Genetic code
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The genetic code is a set of rules, which maps DNA sequences to proteins in the living cell, and is employed in the process of protein synthesis. Nearly all living things use the same genetic code, called the standard genetic code, although a few organisms use minor variations of the standard code.
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Genome expression
The genetic information carried by an organism - its genome - is inscribed in one or more DNA molecules. Each functional portion of a DNA molecule is referred to as a gene. Each gene is transcribed into a short template molecule of the related polymer RNA, which is better suited for protein synthesis. This in turn is translated, by mediation of a machinery consisting of ribosomes and a set of transfer RNAs and associated enzymes, into an amino acid chain (polypeptide), which will then be folded into a protein.
The gene sequence inscribed in DNA, and in RNA, is 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 nucleotide bases grouped into 2 categories, purine and pyrimidine. 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 only consist of one aromatic ring. In RNA however, thymine (T) is substituted by uracil (U) and the deoxyribose is substituted by ribose.
Overall, there are 43 = 64 different codon combinations. 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 a sequence of nucleotide bases, but there thymine takes the place of uracil.)
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 (Asp), and cysteine (Cys) is represented by UGU and by UGC.
Table 1: RNA Codon table
| 2nd base | |||||
|---|---|---|---|---|---|
| U | C | A | G | ||
| 1st base |
U |
UUU (Phe/F)Phenylalanine |
UCU (Ser/S)Serine |
UAU (Tyr/Y)Tyrosine |
UGU (Cys/C)Cysteine |
| C |
CUU (Leu/L)Leucine |
CCU (Pro/P)Proline |
CAU (His/H)Histidine |
CGU (Arg/R)Arginine |
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| A |
AUU (Ile/I)Isoleucine, Start2 |
ACU (Thr/T)Threonine |
AAU (Asn/N)Asparagine |
AGU (Ser/S)Serine |
|
| G |
GUU (Val/V)Valine |
GCU (Ala/A)Alanine |
GAU (Asp/D)Aspartic acid |
GGU (Gly/G)Glycine |
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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
| 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 |
Marshall W. Nirenberg and his lab at the National Institutes of Health performed the experiments which first elucidated the correspondence between the codons and the amino acids for which they code. Har Gobind Khorana expanded on Nirenberg's work and found the codes for the amino acids that Nirenberg's methods could not. Khorana and Nirenberg won a share of the 1968 Nobel Prize in Physiology or Medicine for this work.
Technical details
Stop Codons
In classical genetics, the stop codons were given names: UAG was amber, UGA was opal, and UAA was ochre. 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.
Degeneracy of the genetic code
Many codons are degenerate or redundant, meaning that two or more codons may code for the same amino acid. Degenerate codons typically differ in their third positions; e.g. both GAA and GAG code for the amino acid glutamic acid. 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). The degeneracy of the genetic code is what accounts for the existence of silent mutations.
Degeneracy is required in order to produce enough different codons to code for 20 amino acids and a stop and start codon (at least 22 codons required). Because there are four different bases, triplet codons are the minimum number required to produce at least 22 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 22 codes are required, then 4³ gives 64, which is the minimum number of codons possible.
These properties of the genetic code make it more fault-tolerant for point mutations. For example, four-fold degenerate codons can tolerate any point mutation at the third position; two-fold 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 two-fold degenerate sites adds a further fault-tolerance.
A practical consequence of redundancy is that some errors in the genetic code either only causes a silent mutation or an error that would not affect the amino acid's hydrophilic/hydrophobic property, eg. a codon of XUX (where X = any nucleotide) tends to code for hydrophobic amino acids. Even so, it is a single point mutation which causes a modified haemoglobin molecule in sickle cell anaemia. The hydrophilic glutamate (Glu) is substituted by the hydrophobic valine (Val) which reduces the solubility of ߭globin. This causes haemoglobin to form linear polymers linked by the hydrophobic interaction between the valine groups causing sickle cell deformation of erythrocytes. Sickle cell anaemia is generally not caused by a de novo mutation. Rather it is selected for in malarial regions (in a similar way to thalassemia) as heterozygous people have some resistance to the malarial Plasmodium parasite (heterozygote advantage).
These variable codes for amino acids are possible because of modified bases in the first base of the anticodon, and the basepair formed is called a wobble base pair. The modified bases include inosine and the U-G basepair.
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; the other is tryptophan, specified by the codon UGG.
Phase or reading frame of a sequence
Note that a "codon" is entirely defined by your starting position. For example, the string GGGAAACCC, if read from the first position, contains the codons GGG, AAA and CCC. If read from the second position, it contains the codons GGA and AAC (partial codons being ignored). If read starting from the third position, GAA and ACC. Every DNA sequence can thus be read in three reading frames, each of which will produce a radically different amino acid sequence (in our example, Gly-Lys-Pro, Gly-Asp, and Glu-Thr, respectively). The actual frame a protein sequence is translated in is defined by a start codon, usually the first occurrence of AUG in the RNA sequence. Mutations that disrupt the reading frame (i.e. insertions or deletions of one or two nucleotide bases) severely impair the function of a protein and are thus exceedingly rare in in vivo protein-coding sequences, since they often lead to death before an organism is viable.
Origin of the genetic code
Numerous variations of the standard genetic code are found in mitochondria, which are energy-producing 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 interpretations that 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.
One can ask the question: is the genetic code completely random, just one set of codon-amino acid correspondences that happened to establish itself and be "frozen in" early in evolution, although functionally any other of the near-infinite set of possible transcription tables would have done just as well? Already a cursory look at the table shows patterns that suggest that this is not the case.
Recent aptamer experiments have shown that amino acids have indeed a selective chemical affinity for the base triplets that code for them.1 This suggests that the current, complex transcription mechanism involving tRNA and associated enzymes is a later development, and that originally, protein sequences were directly templated on base sequences. Also, evidence has been found that originally the number of different amino acids used may have been considerably smaller than today.2