Translation (biology)
262401
225844144
2008-07-15T17:41:10Z
Intropy
7481155
Cross link of 'nonsense codons' to 'Stop_codon'
{{MolBioGeneExp}}
'''Translation''' is the first stage of [[protein biosynthesis]] (part of the overall process of [[gene expression]]). Translation occurs in the [[cytoplasm]] where the [[ribosome]]s are located. Ribosomes are made of a small and large subunit which surrounds the mRNA. In translation, [[mRNA|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 acid]]s that form a protein. Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, and small nuclear RNA are not necessarily translated into an amino acid sequence. 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). Amino acids are brought to ribosomes and assembled into proteins.
In activation, the correct amino acid is [[Covalent_bond| covalently bonded]] to the correct [[tRNA| transfer RNA (tRNA)]]. While this is not technically a step in translation, it is required for translation to proceed. The amino acid 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). 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 a [[release factor|releasing factor]] can recognize [[Stop_codon| nonsense codons]] and causes the release of the polypeptide chain. The capacity of disabling or inhibiting translation in protein biosynthesis is used by [[antibiotic]]s such as: [[anisomycin]], [[cycloheximide]], [[chloramphenicol]], [[tetracycline]], [[streptomycin]], [[erythromycin]], [[puromycin]] etc.
==Basic mechanisms==
:''See main articles at [[prokaryotic translation]] and [[eukaryotic translation]]''
The [[mRNA]] carries [[genetic code|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 a specific sequence of amino acids. The ribosome is a multisubunit structure containing [[Ribosomal RNA|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 [[tRNA]]s 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 pair]]ing to specific [[transfer RNA|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 4''n''-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 template DNA base to its RNA complement (note that the complement of A is now U), as shown below. Note that the template strand of the DNA is the one the RNA is polymerized against; the other DNA strand would be the same as the RNA, but with thymine instead of uracil.
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 [[Genetic_code#RNA_codon_table|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, [[protein folding|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 acid]]s 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 [[bioinformatics|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 [http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c 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 [http://www.ncbi.nlm.nih.gov/Taxonomy/ 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===
* [http://www.biology.utah.edu/jorgensen/wayned/ape/ ApE] (Mac, Windows, Unix)
* [[DNA Strider]] (Mac)
* [http://www.expasy.org/tools/dna.html ExPASy Translate Tool] (webserver)
* [http://www.cbs.dtu.dk/services/VirtualRibosome/ Virtual Ribosome] (webserver, cross-platform command-line)
* [http://insilico.ehu.es/translate/ DNA to protein translation] (webserver, 13 genomic codes or custom ones)
Example of computational translation - notice the indication of (alternative) start-codons:
<PRE>
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
</PRE>
==References==
<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.
{{protein biosynthesis}}
{{GeneticTranslation}}
[[Category:Molecular biology]]
[[Category:Protein biosynthesis]]
[[Category:Gene expression]]
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