Nucleic Acids 2 - Video Tutorials & Practice Problems
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Nucleic Acids 2
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The nucleotide monomers in a nucleic acid polymer are connected by phosphodiester bonds. And you can see these here in our diagrams of DNA and RNA. Here is a phosphodiester bond in DNA and here is a phosphodiester bond in RNA. Now, the individual strands of DNA are actually said to be anti parallel to each other. And the way I like to think of this is if you if you look at a strand of DNA and generally speaking, we read the code of DNA in the 5 prime to 3 prime direction. So if you look at a strand of of DNA, you notice that at one end, we have the 5 prime end and the 5 prime end is going to have a phosphate group on it. And the other end, we have a 3 prime end and that's going to have a hydroxyl group on it. So if you notice, on the other side, the 3 prime end and the 5 prime end are actually flipped from the other strand. So if you think about this as an arrow, an arrow that points from 5 prime to 3 prime. You can see if I draw my arrows on the two sides of DNA, they're going in directions. They're parallel to each other but they're pointing in opposite directions and that's what we mean when we say anti parallel. That's basically the definition of the term. So, 2 parallel lines pointing in opposite directions, just like we have here in DNA. If you think of the 3 prime and 5 prime ends as different ends of an arrow. Again, it's important to remember that your 5 prime end is going to be the one with the phosphate group because the phosphate group is attached to the 5 prime carbon of your pentose sugar. Likewise, your 3 prime end is going to be the one with the hydroxyl group because that hydroxyl group is attached to the 3 prime carbon. So, that's where these ends in this naming convention is coming from. It's just coming from the carbon numbers. Now, RNA is actually less stable than DNA and that's because at high pH, this 2 prime hydroxyl group is reactive and it can actually react with, the phosphate group next door basically and what you'll wind up with is some kind of structure that looks like this. You know, I'm kind of half drawing my sugar here but it'll basically react with itself and of course that's bad. It can cause the strand to break in half or whatever. So, because of this, DNA has been favored as the genetic information 3 on the 3 on the 2 prime carbon. So, there are some It's thought that very early life forms would have used RNA as their, genetic storage. But over the course of evolution, DNA has been, like vastly favored by comparison to RNA. Because basically, all life uses DNA. You know, some viruses use RNA, as their genetic information storage. But that begs the question of are viruses even alive and, you know, that's a whole other tangent. So the main point is DNA much more stable and it's all because of, the absence of that 2 prime hydroxyl group. Now, nucleotides and nucleic acids, it's important to remember they have this property where they absorb light, they absorb the maximum amount of light at 260 nanometers. The wavelength, 260 nanometers. This is important because proteins absorb light maximally at 280 nanometers. Nanometers. And you might remember it's actually the amino acids, tryptophan and tyrosine that are doing the most absorption of light at that frequent or at that wavelength. So, this is important because it allows biochemists a really easy way to test for, the presence or absence of DNA versus protein. So if you're trying to isolate something from a cell for example, you're trying to isolate its DNA, you can go through you know the various steps and then test your sample by running it through a spectrophotometer and seeing what lengths it absorbs. If it's only absorbing at 260 and it's not absorbing at 280, then you know you probably got rid of the proteins and you just have your nucleic acids there. So, small property but important fact to know. Now, the two strands of DNA are said to be complementary. And basically, that means that the code on one strand complements the code on the other strand and this is due to specificity of base pairing. And basically, what that means is there are specific rules that guide base pairing and those rules more or less are what we see, below here. So we have in on the left here, we have an adenine that is binding to a thymine. And on the right, you can see that we have a guanine and I'm just going to take myself out of the image so you can see this better. We have a guanine binding to a cytosine. Now, a couple things to note here. 1st, adenine and thymine are forming 2 H bonds. Whereas, guanine and cytosine are forming 3 H bonds. Now, this is important because it's going to result in strands of DNA with higher GC composition having a higher melting temperature or just generally being harder to separate and it literally comes from the fact that they're going to have more hydrogen bonds holding the strands of DNA together making them stick together stronger. Other important thing to note is while while RNA is generally you know in in the areas we're going to be exploring, RNA is generally going to be single stranded. Its bases it can be double stranded first of all but its bases will also form these bonds with DNA during gene expression and during the transcription process. So, what I'm getting to here is that when that happens, adenine will actually be binding with uracil just like we see it, with thymine here and let me like put this in parenthesis. That's not what we're that's not what this image is but, that's what is the presence of this methyl group there. But yeah. So the basic story is because there are these specific base pairing rules, if you have one strand of DNA or just a single strand piece of RNA, you can very easily determine what the complementary strand is In fact, that's how genetic information is transmitted in the cell. So, little thought experiment here. What percentage of DNA is going to be made up of purines and what percentage is going to be made up of pyrimidines? Well, let's think about this for a second. Adenine always pairs with thymine, right? And guanine always pairs with cytosine. Now, adenine and guanine are both purines and thymine and cytisine are both pyrimidines. So, that means that we're always going to have a purine bind to a pyrimidine meaning that DNA is going to be 50% purines 50% pyrimidines. This is actually very important because it means that the, width of the double stranded DNA is going to be consistent. It's always going to have the same width and you can see that, that's determined by the fact that we have the 2 ring structure and the 1 ring structure always binding to each other and that's the width will be the same regardless if it's a GC pair or an AT pair. So always going to be 50% purines, 50% pyrimidines. Now, let's do another little thought experiment here. If a piece of double stranded DNA has 35% adenine and 15% cytosine, how much thymine and guanine is it going to have? Sort of in a similar line of thinking to the last problem, if there's 35 percent adenine, then that means there has to be 35% thymine, right? Because adenine is always going to be bound to thymine. Likewise, if there's 15% cytosine, then there's going to have to be 15% guanine because cytosine always binds to guanine. So, you're going to find those in equal amounts. Now, let's flip the page and talk a little bit more about these ideas we've just explored.