RNA: Questions About Nirenberg, Introns & mRNA

[STAii]

Greetings.
I have a few questions about RNA.

1-In Nirenberg's experiment (building a protein from mRNA made only of U-U-U-U-U ...), how was the protein actually built if it didn't start with AUG (the starting Codon). If the codon AUG is not neccesary for starting the building of a protein, can you please explain how the building starts otherwise ?.

2-During mRNA processing, how are the introns identified ?

3-Why are the introns there from the first place ? If they are not translated to any protein, what is their usage ?
If they have no usage, is it possible that (with time, and evolution) that the introns will go from the original DNA molecule ?

4-As far as i understand, the DNA is transcripted to mRNA, which is then translated to a protein, how does the cell know when it should transceipt a certain part of DNA to mRNA and went it shouldn't (iow, when the protein that the mRNA builds is not needed).

5-Are mRNA molecules re-used after building the protein molecule (iow, if the mRNA stays in the cytoplasm, will it be re-translated .. and re-translted ... and re-translated .. ?).

Thanks in advance (that's all .. for now ).

 

[iansmith]

Originally posted by STAii
Greetings.
I have a few questions about RNA.

1-In Nirenberg's experiment (building a protein from mRNA made only of U-U-U-U-U ...), how was the protein actually built if it didn't start with AUG (the starting Codon). If the codon AUG is not neccesary for starting the building of a protein, can you please explain how the building starts otherwise ?.

Can you point out where you got nirenberg's experirement. I don't know what you are takling about?

Originally posted by STAii
2-During mRNA processing, how are the introns identified ?

introns have a specific sequences at the 5' end, which is the donor, and at the 3' end, which is the acceptor. It goes like this
Exon-5'CG/AGGUA/GAGU---Intron-----T/CNAHN3'-Exon--
________Donor site______________Acceptor site

Originally posted by STAii
3-Why are the introns there from the first place ? If they are not translated to any protein, what is their usage ?
If they have no usage, is it possible that (with time, and evolution) that the introns will go from the original DNA molecule ?

Nobody knows why introns are there but it is observed that there is alternative splicing sites. There could be a different 5' end, 3' end or a different internal structure.

For example, Calcitonin has 2 polyadenylation signals which are tissue specific. In the thyroid the 1st signal will be used whereas in the brain the 2nd signal is used. The exon at 3' end is different.

Originally posted by STAii
4-As far as i understand, the DNA is transcripted to mRNA, which is then translated to a protein, how does the cell know when it should transceipt a certain part of DNA to mRNA and went it shouldn't (iow, when the protein that the mRNA builds is not needed).

There is region upstream of the gene that is called the regulator region. These region control the expression of the DNA. Regulation of the DNA is complex. There can be DNA-protein, DNA-DNA and DNA-RNA interaction that control the expression. For example, some protein are produce only in specific tissues and these protein have a role in promoting tissue specific gene and these gene are can only be express when the protein is present.

Originally posted by STAii
5-Are mRNA molecules re-used after building the protein molecule (iow, if the mRNA stays in the cytoplasm, will it be re-translated .. and re-translted ... and re-translated .. ?).

You are rigth, mRNA is recylce until it is degraded and many ribosomes (translation untis) can bind to the same mRNA strand.

 

[STAii]

Ok, i will come back to questions 2-5. But for now, let me talk about 1.
It is weird that you don't know this experiment.

Marshall W. Nirenberg (b. 1927) is an American biochemist who shared the 1968 Nobel Prize in Physiology or Medicine for his work on deciphering the genetic code.

His experiment is also known as the "Poly-U" experiment.
Mainly, what he did is that he made an RNA molecule made only of Uracil units.
He then got 20 tubes, and put different kinds of Amino acids into the 20 tubes (and also he put Ribosomes, and Enzymes, and other stuff). He put one molecule of this Poly-U RNA into each tube.
He waited, then came back, and found that only one tube had protein made in it (the one with the amino acid phenylalanine).
Anyway, the point is that the protein was made although the RNA did not start with AUG (the starting codon).

 

[Monique]

Well, although AUG is a predominant initiator codon, there are other possibilities such as GUG or CUG. You say the molecule was only composed of Us? This was a eukaryotic or prokaryotic system? Maybe there were impurities? I haven't heard of the experiment before either :S

You might be interested in going through the following tutorial, it is quite nice!
http://www.lsic.ucla.edu/ls3/tutorials/

 

[STAii]

Ok, i am browsing it.
In the meanwhile, you might browse this link too :) http://profiles.nlm.nih.gov/JJ/

 

[iansmith]

I have look at the paper publish by Nirenberg (http://profiles.nlm.nih.gov/JJ/B/B/D/K/_/jjbbdk.pdf). From what I read, it appears that they did not used all the ribosome sub-unit, they only used the 30S fraction or they added a lot 30S rRNA. I think that the start codon was not required because of the condition used during the experiement.

 

[STAii]

Ok, for Q1, i got what i need (not only AUG is a starting codon).
Now, the other questions.
Q2

introns have a specific sequences

good till now

at the 5' end, which is the donor, and at the 3' end, which is the acceptor. It goes like this
Exon-5'CG/AGGUA/GAGU---Intron-----T/CNAHN3'-Exon--
________Donor site______________Acceptor site

You lost me ..

Q5

You are rigth, mRNA is recylce until it is degraded and many ribosomes (translation untis) can bind to the same mRNA strand.

So suppose that the cell does not need a certain protein anymore (or has enough of it after some time), the ribosomes will still build from that protein?

 

[iansmith]

For question 2 i gave you the sequence that is recognize as being the start and end of an intron. So the 5' end of the intron is start and the 3' end is the end. when the intron is cut out the 5' end will be donate to the 3' end which will accept it in order to connect the two exons

Originally posted by STAii

So suppose that the cell does not need a certain protein anymore (or has enough of it after some time), the ribosomes will still build from that protein?

Yeah the cell keeps on build the protein until there is no more mRNA but mRNA is very unsatble so it degraded rapidly.

 

[Monique]

Does this help?
http://www.blc.arizona.edu/marty/411/Modules/Weaver/Chap14/Fig.1432.jpg

let me find a better picture..

 

[Monique]

Basically, small nuclear ribonucleoprotein particles, snRNPs recognize signals (that Ian gave) at the intron/exon boundaries. These snRNPs cause conformational change of the RNA and cleavage.

Four different sites have been found:
5'splice site
3'splice site
branchpoint (in the middle)
polypyrimidine track (after the branchpoint)