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A Science Odyssey: You Try It: DNA Workshop Activity
N2 - A better understanding of the origin and organization of genetic codons is possible based on the metabolic relatedness of amino acids. Amino acids with similar codons (anticodons) usually have the same or similar precursor molecule, even if the amino acids are not related physico-chemically. These observations suggest, that amino acid precursor molecules and enzymes responsible for the synthesis of amino acids "must have seen" the protein synthesis machinery, and played a fundamental role in the codon (anticodon) organization.
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nucleic acids & protein synthesis notes b1 - Biology Junction
We use IR spectroscopy to characterize nSH3 variants labeled with CN or N3 at five different positions. Like carbon-deuterium (C-D) bonds, CN and N3 can provide information about their surrounding protein environment, but unlike C-D, they tend to be perturbative and thus should be used with caution.
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is read in the following way: for the 1st and 2nd base-pairs the wobble-pairs provide uniqueness in the way that U on tRNA always emerges from A on mRNA, A on tRNA always emerges from U on mRNA, etc. For the 3rd base-pair the genetic code is redundant in the way that U on tRNA can emerge from A or G on mRNA, G on tRNA can emerge from U or C on mRNA and I on tRNA can emerge from U, C or A on mRNA. Only A and C at the 3rd place on tRNA are unambiguously assigned to U and G at the 3rd place on mRNA, respectively.
Due to this combination structure a tRNA can bind to different mRNA codons where synonymous or redundant mRNA codons differ at the 3rd base (i.e. at the 5' end of tRNA and the 3' end of mRNA). By this logic the minimum number of tRNA anticodons necessary to encode all amino acids reduces to 31 (excluding the 2 STOP codons AUU and ACU, see ). This means that any tRNA anticodon can be encoded by one or more different mRNA codons (). However, there are more than 31 tRNA anticodons possible for the translation of all 64 mRNA codons. For example, serine has a fourfold degenerate site at the 3rd position (UCU, UCC, UCA, UCG), which can be translated by AGI (for UCU, UCC and UCA) and AGC on tRNA (for UCG) but also by AGG and AGU. This means, in turn, that any mRNA codon can also be translated by one or more tRNA anticodons (see ).
The reason for the occurrence of different wobble-pairs encoding the same amino acid may be due to a compromise between velocity and safety in protein synthesis. The redundancy of mRNA codons exist to prevent mistakes in transcription caused by mutations or variations at the 3rd position but also at other positions. For example, the first position of the leucine codons (UCA, UCC, CCU, CCC, CCA, CCG) is a twofold degenerate site, while the second position is unambiguous (not redundant). Another example is serine with mRNA codons UCA, UCG, UCC, UCU, AGU, AGC. Of course, serine is also twofold degenerate at the first position and fourfold degenerate at the third position, but it is twofold degenerate at the second position in addition. shows the assignment of mRNA codons to any possible tRNA anticodon in eukaryotes for the 20 standard amino acids involved in translation. It is the reverse codon assignment.
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translation: the RNA-directed synthesis of a polypeptide
tRNA: interprets message (codons) along an mRNA molecule and transfers amino acids from the cytoplasm's amino acid pool to a ribosome
anticodon: a nucleotide triplet that base-pairs with a complementary codon on mRNA
wobble: the relaxation of base-pairing rules that allows for the pairing between the 3rd base of a codon and the corresponding base of a tRNA anticodon to not be as strict- more than one codon can code for a specific amino acid
aminoacyl-tRNA synthetase: enzyme that joins each amino acid to the correct tRNA
rRNA: RNA molecules that help construct ribosomal subunits
P-site: holds the tRNA carrying the growing polypeptide chain
A-site: holds the tRNA carrying the next amino acid to be added to the chain
E-site: discharged tRNA's leave the ribosome through this exit site
initiation: brings together mRNA, a tRNA bearing the first amino acid of the polypeptide, and the two subunits of a ribosome
elongation: stage of translation where amino acids are added one by one to the preceding amino acid
termination:final stage of translation that includes elongation continuing until a stop codon in the mRNA reaches the A site of the ribosome
polyribosomes: help a cell make many copies of a polypeptide very quickly
signal peptide: targets the protein to the ER
signal-recognition particle: recognizes the signal peptides of polypeptides targeted to the ER Ribosomes
important factors in the coupling of tRNA anticodons with mRNA codons during protein synthesis
consist of two subunits constructed of mainly rRNA
the ribosome becomes functional when mRNA attaches to the large and small subunits
there are 3 binding sites for tRNA ( P, A, and the E site) and a binding site for mRNA
rRNA is particularly important in protein synthesis because it carries out the ribosomes function and it is the catalyst for peptide bond formation and relationship of subunits to the A and P sites Initiation 1.
Translation (biology) - Wikipedia
Initiation is complete once the initiator tRNA moves to the P site and the A site is open for the next tRNA molecule Elongation purpose is to make the polypeptide chain longer and elongation factors (proteins) are needed
Three steps: CODON RECOGNITION, PEPTIDE BOND FORMATION, AND TRANSLOCATION Codon recognition Hydrogen bonds attach the mRNA codon in the A site to an incoming tRNA anticodon carrying the correct amino acid.
Genetic Code and Amino Acid Translation
Inside every cell, ribosomes read mRNA sequences and hook together protein building blocks called amino acids in the order specified by the code: Groups of three nucleotides in mRNA code for each of 20 amino acids.