Nucleic Acids 2 - Online Tutor, Practice Problems & Exam Prep

Nucleic acids, such as DNA and RNA, are polymers of nucleotides linked by phosphodiester bonds. DNA strands are anti-parallel, with a 5' phosphate end and a 3' hydroxyl end. DNA is more stable than RNA due to the absence of a reactive 2' hydroxyl group. Base pairing rules dictate that adenine pairs with thymine (2 H bonds) and guanine pairs with cytosine (3 H bonds), leading to consistent DNA width. This complementary nature ensures that DNA is 50% purines and 50% pyrimidines, crucial for genetic information transmission.

Nucleic Acids 2

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 antiparallel to each other. And the way I like to think of this is if you look at a strand of DNA and generally speaking, we read the code of DNA in the 5' to 3' direction. So if you look at a strand of DNA, you notice that at one end, we have the 5' end and the 5' end is going to have a phosphate group on it. And at the other end, we have a 3' end and that's going to have a hydroxyl group on it. So if you notice, on the other side, the 3' end and the 5' end are actually flipped from the other strand. So if you think about this as an arrow, an arrow that points from 5' to 3'. You can see if I draw my arrows on the two sides of DNA, they are going in directions. They are parallel to each other but they are pointing in opposite directions and that's what we mean when we say antiparallel. That's basically the definition of the term. So, two parallel lines pointing in opposite directions, just like we have here in DNA. If you think of the 3' and 5' ends as different ends of an arrow. Again, it's important to remember that your 5' end is going to be the one with the phosphate group because the phosphate group is attached to the 5' carbon of your pentose sugar. Likewise, your 3' end is going to be the one with the hydroxyl group because that hydroxyl group is attached to the 3' carbon. So, that's where these ends in this naming convention are 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' 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 on the 3' on the 2' 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' 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 frequency 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, a small property but an 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 the 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 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 cytosine. Now, a couple of things to note here. First, 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. Another important thing to note is while while RNA is generally you know in in the areas we're going to be exploring, 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 are 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, a 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 cytosine 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.

Here’s what students ask on this topic:

What are phosphodiester bonds and how do they function in nucleic acids?

Phosphodiester bonds are the linkages between nucleotide monomers in nucleic acid polymers like DNA and RNA. These bonds form between the 3' hydroxyl group of one nucleotide and the 5' phosphate group of the next nucleotide. This creates a sugar-phosphate backbone that is essential for the structure of nucleic acids. In DNA, these bonds contribute to the stability and integrity of the double helix, while in RNA, they are part of the single-stranded structure. The formation of phosphodiester bonds is catalyzed by enzymes like DNA polymerase during DNA replication and RNA polymerase during transcription.

Why are DNA strands described as anti-parallel?

DNA strands are described as anti-parallel because they run in opposite directions. One strand runs from the 5' to 3' direction, while the complementary strand runs from 3' to 5'. This orientation is crucial for the proper base pairing and the overall stability of the DNA double helix. The 5' end of a DNA strand has a phosphate group attached to the 5' carbon of the sugar, while the 3' end has a hydroxyl group attached to the 3' carbon. This anti-parallel arrangement allows for the complementary base pairing of adenine with thymine and guanine with cytosine.

How does the stability of DNA compare to RNA, and why?

DNA is more stable than RNA primarily due to the absence of a 2' hydroxyl group in its sugar component. In RNA, the presence of the 2' hydroxyl group makes it more reactive and susceptible to hydrolysis, especially under alkaline conditions. This increased reactivity can lead to strand breakage. DNA's stability is further enhanced by its double-stranded structure, which provides additional protection against chemical and enzymatic degradation. This stability is one reason why DNA is the preferred molecule for long-term genetic information storage in most organisms.

What is the significance of base pairing rules in DNA?

Base pairing rules in DNA are crucial for maintaining the structure and function of the molecule. Adenine (A) pairs with thymine (T) via two hydrogen bonds, and guanine (G) pairs with cytosine (C) via three hydrogen bonds. These specific pairings ensure that the DNA double helix has a consistent width and that genetic information can be accurately copied during DNA replication. The complementary nature of base pairing also allows for the accurate transcription of DNA into RNA, which is essential for protein synthesis. These rules are fundamental to the fidelity of genetic information transmission.

How can you determine the presence of DNA versus protein using spectrophotometry?

To determine the presence of DNA versus protein using spectrophotometry, you measure the absorbance of your sample at specific wavelengths. DNA absorbs light maximally at 260 nm, while proteins absorb maximally at 280 nm, primarily due to the amino acids tryptophan and tyrosine. By running your sample through a spectrophotometer and observing the absorbance peaks, you can distinguish between DNA and protein. If the sample shows a peak at 260 nm and not at 280 nm, it indicates the presence of DNA with minimal protein contamination. This method is widely used in molecular biology for nucleic acid purification and quantification.