Protein biosynthesis

Protein biosynthesis (synthesis) is the process in which cells build proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription which are then used for translation. Protein biosynthesis, although very similar, differs between prokaryotes and eukaryotes.

Amino acid synthesis
Amino acids are the monomers which are polymerized to produce proteins. Amino acid synthesis is the set of biochemical processes (metabolic pathways) which build the amino acids from carbon sources like glucose. Not all amino acids may be synthesised by every organism, for example adult humans have to obtain 9 of the 20 amino acids from their diet.

The amino acids are then loaded onto tRNA trains for use in the process of journeying forth to the world beyond.

Transcription
Transcription is the process by which an mRNA template, encoding the sequence of the protein in the form of a trinucleotide code, is transcribed from the genome to provide a template for translation. Transcription copies the template from one strand of the DNA double helix, called the template strand.

Transcription can be divided into 3 stages: Initiation, Elongation and Termination, each regulated by a large number of proteins such as transcription factors and coactivators that ensure the correct gene is transcribed in response to appropriate signals.

The DNA strand is read in the 3' to 5' direction and the mRNA is transcribed in the 5' to 3' direction by the RNA polymerase.

Translation
Protein translation involves the transfer of information from the mRNA into a peptide, composed of amino acids. This process is mediated by the ribosome, with the adaptation of the RNA sequence into amino acids mediated by transfer RNA. Numerous initiation and elongation factors also play a role.

Translation requires a lot of energy, with the hydrolysis of approximately 4 NTP → NDP per amino acid added. (This includes the aminoacylation of the tRNA. Thus, gene expression is highly regulated to ensure that only proteins that are required are translated.

Translation involves 3 processes: initiation, elongation, and termination.

Initiation in prokaryotes
The initiation of protein translation involves the assembly of the ribosome and addition of the first amino acid, methionine.
 * 1) The 30S ribosomal subunit attaches to the mRNA, mediated by IF-1 and IF-3 (initiation factors). The 30S ribosome brings with it the P and A site, but the A site is blocked by IF-1 to prevent binding of tRNA.  It aligns to the Shine-Dalgarno sequence, which positions the first codon (AUG) in the P site.
 * 2) Next, the specific aminoacyl-tRNA for N-formylmethionine (F-Met) is brought into the P site by IF-2. The anticodon of this tRNA will bind to the AUG codon on the mRNA.  Note: this is the only tRNA brought into the P site; all successive aminoacyl-tRNAs will be brought to the A site for peptide elongation.
 * 3) The 50S ribosomal subunit is then brought in to complete the ribosome, and with it, IF-1, IF-2, and IF-3 come off the complex. The A and P site are completed, and the 50S subunit also brings the E (exit) site.zz

Initiation in eukaryotes
The initiation of protein translation in eukaryotes is similar to that of prokaryotes with some modifications.
 * 1) A complex of proteins will connect the 5'cap and 3'PolyA tail, and this complex will recruit the ribosome subunits.
 * 2) There is no Shine-Dalgarno sequence in eukaryotes. Instead, the ribosome scans along the mRNA for the first methionine codon.  Similarly, there is no N-formylmethionine in eukaryotic cells.Also it involves most Mamalian cells than other types of the order in the Animal kingdom.

Elongation
Elongation of protein biosynthesis is fairly similar between prokaryotes and eukaryotes. The following is a description of elongation in prokaryotes.
 * 1) Elongation proceeds after initiation with the binding of an aminoacyl-tRNA to the A site, which is the next codon in the mRNA. The aminoacyl-tRNA is brought to the ribosome through a series of interactions with EF-Tu (an elongation factor).  This step involves the hydrolysis of GTP: EF-Tu-GTP → EF-Tu-GDP  (The hydrolyzed GDP is switched for GTP through another series of reactions with EF-Ts.)
 * 2) The next aminoacyl-tRNA binds to the codon, and the C-terminus of the F-Met undergoes nucleophilic attack by the N-terminus of the second amino acid. The F-Met is now connected to the second amino acid through a peptide bond.
 * 3) The first tRNA (for F-Met) is now uncharged. The entire ribosome complex moves along the mRNA through the action of another elongation factor (EF-G) and the hydrolysis of GTP → GDP.
 * 4) The first tRNA is now in the E site and comes off from the ribosome, while the second tRNA, with the nascent peptide chain, is in the P site. Step 1-4 will repeat as successive amino acids are added.

Termination
Termination of protein biosynthesis occurs when the ribosome comes across a stop codon, for which there is no tRNA. At this point, protein biosynthesis halts and one of three release factors will bind to the stop codon. (Note: In eukaryotes, there is only one release factor that will bind to all three stop codons.) This induces a nucleophilic attack of the C-terminus of the nascent peptide by water - this hydrolysis releases the peptide from the ribosome. The ribosome, release factor, and uncharged tRNA then dissociate and translation is complete.

Events following protein translation
The events following biosynthesis include post-translational modification and protein folding. During and after synthesis, polypeptide chains often fold to assume, so called, native secondary and tertiary structures. This is known as protein folding.

Many proteins undergo post-translational modification. This may include the formation of disulfide bridges or attachment of any of a number of biochemical functional groups, such as acetate, phosphate, various lipids and carbohydrates. Enzymes may also remove one or more amino acids from the leading (amino) end of the polypeptide chain, leaving a protein consisting of two polypeptide chains connected by disulfide bonds.