Codon Chart

1. 01The codon chart at a glance

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   The genetic code is read in codons, three bases of mRNA at a time. Four bases give 64 codons: 61 code for an amino acid and 3 say stop. The chart lays all 64 out in a grid, so any codon can be looked up by its three bases. There are only 20 amino acids, so most are coded by more than one codon.

2. 02The first base picks the row

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   Start with the codon's first base, at its 5′ end, and find its row down the left side: U, C, A or G. Every codon in that row begins with it. The bases are listed in the order U, C, A, G, the order codon tables use by convention; NCBI's tables follow it too, with T written for U.

3. 03The second base picks the column

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   The second base picks the column across the top. Row and column together land on one box of four codons that share their first two bases. For eight amino acids that box is all one amino acid: every codon starting GC is alanine, every codon starting GG is glycine, whatever the third base.

4. 04The third base picks the line, so CAU is histidine

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   The third base picks the line within the box, using the letters at the right. So for CAU: row C, column A, line U, which reads histidine, His, H. Try it with any codon from a sequence. The translation tool linked below does the same lookup for a whole sequence at once.

5. 05AUG, the start codon

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   AUG codes for methionine and is also where translation begins. In eukaryotes the ribosome scans along the mRNA from its 5′ end and usually starts at the first AUG it meets, so almost every new protein starts with methionine, which is often trimmed off later. The bases before the start codon are not translated.

6. 06UAA, UAG and UGA, the stop codons

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   Three codons code for no amino acid. When one of them reaches the ribosome, no tRNA matches it; a release factor binds instead and the finished chain is set free. Their old names, from the mutations they were found in, are ochre (UAA), amber (UAG) and opal (UGA). A mutation that turns a codon into a stop is a nonsense mutation.

7. 07Most amino acids have several codons

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   With 61 codons for 20 amino acids, the code is redundant, or degenerate. Leucine, serine and arginine have six codons each; most have two or four; only methionine and tryptophan have one. Codons for the same amino acid usually differ in the third base, which pairs loosely with the tRNA's anticodon: Crick's wobble. So one tRNA can read several codons.

8. 08One base changed: silent, missense or nonsense

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   Because of the redundancy, a change in the third base often leaves the amino acid the same: a silent mutation. A change that swaps one amino acid for another is a missense mutation. In sickle cell disease the sixth codon of the beta-globin gene reads GUG instead of GAG, so valine replaces glutamate, and the hemoglobin sticks together into fibres.

9. 09Nearly universal, with a few exceptions

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   The same chart serves bacteria, plants and people, which is why a human gene can be read by a bacterium. But there are small variations. In the mitochondria of vertebrates, UGA codes for tryptophan instead of stop, AUA for methionine instead of isoleucine, and AGA and AGG, arginine elsewhere, are listed as stop codons, though in human mitochondria they are now thought to end translation by a frameshift onto a UAG. Some ciliates and yeasts read a codon or two differently.

10. 10mRNA chart or DNA chart

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    This chart is written in mRNA bases, which is what the ribosome reads. A DNA codon chart shows the same code in the coding strand, with T in place of U: AUG becomes ATG. To translate the template strand, take its reverse complement first, then read the result off the chart as DNA.

First base (the row)

The first base of the codon, at its 5′ end, picks the row: U, C, A or G. Read a codon from left to right, as the ribosome reads mRNA from 5′ to 3′.

Second base (the column)

The second base picks the column. The first two bases together often settle the amino acid on their own: every codon beginning GC is alanine, every codon beginning CC is proline.

Third base (the line)

The third base, at the 3′ end, picks the line within the box. It is the base that matters least: for eight amino acids any third base gives the same answer, which is why a mutation here is often silent.

Alanine (Ala, A)

Alanine (Ala, A). Nonpolar, with the smallest side chain after glycine. Four codons, GCU, GCC, GCA and GCG: the third base makes no difference. Made from pyruvate in one step, it carries nitrogen from muscle to the liver in the glucose-alanine cycle.

Arginine (Arg, R)

Arginine (Arg, R). Positively charged. Six codons: CGU, CGC, CGA, CGG, AGA and AGG. The body makes it in the urea cycle, but not always enough, so it is conditionally essential. It is also the source of nitric oxide.

Asparagine (Asn, N)

Asparagine (Asn, N). Polar and uncharged, the amide of aspartate. Two codons, AAU and AAC. Sugar chains are attached to proteins at asparagine in N-linked glycosylation. The first amino acid to be isolated, from asparagus juice, in 1806.

Aspartic acid (aspartate) (Asp, D)

Aspartic acid, or aspartate (Asp, D). Negatively charged. Two codons, GAU and GAC. It feeds the urea cycle, supplies atoms to purines and pyrimidines, and carries reducing power into mitochondria in the malate-aspartate shuttle.

Cysteine (Cys, C)

Cysteine (Cys, C). Polar, with a sulfur-containing thiol group. Two codons, UGU and UGC. Two cysteines can bond across a protein as a disulfide bridge, which holds insulin, antibodies and keratin in shape. Made from methionine's sulfur and serine.

Glutamine (Gln, Q)

Glutamine (Gln, Q). Polar and uncharged, the amide of glutamate. Two codons, CAA and CAG. The most abundant free amino acid in blood, it carries ammonia safely between tissues and donates nitrogen for making nucleotides.

Glutamic acid (glutamate) (Glu, E)

Glutamic acid, or glutamate (Glu, E). Negatively charged. Two codons, GAA and GAG. The hub of nitrogen metabolism, where most amino groups are exchanged, and the brain's main excitatory neurotransmitter. GAG to GUG, glutamate to valine, is the sickle cell mutation.

Glycine (Gly, G)

Glycine (Gly, G). The smallest amino acid: its side chain is a single hydrogen, so it is the only one without a chiral centre. Four codons, GGU, GGC, GGA and GGG. Every third residue of collagen is glycine, and it is an inhibitory neurotransmitter in the spinal cord.

Histidine (His, H)

Histidine (His, H). Positively charged, though its imidazole ring is only partly charged at the pH of the body, which lets it pass protons about in enzyme active sites. Two codons, CAU and CAC. Essential in the diet, and the source of histamine.

Isoleucine (Ile, I)

Isoleucine (Ile, I). Nonpolar and branched, essential in the diet. Three codons, AUU, AUC and AUA; in the vertebrate mitochondrial code AUA is read as methionine instead. One of the three branched-chain amino acids, with leucine and valine.

Leucine (Leu, L)

Leucine (Leu, L). Nonpolar and branched, essential in the diet. Six codons, as many as any amino acid has: UUA, UUG, CUU, CUC, CUA and CUG. The commonest amino acid in proteins, and a signal that amino acids are plentiful, which stimulates protein synthesis in muscle.

Lysine (Lys, K)

Lysine (Lys, K). Positively charged, essential in the diet. Two codons, AAA and AAG. Its side chain is where histones are acetylated and methylated to control genes, and where collagen fibres are cross-linked. The amino acid in shortest supply in cereal grains.

Methionine (Met, M), the start codon

Methionine (Met, M). Nonpolar, with a sulfur in its side chain, and essential in the diet. One codon, AUG, which is also the start codon: nearly every protein is begun with methionine, often removed afterwards. As S-adenosylmethionine it donates methyl groups.

Phenylalanine (Phe, F)

Phenylalanine (Phe, F). Aromatic and nonpolar, essential in the diet. Two codons, UUU and UUC. The body turns it into tyrosine; in phenylketonuria that enzyme is faulty or missing, so phenylalanine builds up and has to be limited in the diet.

Proline (Pro, P)

Proline (Pro, P). Nonpolar, and the only amino acid whose side chain loops back onto the backbone nitrogen. Four codons, CCU, CCC, CCA and CCG. The ring is stiff, so proline bends and breaks helices, and hydroxylated proline strengthens collagen.

Serine (Ser, S)

Serine (Ser, S). Polar, with a hydroxyl group. Six codons: UCU, UCC, UCA, UCG, AGU and AGC. Kinases attach phosphate to serine to switch proteins on and off, serine proteases cut with it, and it is the starting material for glycine, cysteine and many phospholipids.

Threonine (Thr, T)

Threonine (Thr, T). Polar, with a hydroxyl group, and essential in the diet. Four codons, ACU, ACC, ACA and ACG. Like serine it is a site for phosphorylation and for attaching sugars, and like isoleucine it has two chiral centres.

Tryptophan (Trp, W)

Tryptophan (Trp, W). Aromatic, with a large indole ring, and essential in the diet. One codon, UGG, and the rarest amino acid in proteins. The source of serotonin, melatonin and niacin. In the vertebrate mitochondrial code UGA is read as tryptophan too.

Tyrosine (Tyr, Y)

Tyrosine (Tyr, Y). Aromatic, with a phenol group. Two codons, UAU and UAC. Made from phenylalanine, so not essential while that is supplied. Tyrosine kinases phosphorylate it to pass signals, and it is the source of dopamine, adrenaline, thyroid hormones and melanin.

Valine (Val, V)

Valine (Val, V). Nonpolar and branched, essential in the diet. Four codons, GUU, GUC, GUA and GUG. In sickle cell disease a single base change, GAG to GUG, puts valine where glutamate belongs at the sixth position of the beta-globin chain.

Stop codons (UAA, UAG, UGA)

No tRNA carries an anticodon for a stop codon; a release factor binds in its place and the finished chain is let go. Their old names are ochre, amber and opal. UGA can also code for selenocysteine, a 21st amino acid, where the mRNA carries a special signal downstream.

What the chart shows

The standard genetic code, NCBI translation table 1, used by the nuclear genes of nearly every organism. It is written as mRNA codons; a DNA codon chart for the coding strand reads T wherever this one reads U. The abbreviations follow the IUPAC-IUBMB nomenclature.

The 20 amino acids of the standard genetic code, with their abbreviations, their codons, the class of their side chain and whether the diet must supply them.

• Alanine

  Abbreviations

  Ala, A

  mRNA codons

  GCU, GCC, GCA, GCG

  Side chain

  Nonpolar, aliphatic

  In the diet

  Not essential

• Arginine

  Abbreviations

  Arg, R

  mRNA codons

  CGU, CGC, CGA, CGG, AGA, AGG

  Side chain

  Positively charged

  In the diet

  Conditionally essential

• Asparagine

  Abbreviations

  Asn, N

  mRNA codons

  AAU, AAC

  Side chain

  Polar, uncharged

  In the diet

  Not essential

• Aspartic acid (aspartate)

  Abbreviations

  Asp, D

  mRNA codons

  GAU, GAC

  Side chain

  Negatively charged

  In the diet

  Not essential

• Cysteine

  Abbreviations

  Cys, C

  mRNA codons

  UGU, UGC

  Side chain

  Polar, uncharged

  In the diet

  Conditionally essential

• Glutamine

  Abbreviations

  Gln, Q

  mRNA codons

  CAA, CAG

  Side chain

  Polar, uncharged

  In the diet

  Conditionally essential

• Glutamic acid (glutamate)

  Abbreviations

  Glu, E

  mRNA codons

  GAA, GAG

  Side chain

  Negatively charged

  In the diet

  Not essential

• Glycine

  Abbreviations

  Gly, G

  mRNA codons

  GGU, GGC, GGA, GGG

  Side chain

  Nonpolar, aliphatic

  In the diet

  Conditionally essential

• Histidine

  Abbreviations

  His, H

  mRNA codons

  CAU, CAC

  Side chain

  Positively charged

  In the diet

  Essential

• Isoleucine

  Abbreviations

  Ile, I

  mRNA codons

  AUU, AUC, AUA

  Side chain

  Nonpolar, aliphatic

  In the diet

  Essential

• Leucine

  Abbreviations

  Leu, L

  mRNA codons

  UUA, UUG, CUU, CUC, CUA, CUG

  Side chain

  Nonpolar, aliphatic

  In the diet

  Essential

• Lysine

  Abbreviations

  Lys, K

  mRNA codons

  AAA, AAG

  Side chain

  Positively charged

  In the diet

  Essential

• Methionine

  Abbreviations

  Met, M

  mRNA codons

  AUG

  Side chain

  Nonpolar, aliphatic

  In the diet

  Essential

• Phenylalanine

  Abbreviations

  Phe, F

  mRNA codons

  UUU, UUC

  Side chain

  Aromatic

  In the diet

  Essential

• Proline

  Abbreviations

  Pro, P

  mRNA codons

  CCU, CCC, CCA, CCG

  Side chain

  Nonpolar, aliphatic

  In the diet

  Conditionally essential

• Serine

  Abbreviations

  Ser, S

  mRNA codons

  UCU, UCC, UCA, UCG, AGU, AGC

  Side chain

  Polar, uncharged

  In the diet

  Not essential

• Threonine

  Abbreviations

  Thr, T

  mRNA codons

  ACU, ACC, ACA, ACG

  Side chain

  Polar, uncharged

  In the diet

  Essential

• Tryptophan

  Abbreviations

  Trp, W

  mRNA codons

  UGG

  Side chain

  Aromatic

  In the diet

  Essential

• Tyrosine

  Abbreviations

  Tyr, Y

  mRNA codons

  UAU, UAC

  Side chain

  Aromatic

  In the diet

  Conditionally essential

• Valine

  Abbreviations

  Val, V

  mRNA codons

  GUU, GUC, GUA, GUG

  Side chain

  Nonpolar, aliphatic

  In the diet

  Essential

• Stop

  Abbreviations

  Stop, *

  mRNA codons

  UAA, UAG, UGA

  Side chain

  No amino acid: the chain is released

AUG, methionine's one codon, is also the start codon. Essential means the body cannot make it, so food must supply it; conditionally essential means the body usually makes enough, but not in infancy, illness or rapid growth. Side chains are classed as in Lehninger Principles of Biochemistry.

• Codon
• Amino acid
• Translation
• Messenger RNA
• Transfer RNA
• Ribosome
• Peptide bond
• Protein
• Mutation
• Frameshift mutation
• Gene
• Uracil

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• Molecular Biology flashcards

  The subject's terms as a ready-made deck, free to flip through.

• DNA to Protein Translation

  Translate DNA or RNA into protein in any of the six frames, with the standard or a mitochondrial or bacterial code, and get the protein's mass and pI.

• ORF Finder

  Every open reading frame in all six frames, with its position, length and protein, from ATG or any start codon.

• 

  Nucleic acid · PDB 1EHZ

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• NCBI: The Genetic Codes, translation table 1 (the standard code)
• IUPAC-IUBMB Joint Commission on Biochemical Nomenclature: Nomenclature and Symbolism for Amino Acids and Peptides
• Alberts and others, Molecular Biology of the Cell, 4th edition: From RNA to Protein (NCBI Bookshelf)
• National Human Genome Research Institute: Stop Codon (Talking Glossary of Genomic and Genetic Terms)
• Crick: Codon-anticodon pairing, the wobble hypothesis, Journal of Molecular Biology 1966 (PubMed)
• Hatfield and Gladyshev: How selenium has altered our understanding of the genetic code, Molecular and Cellular Biology 2002 (PubMed)
• StatPearls: Biochemistry, Essential Amino Acids, archived chapter (NCBI Bookshelf)
• Watford and Wu: Protein, Advances in Nutrition 2018 (PubMed), on the conditionally indispensable amino acids
• MedlinePlus Genetics: HBB gene (the sickle cell variant, Glu6Val)

Drawn and written by biofideX from these sources.