Nucleic Acids - Online Tutor, Practice Problems & Exam Prep

Nucleic acids, essential macromolecules, include DNA and RNA, which store and encode hereditary information. Nucleotides, the monomers of nucleic acids, consist of a phosphate group, a pentose sugar (deoxyribose in DNA and ribose in RNA), and a nitrogenous base. The five nitrogenous bases are categorized as pyrimidines (cytosine, thymine, uracil) and purines (adenine, guanine). DNA is double-stranded with a double helix structure, while RNA is typically single-stranded. Base pairing occurs via hydrogen bonds, with adenine pairing with thymine (or uracil in RNA) and cytosine pairing with guanine.

Nucleic Acids

So in this video, we're going to do a quick recap on nucleic acids. Recall that nucleic acids are actually one of four major biological macromolecules that compose all cells. Recall from your previous biology courses that the other three 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 one of the major functions of nucleic acids is to store and encode hereditary information. By hereditary, we mean that it can be passed on from one generation of life down to future and newer generations of life. Examples of nucleic acids include DNA, as well as RNA, but it also includes ATP. ATP is adenosine triphosphate, and we know it's the high-energy molecule of the cell, which cells use for energy purposes. We'll talk a lot more about ATP later on in our course, but for now, we're going to be focusing on DNA and RNA.

Now, recall that nucleic acids are polymers of nucleotide monomers. What that means is that nucleotides are the building blocks of nucleic acids, and nucleic acids have directionality. The directionality is referring to when we have a chain of a nucleic acid, the ends of that chain are different. In nucleic acids, those ends are the 5' end and the 3' end. Let's take a look at an example. In our example, what we see is we have a bunch of nucleotide monomers on the left, and through directionality, it has a 5' end on one side and a 3' end on the other. In our next video, we're going to do a refresher on the nucleotide monomer itself. We'll pull out one of these guys and take a look and analyze the monomer. So I'll see you guys in that video.

The Nucleotide

So now that we've refreshed that a nucleotide is the monomer of a nucleic acid, let's now cover the nucleotide itself. Recall that a nucleotide monomer has three different components. It has at least one phosphate group, a pentose sugar or a 5-carbon sugar, and a nitrogenous base. In our image below, we're going to compare DNA and RNA nucleotides. In this left image, we can see that we have a phosphate group shown by this group here, we have a pentose sugar that's shown by this group, and we have a nitrogenous base shown by this group over here. So we've got all three 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. In our next videos, we're going to be talking about the nitrogenous bases themselves. 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.

Nitrogeneous Bases & Base-Pairing

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 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 a purine.

So, in the next section, we're going to 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 third letter of the alphabet, and so the CG 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 antiparallel. So the strands are antiparallel 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 going to compare DNA and RNA directly. So I'll see you guys in that video.

Comparing DNA & RNA

So in this video, we're going to do a quick comparison of DNA and RNA. In the left-hand column, in light blue, we have DNA. In the right-hand column, in light pink, we have RNA. Textbooks usually color-code DNA and RNA accordingly, where DNA is usually bluish and RNA is reddish or pinkish. In the first row, we discuss the strands. DNA is typically a double-stranded molecule, whereas RNA is typically a single-stranded molecule.

Now for the structure and shape, DNA forms a double helix structure, a twisting ladder type of structure we've seen in all our textbooks. The structure of RNA varies greatly and depends on the nucleotide sequence of the RNA molecule. A single-stranded RNA molecule can fold up on itself and hydrogen bond with itself to form complex structures and loops.

The pentose sugar of DNA is deoxyribose. Recall that the 'd' in deoxyribose means 'without,' and 'oxy' means 'oxygen.' So, deoxyribose sugars lack an oxygen atom compared to the pentose sugar of RNA, ribose. As for nitrogenous bases, DNA includes adenine, thymine, cytosine, and guanine. RNA has the same nitrogenous bases, except it uses uracil instead of thymine.

Concerning the function of DNA, it encodes hereditary information. From our abiogenesis lesson, we know that the RNA molecule is more functionally diverse. RNA also encodes hereditary information but has catalytic functions. We will talk more about structures known as ribozymes, RNA molecules with catalytic abilities, later on in our course.

The directionality of a strand, when you give 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. This applies to both DNA and RNA. DNA has two strands that go in opposite directions, a layout referred to as antiparallel strands.

The number of nucleotides in a nucleic acid molecule varies; DNA molecules typically contain millions of nucleotides, depending heavily on the type of organism. In comparison, RNA molecules tend to have between 100 and 1000 nucleotides, making them much smaller than DNA molecules.

We'll be discussing DNA and RNA extensively throughout our biochemistry course, and I'll see you guys in the practice videos.

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

So here's the 3-part practice problem on nucleic acids. And part a asks, what is the assumed directionality of the nucleotide sequence below? Label the ends of the molecule. So recall from our previous videos that if you're given the nucleotide sequence and the directionality is not provided, then you always assume it's from the 5' end to the 3' end. And so the left side here will be the 5' end and the right can be the 3' end. Now for part b, is the sequence above from a DNA or an RNA molecule? And how do you know? So recall that DNA molecules contain thymine nitrogenous bases whereas RNA molecules contain uracil nitrogenous bases instead of having thymines. So if we analyze the sequence above, what we'll notice is that there are an abundance of thymines and the lack of uracils. And so that's an indication that this is a DNA molecule. So the answer here is DNA. And for how do we know, it's because we have the presence of thymines and the lack of uracil nitrogenous bases. Now for part c, it asks, write the complementary sequence of the strand below and include the directionality. So notice that the strand below has the exact same sequence as the strand above. And so we can take part a and apply the directionality to part c. Now to complete this problem, we're going to have to recall the base pairing rules. And recall that adenines always base pair with thymines and guanines pair with cytosines. And so when we apply that to this sequence, we're able to reveal the sequence of the complementary strand. A's always base pair with T's, C's with G's, G's with C's, T's with A's, C's with G's, T's with A's. A's base pair with T's, C's with G's, G's with C's, G's with C's, C's with G's, T's with A's, and A's with T's. And so, the next part is to recall that in a DNA molecule, the strands go in opposite directions, and recall that that's called antiparallel strands. And so what that means is that if the top strand is going from 5' to 3' from left to right, the bottom strand needs to go from 5' to 3' in the opposite direction from right to left. So that means that the right side is the 5' end and the left side is the 3' end. And so the answer to part C is just this green highlighted portion here. And so, I'll see you guys in the next practice problem.

Which of the following nitrogenous bases is a purine?

• A. Cytosine
• B. Uracil
• C. Thymine
• D. Guanine

Here’s what students ask on this topic:

What are the main differences between DNA and RNA?

DNA and RNA differ in several key aspects. DNA is typically double-stranded and forms a double helix structure, while RNA is usually single-stranded. The pentose sugar in DNA is deoxyribose, which lacks one oxygen atom compared to the ribose sugar in RNA. DNA contains the nitrogenous bases adenine, thymine, cytosine, and guanine, whereas RNA contains adenine, uracil, cytosine, and guanine. Functionally, DNA primarily stores and encodes hereditary information, while RNA is more functionally diverse, participating in protein synthesis and having catalytic functions as ribozymes. Additionally, DNA molecules are generally much larger, containing millions of nucleotides, compared to RNA molecules, which typically have 100 to 1000 nucleotides.

What are the components of a nucleotide?

A nucleotide, the monomer of nucleic acids, consists of three components: a phosphate group, a pentose sugar, and a nitrogenous base. The pentose sugar can be either ribose in RNA or deoxyribose in DNA. The nitrogenous base can be one of five types: adenine (A), guanine (G), cytosine (C), thymine (T) in DNA, or uracil (U) in RNA. The phosphate group is attached to the 5' carbon of the pentose sugar, and the nitrogenous base is attached to the 1' carbon. These nucleotides link together via phosphodiester bonds to form the backbone of nucleic acid strands, with the sequence of nitrogenous bases encoding genetic information.

How do nitrogenous bases pair in DNA and RNA?

In DNA, nitrogenous bases pair according to Watson and Crick base pairing rules: adenine (A) pairs with thymine (T) via two hydrogen bonds, and cytosine (C) pairs with guanine (G) via three hydrogen bonds. In RNA, adenine pairs with uracil (U) instead of thymine. These base pairs are crucial for the structure and function of nucleic acids, ensuring accurate replication and transcription processes. The hydrogen bonds between the bases help stabilize the nucleic acid structures, with DNA forming a double helix and RNA often folding into complex shapes.

What is the significance of the 5' and 3' ends in nucleic acids?

The 5' and 3' ends of nucleic acids refer to the directionality of the nucleotide chain. The 5' end 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 directionality is crucial for processes like DNA replication and RNA transcription, as enzymes involved in these processes can only add nucleotides to the 3' end. In DNA, the two strands are antiparallel, meaning one strand runs from 5' to 3' and the other from 3' to 5', which is essential for the double helix structure and function.

What are pyrimidines and purines, and how do they differ?

Pyrimidines and purines are two categories of nitrogenous bases found in nucleic acids. Pyrimidines, which include cytosine (C), thymine (T), and uracil (U), have a single-ring structure. Purines, which include adenine (A) and guanine (G), have a double-ring structure. The structural differences between pyrimidines and purines are crucial for the base pairing rules in DNA and RNA. In DNA, adenine pairs with thymine, and cytosine pairs with guanine. In RNA, adenine pairs with uracil instead of thymine. These pairings are essential for the stability and function of nucleic acid molecules.