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Genetic code

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The genetic code is a mapping that biological cells use to "translate" sequences of three nucleotide bases (called "triplets" or "codons") into amino acids. The mapping indicates, for example, that when the sequence "adenine, adenine, adenine" is encountered, the amino acid lysine should be produced. When the code is followed repeatedly, many amino acids are created, and are strung together to form proteins.

In the process of protein biosynthesis, a sequence of DNA called a gene is first transcribed (copied) into RNA. The RNA is a sequence of repeating units (nucleotide bases). Each position in the RNA may have four possible "values", signified by the four types of bases: adenine, guanine, cytosine and uracil. This sequence of bases encodes a protein. A protein is a sequence of amino acids. There are twenty possible amino acids. The RNA is broken up into units of three, called a codon. Each codon specifies one amino acid. For example, the RNA sequence UUUAAACCC specifies three codons (UUU-AAA-CCC), which each specify one amino acid. This RNA sequence, then, encodes a protein sequence three amino acids in length (as we will see, it encodes Phenylalanine-Lysine-Proline). There are sixty-four possible codons.

Nearly all living things use the same genetic code. The standard version is given in the following tables, which show what amino acid each of the 43 = 64 possible codons specify (Table 1), and what codons specify each of the 20 amino acids involved in translation (Table 2). For instance, GAU codes for the amino acid Asp (asparagine), and Cys (cysteine) is coded for by the codons UGU and UGC. These are called forward and reverse codon tables, respectively. The bases in the table below are adenine, cytosine, guanine and uracil, which are used in the mRNA; in the DNA, thymine takes the place of uracil.

Table 1 : Codon table. This table illustrates the 64 possible codon triplets.
2nd base
U C A G
1st base U UUU Phenylalanine
UUC Phenylalanine
UUA Leucine
UUG Leucine
UCU Serine
UCC Serine
UCA Serine
UCG Serine
UAU Tyrosine
UAC Tyrosine
UAA Ochre Stop
UAG Amber Stop
UGU Cysteine
UGC Cysteine
UGA Opal Stop
UGG Tryptophan
C CUU Leucine
CUC Leucine
CUA Leucine
CUG Leucine
CCU Proline
CCC Proline
CCA Proline
CCG Proline
CAU Histidine
CAC Histidine
CAA Glutamine
CAG Glutamine
CGU Arginine
CGC Arginine
CGA Arginine
CGG Arginine
A AUU Isoleucine
AUC Isoleucine
AUA Isoleucine
1AUG Methionine
ACU Threonine
ACC Threonine
ACA Threonine
ACG Threonine
AAU Asparagine
AAC Asparagine
AAA Lysine
AAG Lysine
AGU Serine
AGC Serine
AGA Arginine
AGG Arginine
G GUU Valine
GUC Valine
GUA Valine
GUG Valine
GCU Alanine
GCC Alanine
GCA Alanine
GCG Alanine
GAU Aspartic acid
GAC Aspartic acid
GAA Glutamic acid
GAG Glutamic acid
GGU Glycine
GGC Glycine
GGA Glycine
GGG Glycine
1The AUG codon both codes for methionine and serves as an initiation site; the first AUG in an mRNA's coding region will be the site where translation into protein begins.

Table 2 : Reverse codon table. This table shows the 20 amino acids used in proteins, together with the codons that code for them.
Ala GCU, GCC, GCA, GCG Leu UUA, UUG, CUU, CUC, CUA, CUG
Arg CGU, CGC, CGA, CGG, AGA, AGG Lys AAA, AAG
Asn AAU, AAC Met AUG
Asp GAU, GAC Phe UUU, UUC
Cys UGU, UGC Pro CCU, CCC, CCA, CCG
Gln CAA, CAG Ser UCU, UCC, UCA, UCG, AGU, AGC
Glu GAA, GAG Thr ACU, ACC, ACA, ACG
Gly GGU, GGC, GGA, GGG Trp UGG
His CAU, CAC Tyr UAU, UAC
Ile AUU, AUC, AUA Val GUU, GUC, GUA, GUG
START AUG, GUG STOP UAG, UGA, UAA

In classical genetics, the STOP codons were given names - UAG was amber, UGA was opal, and UAA was ocher. These names were originally the names of the specific genes in which mutation of each of these stop codons was first detected. Translation starts with a chain initiation or START codon, but unlike STOP codons these are not sufficient by themselves to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes. The most notable of these is AUG, which also codes for methionine. CUG and UUG, and in prokaryotes GUG and AUU, will also work.

It is notable that the standard genetic code contains features which provide for basic forms of error correction. Many codons which differ by only one base still encode the same amino acid and most often the single base that differs is the last one, which happens to be the base which is most often misread by the translation process. Furthermore, amino acids which tend to occur more frequently in proteins on average tend to have more codons which code for them.

Numerous variations on the standard genetic code are found inside mitochondria, energy-burning organelles that were probably derived from symbiotic bacteria. The ciliate protozoa also show some variation in the genetic code: UAG and often UAA code for Glutamine, a variant also found in some green algae, or UGA codes for Cysteine. One more variant is found in some species of the yeast Candida, but interestingly not in all, where CUG codes for Serine. There are also a few "non-standard" amino acids which are substituted for some stop codons in some species of bacteria and archaea; UGA can code for selenocysteine and UAG can code for pyrrolysine. Other non-standard amino acids and codon interpretations may be present but currently unknown.

Despite these variations, the genetic code used by all known life on Earth displays a very large degree of similarity. Since there are many possible genetic codes that are thought to have similar utility to the one used by Earth life, the theory of evolution suggests that the genetic code was established very early in the history of life.

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