Translation (biology)

Translation is the second stage of protein biosynthesis (part of the overall process of gene expression). Translation occurs in the cytoplasm where the ribosomes are located. Ribosomes are made of a small and large subunit which surrounds the mRNA. In translation, messenger RNA (mRNA) is decoded to produce a specific polypeptide according to the rules specified by the genetic code. This uses an mRNA sequence as a template to guide the synthesis of a chain of amino acids that form a protein. Translation is necessarily preceded by transcription. Translation proceeds in four phases: activation, initiation, elongation and termination (all describing the growth of the amino acid chain, or polypeptide that is the product of translation).

In activation, the correct amino acid (AA) is joined to the correct transfer RNA (tRNA). While this is not technically a step in translation, it is required for translation to proceed. The AA is joined by its carboxyl group to the 3' OH of the tRNA by an ester bond. When the tRNA has an amino acid linked to it, it is termed "charged". Initiation involves the small subunit of the ribosome binding to 5' end of mRNA with the help of initiation factors (IF), other proteins that assist the process. Elongation occurs when the next aminoacyl-tRNA (charged tRNA) in line binds to the ribosome along with GTP and an elongation factor. Termination of the polypeptide happens when the A site of the ribosome faces a stop codon (UAA, UAG, or UGA). When this happens, no tRNA can recognize it, but releasing factor can recognize nonsense codons and causes the release of the polypeptide chain. The capacity of disabling or inhibiting translation in protein biosynthesis is used by antibiotics such as: anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, puromycin etc.

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Basic mechanisms

See main articles at prokaryotic translation and eukaryotic translation

The mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. The ribonucleotides are "read" by translational machinery in a sequence of nucleotide triplets called codons. Each of those triplets codes for a specific amino acid.

The ribosome and tRNA molecules translate this code to produce proteins. The ribosome is a multisubunit structure containing 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.

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific 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 base pairing to specific 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 Genetic code to translate the above into a structural formula as used in chemistry.

This will give you the primary structure of the protein. However, proteins tend to fold, depending in part on hydrophilic and hydrophobic segments along the chain. Secondary structure can often still be guessed at, but the proper 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 amino acids such as 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.