DNA Replication (Updated)

0:00 Captions are on! Click CC at bottom right to turn off. DNA. We talk about it so much---it is the ultimate director for cells and it codes for your traits. With a molecule that has a function like that, it makes sense that when you make another cell---like in cell division---you would also need to get more DNA into the new daughter cell. And that introduces our topic of DNA replication, which means, making more DNA. First, let’s talk about where and when. First where---well if it’s in a eukaryotic cell, it occurs in the nucleus. However, remember, not all cells have a nucleus. Such as prokaryotic cells. They don’t have a nucleus. Still both prokaryotic and eukaryotic cells do DNA replicationm but there’s some differences

0:45 between the two that this clip doesn’t go into. Next, when. When does this happen? Well a cell is going to need to do this before it divides so that the new daughter cell can also get a copy of DNA. To get specific, in a eukaryotic cell, that’s going to be before mitosis or meiosis in a time known as interphase. I think DNA replication would actually make a great video game. Still waiting for that to be invented. I’m going to introduce the key players in DNA replication so that you can get some background information. Now, remember, these are just some major key players. There’s a lot to this process. Many of the key players are enzymes. In biology, when you see something end in –ase, you might want to check as it’s very possible that it’s an enzyme.

1:31 Enzymes have the ability to speed up reactions and build up or break down the items that they act on. So here we go with the key players. Helicase- the unzipping enzyme. If you recall that DNA has 2 strands, you can think of helicase unzipping the two strands of DNA. Helicase doesn’t have a hard time doing that. When unzipping, it breaks through the hydrogen bonds that hold the DNA bases together. DNA Polymerase- the builder. This enzyme replicates DNA molecules to actually build a new strand of DNA. Primase- The initializer. With as great as DNA polymerase is, DNA polymerase can’t figure out where to get started without something called a primer. Primase makes the primer so that DNA polymerase can figure out where to go to start to work.

2:18 You know what’s kind of interesting about the primer it makes? The primer is actually made of RNA. Ligase- the gluer. It helps glue DNA fragments together. More about why you would need that later on. Now, don’t feel overwhelmed. We’ll go over the basics of this sequence in order. But remember, like all of our videos, we tend to give the big picture. There are always more details and exceptions to every biological process that we can’t include in such a short video. DNA replication starts at a certain part called the origin. Usually this part is identified by certain DNA sequences. At the origin, helicase (the unzipping enzyme) comes in and unwinds the DNA. Here’s the thing though: you don’t want these strands to come back together.

3:05 So SSB Proteins (which stands for single stranded binding proteins) bind to the DNA strands to keep them separated. And topoisomerase---I always have to slow down when I say that enzyme’s name---keeps the DNA from supercoiling. Supercoiling might sound super and it can be when you’re trying to compact DNA, but it’s something that needs to be controlled during DNA replication. Supercoiling can involve an over-winding of the DNA, and you need the DNA strands to be separated for the next steps. Primase comes in and makes RNA primers on both strands. This is really important because otherwise DNA polymerase won’t know where to start. In comes DNA Polymerase. Ok, before we go on, remember how we said DNA has two strands? They’re not identical; they complement each other.

3:51 In our video that covers DNA structure, we talk about how the bases pair together with hydrogen bonds. The base adenine goes with base thymine and the base guanine goes with the base cytosine. These strands are also anti-parallel so they don’t go in the same direction. What do we mean by direction? Well, with DNA, we don’t say North or South. We say DNA either goes 5’ to 3’ or 3’ to 5’. What in the world does that mean? Well, the sugar of DNA is part of the backbone of DNA. It has carbons. The carbons on the sugar are numbered right after the oxygen in a clockwise direction. 1’, 2’, 3’, 4’ and 5.’ The 5’ carbon is actually outside of this ring structure.

4:38 Now you do the same thing for the other side but keep in mind DNA strands are anti-parallel to each other. So let’s count these---again, clockwise after the oxygen. 1’, 2’ 3’, 4’ 5’. And the 5’ is out of this ring. This strand on the left runs 5’ to 3’ and the strand here on the right here runs 3’ to 5’. We’ll explain why all that matters in a moment. So let’s take that knowledge there and look at DNA replication here. In this image, I labeled the top original strand 3’ to 5’. I labeled this bottom original strand 5’ to 3’. That’s the original DNA that is going to be replicated. DNA is unwinding here thanks to helicase.

5:24 In this example, it will keep unwinding in this direction. Primase places primers. DNA polymerase is building the new strands. Now the thing about DNA polymerase is, when it’s building a new strand, it can only build the new strand in the 5’ to 3’ direction, meaning it adds new bases to the 3’ end on the new strand. See how it’s being built in the 5’ to 3’ direction? This one is called the leading strand. But, take a look down here. So DNA polymerase once again is building a new strand in the 5’ to 3’ direction. But there’s a bit of a problem here. See, as DNA unwinds, because DNA polymerase can only build the new strand in the 5’ to 3’ direction, it has to keep racing up here next to where this unwinding is happening.

6:14 You can see why then this new strand is known as the lagging strand. On this lagging strand, primers have to keep being placed in order for DNA polymerase to build. These fragments that result are known as Okazaki fragments. Primers have to get replaced with DNA bases since the primers were made of RNA. Ligase, the gluing enzyme as I like to nickname it, has to take care of the gaps between the Okazaki fragments, sealing them together. At the end of this replicating, you have two identical double helix DNA molecules from your one original double helix DNA molecule. We call it semi-conservative because the two copies each contain one old original strand and one newly made one.

7:01 One last thing. Surely you have had to proofread your work before to catch errors? In this process, you don’t want DNA polymerase to make errors. If it matches the wrong DNA bases, then you could have an incorrectly coded gene…which could ultimately end up in an incorrect protein---or no protein. DNA polymerase is awesome; it has proofreading ability. Meaning, it so rarely makes a mistake. Which is a good thing. So, remember how we said there is far more detail to this process to explore? The detailed understanding of DNA replication has led to some lifesaving medical treatments that can stop DNA replication in harmful cells including pathogenic bacteria or human cancer cells. We encourage you to explore beyond the basics; check out the further reading suggestions

7:47 in the video details to explore more! Well, that’s it for the Amoeba Sisters and we remind you to stay curious.