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Lecture 4

Cell Biology - Lecture 4 - Video 1 - Notes

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CAS BI 203
Martin Steffen

Lesson 4 – Video 1 [00:00:00.00] 1312 [00:00:01.21] PROFESSOR: Hi. In this lecture, we'll talk in greater detail about DNA structure, 1313 about the arrangement of DNA into a double helix, the organization of DNA into chromosomes, 1314 and the way that genes are arranged on chromosomes. 1315 [00:00:17.67] In DNA, there are 3 basic parts, as we've seen before. We have phosphate groups, 1316 a sugar group-- these two will combine to form the backbone-- and a base, which will encode the 1317 information in the center of the strand. Together, these 3 pieces are called a nucleotide. And the 1318 nucleotides will join together to form a linear sequence of bases which can be read out by 1319 enzymes or other nucleic acid molecules. 1320 [00:00:49.34] It's called a double helix because there are two strands in DNA that base pair with 1321 each other. You have one strand on this side and a second strand going this side. These strands 1322 are anti-parallel That means that the directionality is different. You have a 5 ' end running to a 3 ' 1323 end for one strand, anti-parallel with a 5 ' end running to a 3 ' end over here, with the base pairs 1324 in the center pairing with their partners. 1325 [00:01:27.96] I don't want to give the impression that this is a linear configuration. Again, it's a 1326 double helix. And here we can see a right-handed helix going with and the axis of the double 1327 helix running up and down and the bases interacting with each other in the center of that 1328 configuration. 37 [00:01:55.25] Now, of the four bases in DNA, adenine will always 1329 hydrogen bond with thymine 1330 with two hydrogen bonds. And guanine will interact with cytosine with 3 hydrogen bonds. And a 1331 historically famous way of stating that is Chargaff's rule, which is to say that the amount of 1332 adenine and thymine will always be equal in molar terms. And the G molar content will always 1333 equal to C molar content. 1334 [00:02:35.59] To draw in a little greater detail, again we have the axis running up and down in 1335 the page. And the bases, as they're interacting, are normal both to the axis that we've drawn and 1336 to the plane of the picture, so that the normals, the normal vectors, for each of these planes of 1337 these heterocycles are parallel to the axis of the DNA. 1338 [00:03:13.68] The sugar and phosphates form the backbone. That's the backbone from one 1339 strand. This is the backbone from the other. Remember that these phosphate groups are 1340 negatively charged, so we have polyanions. This has a great deal of electrostatic repulsion 1341 between this strand and that strand. In solution, there would be lots of positively charged 1342 magnesium ions counteracting or binding and screening the negative charges so that you don't 1343 have this electrostatic repulsion between them. Without a divalent cation present, the two strands 1344 will dissociate. 1345 [00:04:01.96] OK, in this slide, we're seeing the double helix with space-filling molecules. You 1346 can see the bases here in the center that we're seeing them on the edge. And you can see the 1347 phosphate sugar backbones, the red and the yellow colors here. You can also notice that between 1348 phosphate backbones there is a smaller section and a larger section. This is the major groove, this 1349 is the minor groove. There is greater accessibility of the edges of the bases in the major groove, 1350 less so in the minor groove. 1351 [00:04:38.39] But when proteins try to read DNA, they're not unfolding it and gaining full access 1352 to it. They have to read the projections of hydrogens, oxygens, carbons, and nitrogens on the 1353 edges here. And that's the way in which the code is read. 1354 [00:05:00.73] There are about 10 base pairs between a full turn of-- 10 or 11-- between a full 1355 turn of the helix. And it's about 3.4 angstroms between each successive stack of spaces in the 1356 double helix. Because you have a double helix with base pairs that are complementary to each 1357 other, this enables you to have two templates for further synthesis, so that when DNA replicates, 1358 these two strands will dissociate and serve as a template for the synthesis of a new strand. This is 1359 termed semiconservative replication. And that just indicates that each new strand has one of the 1360 original strands of DNA and a newly made one, original and nearly made. 1361 [00:05:56.98] Watson and Crick's original paper, which was only a few pages-- two, I believe-- 1362 which they're primarily reporting the structure, at the very end, they have a single sentence 1363 saying that, "It has not escaped our notice that the specific pairing we have postulated 1364 immediately suggests a possible copying mechanism for the genetic material." So they are 1365 remembered not only as having identified the first structure of DNA, but also the first to suggest, 1366 in print, the copying mechanism. 38 [00:06:41.64] Your DNA is organized into chromosomes. You ha 1367 ve about three billion base 1368 pairs. That's an important number for you to remember, three billion base pairs. They are 1369 organized in 23 sets of chromosomes-- 22 autosomes, and one pair of sex chromosomes. Men are 1370 XY, females are XX. 1371 [00:07:10.69] You have two sets of each chromosome. Let's say in chromosome one, you have 1372 one copy of the chromosome from your mother and one copy of the chromosome from your 1373 father. The way they're drawn here and the way they're numbered, they are aligned all but at a 1374 position in the chromosome call the centromere. They are arranged from largest to smallest, even 1375 if it doesn't look like that so much here on the screen. 1376 [00:07:39.35] And in each case, the smaller arm, or the p arm, is above the centromere. And the 1377 longer arm, or the q arm, is below the centromere. The p stands for petite in French. And I'm not 1378 sure what the q stands for. I think it's probably just the next letter in the alphabet. 1379 [00:08:02.62] The last thing you notice here are the black and white banding patterns. And we'll 1380 talk more about that. However, this is what is actually visualized under a light microscope when 1381 the DNA is in a metaphase preparation and has been stained with a fluorescent dye. Those 1382 regions, which are looser and can accept the dye into its structure, will appear whiter or brighter. 1383 And those regions which are very compact, and exclude the dye from entering in its section, will 1384 be dark. 1385 [00:08:45.58] These banding patterns are almost identical in all of us. They're highly similar in 1386 all of us. And when people are referring to particular positions in the chromosome when they 1387 only had microscopy to go by, they have a numbering system for the different bands. That won't 1388 be so obvious for me to show you here in this slide. But two people could talk about a band such 1389 as, for example, 9 p 1-- chromosome 9, arm p, band 1. And then they can go into further detail. 1390 [00:09:34.34] The number of chromosomes is essentially the same in everybody. But it's not, in a 1391 se
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