The genetic code is the set of rules by which information encoded in genetic material (DNA Deoxyribonucleic acid ( /diːˌɒksɨˌraɪbɵ.nuːˈkleɪ.ɪk ˈæsɪd/ (help·info)) (DNA) is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms and some viruses. The main role of DNA molecules is the long-term storage of information. DNA is often compared to a set of or mRNA Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein. In mRNA as in DNA, genetic information sequences) is translated Translation is the first stage of protein biosynthesis . In translation, messenger RNA (mRNA) produced in transcription is decoded to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. Translation occurs in the cell's cytoplasm, where the large and small subunits of the ribosome are located, and bind into proteins Proteins are organic compounds made of amino acids arranged in a linear chain and folded into a globular form. The amino acids in a polymer are joined together by the peptide bonds between the carboxyl and amino groups of adjacent amino acid residues. The sequence of amino acids in a protein is defined by the sequence of a gene, which is encoded (amino acid Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. These molecules contain the key elements of carbon, hydrogen, oxygen, and nitrogen. These molecules are particularly important in biochemistry, where this term refers to alpha-amino acids with the general formula sequences) by living cells The cell is the functional basic unit of life. It was discovered by Robert Hooke and is the functional unit of all known living organisms. It is the smallest unit of life that is classified as a living thing, and is often called the building block of life. Some organisms, such as most bacteria, are unicellular . Other organisms, such as humans,. The code defines a mapping between tri-nucleotide Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides play central roles in metabolism. In that capacity, they serve as sources of chemical energy , participate in cellular signaling (cyclic guanosine monophosphate and cyclic adenosine monophosphate), and are incorporated into sequences, called codons, and amino acids. With some exceptions,^[1] a triplet codon in a nucleic acid sequence specifies a single amino acid. Because the vast majority of genes A gene is a unit of heredity in a living organism. It is normally a stretch of DNA that codes for a type of protein or for an RNA chain that has a function in the organism. All living things depend on genes, as they specify all proteins and functional RNA chains. Genes hold the information to build and maintain an organism's cells and pass genetic are encoded with exactly the same code (see the RNA codon table), this particular code is often referred to as the canonical or standard genetic code, or simply the genetic code, though in fact there are many variant codes. For example, protein synthesis in human mitochondria In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These organelles range from 0.5 to 10 micrometers (μm) in diameter. Mitochondria are sometimes described as "cellular power plants" because they generate most of the cell's supply of adenosine triphosphate (ATP), used as a source of relies on a genetic code that differs from the standard genetic code.

Not all genetic information is stored using the genetic code. All organisms' DNA contains regulatory sequences, intergenic segments, and chromosomal structural areas that can contribute greatly to phenotype A phenotype is any observable characteristic or trait of an organism: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior . Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two. Those elements operate under sets of rules that are distinct from the codon-to-amino acid paradigm underlying the genetic code.

Discovery

After the structure of DNA was deciphered by James Watson James Dewey Watson is an American molecular biologist, best known as one of the two co-discoverers of the structure of DNA, with Francis Crick, in 1953. Watson, Francis Crick, and Maurice Wilkins were awarded the 1962 Nobel Prize in Physiology or Medicine "for their discoveries concerning the molecular structure of nucleic acids and its, Francis Crick Francis Harry Compton Crick OM FRS , was a British molecular biologist, physicist, and neuroscientist, and most noted for being one of two co-discoverers of the structure of the DNA molecule in 1953, together with James D. Watson. He, Watson and Maurice Wilkins were jointly awarded the 1962 Nobel Prize for Physiology or Medicine "for their, Maurice Wilkins Maurice Hugh Frederick Wilkins CBE FRS was a New Zealand molecular biologist, and Nobel Laureate who contributed research in the fields of phosphorescence, radar, isotope separation, and X-ray diffraction. He was most widely known for his work at King's College London on the structure of DNA. In recognition of this work, he, Francis Crick and and Rosalind Franklin Rosalind Elsie Franklin was a British biophysicist, physicist, chemist, biologist and X-ray crystallographer who made important contributions to the understanding of the fine molecular structures of DNA, RNA, viruses, coal and graphite, serious efforts to understand the nature of the encoding of proteins began. George Gamow George Gamow , born Georgiy Antonovich Gamov (Георгий Антонович Гамов), was a Russian-born theoretical physicist and cosmologist. He discovered alpha decay via quantum tunneling and worked on radioactive decay of the atomic nucleus, star formation, stellar nucleosynthesis, big bang nucleosynthesis, cosmic microwave background, postulated that a three-letter code must be employed to encode the 20 standard amino acids used by living cells to encode proteins, because 3 is the smallest integer n such that 4ⁿ is at least 20.^[2]

The fact that codons consist of three DNA bases was first demonstrated in the Crick, Brenner et al. experiment. The first elucidation of a codon was done by Marshall Nirenberg and Heinrich J. Matthaei in 1961 at the National Institutes of Health The National Institutes of Health is an agency of the United States Department of Health and Human Services and is the primary agency of the United States government responsible for biomedical and health-related research. It consists of 27 separate institutes and centers which includes the Office of the Director. Francis S. Collins is the current. They used a cell-free system to translate Translation is the first stage of protein biosynthesis . In translation, messenger RNA (mRNA) produced in transcription is decoded to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. Translation occurs in the cell's cytoplasm, where the large and small subunits of the ribosome are located, and bind a poly-uracil RNA sequence (i.e., UUUUU...) and discovered that the polypeptide Peptides are short polymers of amino acids linked by peptide bonds. They have the same chemical structure as proteins, but only shorter in length that they had synthesized consisted of only the amino acid phenylalanine Phenylalanine is an α-amino acid with the formula HO2CCH(NH2)CH2C6H5. This essential amino acid is classified as nonpolar because of the hydrophobic nature of the benzyl side chain. L-Phenylalanine (LPA) is an electrically-neutral amino acid, one of the twenty common amino acids used to biochemically form proteins, coded for by DNA. The codons. They thereby deduced that the codon UUU specified the amino acid phenylalanine. This was followed by experiments in the laboratory of Severo Ochoa demonstrating that the poly-adenine RNA sequence (AAAAA...) coded for the polypeptide, poly-lysine.^[3] and the poly-cytosine RNA sequence (CCCCC...) coded for the polypeptide, poly-proline.^[4] Therefore the codon AAA specified the amino acid lysine, and the codon CCC specified the amino acid proline. Using different copolymers most of the remaining codons were then determined. Extending this work, Nirenberg and Philip Leder Philip Leder is an American geneticist. He was born in Washington, D.C. and studied at Harvard University, graduating in 1956. In 1960, he graduated from Harvard Medical School revealed the triplet nature of the genetic code and allowed the codons of the standard genetic code to be deciphered. In these experiments various combinations of mRNA Messenger RNA is a molecule of RNA encoding a chemical "blueprint" for a protein product. mRNA is transcribed from a DNA template, and carries coding information to the sites of protein synthesis: the ribosomes. Here, the nucleic acid polymer is translated into a polymer of amino acids: a protein. In mRNA as in DNA, genetic information were passed through a filter which contained ribosomes Ribosomes are the components of cells that make proteins from amino acids. One of the central tenets of biology, often referred to as the "central dogma," is that DNA is used to make RNA, which, in turn, is used to make protein. The DNA sequence in genes is copied into a messenger RNA . Ribosomes then read the information in this RNA and, the components of cells that translate Translation is the first stage of protein biosynthesis . In translation, messenger RNA (mRNA) produced in transcription is decoded to produce a specific amino acid chain, or polypeptide, that will later fold into an active protein. Translation occurs in the cell's cytoplasm, where the large and small subunits of the ribosome are located, and bind RNA into protein. Unique triplets promoted the binding of specific tRNAs to the ribosome. Leder and Nirenberg were able to determine the sequences of 54 out of 64 codons in their experiments.^[5]

Subsequent work by Har Gobind Khorana identified the rest of the genetic code. Shortly thereafter, Robert W. Holley Robert William Holley was an American biochemist, he was awarded the Nobel Prize in Physiology or Medicine in 1968 for describing the structure of alanine transfer RNA, linking DNA and protein synthesis determined the structure of transfer RNA Transfer ribonucleic acid is a small RNA molecule (usually about 74-95 nucleotides) that transfers a specific active amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has a 3' terminal site for amino acid attachment. This covalent linkage is catalyzed by an aminoacyl tRNA synthetase. It (tRNA), the adapter molecule that facilitates the process of translating RNA into protein. This work was based upon earlier studies by Severo Ochoa, who received the Nobel prize The Nobel Prizes are annual international awards bestowed by Scandinavian committees in recognition of cultural and scientific advances. They were established in 1895 by the Swedish chemist Alfred Nobel, the inventor of dynamite. The prizes in Physics, Chemistry, Physiology or Medicine, Literature, and Peace were first awarded in 1901. The in 1959 for his work on the enzymology Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process are called substrates, and the enzyme converts them into different molecules, called the products. Almost all processes in a biological cell need enzymes to occur at significant rates. Since enzymes are selective for their of RNA synthesis.^[6] In 1968, Khorana, Holley and Nirenberg received the Nobel Prize in Physiology or Medicine The Nobel Prize in Physiology or Medicine is awarded once a year by the Swedish Karolinska Institute. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895, awarded for outstanding contributions in Physics, Chemistry, Literature, Peace, and Physiology or Medicine since 1901. The first Nobel Prize in Physiology or for their work.^[7]

Transfer of information via the genetic code

The genome of an organism is inscribed in DNA, or in the case of some viruses, RNA. The portion of the genome that codes for a protein or an RNA is referred to as a gene. Those genes that code for proteins are composed of tri-nucleotide units called codons, each coding for a single amino acid. Each nucleotide sub-unit consists of a phosphate, deoxyribose sugar and one of the 4 nitrogenous nucleobases. The purine bases adenine (A) and guanine (G) are larger and consist of two aromatic rings. The pyrimidine bases cytosine (C) and thymine (T) are smaller and consist of only one aromatic ring. In the double-helix configuration, two strands of DNA are joined to each other by hydrogen bonds in an arrangement known as base pairing. These bonds almost always form between an adenine base on one strand and a thymine on the other strand and between a cytosine base on one strand and a guanine base on the other. This means that the number of A and T residues will be the same in a given double helix, as will the number of G and C residues.^{[8]:102–117} In RNA, thymine (T) is replaced by uracil (U), and the deoxyribose is substituted by ribose.^[8]:127

Each protein-coding gene is transcribed into a template molecule of the related polymer RNA, known as messenger RNA or mRNA. This, in turn, is translated on the ribosome into an amino acid chain or polypeptide.^{[8]:Chp 12} The process of translation requires transfer RNAs specific for individual amino acids with the amino acids covalently attached to them, guanosine triphosphate as an energy source, and a number of translation factors. tRNAs have anticodons complementary to the codons in mRNA and can be "charged" covalently with amino acids at their 3' terminal CCA ends. Individual tRNAs are charged with specific amino acids by enzymes known as aminoacyl tRNA synthetases, which have high specificity for both their cognate amino acids and tRNAs. The high specificity of these enzymes is a major reason why the fidelity of protein translation is maintained.^{[8]:464–469}

There are 4³ = 64 different codon combinations possible with a triplet codon of three nucleotides; all 64 codons are assigned for either amino acids or stop signals during translation. If, for example, an RNA sequence, UUUAAACCC is considered and the reading frame starts with the first U (by convention, 5' to 3'), there are three codons, namely, UUU, AAA and CCC, each of which specifies one amino acid. This RNA sequence will be translated into an amino acid sequence, three amino acids long.^{[8]:521–539} A comparison may be made with computer science, where the codon is similar to a word, which is the standard "chunk" for handling data (like one amino acid of a protein), and a nucleotide is similar to a bit, in that it is the smallest unit.

The standard genetic code is shown in the following tables. Table 1 shows what amino acid each of the 64 codons specifies. Table 2 shows what codons specify each of the 20 standard amino acids involved in translation. These are called forward and reverse codon tables, respectively. For example, the codon AAU represents the amino acid asparagine, and UGU and UGC represent cysteine (standard three-letter designations, Asn and Cys, respectively).^[8]:522

RNA codon table

^A The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins.^[9]

Salient features

Sequence reading frame

A codon is defined by the initial nucleotide from which translation starts. For example, the string GGGAAACCC, if read from the first position, contains the codons GGG, AAA and CCC; and, if read from the second position, it contains the codons GGA and AAC; if read starting from the third position, GAA and ACC. Every sequence can thus be read in three reading frames, each of which will produce a different amino acid sequence (in the given example, Gly-Lys-Pro, Gly-Asn, or Glu-Thr, respectively). With double-stranded DNA there are six possible reading frames, three in the forward orientation on one strand and three reverse on the opposite strand.^[10]:330

The actual frame in which a protein sequence is translated is defined by a start codon, usually the first AUG codon in the mRNA sequence. Mutations that disrupt the reading frame by insertions or deletions of a non-multiple of 3 nucleotide bases are known as frameshift mutations. These mutations may impair the function of the resulting protein, if it is formed, and are thus rare in in vivo protein-coding sequences. Such misformed proteins are often targeted for proteolytic degradation. In addition, a frame shift mutation is very likely to cause a stop codon to be read, which truncates the creation of the protein.^[11] One reason for the rareness of frame-shifted mutations' being inherited is that, if the protein being translated is essential for growth under the selective pressures the organism faces, absence of a functional protein may cause death before the organism is viable.^[12]

Start/stop codons

Translation starts with a chain initiation codon (start codon). Unlike stop codons, the codon alone is not sufficient to begin the process. Nearby sequences (such as the Shine-Dalgarno sequence in E. coli) and initiation factors are also required to start translation. The most common start codon is AUG which is read as methionine or, in bacteria, as formylmethionine. Alternative start codons (depending on the organism), include "GUG" or "UUG", which normally code for valine or leucine, respectively. However, when used as a start codon, these alternative start codons are translated as methionine or formylmethionine.^[13]

The three stop codons have been given names: UAG is amber, UGA is opal (sometimes also called umber), and UAA is ochre. "Amber" was named by discoverers Richard Epstein and Charles Steinberg after their friend Harris Bernstein, whose last name means "amber" in German. The other two stop codons were named "ochre" and "opal" in order to keep the "color names" theme. Stop codons are also called "termination" or "nonsense" codons and they signal release of the nascent polypeptide from the ribosome due to binding of release factors in the absence of cognate tRNAs with anticodons complementary to these stop signals.^[14]

Effect of mutations

Frameshift mutations altering the sequence reading frame, and nonsense mutations causing a stop codon are examples of point mutations. In addition, there may be missense mutations that cause exchange of one amino acid for another. Clinically important missense mutations generally change the properties of the coded amino acid residue between being basic, acidic polar or nonpolar, while nonsense mutations result in a stop codon.^[10]:266

Degeneracy of the genetic code

The genetic code has redundancy but no ambiguity (see the codon tables above for the full correlation). For example, although codons GAA and GAG both specify glutamic acid (redundancy), neither of them specifies any other amino acid (no ambiguity). The codons encoding one amino acid may differ in any of their three positions. For example the amino acid glutamic acid is specified by GAA and GAG codons (difference in the third position), the amino acid leucine is specified by UUA, UUG, CUU, CUC, CUA, CUG codons (difference in the first or third position), while the amino acid serine is specified by UCA, UCG, UCC, UCU, AGU, AGC (difference in the first, second or third position).^{[8]:521–522}

A position of a codon is said to be a fourfold degenerate site if any nucleotide at this position specifies the same amino acid. For example, the third position of the glycine codons (GGA, GGG, GGC, GGU) is a fourfold degenerate site, because all nucleotide substitutions at this site are synonymous; i.e., they do not change the amino acid. Only the third positions of some codons may be fourfold degenerate.^{[8]:521–522} A position of a codon is said to be a twofold degenerate site if only two of four possible nucleotides at this position specify the same amino acid. For example, the third position of the glutamic acid codons (GAA, GAG) is a twofold degenerate site. In twofold degenerate sites, the equivalent nucleotides are always either two purines (A/G) or two pyrimidines (C/U), so only transversional substitutions (purine to pyrimidine or pyrimidine to purine) in twofold degenerate sites are nonsynonymous.^{[8]:521–522} A position of a codon is said to be a non-degenerate site if any mutation at this position results in amino acid substitution. There is only one threefold degenerate site where changing to three of the four nucleotides may have no effect on the amino acid (depending on what it is changed to), while changing to the fourth possible nucleotide always results in an amino acid substitution. This is the third position of an isoleucine codon: AUU, AUC, or AUA all encode isoleucine, but AUG encodes methionine. In computation this position is often treated as a twofold degenerate site.^{[8]:521–522}

There are three amino acids encoded by six different codons: serine, leucine, and arginine. Only two amino acids are specified by a single codon. One of these is the amino-acid methionine, specified by the codon AUG, which also specifies the start of translation; the other is tryptophan, specified by the codon UGG. The degeneracy of the genetic code is what accounts for the existence of synonymous mutations.^{[8]:Chp 15}

Degeneracy results because a triplet code designates 20 amino acids and a stop codon. Because there are four bases, triplet codons are required to produce at least 21 different codes. For example, if there were two bases per codon, then only 16 amino acids could be coded for (4²=16). Because at least 21 codes are required, then 4³ gives 64 possible codons, meaning that some degeneracy must exist.^{[8]:521–522}

These properties of the genetic code make it more fault-tolerant for point mutations. For example, in theory, fourfold degenerate codons can tolerate any point mutation at the third position, although codon usage bias restricts this in practice in many organisms; twofold degenerate codons can tolerate one out of the three possible point mutations at the third position. Since transition mutations (purine to purine or pyrimidine to pyrimidine mutations) are more likely than transversion (purine to pyrimidine or vice-versa) mutations, the equivalence of purines or that of pyrimidines at twofold degenerate sites adds a further fault-tolerance.^{[8]:531–532}

A practical consequence of redundancy is that some errors in the genetic code only cause a silent mutation or an error that would not affect the protein because the hydrophilicity or hydrophobicity is maintained by equivalent substitution of amino acids; for example, a codon of NUN (where N = any nucleotide) tends to code for hydrophobic amino acids. NCN yields amino acid residues that are small in size and moderate in hydropathy; NAN encodes average size hydrophilic residues.^[16][17] These tendencies may result from the shared ancestry of the aminoacyl tRNA synthetases related to these codons.

Even so, single point mutations can still cause dysfunctional proteins. For example, a mutated hemoglobin gene causes sickle-cell disease. In the mutant hemoglobin a hydrophilic glutamate (Glu) is substituted by the hydrophobic valine (Val), that is, GAA or GAG becomes GUA or GUG. The substitution of glutamate by valine reduces the solubility of β-globin which causes hemoglobin to form linear polymers linked by the hydrophobic interaction between the valine groups causing sickle-cell deformation of erythrocytes. Sickle-cell disease is generally not caused by a de novo mutation. Rather it is selected for in malarial regions (in a way similar to thalassemia), as heterozygous people have some resistance to the malarial Plasmodium parasite (heterozygote advantage).^[18]

These variable codes for amino acids are allowed because of modified bases in the first base of the anticodon of the tRNA, and the base-pair formed is called a wobble base pair. The modified bases include inosine and the Non-Watson-Crick U-G basepair.^[19]

Variations to the standard genetic code

While slight variations on the standard code had been predicted earlier,^[20] none were discovered until 1979, when researchers studying human mitochondrial genes discovered they used an alternative code. Many slight variants have been discovered since,^[21] including various alternative mitochondrial codes,^[22] as well as small variants such as Mycoplasma translating the codon UGA as tryptophan and Candida species translating CUG as a serine rather than a leucine.^[23][24] In bacteria and archaea, GUG and UUG are common start codons. However, in rare cases, certain specific proteins may use alternative initiation (start) codons not normally used by that species.^[21]

In certain proteins, non-standard amino acids are substituted for standard stop codons, depending upon associated signal sequences in the messenger RNA: UGA can code for selenocysteine and UAG can code for pyrrolysine as discussed in the relevant articles. Selenocysteine is now viewed as the 21st amino acid, and pyrrolysine is viewed as the 22nd.^[21]

Notwithstanding these differences, all known codes have strong similarities to each other, and the coding mechanism is the same for all organisms: three-base codons, tRNA, ribosomes, reading the code in the same direction and translating the code three letters at a time into sequences of amino acids.

Expanded genetic code

Since 2001, 40 non-natural amino acids have been added into protein by creating a unique codon (recoding) and a corresponding transfer-RNA:aminoacyl – tRNA-synthetase pair to encode it with diverse physicochemical and biological properties in order to be used as a tool to exploring protein structure and function or to create novel or enhanced proteins.^[25][26]

Theories on the origin of the genetic code

Despite the minor variations that exist, the genetic code used by all known forms of life is nearly universal. However, there are a huge number of possible genetic codes. If amino acids are randomly associated with triplet codons, there will be 1.5 x 10⁸⁴ possible genetic codes.^[27] The question arises: why this code? How did it originate?

Phylogenetic analysis of transfer RNA suggests that tRNA molecules evolved before the present set of aminoacyl-tRNA synthetases.^[28]

Theoretically the genetic code could be completely random (a "frozen accident"), completely non-random (optimal) or a combination of random and nonrandom. There are sufficient data to refute the first possibility.^[29] For a start, a quick view on the table of the genetic code already shows a clustering of amino acid assignments. Furthermore, amino acids that share the same biosynthetic pathway tend to have the same first base in their codons,^[30] and amino acids with similar physical properties tend to have similar codons.^[31][32]

There are four themes running through the many theories that seek to explain the evolution of the genetic code (and hence the origin of these patterns):^[33]

• Chemical principles govern specific RNA interaction with amino acids. Aptamer experiments showed that some amino acids have a selective chemical affinity for the base triplets that code for them^[34]. Recent experiments show that of the 8 amino acids tested, 6 show some RNA triplet-amino acid association^{[35] [36]}. This has been called the stereochemical code. The stereochemical code could have created an ancient core of assignments. The current complex translation mechanism involving tRNA and associated enzymes may be a later development, and that originally, protein sequences were directly templated on base sequences.
• Biosynthetic expansion. The standard modern genetic code grew from a simpler earlier code through a process of "biosynthetic expansion". Here the idea is that primordial life "discovered" new amino acids (e.g., as by-products of metabolism) and later back-incorporated some of these into the machinery of genetic coding. Although much circumstantial evidence has been found to suggest that fewer different amino acids were used in the past than today,^[37] precise and detailed hypotheses about exactly which amino acids entered the code in exactly what order have proved far more controversial.^[38][39]
• Natural selection has led to codon assignments of the genetic code that minimize the effects of mutations.^[40] A recent hypothesis^[41] suggests that the triplet code was derived from codes that used longer than triplet codons. Longer than triplet decoding has higher degree of codon redundancy and is more error resistant than the triplet decoding. This feature could allow accurate decoding in the absence of highly complex translational machinery such as the ribosome.
• The biocommunicative approach investigates nucleotide sequences as code, i.e. language-like text, which follows in parallel three (3) kinds of rules: combinatorial (syntactic), context-sensitive (pragmatic) and content-specific (semantic). Natural genome editing from this perspective is competent viral-driven generation and integration of meaningful nucleotide sequences into pre-existing genomic content arrangements and the ability to (re-)combine and (re-)regulate them according to context-dependent (i.e. adaptational) purposes of the host organism.^[42]
• Information-theoretic approaches treat the genetic code in terms of an error-prone information channel. The inherent noise in the channel poses the organism with a fundamental question: how to construct a genetic code that can withstand the impact of noise while accurately and efficiently translating information? These “rate-distortion” models suggest that the genetic code originated as a result of the interplay of the three conflicting evolutionary forces: the needs for diverse amino-acids, for error-tolerance and for minimal cost of resources. The code emerges at a coding phase transition when the mapping of codons to amino-acids becomes nonrandom. The emergence of the code is governed by the topology defined by the most probable errors and is related to the map coloring problem ^[43].

References

1. ^ Turanov AA, Lobanov AV, Fomenko DE, Morrison HG, Sogin ML, Klobutcher LA, Hatfield DL, Gladyshev VN (January 2009). "Genetic code supports targeted insertion of two amino acids by one codon". Science 323 (5911): 259–61. doi:10.1126/science.1164748. PMID 19131629.
2. ^ Crick, Francis (1988). "Chapter 8: The genetic code". What mad pursuit: a personal view of scientific discovery. New York: Basic Books. pp. 89–101. ISBN 0-465-09138-5.
3. ^ Gardner RS, Wahba AJ, Basilio C, Miller RS, Lengyel P, Speyer JF (December 1962). "Synthetic polynucleotides and the amino acid code. VII". Proc. Natl. Acad. Sci. U.S.A. 48: 2087–94. doi:10.1073/pnas.48.12.2087. PMID 13946552.
4. ^ Wahba AJ, Gardner RS, Basilio C, Miller RS, Speyer JF, Lengyel P (January 1963). "Synthetic polynucleotides and the amino acid code. VIII". Proc. Natl. Acad. Sci. U.S.A. 49: 116–22. doi:10.1073/pnas.49.1.116. PMID 13998282.
5. ^ Nirenberg M, Leder P, Bernfield M, Brimacombe R, Trupin J, Rottman F, O'Neal C (May 1965). "RNA codewords and protein synthesis, VII. On the general nature of the RNA code". Proc. Natl. Acad. Sci. U.S.A. 53 (5): 1161–8. doi:10.1073/pnas.53.5.1161. PMID 5330357.
6. ^ The Royal Swedish Academy of Science (1959). "The Nobel Prize in Physiology or Medicine 1959". Press release. http://nobelprize.org/nobel_prizes/medicine/laureates/1959/index.html. Retrieved 2010-02-27.
7. ^ The Royal Swedish Academy of Science (1968). "The Nobel Prize in Physiology or Medicine 1968". Press release. http://nobelprize.org/nobel_prizes/medicine/laureates/1968/index.html. Retrieved 2010-02-27.
8. ^ ^{a b c d e f g h i j k l m} Watson JD, Baker TA, Bell SP, Gann A, Levine M, Oosick R. (2008). Molecular Biology of the Gene. San Francisco: Pearson/Benjamin Cummings. ISBN 0-8053-9592-X.
9. ^ Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene 432 (1-2): 1–6. doi:10.1016/j.gene.2008.11.001. PMID 19056476.
10. ^ ^{a b} Pamela K. Mulligan; King, Robert C.; Stansfield, William D. (2006). A dictionary of genetics. Oxford [Oxfordshire]: Oxford University Press. pp. 608. ISBN 0-19-530761-5.
11. ^ Isbrandt D, Hopwood JJ, von Figura K, Peters C (1996). "Two novel frameshift mutations causing premature stop codons in a patient with the severe form of Maroteaux-Lamy syndrome". Hum. Mutat. 7 (4): 361–3. doi:10.1002/(SICI)1098-1004(1996)7:4<361::AID-HUMU12>3.0.CO;2-0. PMID 8723688.
12. ^ Crow JF (1993). "How much do we know about spontaneous human mutation rates?". Environ. Mol. Mutagen. 21 (2): 122–9. doi:10.1002/em.2850210205. PMID 8444142.
13. ^ Touriol C, Bornes S, Bonnal S, Audigier S, Prats H, Prats AC, Vagner S (2003). "Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons". Biol. Cell 95 (3-4): 169–78. doi:10.1016/S0248-4900(03)00033-9. PMID 12867081.
14. ^ Maloy S (2003-11-29). "How nonsense mutations got their names". Microbial Genetics Course. San Diego State University. http://www.sci.sdsu.edu/~smaloy/MicrobialGenetics/topics/rev-sup/amber-name.html. Retrieved 2010-03-10.
15. ^ References for the image are found in Wikimedia Commons page at: Commons:File:Notable mutations.svg#References.
16. ^ Yang et al. (1990). Michel-Beyerle, M. E.. ed. Reaction centers of photosynthetic bacteria: Feldafing-II-Meeting. 6. Berlin: Springer-Verlag. pp. 209–18. ISBN 3-540-53420-2.
17. ^ Füllen G, Youvan DC (1994). "Genetic Algorithms and Recursive Ensemble Mutagenesis in Protein Engineering". Complexity International 1. http://www.complexity.org.au/ci/vol01/fullen01/html/.
18. ^ Hebbel RP (2003). "Sickle hemoglobin instability: a mechanism for malarial protection". Redox Rep. 8 (5): 238–40. doi:10.1179/135100003225002826. PMID 14962356.
19. ^ Varani G, McClain WH (July 2000). "The G x U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems". EMBO Rep. 1 (1): 18–23. doi:10.1093/embo-reports/kvd001. PMID 11256617.
20. ^ Crick FHC, Orgel LE (1973). "Directed panspermia". Icarus 19: 341–6. doi:10.1016/0019-1035(73)90110-3. "It is a little surprising that organisms with somewhat different codes do not coexist.". (p. 344) (Further discussion)
21. ^ ^{a b c} Elzanowski A, Ostell J (2008-04-07). "The Genetic Codes". National Center for Biotechnology Information (NCBI). http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c. Retrieved 2010-03-10.
22. ^ Jukes TH, Osawa S (December 1990). "The genetic code in mitochondria and chloroplasts". Experientia 46 (11-12): 1117–26. doi:10.1007/BF01936921. PMID 2253709.
23. ^ Santos, M.A.; Tuite, M.F. (1995). "The CUG codon is decoded in vivo as serine and not leucine in Candida albicans". Nucleic Acids Research 23 (9): 1481–6. doi:10.1093/nar/23.9.1481. PMID 7784200.
24. ^ Butler, G. et al.; Rasmussen, MD; Lin, MF; Santos, MA; Sakthikumar, S; Munro, CA; Rheinbay, E; Grabherr, M et al. (2009). "Evolution of pathogenicity and sexual reproduction in eight Candida genomes". Nature 459 (7247): 657–62. doi:10.1038/nature08064. PMID 19465905.
25. ^ Xie J, Schultz PG (December 2005). "Adding amino acids to the genetic repertoire". Curr Opin Chem Biol 9 (6): 548–54. doi:10.1016/j.cbpa.2005.10.011. PMID 16260173.
26. ^ Wang Q, Parrish AR, Wang L (March 2009). "Expanding the genetic code for biological studies". Chem. Biol. 16 (3): 323–36. doi:10.1016/j.chembiol.2009.03.001. PMID 19318213.
27. ^ Michael Yarus (2010) Life from an RNA world, p. 163
28. ^ De Pouplana, L.R.; Turner, R.J.; Steer, B.A.; Schimmel, P. (1998). "Genetic code origins: tRNAs older than their synthetases?". Proceedings of the National Academy of Sciences 95 (19): 11295. doi:10.1073/pnas.95.19.11295. PMID 9736730. PMC 21636. http://www.pnas.org/cgi/content/full/95/19/11295.
29. ^ Freeland SJ, Hurst LD (September 1998). "The genetic code is one in a million". J. Mol. Evol. 47 (3): 238–48. doi:10.1007/PL00006381. PMID 9732450.
30. ^ Taylor FJ, Coates D (1989). "The code within the codons". BioSystems 22 (3): 177–87. doi:10.1016/0303-2647(89)90059-2. PMID 2650752.
31. ^ Di Giulio M (October 1989). "The extension reached by the minimization of the polarity distances during the evolution of the genetic code". J. Mol. Evol. 29 (4): 288–93. doi:10.1007/BF02103616. PMID 2514270.
32. ^ Wong JT (February 1980). "Role of minimization of chemical distances between amino acids in the evolution of the genetic code". Proc. Natl. Acad. Sci. U.S.A. 77 (2): 1083–6. doi:10.1073/pnas.77.2.1083. PMID 6928661.
33. ^ Knight RD, Freeland SJ, Landweber LF (June 1999). "Selection, history and chemistry: the three faces of the genetic code". Trends Biochem. Sci. 24 (6): 241–7. doi:10.1016/S0968-0004(99)01392-4. PMID 10366854.
34. ^ Knight RD, Landweber LF (September 1998). "Rhyme or reason: RNA-arginine interactions and the genetic code". Chem. Biol. 5 (9): R215–20. doi:10.1016/S1074-5521(98)90001-1. PMID 9751648.
35. ^ Michael Yarus, Jeremy Joseph Widmann, Rob Knight (2009) 'RNA–Amino Acid Binding: A Stereochemical Era for the Genetic Code', Journal of Molecular Evolution, 10.1007/s00239-009-9270-1
36. ^ Michael Yarus (2010) Life from an RNA world, p. 170
37. ^ Brooks DJ, Fresco JR, Lesk AM, Singh M (October 2002). "Evolution of amino acid frequencies in proteins over deep time: inferred order of introduction of amino acids into the genetic code". Mol. Biol. Evol. 19 (10): 1645–55. PMID 12270892. http://mbe.oxfordjournals.org/cgi/content/abstract/19/10/1645.
38. ^ Amirnovin R (May 1997). "An analysis of the metabolic theory of the origin of the genetic code". J. Mol. Evol. 44 (5): 473–6. doi:10.1007/PL00006170. PMID 9115171.
39. ^ Ronneberg TA, Landweber LF, Freeland SJ (December 2000). "Testing a biosynthetic theory of the genetic code: fact or artifact?". Proc. Natl. Acad. Sci. U.S.A. 97 (25): 13690–5. doi:10.1073/pnas.250403097. PMID 11087835.
40. ^ Freeland SJ, Wu T, Keulmann N (October 2003). "The case for an error minimizing standard genetic code". Orig Life Evol Biosph 33 (4-5): 457–77. doi:10.1023/A:1025771327614. PMID 14604186.
41. ^ Baranov PV, Venin M, Provan G (2009). "Codon size reduction as the origin of the triplet genetic code". PLoS ONE 4 (5): e5708. doi:10.1371/journal.pone.0005708. PMID 19479032.
42. ^ Witzany G. (2010) Biocommunication and Natural Genome Editing. Springer, Dordrecht
43. ^ Tlusty T (2010). "A colorful origin for the genetic code: Information theory, statistical mechanics and the emergence of molecular codes.". Phys. Life. Rev.. doi:10.1016/j.plrev.2010.06.002. PMID 12270892. http://dx.doi.org/10.1016/j.plrev.2010.06.002.

Further reading

• Griffiths, Anthony J. F.; Miller, Jeffrey H.; Suzuki, David T.; Lewontin, Richard C.; Gelbart, William M. (1999). An Introduction to genetic analysis (7th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-3771-X. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=iga.TOC.
• Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Raff, Martin; Roberts, Keith; Walter, Peter (2002). Molecular biology of the cell (4th ed.). New York: Garland Science. ISBN 0-8153-3218-1. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2.
• Lodish, Harvey F.; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James E. (2000). Molecular cell biology (4th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-3706-X. http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mcb.TOC.

External links

• The Genetic Codes → Genetic Code Tables
• The Codon Usage Database → Codon frequency tables for many organisms
• History of deciphering the genetic code
• Symmetries in the genetic code

Categories: Molecular genetics | Gene expression | Protein biosynthesis

See Also:

• Codex Alimentarius: Encyclopedia
• Genetically Modified Food: Encyclopedia
• Society: Issues: Science and Technology: Biotechnology: Genetics: Genetically Modified Food: Directory
• Society: Issues: Science and Technology: Biotechnology: Genetics: Genetically Modified Food: News: Directory
• Society: Issues: Science and Technology: Biotechnology: Genetics: Genetically Modified Food: Impacts On Hunger: Directory

What Links Here:

Recently Viewed Pages:

• Home
• Kohlrabi: Blogs
• Maize: Blogs
• Meatloaf: Blogs
• Blog Search
• Snacks: Images
• Cherries
• Animal Source Foods
• Sitemap

Most Popular Pages:

• Maize: Blogs
• Kohlrabi: Blogs
• Meatloaf: Blogs
• Genetic Code: Blog Search
• Animal Source Foods
• Cherries
• Sitemap
• Snacks: Images
• Genetic Code: Encyclopedia

Related 'Genetic Code' Searches: