Practice - Nucleic Acids 1 - Video Tutorials & Practice Problems
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Practice - Nucleic Acids 1
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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 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 actually d. And, we kind of briefly touched on this idea in the question above. And the reason that Dee is wrong is because again, RNA has that 2 prime hydroxyl group, right, next to that 3 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, 32 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 prime, non cyclized version, just a 2 prime nucleoside monophosphate just like an a and c or you can get a 3 prime nucleotide monophosphate because the cyclic structure again will break down into equal amounts of the 3 and the 2 prime. 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 o h, 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.