The "Advanced source" of DNA replication.

update: 2015-10-12

Replication!

The source of how we grow, and how we get healed, and how we are even can be twins!

Yes, just like the examples I showed you, even tiny tiny cells in your body replicates and even the DNA inside of it!

Technically, if a DNA is replicating, it means something good might happen!
And this, my friends. Is the stuff we will learn about in today.
The "Advanced source" of DNA replication. Let's get ourselves an egg roll, shall we?

The first thing you know about DNA is the writing I showed you in the last one, whereas the DNA has a part going in the 5` to 3` direction, and the 3` to 5` direction.
DNA has it's deoxyribose backbone and it's four nitrogenous pairs - Adenine, Thymine, Cytosine, Guanine. Because of that, you can easily tell which base pairs are going to be with which base pairs.
There are 8 basic enzymes in order to start you DNA's replication, and those are - Helicase, SSB's, Topoisomerases, RNA primase, DNA polymerase, Sliding DNA clamps, RNAse H, DNA ligase.
And below are the jobs that these enzymes do.

Helicase: This enzyme uses ATP hydrolysis energies to break apart the DNA strands. Their limit is the replication fork, which tells the enzymes where to replicate and where to leave it be.

SSB("Single Strand Binding" proteins): it's job is to make sure that the opened up strands of DNA's doesn't get twisted back to it's normal shape.

Topoisomerases: It makes sure that the other DNA's doesn't get unwounded or get to coiled with each other(Supercoils). This enzyme also uses ATP for it's job, like the Helicase.

RNA primase: Before the other enzymes could start putting in some DNA, it has to have a starting line first, and that 'starting line' is the RNA parts by the RNA primase. Without it, the other enzymes can't do their work of putting the DNA parts.

DNA polymerase and the Sliding DNA clamp duo: Those two are excellent combos. DNA polymerase puts the DNA parts after the 'starting line RNA' that RNA primase has left, and the Sliding DNA clamp makes sure that the DNA polymerase doesn't get side - tracked.

RNAse H: This guy over here removes the RNA parts left by RNA primase.

The second DNA polymerase: Like the first DNA polymerase, this enzyme places DNA blocks in the parts where the RNAse H has removed the RNA parts. It makes Okazaki Fragments in the process, which is a gap between the DNA parts from the RNA places and the original DNA parts.

DNA ligase: This little enzyme fills out the gaps of the Okazaki Fragments, and finishes the replication!

For beginners, teachers shows these enzymes as if they are coming and going on their own, for the sake of simplicity. However, they don't actually just come and go out of nowhere! They are all doing their work based on the structure of the main Holoenzyme!
Look at the 3rd picture which looks like an ant's head with some sort of green stuff stuck on it's antenna, did you got that picture?
Now, I will show you what is the Holoenzyme and what's it's structure.

DNA clamp holder: That's the place where the holoenzyme holds the DNA clamp and uses it and reuses it over and over again.

γ complex(clamp holder): When replication starts, it makes the DNA clamps and holds it in the clamp holder.

τ protein: This protein bundles to hold the DNA polymerases.

That's about it, that's the holoenzyme, and the replication picture is the picture below the holoenzyme picture.
Oh, and one more thing! remember this: 5` to 3` direction is where the enzymes go, so the DNA's have a leading strand and the lagging strand.
The leading strand has no problems for replicating, because it's strand is in the 5` to 3` direction. But the lagging strand is a 3` to 5` direction, so you have to do stuff all over and over again, making a lot of Okazaki Fragments.

Now, with all of this replication stuff done, do you have any questions?
If not, then you could go for a dessert break. And if you have one, you are a wise student! Ok, what's the question? I'll give you one!
Have you ever thought what was the actual stuff that the DNA polymerase places down after the RNA parts? Sure, it's DNA, but what does the actual backbone looks like, and the actual structure, and it's molecule! What are those kinds of stuff, anyways?
And here is the answer - Deoxyribonucleotide triphosphate
This thing - When you look at it, if kinda looks familiar. That's right! it kinda looks like the structure of a DNA nucleotide!
The thing is, instead of having one phosphate group connected with the 5` end, this DTP(Deoxyribonucleotide triphosphate) has 3 phosphate groups!
And I'll tell you why.

DTP is like the DNA nucleotide with 3 phosphate groups instead of one.
Those 3 phosphate groups have a name - The α group phosphate, β group phosphate, and the γ group phosphate.
Whenever replication occurs, the DNA polymerase places this molecule one by one. But here is the thing, whenever the DTP lands on a another DTP, guess what happens to the triphosphate groups?
The β group phosphate, and the γ group phosphate separates from the molecule!
Which gives us a result of the normal DNA nucleotide and 2 individual phosphate molecules!

Well, that's all about replication that I have learned today.
Already on my 3rd page of this activity! What would the 4th one be?
Well, better go and find the flour of videos soon!
See you at next lesson!

By Jane Kim
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