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biosynthesis or chemical transformations?
Chemical transformations I think. Basically curly arrows and the transformation of electrons between atoms.
so you're using coupling reagents like DCC and NHS? I can help you figure out the mechanism, i just need to know what reagents you're using.
I'm not sure what the catalysts/conditions are, just the fact that several amino acids bond to form a polypeptide because of the attraction between the lone pair on nitrogen of one, and the slightly positive carbon atom on the other.
hmm okay, so this (attached) is the mechanism. I assumed this was biosynthesis (i.e. done by a ribosome, so i used tRNA to hold the amino acid, but you can replace it with another leaving group like NHS http://en.wikipedia.org/wiki/N-Hydroxysuccinimide) you can also show the last step (proton transfer) by the negative O on the tRNA taking the proton from the \(-NH^+_2-\).
How does the tRNA come in? I noticed in the diagram that it's drawn attached to one of the amino acids, but I'm slightly confused on where it came from and how it catalyzes the reaction
we'll the catalysis would occur via the ribosome tRNA are mediator molecules for amino acids are to be recognized. i can redraw it using other reagents but i thought this would be less complicated.
I understand that part, just not why the tRNA is already bonded to the amino acid :/
because that's how amino acids are brought to a ribosome during translation (you know, anticodon-codon recognition?).
Oh, we haven't learned that yet but I think I can work with the diagram. thanks!
no problem, i hope thats sufficient. If you have doubts or want the mechanism with the other reagents, just ask.