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* it signals the start of translation
* it codes for the incorporation of the amino acid methionine (Met) into the growing polypeptide chain
The genetic code can be expressed as either RNA codons or DNA codons. RNA codons occur in messenger RNA (mRNA) and are the codons that are actually "read" during the synthesis of polypeptides (the process called translation). But each mRNA molecule acquires its sequence of nucleotides by transcription from the corresponding gene. Because DNA sequencing has become so rapid and because most genes are now being discovered at the level of DNA before they are discovered as mRNA or as a protein product, it is extremely useful to have a table of codons expressed as DNA. So here are both.
Note that for each table, the left-hand column gives the first nucleotide of the codon, the 4 middle columns give the second nucleotide, and the last column gives the third nucleotide.
The RNA Codons
Second nucleotide UCAG
U UUU Phenylalanine (Phe)UCU Serine (Ser)UAU Tyrosine (Tyr)UGU Cysteine (Cys)U
UUC PheUCC SerUAC TyrUGC CysC
UUA Leucine (Leu)UCA Ser UAA STOPUGA STOPA
UUG LeuUCG Ser UAG STOPUGG Tryptophan (Trp)G
C CUU Leucine (Leu)CCU Proline (Pro)CAU Histidine (His)CGU Arginine (Arg)U
CUC LeuCCC ProCAC HisCGC Arg C
CUA LeuCCA ProCAA Glutamine (Gln)CGA Arg A
CUG LeuCCG ProCAG GlnCGG Arg G
A AUU Isoleucine (Ile)ACU Threonine (Thr)AAU Asparagine (Asn)AGU Serine (Ser)U
AUC IleACC ThrAAC AsnAGC Ser C
AUA IleACA Thr AAA Lysine (Lys)AGA Arginine (Arg)A
AUG Methionine (Met) or STARTACG ThrAAG LysAGG Arg G
G GUU Valine ValGCU Alanine (Ala)GAU Aspartic acid (Asp)GGU Glycine (Gly)U
GUC (Val)GCC AlaGAC AspGGC GlyC
GUA ValGCA AlaGAA Glutamic acid (Glu)GGA GlyA
GUG ValGCG AlaGAG GluGGG GlyG
The DNA Codons
These are the codons as they are read on the sense (5' to 3') strand of DNA. Except that the nucleotide thymidine (T) is found in place of uridine (U), they read the same as RNA codons. However, mRNA is actually synthesized using the antisense strand of DNA (3' to 5') as the template. [Discussion]
This table could well be called the Rosetta Stone of life.
The Genetic Code (DNA)
TTTPheTCTSerTATTyrTGTCys
TTCPheTCCSerTACTyrTGCCys
TTALeuTCASerTAASTOPTGASTOP
TTGLeuTCGSerTAGSTOPTGGTrp
CTTLeuCCTProCATHisCGTArg
CTCLeuCCCProCACHisCGCArg
CTALeuCCAProCAAGlnCGAArg
CTGLeuCCGProCAGGlnCGGArg
ATTIleACTThrAATAsnAGTSer
ATCIleACCThrAACAsnAGCSer
ATAIleACAThrAAALysAGAArg
ATGMet*ACGThrAAGLysAGGArg
GTTValGCTAlaGATAspGGTGly
GTCValGCCAlaGACAspGGCGly
GTAValGCAAlaGAAGluGGAGly
GTGValGCGAlaGAGGluGGGGly
*When within gene; at beginning of gene, ATG signals start of translation.
Codon Bias
All but two of the amino acids (Met and Trp) can be encoded by from 2 to 6 different codons. However, the genome of most organisms reveals that certain codons are preferred over others. In humans, for example, alanine is encoded by GCC four times as often as by GCG. Why should this be? The answer is uncertain but probably reflects a greater translation efficiency by the translation apparatus (e.g., ribosomes) for certain codons over their synonyms.
Codon bias even extends to pairs of codons: wherever a human protein contains the amino acids Ala-Glu, the gene encoding those amino acids is seven times as likely to use the codons GCAGAG rather than the synonymous GCCGAA.
Codon bias is exploited by the biotechnology industry to improve the yield of the desired product. The ability to manipulate codon bias may also usher in a era of safer vaccines. Link to a discussion.
Exceptions to the Code
The genetic code is almost universal. The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms. However, some exceptions have been found. Most of these involve assigning one or two of the three STOP codons to an amino acid instead.
Mitochondrial genes
When mitochondrial mRNA from animals or microorganisms (but not from plants) is placed in a test tube with the cytosolic protein-synthesizing machinery (amino acids, enzymes, tRNAs, ribosomes) it fails to be translated into a protein.
The reason: these mitochondria use UGA to encode tryptophan (Trp) rather than as a chain terminator. When translated by cytosolic machinery, synthesis stops where Trp should have been inserted.
In addition, most
* animal mitochondria use AUA for methionine not isoleucine and
* all vertebrate mitochondria use AGA and AGG as chain terminators.
* Yeast mitochondria assign all codons beginning with CU to threonine instead of leucine (which is still encoded by UUA and UUG as it is in cytosolic mRNA).
