DNA and RNA codon tables

A codon table can be used to translate a genetic code into a sequence of amino acids.[1][2] The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis.[2][3] The mRNA sequence is determined by the sequence of genomic DNA.[4] In this context, the standard genetic code is referred to as translation table 1.[3] It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ direction. Different tables with alternate codons are used depending on the source of the genetic code, such as from a cell nucleus, mitochondrion, plastid, or hydrogenosome.[5]

A circular diagram is separated into three rings, broken down into sections labeled with the letters: G, U, A, and C. Each represents a nucleotide found in RNA. The center ring is divided into four areas marked with a unique letter. The second ring is divided into 16 sections also labeled with a nucleotide. They are organized so that the outer edge of the central letters touches four unique nucleotides. The third outer ring, divided into 64 sections labeled with a nucleotide, repeats this. Amino acids are placed outside of the circular diagram and are in contact with specific nucleotides. Using this diagram, one can connect a sequence of three nucleotides with a specific amino acid. For example, given "GUC", one can follow contigous sections of the rings from the center to the outside: from G to U and U to C. This leads the user to the amino acid Alanine.
The standard RNA codon table organized in a wheel
A double helix is situated horizontally. The helix contains vertical letter pairs (e.g. G & C, C & G, and A & T) that represent the base pairs within DNA. The bottom letter of each pair is written below the helix. These letters are in groups of three (triplets). Beneath each triplet is an arrow pointing to the corresponding amino acid. For example, an arrow points from "GCA" to Alanine.
The three consecutive DNA bases, called nucleotide triplets or codons, are translated into amino acids (GCA to alanine, AGA to arginine, GAT to aspartic acid, AAT to asparagine, and TGT to cysteine in this example).

There are 64 different codons in the genetic code and the below tables; most specify an amino acid.[6] Three sequences, UAG, UGA, and UAA, known as stop codons,[note 1] do not code for an amino acid but instead signal the release of the nascent polypeptide from the ribosome.[7] In the standard code, the sequence AUG—read as methionine—can serve as a start codon and, along with sequences such as an initiation factor, initiates translation.[3][8][9] In rare instances, start codons in the standard code may also include GUG or UUG; these codons normally represent valine and leucine, respectively, but as start codons they are translated as methionine or formylmethionine.[3][9]

The first table—the standard table—can be used to translate nucleotide triplets into the corresponding amino acid or appropriate signal if it is a start or stop codon. The second table, appropriately called the inverse, does the opposite: it can be used to deduce a possible triplet code if the amino acid is known. As multiple codons can code for the same amino acid, the International Union of Pure and Applied Chemistry's (IUPAC) nucleic acid notation is given in some instances.

Translation table 1Edit

Standard RNA codon tableEdit

Amino-acid biochemical properties Nonpolar   Polar   Basic   Acidic ↓ Termination: stop codon * Initiation: possible start codon  
Standard genetic code[1][10]
1st
base
2nd base 3rd
base
U C A G
U UUU (Phe/F) Phenylalanine   UCU (Ser/S) Serine   UAU (Tyr/Y) Tyrosine   UGU (Cys/C) Cysteine   U
UUC UCC UAC UGC C
UUA (Leu/L) Leucine   UCA UAA Stop (Ochre) *[note 2] UGA Stop (Opal) *[note 2] A
UUG   UCG UAG Stop (Amber) *[note 2] UGG (Trp/W) Tryptophan   G
C CUU CCU (Pro/P) Proline   CAU (His/H) Histidine   CGU (Arg/R) Arginine   U
CUC CCC CAC CGC C
CUA CCA CAA (Gln/Q) Glutamine   CGA A
CUG CCG CAG CGG G
A AUU (Ile/I) Isoleucine   ACU (Thr/T) Threonine   AAU (Asn/N) Asparagine   AGU (Ser/S) Serine   U
AUC ACC AAC AGC C
AUA ACA AAA (Lys/K) Lysine   AGA (Arg/R) Arginine   A
AUG   (Met/M) Methionine   ACG AAG AGG G
G GUU (Val/V) Valine   GCU (Ala/A) Alanine   GAU (Asp/D) Aspartic acid GGU (Gly/G) Glycine   U
GUC GCC GAC GGC C
GUA GCA GAA (Glu/E) Glutamic acid GGA A
GUG   GCG GAG GGG G

Inverse RNA codon tableEdit

Inverse table for the standard genetic code (compressed using IUPAC notation)[13]
Amino acid RNA codons Compressed Amino acid RNA 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 STOP UAA, UGA, UAG URA, UAR

Standard DNA codon tableEdit

Amino-acid biochemical properties Nonpolar   Polar   Basic   Acidic ↓ Termination: stop codon * Initiation: possible start codon  
Standard genetic code[14][note 3]
1st
base
2nd base 3rd
base
T C A G
T TTT (Phe/F) Phenylalanine   TCT (Ser/S) Serine   TAT (Tyr/Y) Tyrosine   TGT (Cys/C) Cysteine   T
TTC TCC TAC TGC C
TTA (Leu/L) Leucine   TCA TAA Stop (Ochre) *[note 2] TGA Stop (Opal) *[note 2] A
TTG   TCG TAG Stop (Amber) *[note 2] TGG (Trp/W) Tryptophan   G
C CTT CCT (Pro/P) Proline   CAT (His/H) Histidine   CGT (Arg/R) Arginine   T
CTC CCC CAC CGC C
CTA CCA CAA (Gln/Q) Glutamine   CGA A
CTG CCG CAG CGG G
A ATT (Ile/I) Isoleucine   ACT (Thr/T) Threonine   AAT (Asn/N) Asparagine   AGT (Ser/S) Serine   T
ATC ACC AAC AGC C
ATA ACA AAA (Lys/K) Lysine   AGA (Arg/R) Arginine   A
ATG   (Met/M) Methionine   ACG AAG AGG G
G GTT (Val/V) Valine   GCT (Ala/A) Alanine   GAT (Asp/D) Aspartic acid GGT (Gly/G) Glycine   T
GTC GCC GAC GGC C
GTA GCA GAA (Glu/E) Glutamic acid GGA A
GTG   GCG GAG GGG G

Inverse DNA codon tableEdit

Inverse table for the standard genetic code (compressed using IUPAC notation)[13]
Amino acid DNA codons Compressed Amino acid DNA codons Compressed
Ala, A GCT, GCC, GCA, GCG GCN Ile, I ATT, ATC, ATA ATH
Arg, R CGT, CGC, CGA, CGG; AGA, AGG CGN, AGR; or
CGY, MGR
Leu, L CTT, CTC, CTA, CTG; TTA, TTG CTN, TTR; or
CTY, YTR
Asn, N AAT, AAC AAY Lys, K AAA, AAG AAR
Asp, D GAT, GAC GAY Met, M ATG
Asn or Asp, B AAT, AAC; GAT, GAC RAY Phe, F TTT, TTC TTY
Cys, C TGT, TGC TGY Pro, P CCT, CCC, CCA, CCG CCN
Gln, Q CAA, CAG CAR Ser, S TCT, TCC, TCA, TCG; AGT, AGC TCN, AGY
Glu, E GAA, GAG GAR Thr, T ACT, ACC, ACA, ACG ACN
Gln or Glu, Z CAA, CAG; GAA, GAG SAR Trp, W TGG
Gly, G GGT, GGC, GGA, GGG GGN Tyr, Y TAT, TAC TAY
His, H CAT, CAC CAY Val, V GTT, GTC, GTA, GTG GTN
START ATG STOP TAA, TGA, TAG TRA, TAR

Alternative codons in other translation tablesEdit

The genetic code was once believed to be universal:[16] a codon would code for the same amino acid regardless of the organism or source. However, it is now agreed that the genetic code evolves,[17] resulting in discrepancies in how a codon is translated depending on the genetic source.[16][17] For example, in 1981, it was discovered that the use of codons AUA, UGA, AGA and AGG by the coding system in mammalian mitochondria differed from the universal code.[16] Stop codons can also be affected: in ciliated protozoa, the universal stop codons UAA and UAG code for glutamine.[17][note 4] The following table displays these alternative codons.

Amino-acid biochemical properties Nonpolar   Polar   Basic   Acidic ↓ Termination: stop codon *
Comparison between codon translations with alternative and standard genetic codes[3]
Code Translation
table
DNA codon involved RNA codon involved Translation
with this code
Standard translation Notes
Standard 1 Includes translation table 8 (plant chloroplasts).
Vertebrate mitochondrial 2 AGA AGA Stop * Arg (R)  
AGG AGG Stop * Arg (R)  
ATA AUA Met (M)   Ile (I)  
TGA UGA Trp (W)   Stop *
Yeast mitochondrial 3 ATA AUA Met (M)   Ile (I)  
CTT CUU Thr (T)   Leu (L)  
CTC CUC Thr (T)   Leu (L)  
CTA CUA Thr (T)   Leu (L)  
CTG CUG Thr (T)   Leu (L)  
TGA UGA Trp (W)   Stop *
CGA CGA absent Arg (R)  
CGC CGC absent Arg (R)  
Mold, protozoan, and coelenterate mitochondrial + Mycoplasma / Spiroplasma 4 TGA UGA Trp (W)   Stop * Includes the translation table 7 (kinetoplasts).
Invertebrate mitochondrial 5 AGA AGA Ser (S)   Arg (R)  
AGG AGG Ser (S)   Arg (R)  
ATA AUA Met (M)   Ile (I)  
TGA UGA Trp (W)   Stop *
Ciliate, dasycladacean and Hexamita nuclear 6 TAA UAA Gln (Q)   Stop *
TAG UAG Gln (Q)   Stop *
Echinoderm and flatworm mitochondrial 9 AAA AAA Asn (N)   Lys (K)  
AGA AGA Ser (S)   Arg (R)  
AGG AGG Ser (S)   Arg (R)  
TGA UGA Trp (W)   Stop *
Euplotid nuclear 10 TGA UGA Cys (C)   Stop *
Bacterial, archaeal and plant plastid 11 See translation table 1.
Alternative yeast nuclear 12 CTG CUG Ser (S)   Leu (L)  
Ascidian mitochondrial 13 AGA AGA Gly (G)   Arg (R)  
AGG AGG Gly (G)   Arg (R)  
ATA AUA Met (M)   Ile (I)  
TGA UGA Trp (W)   Stop *
Alternative flatworm mitochondrial 14 AAA AAA Asn (N)   Lys (K)  
AGA AGA Ser (S)   Arg (R)  
AGG AGG Ser (S)   Arg (R)  
TAA UAA Tyr (Y)   Stop *
TGA UGA Trp (W)   Stop *
Blepharisma nuclear 15 TAG UAG Gln (Q)   Stop * As of Nov. 18, 2016: absent from the NCBI update. Similar to translation table 6.
Chlorophycean mitochondrial 16 TAG UAG Leu (L)   Stop *
Trematode mitochondrial 21 TGA UGA Trp (W)   Stop *
ATA AUA Met (M)   Ile (I)  
AGA AGA Ser (S) Arg (R)  
AGG AGG Ser (S)   Arg (R)  
AAA AAA Asn (N)   Lys (K)  
Scenedesmus obliquus mitochondrial 22 TCA UCA Stop * Ser (S)  
TAG UAG Leu (L)   Stop *
Thraustochytrium mitochondrial 23 TTA UUA Stop * Leu (L)   Similar to translation table 11.
Pterobranchia mitochondrial 24 AGA AGA Ser (S)   Arg (R)  
AGG AGG Lys (K)   Arg (R)  
TGA UGA Trp (W)   Stop *
Candidate division SR1 and Gracilibacteria 25 TGA UGA Gly (G)   Stop *
Pachysolen tannophilus nuclear 26 CTG CUG Ala (A)   Leu (L)  
Karyorelict nuclear 27 TAA UAA Gln (Q)   Stop *
TAG UAG Gln (Q)   Stop *
TG UGA Stop * or Trp (W)   Stop *
Condylostoma nuclear 28 TAA UAA Stop * or Gln (Q)   Stop *
TAG UAG Stop * or Gln (Q)   Stop *
TGA UGA Stop * or Trp (W)   Stop *
Mesodinium nuclear 29 TAA UAA Tyr (Y)   Stop *
TAG UAG Tyr (Y)   Stop *
Peritrich nuclear 30 TA UAA Glu (E) ↓ Stop *
TAG UAG Glu (E) ↓ Stop *
Blastocrithidia nuclear 31 TAA UAA Stop * or Glu (E) ↓ Stop *
TAG UAG Stop * or Glu (E) ↓ Stop *
TGA UGA Trp (W)   Stop *
Cephalodiscidae mitochondrial code 33 AGA AGA Ser (S)   Arg (R)   Similar to translation table 24.
AGG AGG Lys (K)   Arg (R)  
TAA UAA Tyr (Y)   Stop *
TGA UGA Trp (W)   Stop *

See alsoEdit

NotesEdit

  1. ^ Each stop codon has a specific name: UAG is amber, UGA is opal or umber, and UAA is ochre.[7] In DNA, these stop codons are TAG, TGA, and TAA, respectively.
  2. ^ a b c d e f The historical basis for designating the stop codons as amber, ochre and opal is described in the autobiography of Sydney Brenner[11] and in a historical article by Bob Edgar.[12]
  3. ^ The major difference between DNA and RNA is that thymine (T) is only found in the former. In RNA, it is replaced with uracil (U).[15] This is the only difference between the standard RNA codon table and the standard DNA codon table.
  4. ^ Euplotes octacarinatus is an exception.[17]

ReferencesEdit

  1. ^ a b "Amino Acid Translation Table". Oregon State University. Archived from the original on 29 May 2020. Retrieved 2 December 2020.
  2. ^ a b Bartee, Lisa; Brook, Jack. MHCC Biology 112: Biology for Health Professions. Open Oregon. p. 42. Archived from the original on 6 December 2020. Retrieved 6 December 2020.
  3. ^ a b c d e Elzanowski A, Ostell J (7 January 2019). "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 9 October 2020. Retrieved 21 February 2019.
  4. ^ "RNA Functions". Scitable. Nature Education. Archived from the original on 18 October 2008. Retrieved 5 January 2021.
  5. ^ "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 13 May 2011. Retrieved 2 December 2020.
  6. ^ "Codon". National Human Genome Research Institute. Archived from the original on 22 October 2020. Retrieved 10 October 2020.
  7. ^ a b Maloy S. (29 November 2003). "How nonsense mutations got their names". Microbial Genetics Course. San Diego State University. Archived from the original on 23 September 2020. Retrieved 10 October 2020.
  8. ^ Hinnebusch AG (2011). "Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes". Microbiology and Molecular Biology Reviews. 75 (3): 434–467. doi:10.1128/MMBR.00008-11. PMC 3165540. PMID 21885680.
  9. ^ a b Touriol C, Bornes S, Bonnal S, Audigier S, Prats H, Prats AC, Vagner S (2003). "Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons". Biology of the Cell. 95 (3–4): 169–78. doi:10.1016/S0248-4900(03)00033-9. PMID 12867081.
  10. ^ "The Information in DNA Determines Cellular Function via Translation". Scitable. Nature Education. Archived from the original on 23 September 2017. Retrieved 5 December 2020.
  11. ^ Brenner, Sydney; Wolpert, Lewis (2001). A Life in Science. Biomed Central Limited. pp. 101–104. ISBN 9780954027803.
  12. ^ Edgar B (2004). "The genome of bacteriophage T4: an archeological dig". Genetics. 168 (2): 575–82. doi:10.1093/genetics/168.2.575. PMC 1448817. PMID 15514035. see pages 580–581
  13. ^ a b IUPAC—IUB Commission on Biochemical Nomenclature. "Abbreviations and Symbols for Nucleic Acids, Polynucleotides and Their Constituents" (PDF). International Union of Pure and Applied Chemistry. Retrieved 5 December 2020.
  14. ^ "What does DNA do?". Your Genome. Welcome Genome Campus. Archived from the original on 29 November 2020. Retrieved 12 January 2021.
  15. ^ "Genes". DNA, Genetics, and Evolution. Boston University. Archived from the original on 28 April 2020. Retrieved 10 December 2020.
  16. ^ a b c Osawa, A (November 1993). "Evolutionary changes in the genetic code". Comparative Biochemistry and Physiology. 106 (2): 489–94. doi:10.1016/0305-0491(93)90122-l. PMID 8281749.
  17. ^ a b c d Osawa S, Jukes TH, Watanabe K, Muto A (March 1992). "Recent evidence for evolution of the genetic code". Microbiological Reviews. 56 (1): 229–64. doi:10.1128/MR.56.1.229-264.1992. PMC 372862. PMID 1579111.

Further readingEdit

External linksEdit