This article is part of the series on: Gene expression a Molecular biology topic (portal) (Glossary)

Introduction to Genetics

General flow: DNA > RNA > Protein

special transfers (RNA > RNA, RNA > DNA, Protein > Protein)

Genetic code

Transcription

Transcription (Transcription factors, RNA Polymerase,promoter) Prokaryotic / Archaeal / Eukaryotic

post-transcriptional modification (hnRNA,Splicing)

Translation

Translation (Ribosome,tRNA) Prokaryotic / Archaeal / Eukaryotic

post-translational modification (functional groups, peptides, structural changes)

gene regulation

epigenetic regulation (Genomic imprinting)

transcriptional regulation

post-transcriptional regulation (sequestration, alternative splicing,miRNA)

translational regulation

post-translational regulation (reversible,irreversible)

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Translation is the first stage of protein biosynthesis (part of the overall process of gene expression). Translation is the production of proteins by decoding mRNA produced in transcription. 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. 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 covalently bonded to the correct 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 releasing factor can recognize nonsense codons and causes the release of the polypeptide chain. The 5' end of the mRNA gives rise to the protein's N-terminus, and the direction of translation can therefore be stated as N->C.

A number of antibiotics act by inhibiting translation; these include anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, and puromycin, among others. Prokaryotic ribosomes have a different structure from that of eukaryotic ribosomes, and thus antibiotics can specifically target bacterial infections without any detriment to a eukaryotic host's cells.

[edit] Basic mechanisms

See articles at prokaryotic translation and eukaryotic translation

Diagram showing the translation of mRNA and the synthesis of proteins by a ribosome

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 a specific sequence of amino acids. 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^{[citation needed]}. The rate of translation varies; it is significantly higher in prokaryotic cells (up to 17-21 amino acid residues per second) than in eukaryotic cells (up to 6-7 amino acid residues per second) ^[1]

[edit] Genetic code

Whereas other aspects such as the 3D structure, called tertiary structure, of protein can only be predicted using sophisticated algorithms, the amino acid sequence, called primary structure, can be determined solely from the nucleic acid sequence with the aid of a translation table.

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).

There are many computer programs capable of translating a DNA/RNA sequence into a protein sequence. 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 CTG 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 

[edit] 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 

[edit] Software examples

• ApE (Mac, Windows, Unix)
• Serial Cloner ( A DNA editing and manipulating software for MacOS and Windows)
• DNA Strider (Mac)
• ExPASy Translate Tool (webserver)
• Virtual Ribosome (webserver, cross-platform command-line)
• DNA to protein translation (webserver, 13 genomic codes or custom ones)

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 

[edit] See also

• Expanded genetic code
• Protein methods

[edit] References

• Champe, Pamela C; Harvey, Richard A; Ferrier, Denise R (2004). Lippincott's Illustrated Reviews: Biochemistry (3rd ed.). Hagerstwon, MD: Lippincott Williams & Wilkins. ISBN 0-7817-2265-9. 
• Cox, Michael; Nelson, David R.; Lehninger, Albert L (2005). Lehninger principles of biochemistry (4th ed.). San Francisco: W.H. Freeman. ISBN 0-7167-4339-6.