tronvillain

Thalassemia can also be caused by a point mutation in an intron which prevents splicing, which was what I was talking about. As far as I can tell, these proteins are not functional.

[ January 25, 2002: Message edited by: tronvillain ]</p>

Dr Rick

Thalassemias are the result of unbalanced or inadequate production of the alpha or beta globulins that are the protein constituents of hemoglobin. They represent a spectrum of diseases whose clinical expression depends on the specific defect. Most thalassemias do result in functional albeit abnormal hemoglobin molecules. The total lack of alpha globulin is one thalassemia that is not compatible with life due to a non-functional protein, but I was not aware that it is due to a single base pair mutation or deletion in an intron.

Beta-thalassemia can be due to base-pair changes that affect the splicing of the messenger RNA or mutations within invariant dinucleotides at intron–exon junctions, but the resulting abnormal hemoglobin is functional

Which type of hemoglobinopathy are you referring to?

[ January 25, 2002: Message edited by: rbochnermd ]</p>

davidH

Yo rbochnermd.

You said.

"The total lack of alpha globulin is one thalassemia that is not compatible with life due to a non-functional protein, but I was not aware that it is due to a single base pair mutation or deletion in an intron."

If you look back on page 2 (I think) I posted a passage from a biology text book on the fact that it was based on a single base pair mutation a change of bases not a deletion. It goes into good detail on it.

Ok, so I have now been told by theyeti that mutations in an intron won't affect anything.
ok, please provide evidience for this fact! Experiments or anything else that has been carried out.
Because I go by the evidience I have, and everything seems to point to the fact that they are extremely important. The single base change in the haemoglobin, and the post yellow3 put up about that company. So unless you can provide evidience I can't believe you because the evidience that I have got so far points in the other direction.

If anyone knows where yellow3 is then i'd like him/her opinion. From the experiments that that company is doing I think he/she could spread considerable light on this.

tronvillain

I was thinking of a form of beta thalassemia which is caused by a mutation in a 5' donor splice site that prevents an intron from being spliced out. I suppose I may not be recalling the effects proporly, but it being functional seems unlikely.

theyeti

David, if you think that I claimed that mutations in introns wouldn't affect anything, then I've wasted my time with what I wrote. In the vast majority of cases they won't affect anything. I tried to outline which cases would cause effect and which ones wouldn't, and I tried to explain why this is so. One thing is for sure: introns are not necessary to make proteins, though they are capable of screwing them up in some circumstances. This is evidenced by the fact that bacteria have few or no introns, yet they produce protein just fine.

If you want some published studies, I can dig lots of them up for you, but you need to be more specific on what you're interested in. So far, I have claimed nothing that can't be easily found in most molecular biology text books, so I would suggest you look there.

Since when was a second-hand anecdote considered evidence? I too would like Yellow3 to give some more details on this, because it's highly unusual. Molecular biologists make cDNAs (genes with introns removed) all the time, and they work great for making protein. It's a very basic and indispensible tool -- again, check out any molecular biology text. I would suspect that this unverified exception is probably due to experimental error. Or it could be that that particular gene relied on an intron for some unknown reason, but the fact remains that the overwhelming majority don't.

As for the haemoglobin thing, ignoring the tronvillain vs. Dr. Rick squabble , the point here is that the mutation prevents the intron from being removed. This falls under one of the cases that I talked about concerning splicesites -- a mutation in these regions will have an effect, but this does not at all imply that the intron has a function.

Why? It was an anecdote that I doubt he/she could verify. And more importantly, it's wrong to overgeneralize and claim that the peculiarities of one gene can be applied to all genes, especially considering that we have direct evidence that it isn't.

theyeti

[ January 25, 2002: Message edited by: theyeti ]</p>

Dr Rick

The quote was a description of one of the mutations that can cause beta-thallasemia.

lpetrich

You might want to look at some metabolic pathways some time; they've long seemed very Rube Goldberg to me.

I could track down some URL's; I've seen some discussions of metabolic pathways online.

davidH

ok, so is there an enzyme that cuts the intire intron out? ie. Each different intron has a different enzyme to remove it, or is an intron cut in loads of different places by different enzymes and so the whole intron is removed?

tronvillain

It depends on what you mean by "different intron" - the enzymes depend on conserved areas, but the rest of the intron can vary hugely. An intron is not cut in loads of places since the exons have to be connected.

pseudobug

Hey David,

Those are some pretty good questions you are asking. I would also add that theyeti is giving you some pretty good answers.

As to your first qustion, you are close on the enzyme. Actually, the "enzyme" responsible for intron excision consists of a small ribonucleotide complexed with different proteins. These complexes are known as "snurps" or small ribonucleoprotein complexes. The snurps catalyze the formation of a looping of the pre-mRNA (the intron forms a loop), the excision of the intron and the joining of the exons seperated by the intron by a transesterfication of the exon ends to join them together.

This is likely hard to visualize, so here are some links that go into more detail:

<a href="http://zygote.swarthmore.edu/rna2.html" target="_blank">The Biochemsitry of mRNA splicing (Very good, detailed explanation! )</a>

<a href="http://www.dartmouth.edu/~cbbc/courses/bio4/bio4-lectures/EukGenes.html" target="_blank">RNA Splicing</a>

As to your second question, each intron (as in every single intron contained in every pre-mRNA) DOES NOT have a different enzyme catalyzing the excision of the respective intron. That said, there ARE families of snurps (10-12 I think) that work on specific classes of mRNA based upon the sequence in the exon-intron junctions (I may be wrong about the number).

theyeti is right on the money about mostmutations in introns do not have an effect on the subsequent protein product of the processed mRNA. However, mutations can occur in the at the splicesome junction that cause problems resulting in the deletions, frame shifting, etc. I think that it is also possible to have mutations in the INTERIOR of the intron that prevent proper processing/splicing of the pre-mRNA as well.

Here are some examples of this:
<a href="http://molgen-www.uia.ac.be/ADMutations/DataSource/Mutations.cfm?REF=99" target="_blank">Splice junction mutations causing Alzheimer's</a>
<a href="http://srv2.lycoming.edu/~newman/courses/bio22298/disorderpapers/werners/preliminary.html" target="_blank">Werner’s syndrome</a>

I'm sure that there are many more if one were to look, but it is way out of my balliwick.

One of the really cool things about pre-mRNA processing is differential splicing of mRNA transcripts. This is a different topic altogether, but one of the neat things about i is that it allows an organism to sort of "mix and match different proteins. This is way out of my league, but plays a big role in the immune response.