Generation of DNA nucleotides

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    • #12542
      gs99
      Participant

      My question relates to the base molecules (Adenine, Cytosine, Guanine, Thymine) in DNA.

      The chromosomes are replicated in Synthesis part of cell cycle Interphase.
      About 204 billion atoms are required to complement the two sides of the human genome.

      There is much information about how certain things work in the cell (eg. how proteins are generated). But I’m curious about the chemical level:

      How and where are the base molecules generated?

      Is there a special protein or enzyme that combines the needed atoms into each molecule?

      How does the polymerase obtain the needed molecules to generate the new strands?
      (Does it send a message to a protein that gets the requested molecule. Or does polymerase utilize supply tanks with spigots that inject the proper molecule?)

      Does the cell know in advance that there are sufficient materials available?

      Any comments welcome,

      George

    • #96351
      kolean
      Participant
      quote gs99:

      How and where are the base molecules generated?

      From this article on Nucleotides in Wikipedia, it will tell you that nucleotides can be salvaged from other complexes, or made de novo (from scratch):
      http://en.wikipedia.org/wiki/Nucleotide

    • #96363
      gs99
      Participant

      Thanks for that web page.

      Method 1. "salvaged from other complexes"
      In this page, it states:
      "Salvage pathways are used to recover bases and nucleosides that are formed during degradation of RNA and DNA."
      http://en.wikipedia.org/wiki/Nucleotide_salvage
      Question: Since DNA replication is being done in the cell cycle immediately following formation of the cell, how could there be any degradation of DNA or RNA?
      Is it possible this method is used (only) later in cell life, after may genes have been expressed?

      Method 2. "de novo"
      I failed to mention that I’m not a chemist major; much of the web page is too technical for readers like me.
      I have written computer programs; I’m accustomed to look for objects that have properties and methods (actions).

      So what are the material objects needed to start the process?
      Molecule x and enzyme y

      What is the first method (action)? What does enzyme y do to molecule x? Perhaps the web page calls this Reaction 1?

      There are many web pages that provide great drawings of transcription and translation to explain those things clearly.

      I’m looking for the steps needed to generate one molecule of A, C, G, or T, in simple words.
      Have you seen this kind of information?

      Then, one of the other questions was: How is the newly formed molecule attracted to move when and where it is needed?

    • #96365
      kolean
      Participant

      Wow, so many questions. See if I can tackle a few:

      quote gs99:

      Question: Since DNA replication is being done in the cell cycle immediately following formation of the cell, how could there be any degradation of DNA or RNA?

      DNA replication immediately following formation of the cell is for cells that are only for reproducing themselves (such as stem cells and immune cells) when it is called for in the organism. If the cell has any function in the organism, it will only proceed onto DNA replication when it is needed to be replicated. Most cells have a function to do and perform it, and may not go on to replicating itself. Sometimes the cells just wear out or parts wear out, and the cell proceeds to salvage the parts.

      quote gs99:

      How is the newly formed molecule attracted to move when and where it is needed?

      Proteins in the cell do pretty much everything in the cell. If the protein is not an enzyme catalyzing a reaction to go a certain way (due to environmental conditions and the needs of the cell), it is providing transport or storage for the molecules. Nucleotides are made and transported to the nucleus where they are confined to this part of the cell and are used by the proteins when duplicating the DNA during the S phase.

      quote gs99:

      I’m looking for the steps needed to generate one molecule of A, C, G, or T, in simple words.
      Have you seen this kind of information?

      Google ‘Biosynthesis of Nucleotides’. It is really a complicated biochemical reaction with many steps. And yes, each step has a specific enzyme that takes a basic starting molecule (like the amino acid aspartate) and modifies it in steps, till it is a nucleotide (a nitrogenous base attached to a deoxyribose sugar, which is then phosphorylated three times). It may be too technical for you. You could possibly find it completely explained for you in a biochemistry book that would show the biochemicals and what the enzymes catalyze in each of the reaction steps. And each nucleotide is unique in their biosynthesis, so A, T, G, and C are different.

    • #96375
      gs99
      Participant

      1. Are you saying that DNA replication (S phase) is done only if more cells are needed? That makes sense.
      The new cell enters phase G1, then G0 in which the cell does its main job.
      If more of this cell are needed, it goes into Phase S, G2 and Mitosis.
      This page mentions four resources needed, under "DNA Replication"
      http://www.biology-online.org/1/5_DNA.htm
      Phase S and G2 seem to be needed only before Mitosis.

      2. Until I understand more chemistry, I’m looking for an overview explanation.
      "After Helicase splits the DNA, Polymerase adds about 6 billion A, T, G, or C molecules, resulting in two identical DNA strands."
      Is that correct?
      In a computer program, subroutines would be needed that repeat the steps needed for each nucleotide, such as:
      >Read the nt. on original strand (eg. C)
      >Determine its complement (eg. G)
      >Obtain a new molecule of the complement (eg. G)
      >Attach new molecule to new strand

      3. To do DNA replication efficiently, I’m wondering if (my imagination):
      There are multiple copies of Polymerase, so multiple chromosomes could be processed at the same time.
      Perhaps microtubules are utilized in some way to organize the "production area".
      There are "bucket brigades" of proteins carrying each type of nt. into one or more temporary dispensers connected to the Polymerase.
      Polymerase causes dispenser to release a molecule of needed nt.
      This would be similar to the spider releasing various types of web string material.
      Have you seen any pictures of stained components to shed light on this system (like those that illustrate Mitosis)?

      4. Comments about the chemical formulas for nucleotide metabolism (involving things like IMP, AMP, and GMP)
      http://themedicalbiochemistrypage.org/n … m.html#top
      It’s amazing to me that they discover what enzymes do in each step; this has taken much observation and testing.
      Question: Is there only one occurrence of steps processed for a given amount of source material?
      Or is it possible that multiple "strings" (possibly same or different nt. molecule) are being processed at different stages within the cytoplasm? This would be like various experiments being conducted at the same time in a lab or classroom.

      5. I noticed this interesting statement: "Purine Nucleotide Biosynthesis, The major site of purine synthesis is in the liver."
      http://themedicalbiochemistrypage.org/n … olism.html
      What products are produced in the liver; how are they transported to the cells?
      Are the Final stages to produce each type of molecule always performed in the cell?

      That’s all for now.
      Appreciate any comments on whatever.

    • #96376
      JackBean
      Participant

      2. well, yes, basically, that’s correct

      3. in bacteria, there is only one replication start, but probably there are more polymerases in the cell.
      In human, there are multiple replication starts on each chromosome, which are fired consequently (several of them at a time).

      4. I’m not sure, if I understand your question correctly, but there are definitelly several copies of each enzyme/protein/molecule in each cell.

      5. livers are said to be the factory of the body, there is produced almost everything, what is needed in the body πŸ˜‰

    • #96389
      gs99
      Participant

      4. Evidently many steps are needed to make the nucleotide molecules.
      Note: When I first asked this question, I thought the nt. molecules were made in the cytoplasm (see next item).
      I’m thinking 1.5 billion molecules of each nt. are needed. When the nt. molecules are assembled into DNA they’re handled individually. But it doesn’t seem plausible that they’re generated individually…
      So I thought there must be ways of multiple concurrent production.
      I envisioned many students with there own containers doing various steps.
      Does this occur in the cytoplasm? How would the reactions be "protected" from each other?

      5. It’s reasonable that large volumes of stuff be made in the liver.
      And obviously there are all kinds of reactions happening there!
      But why can’t I find web pages that clearly say this? I’m looking for articles that state:
      a) Liver makes what products of interest to this subject.
      b) They are transported to cells how (eg. red blood cells carry oxygen).
      c) Cells receive products when ready to do replication.
      d) Cells do something to the products if the products from liver are not what’s needed by the polymerase to do replication.

      There are many web pages that clearly describe the mechanics of gene expression (transcription, mRNA, translation). Pictures with stained components help explain mitosis. Where are there similar explanations of DNA replication and nucleotide generation?

    • #96403
      JackBean
      Participant

      4. First of all, there are needed 3 billions of nts in EACH cell πŸ˜‰
      Second of all, as kolean wrote, I think, the cells in our body do not divide usually, so you do not have to generate 3 billion Γ— 10^14 nucleotides πŸ˜‰

      5.
      http://en.wikipedia.org/wiki/Liver#Physiology
      d) if the cell needs 3 BILLIONS of nucleotides. Do you think, it really matter if it gets e.g. one guanine more or less?

      I recommend to look for books Biochemistry by Voet & Voet or by Stryer, Tymoczko and someone… there you can find many pictures and probably also CDs with some animations πŸ˜‰

    • #96409
      gs99
      Participant

      Yes there are many cells in my body that are NOT in the mood to divide today.
      However, there are many times in the history of an organism when cells are prone to divide, correct?

      And evidently, certain cells of the human do continue to divide:
      "Other types of cells, such as epithelial cells, continue to divide throughout an organism’s life and rarely enter G0."
      Under heading "In relation to the cell cycle" at http://en.wikipedia.org/wiki/G0_phase

      Obviously my question relates only to those cells that DO decide to activate Phase "Synthesis" in preparation for Mitosis.

      4.2
      I was thinking of the requirements of EACH cell that divides.
      "two nucleotides on opposite complementary DNA or RNA strands that are connected via hydrogen bonds are called a base pair"
      "The (human genome) is estimated to be about 3 billion base pairs long"
      http://en.wikipedia.org/wiki/Base_pair

      Doesn’t that mean 6 billion nucleotides in the DNA are required for EACH dividing cell?
      That comes to about 1.5 billion of each nt (A, T, C, G).
      Am I looking at this incorrectly?

      5.
      The article you mention
      http://en.wikipedia.org/wiki/Liver#Physiology
      does not include the terms DNA, nucleotide, or purine.
      I’m not sure how it helps at all.

      A linked article mentions several proteins provided by the liver, but I don’t see any devoted to exporting nt stuff.
      http://en.wikipedia.org/wiki/Proteins_p … _the_liver

      I looked for book "Biochemistry" by Voet & Voet. Not in local libraries, including the Community College.
      It is for sale online, so I’ll need to start saving money for that.

      Does anyone know if that book explains clearly in one place how:
      a. the liver produces either nt molecules or things later used for nt construction
      b. how those things are transported from liver to cells
      c. what (if anything) the cell does to those things to enable DNA replication

      There is a place for technical jargon; there is also a place for explanation in common language.
      For example when writing computer programs, instructions are written in code structures of various languages (eg. Visual Basic).
      It’s considered a good professional thing for the programmer to insert comments WHY certain code was utilized.
      The comments do not affect how the program executes, but are helpful to anyone reading the program to understand what’s going on.

      I’m just trying to understand "what’s going on" to generate nucleotides for replication.

      Thanks JackBean, for your help in this mystery.

    • #96411
      kolean
      Participant

      Wanted to add that I think the liver is for the salvage pathway, or the primary processing of ingested DNA/RNA. In your first link, the article said that all nt synthesis starts with PRPP that can be made from ingested nts.

      You also can not ‘see’ nucleotides being processed by staining slides. The chromosomes that you can see during mitosis is when the linear chromosomes are all condensed into a thick rope, and the stain shows up nicely on slides. The other visual of the ‘beads-on-a-string’ DNA is thru the use of the electron microscope. Crystallography and looking at the sequence of the protein is how its structure is proposed.

      This is a cool animation that I found last year:
      http://www.hhmi.org/biointeractive/dna/ … n_vo2.html

      I can also see that the amount of nucleotides is mind bending for you. If you think about all the cells you ingest everyday, you can see why there would even be a surplus of nts in the fluid outside of the cells. In fact you can even get a metabolic disease from the processing of purine metabolism called Gout.
      from the Wikipedia on Gout . . . .
      Uric acid is a product of purine metabolism, and in humans is normally excreted in the urine. Purines are generated by the body via breakdown of cells in normal cellular turnover, and also are ingested as part of a normal diet. The kidneys are responsible for approximately two-thirds of uric acid excretion, with the liver responsible for the rest.

      You also have to take into account that the nitrogenous bases that make up the nts, are also used for alot of metabolic pathways (especially ATP – the energy currency of the body/organism, and it can be converted into other NTPs (nucleotide tri phosphates). There is alot going on in a system that has many checks and balances to keep it at homeostasis, with many functions to perform.

    • #96416
      JackBean
      Participant

      Well, you already have one strain of DNA and replicates only the second one, so divide your number by 2 πŸ˜‰
      Anyway, read, what kolean wrote. Also notice, that billion molecules is only 10^-15 mole, that is really, really, really just a little πŸ˜‰ Notice, that in EACH living cell is every minute produced RNA of at least several thousands if not millions of nts πŸ˜‰

      5. that should just show, that livers are really the factory of the body πŸ˜‰

      Well, you do not have any library around? You don’t have to buy Voet just because of one problem πŸ˜‰

      Unfortunatelly, the nature did not provide any comments and that’s why we study all these things πŸ˜‰

      Asking why in science is a little problematic. You may try to answer, maybe your answer may fit the reality a little, if you’re happy, but may never be sure, what is really reason and what consequence πŸ˜‰

    • #96436
      gs99
      Participant

      JackBean,
      You said "Well, you already have one strain of DNA and replicates only the second one, so divide your number by 2"

      Could you please clarify that?

      In the newly-formed daughter cell from Mitosis, what is in the DNA?
      One double helix strand of DNA.
      3 billion base pairs in human genome, each pair having two nucleotide molecules.
      That makes 6 billion nucleotides, give or take a guanine.
      Is that correct?

      The nucleotides can be A, T, C, or G.
      Assuming random assignments, about 1.5 billion of each.
      Note: The A count equals T count, and C count equals G count.
      (A+T) is probably different than (C+G).
      But my focus is not in exact accounting.
      (Rumor has it that there is some "junk DNA" on chromosome 22 that has final subtotals of each nt type.)

      To replicate the human DNA, how many "new" nucleotides are needed?
      (This is part of the job’s "bill of materials".)

      What number do I divide by 2?

    • #96440
      kolean
      Participant

      Think of the DNA as a terabyte. And instead of 1 and 0 s, it is A, T, C, and G s. Basically a code to program by. Then think of all the coding you would need to do, just to do the basic metabolism of a complex system such as a human.

      And please do not say "junk DNA". There is no such thing. It just shows our ignorance at our DNA knowledge that we don’t know what that sequence of DNA does yet. We have just recently found new ‘genes’ that are really just produce the RNA (made from the ‘junk’ DNA) that is used for regulation. And yes, some of the DNA gets inserted into our genome from outside sources (not just the usual doubling of a DNA from the sliding model), but I figure this is raw material of DNA for the organism to use and develop new systems/programs.

      Again, there is no short supply of nucleotides. They are in high concentration in the cell. Humans ingest cells all day long. And inside cells is DNA. You would only have to worry if you were malnourished/starving, and thus no cells to digest and salvage the nts, and if your ATP (and possibly GTP) weren’t available because they were being used by the metabolic system as energy.

    • #96444
      JackBean
      Participant
      quote kolean:

      Again, there is no short supply of nucleotides. They are in high concentration in the cell. Humans ingest cells all day long. And inside cells is DNA. You would only have to worry if you were malnourished/starving, and thus no cells to digest and salvage the nts, and if your ATP (and possibly GTP) weren’t available because they were being used by the metabolic system as energy.

      Well, I think that in iΓ³ne of Biochemistry books was, that actually any of nt from food is actually used in the body, but these are all build de novo

    • #96452
      gs99
      Participant

      Kolean,
      Thanks for the link to HHMI, and thanks to the people who produce the various media.
      [edited 1/6/10. This link does not show the nucleotides. Please see correction in next post]
      http://www.hhmi.org/biointeractive/dna/ … n_vo2.html
      They almost seem real! I would not have imagined the action of DNA replication being that fast.

      The video reminded me of a sewing machine operation, when attaching two layers of material together.
      In each cycle,
      >The needle with thread "n" is pushed through the material layers.
      >The bobbin with thread "b" (underneath the material) causes a connection to be made between the two threads.
      >A small tool moves the materials exactly the same short distance for the next stitch.
      In reality it goes Very fast, but this shows it in slow motion:
      http://materialmama.wordpress.com/2007/ … ern-ideas/
      With a sewing machine, there is simply one needle thread and one bobbin thread.
      The needle is not concerned about matching things, as polymerase is.

      In the HHMI video, (If I understand correctly) the nts (all four types) appear "floating around" and get attracted somehow at the right time to where the polymerase is making attachments to the DNA strand.
      The nts float in the nucleoplasm, a highly viscous liquid that evidently provides support for all the components.
      But objects normally move slower through liquids.

      My basic question remains: How does one of the needed nt move into position when and where it’s needed?

      —-
      I agree with your "junk DNA" thought. That’s why I put it in parenthesis.

      —-
      I disagree slightly about the 1s and 0s, which are the basic units of information in a typical computer.
      The natural basic units are element atoms (not counting the smaller things being discovered).
      Each nucleotide type is made in a separate way of certain atoms.
      To a non-chemist, these are complicated in themselves.
      But yes, each molecule type could be abbreviated with its letter.

      —-
      "Then think of all the coding you would need to do, just to do the basic metabolism of a complex system such as a human."
      But I try to understand the mechanics of "small" parts, like gene expression and DNA replication.

      When I explain scientific things to others, I try to talk in terms people know.
      When talking about the solar system, I find it useful to envision smaller models.
      Like, if the earth is an inch in diameter, how big is the moon and sun. How far away?
      Students may get a different feeling about the force of gravitation, seeing the objects together.

      To explain small things such as DNA, we need to envision larger.
      If DNA were produced in a factory, typical questions may be:
      How are orders received; from where?
      What does the Bill of Materials look like? How will the raw materials arrive?
      What machines and tools are needed?
      How much energy will be needed?
      How quickly must the job be done?
      What provisions for quality assurance?
      I would like to see a web site dedicated to this subject.
      Where the latest scientific discoveries about DNA replication are explained in language all can understand.
      Videos that can be run in slow motion, and including text.

      —-
      "Again, there is no short supply of nucleotides."
      And they evidently are available in the ratio that is needed, in the nucleus.

      I have found a way to order the book Biochemistry by Voit & Voit, through a state-wide library search facility.
      I’m anxious to see if it answers any of my questions.

      Thanks again Kolean and JackBean

    • #96466
      gs99
      Participant

      I apologize for providing the incorrect link to Howard Hughes Medical Institute.
      The one that I mentioned does not show the nucleotides.
      But this page has a video of "DNA transcription (basic detail)", a similar process to DNA replication.
      http://www.hhmi.org/biointeractive/dna/ … n_vo1.html

      As I looked closer at this video, I noticed the nt "building blocks" appear as two colors, white and yellow. Perhaps to indicate a protein moving each nt through an "intake hole" of the polymerase.
      And at the right time…

      Here’s a possibility:
      All A’s dock at one waiting line, the T’s dock in an adjacent line etc..
      Like people getting onto a roller coaster, each waiting line gets into different cars.
      Only here, the roller coaster has only one "car", the next spot on the DNA string.
      The DNA polymerase controls the "dispensing" of next appropriate nt waiting for its ride.
      That would enable fast operation!

      I’ve found a book "The Way of the Cell", by Franklin M. Harold (Oxford University Press 2001),
      that describes the many ways that proteins function, and other things explained clearly.

      With my background in computers, I noticed this:
      "There are cascades of such "kinases", one switching on the next, and each potentially the target for a signal.
      The common conception of proteins serving either as catalysts or as structural elements is incomplete:
      for many purposes it is more useful to emphasize their roles as computational elements in information-processing networks."
      (page 53, with reference to Bray, 1995)

      Recently I’ve thought of proteins as being computer applications that do the work for an organism.
      Is there an operating system that enables the apps?
      Like the news reporter said, "This story has many moving parts."

    • #96468
      JackBean
      Participant

      The polymerase has simply high affinity for the nts. If the nt fits to the parental strain, it is incorporated, if not, it is released, eventually hydrolysed away, if it was already incorporated.

    • #96482
      kolean
      Participant
      quote gs99:

      Here’s a possibility:
      All A’s dock at one waiting line, the T’s dock in an adjacent line etc..
      Like people getting onto a roller coaster, each waiting line gets into different cars.
      Only here, the roller coaster has only one “car”, the next spot on the DNA string.
      The DNA polymerase controls the “dispensing” of next appropriate nt waiting for its ride.
      That would enable fast operation!

      Now, how would you go about proving this theory?
      What kind of experiment would you perform to show that this is what happens?
      And you could go about this with a model organism, or perhaps just dividing cells in culture (though there is a difference between in vivo and in vitro).

      There are chaperone proteins that help in the proper folding of proteins as they are being translated. RNA also has some help in folding into the proper hairpin structure. Why not help in getting proper nucleotides for processing into the DNA? (You might like to learn about translation: mRNA into a protein structure. There is tRNA that holds onto the amino acid while the polymerase ‘reads’ the mRNA template codon sequence for translation).

      Remember that the DNA polymerase is only one subunit of the whole replication complex (for the initiation and elongation of the DNA replication mechanism).
      I am studying epigenetics and they have just theorized that there is another subunit to add to the replication complex that helps to maintain the methylation status of the DNA during DNA replication.

    • #96488
      gs99
      Participant
      quote :

      Kolean wrote:
      Now, how would you go about proving this theory?

      I don’t have the education and experience to know that.
      I’m just guessing based on how a robotic system might do it.

      The more I learn about proteins, the awe increases.

      I don’t understand how scientists discover what happens within the nucleus, itself being within a cell.
      Microscopes don’t work at that level do they?
      And I would think everything has the same general color, not like the nice pictures we see in the books or the HHMI videos!
      How do they learn how things move from here to there?

      I don’t understand how DNA polymerase can:
      # process each of the billions of nucleotides in sequence (the exact number still being worked out)
      # determine what kind of nucleotide is on the original strand (Could a lab expert identify these molecules easily?)
      # do what’s needed to obtain a new complementary nucleotide (What is there about an A that says: "Give me a T"?)
      # enable the new nt to be connnected to the original nt with hydrogen
      # keep track of what segments are done in reverse
      I’m sure this is not a complete list.
      And it does this accurately and (according to HHMI) very very fast.

      The answer evidently is in your comment about the replication complex; it is a complex mixture of organized things.
      But aren’t they all just a collection of molecules made of amino acids?

    • #96498
      JackBean
      Participant

      The polemerase does not recognise actually anything, everything is done by complementary bonding of paires of nucleotides. If is this bonding strong enough, the polymerase goes on if not, it is released again and searched for new proper nucleotide

      # keep track of what segments are done in reverse
      what?

      But aren’t they all just a collection of molecules made of amino acids?

      Sure, they are, like all enzymes. Aren’t the machines just composed of other pieces? And can they produce them?

    • #96566
      gs99
      Participant
      quote JackBean:

      The polemerase does not recognise actually anything, everything is done by complementary bonding of paires of nucleotides.

      Regarding the important role of new nucleotides, various web sites explain it in different ways:
      >You mention "complementary bonding". I could not find anything about this term.
      Could you please provide a web site that explains?

      >The HHMI movie ignores them altogether.
      http://www.hhmi.org/biointeractive/medi … vo2-lg.mov

      >Talking of transcription (similar process) this page says:
      "As RNA polymerase reads each nt, it brings in the complementary nt and bonds them together forming the mRNA strand".
      http://www-class.unl.edu/biochem/gp2/m_ … ne_a2.html
      Notice it says the polymerase READS each nt.

      >Others say the nucleotides are "attracted".

      DNA replication is done in a liquid, which normally impedes motion of objects.
      How are these nucleotide molecules floating in the nucleoplasm pursuaded to move quickly at the right time to where they are needed?

      quote JackBean:

      keep track of what segments are done in reverse
      what?

      I probably used the wrong words. I was referring to the additional steps completed in the lagging strand, where synthesizing is done "backward".
      "Two polymerase enzymes are required, one for each parental DNA strand.
      Due to the antiparallel nature of the DNA strands, however, the polymerase enzymes on the two strands start to move in opposite directions."
      http://www.wiley.com/college/pratt/0471 … index.html

      The Primase enzyme is utilized often in the lagging strand.
      It has the ability to move itself "down the line" and generate short segments of RNA primer as needed.
      Now how does this collection of atoms know when and how to do that?

      The initial experience of chemistry is to learn the characteristics of elements and compounds.
      Something happens when mixing four grams of this with a liter of that.
      And matter normally has standard properties when in a solid, liquid, or gaseous state.

      But in biochemistry, it seems to be different.
      A single molecule comprised of atoms or other molecules (eg. DNA polymerase, Primase enzyme) has the ability to do things on its own!

      One web site claims there may be thirty different tools (proteins, enzymes etc.) working together in DNA replication. Another uses the term "military precision".

      There are various claims about multiple processing. Most web sites show only a single replication fork.
      One claims there are hundreds of concurrent DNA replication activities in a cell.
      Is the DNA separated into chromosomes when replication occurs?
      There are also various claims about the speed.
      I appreciate the internet, but sometimes it’s difficult to know what’s the latest information.

    • #96574
      JackBean
      Participant

      >Others say the nucleotides are "attracted".
      This is the complementary bonding. Complementary bonding (or binding) means, that A binds always T and C binds always G and vice versa πŸ˜‰
      http://www.elmhurst.edu/~chm/vchembook/ … sepair.gif
      This is due to spatial restrictions and H-bonding restrictions (position of donors and acceptors).

      You are still NOT understanding, that the solution in cell is actually very dense, containing many molecules.

      As I mentioned above, in bacteria you have only one replication origin, so you have only one replication at a time (although after some time, new replication can start, although the previous did not finish yet), but in humans you have replication origin each 3-300 thousands of bps. These are fired several of them at a time in a coordinated manner.
      The speed of replication varies in dependence of polymerase.

    • #96600
      gs99
      Participant

      Polymerase Chain Reaction (PCR) seems to provide some insight.
      http://en.wikipedia.org/wiki/Polymerase_chain_reaction

      Why Taq is utilized
      http://en.wikipedia.org/wiki/Taq_polymerase

      And a Virtual lab where anyone can do it:
      http://learn.genetics.utah.edu/content/labs/pcr/
      These contents are placed into the pcr tube:
      # extracted DNA (to be copied)
      # Primer 1
      # Primer 2
      # New nucleotides (ATCG building blocks)
      # DNA polymerase
      The pcr tube is then put into the DNA Thermal Cycler.
      The Cycler automatically changes the temperature in cycles to simulate what happens in the cell nucleus.
      Many copies of a specific DNA segment are thereby generated.

      (1) I noticed that no additional proteins were needed to facilitate movement of the nucleotides.
      That seems in opposition to my guess that "proteins" were utilized.
      I still am curious how they move, as if by magnetic force.

      (2) The new nucleotides are not attracted automatically to complementary nts on their own.
      Otherwise, why is DNA Pol needed?

      (3) The DNA Pol "read the DNA code and then attach matching nucleotides".
      This seems in opposition to what JackBean said:
      "The polemerase does not recognise actually anything"

    • #96601
      JackBean
      Participant

      Well, I’m not master in these things, probably MrMistery could shed some light into this topic…

      (1) that’s, why there is temperature change, not to need other proteins…

      (2) Pol is used for the same thing as other enzymes – to catalyse reaction, to speed it up

    • #96616
      gs99
      Participant

      (Edit 1/15/10. There was a post that originally appeared before this one, from "rania".
      It was later recognized as a bot and therefore deleted. See 1/13/10 post by mith)

      quote Rania:

      Why don’t you just buy these?

      I’m interested only in the interaction of DNA Polymerase with nucleotides.

      All the diagrams show sequential processing, where DNA Pol:
      (1) "reads" the nt on the template
      (2) determines the complement
      (3) "obtains" a copy of that complement nt molecule (as a neucleoside triphosphate)
      (4) attaches the new molecule to the new DNA strand
      (5) proceeds to the next nt on the template
      In step 4, it appears that two phosphates are removed from each new nt molecule and hydrogen bonds are added.
      http://en.wikipedia.org/wiki/File:DNA_polymerase.svg

      Any of that incorrect?

      Being a computer programmer, I can easily visualize "sequential processing".
      But – not being a chemist – I’m looking for the operational mechanics.
      How does DNA Pol "obtain" the appropriate nt molecule?

      I’m aware of the four "natural forces". Are there additional forces at play here?

      The answer seems to preclude any other proteins, since this part of DNA replication works in PCR where known objects are included.

      ps. to Rania,
      Thanks for your reply,

      quote Rania:

      Let us know when you figure it out.

      but everything that followed the first occurrence of that sentence was completely over my head.
      At least I couldn’t see that it applied to my question.
      Welcome to the forum!

    • #96622
      kolean
      Participant

      You definitely need to know about chemistry, especially organic chemistry. There are covalent bonds, such as the bonds for the amino acids to form a protein. This protein then has amino acid side chains that will stick out of the surface of the protein (globular especially) and some that will be inside of clefts, and perhaps a metal ion will also be inside. Now when the protein is specialized for a function, like the DNA pol, it has specific placement of the amino acid side chains, so that there will be certain forces to attract specific charged/uncharged molecules to the function it is to do. The complementary binding of the nucleotides A to T is not covalent binding (sharing of an electron), but opposite attraction in hydrogen bonding.
      http://upload.wikimedia.org/wikipedia/c … ir.svg.png
      this shows the hydrogen bonding: hydrogen has a positive force, while the oxygen has a negative force, and since they are opposites, they attract to each other. Though not enough to swap electrons and bond covalently.

      And because there is no covalent bonding (though the phosphate backbone will covalent bond to the next nucleotide incorporated into the strand), it has to be guided to the right space of forces around it, and has to be especially complementary (correct hydrogen bonding to the correct complementary base) bound before that catalyzed reaction of nucleotide addition takes place.

    • #96623
      gs99
      Participant
      quote kolean:

      You definitely need to know about chemistry, especially organic chemistry.

      Agreed!

      quote kolean:

      Now when the protein is specialized for a function, like the DNA pol, it has specific placement of the amino acid side chains, so that there will be certain forces to attract specific charged/uncharged molecules to the function it is to do.

      Awesome!

      I assume each side chain operates by a specific force to do a specific activity, is that correct?
      So a specific side chain doesn’t do multitasking?
      I didn’t find any details for this. I’m remembering they are a collection of atoms…

      I’m guessing these steps that need to be done by the side chains:

      A moves the DNA pol to the beginning of the template
      (or the DNA pol attracts the beginning of the template) (Either way, this is the first "attraction" to get things rolling)
      B maintains proper closeness to the template
      (These objects are floating in nucleoplasm; there are no handrails to hold as astronauts have on a space walk)
      C reads the template nt, and gives message to
      D that determines what is the complement, gives message to
      E that turns on forces to attract a complement neucleoside triphosphate floating in the area
      (Or possibly E has additional parts for each type: Ea, Et, Ec, and Eg)
      F grabs the new molecule and positions it for an "operation"
      G removes two phosphates
      H guides the molecule to the right space of forces around it, so covalent bonds can be made at the backbone end
      I attracts the proper hydrogen atoms to connect the two nt molecules
      J grabs the template somehow and moves it to the next nt

      The side chains are on different sides of the DNA pol
      http://upload.wikimedia.org/wikipedia/e … TaqPol.jpg
      so I assume the forces are exerted from various sides.
      This may sound simple, but doesn’t that complicate handling of the molecules?

      Some of these steps are cell-like (eg. sending messages), but how else do these simple side chains work with each other?

      Kolean, is this what you meant?
      Thanks again for your direction.

      ps, My Voet "Biochemistry" book is in. I’ll be taking some time to review it.

    • #96631
      JackBean
      Participant
      quote gs99:

      The side chains are on different sides of the DNA pol
      http://upload.wikimedia.org/wikipedia/e … TaqPol.jpg

      Which side chains do you mean? Do you realize, that on the picture is only the C-alpha backbone and no amino acid’s side chains?

      Look to the Voet, read it carefully from the very first page. After will you have some insight into basic chemistry and biochemistry come back and ask πŸ˜‰

    • #96646
      gs99
      Participant
      quote JackBean:

      Which side chains do you mean? Do you realize, that on the picture is only the C-alpha backbone and no amino acid’s side chains?

      This page indicates that all amino acids have side chains.
      http://en.wikipedia.org/wiki/File:Amino_acids.png

      Kolean had said (DNA pol) "has specific placement of the amino acid side chains, so that there will be certain forces to attract specific charged/uncharged molecules to the function it is to do."

      I got the impression that the "certain forces" relate to the side chains; perhaps I’m mistaken.

      Are there different definitions of "side chains"?

      At any rate, I was envisioning the various steps done by the DNA pol enzyme, not taking anything for granted. In slow motion, recognizing everything that it does.

      Can anybody reading this (with advanced knowledge of biochemistry) explain in common language how DNA pol performs the steps I mentioned?

      If you can explain it, should you be entitled to a Nobel prize?

    • #96648
      JackBean
      Participant

      I know, that all AAs have side chains, but I’m asking, whether you know, what are these side chains, as you’re talking about them and refering to picture, where they are NOT.

    • #96650
      kolean
      Participant

      Check this out:
      http://en.wikipedia.org/wiki/File:Proteinviews-1tim.png
      This is the same enzyme/protein, but biochemists show it different ways. The last one is the one I was talking about. See how the blue is for the side chains that have a basic charge, and red is for acidic side chains, and polar is green, and nonpolar is white, and these are only on the surface (that is why it is called a surface view) and that is what can interact with other proteins. But not only do you have the different charges from the side chains, you also have the shape and the space the amino acids side chains occupy and don’t occupy. I like to think of it as a collosal puzzle with many tiny pieces that all fit together somehow, and it is not static – but moving also!
      oh yeah, check out the diagrams of amino acids and their side chains:
      http://en.wikipedia.org/wiki/File:Amino_acids.png
      (and that is a backbone diagram of amino acids. you’ll have to know that there are hydrogens missing, and every intersection has a carbon atom there).

    • #96654
      mith
      Participant

      sorry, rania is a bot. post has been deleted.

    • #96663
      gs99
      Participant
      quote mith:

      sorry, rania is a bot. post has been deleted.

      When I first read that post, I wondered about the content.
      From the initial question – Why don’t you just buy these? – I didn’t know where it was coming from.
      And then certain things that followed, the sentence that was repeated and other verbiage that seemed to be from other discussions.
      The appearance was something not edited by a normal person.
      I did make a comment. If I understand what a bot is, I feel better now. I had been concerned about hurt feelings.
      Thanks for your efforts.

    • #96668
      gs99
      Participant
      quote kolean:

      See how the blue is for the side chains that have a basic charge, and red is for acidic side chains, and polar is green, and nonpolar is white, and these are only on the surface (that is why it is called a surface view) and that is what can interact with other proteins.
      quote JackBean:

      I know, that all AAs have side chains, but I’m asking, whether you know, what are these side chains, as you’re talking about them and refering to picture, where they are NOT.

      From my observation, it seems there is a difference of opinion here.
      I’m not going to focus on that, because I don’t have the training to understand it today.

      But I have come to a conclusion about my questions and would welcome your comments.

      This morning, I came to this comparison of chemistry and biochemistry. This is not something I’ve seen in a book or on a web page.

      CHEMISTRY
      Heating the PCR tube to 95c to separate the DNA double helix.
      I’m guessing that no matter what is in the PCR tube, hydrogen bonds will be dissolved, including those in DNA.

      BIOCHEMISTRY
      The enzyme Helicase (along with other enzymes etc.) is sent to a specific point in the DNA.
      The cell knew it would be needing these proteins, so it generated them ahead of time.
      At the correct time, these proteins are activated and move to where they are needed.
      With no change of temperature, Helicase proceeds to separate the DNA in its own way.
      That’s just one small (but very important) role in DNA replication.

      My conclusion is that proteins have "micro-intelligence" that activates whatever forces they have.
      The Amino Acids are made of ordinary atoms.
      A chemist could mix these elements in a zillion ways, changing temperatures etc. and they still couldn’t do anything special.
      But combine them in the special patterns of a protein, and things happen!
      They can move. They can read. They can change other molecules. With "military precision".
      Cells are viewed as the smallest living thing.
      But the animations produced by HHMI and others portray proteins (and other components within the cell) acting as if they were alive.
      Proteins made of molecules, made of atoms.

      If this were a movie, the credits would take hours.

    • #96672
      jonmoulton
      Participant

      gs99, invoking "micro-intelligence" isn’t needed to explain the arrival of activated nucleotides during replication. The Polymerase doesn’t "send out for" the right nucleotide triphosphate; instead, random nucleotide triphosphates bump into the template nucleotide. If the nucleotide triphosphate hydrogen bonds correctly with the template nucleotide, the new phosphodiester linkage forms. If the nucleotide triphosphate is the wrong one then usually it will not slip into the correct orientation to form the new bond, so it is quickly displaced and another random activated nucleotide slips into position at the polymerase active site and bumps against the template nucleotide. Eventually (in a tiny fraction of a second) a correct nucleotide is fitted and reacted and the polymerase advances. If a mistake is made (and this sometimes happens), it is almost always caught by the "proofreading" function of the polymerase and corrected. If not, a mutation has occurred (a rare event). The process is driven by diffusion and thermally-driven shaking and collision, not any form of intelligence on the part of a protein. If you put a thousand Lego blocks in a sack, roll it around and dump out the blocks, some of them will have fit together. It is really a similar process, with greater selectivity about which parts fit together and happening at the blazing speed of molecular interactions.

    • #96708
      gs99
      Participant
      quote jonmoulton:

      another random activated nucleotide slips into position at the polymerase active site and bumps against the template nucleotide.

      (1) Seems like a lot of "slipping into position" and "bumping" with incorrect molecules.
      This results in a 75% failure rate. And worse if the nt triphosphates aren’t consistently homogenized.
      That doesn’t sound good for an organism to survive.

      (2) Why is randomness used here when it’s not used elsewhere?
      All that I’ve read indicates specific things happening, and happening in a specific sequence.
      Do the proteins fold in random ways?
      Do Single-strand binding proteins decide to appear randomly?
      Does Primase operate randomly?

      Various web sites describing the cell and proteins give a strong impression that randomness is not involved.
      For example, this recent article had headlines:
      "Scientists Uncover Role of Protein Critical for Activating DNA Replication",
      http://www.sciencedaily.com/releases/20 … ience+News)
      and the article includes this comment:
      "In multicellular organisms, the duplication of the DNA in chromosomes starts at multiple sites, called origins, within the genome.
      For the genome to retain its integrity each time a cell divides, it’s crucial that each origin "fires," or becomes active, just once and only during a timeframe in the cell cycle known as the S-phase.
      A large number of proteins cooperate and interact with military precision to ensure this "once-only" condition."

      quote jonmoulton:

      The Polymerase doesn’t “send out for” the right nucleotide triphosphate;

      Many web sites like this one from University of Nebraska give the opposite impression.
      In this case, it’s explaining Transcription:
      http://www-class.unl.edu/biochem/gp2/m_ … ne_a2.html
      "As RNA polymerase reads each nucleotide it brings in the complementary nucleotide and bonds them together forming the mRNA strand."
      There are a lot of web sites apparently giving wrong information to the public!

      quote jonmoulton:

      The process is driven by diffusion and thermally-driven shaking and collision

      http://highered.mcgraw-hill.com/sites/0 … works.html
      The end result of diffusion is a scattering of molecules.
      How does that drive the appropriate nucleotide to where it’s needed?
      And what exactly is "thermally-driven shaking and collision"? (no results in Google)
      Can you please explain these buzz words to the class?

      quote jonmoulton:

      invoking “micro-intelligence” isn’t needed

      See first definition: "to call for with earnest desire"
      http://dictionary.reference.com/browse/invoke
      I posted a question here about nucleotides in DNA replication, "calling for help", you might say.
      I have an earnest desire to obtain answers; hoping some reader would volunteer information.
      In preparing various posts, I never thought of the word "invoke", but I see that it could fit.
      That’s how a forum works. And I appreciate all the replies, especially those with references.

      So what did you think of my comparison of biochemistry with chemistry?
      You may know, I do not have training in either; just read books and web pages.

      I thought myself clever in noticing that in PCR, DNA pol is the only protein.
      Therefore, I was apparently incorrect in thinking that a separate protein "delivers" the nucleotide to DNA pol. In scientist fashion, I published the results.
      (The reasoning came from Translation, where tRNA "brings" the Amino Acids to Ribosome, according to something I read somewhere. Has that been changed also? If it is done randomly with 20 some possibilities, what is the failure rate?)

      Back to biochemistry being different than chemistry.
      Atoms brought together in a special way. (synthesis of protein)
      Working together. Signalling one another. Cooperating.
      Can anybody argue that it doesn’t happen?
      How many times in this discussion has it been mentioned about how many proteins may be needed to accomplish DNA replication?
      Which protein would you say is expendible?
      Can a chemist with a masters degree prepare a mixture of these same elements to do the same work?

      Perhaps we could call it "micro-works" – they do the work!

      All living things – from bacteria to elephants – have "micro-works",
      or whatever.

    • #96711
      JackBean
      Participant

      The chemical reactions are all driven by random moves and random collisions, just proteins are catalysts, they speed up the reaction, helping all molecules to react in the correct orientation and stuff like that.
      If you had e.g. ethene and hydrogen, nothing will happen. But add some platinum and you will get ethane. That is catalysis. But the platinum is still not alive πŸ˜‰

    • #96720
      gs99
      Participant
      quote JackBean:

      If you had e.g. ethene and hydrogen, nothing will happen. But add some platinum and you will get ethane.

      You’re right, there are countless examples in chemistry, I’m sure.

      But don’t you agree that in biochemistry, things happen at a different level?
      Isn’t the difference illustrated well by comparing
      > PCR step #1 heat to 95c to break the hydrogen bonds (chemistry)
      > In life, Helicase etc. doing a similar thing but at certain places, in an organized way?

      quote JackBean:

      (Proteins) helping all molecules to react in the correct orientation and stuff like that.

      Yes, but each molecule in its time, not all in one bang! All the explanations I’ve seen talk about sequential processing, moving the DNA template through DNA pol like a movie film through a projector. Are these incorrect?

      http://en.wikipedia.org/wiki/DNA_polymerase
      says: "the polymerase "reads" an intact DNA strand as a template and uses it to synthesize the new strand."

      I think most people reading that web page conclude that the protein actually READS!
      http://en.wikipedia.org/wiki/Reading_(process)
      says: "Reading is a complex cognitive process of decoding symbols for the intention of deriving meaning (reading comprehension) and/or constructing meaning."

      http://en.wikipedia.org/wiki/Proofreading_(biology)
      Not only does it read, but it proofreads!
      What chemical reaction does that?

      What conclusion does a student reach when reading these web pages?
      Are the pages incorrect?

    • #96726
      JackBean
      Participant

      IMHO they are misunderstood. Or maybe overestimated…

    • #96748
      gs99
      Participant

      OK, let’s say all the websites I provided are "incorrect".
      (If they are, a lot of people are being deceived.)

      Are there any websites that explain nucleotides coming together by random "slipping" and "bumping",
      driven by "diffusion" and "thermally-driven shaking and collision"?
      I searched with various combinations in Google but couldn’t find anything.

      Or is the correct information only found in one book by Voet?
      (Which I hope to get my copy very shortly…)

    • #97037
      gs99
      Participant

      An update after reviewing book "Biochemistry" by Voet.
      The edition sent to me from state university library is 1990; there may be new discoveries since then.
      In the section "Enzymes of Replication" I see no mention of "random bumping" or that the process is driven by diffusion and thermally-driven shaking and collision.
      It doesn’t explain what I was looking for – how the appropriate nt molecule is "brought into" the precise spot of connection into the DNA strand.

      I have found a few web pages that mention the random concept, like this one.
      http://blc.arizona.edu/courses/181Lab/M … NAPol.html
      but there’s no date or references.

      And I thought of a further complication.
      As these nt molecules are floating, aren’t they in all kinds of positions?

      I envision this demo:
      A round container filled with a liquid. Place forty ping pong balls in the liquid.
      Ten balls are red, ten are blue, ten are white, ten are yellow.
      Each ball has an "X" on one side.
      Vibrate the liquid to encourage bumping. (I’m not sure how this is done in vivo.)
      How long will it take a red ball with its "X" bumping into a predetermined spot "Z" on the container’s side?
      If the balls are in a crowded environment, they would have a problem changing position.
      If they could move easily, they may be bounced past spot "Z" easier.

      If this is not the "correct" simulation, what should it be?

    • #97039
      kolean
      Participant

      I am with Jack Bean in that they are overly simplified. And right now I do not know of any website that would do it justice to the reality of it. There is just so much going on, but as scientists we usually study one or two aspects of the situation.

      You need to learn the alphabet first. You are already to make novels because you have stories to tell, but you do not even know about words yet.

      You have yet to grasp the concept that these molecules have shape and charge. Everything is not a random ‘bounce’. You have to take into account that most biological reactions take place where there is water. Water is very polar, and can even form clathrins around certain other charge molecules. It can hold a protein in place with all of its hydrogen bonding. So much info to look at. Keep building upon it.

      A better analogy is to look at the macro. How does a city run smoothly? How does everybody get into there cars in the morning and drive to work? How are you able to go thru a drive thru for lunch and get exactly what you ordered? And all the other 30 cars behind you? What happens if you did not get what you exactly ordered? Do you check your bag as it is presented to you at the window? and notice you got onion rings when you wanted fries? Do you hold up the whole process and wait to get your fries? (proofreading here) Or do you just accept the onion rings because it is all good and you proceed on your merry way (mutation that may not cause any trouble), Do you take your bag and not notice till you are just about to go out of the parking lot, and so you park the car and go in and correct the mistake then (not proofreading here, but mismatched corrections by other enzymes that notice a ‘bump’ in the DNA complementary binding). Or do you eat the onion rings because you haven’t had them in such a long time and they smell wonderful, only to remember that you are allergic to them and you either get sick (mutation that causes some harm) or get in a car crash and die (apoptosis – cell death).
      Well it is just one analogy. . . . may not be a scientific one, but I liked it!

    • #97044
      JackBean
      Participant

      gs:
      first of all, read first about enzymes in common, how they work, ways, how they catalyze and stuff…
      second: from your link:
      The Big Job:Adding nucleotides
      How does Polymerase know which nucleotide to add? The short answer is, it doesn’t. There is no reason to believe that DNA Polymerase ever achieves direct knowledge of the nucleotide it is adding! Indeed, it has been elegantly demonstrated that it can add a slew of nucleotides outside of the canonical Big 4 it’s used to. How, then, does it achieve "chemically impossible" low rates of error?

      So, read the link carefully, I think there are the answers (athough I haven’t read it whole).

      kolean: nice analogy :o)) I like it πŸ™‚

    • #97050
      gs99
      Participant
      quote kolean:

      Everything is not a random ‘bounce’.

      That’s what I’ve been thinking! There’s gotta be something more than "random"!
      But several references in this thread (including my recent arizona.edu link) give the impression that randomness is the primary factor.

      quote kolean:

      Water is very polar, and can even form clathrins around certain other charge molecules.

      http://en.wikipedia.org/wiki/Clathrin
      "Clathrin is a protein which plays a major role in the formation of coated vesicles"
      In PCR, I don’t see clathrin proteins as an ingredient, yet the DNA pol does its work.
      Do you know of a publication that says clathrins are utilized in DNA replication?

      quote kolean:

      And right now I do not know of any website that would do it justice to the reality of it.

      This is amazing to me, that a simple part of DNA replication is not explained in a standard website.
      Someone said "If you can’t explain it, you evidently do not understand it."

      quote kolean:

      There is just so much going on, but as scientists we usually study one or two aspects of the situation.

      The movement of the appropriate nt to the DNA strand is just "one aspect" of DNA replication.
      And it apparently cannot be explained in everyday language.

      quote kolean:

      A better analogy is to look at the macro. How does a city run smoothly?

      I think everybody appreciates every-day comparisons to explain things that are super big or super small.
      But there’s a few questions.
      If the restaurant is the DNA pol, I the customer am the DNA strand to be replicated, and the actual food given me is the nucleotide…
      (1) I know how to drive my car to where drive-thru orders are taken.
      —–the DNA pol and strand meet at the right place. Not by accident. A primer has to go there first.
      (2) I communicate my order.
      —– many web pages say the DNA pol "reads", but evidently not the way humans read.
      (3) The workers prepare the food items I ordered.
      (4) The workers deliver the food to me in my car.
      —– If steps 3 and 4 are done randomly in DNA replication there is a 75% chance of failure.
      How long will a restaurant stay in business with that many mistakes?
      For the fast food restaurant to work, intelligence is needed by customers and the workers.
      How does that relate to proteins and inanimate molecules?

      What inanimate objects could be used instead of ping pong balls? We all know that molecules are not perfect spheres. And they have atoms with powerful attractions.
      Why is it so difficult in providing a model of this process? I would think it would be a piece of cake for people learning it for years.

    • #97051
      JackBean
      Participant
      quote JackBean:

      first of all, read first about enzymes in common, how they work, ways, how they catalyze and stuff…

      DO IT!!!

      quote gs99:

      quote kolean:

      Everything is not a random ‘bounce’.

      That’s what I’ve been thinking! There’s gotta be something more than “random”!
      But several references in this thread (including my recent arizona.edu link) give the impression that randomness is the primary factor.

      this means, that there are forces, which direct adenine to thymine and vice versa and guanine to cytosine and vice versa

      by clathrin, kolean meant some clusters, not the proteins.

    • #97054
      gs99
      Participant
      quote JackBean:

      first of all, read first about enzymes in common, how they work

      I obtained a book you suggested: "Biochemistry" by Voet & Voet.
      It assumes that the reader has completed one year of college chemistry and a semester of organic chemistry. I have neither of these; the text is far too advanced for me.
      But I did read sections about enzymes, nucleotides, and DNA replication.
      If anybody can refer me to a specific page that talks about my questions, please let me know.
      I’ll need to return this book by Feb 4.
      But I’ll continue reading various books…

      quote JackBean:

      this means, that there are forces, which direct adenine to thymine and vice versa and guanine to cytosine and vice versa

      I knew they had to match. But what kind of attractive forces are they?
      http://en.wikipedia.org/wiki/Fundamental_interaction
      says "The four known fundamental interactions are electromagnetism, strong interaction, weak interaction, and gravitation."
      Is the ATCG force one of these or still another type?
      In a PCR tube that has all four deoxynucleoside triphosphates, why don’t they bond to each other immediately upon contact?
      Or does DNA pol turn on the attraction? Or is it a random attraction?
      Love at first sight?

      quote JackBean:

      by clathrin, kolean meant some clusters, not the proteins.

      http://en.wikipedia.org/wiki/Clathrin
      says: "Clathrin facilitates the formation of small vesicles in the cytoplasm."
      How do clathrin clusters relate to DNA replication?

      Thanks JackBean and Kolean for your patience.

    • #97058
      JackBean
      Participant

      Voet: read part I, chapters 1 (not needed), 2 and 3; part III, chapters 13, 14 and 15
      you may have other numbering, because I have third edition, what I doubt about yours. But I think the chapters in the beginning are the same.

      forces: we are not talking about such interactions. I mean, they belong to one of these groups, but in chemistry (and biochemistry) we recognize H-bond, ionic interaction, hydrophobic interaction, van der Waals interaction etc.
      The interactions responsible for base pairing are hydrogen bonds. These are weak (do not confuse with weak interactions from physics), about 100-1000-times weaker, than covalent bonds, but because there are (at least) thousands of nt in the strand, so together they are quite strong and hold it together.

      clathrin: as I told you, kolean didn’t mean (I guess) the proteins clathrins!!!

    • #97102
      gs99
      Participant
      quote JackBean:

      Voet: read part I, chapters 1 (not needed), 2 and 3; part III, chapters 13, 14 and 15

      My 1990 edition has these Parts and Chapters of interest:
      Part I
      1 Life
      2 Aqueos Solutions
      3 Thermodynamic Principles: A Review
      Part III
      12 Introduction to Enzymes
      13 Rates of Enzymatic Reactions
      14 Enzymatic Catalysis
      15 Iintroduction to Metabolism
      Part V
      31 DNA Replication

      First page of chapter 31, first paragraph (Page 948) says:
      "The general outlines of most of these processes have been elucidated although, as will become apparent, the details are largely obscure."
      (italics added)
      I’m really glad I didn’t buy this book! I thought it was supposed to have the clear answers!

      quote JackBean:

      clathrin: as I told you, kolean didn’t mean (I guess) the proteins clathrins!!!

      I’m confused as to what kolean was explaining.
      What other clathrins are there?
      What I’ve read about clathrin is that it provides structure material (scaffolding), for vesicles.
      Biochemistry page 303 says "The vehicles in which proteins are transported between the RER, the Golgi apparatus, and their final destinations are coated vesicles.
      These membranous sacs are encased on their outer face by a polyhedral framework of the nonglycosylated protein clathrin, which is believed to act as a flexible saffolding in promoting vesicle formation."
      As I mentioned before, web pages say this is done in the cytoplasm.
      That’s very interesting, and I intend to study it more because I’ve been wondering how these proteins are forwarded as needed.
      But how does that relate to DNA rep?

      quote JackBean:

      forces: we are not talking about such interactions.

      I understand that hydrogen bonding is weaker than the Sugar-phosphate backbone. I understand that A molecules match up with T molecules etc..
      But that’s after the fact of what I’m asking about.

      My question is:
      How do the appropriate Deoxynucleoside Triphosphates find their way into the place where DNA pol is affixing them to the DNA template (spot "X")?

      Each DT has a unique shape, not at all resembling a smooth ping pong ball.
      Each DT can be floating in any which three-dimensional direction. Is that correct?
      How is the appropriate DT brought into X at the right time?

      Some replies have been:
      "The process is driven by diffusion and thermally-driven shaking and collision, not any form of intelligence on the part of a protein."
      "The chemical reactions are all driven by random moves and random collisions."
      "Water is very polar, and can even form clathrins around certain other charge molecules."
      "this means, that there are forces, which direct adenine to thymine and vice versa and guanine to cytosine and vice versa"

      The Arizona.edu link
      http://blc.arizona.edu/courses/181Lab/M … NAPol.html
      says "To the contrary, the open binding site of DNA Polymerase is like an available parking spot–anything can drive in."
      We talked about driving into a fast food drive-thru lane.
      How does any DT molecule know how to drive itself into the parking spot?
      What motivation does it have to get involved with DNA pol?
      I would think it’s difficult for DT molecules to "park", with their non-smooth surfaces and charges.
      And then after getting parked and it’s the wrong one, it must be ejected!
      Hey, you with the polka dots, out of the pool!

      The DNA replication is evidently done fast and accurately.
      "Random" doesn’t sound right to me. Like a game of chance, depending on luck.
      (Are the DTs of random design or are they consistent and in a favorable mixture?)
      Perhaps we’ll get clear answers with a better kind of microsope.

      It has been interesting and I appreciate all the replies.
      But I’ll be taking leave to learn more "words".

    • #97123
      JackBean
      Participant

      That doesn’t make any sense to reply here, because YOU WILL BE STILL SAYING THE SAME THINGS AND NOT READING THE BOOK!!!
      Just read, how enzymes work in common, how they procced through the reaction and stuff

    • #97132
      kolean
      Participant

      I think I am getting off this merry-go-round. You need to just read and take it all in. Do not fight it just yet, put it on the back burner. Let it simmer.

    • #97310
      gs99
      Participant

      I still have not seen an explanation for this statement:

      quote kolean:

      Water is very polar, and can even form clathrins around certain other charge molecules. It can hold a protein in place with all of its hydrogen bonding.

      The book "Biochemistry" by Voet & Voet (1990) refers to clathrin only as a protein.

      How can water itself form a protein?

      quote JackBean:

      as I told you, kolean didn’t mean (I guess) the proteins clathrins!!!

      What other clathrins are there?

    • #97312
      JackBean
      Participant

      I knew, I should lock it here.

      I told you already, instead of clathrin, put into the sentence cluster.

    • #97319
      gs99
      Participant

      Yes, you did mention that.
      But I didn’t find anything substantial about water "clusters".
      Not mentioned in the book by Voet.

      http://en.wikipedia.org/wiki/Water_cluster
      says: "So little is understood about water clusters in bulk water that it is considered one of the unsolved problems in chemistry."

      But we’re to accept that water forms "clusters" at the right time to move molecules into DNA pol.

      Aren’t you curious as to how that happens?

      And without a reply from kolean, we really don’t know what was meant, do we? Is it possible that kolean knows something that you don’t?

    • #97320
      JackBean
      Participant

      for sure she knows something I don’t πŸ˜†

      look for hydration sheath. That are water molecules, which surround every dissolved molecule

    • #97435
      jonmoulton
      Participant

      Clathrate. Specifically, water clathrate.

      I hope this helps with the (water cluster)(hydration sheath)(clathrin) discussion. Clathrin is a protein that forms an ordered structure around invaginating membranes during some forms of endocytosis, in a manner analogous to a clathrate. A clathrate is a geometrically ordered, hydrogen-bonded cage of water surrounding an insoluble substance immersed in water.

      Argument for clathrate formation at hydrophobic biomolecular surfaces:
      http://www.pnas.org/content/92/18/8308.abstract
      http://www.pnas.org/content/92/18/8308.full.pdf

      Argument against clathrate formation at hydrophobic biomolecular surfaces:
      http://ww2.chemistry.gatech.edu/~lw26/b … LDW_30.pdf

      This doesn’t address water, but the idea is similar: http://en.wikipedia.org/wiki/Clathrate

      Nice discussion in the context of biomolecules:
      http://www.i-sis.org.uk/TIOCW.php

      Here is older work describing stable water clathrates: http://www.jstor.org/pss/100444
      Note that the water clathrates that are thought to blanket hydrophobic regions of biomolecules are not as stable as those described in this paper.

      You can chill a mixture and make the clathrate more stable: http://bit.ly/9ds6AT

      Nice pictures. I doubt such complete complexes could form stably at room temperature, but this shows the extreme case of hypothetical orderliness in a water clathrate. http://www.btinternet.com/~martin.chapl … hrate.html

      This describes gas hydrates instead of water ordered around biomolecules:
      http://chem.ps.uci.edu/~kcjanda/Group/g … cture.html

      That’s as far as I’m ready to go now. Best wishes stalking reality!

    • #97467
      gs99
      Participant

      Thanks jonmoulton for that clarifying information and references.

      quote jonmoulton:

      A clathrate is a geometrically ordered, hydrogen-bonded cage of water surrounding an insoluble substance immersed in water.

      Still not sure what kolean had in mind.

      My basic interest has been the rapid motion of the nucleotides toward their parking space in the DNA pol.

      Could water clathrates play a part in this?
      Since they seem to be closed "structures", my initial guess is no.

    • #97476
      jonmoulton
      Participant

      I don’t see a mechanism by which clathrates would speed the motion of nucleotides toward the polymerase active site.

      There are several factors which might increase the rate of nucleotide triphosphate (NTP) entry into the active site beyond the rate predicted from simple diffusion. For these, I am speculating. The polymerase itself might have sites on its surface with some affinity to NTPs, allowing the NTPs to "queue up" by the active site. I am also thinking of the interaction of Dicer and Argonaute, where Dicer associates with Argonaute and loads a newly-matured miRNA strands directly into Argonaute’s RNA binding domain — perhaps there is another protein that catches NTPs and loads them onto polymerase. There is lots of higher-order structure in cells that is just being explored, regions of protein interaction that lead to non-average composition; I expect these regions of local order are the rule rather than the exception. Perhaps there are yet-to-be described interactions between NPTs and cellular components that tend to concentrate NTPs near a polymerase, increasing the rate of productive collision between NTPs and polymerase by increasing the local concentration of NTPs.

      However, none of these potential mechanisms need to pre-sort the NTPs so that the complementary nucleotide is always the next loaded onto the polymerase. The cell doesn’t need to get the correct nucleotide for pairing, it just needs a steady supply of ATP, CTP, GTP and TTP; the Watson-Crick pairing that occurs (or, 3/4 of the time, doesn’t occur) at the site of strand elongation is sufficient to elongate the strand rapidly and fairly accurately (and with the polymerases proofreading activity, the accuracy is increased). Get ALL the nucleotide triphosphates to the polymerase and let the polymerase and template strand sort them out.

    • #97480
      gs99
      Participant
      quote jonmoulton:

      Get ALL the nucleotide triphosphates to the polymerase and let the polymerase and template strand sort them out.

      Sounds like a plan!

      Thanks for all the replies by everybody. It’s been very informative and interesting.
      Lots more to learn.

      One day we might have a microsope that will show all this in living color,
      and we’ll play it in slow motion.
      Details at 11.

    • #97484
      JackBean
      Participant

      hardly as we are limited by the wavelength. Maybe NMR…

    • #97513
      gs99
      Participant

      When glass was discovered 2000 years ago, it paved a way to the common microscope.

      When Alexander Bell made the first telephone, he probably didn’t envision the sound wave being digitized. Yet the sounds we make on the phone are broken up into tiny parts and then reassembled, enabling many conversations on one wire. Motion pictures are digitized.

      I have confidence that someone will discover a similar process with light waves, to provide a "fractionated" light wave or whatever to resolve current microscope restrictions.

      Then we’ll see "what’s happening".

    • #97515
      JackBean
      Participant

      There’s limitation of the resolution. Trust me, easier would be to do real-time electron microscope or NMR of such complicated mix.

    • #97548
      gs99
      Participant

      Those who invent and discover seem to go beyond "limitations":
      Years ago, the staff at Bell labs discovered a way to have more than one conversation on a telephone wire!
      I have a complete motion picture stored on a small piece of plastic; I can play it on a computer at home!

      At this point, it seems we need a "microscope" that can see what’s happening in the molecules of a live specimen.

      I don’t know about you, but I surely cannot predetermine the technologies.

      But somewhere, a genius will get the insight.

    • #97550
      mith
      Participant

      you do understand that since we can’t create energy out of nothing(law of conservation) that even in the future, we wouldn’t be able to create energy ?

      this isn’t a technology issue, it’s a limit of physics.

    • #97568
      gs99
      Participant

      You’re saying we have reached our limit of learning and developing new things?

      Haven’t we been at this crossroads before?

      Don’t worry that we don’t have the answer right now; it will come.
      And the law of conservation will not be broken.

    • #97572
      JackBean
      Participant

      any of us is saying, that we reached limit of all learning, just that some things are a little behind the Universe laws as we know them nowadays…

    • #97621
      gs99
      Participant
      quote JackBean:

      any of us is saying, that we reached limit of all learning

      What does "any of us is saying" mean?
      More sensible (to me): "None of us are saying that we reached limit of all learning".

      quote JackBean:

      some things are a little behind the Universe laws as we know them nowadays…

      If you mean "current microscope technology is lagging a little behind",
      I agree.

      The answer probably will be in quantum physics, for example:
      http://www.sciencedaily.com/releases/20 … 172255.htm

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