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So confused with 5' to 3' end of DNA molecule

  1. Nov 18, 2009 #1
    Hello everyone,

    Quick questions. What do they mean by different polarities in anti parallel DNA strands. Are they referring to some chemical polarity or simply the fact they run in opposite directions.

    I'm confused with DNA replication. DNA polymerase can only synthesize DNA in 5' to 3' direction. I don't understand how this could cause a lagging strand.

    For example

    5'------------------------3' (1st strand)
    3'------------------------5' (2nd strand)

    Can't two DNA polymerases work in opposite directions in DNA replication. One from 5' to 3' in the first strand(moving to the left) and the other 5 to 3 in the second strand(moving to the right)

    They say that RNA polymerase can only synthesize RNA from 5' to 3' direction.

    5'------------------------3' (1st strand)
    3'------------------------5' (2nd strand)

    So that makes the second strand the template strand. My question is can't RNA polymerase use the first strand as the template strand by synthesizing in the opposite direction (to the left)

    Basically what I'm asking is in a DNA molecule only one strand that has genes is used all the time. I mean in transcription do they only use one DNA strand all the time or do they use the other one as well for some genes. Is one DNA strand wasted in transcription?

    Basically what I'm asking is in a DNA molecule only one strand that has genes is used all the time. I mean in transcription do they only use one DNA strand all the time or do they use the other one as well for some genes. Is one DNA strand wasted in transcription?

    Thanks a lot :smile:
    Last edited: Nov 18, 2009
  2. jcsd
  3. Nov 18, 2009 #2
    The 5' end has the terminal phosphate (-PO4) group and the 3' end a terminal hydroxyl group (-OH). In multicellular life only one strand is transcribed. The other is not wasted, just ignored during this process. It would code for an entirely different protein if transcribed. Both strands are used in DNA replication. WIKI has a good article on DNA.
  4. Nov 18, 2009 #3


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    They are referring to the chemical polarity of the nucleotide molecule. Nucleotides in nucleic acids are strung together by connecting the 5' OH of one sugar molecule to the 3' OH of another sugar molecule via a bridging phosphate moiety (referred to as a phosphodiester bond). One end of the DNA molecule will have a free 5' phoshpate and is referred to as the 5' end and one end of the molecule will have a free 3' OH and is referred to as the 3' end.

    Consider this analogy. If you've ever played with Lego bricks, you know that one side of the bricks have raised pegs and the other side of the bricks have indentations into which the pegs fit. Let's call the side with the raised pegs the 5' end and the side with the indentations the 3' end. If you build a linear chain of Lego bricks, you can immediately see that it will have a polarity: there will be a 5' end and a 3' end.

    Yes, that is correct. In theory, you could have two polymerases working from opposite ends of the genome to replicate the DNA strand. In fact, a few viruses that carry double stranded DNA genomes use this strategy to replicate their genomes.

    Why do more complicated organisms not use this strategy? Well, the DNA of humans (and even bacteria) is too long for this strategy to work efficiently.

    Instead, most organisms create a replication fork. Special enzymes disrupt the base pairing in the middle of a DNA molecule creating two replication forks. At the replication fork, you have a double stranded DNA that gets split into two single strands. At the replication fork, you have a molecular assembly consisting of two polymerases (one to copy the leading strand and one to copy the lagging strand), the helicase (which unzips the DNA to move the replication fork forward), and many other proteins involved in DNA replication. Having a physical association of these different proteins into one macromolecular assembly probably aids in the coordination of their activities and makes DNA replication more efficient (see this video showing a model of how the complex works:

    Why is this strategy more efficient than copying from the ends? Well, since replication can begin in the middle of a linear DNA, you can have multiple replication forks throughout the long DNA molecule. Thus, DNA replication occurs in a massively parallel process with many polymerase molecules working at the same time instead of having just two working from the ends onward.

    It can. If the 1st strand is the template strand, RNA polymerase will move along the first strand right to left in order to copy the DNA. If the 2nd strand is the template strand, RNA polymerase will move along the 2nd strand from left to right.

    The template sequence for a gene could be on either strand. If one gene is on one strand it does not necessarily mean that neighboring genes will be on the same strand. From the point of view of transcription, the non-template strand is "wasted" because it is not involved at all in transcription. However, it is not wasted in the sense that it serves as a means to prevent mutations by acting as an independent backup "copy" of the information on the template strand.
    Last edited by a moderator: Sep 25, 2014
  5. Nov 18, 2009 #4
    This can be a confusing topic but here's the low-down :-p

    First off, you should read up on the difference between DNA replication and transcription. They are similar, however one is used for eventually making proteins, and one is purely maintaining genetic materials and preparing for a mitotic or meiosis event.

    Polymerases are just enzymes. They read the genetic code and, after reading it, make a complementary copy to it.

    In the same way that this sentence only makes sense to you if you read it from left to right, D/RNA only makes sense to a polymerase molecule if it is read from 3' to 5'. Polymerases can only bind to strands of DNA that have a 3' OH group on them.

    Now, that is to say that the polymerase moves and reads from 3' to 5'. As you know, the polymerase synthesizes a complementary strand WHILE it reads. This complementary strand is MADE backwards from 5' to 3'.

    Now, to explain the leading/lagging strands.

    5'------------------3' lagging strand

    3'------------------5' leading leading strand

    in DNA replication, both strands will be used by a polymerase molecule, but remember that polymerase molecules can only read DNA from the 3' to the 5' direction.

    Before DNA can be transcribed it must be unwound. This unwinding is performed by the DNA helicase molecule. So DNA that is being transcribed looks like

    5'----#\ /---\ /---
    3'------/*\---/ \---

    Now, the * in the picture represents the helicase molecule, which unwinds this double helix. As you can see, the bottom strand starts with the 3' end, so a polymerase molecule can attach itself right at the beginning and transcribe all the way to the end of the DNA strand, impeded only by the helicase. The lagging strand is different however. If you notice, right before the * (helicase) there is #. Before DNA polymerase can bind to this, a primer must be added. This is done by DNA primase. Once this is done, a polymerase molecule can bind to that part of the DNA and transcribe until it reaches the end of the DNA molecule. By the time it reaches the end of the DAN strand, the helicase molecule has exposed more of the DNA strand for transcription. Again, DNA primase comes in and lays down a primer for the polymerase to bind to. The polymerase then transcribes until it has reached its previous starting point. This continues all the way until the entire DNA molecule has been unwound. At the end of this reaction, you have one complete leading strand that has been synthesized and a lagging strand that is make up up hundreds of smaller fragments (called okazaki fragments) these fragments are joined up together by DNA ligase to form a complete strand of DNA.
    Last edited: Nov 18, 2009
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