Translation is the second process of protein biosynthesis (part of the overall process of gene expression). In translation, Messenger RNA (mRNA) is decoded to produce a specific polypeptide according to the rules specified by the genetic code. Translation is necessarily preceded by transcription. Similarly to 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). activation - Involves the joining of the correct amino acid to the correct tRNA, The AA is joined by its carboxyl group to the 3' OH by an ester bond. initiation - Small subunit of ribosome binds to 5' end of mRNA with the help of initiation factors (IF). Elongation - Next AA in line will form complex with elongation factor and GTP. Termination - When A site faces a nonsense codons (UAA, UAG, UGA) no tRNA can recognize it, but releasing factor can recognize nonsense codon 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 and tetracycline. An overview of protein synthesis. ... Gene expression, also called protein expression or often simply expression is the process by which a genes DNA sequence is converted into the structures and functions of a cell. ... 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. ... RNA codons. ... Transcription is the process through which a DNA sequence is enzymatically copied by an RNA polymerase to produce a complementary RNA. Or, in other words, the transfer of genetic information from DNA into RNA. In the case of protein-encoding DNA, transcription is the beginning of the process that ultimately... Peptides are the family of molecules formed from the linking, in a defined order, of various amino acids. ... An antibiotic is a drug that kills or slows the growth of bacteria. ... 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 (or 2,2-dichlor-N-[(aR,bR)-b-hydroxy-a-hydroxymethyl-4-nitrophenethyl]acetamide) is an antibiotic that was derived from the bacterium Streptomyces venezuelae and is now produced synthetically. ... Tetracycline is a broad-spectrum antibiotic produced by the streptomyces bacterium, indicated for use against many bacterial infections. ...

Basic mechanisms

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 interaction of mRNA in a eukaryote cell. ... RNA codons. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... A non-coding RNA (ncRNA) is any RNA molecule that functions without being translated into a protein. ... An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... 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. TIM is catalytically perfect, meaning its conversion rate is limited, or nearly limited to its substrate diffusion rate. ... 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. ... Headline text this website sucks your mothers dickIn molecular biology, two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair (often abbreviated bp). ... 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. ...

Prokaryotic translation

Main Article: Prokaryotic translation 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. ...

Prokaryotes have no nucleus, so mRNA can be translated while it is still being transcribed. The translation is said to be polyribosomal when there is more than one active ribosome. In this case, the collection of ribosomes working at the same time is referred to as a 'polysome'.

Initiation

Initiation of translation involves the small ribosomal subunit binding to the 'start' codon on the mRNA, which indicates where the mRNA starts coding for the protein. This codon is most commonly an AUG, but alternative start codons are common in prokaryotes. In bacteria, the protein starts instead with the modified amino acid N-formylmethionine (f-Met). In f-Met, the amino group has been blocked by a formyl group to form an amide, so this amino group cannot form a peptide bond. This is not a problem because the f-Met is at the amino terminus of the protein. In prokaryotes the binding of the small subunit to the correct place on the mRNA is facilitated by base pairing to a series of bases known as the Shine-Dalgarno sequence, located about 7 nucleotides before the start site. Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Domain Archaea - Archaebacteria Bacteria - Eubacteria Prokaryotes (from Old Greek pro- before + karyon nut or kernel, referring to the cell nucleus, + suffix -otos, pl. ... Phyla/Divisions Actinobacteria Aquificae Bacteroidetes/Chlorobi Chlamydiae/Verrucomicrobia Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Deinococcus-Thermus Dictyoglomi Fibrobacteres/Acidobacteria Firmicutes Fusobacteria Gemmatimonadetes Nitrospirae Omnibacteria Planctomycetes Proteobacteria Spirochaetes Thermodesulfobacteria Thermomicrobia Thermotogae Bacteria (singular, bacterium) are a major group of living organisms. ... N-Formylmethionine is an amino acid found in all living cells. ... In chemistry, especially in organic chemistry and biochemistry, an amino group is an ammonia-like functional group. ... Amide functional group In chemistry, an amide is one of two kinds of compound. ... The Shine-Dalgarno Sequence (AGGAGGU) is the signal for initiation of protein biosynthesis in bacterial mRNA. It is located 5 of the first coding AUG, and consists primarily, but not exclusively, of purines. ...

Elongation

The large 50S subunit forms a complex with the small 30S subunit, and elongation proceeds. Firstly, the Met-tRNAi enters the P-site of the ribosome and base-pairs with the AUG codon. Then another aminoacylated tRNA enters the A site of the ribosome and base pairs with the mRNA. Correct base pairing between mRNA codon and the tRNA anti-codon results in accommodation of the tRNA. Ribosome catalyzed peptidyl transfer joins the two adjacent amino acids by a newly formed peptide bond; the amino acid on the P site leaves its tRNA and joins the mRNA at the A site. Finally translocation occurs; shifting the peptidyl tRNA into the P-site leaving the A-site empty for a newly incoming tRNA.

Termination

This procedure repeats until the ribosome encounters one of three possible stop codons, where translation is terminated. This stalls protein growth, and release factors, proteins which mimic tRNA, enter the A site and release the protein into the cytoplasm.

Recycling

Once the nascent protein is released in termination, Ribosome Recycling Factor and Elongation Factor G (EF-G) function to release the mRNA from ribosomes. This "recycles" the ribosomes for additional rounds of translation. Ribosome Recycling Factor (RRF) is a protein found in bacterial cells as well as eukaryotic organelles, specifically mitochondria and chloroplasts. ...

Eukaryotic translation

Main Article: Eukaryotic translation 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. ...

In eukaryotes, transcription occurs in the nucleus, then the mRNA moves to the cytoplasm for the translation to occur. The mRNA is spliced with 5' cap and 3' poly-A-tail and then transported. Initiation is described well below, elongation and termination proceed similarly to that in prokaryotes. In cell biology, the nucleus (from Latin nucleus or nuculeus, kernel) is found in all eukaryotic cells and contains the nuclear genes which form most of the cells genetic material. ... Cytoplasm is like jelly-like material that fills cells. ... In genetics, splicing is a modification of genetic information after transcription, in which introns are removed and exons are joined. ...

Initiation

The cap-dependent initiation

Initiation of translation involves an interaction of some proteins with a special tag bound to 5'-end of the mRNA molecules. The protein factors bind the small ribosomal subunit. The subunit accompanied by some of those protein factors moves along the mRNA chain towards its 3'-end and scans for the 'start' codon (mostly AUG) on the mRNA, which indicates where the mRNA starts coding for the protein. The sequence downstream between the 'start' and 'stop' codons is then translated by the ribosome into the aminoacid sequence -- thus a protein is synthesized. In eukaryotes and archaea, the amino acid encoded by the start codon is methionine. The initiator tRNA charged with Met forms part of the ribosomal complex and thus all proteins start with this amino acid (unless it is cleaved away by a protease in some subsequent steps). Figure 1: Ribosome structure indicating small subunit (A) and large subunit (B). ... Kingdoms Animalia - Animals Fungi Plantae - Plants Protista A eukaryote is an organism with a complex cell or cells, in which the genetic material is organized into a membrane-bound nucleus or nuclei. ... Phyla / Classes Phylum Crenarchaeota Phylum Euryarchaeota     Halobacteria     Methanobacteria     Methanococci     Methanopyri     Archaeoglobi     Thermoplasmata     Thermococci Phylum Korarchaeota Phylum Nanoarchaeota Archaea (; from Greek αρχαία, old ones; singular Archaeum, Archaean, or Archaeon), also called Archaebacteria (), is a major division of living organisms. ... An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... Methionine (Met, M. C5H11NO2S) is an essential nonpolar amino acid, and a lipotropic. ...

The cap-independent initiation

The best studied example of the cap-independent mode of translation initiation in eukaryotes is the Internal Ribosome Entry Site IRES approach. What differentiates cap-independent translation from cap-dependent translation is that cap-independent translation does not require the ribosome to start scanning from the 5' end of the mRNA cap until the start codon. The ribosome can be trafficked to the start site by ITAFs (IRES trans-acting factors) bypassing the need to scan from the 5' end of the untranslated region of the mRNA. This method of translation has been recently discovered, and has found to be important in conditions that require the translation of specific mRNAs, despite cellular stress or the inability to translate most mRNAs. Examples include factors responding to apoptosis, stress-induced responses. IRES (Internal Ribosome Entry Site) were first discovered in +RNA viruses in 1986 in the labs of Sonenberg and Wimmer. ...

Translation by hand

It is also possible to translate either by hand (for short sequences) or by computer (after first programming one appropriately), 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 T 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 Amino acid to translate the above into a structural formula as used in chemistry. An amino acid residue is what is left of an amino acid once a molecule of water has been lost (an H+ from the nitrogenous side and an OH- from the carboxylic side) in the formation of a peptide bond. ... Many chemical compounds, especially hydrocarbons, can exist in different geometric configurations. ...

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, though chemical simulations currently are able to guess right about 70% of the time^{[citation needed]}. A protein primary structure is a chain of amino acids. ... Protein folding is the process by which a protein structure assumes its functional shape or conformation. ... 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. ...

External Links

• Translation of DNA to an Amino Acid Sequence Web Page to translate a DNA Sequence to a Protein
• Translation Termination Review Excellent Translation Termination Review.