Lecture 7:  09-01-06


Amino Acids (continued)


Methionine, (Met), M:


      Methionine is one of the sulfur containing amino acids other than cysteine.


      It has a large aliphatic side chain, which has a thioether.


The methyl group of methionine:

      In general the methyl group is a highly inert group.


      This inert behavior is due to the tetrahedral carbon, which has its octet complete making.


      Thus it needs to be activated in order to react with other compounds.


      The sulfur bonded to the methyl group in methionine activates the methyl group.


Why is methionine essential?

Methylation of proteins (post-translational modifications of proteins), DNA and other biological molecules is an essential modification, which serves as a means to alter the susceptibility of proteins and DNA to various reactions, which in turn induces or suppresses various pathways downstream.


Reactions that involve methionine:

      Methionine is one of the common methyl group donors in the cell.





Let us begin with understanding how methionine gets this special status to be the initiator of protein synthesis.  We all know that protein synthesis comprises of following steps:



There are special RNAs called tRNAs (transfer RNAs) that carry an amino acid as a cargo on its head.

      tRNAs act as an adaptor molecule by carrying amino acids.


      There are 20 different tRNAs to carry 20 different amino acids.


      So, there are 64 codons, out of which 1 is a start codon and 3 are stop codons.


      Start codon- AUG and Stop codons- UAA, UGA and UAG.



What does a tRNA do?

      A tRNA reads the codon, which is a triplet code.


      It carries amino acids on its amino acid attachment site.


      It locates and binds the protein synthesis machinery called ribosome.


      Then they bind the codons on the mRNA that are specific for each amino acid.


      tRNA also carries the growing polypeptide chain.


Wait a second! How methionine is connected with protein synthesis and tRNA?

The answer is that methionine is the starting amino acid in a protein chain and the codon for methionine is AUG, which is the start codon.

The above figure shows how an mRNA looks like with a start codon and a stop codon.


      By convention the right hand side is the 5 side and left side is the 3 side.


      The protein synthesis starts at AUG and ends at UAA.


      UAA is the most common stop codon and there are no tRNAs that bind to it.


How does a tRNA carrying a methionine know where to start?


      The accuracy of translation depends on the Watson and crick base pairing.


      The ribosome is made up of large and small protein subunits and a type of RNA called ribosomal RNA (rRNA).


      The 3 end of rRNA hangs free which is complimentary to the region upstream of AUG of mRNA.


      This region is called the Shine-Dalgarno sequence in prokaryotes.


      The small subunit of ribosome binds first and then followed by the large subunit forming a tunnel and then the special Methionyl- tRNA binds to the ribosome.


      The growing polypeptide chain escapes the ribosome through this tunnel during protein synthesis.


The figure below depicts the steps in protein synthesis:



      The methionine when it is attached to the initiator methionine tRNA, can be formylated.  A second Methionine tRNA that cannot be formylated inserts methionine in internal positions in growing polypeptides.


      The formylation of the methinoine blocks the amino group of the methionine and prevents it from any reaction on the amino side and allows it to bind only to the P-site.



      Subsequently the second amino acyl-tRNA enters at the A site and the peptide bond is formed between the two amino acids.


How does this process take place in Eukaryotes? What are the contrasting features in the initiation of protein synthesis?


      In eukaryotes the methinoine is not formylated and the initiating amino acid is methionine and not formyl-methionine.


      In eukaryotes the mRNA forms a hairpin loop like structure with itself by base pairing, whereas in prokaryotes the second strand comes from the ribosomal RNA.


      This loop is formed upstream of the start codon AUG.


      In eukaryotes the initiator tRNA itself is mutated and so binds only to the P-site and thus there is no need for it to be formylated.


      After initiation of protein synthesis, the methionine is cleaved off by an enzyme, since it is not present in the mature polypeptide.


      But if a protein sequence has a methionine as the first amino acid, then the mRNA would have two AUG codons and the first methionine is cleaved prior to release of the mature protein from the ribosome complex.