DNA Replication

DNA Replication

The blog embeds a couple of videos that I think will really help you follow what happens. The first time you look at the advanced one, you will have trouble following it. Then, they the more basic one…then come back to the advanced one, along with the blog. This should get the material across to you.

Let me lay out the basics:

Since DNA is two complimentary strands, each strand contains the information to specify the other. Thus, it seemed logical from the first time the structure was determined that the two strands would separate and new subunits (deoxyribonucleotides) would be added to make each new strand, using the other old strand as a template. Each new double helix would therefore really be one old strand and one new one.
Here is the basic idea in video. Like most of the videos I will link, these come from the Howard Hughes Medical Institutes (HHMI).

The first problem:

So, one strand is the template for the other. New bases are added one at a time via a simple chemical reaction we have talked about, mediated by a complicated enzyme machine (comprising many different proteins).
The problem is that the chemistry requires that a new subunit can only be added to the 3’ end. So, if you are moving along a replication fork, one strand cannot be replicated easily…the fork is moving the wrong way and it has to be replicated “backward.”
Here’s a more basic video that shows you how an Origin of replication might work and some detail, but in a much simpler form.

Notice that there is a second problem. As the video says, you need a short RNA primer to begin each section when synthesizing the lagging strand. This is put down by an enzyme called “primase.” That has to be done every time an new Okazaki fragment starts.
Go back and look at the really cool video from above. I think you should look at it again, now that you have seen the simple one.

Here are the details of the problem

If you care...The unit of DNA polymerization (Synthesis) is a deoxyribonucleoside triphosphate. In the image, the “Base” would be either A, T, C or G, depending on what was on the template strand. Just like ATP, these molecules have high-energy (unstable, that is) bonds joining the phosphates. This can therefore be used in transfer reactions, just like enzymes transfer phosphates from ATP in reactions we have studied.
Here is a specific example, deoxyATP
The next base that comes in will use the high-energy triphosphate it carries to attack the 3’ OH.
And forms this:

Thus, as we said, we must add DNA to the growing 3’ end.