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A ribosome binding site, or ribosomal binding site (RBS), is a sequence of nucleotides upstream of the start codon of an mRNA transcript that is responsible for the ...
The ribosome catalyzes ester-amide exchange, transferring the C-terminus of a nascent peptide from a tRNA to the amine of an amino acid. These processes are able to occur due to sites within the ribosome in which these molecules can bind, formed by the rRNA stem-loops. A ribosome has three of these binding sites called the A, P and E sites:
The ribosome contains three RNA binding sites, designated A, P, and E. The A-site binds an aminoacyl-tRNA or termination release factors; [ 50 ] [ 51 ] the P-site binds a peptidyl-tRNA (a tRNA bound to the poly-peptide chain); and the E-site (exit) binds a free tRNA.
Cross-linking immunoprecipitation (CLIP) methods are used to stringently identify direct RNA binding sites of RNA-binding proteins in a variety of tissues and organisms. In this section, three classes of the most widely studied RNA-binding domains (RNA-recognition motif, double-stranded RNA-binding motif, zinc-finger motif) will be discussed.
The ribosome facilitates decoding by inducing the binding of complementary transfer RNA (tRNA) anticodon sequences to mRNA codons. The tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is "read" by the ribosome. Translation proceeds in three phases:
The ribosome has three binding sites for tRNA molecules that span the space between the two ribosomal subunits: the A (aminoacyl), [24] P (peptidyl), and E (exit) sites. In addition, the ribosome has two other sites for tRNA binding that are used during mRNA decoding or during the initiation of protein synthesis.
The ribosome can localize to the start site by direct binding, initiation factors, and/or ITAFs (IRES trans-acting factors) bypassing the need to scan the entire 5' UTR. This method of translation is important in conditions that require the translation of specific mRNAs during cellular stress, when overall translation is reduced.
In these hybrid states of binding, acceptor and anti-codon ends of tRNA are in different sites (A, P and E). Using chemical probing methods, a set of phylogenetically conserved bases in ribosomal RNA where the tRNA binds has been examined, and is suggested to be directly involved in the binding of tRNA to the prokaryotic ribosome. [6]
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