Nucleic Acids - Video Tutorials & Practice Problems
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Nucleic Acids
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So in this video, we're gonna do a quick recap on nucleic acids. So recall that nucleic acids are actually one of 4 major biological macromolecules that compose all cells. So recall from your previous biology courses that the other 3 are proteins, carbohydrates, and lipids, and we'll talk about each of those in separate videos as we move forward in our course. Now, recall that nucleic acids, one of their major functions is to store and encode hereditary information. And by hereditary, we mean that it can be passed on from 1 generation of life down to future and newer generations of life. And examples of nucleic acids include DNA, as well as RNA, but it also includes ATP. An ATP is adenosine tri phosphate, and we know it's the high energy molecule of the cell, and energy, cells use it for energy purposes. And we'll talk a lot more about ATP later on in our course, but for now, we're gonna be focusing on DNA and RNA. Now, recall that nucleic acids are polymers of nucleotide monomers. So what that means is that, nucleotides are the of nucleic acids, and nucleic acids have directionality. And the directionality is referring to when we have a chain chain of a nucleic acid, the ends of that chain are different. And in, nucleic acids, those ends are the 5 prime end and the 3 prime end. So let's take a look at an example. And in our example, what we see is we have a bunch of nucleotide monomers on the left, and through directionality. It has a directionality. It has a 5 prime end on one side and a 3 prime end on the other. And so in our next video, what we're gonna do is do a refresher on the nucleotide monomer itself. So we'll pull out one of these guys, and we'll take a look and analyze the monomer. So I'll see you guys in that video.
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The Nucleotide
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So now that we've refreshed that a nucleotide is the monomer of a nucleic acid, let's now cover the nucleotide itself. So recall that a nucleotide monomer has 3 different components. It has at least 1 phosphate group. It has a pentose sugar or a 5 carbon sugar, and it has a nitrogenous base. And so in our image below, what we'll see is we're gonna compare DNA and RNA nucleotides. And on this left image, we can see that we have a phosphate group shown by this group here, we have a pentoseugar that's shown by this group, and we have a nitrogenous base shown by this group over here. So we've got all 3 different components and we've got a nucleotide. And in particular, what we have is a ribose sugar. And because it's a ribose sugar, that means that at this position, what we have is a hydroxyl group or an oxygen, but nucleotide of a ribo, is a nucleotide of a ribonucleic acid, or an RNA molecule. So this is an RNA nucleotide. Now over here on the right image, we see that we also have a phosphate group, a pentose sugar, and a nitrogenous base. However, this particular pentose sugar is a deoxyribose sugar. And so the d here means without and the oxy means oxygen. So the deoxyribose is missing one oxygen in comparison to the ribose sugar. And so at this position, instead of having a hydroxyl group, it just has a hydrogen atom here. And because of that, this molecule, this nucleotide is from a deoxyribonucleic acid, or from a DNA molecule. So this is a DNA nucleotide. And so in our next videos, what we're gonna be talking about are the nitrogenous bases themselves. So we'll talk about the nitrogenous bases, and we'll talk about how they base pair and the different types. So I'll see you guys in that next video.
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Nitrogeneous Bases & Base-Pairing
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So now that we've reviewed the nucleotide monomer, we can talk about the nitrogenous bases and the base pairs they form. In DNA and RNA, they differ in several different ways including the nucleotides and the nitrogenous bases that they use, but we'll talk about the differences between DNA and RNA in our next video. Now in this video, I want you guys to know that there are 5 different nitrogenous bases that can be grouped either as pyrimidines or as purines. And these nitrogenous bases can pair with one another via hydrogen bonds, and they do so according to Watson and Crick base pairing rules, where recall Watson and Crick are the names of the scientists that help discover the rules. So if we take a look at our example below, notice the 5 nitrogenous bases are lined up horizontally, cytosine, thymine, uracil, adenine, and guanine, and these can be abbreviated by the first letter of the nitrogenous base. Now, I don't want you guys to memorize the structures of these nitrogenous bases just yet. In this video, I just want you to know how they're grouped. So notice the first three nitrogenous bases are grouped as as pyrimidines, and the next 2 are grouped as purines. So you might be asking, Jason, how am I supposed to memorize how these nitrogenous bases are grouped? And I can tell you what helps me memorize it. And so, pyrimidines, pie, kinda sounds like a pie. And so up here I took a picture of a pie that my mom baked for me last week. Nah. I'm just kidding. I got this from the Internet. But notice how this pie has a single ring structure to it, just like the pyrimidines do. And if we compare that to the purines on the other hand, they don't have a pie like structure, they have a double ring structure that doesn't look like a pie. And so pyrimidines have a single ring pie like structure. Now, the other thing that helps me remember is that pyrimidines has a y in it and so does cytosine and thymine. And y's are unique letters to these two nitrogenous bases. And, I know that cytosines and thymines are pyrimidines because they have Y's in them. Now, uracils do not have Y's in them. However, we know from our previous bio courses that uracils replace thymines in RNA molecules. So I'm already associating uracils with thymines and I know to group uracils with thymines as pyrimidines. Now, there are only 5 nitrogenous bases, and what isn't a pyrimidine must be appearing. So, in the next section, we're gonna talk about how these, nitrogenous base pairs form, how they pair with one another in a DNA molecule. And so recall, adenines always pair with thymines and cytosines always pair with guanines. And we've already mentioned that these, nitrogenous bases pair via hydrogen bonds. However, what you may not have recalled is that adenines and thymines, they form 2 hydrogen bonds in the base pair represented by 2 dotted lines here, and guanines and cytosines form 3 hydrogen bonds in their base pair. And a good way to remember this is that cytosine is the 3rd letter of the alphabet, and so the c g base pair forms 3 hydrogen bonds, and that means the other base pair must be forming 2 hydrogen bonds. And so, if we take a look at our DNA molecule over here, notice that adenines always pair with thymines and the guanines always pair with cytosines throughout the entire molecule. And also recall that DNA molecules have directionality. And so if I indicate this is the 5 prime end of 1 strand, the opposite end of the strand must be the 3 prime end. And also recall from your previous bio courses that the 2 strands in a DNA molecule go in opposite directions, and so that is called anti parallel. So the strands are anti parallel and what that means is, if this strand goes from 5 prime to 3 prime in this direction, the other strand must go from 5 prime to 3 prime in the opposite direction, which means that this is the 5 prime end and this would be the 3 prime end. And so in our next video, we're gonna compare DNA and RNA directly. So I'll see you guys in that video.
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Comparing DNA & RNA
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So in this video, we're gonna do a quick comparison on DNA and RNA. And so, in the left hand column in light blue, we have DNA. And in the right hand column in light pink, we have RNA. And so usually textbooks color code DNA and RNA accordingly where DNA is usually bluish and RNA is usually pinkish ish or reddish. And so in the first row, what we have is the strands. And we know that DNA is usually a double stranded molecule, whereas RNA is usually a single stranded molecule. Now for the structure and shape, we know that DNA usually forms a double helix structure, which of course is this twisting ladder type structure that we've seen in all our textbooks. Now the structure of RNA varies greatly, and it depends on the nucleotide sequence of the RNA molecule. And so you can have a single stranded RNA molecule that actually folds up on itself and hydrogen bonds with itself to form complex structures and loops. Now the pentoseugar of DNA is deoxyribose. And recall that the d part of deoxyribose means without, and oxy means oxygen. And so deoxyribose pentose sugars lack an oxygen atom in comparison to the pentose sugar of RNA ribose. Now, nitrogenous bases of DNA include adenines, thymines, cytosines, and guanines. And RNA has the same exact nitrogenous bases, except it uses uracils instead of using thymines. Now for the function of DNA, we know that it encodes hereditary information. And from our ABO Genesis lesson, we know that the the RNA molecule is more functionally diverse. So RNA encodes hereditary information, but it also has catalytic functions. And there are these structures known as ribozymes, which we'll talk more about later on in our course, that are RNA molecules with catalytic abilities. Now the directionality of a strand, whenever you're giving a nucleic acid sequence and the directionality is not indicated, you always assume the direction is from the 5 prime end to the 3 prime end. And that applies to both DNA and RNA, so 5 prime 2, 3 prime. Now recall that DNA has 2 strands that go in opposite directions. And so this, of course, is referring to antiparallel strands. Now the number of nucleotides in a nucleic acid molecule, depends on if it's DNA or RNA. Usually DNA are a large molecules that contain millions of nucleotides. But that depends heavily on the type of organism that it is. Now, RNA molecules tend to have 100 to 1000 of nucleotides. And so in comparison, RNA molecules are much smaller than DNA molecules. And so we'll be talking a lot more about DNA and RNA throughout our biochemistry course, and I'll see you guys in the practice videos.
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Problem
Problem
A) What is the assumed directionality of the nucleotide sequence below? Label the ends of the molecule.
A C G T C T A A A C G G C T A
B) Is the sequence above from a DNA or RNA molecule? How do you know?
C) Write the complementary sequence to the strand below (include the directionality).
A C G T C T A A A C G G C T A
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Problem
Problem
Which of the following nitrogenous bases is a purine?