Hi. In this video series, we'll be going over the major topics for biochemistry exam 3, including nucleic acids, DNA sequencing, lipids, membrane structure, and membrane transport. Now let's get started with nucleic acids. Nucleic acids are made of 3 components: phosphate groups, which you can see pictured right here, a 5 carbon sugar and that 5 carbon sugar will be ribose, like you see on the left here, if it's RNA, and you can tell that it's ribose because it will have a hydroxyl group on the 2' carbon there, and if you are dealing with DNA, you'll have deoxyribose which is pictured here on the right and you can see that deoxyribose is missing a hydroxyl group on that 2' carbon there. Hence, the deoxy part of its name. In its place, there's just a hydrogen.
Now, the code part of DNA comes from the nitrogenous bases that can be present, and there are actually 5 nitrogenous bases that will appear in DNA and RNA, going from left to right here: Adenine, Guanine, Cytosine, Uracil, and Thymine. Now, Adenine and Guanine are purines. Whereas, Cytosine, Uracyl, and Thymine are pyrimidines. A nice way to remember the purines and the pyrimidines is using the mnemonic device for adding an "iguana pure as gold". And for the pyrimidines, you use the mnemonic "cut pie" and hopefully that'll help you remember your purines from your pyrimidines. Now, it's important to note that Uracil is only present in RNA and Thymine is only present in DNA. So, I'm just going to put "RNA" here and "DNA" there, just so we know that one is present in one and the other in the other, and they essentially replace each other in each structure. So in RNA, you have Uracil in place of Thymine and in DNA, you have Thymine in place of Uracil. And there actually is a biochemical reason for that, and it has to do with the fact that if Cytosine, which you can see right here, if Cytosine is bombarded with UV light, this amino group can actually get deaminated and turn into a carbonyl like we see in Uracil. So basically, Cytosine can be mutated into Uracil by UV light. Now if this happens, it's hard for your cells to tell which is the mutation because that new Uracil looks like a normal base to it. So it can confuse the cell. However, Thymine has this methyl group there. So if a Cytosine gets mutated to a Uracil in DNA, your cells will be able to tell. And that's because if Cytosine gets mutated into Uracil, your cells know that Uracil is not supposed to be there because they're supposed to have Thymine, and Thymine has that methyl group on it.
So, I know it's kind of a lengthy explanation but just a nice little kind of a side story as to why this is the case because often in science, we really want to think about those why questions. Now moving on, nucleic acids are actually polymers and they're polymers of nucleotides. And here we have to get a little careful about our language because we're going to use terms that sound quite similar to each other but actually mean different things. So nucleotides are like what you see here on the left. This is a nucleotide. And it's a nucleotide because it has a phosphate group present. Whereas, if it did not have this phosphate group like we see right here, it would be considered a nucleoside like you see written there. So if you just have the pentose sugar attached to the base, that's a nucleoside. Bind the you actually have to use nucleotide triphosphates to synthesize them. And the reason for that is because this bond right here, this high-energy bond between the phosphate groups will actually be cleaved to provide the energy for the polymerization reaction. DNA polymerase relies on the energy from cleaving this bond in order to continue synthesis. So, even though technically, new nucleic acids are polymers of nucleotides, you have to use nucleotide triphosphates to actually make them. And it's worth noting that nucleotides and of course nucleosides use a somewhat unique system. So you might notice looking over here at our sugar in our that all the numbers have a prime symbol next to them. So, this is the 1 prime carbon, the 2 prime carbon, 3 prime carbon, 4 prime, and 5 prime.
Now, the reason for that, for using the prime symbol there is because the first carbon, carbon number 1 is actually, actually comes from the base, not from the sugar. So rather than starting this carbon at like carbon number 10 in the case of this, nucleotide we have here, we started at 1 again and we just put a prime symbol there. So it's basically just to make the carbon numbering easier and to keep the numbers below 10. You know, so this is a unique you probably won't really see anything like this outside of numbering nucleotides. So, you know, don't worry about it too much but you do need to know the numbers of all the carbons in a nucleotide. So moving on, you can actually see down below here we have all of the bases and all of the bases have their carbons numbered and you can see that the carbon numbering of the bases is it's a little different between the purines and the pyrimidines. And again, you need to know the numbering of all of these bases. Fortunately, you basically only have to memorize 2 numbering systems as the numbering for the pyrimidines is consistent with each one and likewise the numbering with the purines is consistent with both of them. So you just have to memorize the purine and pyrimidine numbering and of course also know the numbering for your pentose sugar. Lastly, these phosphate groups on the nucleotide, the nucleotide triphosphate here, these phosphate groups have their own naming convention. We don't just call them 1, 2, 3. We actually call them the alpha, beta, and gamma phosphate groups. So, you know, couple things to memorize here in terms of the numbering and naming of these molecules, and there's really no two ways about it. You just have to memorize this information because it's going to be important for the conversations down the line and for you to be able to determine the structures of molecules given a certain name. Alright. That's all I have for this page. Let's move on.
