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Lecture 5

Cell Biology - Lecture 5 - Video 1.1 - Notes

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Boston University
CAS BI 203
Martin Steffen

Lesson 5 – Video 1a [00:00:00.00] 1600 [00:00:00.68] Hi. In this video we will study DNAreplication, which is the process of DNAa 1601 making a copy of itself to pass on to a new cell. The specific topics we'll talk about is that DNA 1602 is the template for DNAsynthesis. We'll talk about four required elements for DNA replication. 1603 We won't be able to stress enough that DNAis always synthesized in the 5 ' to 3 ' direction. This 1604 will cause some problems for DNAsynthesis, as you'll see. 1605 [00:00:36.07] As DNAis synthesized there are going to be leading and lagging strands because 1606 of the requirement that DNAis always synthesized 5 ' to 3 '.And in a second video we'll talk 1607 about the problem of DNAand telomeres. Remember that was one of the 3 essential elements of 1608 chromosomes. There's a problem replicating telomeres.And then we'll also talk a little bit about 1609 organisms which don't have DNAgenome genomes. They have RNAgenomes.And what that 1610 means for our view of biology and what opportunities that gives us for biotechnology. 1611 [00:01:16.89] So in today's lecture, replication, we'll talk about DNAto DNA. In the next set of 1612 lectures on Wednesday, we'll talk about transcription and translation. These are words you have 1613 to memorize. Replication, transcription, translation. On this slide we see a double- stranded piece 1614 of DNAthat's going to get replicated three times into eight copies of itself. 1615 [00:01:47.48] The key point here being, again, that DNAreplication to semi- conservative, 1616 meaning each of the daughter strands gets one of the original gold-colored strands and it 1617 synthesizes a new, approximately dark red strand.And as you can see, each of the daughter cells 1618 from any parent has one of the original strands and makes new ones. Just as a little preview, we'll 1619 mention that DNAreplication is not perfect, that errors get made, and errors are mutations and 1620 these can cause diseases such as cancer.And so certain cells have actually learned to hold on to 1621 the original strand. Stem cells have asymmetric DNAsynthesis, but that is pretty rare in biology. 45 [00:02:45.34] On this slide we see for requirements for DNAa replication. 1622 Replication requires 1623 an origin of replication, the site for it to begin. It will not begin randomly any place. DNA 1624 polymerase always requires a primer to get the strand going. That's a requirement of DNA 1625 polymerase. This is in contrast when enzyme we'll meet later today, in fact, RNA polymerase, 1626 which does not need a primer to start its synthesis. 1627 [00:03:18.01] All polymerases need a template from which to copy, and all nucleic acid 1628 synthesis goes in the 5-' to 3-' direction.And we'll again see some of the challenges that causes 1629 for the replication machinery. On this slide we see a growing strand of DNAin red here. Here is 1630 the end of the existing piece of DNA. This is the 3 ' hydroxyl.Again, 1 ', 2 ', 3 ', 4 ', 5 '. 1631 [00:03:55.89] Again, the "primes" are important because those are the positions of the sugar. The 1632 numbers without "primes" are for the bases. So you have the 3 ' hydroxyl group.Anew 1633 nucleotide comes in and it will allow the hydroxylate group to attack this first phosphate group. 1634 You're going to cleave pyrophosphate out and you're going to have a connection between the 3 ' 1635 carbon and the 5 ' carbon. 1636 [00:04:26.87] This connection will only occur if you are bringing the proper base to base pair 1637 with the existing base on the template strand. In this case G is on the template strand and C is the 1638 nucleotide that you're bringing in. Notice also that the template strand is anti-parallel to the 1639 growing strand.And that's depicted both explicitly with the labeling here and also in this 1640 particular instance with the sugars being drawn upside down. 1641 [00:05:00.33] If you were to bring in a base they didn't base pair with G, say anA, 999 times out 1642 of 1,000 the polymerase would not incorporate it here at the growing 3 ' hydroxyl group. 1643 Mistakes do happen very rarely, but most of the time that would get rejected. On this slide, you 1644 see the second of the four requirements, and that is that DNAsynthesis begins at replication of 1645 origins. This is a sequence, a piece of DNAa that is defined by a specific sequence. The 1646 sequences is recognized by certain proteins that bind to the replication of origin, and these 1647 proteins help unwind the DNAstrands, creating a bubble. 1648 [00:05:51.77] And now you're going to be exposing bases and allowing them to get replicated. 1649 One important thing to remember here is that there are going to be four replication processes. 1650 There's going to be a replication process going in this direction on this strand, there's going to be 1651 a second one at that position going in that direction, there's going to be a third replication event 1652 going that way, and a fourth replication process going on at that end. So this is one replication 1653 bubble. There are two replication forks. Here's one replication fork, here's a second replication 1654 fork, and at each replication fork both strands are being copied. So four simultaneous replication 1655 processes. 1656 [00:06:45.50] Here's a schematic of a growing replication bubble. Let's focus for the beginning 1657 just on the leading strand. We'll talk about the lagging strand in a second. The first thing I want 1658 to point out is that we can deduce the directionality of the DNAbecause of the fact that the 1659 leading strand is growing in this direction. We know that the leading strand has to be 5 '. DNA 1660 grows 5 ' to 3 '. 46 [00:07:17.11] That DNAa is anti-parallel, so if this is going 5 ' 1661 to 3 ' in this direction, this top 1662 strand is 5 ' over here and 3 ' over here. So it's growing in the 5 ' to 3 ' direction. Since DNAis 1663 anti-parallel you know that this is the 5 ' end of this strand and this is the 3 ' end of this strand. 1664 And again, since this is anti-parallel 5 ' over here for this growing strand on the bottom. This is 1665 the 5 ' end and this is the 3 ' end. 1666 [00:07:50.61] Now I'm going to erase some of these markings so that I don't get too confused. 1667 OK, so I have erased some of those markings.And now let's imagine what's going to happen as 1668 this strand keeps growing. This strand will have to burrow in to the center here to keep this 1669 unwinding, to keep copying the strand.And it will just keep on going for as long as there is a 1670 template to be copied. 1671 [00:08:21.97] This motion is depicted sort of in these three snapshots. The smallest bubble, a 1672 little larger bubble, and a larger bubble, just because as you keep unwinding at this location and 1673 this location to keep copying, the bubble will get larger and larger as you're copying it. And as 1674 you can see for the leading strand, as the bubble gets larger, it just keeps extending and it keeps 1675 getting larger and keeps getting larger. Same thing is true on this end. The leading strand on the 1676 bottom is just going, going, going, and it will just continue to make a very long strand as long as 1677 it is needed. 1678 [00:09:05.17] The problem for the lagging strand is that it synthesizes in the wrong direction.As 1679 this bubble grows larger going in this direction, on the bottom in the lagging strand, you are still 1680 required to synthesize in the 5 ' to 3 ' direction. So what happens is, the polymerase jumps ahead, 1681 sequences back, jumps ahead, sequences back, jumps ahead, sequences back. We'll see that 1682 better on another slide. But the point here is just no that's a lagging strand has to put down many 1683 primers and it can synthesize many small little pieces of DNA, which then later on will have to 1684 get stitched up. 1685 [00:09:50.74] In this picture, we see half of a replication bubble. We see one replication fork. 1686 The rest of the replication bubble would be here, on this side.And as this replication fork moves 1687 out wider and wider, farther and farther away from the center of the origin of replication, we're 1688 going to look at the consequences. Now, I have to apologize. These figures are not very related. 1689 [00:10:17.49] Notice that down here we have 5 ' at the top, and here it's a 3 '. So you'd have to 1690 flip this over for these two to relate. That's not important. This is the orientation that we showed 1691 in the previous slide. Here we have a leading strand synthesizing 5 ' to 3 ' and it's going to just 1692 continue to synthesize as long as you can go. The first amount of material that's synthesized is in 1693 dark red. Then we look at it a little later and you can see that in lighter red or pink there is 1694 additional synthesis, so the most recently synthesized base of the leading strand is the one that's 1695 furthest most near the replication fork
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