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In the production of a protein molecule, there have to be a ready supply of free-floating amino acids. When a given codon for adjoining, say, serine comes up, how are the serine molecules found out of a soup of 20 different types of amino acids?

For example, 

Meleagris gallopavo (turkey) small muscular protein
NCBI Reference Sequence: XP_010724014.1  88aa GI: 733873411

 1 mskqpashvk aiqaninipm gafrpgaghp hkrkevtpee veesvpatee ekdkkhlpga
61 iklpgpavnl seiqniksel kfvpkaeq

has 9 alanines, 1 aspartate, 11 glutamates, 2 phenylalanines, 5 glycines, 4 histidines, 6 isoleucines, 11 lysines, 4 leucines, 2 methionines, 4 asparagines, 10 prolines, 4 glutamines, 2 arginines, 5 serines, 2 threonines, 6 valines, 0 tryptophans, 0 cysteines, 0 tyrosines.

So the cell would deplete glutamates much faster than aspartates and obviously infinitely faster than tryptophans. So, as the concentration of glutamates drops drastically with the production of each new turkey muscle polypeptide strand, getting diluted by the nonreactants tryptophan, cysteine, tyrosine, wouldn't the reaction rate get exponentially slow?

And when the last available glutamate residue gets attached, and if it happens before the polypeptide is complete, yet it needs one more glutamate to complete the chain, what signals the ribosome to "stop looking for more glutamates"?

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  • $\begingroup$ Under normal conditions, it will not run out. Glutamate can be synthesized by the cell, so as long as there is a nitrogen and a carbon source, you can make it. Also the cell is degrading proteins all the time and those amino acids get recycled by the cell. $\endgroup$
    – AMR
    Commented Oct 8, 2015 at 5:18

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When cells run out of amino acids, more and more of their tRNAs remain uncharged. This elevated ratio of uncharged/charged tRNAs trigger complex signalling pathways that control amino acid biosynthesis, general reduction of translation, halting ribosome biosynthesis, autophagy (includes ribophagy - digestion of ribosomes) to recycle cells' components, etc. This can be clubbed into general amino acid control (GAAC) and involves the super important regulatory kinase protein called as Target of Rapamycin (TOR) and other transcription factors. The regulation of amino acids level is one of the most basic and important features of cellular metabolism and can be found conserved from yeast to humans. In addition to GAAC, there can be pathways for some specific amino acids as well.

There is not shortage of scientific literature. To start with you can read following article:

http://www.cell.com/trends/cell-biology/abstract/S0962-8924(14)00036-1 http://jcb.rupress.org/content/206/2/173.full

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For the most part, there is no signal to a ribosome to "stop looking for more glutamates". If there is a shortage of a needed amino acid that prevents a ribosome from continuing elongation of a polypeptide, the ribosome simply waits for the needed tRNA-amino acid complex to become available.

The main effect of a lack of amino acids for protein synthesis is to cause inhibition of new initiations of translation of mRNAs into proteins. This form of translational regulation occurs when a protein called GCN2 senses the lack of an essential amino acid, which causes it to disable the initiation factor needed for a ribosome to start translating a new mRNA strand.

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  • $\begingroup$ And what about the No-Go decay mechanism? $\endgroup$
    – ktyagi
    Commented Aug 2, 2017 at 15:49

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