DNA Building Blocks

DNA Replication Part 2

Estimated read time: 1:20

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    Summary

    In this informative episode by Marty Frolick, part 2 of the DNA replication process is discussed in detail, continuing from where part 1 left off. The video walks through the role of various enzymes, including helicase, primase, and DNA polymerase, in unzipping the DNA strands and forming new ones. The process involves the leading and lagging strand dynamics, highlighting the Okazaki fragments and how DNA ligase ensures the final pieces come together seamlessly. The session takes an animated approach to elucidate this complex biological process.

      Highlights

      • Helicase does the heavy lifting by unzipping the DNA strands. 💪
      • Primase sets the stage by inserting RNA primers. 🎬
      • DNA polymerase III constructs the new DNA strand, following the blueprint. ⚙️
      • The formation of Okazaki fragments is part of the lagging strand's unique replication journey. 🧩
      • DNA ligase acts like the glue, sealing all the DNA pieces into one coherent strand. 📎

      Key Takeaways

      • The helicase enzyme unzips DNA strands, allowing replication to begin. 🚀
      • DNA polymerase III builds the new DNA strands, following the primer's lead. 🎨
      • Okazaki fragments form on the lagging strand due to replication directionality. 🔄
      • DNA polymerase I replaces RNA primers with DNA nucleotides to ensure a complete strand. 🖌️
      • DNA ligase ties the DNA segments together, creating a continuous strand. 🔗

      Overview

      In Marty Frolick's tutorial on DNA Replication Part 2, the journey of DNA replication is explored with focus on the specific enzymes involved. Starting from where we left off in part 1, this lesson illustrates the essential role of helicase in unwinding the DNA strands, setting the stage for replication.

        DNA polymerase III plays a key role in assembling new DNA strands by following primers set by primase, effective both on the leading and lagging strands. However, due to the directional constraints of DNA replication, Okazaki fragments appear on the lagging strand, requiring additional steps to form a complete, uninterrupted DNA strand.

          The episode smoothly transitions into the role of DNA polymerase I, replacing RNA primers with DNA, and concludes with DNA ligase, which ensures that all DNA fragments are joined, securing a complete replication process. With engaging animations and clear explanations, Marty makes this complex process educational and accessible.

            Chapters

            • 00:00 - 01:00: Introduction and Review of Part 1 The chapter begins by revisiting the ending of Part 1, focusing on the continuation of a DNA module discussion. It details the process of drawing the top strand of a DNA molecule that has been opened up. The bottom strand was illustrated as green in previous discussions. The conversation includes a brief mention of the helicase enzyme and its implications in this context.
            • 01:01 - 02:00: Role of Helicase and Primase The chapter discusses the role of helicase and primase in molecular biology. It describes helicase as a protein enzyme responsible for opening or unzipping DNA strands. The chapter uses a visual representation, likening helicase to a 'big chunky protein' that operates on a specific part of the DNA molecule, moving in a particular direction as it functions.
            • 02:01 - 05:00: DNA Polymerase III and Okazaki Fragments This chapter discusses the process of DNA replication focusing on DNA Polymerase III and the formation of Okazaki fragments. It highlights the importance of directional markers in understanding how the strands are oriented, with the top strand directed from 3' to 5' and the complementary green strand from 5' to 3'. The chapter explains the roles of helicase and primase in unwinding the DNA and inserting primers, respectively, setting the stage for the synthesis of Okazaki fragments by DNA Polymerase III on the lagging strand.
            • 05:01 - 07:00: Role of DNA Polymerase I The chapter discusses the function and importance of RNA primers in the replication process of DNA. Due to the uni-directional movement of enzymatic processes along the DNA molecule, primers are necessary for initiating this movement. The speaker explains the placement of the primers at the start and illustrates their function, acknowledging their critical role in facilitating enzyme activity. The use of different colors to highlight the primers indicates an effort to visually clarify how these elements work within DNA replication.
            • 07:01 - 09:00: Finalizing with DNA Ligase In the chapter titled 'Finalizing with DNA Ligase', the focus is on the process of DNA synthesis, specifically the role of DNA ligase. The transcript describes how primers provide a starting point for DNA Polymerase III to begin assembling a new strand of DNA. It emphasizes the sequence of events where the primer is placed, allowing the polymerase to add complementary nucleotides, thus continuing the extension of the DNA strand. The narrative likely continues beyond this excerpt to include the ligation step that finalizes the DNA strand assembly.
            • 09:01 - 11:00: Summary and Conclusion The chapter describes the movement and function of DNA polymerase in relation to helicase. It uses a visual aid by introducing an 'orangy' color to depict the DNA polymerase, emphasizing its direction and action. The summary focuses on how DNA polymerase follows the helicase as they move along the DNA strand.

            DNA Replication Part 2 Transcription

            • 00:00 - 00:30 okay so we are continuing from part one where uh where we left off so we're going to draw this top strand of this dna molecule that's been opened up and the bottom strand was green you said so the bottom strand was something like this and what had happened is the we had the helicase
            • 00:30 - 01:00 protein enzyme which had opened up or unzipped okay um we can draw him i think he was red so the helicase is operating here at this point so we'll shade him in with our crayon just so he looks like a big chunky protein working on that part of the molecule and he's moving of course in a in the direction oh yeah we should put
            • 01:00 - 01:30 the directional uh markers in too so let's do that first and i believe the top strand in our previous example was the three here and the five here is that right we're good because we can't mess that up or it'll really screw things up and then we had the five end here and the three end down here for the green so what we had done is we had seen that after the helicase opens this up primase comes in and inserts these
            • 01:30 - 02:00 little rna primers so i'm going to use a different color this time because last time i was using that lime green and it wasn't showing up very well so i'm going to change to this really bright yellow for the primers okay so a primer was put here at the start and it's because the movement of these enzymes along the molecule is one direction only so i'll put in this piece of primer here and of course we have these little bases that are excuse me
            • 02:00 - 02:30 are being ready to attach now the primer inserts this piece which is now serves as a starting point for the dna polymerase iii which would attach here at this point and begin to assemble uh the piece of dna that goes sort of with this section so i'll put it here and i don't forget what color i use for
            • 02:30 - 03:00 dna polymerase do you remember let's use something sort of different i think it was an orange actually let's use this orangy color so here's the dna polymerase right here and of course it's moving this way right and the helicase is moving this way so it's basically following the helicase and so we'll color that into with our crayon and we'll get that nice sort of what was it orangey color
            • 03:00 - 03:30 there he is and of course what he's doing is building this this other strand this green strand assembling it uh it's on to the purple string so we'll put some black little markers for our bases in there the base pairs here okay on the bottom however because these enzymes are always moving in the same direction
            • 03:30 - 04:00 they have to basically move backwards so what has to happen on the bottom is the primase has to insert a starting piece of rna here but it also has to have other pieces or markers that tell the polymerase where to stop so all along the bottom every so often you will get a marker in other words right here this marker is put here why is it put there well that's right behind the helicase you can't put it any further ahead so it inserts the marker but a little
            • 04:00 - 04:30 later if you imagine this animated that marker next to the helicase will be the one way down here right and so it will leave behind it and then they'll put another one in further on another one sort of always inserting them right behind the helicase which produces this staggered effect and so we get these little rna primer pieces all sort of staggered along and this is where we sort of left off and i'll put these guys underneath here
            • 04:30 - 05:00 and then of course on the bottom we also have a dna polymerase so let's put him in there sorry sorry well yeah but so what would happen is a dna polymerase would be working here but it would also be working on the other section so on this one he's going to go this way on this one he's been working longer so
            • 05:00 - 05:30 i'm going to put him near the end he's pretty much done he's he's gone as far as he can go right he's kind of hit the wall he's hit the next primer and i'll shade those in kind of showing what's happening as time goes on right so remember this is you have to think about this as an animated process and so his job is to reassemble and he'll be assembling this nice purple so he's assembled he's going to start to
            • 05:30 - 06:00 assemble the purple but i'm only going to draw a little bit because obviously he hasn't gone that far but this guy has gone almost all the way to the end so they are building these purple sections which are essentially the top pieces of our original dna strand so those are the rna polymerase threes remember that rna polymerase three and that's where we sort of left off and we said that on the top we get a
            • 06:00 - 06:30 nice smooth piece of dna that's being made that'll follow the helicase the only thing that we have to worry about is just one little piece of primer rna at the start but on the bottom because we have to keep going backwards every time the helicase moves an rna is inserted and then it moves a little more and rna is inserted you get these fragments and we call them okazaki fragments so these pieces right here of dna that are like the purple piece there
            • 06:30 - 07:00 it's called an okazaki fragment named after the scientists who sort of discovered or isolated that and that's about as far as we got all right let's carry on so now i'm going to redraw sort of the next picture and uh i'll just move down a bit more [Laughter]
            • 07:00 - 07:30 uh yeah purple on top so here's where we're at we have a purple strand at the top and the gila caves is on its way we have a green strand on the bottom like that and uh we have a little piece of rna that's been put here and on on the other side we have these little pieces of rna that have been attached sort of all
            • 07:30 - 08:00 along maybe there's another one starting right here and we have on the top a nice piece of dna that's being made all the way to here now so the dna polymerase 3 is just working along and the top is looking good oops all right we'll put in some lines for our bases
            • 08:00 - 08:30 so the top part is looking good the bottom part however only has [Laughter] these little guys and because it's working backwards it's got pieces of dna that have been inserted this way this one will be finished this one over here might still be going right so it's on it's kind of being
            • 08:30 - 09:00 built you can imagine that there's a little um there's a little dna polymerase working along there right and so we have all this whoops colors thicknesses and that one's not quite done so it's being built so this is what it's looking like it's
            • 09:00 - 09:30 getting there so next what we have to do is we have to change the little bits of rna into the corresponding dna and so what happens here is another enzyme called dna polymerase one right they're called one and two and three because of the order in which they were discovered so that's not anything to do with their function it's just the way they're called so what it does is it removes the rna nucleotides so now we need another enzyme
            • 09:30 - 10:00 let's use a new color maybe this really light blue or something and let's draw an enzyme that would be sort of operating here moving along this little rna fragment this one will be almost done so we'll put it because it started sooner right and we'll color those in with our crayon
            • 10:00 - 10:30 that's not super visible but you get the idea um while we're at it we'll need one at the top too so let's do that one it's got there's a piece up there that has to be fixed so this one will be almost done as well right okay and we're coloring in so this is dna polymerase
            • 10:30 - 11:00 one i'll write that next to it in a different i'm just in black because it's a dna i'm going to put p for polymerase and a 1. okay dna polymerase one we've already seen polymerase so you know what that means and you can see it's working here and in every case it's moving uh along that little fragment in this direction
            • 11:00 - 11:30 so what would the result would be is that it would be changing so i'm going to rewrite this as green you see these would all be turning into dna pieces because this is this one's just getting started oh those should be purple crap on the bottom right green on the top these are turning into purple pieces so the dna polymerase one's job is to change the rna primer pieces into regular dna yeah
            • 11:30 - 12:00 yep oh yeah no sorry good point went too fast the one on the top is obviously going in the opposite direction right this one would be going so yeah let me have to redraw that hang on good point rats that's what happens when you don't stay focused so this one is actually by the time it's done it's moving the other way so let's redraw that guy uh
            • 12:00 - 12:30 he'll be very close to the end of that fragment here the ones on the bottom are okay but he's actually going this way and so the effect would be we would still have yellow primer well right sort of here and he would be inserting the green all along here so it would look more like that right that's that's a good correction
            • 12:30 - 13:00 and it would be nearly done so we could maybe put the green almost over there finishing up that piece okay now we're doing better they're changing the rna pieces they're disassembling one nucleotide at a time and reassembling a dna nucleotide in its place and over here we would still have our little brown dude
            • 13:00 - 13:30 still working so here he is this is the dna polymerase three who's still chugging along here uh finishing up that okazaki segment right so that's kind of happening yes yeah so it's not a sequential thing it's continuously happening all sort of at the same time however certain things have to happen first
            • 13:30 - 14:00 so as this opens as the helicase moves down immediately the primases will come in and start putting in the yellow pieces of of rna as the helicase moves on those will move along with it and keep doing that leaving behind all these open section which then will have the dna polymerase threes will come in and start attaching dna according to where those primers are placed once they're done the helicase is moved
            • 14:00 - 14:30 even further right all the other stuff is moving down the line so they're going to go down the line and keep working down the line it's like it's like a an assembly line this essentially and then what happens is this stage where the dna polymerase 1 comes in and changes it so then there's basically only two things left or one thing left what we now have then is this once this is finished the way down the line we have this
            • 14:30 - 15:00 okay and um if i continue this picture way down here okay so now we have all of this all the rna is gone and there's now another protein and what this protein does um is it comes along and it joins
            • 15:00 - 15:30 whoops black so let's put all these pieces in here i should have left a little space and i didn't so because the bottom piece here was i'm going to put a little space right there that used to be the rna fragment it's been replaced by dna now remember and this is all just normal along the bottom we'll have several little spots that were replaced by
            • 15:30 - 16:00 dna segments like this so the little rna primers are are replaced but they're not totally attached here we go they're not totally attached
            • 16:00 - 16:30 so what has to happen now is one final enzyme called ligase has to come along dna ligase and dna ligase is going to attach each of these little sort of fragments together so let's get yet another color perhaps a nice purpley mauve color and let's draw right here
            • 16:30 - 17:00 and here and here this dna ligase so we'll call it dna ligase what's a ligature is there anybody going to be a doctor soon doctors often refer to stitches as ligatures because what do they do they close up they stick things together right a ligature is a way of tying things together specifically and so ligase is an enzyme that ties
            • 17:00 - 17:30 things together so you can remember that based on that so what it's doing is it's essentially working on the gap so what i'm going to do is in black i'm just going to put the gaps here just so you can still see them right but they would just be purple or green they'd be filling in the gap forming bonds and making the dna completely finished and essentially the same as it was before
            • 17:30 - 18:00 okay and that's the basic process so to review the whole process in summary helicase opens molecules unwinds once the section has been unwind and wound then the rna primases
            • 18:00 - 18:30 can move in and begin to assemble the little rna marker pieces on the leading strand only one is needed and in fact um again i'd have to double check on this but i think this one never actually gets turned into dna just as a technicality because it's a marker it's not it's not a it's not a red as uh i'm not sure if that does or not i'll have to look that one up for you but the point is is that it produces these marker rnas which essentially are telling the
            • 18:30 - 19:00 dna polymerase three where to begin its assembly of the dna so after the primase is gone in this picture we see the dna polymerase iii building the pieces of dna in their place on the leading strand it simply chugs ahead and follows the helicase making a nice long uninterrupted strand of dna but on the bottom because it has to go from the five to the three end uh sorry the three to the five now
            • 19:00 - 19:30 here's here's the thing right the confusing part of the five and three is on which strand are you talking are you talking about the strand it's riding on or the strand that it's building because the strand it's riding on if you look at the one on the bottom it's riding on the green strand and it's going from three to five but it's building from five to three isn't it so you just have to keep track of that in your mind they ride from three to five they build
            • 19:30 - 20:00 from five to three right so the piece if i i right here this piece that it's making is moving from right to left in the five to three direction but it's riding on the green piece down below in the three to five direction so just kind of remember that and make sure that you keep that straight in your mind so these guys are building this on the bottom now i'm a lagging strand we have this incidence of getting fragments of dna because obviously when this gets to here it has to stop
            • 20:00 - 20:30 because of the other marker and so therefore we get the okazaki fragments and then afterwards we have the dna polymerase one which comes in and replaces the fragments of rna with dna producing a nice even chain on both sides and then the last step is dna ligase which has to come in and actually bond those segments of dna that were replaced by the dna polymerase one but they're actually
            • 20:30 - 21:00 stuck to the ones next to them and now we have a nice complete picture of dna and it's being replicated okay up so dna polymerase iii its job is to assemble dna fragments in the open space that's left see this this here
            • 21:00 - 21:30 is an open space there's nothing there and so what it's doing is it's enabling so nucleotides would be floating around in the mix right they're floating around in this in the nuclear cytoplasm or cytosol and so what's happening is as one floats by this enzyme has an active site that allows it to attach and grab and therefore it can attach to the bottom strand so it's building the dna strand along this sort of open-ended
            • 21:30 - 22:00 gap it's building dna the dna polymerase one however is not doing that what it's doing is it's changing the rna pieces into dna there's no gap here there's an rna piece that has to be eliminated so its enzyme has the right active sites to break apart the rna piece nucleotide that's bonded there and also bring in a dna nucleotide get rid of the yellow that's exactly what they're doing
            • 22:00 - 22:30 so now it's because remember the yellow is rna right and now when it's done it's all dna it's all copied like this and then the ligase ties everything together and that's essentially the way it works okay all right and that's where we'll stop dna replication