Genetic code

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.

External Links

• Online DNA → Amino Acid Converter (http://www.geneseo.edu/~eshamb/php/dna.php) by bdesham