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). An overview of protein synthesis. ... Gene expression, or simply expression, is the process by which the inheritable information which comprises a gene, such as the DNA sequence, is made manifest as a physical and biologically functional gene product, such as protein or RNA. Several steps in the gene expression process may be modulated, including the... Organelles. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... The interaction of mRNA in a eukaryote cell. ... Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ... For a non-technical introduction to the topic, see Introduction to Genetics. ... This article is about the class of chemicals. ... A micrograph of ongoing gene transcription of ribosomal RNA illustrating the growing primary transcripts. ... Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ...

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. Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... The release factor is a protein that recognises the termination codon or stop codon in a mRNA sequence. ... Staphylococcus aureus - Antibiotics test plate. ... Anisomycin is an antibiotic produced by Streptomyces griseolus which can arrest gene expression by inhibiting protein synthesis. ... Cycloheximide (IUPAC designation 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione) is an inhibitor of protein biosynthesis in eukaryotic organisms, produced by the bacterium Streptomyces griseus. ... Chloramphenicol is a bacteriostatic antibiotic originally derived from the bacterium Streptomyces venezuelae, isolated by David Gottlieb, and introduced into clinical practice in 1949. ... Tetracycline (INN) (IPA: ) is a broad-spectrum antibiotic produced by the streptomyces bacterium, indicated for use against many bacterial infections. ... Streptomycin is an antibiotic drug, the first of a class of drugs called aminoglycosides to be discovered, and was the first antibiotic remedy for tuberculosis. ... Erythromycin is a macrolide antibiotic which has an antimicrobial spectrum similar to or slightly wider than that of penicillin, and is often used for people who have an allergy to penicillins. ... Puromycin is an antibiotic that is a potent inhibitor of translation. ...

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. Translation is the process in cells by which messenger RNA is read by a ribosome, and by utilising tRNA a protein is built according to the genetic code of the mRNA. This varies between prokaryotic and eukaryotic cells. ... The process of initiation of translation in eukaryotes. ... The interaction of mRNA in a eukaryote cell. ... For a non-technical introduction to the topic, see Introduction to Genetics. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... This article is about the class of chemicals. ...

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. Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Ribosomal RNA (rRNA), a type of RNA synthesized in the nucleolus by RNA Pol I, is the central component of the ribosome, the protein manufacturing machinery of all living cells. ...

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. This article is about the class of chemicals. ...

Aminoacyl tRNA synthetase (an enzyme) catalyzes the bonding between specific tRNAs and the amino acids that their anticodons sequences call for. An aminoacyl tRNA synthetase (abbreviated aaRs) is an enzyme that catalyzes the binding of a specific amino acid to a tRNA to form an aminoacyl-tRNA. The synthetase hydrolyzes ATP to bind the appropriate amino acid to the 3 hydroxyl of the tRNA molecule. ... Ribbon diagram of the enzyme TIM, surrounded by the space-filling model of the protein. ... Transfer RNA (abbreviated tRNA) is a small RNA chain (74-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ... In chemistry, an amino acid is any molecule that contains both amino and carboxylic acid functional groups. ...

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. Base pairs, of a DNA molecule. ... Transfer RNA Transfer RNA (abbreviated tRNA), first hypothesized by Francis Crick, is a small RNA chain (73-93 nucleotides) that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. ...

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.

It is also the process whereby ribosomes use the sequence of codons in mRNA to produce a polypeptide with a particular sequence of amino acids.

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. For a non-technical introduction to the topic, see Introduction to Genetics. ... The structural formula of a chemical compound is a graphical representation of the molecular structure showing how the atoms are arranged. ...

This will give you the primary structure of the protein. However, proteins tend to fold, depending in part on hydrophilic and hydrophobic segments alóng the chain. Secondary structure can often still be guessed at, but the proper tertiary structure is often very hard to determine. A protein primary structure is a chain of amino acids. ... Protein folding is the process by which a protein assumes its characteristic functional shape or tertiary structure, also known as the native state. ... The adjective hydrophilic describes something that likes water (from Greek hydros = water; philos = friend). ... In chemistry, hydrophobic or lipophilic species, or hydrophobes, tend to be electrically neutral and nonpolar, and thus prefer other neutral and nonpolar solvents or molecular environments. ... A representation of the 3D structure of the Myoglobin protein. ... In biochemistry, the tertiary structure of a protein is its overall shape. ...

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 protien, which is coded for by a conventional stop codon in combination with a downstream hairpin (SElenoCysteine Insertion Sequence, or SECIS). This article is about the class of chemicals. ... Skeletal formula of L-selenocysteine Space-filling model of L-selenocysteine Selenocysteine is an amino acid that is present in several enzymes (for example glutathione peroxidases, tetraiodothyronine 5 deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases and some hydrogenases). ...

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. Map of the human X chromosome (from the NCBI website). ... Methionine is an α-amino acid with the chemical formula HO2CCH(NH2)CH2CH2SCH3. ... Leucine is one of the 20 most common amino acids and coded for by DNA. It is isomeric with isoleucine. ...

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: Kingdoms Eukaryotes are organisms with complex cells, in which the genetic material is organized into membrane-bound nuclei. ... Typical divisions Ascomycota (sac fungi) Saccharomycotina (true yeasts) Taphrinomycotina Schizosaccharomycetes (fission yeasts) Basidiomycota (club fungi) Urediniomycetes Sporidiales Yeasts are a growth form of eukaryotic microorganisms classified in the kingdom Fungi, with approximately 1,500 species described. ... The GenBank sequence database is an annotated collection of all publicly available nucleotide sequences and their protein translations. ...

 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 

... Typical divisions Ascomycota (sac fungi) Saccharomycotina (true yeasts) Taphrinomycotina Schizosaccharomycetes (fission yeasts) Basidiomycota (club fungi) Urediniomycetes Sporidiales Yeasts are a growth form of eukaryotic microorganisms classified in the kingdom Fungi, with approximately 1,500 species described. ... This article is about the fungi known as molds. ... Protozoa (in Greek protos = first and zoon = animal) are single-celled creatures with nuclei that show some characteristics usually associated with animals, most notably mobility and heterotrophy. ... Classes Anthozoa - Corals and sea anemones Cubozoa - Sea wasps or box jellyfish Hydrozoa - Hydroids, hydra-like animals Scyphozoa - Jellyfish Cnidaria is a phylum containing some 10,000 species of relatively simple animals found exclusively in aquatic environments (most species are marine). ... Species M. genitalium M. hominis M. pneumoniae etc. ... To meet Wikipedias quality standards and make it more accessible, this article may require cleanup. ... Invertebrate is an English word that describes any animal without a spinal column. ... Classes Karyorelictea Heterotrichea Spirotrichea Litostomatea Phyllopharyngea Nassophorea Colpodea Prostomatea Oligohymenophorea Plagiopylea See text for subclasses. ... Hole in the Head Disease, commmonly known as HITH, is a fish disease that affects most cichlids. ... Classes Subphylum Homalozoa Gill & Caster, 1960 Class Homostelea Class Homoiostelea Class Stylophora Gill & Caster, 1960 Class Ctenocystoidea Robison & Sprinkle, 1969 Subphylum Crinozoa Class Eocrinoidea Jaekel, 1899 Class Paracrinoidea Regnéll, 1945 Class Cystoidea von Buch, 1846 Class Blastoidea Class Crinoidea Subphylum Asterozoa Class Ophiuroidea Class Asteroidea Subphylum Echinozoa Helicoplacoidea †  ?Arkarua... Classes Monogenea Trematoda Cestoda Turbellaria Wikimedia Commons has media related to: Platyhelminthes Wikispecies has information related to: Platyhelminthes The flatworms (Phylum Platyhelminthes from the Greek platy, meaning flat and helminth, meaning worm) are a phylum of relatively simple soft-bodied invertebrate animals. ... Plant cells with visible chloroplasts. ... Orders Aplousobranchia Enterogona Phlebobranchia Pleurogona Stolidobranchia Ascidiacea (commonly known as the ascidians) is an order in the Urochordata subphylum of sac-like marine filter feeders. ... Blepharisma is a genus of heterotrich ciliates (a type of protista) which contains many species. ... Orders not necessarily a complete list Azygiida Echinostomida Opisthorchiida Plagiorchiida Strigeata Strigeatida Trematodes are also known as flukes. ...

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.