How does replication occur in the antiparallel DNA molecule? In this lesson, explore the significance of the leading and lagging strands, and learn how Okazaki fragments and RNA ligase make DNA replication possible.
Review of DNA Polymerase
So far in our discussions about DNA replication, we’ve talked about a handful of enzymes that help us by changing and moving parts of the DNA molecules.
One of the most important enzymes here is DNA polymerase. This enzyme is the one that carries the individual nucleotides to the side of replication. DNA polymerase builds the daughter strand by matching new nucleotides to their complementary bases on the parent strand.
When scientists first began studying how DNA polymerase works, they assumed that it always added nucleotides in a continuous fashion.
That is, they thought the enzyme always followed right behind the replication fork, laying down nucleotides as soon as the parent strands were exposed. But in the 1960s, a molecular biologist named Reiji Okazaki challenged that view. He and his colleagues had begun to think that the action of DNA polymerase was not always continuous.
Their ideas stemmed from a combination of discoveries they’d made in the lab and a thorough knowledge of the structure of DNA.
Okazaki and the Antiparallel Problems
Okazaki understood the DNA molecule, and he knew that DNA backbones run in opposite directions. Remember that the strands in a DNA molecule are oriented antiparallel to one another. You can think of the two strands like arrows, with the arrowhead of one strand matching up with the tail of the other strand. Scientists name the ends of the DNA strands according to the carbons in the sugar ring. One end is called the 3′ end, and the other is called the 5′ end.
So on any complete molecule of DNA, one strand will run from 3′ to 5′, and the other will run from 5′ to 3′.
Okazaki and his colleagues knew something was wrong. Remember, enzymes can be picky about how they do their jobs! So for one of the parental strands of DNA, replication occurs just like we always thought, with DNA polymerase working continuously to add on the nucleotides. But it looks like bad luck for the other strand, which runs in the 5′ to 3′ direction.
If DNA polymerase can’t replicate that way, then how does the other parent strand get replicated, too?
Leading Strand and Lagging Strand
Before we go on, we should give a name to each of the two strands we’re talking about. The first one is called the leading strand. This is the parent strand of DNA which runs in the 3′ to 5′ direction toward the fork, and it’s able to be replicated continuously by DNA polymerase. The other strand is called the lagging strand. This is the parent strand which runs in the 5′ to 3′ direction toward the fork, and it’s replicated discontinuously. Now let’s talk about the difference between continuous and discontinuous replication.When DNA helicase opens up the replication fork, the result is two parent strands that are exposed and waiting for new nucleotides to be added on.
The leading strand’s free end is a 3′ end, and the end that’s nearest to the replication fork is the 5′ end. So, DNA polymerase can simply start at the free end, working in the 3′ to 5′ direction, and run continuously toward the replication fork.As DNA polymerase does its job, DNA helicase is still moving down the line, opening the replication fork more and more. So, the two enzymes work in sync with each other. The more DNA helicase splits open the fork, the more DNA polymerase keeps adding on daughter nucleotides.
This is what it means for DNA replication to work in a continuous fashion. But this only occurs on the leading strand.Now let’s look at the lagging strand.
When the replication fork is open, its 3′ end lies at the base of the fork, and the 5′ end lies at the opposite end. With this orientation, DNA polymerase has no problem moving into the base of the fork and replicating straight toward the 5′ end. The problem arises when DNA helicase moves forward, exposing even more lagging strand in front of the point that DNA polymerase began doing its job.
DNA polymerase can’t go backwards and fill in that spot. It only works in the 3′ to 5′ direction. So at this point, it’s basically run out of track.
This is where Reiji Okazaki comes into the picture. He hypothesized that in this situation, DNA polymerase would quit its job once it ran out of space, and then swing back to the base of the fork – that is, the new base of the fork, now that it opened a little bit more – and then it would begin again from there, until it reached the point where it had begun the first time.In this fashion, DNA polymerase would be able to replicate the lagging strand of the DNA molecule, simply by making short lengths at a time. Okazaki and his colleagues worked with the bacteria E.
coli to find out whether this hypothesis was correct. Eventually they proved their theory of discontinuous replication, and the short lengths of DNA came to be known as Okazaki fragments. So the Okazaki fragments are the short pieces of daughter DNA that are made on the lagging strand by DNA polymerase.
Okazaki’s hypothesis was challenged by the fact that nobody understood how the fragments joined together. Even though DNA polymerase is perfectly capable of making multiple fragments, it can’t actually join the adjacent fragments together. But it turns out there’s another enzyme here to help us out. This one’s job is to tie, or bind, the Okazaki fragments to each other.
The fancy scientific word for ‘tie’ is ‘ligate.’
So the name for this enzyme comes from the word ‘ligate’ and, like all the other enzymes, ends with the suffix –ase.
The resulting name is DNA ligase. DNA ligase is the enzyme that binds adjacent Okazaki fragments on the lagging strand, resulting in a continuous daughter strand where DNA polymerase had worked in a discontinuous fashion.
Summary and Review
The dance of the Okazaki fragments and DNA ligase only make the process of DNA replication more complicated than we ever thought. But believe it or not, the details do all come together in the end.
Later, we’ll take a complete walk-through of DNA replication. But for now, let’s review what we’ve learned about the lagging strand of DNA.When replication begins, the two parent DNA strands are separated. One of these is called the leading strand, and it is replicated continuously in the 3′ to 5′ direction. The other strand is the lagging strand, and it is replicated discontinuously in short sections. These sections are called Okazaki fragments, and they are short lengths of DNA. Okazaki fragments are made by DNA polymerase working for short distances in the 3′ to 5′ direction.
The fragments are bound together by the enzyme DNA ligase in order to complete replication in the lagging strand of DNA.