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Structure and Topology of DNA – DNA, RNA and the Genetic Code

by Kevin Ahern, PhD
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    00:00 made, and it's the way that messenger RNA is translated into protein.

    00:01 Now, the structure of DNA was determined by Watson and Crick back in 1953 using data from Rosalind Franklin. The form of DNA that they described is the one that we know today as the most common form of DNA. It's referred to as the B form of DNA and it contains about 10.5 base pairs per turn of the helix. We can see in the Watson-Crick structure, for example, the bases are located on the inner portion of the DNA molecule. We see the phosphates and sugars are located on the outside. Now this turns out not to be random. Phosphates and sugars are very hydrophilic, the bases by comparison are relatively hydrophobic, although not overly hydrophobic, but by this arrangement the outside hydrophilic molecules can interact with water where the bases on the inside don't have to interact with water as much. Other components we see of the double helix include two grooves, a major groove that is a bigger groove as you can see here and another groove called the minor groove.

    01:00 These grooves are very important places for proteins to bind, that actually can read the sequence of DNA.

    01:08 Now we see here a double helix of DNA that has been expanded and this shows us a little bit more about the information of the structure of a double helix. DNA strands are what we refer to as anti-parallel, meaning that they're oriented in opposite directions, five prime to three prime of one strand going opposite of five prime to three prime of the other strand. This opposite polarity is a very important consideration in terms of their structure, the base pairs of course; adenine pairs with thymine and guanine pairs with cytosine.

    01:41 In RNA, the thymine is of course replaced by uracil, but uracil pairs with adenine just like thymine does. You can see in this structure, the hydrogen bond that actually help hold together the individual bases in a base pairing interaction. On the left we see the hydrogen bonds between adenine and thymine and you'll notice that there are two hydrogen bonds that help to stabilize this base pairing interaction. On the right side we see that guanine and cytosine pair with three double bonds, meaning that there's more strength to the base pairing between guanine and cytosine, than there is between adenine and thymine. That turns out to be very important when we get to talking about transcription, where the individual double helices have to be pulled apart and it's easier to pull apart As and Ts, than it is to pull apart Gs and Cs.

    02:33 Now, there are in fact other forms of DNA besides the B form that was described by Watson and Crick. We know of two other major forms of DNA that occur, they're referred to as A form and the Z form. The A form and the B form are shown on the left side of this slide and they have what's described as a right-handed helix. The handedness of a helix isn't something that we need to go into terribly here, but it relates to the way that the strands interact with each other, it turns out that strands can interact in two different ways, one being referred to as right-handed and that's what's seen with the A and the B forms of DNA. And the Z form which is shown on the right side of the image has a left-handed configuration.

    03:13 Now, DNA because it has interwound strands has some considerations with respect to topology.

    03:22 Topology is very important because we think of the strands interacting and wound with each other. If we were to take for example, a rubber band and take and twist a part of the rubber band, what we would see is that the rubber band would coil up. And the reason it would coil up would be because we've change the topological nature of that and the rubber band is responding to what we've done to it. DNA occurs in a couple forms, so in the relaxed form of DNA as you see on the left, we have pure Watson-Crick type base pairing, 10.5 base pairs per turn. But if we were to take those individual strands and peel them apart in some way, then the portion away from the peel would have a lot more bases per turn, which would give some tension to the molecule. Molecules that have tension of course relieve tension in a couple of ways. One of the ways in which they can relieve the tension is by forming super helices such as you see on the right. The super helix is a way of responding to that tension to relieve the tension, even though it might look like it's actually more tight, it actually is less. Now importantly, the cell has enzymes called topoisomerases that can actually alter the tension of a DNA strand, either increase it or decrease it. Cells tend to leave DNA somewhat super helical and the reason that they do that is it's more compact.

    04:50 The central dogma we've talked about says that DNA makes RNA, makes protein and we can see that depicted here and we reminder ourselves of course that DNA replicates itself and some viruses actually replicate themselves that contain RNA, that's what you see the very bottom there. We also know that there is also a way that RNA can be made back into DNA and that was something that wasn't realized when the central dogma was first described.

    05:18 We're not going to talk about that here.

    05:22 Now, DNA replication is a very essential process for cell to undergo because of course the


    About the Lecture

    The lecture Structure and Topology of DNA – DNA, RNA and the Genetic Code by Kevin Ahern, PhD is from the course Biochemistry: Basics.


    Included Quiz Questions

    1. They all are used by RNA polymerase
    2. They all contain at least one phosphate
    3. They all contain deoxyribose
    4. They all contain at least one base
    1. They have directional polarities arising the sugars they contain
    2. They contain phosphodiester bonds that join the bases
    3. They have a positively charged phosphate backbone
    4. They contain peptide bonds
    1. 12 (6 dimers)
    2. 10
    3. 11
    4. 10.5
    5. 8

    Author of lecture Structure and Topology of DNA – DNA, RNA and the Genetic Code

     Kevin Ahern, PhD

    Kevin Ahern, PhD


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