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Revision as of 12:37, 24 February 2012
Translation is the third stage of protein synthesis and proceeds in four phases: activation, initiation, elongation and termination. Activation occurs when an amino acid is covalently bonded to a tRNA.  Initiation follows when the ribosome binds to the 5' end of mRNA. This allows translation to build a particular protein. This process is halted once a stop codon (UAA, UAG, or UGA) is reached because no tRNA can bind to these codons. What does recognize this codon is a "release factor" protein that disassembles the ribosome/mRNA complex.
An illustration of this process is shown as follows:
Shown above is a ribosome translating a protein that is secreted into the endoplasmic reticulum. tRNAs are colored dark blue.
Bacterial Ribosome Binding Sites
A ribosome binding site (RBS) is a region 6-7 nucleotides upstream of the start codon AUG in prokaryotes called the Shine-Dalgarno sequence (5′–GGAGGU–3′). The ribosome will base pair with this site through its own rRNA as well at the start codon using tRNA. What makes this an interesting topic of research is the fact that the Shine-Dalgarno sequence is not the "optimal" RBS for all expression processes. In other words, a RBS affects the rate at which a particular Open Reading Frame (ORF) is translated. There are two general ways in which this happens: i) the rate at which ribosomes are recruited to the mRNA and initiate translation is dependent on the sequence of the RBS and ii) the RBS can also affect the stability of the mRNA, thereby affecting the number of proteins made over the lifetime of the mRNA.
RBS Sequence Design
The first variable to be taken into account should be the sequence of the RBS itself, specifically to what degree the RBS is complementary to the free end of the 16s rRNA. If this hybridization is highly favorable, then the time needed to complete the initiation phase will be reduced allowing elongation to proceed. Obviously the start codon AUG must be upstream of the RBS and needs to lie 6-7 nt. The reason for such a specific distance is due to the geometry of the ribosome and where it attaches itself to the mRNA. Not only is the exact sequence of the RBS important, but the overall sequence of the mRNA will affect translation rates. Secondary structure in mRNA has been shown to affect translation rates  due to competitive binding of the RBS by the ribosome as well as other nucleotides in the mRNA. Many attempts have been made to computationally predict the best sequence to minimize secondary structure in DNA/RNA. CircDesigNA is one such tool .
Genetic code is defined by a sequence of three nucleotides, called codons. These codons can serve three functions. 1) The start codon, AUG is used to initiate translation 2) Specific codons stop translation by not coding for anything 3) They serve as a template to allow the binding of amino acids to form a protein. Crick and Brenner et al. were the first to show that codons existed and that they coded for specific amino acids. [3, 4, 5]
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Initiation of protein synthesis in bacteria.
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Overview of high-level translation initiation.