In this video, we're going to focus on DNA replication. The first thing that you need to know is that DNA replication is semi-conservative. What does that mean?
So looking at the strand on the left, that is the original strand. You can call it the old strand. And on the right, it was replicated.
We have two new strands. In each new copy, we could see there's one red strand. and one blue strand. So we have one old strand, that's the red one, and one new one, that's the blue one.
So thus DNA replication is semi-conservative. Each new strand retains one original copy, and it has one new copy. Number two, the two DNA strands are anti-parallel. This means that they run in opposite directions.
So from left to right, one of the strands run in the 5 to 3 direction, and the other one goes in the 3 to 5 direction from left to right. Now, the DNA strands are also complementary. They have complementary base parent. So for instance, let's say that the nucleotide sequence of the first strand is A, T, T, G, A, T, C. If we know the sequence of one strand, we can predict the sequence of the other strand. Now in DNA you need to know that A always pair up with T and G always pair up with C and vice versa.
So here we have A, A is going to pair up with T, T is going to pair up with A, G is going to pair up with C, A is going to pair up with T, and C will pair up with G. So given the information of one strand, we can write the nucleotide sequence of another strand. And so that's the idea of complementary base pairing in DNA. Now the next thing you need to know are what holds nucleotides together.
And the answer is hydrogen bonds. Between adenine and thymine, there are two hydrogen bonds. And you need to know that between guanine and cytosine, there are three hydrogen bonds holding them together.
So those H bonds are holding the DNA strands together. Now, there's a lot of other stuff that we need to talk about. One of which is that DNA replication usually proceeds bidirectionally.
So what does that mean? Well, let me draw a picture that will illustrate this concept. So this bubble that you see between the two strands, that is the origin of replication.
In red, This is a new strand being produced. Now in bidirectional DNA replication, the strands can be produced in both directions. Bi means two. Now another example of replication is unidirectional replication. So that occurs when the strand is being synthesized in one direction.
So here's a picture of... the replication fork that I decided to draw ahead of time. And the first thing that we're going to talk about is the helicase enzyme. Helicase separates the two strands, and it does so by breaking the hydrogen bonds that hold the nucleotides together. As helicase separates the two strands, torsional strain is created ahead of the replication fork.
And as a result, an enzyme is needed. DNA gyrase, which is a type of topoisomerase. And these types of enzymes, they can reduce the torsional strain and even relieve positive supracolin that could form in the DNA strand ahead of the replication fork.
So I'm going to put T for a topoisomerase enzyme. So you might see DNA gyrase here as well, but keep in mind that DNA gyrase is a type of... topoisomerase enzyme.
Next, we have the SSB proteins, the single-stranded binding proteins. These SSB proteins, they protect the two strands from cleavage. They also stabilize the two strands, preventing them from snapping back together. Now, DNA replication requires an RNA primer to begin.
So I'm going to draw the RNA primer in green. The RNA primer is basically a sequence of RNA nucleotides. DNA polymerase III, once it sees the RNA primer, it begins to synthesize the new strand in the 5 to 3 direction. This strand here is called the template strand, and that strand runs in the 3 to 5 direction.
But DNA, I mean... DNA polymerase 3 is going to build the new strand in the 5 to 3 direction. So make sure you understand that. DNA polymerase 3 adds nucleotides in the 5 to 3 direction.
Now the enzyme that creates the primer is known as primase. Now DNA replication is semi-discontinuous. Now what does that mean?
What does it mean that DNA replication is semi-discontinuous? Well we need to talk about the other strand. So the first template strand on top runs in a 3 to 5 direction, which means the template strand on the bottom runs in the 5 to 3 direction. DNA polymerase 3 only adds nucleotides in the 5 to 3 direction.
So once a primer is added to this strand, DNA polymerase III is going to work in this direction, that is in the 5 to 3 direction. Now, notice that this strand, this strand, by the way, is called the one in red. This is called the leading strand. And this one here is called the lagging strand.
The leading strand moves in the same direction. as the replication fork. The lagging strand moves in the opposite direction of the replication fork.
So as the replication fork continues to move forward, you're going to have more space here. So what's going to happen is a new RNA primer is going to join here and then DNA polymerase is going to start there producing or adding nucleotides in this direction. So in the leading strand, DNA is synthesized continuously.
It only needs one primer to start and it just keeps on going. It follows the replication fork. On the lagging strand, it doesn't synthesize a new strand continuously.
The replication is discontinuous, as you can see here with that empty space. So that's why DNA replication is said to be semi-discontinuous. It's continuous in the leading strand but discontinuous in the lagging strand.
The prefix semi-means half. So it's half-continuous, half-discontinuous. So technically you could say semi-discontinuous or semi-continuous. Both words will accurately represent DNA replication. Now, DNA polymerase 1 removes the RNA primer and replaces it with DNA.
So after replication, when it's almost finished, this part, this RNA primer, gets removed. And so I'm going to replace that with a red color. So it's been replaced by DNA polymerase 1. Well, I mean, DNA polymerase 1 replaces the RNA primer with DNA material.
Now, once that happens, you're going to have some spaces in between. By the way, these fragments are called Okazaki fragments. Hopefully I spelled that correctly. Now, another enzyme called DNA ligase seals the nick between the Okazaki fragments.
And so there you have DNA replication. So that's the whole process there. Now some other things that you want to know is that DNA polymerase 1 and 3, they have 3 to 5 exonuclease activity.
An exonuclease enzyme is an enzyme that can remove nucleotides from a strand starting at one end of the strand. So this 3 to 5 exonuclease activity, it describes the proofreading ability. of these two enzymes.
So when DNA polymerase III is synthesizing a new strand, if it makes a mistake, It can stop, remove the wrong nucleotide, and replace it with the right one. So that would be the proof-reading ability of DNA polymerase III. Now, DNA polymerase I, not III, has the 5 to 3 exonuclease activity, which plays a role in DNA repair. So those are some things that you want to know with regard to DNA replication.
So just to review, DNA ligase is the enzyme that seals the nicks between Okazaki fragments. And then DNA polymerase 1 is the enzyme that removes the RNA primer and replaces it with DNA material prior to ligase sealing the nicks. And then also DNA polymerase 3 is the enzyme that builds the new DNA strand during elongation. So make sure you understand the functions of those enzymes.
And so that's basically it for DNA replication. Now let's work on some practice problems for the sake of review. Feel free to pause the video if you want to try this mini quiz. Number one, which of the following statements is false?
So let's look at A, DNA replication is semi-conservative. Would you say that's a true statement or a false statement? Now that statement is true. DNA replication is semi-conservative. If you recall, we start with an old DNA strand, and once we create two copies, each copy will have one old DNA strand, and each copy will have one new DNA strand.
So it's semi-conservative in that each new copy has one old strand and one new strand. Some other ideas of DNA replication are conservative and dispersive replication. Now, B, helicase is the enzyme that separates the two DNA strands during replication. Is that true or false?
So that is also a true statement. Helicase is the enzyme that breaks the hydrogen bonds between the nucleotides that are holding the two strands together. And that's how it separates them during replication.
Here is a visual illustration of that. So here are the hydrogen bonds holding the two strands together. And here is helicase, which is about to break those hydrogen bonds. This is going to open the DNA strand and separate into two parts.
Now, DNA replication is continuous. Is that true or false? So this is a false statement.
DNA replication is semi-discontinuous, or you could say semi-continuous. The leading strand is produced continuously in the direction of the replication fork. The lagging strand is produced discontinuously in the opposite direction of the replication fork. Because the leading strand is produced continuously and the lagging strand is produced discontinuously, overall. DNA replication is said to be semi-discontinuous.
So we know the other statements must be true. DNA polymerase III adds nucleotides on the leading strand in the 5 to 3 direction. And E, Okazaki fragments are short sequences of nucleotides found on the lagged strand during replication. So these would be the Okazaki fragments. So the answer for this problem is C.
That is the false statement. Number two, which of the following enzymes is used to reduce torsional strain during DNA replication? Is it helicase, primase, DNA ligase, DNA polymerase I, or topoisomerase?
What would you say? So feel free to pause the video to work on it. So we know the answer is not A. As we said before, helicase is the enzyme that breaks the hydrogen bonds, thus separating the two strands.
So A is out. Primase is the enzyme that synthesizes the RNA primer representing green. Ligase is the enzyme that seals the nicks that are formed in between the Okazaki fragments. So ligase will be here. DNA polymerase 1 is the enzyme that removes the RNA primer and replaces it with DNA material.
The answer is E The topoisomerase enzyme is the enzyme that relieves the torsional strain that is built up when helicase separates the two strands. So E is the correct answer. Number three, which of the following statements is false?
So let's go through each one, one at a time. Looking at answer choice A, DNA strands possess complementary base pairing. Is that true or false? This is a true statement. So if the first strand has, let's say, the nucleotide sequence A, G, T, T, G, C, A, T, G, what's going to be the nucleotide sequence of the other strand?
It's going to run in the other direction. A always pairs up with T. C always pairs up with G.
So we'll get this sequence. And so this is an example of complementary base parent. And don't forget that there's two hydrogen bonds between adenine and thymine.
And there's three hydrogen bonds between guanine and cytosine. Now, B, DNA strands run in anti-parallel directions. That's a true statement. If one strand goes in the 5-3 direction, the other strand is going to run in the opposite direction. So they're anti-parallel.
Now, look at that part C. DNA gyrase can reduce positive supracoils in DNA replication. That's also a true statement.
Keep in mind... DNA gyrase falls in the category of topoisomerases. I always have issues saying that word. So DNA gyrase, a type of topoisomerase, can reduce positive supracoils and can reduce torsional strain ahead of the replication fork in DNA replication. Sometimes my words just don't flow smoothly off my tongue.
What can I say? It just, it happens. Now let's move on to part D. SSB proteins, or single-stranded binding proteins, stabilizes the two DNA strands, preventing them from snapping back together. That is a true statement.
So earlier in the video, the SSB proteins were here. and they prevent the two strands from snapping back together. They also protect the strands from cleavage, so keep that in mind. And then E, DNA polymerase III has 3-5 and 5-3 exonuclease activity. Because it's the last one, we know this has to be the answer.
So there has to be something false with this statement. So what's the part, what's wrong with that statement? You need to know that DNA polymerase 1 has both 3 to 5 exonuclease activity and 5 to 3 exonuclease activity. DNA polymerase 3 only has 3 to 5 exonuclease activity.
It doesn't have the 5 to 3 exonuclease activity. The 3 to 5 exonuclease activity... has to do with the proofreading functions of DNA polymerase 1 and 3. They can both do that. DNA polymerase 1 can remove the RNA primer and it can also function in DNA repair. This is due to the 5 to 3 exonuclease activity of DNA polymerase 1. And so that's why E is false.
It's because DNA polymerase 3 doesn't have the 5 to 3. exonuclease activity.