and the malleability of the genetic code. Journal of Molecular Biology 235: 1377–1380.
    Seilhamer JJ and Cummings DJ (1982) Altered genetic code in Paramecium mitochondria: possible evolutionary trends. Molecular and General Genetics 187: 236–239.
    Soma A, Ikeuchi Y, Kanemasa S et al. (2003) An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Molecular Cell 12: 689–698.
    Speyer JF, Lengyel P, Basilio C et al. (1963) Synthetic polynucleotides and the amino acid code. Cold Spring Harbor Symposia on Quantitative Biology 28: 559–567.
    Steitz JA (1969) Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature 224: 957–964.
    Takemoto C, Spremulli LL, Benkowski LA et al. (2009) Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system. Nucleic Acids Research 37: 1616–1627.
    Terzaghi E, Okada Y, Streisinger G (1966) Change of a sequence of amino acids in phage T4 lysozyme by acridine-induced mutations. Proceedings of the National Academy of Sciences of the USA 56: 500–507.
    Watson JD and Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171: 737–738.
    Webster RE, Engelhardt DL and Zinder ND (1966) In vitro protein synthesis: chain initiation. Proceedings of the National Academy of Sciences of the USA 5: 155–161.
    Wilkins MHF, Stokes AR and Wilson HR (1953) Molecular structure of deoxypentose nucleic acids. Nature 171: 738–740.
    Yamao F, Muto A, Kawauchi Y et al. (1985) UGA is read as tryptophan in Mycoplasma capricolum. Proceedings of the National Academy of Sciences of the USA 82: 2306–2309.
    Yokobori S, Ueda T and Watanabe K (1993) Codons AGA and AGG are read as glycine in ascidian mitochondria. Journal of Molecular Evolution 36: 1–8.
    Yokogawa T, Suzuki T, Ueda T et al. (1992) Serine tRNA complementary to the nonuniversal serine codon CUG in Candida cylindracea: evolutionary implications. Proceedings of the National Academy of Sciences of the USA 89: 7408–7411.
 Further Reading
    book Judson HF (1979) The Eighth Day of Creation, The Makers of the Revolution in Biology. New York: Simon and Shuster.
    book Osawa S (1995) Evolution of the Genetic Code. Oxford: Oxford Science.
    Sanger F, Coulson AR, Friedmann T et al. (1978) The nucleotide sequence of bacteriophage X174. Journal of Molecular Biology 125: 225–246.
    book The Genetic code (1968) Cold Spring Harbor Symposium on Quantative Biology, vol. 31. USA: Cold Spring Harbor Laboratory.
    Weigert MG and Garen A (1965) Base composition of nonsense codons in E. coli. Evidence from amino-acid substitutions at a tryptophan site in alkaline phosphatase. Nature 206: 992–994.

Related Sub-Topics:

Translation and Protein synthesis | Translation of RNA | DNA Structure and Function | Genetic Code | History
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Article Title: Genetic Code: Introduction
 
How to Cite close
Watanabe, Kimitsuna, and Yokobori, Shin‐ichi(Oct 2011) Genetic Code: Introduction. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0000809.pub2]