dadamowiki

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Genomics

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Description

A process by which the sequence of nucleotides in a messenger RNA molecule directs the incorporation of amino acids into a protein.

Translation is the second process of protein biosynthesis (part of the overall process of gene expression). In translation, messenger RNA 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 three phases: initiation, elongation and termination (all describing the growth of the amino acid chain, or polypeptide that is the product of translation). The capacity of disabling or inhibiting translation in protein biosynthesis is used by antibiotics such as: anisomycin, cycloheximide, chloramphenicol and tetracycline.

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 protein. 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 tRNA's carry are then used to assemble a protein.

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 can not 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.

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.

[[Eukaryote|Eukaryotic]] translation

In [eukaryote? eukaryote]s, 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.

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 [eukaryote? eukaryote]s 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).

The cap-independent initiation

The best studied example of the cap-independent mode of translation initiation in [eukaryote? eukaryote]s 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.

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.

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.

Attribution

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