how does DNA replication initiate?

Discussion in 'Biology & Genetics' started by Rick, Oct 25, 2001.

  1. Rick Valued Senior Member

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    how does cell realize that it is time for protien synthesis via DNA,or may be DNA replication via seperation of strands and using primase to synthesize another strand?
     
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  3. Ana Registered Senior Member

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    why and how....

    WHY:

    DNA replication occurs because cells need to divide in order to replace old and dying cells, right? The nucleus is the cell's control center, so that must be duplicated in order to have the cell divide into two identical daughter cells...and the nucleus has the chromatin (genetic material--the instructions that direct the functions of a cell)....the DNA (which is a nucleic acid found in the chromatin) is duplicated so that the two daughter cells have identical genetic material (for stability purposes--so it can survive).

    Then I found this for ya: the HOW (which I believe was your question)

    "In bacteria, the concentration of the initiator protein, DnaA, is a critical factor
    in determining when initiation of DNA replication occurs. The regulatory mechanisms that provide sufficient DnaA protein for the correct frequency and spacing of initiation events depending on growth rate, growth phase, stage in the cell cycle, and starvation conditions are being studied. A recent discovery suggests that the synthesis of DnaA may be controlled by another protein, Fis. Fis is itself growth phase regulated; thus, it may act
    as a sensor of the growth conditions of the cell. The objectives of this proposal are to delineate the Fis binding sites in the dnaA promoter . . ."

    Hope this helps.
     
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  5. Ana Registered Senior Member

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    uhg...

    Wait, what was the question again? Did I answer anything?
     
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  7. Counterbalance Registered Senior Member

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    zion,

    I had a little trouble understanding precisely what you were asking, too. I suspect Ana nailed it for you; nonetheless, the information below is straight from the fifth edition of Biology, by Peter H. Raven and George B. Johnson. It's simply a brief run down (of part) of the initiation of the replication process. Various proteins are involved, including primase.

    ~~~


    "Step One: Initiating replication. The binding of initiator proteins to the replication origin start an intricate series of interactions that opens the helix.

    Step Two: Unwinding the duplex. After initiation, “unwinding’ enzymes called helicases bind to and move along one strand, shouldering aside the other strand as they go.

    Step Three: Stabilizing the single strands. The unwound portion of the DNA double helix is stabilized by single-strand binding protein, which binds to the exposed single strands, protecting them from cleavage and preventing them from rewinding.

    Step Four: Relieving the torque generated by unwinding. For replication to proceed at 1000 nucleotides per second, the parental helix ahead of the replication fork must rotate 100 revolutions per second! To relieve the resulting twisting, called torque, enzymes known as topisomerases--or, more informally, gyrases-- leave a strand of the helix, allow it to swivel around the intact strand, and then reseal the broken strand.

    2. Building a primer. New DNA cannot be synthesized on the exposed templates until a primer is constructed, as DNA polymerases require 3’ primers to initiate replication. The necessary primer is a short stretch of RNA, added by a specialized RNA polymerase called primase in a multisubunit complex informally called a primasome. Why an RNA primer, rather than DNA? Starting chains on exposed templates introduces many errors; RNA marks this initial stretch as “temporary,” making this error-prone stretch easy to excise later. ....”

    “Replication takes approximately eight hours in human cells, but if there were only one origin, it would take 100 times longer. Regulation of the replication process ensures that only one copy of the DNA is ultimately produced. How a cell achieves this regulation is not yet completely clear. It may involve periodic inhibitor or initiator proteins on the DNA molecule itself.

    ~~~

    Counterbalance
     
  8. Rick Valued Senior Member

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    Re: uhg...

    you answered my question correctly,thanks.

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    ,i didnt know about Fis protein that you mentioned.i"ll have to find out.
     
  9. Rick Valued Senior Member

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    hi,is the single strand binding protein same as swirling protein.also do you know anthing about Fis protein,that ana mentioned?
     
  10. Counterbalance Registered Senior Member

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    373
    zion,

    Ana knows more about it than I do. In the meantime, (until she gets a chance to drop in here again), here are three links that can provide various and sundry info on FIS--plus links to other pages. You know best what you're looking for, so I'll let you pick and choose.

    Btw... if these don't work well, try dropping the "html" part at the end.



    http://www.fccc.edu/research/reports/report96/feng.html

    http://www.doe-mbi.ucla.edu/People/Dickerson/Gallery/FIS.html

    http://www.zi.biologie.uni-muenchen.de/institute/IGM/genetik/ginfisgr.html

    Good luck

    ~~~

    Counterbalance
     
  11. Counterbalance Registered Senior Member

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  12. esp Registered Senior Member

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    908
    counterbalance....

    The four steps you mentiond earlier sound a lot like Prophase, Metaphase, Anaphase and Telephase in the replication process of chromasomal pairs.
    Is this right?
    It's a while since I studied genetics and cellular biology.

    One other thing-

    Is the self replication different any in MIOSIS from MITOSIS?
     
    Last edited: Dec 11, 2001
  13. Chagur .Seeker. Registered Senior Member

    Messages:
    2,235
    Help! Confused ...

    Re. post by Ana: "DNA replication occurs because cells need to divide in order to replace old and dying cells, right?"

    I don't think so ... but its been a very long while.

    Any input appreciated.

    Take care.
     
  14. esp Registered Senior Member

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    Re: Help! Confused ...

    I'm not totally certain, but I think if I remember rightly, that this reason is valid.
     
  15. Stryder Keeper of "good" ideas. Valued Senior Member

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    I always go down to the building blocks to explain something like that. I know the topic is Genetics but I usually look at something atomically and then wonder about it's quanta interactions.

    For instance, an Enzyme causes a change in cellular structuring, to me thats an Enzyme causes an atomic breakdown through the lesser strengthed bondings (like Hydrogen), that then rebond to some other chemical that seemed more appealing for its "bond strength". The bonds break because they become unstable.

    My understanding there is that a radioactive material eventually decays, when a frequency of an atoms resonance and bond becomes interrupted it too decays breaking a bond.

    In truth DNA replicates from the DNA splitting apart bond by bond and having freefloating materials that attach themselves to those now broken bonds to create a new strand. Those freefloating parts are from proteins as proteins are used to nurish reproduction and repairing what DNA is already there.

    (In fact Virii are Protein based when they attack, and this is why Virii can attack particular organs in the body, as the protein that would be used to repair and replicate is replaced with the virated protein, which causes a replication of the virus, a possible mutation and the damaging of healthy cells.)
     
  16. scilosopher Registered Senior Member

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    435
    Zion are you interested in prokaryotes or eukaryotes? They're somewhat different.

    Bacteria have a circular chromosome and sometimes plasmids which are extra add ons and typically carry things like antibiotic resistance. The bacterial chromosome has a single origin of replication (starting with the sequence GATC) where replication starts. dnaA binds to the origin or oriC 4 times beginning the unwinding process. Then SSB binds to the single stranded part to keep it from reannealing. There are helicases and topoisomerases which unwind and deal with supercoiling issues respectively (if you take two pieces of string which are wound around eachother and unwind a small region you superwind the rest which can result in coils of coils like a telephone cord that's wound up on itself). The main work is done by DNA polymerase which is primed with short bits of RNA. There are at least three DNA polymerases with slightly different roles. As all replication goes 5' -> 3' at each of the forks formed on either side of the origin one side has to synthesize lots of short fragments (okazaki fragments) which get stitched back together while the other side copies continuously.

    Eukaryotes have a nucleus and chromosomes. Because they have orders of magnitude more DNA to replicate they have hundreds of origins of replication on each chromosome and use slightly different machinery. But the overall process is similar.

    Multicellular organisms, which are all eukaryotes, do use division to handle the problem of cells dying off though in many cases stem cells are the only ones that divide to replace the dying cells, not the ones having trouble.
    Bacteria generally divide whenever there is enough food to do so.

    There is definitely no transcription from the DNA during replication, but there may be residual protein synthesis from mRNA already present in the cell.
     
    Last edited: Dec 13, 2001
  17. Counterbalance Registered Senior Member

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    373
    ~~~

    Esp & zion...

    The following is taken from the same text by Raven and Johnson:

    ( Wish I could keep it all straight and provide the info without referencing, but at least this way it's more like getting it from the experts.

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    )



    "Meiosis and fertilization together constitute a cycle of reproduction. Two sets of chromosomes are present in the somatic cells of adult individuals, making them diploid cells, but only one set is present in the gametes, which are thus haploid. Reproduction that involves this alternation of meiosis and fertilization is called sexual reproduction....

    "The mechanism of cell division varies in important details in different organisms. This is particularly true of chromosomal separation mechanisms, which differ substantially in protist and fungi from the process in plants and animals. Meiosis in a diploid organism consists of two rounds of division, mitosis of one. Although meiosis and mitosis have much in common, meiosis has two unique features: synapsis and reduction division.

    "...To be effective, DNA replication must be fast and accurate. The machinery responsible has been the subject of intensive study for 40 years, and we now know a great deal about it. The replication of DNA begins at one or more sites on the DNA molecule where there is a specific sequence of nucleotides called a replication origin. There the DNA replication enzyme DNA polymerasee III and other enzymes begin a complex process that catalyzes the addition of nucleotides to the growing complementary strand of DNA."

    The proteins listed in one of my prior posts are proteins involved in bacterial DNA replication.

    Eukaryotic DNA Replication

    "In eukaryotic cells, the DNA is packaged in nucleosomes within chromosomes. Each individual zone of a chromosome replicates as a discrete section called a replication unit, or replicon.... Each replicon unit has its own origin of replication, and multiple units may be undergoing replication at any time.... Each unit replicates in a way fundamentally similar to prokaryotic DNA replication, using similar enzymes. The advantage of having multiple origins of replication in eukaryotes is speed...."

    "Eukaryotic cells store hereditary information within the nucleus. " I believe Ana's post alluded to this.

    "When the nucleus is transplanted into another cell, the herediatry specifications of the organisms are also transplanted. In viruses, bacteria, and eukaryotes, the hereditary information resides in nucleic acids. The transfer of nucleic acids can lead to the transfer of hereditary traits. The hereditary material is DNA in all cellular organisms and some viruses; it is RNA in other viruses. When radioactively labeled DNA viruses infect bacteria, the DNA, but not the portein coat of the viruses, enters the bacterial cells, indicating that the hereditary material is DNA rather than protein....

    "How does DNA replicate?

    (During the S phase of the cell cycle, the hereditary message in DNA is replicated with great accuracy....)

    'G-1' is the primary growth phase of the cell. For many organisms, this encompasses the major portion of the cell's life span.

    'S' is the phase in which the cell synthesizes a replica of the genome.

    'G-2' is the second growth phase, in which preparations are made for genomic separation. During this phase, mitochondria and other organelles replicate, chromosomes condense, and microtubules begin to assemble at a spindle.

    'M' is the phase of the cell cycle in which the microtubular appartus assembles, binds to the chromosmes, and moves the sister chromatids apart. Called mitosis, this process is the essential step in the separation of the the two daughter genomes.... Although mitosis is a continuous process, it is tradionally subdivided into four stages: prophase, metaphase, anaphase, and telophase.

    'C' is the phase of the cell cycle when the cytoplasm divides, creating two daughter cells. This phase is called cytokinesis. In animal cells, the microtubule spindle helps position a contracting ring of actin that constricts like a drawstring to pinch the cell in two. In cells with a cell wall, such as plant cells, a plate forms between the dividing cells.

    "Most of the variation in the length of the cell cycle from one organism or tissue to the next occurs in the 'G-1' phase. Cells often pause in 'G-1' before DNA replication and enter a resting state called 'G-0' phase; they may remain in this phase for days to years before resuming cell division...."

    ~~~

    Hopefully that will clarify things a little.


    Counterbalance

    p.s. The spell-checker appears to be stuck in 'G-0' phase tonight. Please forgive any typos.

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  18. Rick Valued Senior Member

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    OK.

    bye!
     
  19. Rick Valued Senior Member

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    Actually i have studied all this stuff in great details starting with mendellian genetics to other stuff,but i could never grasp exactly at what time and when DNA realises it has to start replication,since now i am busy with my Engineering semesters so i have lost touch...
    so that information was pretty enlightning...thanks once again.
    conjured up my memories.
    bye!

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