D1.1 HL DNA Replication [IB Biology HL]

this is the video for the higher level content from D 1.1 on DNA replication let's do a quick review of nucleotide structure so this is a nucleotide and it consists of deoxy ribos if we're talking about DNA or ribos if we were talking about RNA a nitrogenous base and a phosphate group now this deoxy ribos is a five carbon sugar and the carbons are numbered 1 2 3 4 and and five and new nucleotides can only be added to the three prime end so if I go back and I number those nucleotides again 1 2

3 4 and the fifth one is up here that means I can only add new nucleotides to the three prime end I like to think of that as like the bottom of the house so if I'm applying that knowledge to this view this molecular view of a DNA strand let's first identify where the five Prime and three prime ends are on this strand the five Prime end is up here okay so the five Prime end and the three prime end again here's the bottom of the house and the top of the house I kind of

like to think of it and the other strand is anti-parallel so that means it's running in the opposite direction so the three prime end is up here and the five Prime end is down here new nucleotides can only be added to the three prime end so again what that means is that on this strand I can add new nucleotides down here on this strand I can add them here no nucleotides can be added to the five Prime end so we say that replication happens in the five Prime to 3 Prime Direction and honestly if you

have to remember just one thing about replication this is a really good one to remember because lots of things happen in the five Prime to three prime Direction DNA replication transcription translation so understanding this Concepts will be very important moving forward let's take a look at replication in real time so I want you to imagine that DNA helicase that enzyme that breaks the hydrogen bonds is working right here and it's breaking these hydrogen bonds going in this direction right so it'll eventually be working its way this way well this creates something called a replication fork

the replication fork is right here it's the point of separation from uh between those strands replication is going to move in the direction of that replication fork so overall replication will be happening this way on the leading strand that is continuous and here's why the leading strand is going to be the one that moves in the five Prime to three prime Direction remember we can only add new nucleotides to that three prime end so imagine DNA polymerase is adding adding adding nucleotides every time it does it it's adding something to the three prime end and

you can picture this building a strand continuously and that's going to move towards that replication fork so this is new Pro no problem notice how our new strand is being built in the five Prime to thre Prime Direction and it's anti-parallel to that parent strand on the other strand though we have a little bit of a problem so imagine this parent strand here and I'll use let's say blue here so this parent strand is three prime to five Prime and this other one would be five Prime to 3 Prime well that means that my new

strand is going to have to be five Prime on this end and three Prime on this end remember the original Strand and the New Strand have to be anti-parallel the problem is is that new nucleotides can only be added to the three prime end so we cannot add them continuously towards the replication fork we have to add them in short segments called okazaki fragments and this is going to happen away from the replication fork and we call call this strand that we are making the lagging strand so it works a little bit something like this

after separation a strand A short segment called an okazaki fragment I'll highlight that in green is laid down again in the five Prime to three prime Direction then another short segment is laid down again in the five Prime to three prime Direction and then another short segment is laid down in the five Prime to three prime Direction so all although we can only add things to the three prime end overall it's still progressing towards the replication fork so again it looks something like this this way and then it jumps over here and then an okazaki

fragment and then it jumps over here an okazaki fragment so overall still progressing towards the replication fork still only adding things to the three prime end just in short segments called okazaki fragments discontinuously on that lagging strand the DNA replication process is highly dependent on several enzymes and lucky for us we have a way of recognizing that look they all end in this suffix as e so that's very helpful to remember one of the enzymes that you do have to know that is not listed here is helicase that was covered in the standard level portion

of this topic helicase of course breaks those hydrogen bonds to separate the parent strands DNA primase is an enzyme that lays down a primer a primer is a segment of RNA nucleotides that acts as a signaling um molecule to tell enzymes where to start the replication process so that primer is very important so DNA primase is going to lay down a primer to let DNA polymerase know where to start synthesizing that next um strand in the standard level uh topic we learned that there was just DNA polymerase and it synthesized a new strand now let's

dive a little bit more into some detail here there are actually two different types of DNA polymerases that we're responsible for knowing DNA polymerase 3 is the enzyme that adds new nucleotides in a five Prime to thre Prime Direction so it's here in green again on the leading strand that is going to be continuous on on the lagging strand it's going to start wherever there's an RNA primer so there would have been one here or there is one right here and it's going to continue in a five Prime to three prime Direction so adding new

nucleotides using the rules of complimentary base pairing in the five Prime to three prime Direction it also attaches those nucleotides together by forming a bond between the phosphate of one nucleotide and the sugar of another nucleotide DNA polymer one is the enzyme that removes all of these RNA primers so again these primers were there for like the starting point and then they need to be replaced with proper DNA nucleotides so this DNA polymerase 1 which you'll see here in blue is the enzyme that is going to pluck out those RNA nucleotides and replace them with

the correct DNA nucleotides and the last enzyme in this this uh sequence is DNA ligase now a lot of students like to think as ligase as like the glue okay but there's not an actual glue this liase is responsible for making connections between the phosphate of one nucleotide and the sugar of another again those are called phosphodiester bonds if you've already studied the topic on DNA structure and this is going to help us connect all of those okasaki fragments which means that we need need to seal some people say sealing the Nyx sealing these segments

of um DNA together so we're looking at making connections between the um segments of DNA that were laid down by DNA polymerase 3 and the nucleotides that were then replaced by DNA polymerase 1 so this DNA ligase is going to run through and make sure that all of those nucleotides are bonded together properly it's very important that at the end of replication we have two identical molecules that the base sequence in the parent strands of DNA have been conserved so errors in replication could result in mutations while mutations can sometimes be beneficial a lot of

the times they are harmful so it's important um to recognize and fix any of them and prevent them from causing changes in the DNA sequence this is done by DNA polymerase 3 so as DNA polymerase 3 is running along and adding new nucleotides it's also proofreading it recognizes any mismatches and replaces the incorrect nucleotide with the correct one so let's say by accident a t is laid down instead of a c then DNA polymerase 3 would then recognize that mismatch and replace it this is the way that continuity is um provided throughout this process and

by the end of DNA replication we should have two identical strands