How do enzymes assist in starting DNA replication? In this lesson, we explore the work of a contributing enzyme, DNA polymerase, and learn how the RNA primer is made by the action of RNA primase.
DNA Replication and the Zipper Model
So far we’ve been talking about DNA replication by using a zipper as an example. It really is one of the closest things we have to help us understand how DNA replication works. We talked about how the DNA molecule splits apart during semi-conservative replication and how the enzyme helicase acts just like a zipper slider to separate the DNA right down the middle. Helicase breaks the hydrogen bonds just like the wedge in the slider breaks apart the teeth on a zipper.
But we didn’t get to talk about how the daughter strands are put together on top of the parent template. So, in this lesson we’re going to continue with the steps of DNA replication, and we’ll keep thinking of it being similar to the form of a zipper.Imagine if your best friend gave you one side of a zipper tape, and he asked you to complete the zipper by attaching the other side.
But instead of giving you an entire zipper tape, what if he only gave you a bunch of little teeth that weren’t connected to each other? You would have a lot of work to do! You’d have to slide those little metal teeth in between the grooves on the zipper tape one at a time until you completed the opposite half of the zipper.That’s sort of how it is with DNA replication. Once the parent DNA has been split into a replication fork, a daughter strand has to be built onto the parent strand one nucleotide at a time. The ‘hands’ that work to grab those little nucleotides and arrange them into their spaces are actually a special type of enzyme. The enzyme is called DNA polymerase.
DNA polymerase sounds like a really long word, but if you break it down, it actually makes a lot of sense, and it’s easy to remember. The suffix –ase simply tells you that this molecule is an enzyme, or a protein that helps with chemical reactions. The word root ‘polymer’ refers to any large molecule that is made of many smaller parts, or monomers. And you already know that DNA stands for deoxyribonucleic acid.
So, if you add up all of the parts of the word, then you can see that DNA polymerase is an enzyme that helps put together the small parts of the DNA molecule. Those small parts, of course, are the nucleotides.DNA polymerase is like a vehicle that buses in the individual nucleotides. It builds the daughter strand of DNA according to the template set up by the parental strand. For every cytosine, it lays down a guanine, and for every guanine, it lays down a cytosine. For every thymine, it lays down an adenine, and for every adenine, it lays down a thymine. Each daughter nucleotide is attached, one at a time, by DNA polymerase.
Now, most enzymes, especially DNA polymerase, are a bit picky when it comes to doing their job. They want all the conditions to be just right, and they’ll only help with a chemical reaction when they have everything go their way. The job of DNA polymerase is to add daughter nucleotides onto the exposed bases of a parent strand.But since it’s so picky, it won’t just start adding nucleotides on its own.
It has to attach them onto the end of a newly synthesized daughter strand. Now how is that supposed to work? It’s sort of like if I said, ‘I’m not going to go grocery shopping until somebody buys me some groceries first.’ DNA polymerase basically refuses to do its job until part of its job is already done!
RNA Primase and the RNA Primer
Wouldn’t it be nice if we had another helper to solve this problem? Well, fortunately, we do, and it’s yet another enzyme. It’s called RNA primase. The job of RNA primase is to make, or synthesize, a primer for replication to start. First, it waits for DNA helicase to open a replication fork. Then, it swings in behind helicase to lay down a primer.
What’s a primer? Well, a primer is a short polynucleotide segment that primes, or prepares, the way for DNA replication by helping DNA polymerase to get started in doing its job.
The primer is made out of RNA, so it’s called an RNA primer.Let’s go through that again because it gets a little confusing here. The RNA primer is a short strand of RNA that initiates DNA replication.
So, the primer that initiates DNA replication isn’t even made out of DNA! Don’t get confused about the difference between the RNA primer and the RNA primase. Again, the enzyme that puts together the RNA primer is called RNA primase. Just remember that the one with –ase is the one that’s the enzyme.
Just like DNA polymerase buses in the DNA nucleotides, RNA primase buses in the RNA nucleotides in order to build the RNA primer. It builds up a segment of RNA according to the template, just like before. For every cytosine, it lays down a guanine, and for every guanine, it lays down a cytosine. For every thymine, it lays down an adenine, and for every adenine, it lays down a… no, it doesn’t lay down a thymine! Here’s one spot where things are a bit different. Remember, this is RNA we’re talking about.
There is no thymine in RNA. Instead, it lays down a uracil.This segment of RNA might only get about 10 nucleotides long before DNA polymerase feels ready to start putting on DNA. So, it finally gets itself over to the RNA primer and begins to attach the actual DNA nucleotides that will become the daughter strand. The RNA primer isn’t needed anymore once DNA polymerase is doing its job.
So, it actually gets removed, and later, DNA polymerase will come back around and make sure that spot is filled in with DNA.
As you’re learning about these enzymes, it’s easy to get confused about which enzyme has which job to do. Scientific terminology can all begin to sound the same. So remember, there is usually a hint about the job they do inside of the enzyme’s name. For example, DNA polymerase is responsible for making a polymer of DNA and RNA primase is responsible for making a primer out of RNA.
Now I know I made DNA polymerase sound like a picky, lazy bum, but it’s actually a pretty efficient enzyme. Remember that it has to synthesize that daughter strand of DNA by the rules of complementary base pairing. If it makes a mistake by mispairing a base, like attaching cytosine to adenine, for example, that could cause a harmful or even deadly mutation.
Fortunately, incorrect pairings only occur in about one in a billion nucleotides.For the mispairings that do occur, DNA polymerase goes back for a proofreading step and fixes all the mistakes. It’ll even check for any damage that may have been caused by radiation, like ultraviolet light and x-rays. This kind of damage can be repaired by DNA polymerase and other enzymes that we have in our bodies.
So really, DNA polymerase is a valuable enzyme.
Believe it or not, there are even more things to understand about DNA replication before we can complete the picture. But for now, let’s summarize what we’ve learned in this lesson. DNA polymerase is the enzyme responsible for adding the daughter nucleotides to the parent DNA strand. In order to help it get started in its process, an RNA primer is built upon the parent strand at the base of the replication fork. The enzyme responsible for building that RNA primer is RNA primase.
Once replication has begun by DNA polymerase, the RNA primer is removed and the daughter strand is eventually completed from one end to the other.
You will be able to describe the functions of DNA polymerase, RNA primer and RNA primase in the process of DNA replication at the conclusion of this video lesson.