Translation (biology)

Basic mechanisms

See main articles at eukaryotic translation

The mRNA carries amino acid.

The ribosome and tRNA molecules translate this code to produce proteins. The rRNA and proteins. It is the "factory" where amino acids are assembled into proteins. tRNAs are small noncoding RNA chains (74-93 nucleotides) that transport amino acids to the ribosome. tRNAs have a site for amino acid attachment, and a site called an anticodon. The anticodon is an RNA triplet complementary to the mRNA triplet that codes for their cargo amino acid.

tRNAs and the amino acids that their anticodons sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary tRNA anticodons. The amino acids that the tRNAs carry are then used to assemble a protein. The energy required for translation of proteins is significant. For a protein containing n amino acids, the number of high-energy Phosphate bonds required to translate it is 4n-1.

Translation by hand

It is also possible to translate either by hand (for short sequences) or by computer (after first programming one appropriately, see section below), this allows biologists and chemists to draw out the chemical structure of the encoded protein on paper.

First, convert each DNA base to its RNA complement (note that the complement of A is now U):

DNA -> RNA
 A  ->  U
 T  ->  A
 G  ->  C
 C  ->  G

Then split the RNA into triplets (groups of three bases). Note that there are 3 translation "windows" depending on where you start reading the code. Finally, use the table at structural formula as used in chemistry.

This will give you the tertiary structure is often very hard to determine.

This approach may not give the correct amino acid composition of the protein, in particular if unconventional selenocysteine are incorporated into the protein, which is coded for by a conventional stop codon in combination with a downstream hairpin (SElenoCysteine Insertion Sequence, or SECIS).

Translation by computer

Many computer programs capable of translating a DNA/RNA sequence into protein sequence exist. Normally this is performed using the Standard Genetic Code; many bioinformaticians have written at least one such program at some point in their education. However, few programs can handle all the "special" cases, such as the use of the alternative initiation codons: For example the rare alternative start codon TTG codes for Methionine when used as a start codon and for Leucine in all other positions.

Example: Condensed translation table for the Standard Genetic Code (from the NCBI Taxonomy webpage).

   AAs  = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
 Starts = ---M---------------M---------------M----------------------------
 Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Translation tables

Even when working with ordinary Eukaryotic sequences such as the Yeast genome, it is often desired to be able to use alternative translation tables -- namely for translation of the mitochondrial genes. Currently the following translation tables are defined by the NCBI Taxonomy Group for the translation of the sequences in GenBank:

 1: The Standard 
 2: The Vertebrate Mitochondrial Code 
 3: The Yeast Mitochondrial Code 
 4: The Mold, Protozoan, and Coelenterate Mitochondrial Code  and the Mycoplasma/Spiroplasma Code 
 5: The Invertebrate Mitochondrial Code 
 6: The Ciliate, Dasycladacean and Hexamita Nuclear Code 
 9: The Echinoderm and Flatworm Mitochondrial Code
10: The Euplotid Nuclear Code 
11: The Bacterial and Plant Plastid Code 
12: The Alternative Yeast Nuclear Code 
13: The Ascidian Mitochondrial Code 
14: The Alternative Flatworm Mitochondrial Code 
15: Blepharisma Nuclear Code 
16: Chlorophycean Mitochondrial Code 
21: Trematode Mitochondrial Code 
22: Scenedesmus obliquus mitochondrial Code 
23: Thraustochytrium Mitochondrial Code

Software examples

• ApE (Mac, Windows, Unix)
• DNA Strider (Mac)
• ExPASy Translate Tool (webserver)
• Virtual Ribosome (webserver, cross-platform command-line)

Example of computational translation - notice the indication of (alternative) start-codons:

VIRTUAL RIBOSOME
----
Translation table: Standard SGC0 

>Seq1
Reading frame: 1

    M  V  L  S  A  A  D  K  G  N  V  K  A  A  W  G  K  V  G  G  H  A  A  E  Y  G  A  E  A  L  
5' ATGGTGCTGTCTGCCGCCGACAAGGGCAATGTCAAGGCCGCCTGGGGCAAGGTTGGCGGCCACGCTGCAGAGTATGGCGCAGAGGCCCTG 90
   >>>...)))..............................................................................))) 

    E  R  M  F  L  S  F  P  T  T  K  T  Y  F  P  H  F  D  L  S  H  G  S  A  Q  V  K  G  H  G  
5' GAGAGGATGTTCCTGAGCTTCCCCACCACCAAGACCTACTTCCCCCACTTCGACCTGAGCCACGGCTCCGCGCAGGTCAAGGGCCACGGC 180
   ......>>>...))).......................................)))................................. 

    A  K  V  A  A  A  L  T  K  A  V  E  H  L  D  D  L  P  G  A  L  S  E  L  S  D  L  H  A  H  
5' GCGAAGGTGGCCGCCGCGCTGACCAAAGCGGTGGAACACCTGGACGACCTGCCCGGTGCCCTGTCTGAACTGAGTGACCTGCACGCTCAC 270
   ..................)))..................)))......))).........)))......)))......)))......... 

    K  L  R  V  D  P  V  N  F  K  L  L  S  H  S  L  L  V  T  L  A  S  H  L  P  S  D  F  T  P  
5' AAGCTGCGTGTGGACCCGGTCAACTTCAAGCTTCTGAGCCACTCCCTGCTGGTGACCCTGGCCTCCCACCTCCCCAGTGATTTCACCCCC 360
   ...)))...........................))).........))))))......))).............................. 

    A  V  H  A  S  L  D  K  F  L  A  N  V  S  T  V  L  T  S  K  Y  R  *  
5' GCGGTCCACGCCTCCCTGGACAAGTTCTTGGCCAACGTGAGCACCGTGCTGACCTCCAAATACCGTTAA 429
   ...............))).........)))..................)))...............*** 

Annotation key:
>>> : START codon (strict)
))) : START codon (alternative)
*** : STOP

References

• Pamela C Champe, Richard A Harvey and Denise R Ferrier (2005). Lippincott's Illustrated Reviews: Biochemistry (3rd ed.). Lippincott Williams & Wilkins. ISBN 0-7817-2265-9.
• David L. Nelson and Michael M. Cox (2005). Lehninger Principles of Biochemistry (4th ed.). W.H. Freeman. ISBN 0-7167-4339-6.

v • d • e Protein biosynthesis
Biochemical Processes: Amino acid synthesis - tRNA synthesis Molecular Biology Processes: Transcription - Post-transcriptional modification - Translation

v • d • e Eukaryotic) - Kozak consensus sequence