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Current time:0:00Total duration:9:57

Antiparallel structure of DNA strands

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Video transcript

in the video on the molecular structure of DNA we saw that DNA was made up is made up typically made up of two strands where the the backbone of each of the strands is made up of phosphate alternating between a noose and different colors a phosphate group and then you have a sugar you have a you have a phosphate group and then you have a sugar and then you have a sugar and then you have a phosphate group and then you have a sugar and so I could draw the strand something like this so phosphate and then we have a sugar clip so let me so let me just draw all the phosphates ahead of time so you have the phosphates on that end and then you have the sugars and you see the same thing on the on the other strand as well where we have phosphate phosphate with the sugar then another phosphate then a sugar then another phosphate let me circle the sugars as well so you have a sugar there and then you have the sugar there as well so on the other strand it's also going to look like this so let me draw the phosphates I'm just abstracting them now so the phosphate and then you have the sugars in between the phosphates and what links them you can think of them as the rungs on the ladder these are the complementary nitrogenous bases and the reason why we call them nitrogenous bases I actually forgot to talk about in the last videos is that these nitrogen's are really electronegative and they can take up more hydrogen protons they have they have an extra lone pair the nitrogen's have an extra lone pair that can be used up under the right conditions to potentially stop up more hydrogen protons now a lot of people ask well if you have these nitrogenous bases here why is DNA called an acid why is it called an acid well the first thing is that the the basic properties of the nitrogenous base are offset to to a good degree based on the fact that they're able to hydrogen bond with each other and that's actually Able's that's what actually forms these these rungs the the rungs of the ladder when these complementary nitrogenous bases form these hydrogen bonds with each other but even more the reason why we call it an acid is the phosphate groups when they're protonated are acids now the reason why we tend to draw them deprotonated is what they're so acidic that if you put them in a in a in a neutral solution they're going to be deprotonated so this would this is the form that you're more likely to find it in the nucleus of an actual cell once it's actually already be deep once it's already deprotonated but in general phosphate groups are considered acidic and if I were to draw a kind of a more pure phosphate group and I talked about this already in the last video I would have I would have it protonated and so I wouldn't draw that negative charge like that so that's just a review of view of last time but let's actually actually just let me just I already started abstracting it let's abstract it further so let's let's draw the nitrogenous bases a little bit so I have I have thymine here and I will do thymine in this green color so this right over there is thymine so this is attached to the mean and the complementary the complimentary nitrogenous base to thymine is adenine is adenine which I will do let's see I'm running out of colors here let's see adenine I'll do this in an orange color it's got so many nitrogen's on it so actually so let me so it actually should include that hydrogen right over there so this right over here is adenine adenine and they form that you have these hydrogen bonds between them right over here because if partially negative and positive charges on either end that are attracted to each other and then we go to this rung one rung below it and what is going on well let's see we have I really am running out of colors here we have this this nitrogenous base is cytosine this nitrogenous base right over here is cytosine this nitrogenous base here is cytosine and it is paired up with guanine it is paired up with guanine the guanine in this color so it is it is paired up with guanine right over there and we even saw this in the in the introductory video to DNA now you might say oh look these two strands see parallel to each other and in some ways that is that is true but there might be something other than another interesting thing that you might have noticed is the direction in which they they are oriented I guess it's the best way to phrase it if we edit and you especially see that when you focus in on the sugars notice the the sugar is over here the deoxyribose this is or the things that are the parts of the nucleotide that come from deoxy ribose you see the oxygens on the top of the ribose on the top of these five-member rings the oxygen is on top well on this side the oxygen is on the bottom and so they are actually in different orientations here the oxygens pointing up here the oxygen is pointing down and to get a little bit more concrete about that we can number the carbons on the ribose to think about the directions and use those numbers of the carbons to to describe the different directions so let's number our carbons so when ribose so this is rye but these are both ribose we saw that in the molecular structure of DNA videos when we're talking about DNA we're talking with deoxyribose so it does not have it does not have a it does not instead of having a hydroxyl group on the number two carbon it just has a it just has a hydrogen so instead of having a hydroxyl group on the number two carbon it just has a hydrogen but let's actually number them so this is the 1 prime carbon starting at the carbonyl group let me do that in a different color so this is the 1 prime carbon and I'm just numbering them starting at the carbonyl group 1 prime 2 prime three prime 4 prime 5 prime and then when you look at it as a ring this was the 1 prime this is the 2 prime this is the 3 prime this is the 4 prime this is the 5 prime or if you were to number them on this diagram right over here actually in the DNA molecule this is the 1 prime this is the 2 prime carbon this is the 3 prime carbon this is the 4 prime carbon and this is the 5 prime carbon and so one way to think about it is we go fasta fête group and it's connected it's connected with what we call phosphodiester linkages phosphodiester linkage is that that's what's less essentially allowing these backbones to link up but we're going from phosphate to five prime carbon to and then through the sugar we go from to the three prime carbon then we go to another phosphate then we go to the five pi prime carbon let me label that this is the five prime carbon then we go to the three prime carbon and that just comes straight out of just numbering these starting with the carbon that was the number one carbon foot when in a straight chain form it's at the carbonyl it for it's part of the carbonyl group but you see we're going from five we go phosphate five prime three prime phosphate five prime three prime phosphate so one way to describe the orientation is saying hey we're going in the direction from five prime to three prime so we could say we could say that we're going from five prime we're going from five prime to three prime that way on the left-hand chain and what are we doing on the right-hand chain well let's number them again so this is the 1 prime carbon now this thing relative to this is upside-down it's inverted so one prime two prime three prime four prime five prime I can do it up here one prime carbon two prime carbon three carbon four prime carbon five prime carbon here you're going from phosphate three prime five prime phosphate three prime five prime phosphate so the way that the sugars are oriented if you're going from top to bottom the way we're looking here you're going from three prime to five prime so on the right hand side you are it's three prime five prime and so if you want to draw an arrow from five prime to three prime you could you could look at it like that and so you could say these are parallel but since they are essentially oriented in they're pointing in different directions even though they're actually parallel we would call the structure of DNA and tie parallel so this would be an anti anti anti parallel structure of DNA so these two strands they're complementary they're defined by each other the thymine bonds with the adenine the cytosine bonds with the guanine or they they they they're they are tracted to each other through these hydrogen bonds but the two backbones they're pointed in different directions and another interesting thing to think about since we're talking about the molecular structure of DNA is how do these things form how do these things know to orient the in this way and part of what plays part of that role is the fact that these phosphate groups are negative so you think these things that have outright negative charge they're going to try to get as far away from each other as possible and then when they you know they just keep kind of orienting getting far away from each other and these are long these are very very very very long molecules in the introductory video to DNA we talked about how long these these chromosomes are how many base pairs we actually have in these are long molecules so all of these phosphate groups on either strand they want to get away from each other and then these things want to these things want to get close to each other because of the hydrogen bonds and so that's what helps form this actual ladder structure so DNA fascinating molecule we could speak for days about it it's actually mind-blowing when you think about its implications for for who we are but hopefully this gives you a better sense of what it is molecular Lily molecular lis I cannot say it molecular Li
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