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Genetic code
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Genetic code

The genetic code is a mapping that biological cellss use to translate a sequence of RNA codons into a sequence of amino acids. Nearly all living things use the same genetic code, called the standard genetic code, and all use small variations of it.

This translation is the latter stage of protein biosynthesis. The first stage is transcription, where a sub-sequence of DNA called a gene is rewritten into an RNA. An RNA is a sequence of repeating nucleotide bases: adenine, guanine, cytosine and uracil. The RNA is divided into non-overlapping groups of three bases, called codons. Each codon is then translated to a particular amino acid. Thus a codon is said to code for that amino acid in the genetic code. There are 43 = 64 codons. For example, the RNA sequence UUUAAACCC contains the codons UUU, AAA and CCC, each of which specifies one amino acid. So, this RNA sequence represents a protein sequence, three amino acids long. (DNA is also sequence of nucleotide bases, but there thymine takes the place of uracil.)

The standard genetic code is shown in the following tables. shows what amino acid each of the 64 codons specifies. 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 GAU represents the amino acid asparagine (Asp), and cysteine (Cys) is represented by UGU and by UGC.

Table 1: Codon table

This table shows the 64 codons and the amino acid each codon codes for.
2nd base
U C A G
1st
base
U UUU Phenylalanine
UUC Phenylalanine
UUA Leucine
UUG Leucine, Start
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, Start
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, Start2
AUC Isoleucine
AUA Isoleucine
AUG Methionine, Start1
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, Start2
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 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.
2This is a start codon for prokaryotes only.

Table 2: Reverse codon table

This table shows the 20 amino acids used in proteins, and the codons that code for each amino acid.
Ala A GCU, GCC, GCA, GCG Leu L UUA, UUG, CUU, CUC, CUA, CUG
Arg R CGU, CGC, CGA, CGG, AGA, AGG Lys K AAA, AAG
Asn N AAU, AAC Met M AUG
Asp D GAU, GAC Phe F UUU, UUC
Cys C UGU, UGC Pro P CCU, CCC, CCA, CCG
Gln Q CAA, CAG Ser S UCU, UCC, UCA, UCG, AGU,AGC
Glu E GAA, GAG Thr T ACU, ACC, ACA, ACG
Gly G GGU, GGC, GGA, GGG Trp W UGG
His H CAU, CAC Tyr Y UAU, UAC
Ile I AUU, AUC, AUA Val V 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 codon (start codon). But unlike stop codons, these are not sufficient to begin the process; nearby initiation sequences are also required to induce transcription into mRNA and binding by ribosomes. The most notable start codon is AUG, which also codes for methionine. CUG and UUG, and in prokaryotes GUG and AUU, also work.

Many codons are redundant; i.e., two codons may code for the same amino acid. This redundancy is confined to the third position, e.g. both GAA and GAG code for the amino acid glutamine. A codon is said to be four-fold degenerate if any nucleotide at its third position specifies the same amino acid; it is said to be two-fold degenerate if only two of four possible nucleotides at its third position specify the same amino acid. In two-fold degenerate codons, the equivalent third position nucleotides are always either two purines (A/G) or two pyrimidines (C/T).

These properties of the genetic code make it more fault-tolerant for mutations. For example, four-fold degenerate codons can tolerate any mutation at the third position; two-fold degenerate codons can tolerate one out of the three possible 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 two-fold degenerate sites adds a further fault-tolerance.

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 transcription.

Numerous variations of the standard genetic code are found in mitochondria, energy-burning organelles. Ciliate protozoa also have 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. Another variant is found in some species of the yeast candida, where CUG codes for Serine. In some species of bacteria and archaea, a few non-standard amino acids are substituted for standard stop codons; UGA can code for selenocysteine and UAG can code for pyrrolysine. There may be other non-standard amino acids and codon interpretations but are not known.

Despite these variations, the genetic codes used by all known forms of life on Earth are very similar. 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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