Practice - Nucleic Acids 1: Study with Video Lessons, Practice Problems & Examples

Nucleic acids consist of purines and pyrimidines, with purines (adenine and guanine) having two rings and pyrimidines (cytosine, uracil, thymine) having one. Nucleotides are linked by phosphodiester bonds between the 3' hydroxyl and 5' carbon of sugars. RNA's 2' hydroxyl makes it susceptible to alkaline hydrolysis. Nucleic acid bases are roughly planar, allowing for stacking interactions, which maintain uniform DNA width. A pairs with T or U, while C pairs with G, with A-T forming two hydrogen bonds and C-G forming three, crucial for DNA stability.

Practice - Nucleic Acids 1

Hi. In these videos, we will be going over questions similar to those that you will see on your biochemistry exam 3. Before each question, you should actually pause the video and try to answer it yourself. Let's begin by looking at some questions relating to nucleic acids. And again, you should pause the video now and try to answer question 1 on your own. The answer to question 1 is e. Purines have 2 rings while pyrimidines have 1 ring. But purines and pyrimidines actually share a ring and that is this 6-membered ring right here that contains 2 nitrogens. And in the case of purines, this is actually fused to a 5-membered ring that contains 2 nitrogens and you can see it's conjugated and the numbering scheme is like I'm drawing here and it's here at the 9 position where the base will actually be linked to the one-prime carbon of whatever sugar is being used whether it's ribose or deoxyribose. And pyrimidines, again, they're just that 6-membered ring with the 2 nitrogens like that and they're numbered the same way. Oops. Number the same way. The difference is they're actually attached at the one position to the one-prime carbon on the sugar. And, while purines come in only 2 flavors, adenine and guanine, pyrimidines come in 3. Cytosine, uracil, and thymine. And nice way to remember this is with the mnemonic pure as in purines as gold and cut pi as in pyrimidines. Pretty easy to remember. Alright. Question number 2. The answer to question number 2 is e. The units are linked together between the 3-prime hydroxyl of one sugar. So I'm Here's the 3-prime group and that is where you're gonna have your phosphodiester bond and that attaches to the 5-prime carbon of this other sugar. Alright. Just to take a look at the wrong answer choices here, phosphodiester bonds don't link bases. Those are linked by hydrogen bonds of course. Only RNA is susceptible to alkaline hydrolysis. And that is of course because of the presence of that 2-prime hydroxyl in addition to 3-prime hydroxyl. Uncharged at neutral pH, no way. Phosphates, guys. Negative charge, guys. And form between the planar rings of the nucleotide bases. Again, no. The, nucleotide bases have, these hydrophobic stacking forces but no phosphodiester bonds between them. Alright. Question number 3. The answer to question number 3 is actually d. And, we kind of briefly touched on this idea in the question above. And the reason that d is wrong is because again, RNA has that 2-prime hydroxyl group, right, next to that 3-prime hydroxyl group and that 3-prime hydroxyl group will, participate in the phosphodiester bonds. Right. I'm kind of abbreviating the structures here. Not trying to draw the whole thing. And in alkaline conditions, you can get a reaction that leads to cyclization and what you wind up with is this. So here's our 2-prime, here's our 3-prime and you have a cyclized molecule. I'm not drawing the whole thing out here. Again, but all I'm trying to show is that you get cyclization there. You don't get it between 3-prime and the 5-prime position. And this structure, this, 2',3'-cyclized molecule, this actually breaks down to equal amounts of the 3-prime nucleotide monophosphate and the 2-prime nucleotide monophosphate. So, you can get b. You can get a 2',3'-cyclized version or you can get a 2'-non-cyclized version, just a 2'-nucleoside monophosphate just like an a and c or you can get a 3'-nucleotide monophosphate because the cyclic structure again will break down into equal amounts of the 3' and the 2'. Alright. Question number 4, this question, you might have noticed, actually has 2 correct answer choices, b and d, and the reason for this is if we take a look at our molecule, take a look at our piece of DNA here, that p right here, that means this is the 5-prime end. And that means that the a is on the 3-prime end. Now, the 3-prime end again it always ends in an OH, right? Just like we saw up here before and in previous examples. The 3-prime end of our molecule is always gonna have an OH group and that's actually the site of, the reaction with the new nucleotide. That's where you'd actually, attach a nucleotide triphosphate. Right? Anyhoo, in addition to that, it's always convention that DNA is written from the 5'-prime end to the 3'-prime end. This p is just sort of confirming that this is the 5-prime end. If you count, it's actually 6 phosphates just in case you, looked at that and know this, you can't really say this violates Chargaff's rules because Chargaff's rules are pertaining to double-stranded DNA. And, you wouldn't have a phosphate on the 3'-prime end because phosphate is on the 5-prime end and the hydroxyl is on the 3-prime end. Alright, moving on to question number 5. And the answer to Question number 5 is d, roughly planar. Nucleic acid bases are roughly planar. In the structure, it kind of looks something like this. I mean bear with my drawing here but if we imagine these circles I'm drawing as the nucleic acid bases, they basically, sit parallel to each other. So if we were like, you know, looking down on it, it would be like one on top of the other more or less. Right? So anyways, they are roughly planar. They kind of lay flat and they stack on each other. Anyhoo. Taking a look at the wrong answer choices. Proteins absorb UV light 280 nanometers. Nucleic acid bases absorb it at 260 nanometers. So jump out of the image here. 280 is proteins. They are not all the same size, right? There are 2 ring varieties and 3 ring varieties as we just saw and that's actually pretty important because if you noticed, purines are always paired with pyrimidines and that keeps this width The width of the DNA molecule uniform. Pretty cool. And, pattern you might have noticed is that, in biological systems shape is a very important thing. Shape is often used to convey information and in order for molecules to interact. So having a uniform width allows, our cells to look for problems in DNA when the, you know, if the width becomes, non-uniform. If you have a purine bound to a purine or a pyrimidine bound to a pyrimidine, it'll be able to tell because the width of the DNA molecule will change. And lastly, e I mean as we just said purines always pair to pyrimidines and furthermore, you always have A pairing to T or U if it's RNA and C always pairing with G. And of course A and T form 2 hydrogen bonds, C and G form 3 hydrogen bonds. Alright, let's flip the page.

Here’s what students ask on this topic:

What is the difference between purines and pyrimidines in nucleic acids?

Purines and pyrimidines are the two types of nitrogenous bases found in nucleic acids. Purines, which include adenine (A) and guanine (G), have a two-ring structure consisting of a six-membered ring fused to a five-membered ring. Pyrimidines, which include cytosine (C), uracil (U), and thymine (T), have a single six-membered ring. This structural difference is crucial for the pairing and stability of DNA and RNA. Purines pair with pyrimidines through hydrogen bonds: A pairs with T (or U in RNA) forming two hydrogen bonds, and C pairs with G forming three hydrogen bonds.

How are nucleotides linked together in nucleic acids?

Nucleotides in nucleic acids are linked together by phosphodiester bonds. These bonds form between the 3' hydroxyl group of one sugar and the 5' carbon of the next sugar. This linkage creates a sugar-phosphate backbone, with the bases extending from this backbone. The phosphodiester bond is crucial for the structural integrity of nucleic acids, allowing for the formation of long chains of nucleotides that make up DNA and RNA.

Why is RNA more susceptible to alkaline hydrolysis than DNA?

RNA is more susceptible to alkaline hydrolysis than DNA due to the presence of a 2' hydroxyl group in its ribose sugar. Under alkaline conditions, this 2' hydroxyl group can attack the adjacent phosphodiester bond, leading to the cleavage of the RNA strand. DNA lacks this 2' hydroxyl group, having only a hydrogen atom at the 2' position, which makes it more stable under similar conditions.

What is the significance of base pairing in DNA stability?

Base pairing is crucial for DNA stability. Adenine (A) pairs with thymine (T) through two hydrogen bonds, and cytosine (C) pairs with guanine (G) through three hydrogen bonds. These specific pairings ensure that the DNA double helix has a uniform width, which is essential for the proper functioning of biological processes. The hydrogen bonds between the bases also contribute to the overall stability of the DNA molecule, making it less prone to denaturation and damage.

What are the stacking interactions in nucleic acids, and why are they important?

Stacking interactions in nucleic acids refer to the hydrophobic interactions between the planar bases that lie parallel to each other in the DNA or RNA structure. These interactions help stabilize the nucleic acid structure by minimizing the exposure of hydrophobic bases to the aqueous environment. Stacking interactions are important because they contribute to the overall stability and integrity of the nucleic acid molecule, ensuring proper function and replication.