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Natural Science Forum / Biology / Microbiology / June 2006Structure of phosphate group in DNA?
What does the phosphate backbone look like in DNA? The first diagram here: http://www.emc.maricopa.edu/faculty/farabee/biobk/BioBookDNAMOLGEN.html, list a triphosphate. However, in this complete structure of DNA: http://www.emc.maricopa.edu/faculty/farabee/biobk/BP2.gif, there is only one phosphate and not three. What happened to the other two go? What is the correlation between the three phosphates in the first image and the one phosphate in the second image? Thanks, Brett Look up the process of DNA synthesis. All will be clear. > What does the phosphate backbone look like in DNA? The first diagram > here: [quoted text clipped - 8 lines] > Thanks, > Brett  SignatureLarry D. Farrell, Ph.D. Professor of Microbiology Idaho State University -- Posted via a free Usenet account from http://www.teranews.com > What does the phosphate backbone look like in DNA? The first diagram > here: [quoted text clipped - 8 lines] > Thanks, > Brett three phosphates = high energy one phosphate = low energy The energy from the phosphodiester bond is used to covalently link molecules together with the help of an enzyme. During the process of DNA synthesis, nucleotides are in the "tri-phosphate" form. That is, each nucleotide has 3 phosphate groups. However, as DNA polymerase adds on each nucleotide to the growing DNA chain, it has to find energy to do this, and it acquires energy by cleaving off two of the phosphate groups. This reaction provides the energy required to drive DNA synthesis. As a result, the sugar-phosphate backbone of DNA only has 1 phosphate for each nucleotide ("mono-phosphate" form). This is also the reason that the very extreme 5' end of a DNA strand has 3 phosphate groups on it. --Alex ************* Alex B. Berezow, Grad Student Dept. of Microbiology University of Washington School of Medicine Seattle, WA 98195 Very nice. Thanks for the references. I'm wondering where the DNA ligase gets its energy from if the polymerase is taking everything. But I believe some reading on phosphodiester bonds will probably answer that question and lead in me in the right direction. Since we're talking about DNA, how does the radius here (bottom of article) http://www.nature.com/nature/journal/v406/n6793/full/406251a0.html get a 4? 23.7/4=5.92 Å Also, the article mentions: "...there is a critical pitch-to-radius ratio (p/r=2=6.28) above which the line of contact between the tubes is straight, and below which it is helical." What is meant by, "above which the line of contact between the tubes is straight"? It's a great article but I can't find other references on the goemetric structure of DNA with this kind of detail. Thanks, Brett >Very nice. Thanks for the references. > >I'm wondering where the DNA ligase gets its energy from Look at the cofactors used by ligase. >if the >polymerase is taking everything. means what?? bob > It's a great article but I can't find other references on the goemetric > structure of DNA with this kind of detail. There's a good reason for that: No one really cares/understands. At least no one in microbiology. A biochemist would have a field day with a paper like that.....so if you're really interested in the detailed structures of molecules, you might want to ask a biochemist. Or maybe a structural biologist. --Alex ************************* Alex B. Berezow, Grad Student Dept. of Microbiology University of Washington School of Medicine Seattle, WA 98195 >Since we're talking about DNA, how does the radius here (bottom of >article) >http://www.nature.com/nature/journal/v406/n6793/full/406251a0.html get >a 4? > >23.7/4=5.92 Å Think of two strands lying side by side. 23.7 is the width -- of two strands. Diameter of one strand is half that. Radius of one strand is half of that diameter. >Also, the article mentions: >"...there is a critical pitch-to-radius ratio (p/r=2=6.28) above which [quoted text clipped - 3 lines] >What is meant by, "above which the line of contact between the tubes is >straight"? Not sure how to explain something like that in words. Pictures/models help. Did you read the article this comes from? >It's a great article but I can't find other references on the goemetric >structure of DNA with this kind of detail. ?? What are you looking for? Have you read the actual article this little news story refers to? Have you read the other references? Have you done a citation search on the main article? There was a book a few years back on DNA structure using simple geometric models as approximations. Don't remember for sure, but I think one author may have been Calladine. Might be a good book for you. Remember, this is a simplified approximation to DNA structure, not "detail". If that is what you want, fine. DNA helix is not regular. bob >>Since we're talking about DNA, how does the radius here (bottom of >>article) [quoted text clipped - 34 lines] > > bob indeed it's not at all regular, having other helical configurations than you typically see in textbooks. I think you might be interested in adding the z form to your search >> There was a book a few years back on DNA structure using simple >> geometric models as approximations. Don't remember for sure, but I [quoted text clipped - 9 lines] >you typically see in textbooks. I think you might be interested in >adding the z form to your search Just in case the OP is still around (or anyone else is listening)... I think it is useful to distinguish two kinds of variation in DNA structure. One is the different basic forms, such as A, B, Z -- which are distinct helical forms. But also, within a sequence of "common" B-form DNA, the details depend on the specific base pairs (and neighbors). This micro-variability of DNA has been well studied with crystals of known structure oligos. It is also important when getting into the details of how proteins recognize DNA bases. Students are sometimes not made aware of this level of variability in "basic" mol biol. Then there are special issues, such as some sequences being easier to bend. bob >During the process of DNA synthesis, nucleotides are in the >"tri-phosphate" form. That is, each nucleotide has 3 phosphate groups. [quoted text clipped - 7 lines] >This is also the reason that the very extreme 5' end of a DNA strand >has 3 phosphate groups on it. Oh come on. You gave such a great answer above, and then this. Not true for DNA -- but it is true for RNA. DNA polymerase is unable to initiate a new chain; it only adds a nucleotide to a growing chain (or something that looks like a growing chain). Thus there can not be a deoxyribonucleotide triphosphate at the 5' end of DNA. There is a ribonucleotide triphosphate at the 5' end of RNA -- at least it is made that way. The most common method of initiating DNA synthesis is to make a small RNA chain at the desired start location, then extend it with deoxynucleotides, then go back and trim out the RNA and fill the gap in with deoxy-nucleotides. (And you knew that, too, yes? :-) ) Ok, now that I have been so bold, and put myself out on a limb... Is there any exception yet known? Is there any DNA Polymerase that can truly initiate a new chain? bob > Thus there can not be a deoxyribonucleotide triphosphate at the 5' end of DNA. There > is a ribonucleotide triphosphate at the 5' end of RNA -- at least it is made that way. You're absolutely right. My bad. I had this image in my head of an undergraduate bacterial genetics exam where I was made to draw an oligo, and I had to place a tri-phosphate at the 5' end. I forgot that must have been RNA, not DNA. > The most common method of initiating DNA synthesis is to make a small > RNA chain at the desired start location, then extend it with > deoxynucleotides, then go back and trim out the RNA and fill the gap > in with deoxy-nucleotides. > > (And you knew that, too, yes? :-) ) Yes, I did know that. :) > Ok, now that I have been so bold, and put myself out on a limb... Is > there any exception yet known? Is there any DNA Polymerase that can > truly initiate a new chain? I think so. Aren't there viral DNA polymerases that don't require a primer? I'm wanting to say reverse transcriptase doesn't need a primer. It's been a while since I've had virology....and all I remember from it is that many viruses have really strange mechanisms of replication. On this webpage: http://www.web-books.com/moBio/Free/Ch4J1.htm it doesn't look like reverse transcriptase requires a primer....unless that tRNA is doing something I don't know about. --Alex ************************* Alex B. Berezow, Grad Student Dept. of Microbiology University of Washington School of Medicine Seattle, WA 98195 >> Ok, now that I have been so bold, and put myself out on a limb... Is >> there any exception yet known? Is there any DNA Polymerase that can [quoted text clipped - 10 lines] >it doesn't look like reverse transcriptase requires a primer....unless >that tRNA is doing something I don't know about. As you noted later, the tRNA typically does serve as a primer. Further some viral DNA Pol use an -OH group of a "primer protein" to elongate from. The general picture is that the viruses show the great lengths DNA Pols will go to to get around their inability to initiate (to lay down an initial dNTP). However, incubating your post finally made me go back and look up something that was lurking in the back of my mind. I have the following ref and comment in my files (and have done no further follow-up on it.): C-C Chiang & A M Lambowitz, The Mauriceville retroplasmid reverse transcriptase initiates cDNA synthesis de novo at the 3' end of tRNAs. Mol Cell Biol 17:4526, 8/97. We show that [this] reverse transcriptase ¼ has the unprecedented ability for a DNA polymerase to initiate DNA synthesis at a specific site in a natural template without a primer. (From the abstract of an earlier paper.) Thus another common generality falls. This new result is interesting from an evolutionary perspective. RNA polymerase can initiate, and the first DNA Pol presumably evolved from an RNA Pol. Thus it is reasonable (even expected) that a primitive DNA Pol might be found that initiates. The failure of common modern DNA Pols to initiate would seem to reflect the loss of a feature. -- Any follow-up on that would be welcomed. There is an "argument" why DNA Pol does not initiate. One might expect the error rate to be higher for the first few nucleotides of a new chain (Floppy end problem). Thus allowing DNA Pol to initiate would not be good for genomic stability. bob > Any follow-up on that would be welcomed. Well, I don't think I can provide much follow-up. I was certainly in complete ignorance of this enzyme. The authors do point something out in the introduction that I found quite stunning: "The Mauriceville plasmid is a novel retroelement found in the mitochondria of certain Neurospora strains isolated from nature (1, 8)." Neurospora?? I'm VERY surprised that such a unique enzyme would be in a fungus. It's always seemed to me that the eukaryotes have one thing in common: rather boring biology (at least at the cellular level). The truly unique molecules (in my opinion) have almost exclusively been bacterial or viral. I would have bet anyone $100 that such a strange enzyme would have been found in a virus. --Alex ************************** Alex B. Berezow, Grad Student Dept. of Microbiology University of Washington School of Medicine Seattle, WA 98195 >>Any follow-up on that would be welcomed. > [quoted text clipped - 20 lines] > University of Washington School of Medicine > Seattle, WA 98195 Note that RT activity has been noted in humans regardless of viral infection. The fact that an RT gene is present perhaps indicates the historical infection of neurospora by a virus which uses RT. Horizontal gene transfer is what im trying to say. >> Any follow-up on that would be welcomed. > >Well, I don't think I can provide much follow-up. Of course, you have no obligation to do any follow-up, but occurs to me... You do know about doing citation searches (on what is now called Web of Science), which gives you all the articles that have cited the given article??? A great tool. If you don't know about it, check with your reference librarian. >I was certainly in >complete ignorance of this enzyme. The authors do point something out [quoted text clipped - 10 lines] >bacterial or viral. I would have bet anyone $100 that such a strange >enzyme would have been found in a virus. I agree with the general spirit of your point. As Mike has noted, this particular case involves a mobile element, so its real affinity may be complex. And certainly among the eukaryotes, the place for novelty would be with the microbes. Remember, the first antibiotics came from fungi. bob Bob, I meant to ask you in my last post....are you a prof? If so, what institution? --Alex >Bob, > >I meant to ask you in my last post....are you a prof? If so, what >institution? I'm mostly retired at this point. Background in chem/mol biol in the 60s. 20 yr in biotech industry. Taught various places, including mol biol at Extension for UC Berkeley for many years. (I actually got the Mauriceville item by going back to my chapter handout for DNA replication last time I taught that -- in 2001.) http://www.geocities.com/b_bruner/ if you want to look around. Remember, I have not kept the mol biol up much since 2001, but contributions for good web links (from your dept?) are welcomed. bob but contributions for good web links (from your > dept?) are welcomed. > > bob I can't say it's a GOOD weblink....it's A weblink. I made this website for my lab last summer, but haven't gotten around to putting up anything under "Research" or "Photos." Most of the information about what we do is under "Lab Members," which gives an extremely brief little blurb on what each of us does. It also hasn't been updated since Oct. 2005. I plan to add to and/or update the website.....but this is certainly last on my priority list as a grad student. This website was more for fun and free advertisement. But, here it is if you want to check it out: http://staff.washington.edu/alexbb/ --Alex *************************** Alex B. Berezow, Grad Student Dept. of Microbiology University of Washington School of Medicine Seattle, WA 98195 >>>Ok, now that I have been so bold, and put myself out on a limb... Is >>>there any exception yet known? Is there any DNA Polymerase that can [quoted text clipped - 45 lines] > > bob I regularly use reverse transcriptase from maloney murine leukemia virus and I require primers. It's interesting that there is an RT that requires no primers, but like was mentioned is probably error prone, and I imagine the initiation kinetics of primerless cDNA synthesis suck. So it probably wouldn't be used as a lab tool, especially considering that polyT primers are probably the cheapest you can buy. Neat though. > Ok, now that I have been so bold, and put myself out on a limb... Is > there any exception yet known? Is there any DNA Polymerase that can > truly initiate a new chain? Okay, it looks like that tRNA is acting like a primer. I'm not sure, then. My guess is there's some viral polymearse that doesn't require a primer. |
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