Codon degeneracy
Degeneracy or redundancy
Background
Degeneracy of the genetic code was identified by Lagerkvist.[3] For instance, codons GAA and GAG both specify glutamic acid and exhibit redundancy; but, neither specifies any other amino acid and thus are not ambiguous or demonstrate no ambiguity.
The codons encoding one amino acid may differ in any of their three positions; however, more often than not, this difference is in the second or third position.[4] For instance, 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); and the amino acid serine is specified by UCA, UCG, UCC, UCU, AGU, AGC (difference in the first, second, or third position).[2]: 521–522
Degeneracy results because there are more codons than encodable amino acids. 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 (20 amino acids plus stop) and the next largest number of bases is three, then 4³ gives 64 possible codons, meaning that some degeneracy must exist.[2]: 521–522
Terminology
A position of a codon is said to be a n-fold degenerate site if only n of four possible nucleotides (A, C, G, T) at this position specify the same amino acid. A nucleotide substitution at a 4-fold degenerate site is always a
A less degenerate site would produce a
A position is said to be non-degenerate if any mutation at this position changes the amino acid. For example, all three positions of methionine's AUG are non-degenerate, because the only codon coding for methionine is AUG. The same goes for tryptophan's UGG.[2]: 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 each. 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.
Amino acid | DNA codons | Compressed | Amino acid | DNA codons | Compressed | |
---|---|---|---|---|---|---|
Ala, A | GCU, GCC, GCA, GCG | GCN | Ile, I | AUU, AUC, AUA | AUH | |
Arg, R | CGU, CGC, CGA, CGG; AGA, AGG | CGN, AGR; or CGY, MGR |
Leu, L | CUU, CUC, CUA, CUG; UUA, UUG | CUN, UUR; or CUY, YUR | |
Asn, N | AAU, AAC | AAY | Lys, K | AAA, AAG | AAR | |
Asp, D | GAU, GAC | GAY | Met, M | AUG | ||
Asn or Asp, B | AAU, AAC; GAU, GAC | RAY | Phe, F | UUU, UUC | UUY | |
Cys, C | UGU, UGC | UGY | Pro, P | CCU, CCC, CCA, CCG | CCN | |
Gln, Q | CAA, CAG | CAR | Ser, S | UCU, UCC, UCA, UCG; AGU, AGC | UCN, AGY | |
Glu, E | GAA, GAG | GAR | Thr, T | ACU, ACC, ACA, ACG | ACN | |
Gln or Glu, Z | CAA, CAG; GAA, GAG | SAR | Trp, W | UGG | ||
Gly, G | GGU, GGC, GGA, GGG | GGN | Tyr, Y | UAU, UAC | UAY | |
His, H | CAU, CAC | CAY | Val, V | GUU, GUC, GUA, GUG | GUN | |
START | AUG, CUG, UUG | HUG | STOP | UAA, UGA, UAG | URA, UAR |
Implications
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 withstand silence mutation rather than Missense or Nonsense 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.[2]: 531–532
A practical consequence of redundancy is that some errors in the genetic code cause only a synonymous mutation, or an error that would not affect the protein because the
These variable codes for amino acids are allowed because of modified bases in the first base of the
See also
References
- ^ "The Information in DNA Determines Cellular Function via Translation | Learn Science at Scitable". www.nature.com. Retrieved 2021-07-14.
- ^ ISBN 978-0-8053-9592-1.
- ^ Lagerkvist, U. (1978.) "Two out of three: An alternative method for codon reading", PNAS, 75:1759-62.
- PMID 18495942.
- ISBN 3-540-53420-2.
- ^ Füllen G, Youvan DC (1994). "Genetic Algorithms and Recursive Ensemble Mutagenesis in Protein Engineering". Complexity International. 1. Archived from the original on 2011-03-15.
- PMID 11256617.