theyeti

There is what's known as the spliceosome that cuts spliceosomal introns out. The splicosome is a protein/RNA complex -- it's actually the RNA that has the catalytic activity. The same spliceosome that cuts out one intron will cut them all out. If you needed a separate splicosome for each one, then it would be impossible, because each gene that codes for part of the spliceosome would need several spliceosomes itself, and so on to infinity.

And to answer your second question, no, it does not get cut at lots of places. There are very short conserved sequences on the ends that are recognized by the spliceosome, and the rest appears to be "junk". On the 5' end of the intron, only the first 6 base pairs are conserved, and only the first two of those are the invariant GU. On the 3' end, the last 3 bases are conserved, with the last two the invariant AG. There is also a pyrimidine rich region on the 3' end of about 15bp just upstream, and another 5 conserved bases just 5' of that, with only one, the "branch point", an invariant A. So at most, there are about 30 conserved bases with only 5 of them invariant and yet the intron can be hundreds of bases long.

Now this is important: not all introns require a spliceosome to be removed. Both group I and group II introns are self-splicing. What they do is they fold into a secondary structure such that their own RNA is able to catalyse their removal. Now group I introns are rare and non-homologous to the others, so I won't go into them. But group II introns form a secondary structure that is higly similar to that of the spliceosome, and their catalytic mechanisms are identical. There is strong evidence that the snRNAs that make up the spliceosome are directly descended from group II introns.

And other than that, there is evidence that group II introns are descended from retrotransposons. In fact, group II introns ocassionaly retrotranspose themselves. And if they happen to insert into a coding sequence, it's okay, because they remove themselves after transcription!

theyeti

davidH

Thanks for the answers, it helps clear a few things up.
Sorry I haven't replied for ages - I was off sick.

ok, so except in a rare case the mutation in an intron will wreck everything.

So you believe that only mutations in an exon would bring about the changes you believe to have happned in evolution - yeah, because the exon is the DNA that would have have to have been altered for this to happen.

How much of a percentage of the DNA is made up of introns? (any examples will do).

Another question here,
What type of mutations must have occurred and what were they caused by?

Cause in my reading so far I have come across the following:

I also read the following.

"Deletion - leads to an absence of certain genes, infact all but the shortest deletions are usually fatal.

Inverson - chromosome breaks and middle piece turns around, this often disrupts gene regulation but very occasionally the resulting change may benefit the organism.

Duplication - is frequently harmful."

Then finally this;

"It is characteristic of mutations that they are comparatively rare, at least from the perspective of a particular gene. In most organisms the mutation rate at any given locus varies between 1 and 30 mutations per million gametes. The exact number is veriable since genes at different loci have different mutation rates. Low mutation rates bears witness to the tremendous accuracy with which DNA replicates."

So if mutations are extremely rare, and the mutations that are useful are even rarer doesn't that make the odds vast? Especially if the introns are a large percentage of the DNA.

I'd like your views on this.

Thanks.

scigirl

NO!!!!! It's the other way around. Most mutations in an intron will go unnoticed. Remember, the introns are the non-coding parts of the DNA!

Yes there are cases where a mutation in the intron messes up the gene. Such as the cases we have been discussing. These are RARE!

Actually, I think gene duplication provides a huge source for evolution. And introns have NOTHING to do with gene duplication. Read my second to last post to Douglas <a href="http://iidb.org/cgi-bin/ultimatebb.cgi?ubb=get_topic&f=8&t=000008" target="_blank">here</a> (look for the pictures I drew of chromosomes) to explain this phenomenon. Keep in mind--duplication allows for one gene to mutate (as long as the other one stays the same). Harmful mutations to the duplicated gene will do nothing. Beneficial mutations however allow the organism to have two different gene products that could potentially give them a new function (such as a new form of hemoglobin).

Good question. We do not know the exact answer yet. Obtaining the raw sequence of DNA does not automatically tell you where the introns are, or even where the genes are. You have to compare the cDNA libraries back to the genomic sequence, which can be a long, painstaking process.

I'll try to find a reference later. I know I learned about this in my Functional Genomics class last year, but my notes are at work right now. I do remember though, that the appearance of introns did correlate with evolutionary theory.

Occurred to cause evolution you mean? Read my post to douglas-I outline several.

If you allow say only, 6000 years, then you are correct. There wasn't enough time for a large amount of mutations to accumulate.

If you allow for millions of years (like mainstream science does), and if you are familiar with gene duplication and other phenomenon you have not mentioned, than yes, we have had enough time for the mutations to accumulate.

Introns are not a large percentage of the DNA. Genes themselves (which include introns) only account for about 1% of our entire genome.

scigirl

DNAunion

DNAunion: Natural selection does not remove bases from DNA. “Chance” does. Natural selection can only retain the change (if it proves beneficial), NS cannot create it.

DNAunion: Not usually: a frameshift's effects are typically limited to the gene it occurred in (assuming the loss of a base pair occurred in a gene sequence). The number of triplets affected would depend upon where along the gene’s length the loss of a base occurred.

DNAunion: That depends. If the frameshift mutation affects a “regulatory gene” – such as one that codes for a transcription factor – it could have far-reaching consequences. For example, in prokaryotes, if a frameshift mutation occurs in a repressor gene (and sufficiently alters the conformation of the protein that the gene encodes so that it no longer binds to the operator), then a whole operon - a whole series of related genes - could be affected.

DNAunion: The way I took the original question it didn’t really deal with a shot-in-the-dark mutation: one that occurred at a randomly selected base pair. It dealt with a mutation that occurred anywhere along the strand. Basically, anywhere the person asking the question felt like making it occur. I assume he meant in a gene.

DNAunion

DNAunion: No there aren’t. DNA replication creates a copy of all DNA: DNA polymerases do not exclude introns (they don’t even know what they are).

You INDIRECTLY say this in a minute (by saying that you are talking about RNA and not DNA), but DavidH just told you that he is not all that familiar with this stuff. Your answering “[Yes] there are” to his question about DNA replication is misleading. Are you trying to confuse him, or help him?

DNAunion: I assume in relation to the enzyme that “turns RNA into DNA” you are referring to reverse transcriptase. That enzyme is not “the” enzyme used in PCR for amplification (that would be Taq polymerase, or some similar DNA polymerase).

[ February 02, 2002: Message edited by: DNAunion ]</p>

DNAunion

DNAunion: Actually, there was just a post made about a week ago at ARN that gave a link to an article that mentioned increased interest in intronic RNA. The focuse of the articlw was that very small RNAs with no previously known function have been found to play regulatory roles in the cell. Here is a quote from the article that pertains to introns.

scigirl

Ahh, yes. I guess I just assumed he meant RNA. Sorry if I contributed to the confusion!

Yes, we are not talking about DNA replication, but gene expression. When an RNA is made, it is copied from the DNA, then later modified by enzymes (intron splicing, etc). When DNA is replicated, nothing is spliced out.

Ever heard of RT-PCR? Please explain to me how Taq can amplify RNA.

scigirl

Edited to add:
I went and re-read my post to DavidH, and I had stated here: "Scientists...take advantage of these enzymes to "engineer" DNA. For instance, the weird viral enzyme that turns RNA into DNA (like in HIV) is used in a proceedure called PCR to study gene expression. "
I was not claiming that RT is the ONLY enzyme used in PCR, I said it was a tool to study gene expression. I am well aware of the different types of enzymes.

Furthermore, I find your comment, "are you trying to confuse David" rather insulting. A "you screwed up here scigirl" would have been sufficient, without assuming my motives.

I spend a lot of time here trying to explain complex concepts to people who have no or little understanding of biology, so naturally I will not sound as eloquent or detailed as the Lodish textbook. Anyone here who actually knows me will realize my motivations here are anything but trying to confuse people.

scigirl

[ February 02, 2002: Message edited by: scigirl ]</p>

excreationist

In case no-one has offered a link this good, here's a good link:
<a href="http://www.ultranet.com/~jkimball/BiologyPages/G/GenomeSizes.html" target="_blank">Genome Sizes</a>
It talks about the exact number of base pairs and genes of many viruses and life-forms.
Some species have a lot more DNA than we do (e.g. amphibians have about 30 times as much) but this is mostly repetitive DNA.

DNAunion

DNAunion: Please point out to me where I stated that Taq can amplify RNA.

scigirl

You didn't. And equally, I did not state that RT was "the" enzyme in PCR.

I do not wish to get into a silly "you said this I said that" pissing contest with you, so hopefully this post will clear this issue up. The point is--You and I both know enough about how PCR works. I brought up PCR to illustrate how molecular biologists use a naturally occuring enzyme to study biology. That post was not meant to be a thesis on the details of PCR.

This thread was started by DavidH, and many of us have been attempting to educate him about very complex genetic concepts. So far, I think we have been successful.

If you read the threads that led up to my reply you critiqued, you will see we had been talking about introns, and how they work. So I just (unfortunately) made an assumption about what he meant by "dna replication" and I made an error. I stand corrected.

scigirl