Are charged tRNAs being sorted entering the ribosome?

[SStell]

Can someone shed some light on how charged tRNAs being escorted into the ribosome by EF-Tu are sorted out if in fact they are?

 

Do all 20+ types just go in haphazardly and fit or not fit the mRNA template or are they some how selected for entrance.

 

Is there some type of ribosomal conformation change that only let's in certain types depending on the code being needed?

 

It seems to be somewhat inefficient to have to go through numerous tries for each and every amino acid installation.

 

If it is completely random this could go through way more than just 20 tries for each correct one.

If you have a 20 sided dice and you need a '3'. How many times can you throw it without getting that 3, it could be scores and scores could it not?

 

Is there some type of sorting based on the class of the tRNA synthetases that were involved?

 

Just really curious about the whole thing.

[BabcockHall]

The process of choosing the correct codon/anticodon pair proceeds by two steps. The first step is recognition, and some non cognate tRNA molecules are rejected at this point. Then Ef-Tu hydrolyzes GTP, and additional non cognate tRNAs are rejected at this proofreading step. The process is called kinetic proofreading.

[SStell]

Babcock, do the first and second steps happen inside the ribosome?

Again I think that this would be an extremely inefficient way of doing things but if that is how it works- then that is how it works.

It would on average go through 20 incorrect attempts before getting the right one.

Life seems to have overcome inefficiencies quite often and I just find it hard that this most important activity would rely on pure chance and cause a bottleneck every time.

[BabcockHall]

Yes, they happen at the ribosome. I don't see why there would necessarily be twenty attempts. I don't look upon it any differently than I look upon an enzyme's choosing the correct substrate. In this case the enzyme is the ribosome and the substrate is the aminoacyl tRNA.

[SStell]

The twenty attempts is because there are at least 20 distinct types of tRNAs and only one is of any use at that particular time.

If there are a few hundred or thousand tRNAs swarming about the entrance to the ribosome all being imported into it with the EF-Tu but only one out of every twenty has the proper anticodon then on average there would be about 20 wrong ones.

There could be a hundred wrong ones.

I am just having a difficult time seeing that as a reasonable system.

I was thinking there might be some conformational change in the ribosome that only allows certain tRNA in at a particular time.

For example, if the mRNA codes for ATG then maybe only tRNAs with a T for the first anticodon letter would be allowed in, thus reducing the number of wrong attempts from an average of 20 down to an average of five.

Or even only allowing tRNAs in that have a purine as the first letter or just a pyrimidine, thus cutting the chances down to 1 in 10. Many species have more than 20 types of tRNAs ( I think ), some with a lot more due to there being 62 possible codon possibilities.

I am just barking up trees to see if there is anything in them. Thanks.

 

I agree that the ribosome is an enzyme but it is a very big complex one.

It has some sort of channel that everything must travel down and to have only a 1 in 20 chance seems to be inefficient to me.

But like I said, if that is how it works then there ya go.

[BabcockHall]

Protein synthesis appears to be a compromise between speed and fidelity. There is at least one ribosomal mutation that makes the process slower but more accurate.

EDT

My comment about substrates in a previous message might mislead the unwary. All enzymes can reject a incorrect (non cognate) substrate via dissociation, but only a few enzymes proofread, and kinetic proofreading is a subset of all proofreading mechanisms.

Edited October 19, 2015 by BabcockHall

[CharonY]

Note that tRNA abundance is quit diverse. Together with codon bias the false pairing rate is much lower for common and lower for rare pairings. This, btw. is another way to control protein synthesis rates.

[SStell]

Am I completely confused on this one in twenty crap shoot?

 

I opened a new topic on the percent abundances of tRNA codes etc and any information on this is helpful to me.