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Current time:0:00Total duration:13:01

Molecular structure of DNA

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Video transcript

we already have an overview video of DNA and I encourage you to watch that first but what I want to do in this video is dig a little bit deeper actually get into the molecular structure of DNA and just as a starting point let's just remind ourselves what DNA stands for all right the different parts of the word in different colors so it stands for deoxy deoxyribonucleic ribonucleic ribonucleic acid ribonucleic acid so I'm just going to put this on the side and now let's actually look at the molecular structure and how it relates to this actual name deoxyribonucleic acid so DNA is just a jump trip for a nucleic acid and it's the term nucleic it comes from the fact that it's found in the nucleus it's found in the nucleus of eukaryotes so that's where the the nucleic comes from and we'll talk about in a second why it's called an acid but I'll wait on that and now each DNA molecule is made up of a chain of what we call nucleotides so what we call nucleotides so it's made up of nucleo nucleo nucleotides so what does the nucleotide look like well what I have right over here is I have two strands I've zoomed in two strands of DNA or I've zoomed in two strands of DNA so you could view this side right over here as one of the one of the I guess you could say the backbones of one side of the ladder this is the other side of the ladder and then each of these bridges and I will talk about what molecules these are these are kind of the rungs of the ladder and a nucleotide let me separate off a nucleotide so nucleotide would so what I am what I am cordoning off what I am coordinating off right over here could be considered could be considered a nucleotide so that's one nucleotide and then it's connected to another it's connected it's connected to another another nucleotide another nucleotide right over here and on the right hand side we have a nucleotide we have a nucleotide right over there and then actually I want to do it let me do a little slightly different we have a we have a nucleotide right over here on the right side and then right below that we have another we have another nucleotide we have another nucleotide so depicted here we essentially have four nucleotides these two are on this left side of the ladder these two are on the right side of the ladder now let's think about the the different pieces of that nucleotide so the one thing that might jump out at you is we have these phosphate groups so this is a phosphate group right over here this is a phosphate group right over here each of these nucleotides have a phosphate group so this is a phosphate group over here and this is a phosphate group over here now the phosphate groups are actually what make DNA or actually what make nucleic acid and acid and you might say wait wait the way you've drawn it Sal you have a negative charge something with a negative charge would attract protons it would stop up protons how can you call this an acid this actually looks more basic and the reason why they that's DNA is typically drawn with these negative charges here is that it's so acidic and if you put it in into a into a neutral solution it's actually going to lose its hydrogen's actually the DNA if we actually want to be formal about it the DNA molecules would actually have its phosphates protonated like this but it so badly wants to lose these hydrogen these hydrogen protons so typically would be let me let me draw it like this let me get rid of the negative charge just on this one whoops just on this phosphate group over here so if you get rid of the negative charge and if this was bounded this is bonded to a hydrogen this so badly wants to grab these electrons so this oxygen can grab these electrons and then this hydrogen will just be grabbed by another water molecule or something or so so the proton will be let go that's why we call it an acid so if it wasn't in a solution it would have the hydrogen's and but it would be very acidic as soon as you put it into a neutral solution it's going to lose those hydrogen's so the phosphate groups are what make it are what make it an acid but it's confusing sometimes because usually when you see it depicted you see it with these negative charges and that's because it has already it has already lost its hydrogen proton you're actually depicting you're actually depicting the conjugate base here but that's where it gets its acidic name from because it starts protonated or it gets in this acid form its protonated but it readily loses it and so that's why it has it's that's where it gets the name acid form from so each of these each of these nucleotides they have a phosphate group now the next thing you might notice the next thing you might notice is the next thing you might notice is this group right over here it is a cycle it is a ring and it looks an awful lot like a sugar and that's because it is a sugar so this sugar is based on it's a five carbon sugar what I have depicted here this sugar this is ribose so this sugar right over here is ribose this is when it's as when it's just as a straight chain and like many sugars it can take a cyclical form actually could take many different cyclical forms but the one that's most typically described is when you have that line which you number the carbons because carbon numbering is important when we talk about DNA if we start at the carbonyl group right over here we call that the one carbon or the one prime carbon one prime two prime three prime four prime and five prime that's the five prime carbon and so you form your you form the cyclical form of ribose is if you have the oxygen you have the oxygen right over here on the four prime carbon it uses one of its lone pairs it uses one of its lone pairs to form a bond to form a bond with with the one prime with the one prime carbon and I drew it that way because it kind of does bend the whole molecule is going to have to bend that way to form this structure and then when it forms that bond the carbon can let go of one of these double bonds and then that can then the oxygen the oxygen can use that the oxygen can use those electrons to go grab a hydrogen proton from someplace so tune a bond to a hydrogen proton so when it does that you're in this form and this form just to be clear of what we're talking about this is the one prime carbon one prime to prime three prime four prime and five five prime carbon and where we see this bond this is the one prime carbon it was part of a carbonyl now it lets it lets go of one of those double bonds so that this oxygen can form a bond with a hydrogen proton so let go of a double bond there so that this could form a bond with a hydrogen proton so this hydrogen proton is that hydrogen proton right over there and this green this green bond that gets formed between the four prime carbon and or between the oxygen that's attached to the four prime carbon and the one prime carbon that's this that's this bond right over here this oxygen is that oxygen right there notice this oxygen is bound to the four prime carbon and now it's also bound to the one prime carbon and it was also attached to a hydrogen it was also attached to a hydrogen so that hydrogen is there but then that could get nabbed up by another passing water molecule to become hydronium so it can get it can get lost and you know net-net it grabs up a hydrogen proton right over here and so it can lose a hydrogen proton right there so it's not adding or losing net-net and so you form this cyclical form and the cyclical form right over here is very close to what we see in a DNA molecule it's actually exactly what we would see in an RNA molecule and ribonucleic acid and so what do we think we're talking about when we say deoxy ribose nucleic acid well you could start with you have a ribose here but if we got rid of one of the oxygen groups in particular one of well actually if we just got rid of one of the oxygens we replace our hydroxyl with just a hydrogen well then you're going to have deoxyribose and you see that over here this this five-member ring you have four carbons right over here it looks just like this the hydrogen's the hydrogen's are implicit to the carbons we've seen this multiple time the carbons are at at where these lines intersect or I guess at the edges or maybe and also and also where these were these lines and right over there but you see this does not have an O a this this molecule if we compare these two molecules if we compare these two molecules over here we see that this this guy has an O H and this guy implicitly just has this has an OHA eh this guy implicitly has just two hydrogen's over here so he's missing an oxygen so this is deoxyribose so deoxyribose deoxyribose doesn't have this oxygen it does not have the oxygen on the two prime carbon so this if you get rid of that this is deoxyribose so let me circle that so what where this thing right over here this thing right over here that is deoxyribose d oxy or it's based on deoxyribose so I guess before it bonded to these other constituents you could consider this deoxy deoxyribose and so that's where the deoxy ribose from and then the last piece of it the last piece of it is this this chunk right over here and these we call nitrogenous bases so nitrogenous nitrogenous nitrogenous bases and you can see we have different types of nitrogenous bases this is a nitrogenous base this is this right over here is a different nitrogenous base this right over here is another different nitrogenous base notice this one only has one ring this one has one ring this one has two rings this one over here has two rings and we have different names for these nitrogenous bases the ones with two rings the general categorization we call them purines so a nitrogenous base is if you have two rings if you have two rings we call them purines that's a general classification term let me make sure purines and if you have one ring I'm able to write it this way one ring one ring we call these pyrimidines per rim medine per rimma Dean's we call these pyramids and these particular these two on the right these two purines this one up here this is adenine and we talked about how they pair in the overview video on DNA but this one right over here is adenine this nitrogenous base this one over here is guanine that is guanine and then and so and then over here over here this single ring the single ring nitrogenous base which makes it a pyrimidine this is thymine this right over here is the I mean this is thymine and then last but not least if we're talking about DNA where we get to go into RNA we're also going to talk about uracil but when we talk about DNA this one over here is cytosine say cytosine and you can see the way it's structured the thymine is attracted to adenine it bonds with adenine and cytosine bonds with guanine so how are they bonding well the good the way that these nitrogenous bases form the rungs of the ladder how they're there how they want they're drawn to each other this is our good old friend hydrogen bonds and this all comes out of the fact that nitrogen is quite electronegative so when nitrogen is bound to a hydrogen you're going to have a partially negative charge at the nitrogen let me do this in green you're going to have a partial negative charge of the nitrogen and a partially positive charge at the hydrogen and then oxygen we've always talked about as being electronegative so it has a partial negative charge so the partial negative charge of this oxygen is going to be attacked attracted the partial positive charge of this hydrogen and so you're going to have you're going to have a hydrogen bond and that same that's going to happen between this hydrogen which is going to it's hydro its electrons are being hogged by this nitrogen and this nitrogen with its with who which itself hogs electrons so that forms a that forms a hydrogen bond and then down here you have a hydrogen that has a partially positive charge because it's electrons are being hogged and then you have this oxygen with a partially negative charge they're going to be attracted to each other that's a hydrogen bond same thing between this nitrogen and that hydrogen and same thing between this oxygen and that hydrogen and that's why cytosine and guanine pair up and that's why thymine and adenine pair up and we talk about that as well in that in the overview video of DNA