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DNA and protein synthesis: Peptide folding - Fastbleep
The other approach is to introduce backbone protecting groups which will prevent the formation of hydrogen bonds. Such protection is made by the introduction of the Hmb group on the αnitrogen . It has been shown that the presence of a Hmb unit every 6-7 residues is sufficient to disrupt the peptide aggregation . The Hmb protected amino acid is introduced under the form of N,O-bis-Fmoc-N-(2hydroxy-4-methoxybenzyl) derivative, the O-Fmoc protection being cleaved during the following piperidine treatment. At the end of the synthesis the Hmb group is cleaved in the final TFA cleavage.
For example, polypeptides (proteins) result from the linking of amino acids by peptide bonds and polysaccharides result from the linking of sugars by glycosidic bonds.
A covalent bond formed between amino acids during protein synthesis.
As mentioned above, the generation and disappearance of Fmoc based chromophors allows the monitoring of the synthesis. Furthermore, samples may be taken to determine the load of Fmoc peptide. The completion of the deprotection reaction may be checked by cleaving samples and analyzing the obtained peptide.
The 30S subunit consists of one molecule of 16S rRNA, and 20 different proteins of various sizes. This unit is responsible for formation of the initiation complex, performs the decoding of the genetic information, and controls the fidelity of codon-anticodon interactions. The large subunit consists of 2 RNA molcules: 23S and 5S rRNA, and 34 proteins. This subunit catalyzes the reactions of peptide bond formation and peptide release. It also provides the path for the nascent polypeptide chain through a tunnel.
Peptide Sequencing and Synthesis
Which amino acid that is going to be incorporated into the growing peptide chain is determined by the codon (a triplet of bases) on the mRNA (fig 2). Many amino acids have several codon options, so each amino acid can be incorporated by a set of different codons. For example, the amino acid lysine has two codons and serine has 6 different codons. Codons for the same amino acid tend to have the same nucleotides for the two first positions and only differ in the third position. Only two amino acids, tryptophan and methionine, have one single codon. The codon for methionine is also a start signal for protein synthesis. There are also several stop codons, which are used as a signal when the protein message is ending. These are decoded not by a tRNA but by a protein called release factor.
The polypeptide chain is transferred from the P-site tRNA to the free amino group of the amino acid attached to the A-site tRNA, forming a new peptide bond. This reaction is catalysed by the peptidyl transferase center of the large ribosomal subunit. This reaction is followed by a series of large conformational changes, which shift the two tRNAs into the P and E sites of the large subunit, so the tRNA which previously was in the A-site is now in the P-site and the E-site is bound with the former tRNA of the P-site. Through large conformational changes catalysed by the protein EF-G, the mRNA moves by three nucleotides with respect to the the small ribosomal subunit together with the tRNAs so that the ribosome is ready to enter the next round and accept a new tRNA. These three steps are repeted in a so-called until the ribosome reaches a stop codon, where synthesis is stopped and the protein chain is released. Procaryotic ribosomes are remarkably efficient: within a bacterial cell, one ribosome can add 20 amino acids to a growing polypeptide chain every second.
The ribosome is helped both at the start and end of translation by specialized proteins called initiation factors and release factors, respectively.
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Protein Synthesis -Translation and Regulation
Peptide aldehydes are a common feature of enzyme inhibitors, for example HIV protease inhibitors, or caspase inhibitors (see diagram). Peptide aldehydes are also used in chemoselective ligation, for example in the production of peptide dendrimers. They are also used in the formation of reduced peptide bonds (pseudo peptide bond peptidomimetics).
Translation is the RNA directed synthesis of polypeptides
Cyclic peptides can be produced by forming a disulphide bond between two cysteine residues, or by head-to-tail or side chain cyclisation, forming an amide bond. Using special protecting groups, it is possible to cyclise between two specific cysteines in a peptide, thus it is possible to have more than one disulphide in a peptide.
This process requires all three classes of RNA
We have great expertise in the synthesis of peptides containing N-methyl amino acids. The methyl group replaces a H-bond donor, so is useful for destabilising secondary structure and peptide aggregation.
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