| From: Di | 3/01/00
1:51:23 |
| Subject: DNA | post id:
22969 |
| I am a little confused by the
term "junk DNA". What is it's purpose? It has to have one doesn't it? | |
| From: Dr. Ed G (Avatar) | 3/01/00
1:58:28 |
| Subject: re: DNA | post id:
22973 |
| I don't believe there is a clear
cut or unequivocal explanation for it, but given that most of our DNA is
actually junk DNA it is fairly reasonable to expect some
explanation. One explanation that I tend to like is that it represents a backload/backup of genetic variation. Much of it represents previously (in evolutionary history) active genes which have simply been turned off. Perhaps it is more likely that useful new traits can be formed through the random reactivation of old genes than in the random mutation of new ones. | |
| From: Dr. Ed G (Avatar) | 3/01/00
2:21:56 |
| Subject: re: DNA | post id:
22982 |
| Hmmm... now I don't remember...
we haven't total excluded the chance that it has some active chemical
effect, though I suspect this is unlikely given I don't believe its ever
been observed to result in messenger RNA (so it cannot have any effect on
the production of proteins). Dr. Paul is possibly the one to answer this
one I suspect. | |
| From: Chris W (Avatar) | 3/01/00
9:54:56 |
| Subject: re: DNA | post id:
23001 |
| I've always wondered what
delineates a gene amongst many other in a continuous strand of
DNA. | |
| From: Stephen Bosi | 3/01/00
10:43:16 |
| Subject: re: DNA | post id:
23012 |
| Crudely speaking a single gene is
a unit of genetic material responsible for a single protein. In the simplest view, the beginning of the gene is marked by a kind of "capital letter" sequence adenine-thymine-guanine (or ATG which can also code for the amino acid methionine). Another sequence that can act as a capital letter is guanine-thymine-guanine (or GTG which can also code for the amino acid valine). The "full-stop" sequences are TAA, TAG and TGA. The situation is a little more complex in reality. The term "operon" refers to the complete unit of the genome which codes for the protein plus all the extra regulatory machinery built into the gene which controls the rate at which the gene is transcribed into protein. A single operon is probably a more precise idea than a single "gene". The word "gene" is actually very old and no-one had a very clear idea of what it was when the idea was first coined. | |
| From: Rapunzel | 4/01/00
12:37:01 |
| Subject: re: DNA | post id:
23259 |
Eukaryotic DNA strands contain structural genes which code for polypeptide products, as well as regulatory sequences, sequences which code for tRNA and rRNA, and "spacer" regions between genes. Most eukaryotic genes themselves have coding regions (exons) separated by "nonsense" regions (introns, also called intervening sequences). As translation of DNA into RNA is sequential, the initial RNA read out from the DNA, called pre-mRNA, is littered with intron "nonsense" sequences which have to be enzymatically removed. Then the exon-coded sections have to be spliced together in the correct sequence to produce the mature, functional mRNA which can exit the nucleus and direct the translation process in the ribosomes. The length of introns ranges from 60 to 100 000 nucleotides, and as a single gene can have 50 introns, most genes are much larger than would be expected from the size of their polypeptide products. The role of introns is still unclear. It may be that introns are just "garbage" sequences, devoid of any function and in effect genetic parasites; but it has also been postulated that intron-exon sequences may have a role in controlling the flow of information from nucleus to cytoplasm and in controlling cellular differentiation. Eukaryotes do not appear to possess operons or comparable mechanisms which have been described for prokaryotes (i.e. bacteria), and the transcription and translation processes take place in different regions of the cell (the nucleus and cytoplasm respectively). In prokaryotes, the transcription-translation process is intimately coupled; both take place in the cytoplasm as there is no nucleus; and this makes gene control technically simpler for them than is the case in eukaryotes. In the case of eukaryotes, therefore, the question of gene regulation is more complex, and as yet more poorly understood. Besides the possible role of intron-exon sequences, gene regulation in eukaryotes may also involve alkaline nuclear proteins called histones, alternative forms of DNA, e.g. left-coiling DNA (Z-DNA), hormone-mediated transcription activators, repressor substances, and other mechanisms. The fact that many introns are near-copies of the neighbouring exons has led to evolutionary proposals. For example, introns may serve as the raw material from which new functional genes may evolve, or from which genes lost by mutation may have a chance of being recovered. Prokaryotic (i.e. bacterial) DNA is not studded with introns. It has actually been suggested that the genetic organisation involved in eukaryotes represents an ancestral organisation from which present-day prokaryotes have evolved. This is a debatable hypothesis as common thinking has the eukaryotes evolving from the prokaryotes, but it is an interesting hypothesis nevertheless. Proponents of the hypothesis point out that bacteria have probably evolved in response to circumstances selecting for rapid growth and cell division, and that this evolution may have been accomplished by the fusion of the nucleus and cytoplasm and the consequential coupling of the transcription and translation processes, thereby also forcing the elimination of introns. Further support for this hypothesis has been argued based on the organisation of mitochondrial genomes in "lower" eukaryotes such as fungi and "higher" eukaryotes such as mammals. Mitochondria (and chloroplasts) are generally accepted to have evolved from ancestors of present-day prokaryotic cells which developed a symbiotic relationship with the ancestors of eukaryotic cells. And interestingly enough, the mitochondrial genomes of fungi contain introns that have to be spliced from the primary RNA transcripts within the mitochondria. The mitochondrial genomes of the fungi may not have evolved far from the ancestral prokaryotic genetic organisation. On the other hand, the mitochondria of humans exhibit a highly compact genetic organisation in which introns are conspicuously absent and from which nonessential sequences have apparently been almost totally eliminated. This situation suggests to the proponents of the hypothesis that highly evolved eukaryotic cells possess mitochondria whose genomes have likewise evolved far from the ancestral condition. They hold that if mitochondria have evolved from an ancestral prokaryote, that prokaryote must have had a genome organisation more like that of modern eukaryotes than that of modern prokaryotes. Debatable, but interesting. :-) | |
| From: Di | 4/01/00
13:53:20 |
| Subject: re: DNA | post id:
23273 |
| That is interesting. I am
particularly interested in the bacterial DNA. I might be a little confused, but if something has less time to evolve, wouldn't it be a little messier or would it just have smaller changes? P.s. please forgive me, I just don't have the vocab for this subject, always wanted to do bio. | |
| From: Rapunzel | 4/01/00
23:02:12 |
| Subject: re: DNA | post id:
23580 |
I personally tend to think that the idea of simplicity preceding complexity is more logical. If introns are near-copies of exons, why would it make sense for them to be there at the beginning? I can better imagine introns accumulating with time than being there at the outset. Not that what I can imagine necessarily gets us closer to the truth! There are a few ideas I would like to run past the proponents of the hypothesis discussed in the previous post. One of things that occurred to me is that the generation time of fungi is much shorter than the generation time of the "more highly evolved" organisms such as mammals. So, if you start both paths at a point in time X, I think it's the fungi which will have gone through more generations (even if they haven't evolved as much), and so, the fungal mitochondria should also have gone through more generations than the mammalian ones. Not that the number of generations is necessarily proportional to the amount of evolving an organism is going to do - as illustrated by the cases of fungi versus mammals. If the ecological niche of a species is relatively stable, it isn't under pressure to evolve very much. However, the number of generations is important in providing opportunities for genetic mutations to occur - and whether such mutations are likely to be favourable is probably inversely proportional to the stability of the niche. At any rate, it is conceivable that the fungal mitochondria may in fact be more highly evolved than those of mammals, even if the organisms harbouring them are less evolved. The obvious argument against that, of course, is that as far as the mitochondria are concerned, their niche has changed more in the evolutionary pathway of the mammals than in the evolutionary pathway of the fungi. On the other hand, out of the current niches for mitochondria, mammalian ones may actually be more stable than fungal ones, because mammalian homeostasis is more tightly controlled than fungal homeostasis. Maybe there is a simpler explanation - fungal mitochondria went one way, mammalian mitochondria the other for reasons of different requirements posed by the cellular machineries of fungi versus mammals, or perhaps just by chance. Or maybe endosymbiosis wasn't an isolated event, and mitochondria got encorporated multiple times into several different lineages of ancestral eukaryotic cells. I'm just thinking out loud here, and my thinking may be a bit muddled because unfortunately my brain is pretty ordinary today. Ed's opinion on all this would be interesting. Can we borrow your brain, Ed? | |
| From: Dr Paul (Avatar) | 7/01/00
10:07:57 |
| Subject: re: DNA | post id:
24233 |
| Hi Rapunzel, Great answers, great answers. Could there be a role in the introns for determining an altered output of a gene sequence. In the higher plant photosystem II, two of the many polypeptides are closely related. Indeed, they come essentially from the same gene sequence (or highly overlapping regions of the chloroplast genome) . Maybe in some instances, the introns are there for gene product storage overlap. The two polypeptides are a chlorophyll binding inner antennae (light harvesting) protein and one of the two reaction centre proteins binding the essential electron transfer reaction components. The gene is apparently processed slightly differently to obtain copies of each polypeptide. No one in the PS field knows an exact answer as to why this should be apart from limited storage space in the chloroplast genome. Paul | |
| From: michael c | 7/01/00
11:36:18 |
| Subject: re: DNA | post id:
24258 |
| Hi Rapunzel, I'm interested in the theories you have proposed for the differences between fungal and mammalian mitochondria. One thing that comes to mind when you mention that mammals have a more tightly controlled homeostasis is that this really only refers to the changes to the environment that the cells are in. There are a greater variety of cell types in a mammal that all have to be able to use the same mitochondria, everything from muscle cells to adipose cells, neurons to osteoclasts, epithelial cells to lymphocytes. Compared to a fungal mitochondria, a mammalian mitochondria has to be able to function in a greater variety of cell types. I wonder if this versatility might be a contributing factor to the economy of genetic information in the mammalian mitochondria. It makes sense to say that the fungal mitochondria have had more generations to introduce variation, not only in terms of reproductive rate, but also overall time scale. Fungi have been around a lot longer than mammals! Actually that also makes me wonder what effect the reproductive methods would have. Fungi are capable of both sexual and asexual reproduction, whereas us mammals are limited to the one method. Michael C J By the way, this thread is giving me flashbacks to 2nd year Biochem, which is the last time I had to think seriously about this stuff. It's always good to get those dusty neurons firing again! | |
| From: Rapunzel | 8/01/00
22:47:24 |
| Subject: re: DNA | post id:
24643 |
Hello Michael Thank you for your thought-provoking post. It's good to get some discussion going on these kinds of questions, they're so hairy! I'm interested in the theories you have proposed for the differences between fungal and mammalian mitochondria. I didn't propose any theories, I was just engaging in some speculation! (Big difference.) And asking for other people's input… Thanks for your input. :-) One thing that comes to mind when you mention that mammals have a more tightly controlled homeostasis is that this really only refers to the changes to the environment that the cells are in. There are a greater variety of cell types in a mammal that all have to be able to use the same mitochondria, everything from muscle cells to adipose cells, neurons to osteoclasts, epithelial cells to lymphocytes. Compared to a fungal mitochondria, a mammalian mitochondria has to be able to function in a greater variety of cell types. That's a good point, but are the particular "niches" the mitochondria occupy in those very different cells necessarily that different? And necessarily more different than the "niches" occupied by fungal mitochondria? That's a question I haven't got an answer to at the moment. I will have to think more, and maybe read more. Homeostasis versus cell specialisation, and how that influences mitochondria… I wonder if this versatility might be a contributing factor to the economy of genetic information in the mammalian mitochondria. Maybe, but as with all these speculations we are engaging in, the ultimate question is, why/how? It makes sense to say that the fungal mitochondria have had more generations to introduce variation, not only in terms of reproductive rate, but also overall time scale. Fungi have been around a lot longer than mammals! Fungi may have been around longer than mammals, but does that mean that the ancestors of fungi were around for longer than the ancestors of mammals? I think not. Actually that also makes me wonder what effect the reproductive methods would have. Fungi are capable of both sexual and asexual reproduction, whereas us mammals are limited to the one method. As far as reproduction is concerned, it doesn't make much difference to the mitochondria whether reproduction is asexual or sexual (other than the indirect effect this has through the evolution of the cells that house them). In sexually reproducing organisms, the zygote's mitochondria come from the female line, as the male gamete has little cytoplasm and mainly contributes nuclear material to the new individual. Mitochondria are self-replicating organelles. In humans, mitochondrial DNA directs the synthesis of 13 of the proteins responsible for mitochondrial function; but the remaining 50-odd proteins required for cellular respiration within the mitochondria are coded for by the nuclear DNA. Increased ATP requirements by a cell result in mitochondria splitting by simple fission to increase their numbers, then growing to their former size. The sharing out of genetic information between the mitochondrial and nuclear genomes appears to suggest that human mitochondria have surrendered part of their independence. But then, it would appear that every form of symbiosis results in a reduction of the independence of the participants. Cheers Rapunzel | |
| From: michael c | 10/01/00
10:17:09 |
| Subject: re: DNA | post id:
25015 |
| Hi Rapunzel, I didn't propose any theories, I was just engaging in some speculation! (Big difference.) And asking for other people's input… Thanks for your input. :-) oops, sorry! Speculation*slaps forehead* :-) Fungi may have been around longer than mammals, but does that mean that the ancestors of fungi were around for longer than the ancestors of mammals? I think not. Good point, I was thinking in limited terms. Of course the ancestors would be the same, especially if we are accepting the hypothesis that a single ancestor entered into the symbiotic relationship. As far as reproduction is concerned, it doesn't make much difference to the mitochondria whether reproduction is asexual or sexual (other than the indirect effect this has through the evolution of the cells that house them). Well it was the indirect effect of the evolution of the cell that I was thinking of, but don't ask for specifics because I was just throwing another idea around. ......the ultimate question is, why/how? Which is probably what got most of us here in the first place! Michael C J | |
| From: Rapunzel | 13/01/00
23:13:31 |
| Subject: re: DNA | post id:
26215 |
Hi Paul Could there be a role in the introns for determining an altered output of a gene sequence. In the higher plant photosystem II, two of the many polypeptides are closely related. Indeed, they come essentially from the same gene sequence (or highly overlapping regions of the chloroplast genome) . Maybe in some instances, the introns are there for gene product storage overlap. The two polypeptides are a chlorophyll binding inner antennae (light harvesting) protein and one of the two reaction centre proteins binding the essential electron transfer reaction components. The gene is apparently processed slightly differently to obtain copies of each polypeptide. No one in the PS field knows an exact answer as to why this should be apart from limited storage space in the chloroplast genome. Paul, that sounds plausible to me, just one thing: If there is such a limitation on storage space in chloroplast genomes (and I'm not an expert on chloroplast genomes), then why would there be introns in those genomes? - Do you know much about chloroplastic introns? Are there significant differences in their intron:exon ratios depending on the line of autotrophs they are found in, as is the case in animal mitochondria? Regards Rapunzel | |