What would this be
- Thread starter ELOGE1174
- Start date
There are multiple RNA polymerases but I imagine you are referring to RNA polymerase II, the eukaryotic RNA polymerase that catalyses synthesis of mRNAs and a few small nuclear RNAs.
Since transcription of mRNA is necessarily for almost every cell type (although it’s probably safe to say all cell types), reducing the efficiency of RNA pol II will have a dramatic negative effect on a cell, if not a lethal effect. This is true of most “housekeeping genes” (ie. genes that encode proteins that play a role in necessary cellular processes like DNA replication and repair, metabolism, protein synthesis etc). RNA pol II forms a transcription complex with a variety of other transcription factors. A mutation that alters the function of a specific transcription factor protein will influence transcription of the specific genes for which it acts, but RNA pol II is present in the transcription complexes for all genes, so it is fundamentally important for cellular functioning.
A base pair substitution does not always cause a change in the corresponding amino acid sequence of the protein due to the degeneracy of the triplet code. Base pair substitutions that do not alter the amino acid encoded by that codon are said to be "silent" and have no effect on protein function. If a base pair substitution does cause a changed amino acid, then this may or may not have an effect on protein function. If depends on a lot of things, such as the nature of the changed amino acid and where in the protein that substitution occurs.
Since transcription of mRNA is necessarily for almost every cell type (although it’s probably safe to say all cell types), reducing the efficiency of RNA pol II will have a dramatic negative effect on a cell, if not a lethal effect. This is true of most “housekeeping genes” (ie. genes that encode proteins that play a role in necessary cellular processes like DNA replication and repair, metabolism, protein synthesis etc). RNA pol II forms a transcription complex with a variety of other transcription factors. A mutation that alters the function of a specific transcription factor protein will influence transcription of the specific genes for which it acts, but RNA pol II is present in the transcription complexes for all genes, so it is fundamentally important for cellular functioning.
A base pair substitution does not always cause a change in the corresponding amino acid sequence of the protein due to the degeneracy of the triplet code. Base pair substitutions that do not alter the amino acid encoded by that codon are said to be "silent" and have no effect on protein function. If a base pair substitution does cause a changed amino acid, then this may or may not have an effect on protein function. If depends on a lot of things, such as the nature of the changed amino acid and where in the protein that substitution occurs.
Indeed, Hercules did answer the question. So much so that I cannot add anything to it. Hence I will just repeat the obvious.
With a deleterious mutation in the RNA polymerase (if RNA polymerase was one protein) you are pretty much looking at a dead cell.
With a deleterious mutation in the RNA polymerase (if RNA polymerase was one protein) you are pretty much looking at a dead cell.
The code is optimized to maximize error repair. A substition is not always a deleterious mutation and a deleterious mutation is usually just selected out anyways. With a deleterious mutation in the RNA polymerase, if it is in the alpha subunit then it would have no effect at all on transcription. Also, given the fact that most polymerases are polycistronic, the mutation might effect the translation of one gene but not the other.
Positive and negative regulators have a profound effect on whether or not the polymerase will bind to the promoter, thus if there is a mutation in the binding site for the regulator, expression may or may not occur. Loss of function of a negative regulator would still allow expression. Also have to take into consideration the difference between mRNA and the pre-mRNA in the polymerase and what part the mutation effects. Also reverse transcription of deleterious mRNAs can generate pseudogenes that may or may not be advantageous. There is also a big difference between the more compact usually-faithfully reproduced genome of prokaryotes (debateable) and the much larger diverse more-variable eukaryote genome. And in eukaryotes you have to consider whether it's RNA polymerase I, II, or II that we're taking into consideration. There is also an environmental factor that has an effect on determining which codon sites are used or not used.
I think the regulatory network is extremely important as it acts as a modulator in the whole process, and there are varying degrees of mutation, whereby some might be advantageous while others partially surpressed while others just edited out. Evolution occurs by changes in the polymerase pathway. This is a very complex subject, but an "all-or-nothing" answer is certainly not adequate, and a distinction needs to be made between deleterious RNA polymerase and substitutions, which I haven't addressed.
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I was just reviewing some of this in my textbooks on regulatory networks and thought I'd add some of the research findings done on E. coli. They talk about conditional lethal mutations in which high temperatures provide critical evidence for the importance of a global regulatory network and mechanisms. The conditional mutants described have a defect in the rpoH gene that encodes an alternate RNA polymerase sigma factor (sigma 32 rather than 70). Under normal physiological conditions the sigma factor is active in the cell, however at high temperatures an alternate sigma factor functions that recognizes different promoter sequences. In this example, sigma 32 mediates the heat shock response by binding to the core RNA polymerase and allowing it to initiate transcription. This would be an example where a regulatory mutant substitution is advantageous by providing activation of transcription over a much wider temperature range.
Positive and negative regulators have a profound effect on whether or not the polymerase will bind to the promoter, thus if there is a mutation in the binding site for the regulator, expression may or may not occur. Loss of function of a negative regulator would still allow expression. Also have to take into consideration the difference between mRNA and the pre-mRNA in the polymerase and what part the mutation effects. Also reverse transcription of deleterious mRNAs can generate pseudogenes that may or may not be advantageous. There is also a big difference between the more compact usually-faithfully reproduced genome of prokaryotes (debateable) and the much larger diverse more-variable eukaryote genome. And in eukaryotes you have to consider whether it's RNA polymerase I, II, or II that we're taking into consideration. There is also an environmental factor that has an effect on determining which codon sites are used or not used.
I think the regulatory network is extremely important as it acts as a modulator in the whole process, and there are varying degrees of mutation, whereby some might be advantageous while others partially surpressed while others just edited out. Evolution occurs by changes in the polymerase pathway. This is a very complex subject, but an "all-or-nothing" answer is certainly not adequate, and a distinction needs to be made between deleterious RNA polymerase and substitutions, which I haven't addressed.
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I was just reviewing some of this in my textbooks on regulatory networks and thought I'd add some of the research findings done on E. coli. They talk about conditional lethal mutations in which high temperatures provide critical evidence for the importance of a global regulatory network and mechanisms. The conditional mutants described have a defect in the rpoH gene that encodes an alternate RNA polymerase sigma factor (sigma 32 rather than 70). Under normal physiological conditions the sigma factor is active in the cell, however at high temperatures an alternate sigma factor functions that recognizes different promoter sequences. In this example, sigma 32 mediates the heat shock response by binding to the core RNA polymerase and allowing it to initiate transcription. This would be an example where a regulatory mutant substitution is advantageous by providing activation of transcription over a much wider temperature range.
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RNA polymerase is a protein enzyme, not a gene. Clarify.
Okay, since most proteins are too large to pass into the cell through the cell membrane, each cell makes it's own proteins. Being that RNA Polymerase is such a protein (several proteins, in fact), the cell must create the RNA Polymerase from genes found along the DNA strand. If a mutation were to happen in part of the DNA strand that codes for RNA polymerase, then the resulting transcription product (mRNA) would be mutated, and thus the resulting translation product (protein) would also be mutated.
This is what he/she is referring to. There is a deleterious mutation in the DNA that codes for the RNA Polymerase. How's that?
This is what he/she is referring to. There is a deleterious mutation in the DNA that codes for the RNA Polymerase. How's that?
Oh dear, Idle Mind ... 
Don't play the troll's game. Just ignore the fool.
Don't play the troll's game. Just ignore the fool.Easily resolved.
A deletion has taken place in the quoted sentence.
The deletion of a single word.
"For."
Better?
(Of course, this overlooks the fact that polymerase is actually composed of multiple subunits which are coded by multiple genes, but we can accept that the thread starter didn't know this, yes?)
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I'm trying to give him the benefit of the doubt...Oh dear, Idle Mind ...
kebabotronic
Registered Member
Or the poster forgot for instance to add 'β' after polymerase.
Gene is a flexible word. It means different things to different people. The entire Polymerase complex can be said to be coded by a gene, although this wouldn't be the standard definition.
In this case it seems futile to discuss whether or not RNA polymerase is a gene since the question has already been answered. The subunits are definitely coded by genes. The whole polymerase complex is also genetically coded. You may call it a gene. No biologist will shoot you for that. Maybe one or two will protest.
And how do we handle the opposite case then? Are the non-coding regions not part of the gene suddenly anymore? What about different splice forms? Are the parts of the gene that are spliced out not part of the gene?
It's not wise to let yourself be trapped by rigid thinking in biology.
Oh dear, Idle Mind ...
You want to call me a fool, bucko, you come here and say it to my face. I'm not going to waste my time answering a muddled up unclear question, except to give the most obvious-related answer. And that I did. Clearly, by ignoring regulation outright, your's was the foolish answer. If the thread starter wants to clarify the question, then I'll answer it. You got problem with that? The fool who hides behind his computer screen antagonizing others, here another case in point, with a colorful array of bells and whistles. Grow up, rock-head, now we're going to see ten more foolish posts of unproductive nonsense that you can roll around it, like the foolish pig that you are, hence your call name.
Don't do "me" any favors. I'm assuming you're referring to ELOGE1174's post. Nothing in what I posted has any "doubt." So who are you "giving the benefit of a ddoubt to"? If that's what you assume ELOGE1174 meant, then its a good reply.
HR: Is that okay with you pighead? You're as "make-believe" and fictious as your mythological name implies, and far from being divine. lol
Fine, I won't. I'll go back to being blunt with you. I didn't say that your post contained doubt, but I was mistaken in thinking you wanted to learn something. I clarified something in Eloge's post, and you said it wasn't clear enough. Hence, I made an effort to clear it up for you even more.
Praise the Lord!
...oh. -.-
Wrong. Your answer was needlessly complex. The question mentioned nothing of regulation. It specifically asked what the effect of deletion and substitution mutations in the RNA Polymerase gene would have.
He didn't ignore regulation. Hercules answered the question perfectly, and thus your reply was completely unnecessary. If Eloge wanted to learn more, he would have asked, yes?
This is a ridiculously simplified answer that ignores well over a hundred regulatory mutation factors that can alter the process along the way. Yes, transcription-translation is an intracellular process and that's basically all that you've said here, although there are exceptions, as in the case of RNA polymerase being introduced into the cell from viruses. But that is not what we're talking about. Your reply her belongs in a grade school textbook, and it is definitely a reflection of an idle mind. Again, this is an extremely complex process that cannot be addressed suficiently without knowing what the question is, unless you care to write a textbook. I sent and email to ELOGE1174, asking him to clarify. By the way, I never read line-by-line criticisms as I have no time to waste on that type of immaturity. Doing so is just simply an unproductive immature waste of time.
Valich, what on earth is your problem? All Eloge asked, was what would happen if there was a deleterious mutation in the gene that codes for RNA polymerase. What would it mean to the cell. Then, in part 2, he asks what would happen if there was a substitution in the gene that codes for RNA Polymerase. Nowhere did they ask about regulatory controls, nowhere did they ask about cofactors.
Also, we separate out quotes not to be immature, but to make it clear to the reader which part of their post we are responding to. We do it to make things easier to understand.
As for your ad hominem attack on me (real clever on the pun, by the way), what have I done to warrant such disrespect? Because I simplified a response? Who knows what level of understanding of a certain subject another poster has. Maybe Eloge will benefit from such information. Maybe not. But, I'm sure there are other readers out there who will, and if it helps even a single person learn something, then I've done all I intended to do.
So please, if reading responses to topics that you post in is a waste of time, please do us all a favour and relieve us of your presence. I'm sure it will be sorely missed.
Also, we separate out quotes not to be immature, but to make it clear to the reader which part of their post we are responding to. We do it to make things easier to understand.
As for your ad hominem attack on me (real clever on the pun, by the way), what have I done to warrant such disrespect? Because I simplified a response? Who knows what level of understanding of a certain subject another poster has. Maybe Eloge will benefit from such information. Maybe not. But, I'm sure there are other readers out there who will, and if it helps even a single person learn something, then I've done all I intended to do.
So please, if reading responses to topics that you post in is a waste of time, please do us all a favour and relieve us of your presence. I'm sure it will be sorely missed.