Introduction to DNA Replication - Online Tutor, Practice Problems & Exam Prep

DNA replication initiates at specific sequences known as the origin of replication (ori). Prokaryotes possess a single circular chromosome with one ori, while eukaryotes have multiple linear chromosomes with numerous origins. The process involves unwinding DNA at replication forks, facilitated by enzymes like topoisomerase, which relieves supercoiling, and helicase, which separates strands by breaking hydrogen bonds. Single-stranded binding proteins (SSBs) stabilize the unwound DNA, preventing reannealing. This semi-conservative replication results in two identical DNA molecules, essential for cellular division and genetic continuity.

Introduction to DNA Replication

In this video, we're going to begin our introduction to DNA replication. It's important to keep in mind as we move forward in our course and continue to talk more about DNA replication that there is actually much more information known about prokaryotic DNA replication than about eukaryotic DNA replication. For that reason, as we move forward in our course, we're mainly going to focus on prokaryotic DNA replication. However, it is also important to remember that scientists believe that most of the DNA replication process is fundamentally similar in both prokaryotes and eukaryotes. Even though moving forward, we're mainly focusing on prokaryotic DNA replication, it's crucial to note that most of the process is fundamentally similar in both.

As we proceed in our course, we'll try to point out some of the key differences between prokaryotic and eukaryotic DNA replication. In both types of replication, DNA replication occurs via a semi-conservative process, which we introduced in our last lesson video. Semi-conservative DNA replication suggests that the old parental strands in the original DNA molecule are going to separate from one another, and each will act as a template in the synthesis of new DNA strands that are complementary to the old parental strands. If we take a look at our image below, we're showing another image of semi-conservative DNA replication. Notice on the far left, we start with just one DNA molecule.

This is the original DNA molecule. By the end of this DNA replication process, we end up with two DNA molecules, one here and one here. The DNA strands in the old parental DNA molecule are going to separate from one another. You can see the separation beginning here. As these old original DNA strands separate from one another, they act as templates to build new DNA that is complementary to it.

You can see the new DNA here is this yellow strand being built using the old blue strand as a template. This process will continue, ultimately resulting in two DNA strands that are identical to each other and identical to the original since it's built via complementary base pairing. We'll be able to talk more about the mechanism of this semi-conservative DNA replication as we move forward in our course. We'll start off by introducing the DNA replication components. I'll see you all in our next lesson video to talk about that.

Components of DNA Replication

In this video, we're going to briefly introduce some of the most important components of DNA replication. It turns out that DNA replication is actually a relatively complex process that requires a host of multiple enzymes and proteins working together. Notice down below we have this table that shows you some of the most important enzymes and proteins involved in DNA replication along with their functions. It's important to note here in this video we're only going to briefly introduce these enzymes and proteins and their functions. But as we move forward in our course in their own separate videos, we're going to talk about each of these enzymes and proteins in more detail along with the details of their functions.

Keep in mind that this is just a brief introduction and you can use this table down below as a reference moving forward as we cover these different enzymes and proteins in more detail. What you'll notice is over here in this column, what we're going to show you is the shape that we're going to use here in Clutch Prep to represent each of the individual enzymes and proteins. Of course, we have the name of the enzyme and protein in this column, and then we have the function of the enzyme or protein in this column here. The first enzyme that we're showing you here is going to be topoisomerase. Topoisomerase is also sometimes referred to as DNA gyrase in prokaryotes, and you may see your textbooks or your professor refer to it as that.

Its function is to relieve DNA supercoiling ahead of the replication fork. We'll talk more about what DNA supercoiling is and the function of topoisomerase and DNA gyrase in their own separate video as we move forward. And that again goes for all of these enzymes and proteins. The next enzyme that we're showing you is represented with this yellow triangle here at Clutch Prep, and it is helicase. Helicase's function is to unwind the DNA double helix at the replication fork.

Next what we have are these little orange circles and these represent our single stranded binding proteins. As their name implies, these single stranded binding proteins are going to bind to and stabilize single stranded DNA. Next what we have is this pink structure which is going to be Primase. As the Primase name implies, it is going to create RNA primers, which act as a starting point for DNA synthesis. Next, what we have is this light blue circle here, which represents DNA polymerase III in prokaryotic organisms, and this is the main DNA polymerase that's responsible for building a new strand of DNA using the old strand of DNA as a template. But there are multiple DNA polymerases and this DNA polymerase is, going to be DNA polymerase I in prokaryotes and its job is to replace RNA primers with DNA.

Notice that DNA Polymerase II is not mentioned here on this list and that's because DNA Polymerase II is not one of the most important components of DNA replication and it has a slightly different function that we're not really going to cover in this course. The last protein, the last component that's very important for DNA replication is going to be DNA ligase. DNA ligase's function is to covalently join together what are known as Okazaki fragments in the lagging DNA strand. This will make a lot more sense, these functions, and these enzymes and proteins will be cleared up as we move forward and talk about them in more detail in their own separate videos. But again, this here concludes our brief introduction to some of the most important components of DNA replication that we're going to encounter moving forward.

We'll be able to talk more about these as we move forward in our course. So I'll see you all in our next video.

Origin of Replication

In this video, we're going to introduce the origin of DNA replication or just the origin of replication. And so DNA replication actually begins at a specific set of DNA sequences that are collectively referred to as the Origin of Replication or just the ori for short. And so it turns out that prokaryotic cells have a small circular chromosome, and these small circular chromosomes of prokaryotic organisms have just one single origin of replication on their chromosome. Whereas eukaryotic organisms have larger linear chromosomes, and these larger linear chromosomes of eukaryotes actually have multiple origins of replication. In some cases, they can have up to 100 of origins of replications or more.

And so if we take a look at our image down below, notice on the left-hand side over here, what we're showing you is prokaryotic DNA replication, and on the right-hand side over here, what we're showing you is eukaryotic DNA replication. And what you'll notice is that the chromosome of prokaryotes is circular. And, the circular chromosome of prokaryotes only has just one single origin of replication. One origin of replication. Now if we take a look over here at the eukaryotic chromosome, notice that its chromosome is linear, and the linear chromosome actually has 2 origins of replication in this image, but again they can have many origins of replication, so multiple origins of replication.

And so what you'll see here is that the darker blue molecules represent the old original parental DNA strands, and, as DNA replication proceeds, it's going to occur and begin at this origin of replication. And so what you'll notice here in this image is that the new DNA strands are, in the light blue color and, of course, these little pink structures are representing RNA primers, which we're going to talk more about the functions of these RNA primers, as we move forward in our course. But the point here is that the origin of replication is where DNA replication is going to begin the process. And so, you can see over here, in the eukaryotic DNA replication image that, once again, the origin of replication is going to represent the starting place where DNA replication is going to begin and proceed. And so, this here concludes our brief introduction to the origin of replication, this set of DNA sequences that marks the beginning of DNA replication.

And we'll be able to talk more and more about DNA replication as we move forward in our course. So I'll see you all in our next video.

Replication Forks

In this video, we're going to introduce replication forks. Recall from our last lesson video that DNA replication begins at a specific set of DNA sequences called the origin of replication or just the ori for short. It turns out that many different proteins are going to bind to this origin of replication and those proteins are going to separate the 2 strands of DNA, unwinding the DNA so that DNA replication can begin. This unwinding forms a replication fork, which is sometimes also referred to as a replication bubble. Replication forks are really just these Y-shaped regions that are at the end of the bubble where DNA is unwound.

We'll be able to see the replication forks down below here in our image. If we take a look at this image, what you'll notice is that over on this side, we're showing you this replication fork. You can see that the DNA strands have unwound, so we have the old original DNA strand, which is a darker blue color, and you'll see that they're starting to be separated here. There's a separation of these two strands. The separation of these two strands creates the replication forks, or the replication bubbles.

You'll notice that at each of these positions on each side of this unwinding is a replication fork. The replication forks are indicated with these yellow backgrounds that you see here and over here, and you'll notice the Y-shaped regions at the end of the bubble where DNA is unwound. You'll notice that it does kind of create somewhat of a bubble. From here to here there's a little bit of a bubble and sometimes it's referred to as the replication bubble.

What you'll notice here is that DNA replication is actually going to proceed bidirectionally. Bidirectionally just means that it's going to occur in both directions, at each replication fork. You'll see that the direction of DNA replication, and the replication fork is going to be indicated by these red arrows. DNA replication is going to proceed in this direction at this replication fork and it will also proceed in this direction for this replication fork as well. That's important to keep in mind moving forward because we're going to talk about DNA replication at just one replication fork, but we have to keep in mind that DNA replication occurs at the other replication fork in the opposite direction.

DNA replication proceeds bidirectionally in both directions at each replication fork. Once again, we're going to talk more about the process of DNA replication, involving these RNA primers and these different strands as we move forward in our course. But for now, this here concludes our video introducing the terms replication forks, and we'll be able to get some practice applying these concepts as we move forward in our course. I'll see you all in our next video.

Which of the following is incorrect regarding DNA replication forks?

• A. DNA replication forks begin forming at the origin of replication (ORI).
• B. DNA replication forks are caused by helicase separating two complementary strands of DNA.
• C. There are two replication forks found in each replicating prokaryotic chromosome.
• D. DNA replication forks are found at both ends of the replication 'bubble'.
• E. None of the above are incorrect.

Unwinding the DNA: Topoisomerase, Helicase & SSBs

In this video, we're going to talk about some of the enzymes and proteins involved with the unwinding of the DNA during DNA replication, and these include the enzymes topoisomerase and helicase, as well as the protein single stranded binding proteins or SSBs. It turns out that several different proteins participate in the unwinding of the DNA during DNA replication. Of course, the unwinding of the DNA just refers to the separation of the 2 strands of DNA. These include the proteins, these 3 proteins that are listed down below, 1, 2, and 3, and the first of these 3 is topoisomerase, which is also sometimes referred to as DNA gyrase in prokaryotes. Topoisomerase or DNA gyrase, its function is to cut and rejoin the DNA in order to relieve strain that's caused by DNA supercoiling.

DNA supercoiling or just supercoiling can actually inhibit DNA replication and therefore supercoiling must be relieved in order for DNA replication to proceed normally. If we take a look at our image down below, on the left, we're showing you some DNA supercoiling here. You can see that we're showing you a DNA molecule, but the DNA molecule here is supercoiling and so this structure that you see here is a DNA supercoil. The DNA supercoil is going to, again, cause strain and it can inhibit DNA replication, and so this DNA supercoil must be relieved in order for DNA replication to proceed. That is the function of the DNA gyrase or the topoisomerase which is right here ahead of the replication fork over here.

The DNA gyrase's job is to again eliminate or remove the DNA supercoils. The DNA supercoiling can be better understood by thinking about the supercoiling of one of these old telephone wires. This old telephone wire will supercoil just like the DNA molecule has a tendency to supercoil. The topoisomerase is going to help with getting rid of and eliminating the DNA supercoils. Now the second protein involved with the unwinding of the DNA is helicase, and helicase unwinds the DNA by breaking hydrogen bonds.

The hydrogen bonds are forming between the 2 DNA strands. When helicase breaks these hydrogen bonds between the two strands, it separates the strands. So helicase is going to help create single stranded DNA. If we take a look at our image down below, what you'll notice is that the helicase is represented as this yellow triangle, and its job is to break the hydrogen bonds that hold the 2 DNA strands together. It separates the 2 DNA strands creating single stranded DNA.

This is where the third proteins come into play, the single stranded binding proteins, which are abbreviated as just SSBs. These single stranded binding proteins, or SSBs, are going to bind to the single stranded DNA to prevent the reannealing of the DNA, to prevent those hydrogen bonds from reforming. They're also going to prevent the degradation of each of these single stranded DNA molecules since single stranded DNA within cells tends to be degraded. These single stranded binding proteins will bind to the single stranded DNA, prevent reannealing and degradation of each of the separated DNA strands. When we take a look at our image down below, notice that the single stranded binding proteins are these orange circles here that are binding to the single stranded DNA that's being separated here.

These are the proteins that are going to be important for the unwinding of the DNA and the separation of the two strands of DNA so that they can serve as templates for building the brand new DNA strands. This here concludes our lesson on the unwinding of the DNA, and we'll be able to get some practice applying the concepts that we've talked about here as we move forward in our course. So I'll see you all in our next video.

What is the function of the enzyme topoisomerase in DNA replication?

• A. Relieving strain in the DNA ahead of the replication fork caused by the untwisting of the double helix.
• B. Elongating new DNA at a replication fork by adding nucleotides to the existing chain.
• C. Reattaching the hydrogen bonds between the base pairs in the double helix.
• D. Building RNA primers using the parental DNA strand as a template.

Here’s what students ask on this topic:

What is the origin of replication in DNA replication?

The origin of replication, often abbreviated as ori, is a specific sequence of DNA where replication begins. In prokaryotes, which have a single circular chromosome, there is typically one origin of replication. In contrast, eukaryotes have multiple linear chromosomes, each with numerous origins of replication. These origins are crucial because they mark the starting points where the DNA double helix unwinds, allowing replication machinery to access the DNA strands and begin synthesizing new DNA. The presence of multiple origins in eukaryotes helps to ensure that the entire genome is replicated efficiently within the limited time frame of the cell cycle.

What are the key enzymes involved in DNA replication?

DNA replication involves several key enzymes, each with a specific function. Topoisomerase (or DNA gyrase in prokaryotes) relieves supercoiling ahead of the replication fork. Helicase unwinds the DNA double helix by breaking hydrogen bonds between the strands. Single-stranded binding proteins (SSBs) stabilize the unwound DNA, preventing reannealing. Primase synthesizes RNA primers to provide starting points for DNA synthesis. DNA polymerase III (in prokaryotes) extends the new DNA strand by adding nucleotides complementary to the template strand. DNA polymerase I replaces RNA primers with DNA. Finally, DNA ligase joins Okazaki fragments on the lagging strand, ensuring a continuous DNA molecule.

What is the difference between prokaryotic and eukaryotic DNA replication?

Prokaryotic and eukaryotic DNA replication share fundamental similarities but also have key differences. Prokaryotic cells have a single circular chromosome with one origin of replication, while eukaryotic cells have multiple linear chromosomes with numerous origins of replication. This allows eukaryotic cells to replicate their larger genomes more efficiently. Additionally, the replication machinery in eukaryotes is more complex, involving multiple types of DNA polymerases and additional regulatory proteins. Despite these differences, the basic mechanism of semi-conservative replication, where each parental strand serves as a template for a new complementary strand, is conserved across both types of organisms.

What is the role of helicase in DNA replication?

Helicase plays a crucial role in DNA replication by unwinding the DNA double helix. It does this by breaking the hydrogen bonds between the two DNA strands, creating single-stranded DNA templates necessary for replication. This unwinding occurs at the replication fork, a Y-shaped region where the DNA is separated into two single strands. By unwinding the DNA, helicase allows other replication enzymes, such as DNA polymerase, to access the single-stranded DNA and synthesize new complementary strands. Without helicase, the replication machinery would not be able to function effectively, as the DNA strands would remain tightly coiled and inaccessible.

What is semi-conservative DNA replication?

Semi-conservative DNA replication is a process where each of the two new DNA molecules formed contains one original (parental) strand and one newly synthesized strand. During replication, the two strands of the original DNA molecule separate, and each serves as a template for the synthesis of a new complementary strand. This results in two DNA molecules, each composed of one old and one new strand. This method of replication ensures genetic continuity, as each new DNA molecule is identical to the original, preserving the genetic information across generations of cells.