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Natural Science Forum / Biology / Biology / August 2006Algorithm used by cell nucleus?
Hi all, a couple of questions about the process used by the cell nucleus to read DNA: -does any part of a cell contain an algorithm for how the DNA is processed? -any book / web site / paper that you would recommend that discusses this process? thanks! jj >Hi all, > [quoted text clipped - 3 lines] >-does any part of a cell contain an algorithm for how the DNA is >processed? What part of the processing is of interest? Standard base pairing determines the information readout. Protein and RNA recognition guide choice of sites. >-any book / web site / paper that you would recommend that discusses >this process? Any molecular biology book. Or start with a basic biology book. If you want to buy one, you might start with Clark & Russell, Molecular Biology made fun and simple. bob Hi bob, this reply touches on what I was looking for: > Standard base pairing determines the information readout. Protein and > RNA recognition guide choice of sites. What I meant to ask was: Where in the cell is the "code" that reacts to the type of protein or RNA and then determines what should be done? Basically what I am looking for is similar to the firmware on e.g. a CD-ROM drive. Something that takes care of the low-level processing of data. Data (in this case DNA) is equal to a CD-ROM that has been inserted into a drive. What part in the cell handles the role of the "firmware"? thanks again, jj > >Hi all, > > [quoted text clipped - 18 lines] > > bob >Hi bob, > [quoted text clipped - 5 lines] >Where in the cell is the "code" that reacts to the type of protein or >RNA and then determines what should be done? I suppose, in biol terms, you are asking what tells a gene whether or not it should function? A complex of proteins forms at and around the initiation site in the gene. (For simplicity, let's leave the RNA out of this.) In the simplest of cases, it may be as simple as a protein recognizing a site on the DNA. In real cases, there may be a very extensive complex, involving both protein-protein and protein-DNA interactions. >Basically what I am looking for is similar to the firmware on e.g. a >CD-ROM drive. Something that takes care of the low-level processing of >data. Data (in this case DNA) is equal to a CD-ROM that has been >inserted into a drive. Maybe because I do not what low level processing on a CD means, I am not sure how useful this analogy is. The part I described above is the part that tells the read-head where to read (I think). bob >What part in the cell handles the role of the "firmware"? > [quoted text clipped - 24 lines] >> >> bob Hi Bob, thanks for your reply. The low-level stuff that a CD-Rom drive firmware handles is for example turning the laser on and off, moving the read head to different locations on the disk, and ejecting the disk. For example, the action of moving the read head to different locations on the disk could not happen without the action being coded in the firmware. For this reason I was curious how the control tasks were accomplished in case of the 'DNA read-head'. I wanted to ask a couple of follow up questions: a. when the DNA read-head recognizes a protein (for example), how does the recognition occur? I assume there is no database somewhere within the cell that contains a list of "approved" proteins (correct me if I am wrong). Is the recognition 'inbuilt' into the chemical interaction between the read-head and the protein? b. when you say "what tells a gene whether or not it should function", is it so that a gene that is not supposed to function is skipped by the 'DNA read-head'? or is it read just as the rest and skipped later? c. if the answer to "b" is "skipped", how does the DNA read-head know how many base pairs to skip to get to the next gene? d. this is not related to the rest, but I'm asking because of not having found much info on this elsewhere: is the DNA stored in a spherical form and then unraveled from that for parsing? apologies for many questions jj >Hi Bob, > [quoted text clipped - 5 lines] >of moving the read head to different locations on the disk could not >happen without the action being coded in the firmware. As to the read head moving to different locations... I think we could say it occurs largely by random diffusion -- checking at each point whether this is the right place. Now, can you get a CD drive to work that way? (see your c. below) >For this reason >I was curious how the control tasks were accomplished in case of the [quoted text clipped - 8 lines] >am wrong). Is the recognition 'inbuilt' into the chemical interaction >between the read-head and the protein? yes You may know, at least vaguely, that the two strands of DNA recognize each other (are complementary) by hydrogen bonding. Proteins interact with DNA by similar hydrogen bonding. (There is more to it, but that is a useful start.) Chemically, both DNA and proteins have H-bond donating groups and H-bond accepting groups. >b. when you say "what tells a gene whether or not it should function", >is it so that a gene that is not supposed to function is skipped by the >'DNA read-head'? or is it read just as the rest and skipped later? Well, either can happen. The simple view is that a gene is on DNA, a temporary copy is made onto RNA ("transcription"), and then that RNA copied is "translated" into protein. Most commonly, regulation is at the level of transcription. But it can also be at the level of translation: make the mRNA, and then regulate how that mRNA gets used. These are separate questions. >c. if the answer to "b" is "skipped", how does the DNA read-head know >how many base pairs to skip to get to the next gene? As hinted earlier, interaction of the transcription apparatus with the DNA is more or less random access -- diffuse, collide, check. (There is a possibility that some of this is 1-D diffusion along the length of the DNA. A minor point for now, I think.) Gene spacing is not regular. Each gene (or at least each transcription unit) must have its own start (and stop) signals. >d. this is not related to the rest, but I'm asking because of not >having found much info on this elsewhere: is the DNA stored in a >spherical form and then unraveled from that for parsing? Oh, that is actually quite complex. But let's start simple. DNA is topologically linear. The two strands are wound around each other in a plectonemic helix. The genetic information -- the base pairs -- is "inside". Fortunately, the bases are somewhat visible from the outside, which is why proteins can recognize base sequences. But actual DNA processes involving base pairing do require that the strands be separated. In fact, the proteins that form the initiation complex help to open the DNA up. There are also higher levels of DNA organization, especially in higher cells; these have additional processes for turning DNA on and off at those levels. >apologies for many questions That's fine. All sorts of people post here. It is often hard to know what to do with an initial short post. But you have followed up and turned it into a conversation. I gather you are something of an "engineer", and discussion such as this across traditional boundaries can be interesting, perhaps even worthwhile -- though awkward. bob thanks for your detailed answers, Bob. Very appreciated. |
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