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Molecular structure of DNA

IST‑1 (EU)
IST‑1.A (LO)
IST‑1.A.1 (EK)
IST‑1.K.1 (EK)
IST‑1.K.2 (EK)
IST‑1.L (LO)
SYI‑1 (EU)
SYI‑1.B (LO)
SYI‑1.B.2 (EK)
SYI‑1.C (LO)
SYI‑1.C.1 (EK)
Molecular structure of DNA. Nucleotide. Nitrogenous base, phosphate.

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  • aqualine ultimate style avatar for user Ananya Singhal
    Where did the oxygen from 1st carbon in deoxyribose go when in DNA?
    (26 votes)
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  • orange juice squid orange style avatar for user LaFontaine
    just by looking at the site of H-bonding, can't we say that G can bond with both A and T as they both have three sites where H- bonding can happen?
    (15 votes)
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    • leaf green style avatar for user S Sinclair
      Also, a pyrimidine is always H bonded to a purine so that the diameter/width of the DNA molecule is consistent throughout the molecule. 2 purines would make the DNA bulky in parts and 2 pyrimidines would make it very narrow. By always pairing a 1 ring base with a 2 ring base the width is constant. Additionally, the GC and AT base pairs have optimal hydrogen bonding. All other arrangements are suboptimal.
      (22 votes)
  • duskpin ultimate style avatar for user RacheLee
    Can DNA be either single or double stranded?
    (0 votes)
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  • female robot grace style avatar for user Billy Wright
    At , Sal begins to discuss the linear-to-ring configuration of ribose. Apparently, ribose can take more than one cyclical form. Why is it that in a nucleotide the oxygen of the 4' carbon bonds with 1'? Why not another? Is this necessary to the structure of DNA/RNA?
    (8 votes)
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    • leaf blue style avatar for user Kevin D. Fettel
      Great question!

      For an intramolecular attack, the stability of a ring structure is important! The least amount of ring strain occurs in structures that can form six membered rings (i.e. as in cyclohexane) chair conformational isomers. Angle strains occur when cyclic molecules are forced to deviate from the ideal sp3 hybridized (i.e. tetrahedral) bond angle of 109.5 degrees.

      A four-membered ring produces a substantial bond angle (i.e 90 deg.) and an eclipsing steric strain, and are therefore not very stable.

      A five-membered ring, while not as stable as a six-membered ring, is still stable enough to form.
      (5 votes)
  • duskpin ultimate style avatar for user Jack Smith
    Why does cytosine only bond with guanine and thymine only bond with adenine? Is that based on the chemical structure?

    Thanks to anyone who answers,
    (6 votes)
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  • orange juice squid orange style avatar for user Bas Munting
    why is he using the accents when numbering the carbon atoms in the ribose(around )?
    (4 votes)
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  • starky ultimate style avatar for user Vedant
    At about what is hydronium?
    (2 votes)
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    • leaf green style avatar for user colin
      Hydronium is H30. A water molecule is H20. When some molecular structure release a hydrogen ion (hydroxide), the water molecule, being electronegative (hoging electrons), take the hydroxide, thus forming Hydronium, with three Hydrogen molecules and one Oxygen molecule.
      (10 votes)
  • starky ultimate style avatar for user Rubujo
    Why in the Phosphate group, phosphorus form 5 covalent bonds? wouldn't just 3 fill it's outermost shell?
    (3 votes)
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    • female robot grace style avatar for user tyersome
      Yes there are compounds where phosphorous forms three bonds (this is associated with an oxidation state of +3 or -3), but this element seems to prefer an oxidation state of +5.

      The formation of these "extra" bonds is due to hypercoordination (aka. hypervalency, but that may not be a good term to use) and is commonly seen for elements in the 3rd period and beyond.

      This is quite complicated to explain, but the current consensus is that the phosphorous in phosphate doesn't actually end up with more than 8 "valence" electrons due to electron withdrawing effects by the oxygens.
      (Note: You will find explanations for this that invoke hybridization with d-orbitals, but this has been shown to not be true.)

      The wikipedia article on hypercoordination seems like a reasonable place to learn more:

      You might also find this section of wikipedia article on phosphorus helpful:

      Does that help?
      (8 votes)
  • starky ultimate style avatar for user Stef Bracke
    at , what is the symbol Sal is writing for 'partial' ?
    (3 votes)
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  • orange juice squid orange style avatar for user Cameron
    At , Sal says that the Ribose is deoxy because it is missing the 2' carbon's oxygen. Isn't the deoxy Ribose also missing the 1' oxygen by being bonded to the nitrogeneous base and the 5' and 3' oxygens by being bonded to the phosphates?
    (6 votes)
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Video transcript

- [Voiceover] We already have an overview video of DNA and I encourage you to watch that first. What I want to do in this video is dig a little bit deeper. Actually get into the molecular structure of DNA. This is a starting point. Let's just remind ourselves what DNA stands for. I'm gonna write the different parts of the word in different colors. It stands for deoxy. Deoxyribonucleic. Ribonucleic. Ribonucleic acid. Ribonucleic acid. So I'm just gonna 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. DNA is just a junction for nucleic acid and it's the term nucleic that comes from the fact that it's found in the nucleus. It's found in the nucleus of eukaryotes. That's where the nucleic comes from and we'll talk about in a second why it's called an acid but I'll wait on that. Now each DNA molecule is made up of a chain of what we call nucleotides. What we call nucleotides. It's made up of nucleo, nucleo, nucleotides. What does a nucleotide look like? Well, what I have right over here is I have two strands, I've zoomed two strands of DNA or I've zoomed in two strands of DNA. You could view this side right over here as one of the, I guess you can 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. A nucleotide, let me separate off the nucleotide. A nucleotide would... What I am cordoning off, what I am cordoning off right over here could be considered, could be considered a nucleotide. That's one nucleotide and then it's connected to another. It's connected to another nucleotide. Another nucleotide right over here. 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 it slightly different. 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. 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 different pieces of that nucleotide. The one thing that might jump out at you is we have these phosphate groups. This is a phosphate group right over here. This is a phosphate group right over here. Each of these nucleotides have a phosphate group. 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 an acid. 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 sap up protons. How can you call this an acid? This actually looks more basic. The reason why its DNA is typically drawn with these negative charges here is that it's so acidic and that if you put it in into a neutral solution, it's actually going to lose its hydrogens. 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 protons so it typically would be, 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. 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. These oxygen can grab these electrons and then these hydrogen will just be grabbed by another water molecule or something so the proton will be let go. That's why we call it an acid. If it wasn't in a solution it would have the hydrogens but it would be very acidic as soon as you put it into a neutral solution it's going to lose those hydrogens. 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 lost its hydrogen proton. 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, it's protonated but it readily loses it. And so that's why it has its, that's where it gets the name acid form from. 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. This sugar is based on, it's a five-carbon sugar. What I have depicted here, this sugar, this is ribose. This sugar right over here is ribose. This is when it's just as a straight chain and like many sugars, it can take a cyclical form. Actually it can take many different cyclical forms but the one that's most typically described is when you have that. Let me number the carbons because carbon numbering is important when we talk about DNA. But if we start 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. You form the cyclical form of ribose as 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 the one prime. With the one prime carbon and I drew it that way because it kind of does bend. The whole molecule's 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 some place. To nab on to a hydrogen proton. 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, two prime, three prime, four prime and five prime carbon. Where we see this bond, this is the one prime carbon. it was part of a carbonyl. Now it lets go of one of those double bonds so that this oxygen can form a bond with a hydrogen proton. It let go of a double bond there so that this could form a bond with a hydrogen proton. This hydrogen proton is that hydrogen proton right over there and 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. It was also attached to a hydrogen. It was also attached to a hydrogen so that hydrogen is there but then that can get nabbed up by another passing water molecule to become hydronium so it can get lost. It grabs up a hydrogen proton right over here and so it can lose a hydrogen proton right there. It's not adding or losing in that net. 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 what we would see in an RNA molecule, in a ribonucleic acid. And so what do we think we're talking about when we say deoxyribonucleic acid. Well, you can start with you have a ribose here but if we got rid of one of the oxygen groups and in particular one of... Well, actually if we just got rid of one of the oxygens we replace a hydroxyl with just a hydrogen, well then you're gonna have deoxyribose and you see that over here. This five-member ring, you have four carbons right over here. it looks just like this. The hydrogens are implicit to the carbons, we've seen this multiple time. The carbons are at where these lines intersect or I guess at the edges or maybe and also where these lines end right over there. But you see this does not have an... This molecule if we compare these two molecules, if we compare these two molecules over here, we see that this guy has an OH, and this guy implicitly just has... This has an OH and an H. This guy implicitly has just two hydrogens over here. He's missing an oxygen. This is deoxyribose. 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. This thing right over here, this thing right over here, that is deoxyribose. Deoxy or it's based on deoxyribose I guess before it bonded to these other constituents. You could consider this deoxyribose. That's where the deoxyribo comes from and then the last piece of it, the last piece of it is this chunk right over here. These we call nitrogenous bases. Nitrogenous. Nitrogenous. Nitrogenous bases. You could see we have different types of nitrogenous bases. This is a nitrogenous base. 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. Nitrogenous bases 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. If you have one ring. Anyway, I'll just write this way. One ring. One ring, we call these pyrimidines. Pyrimidine. Pyrimidines. We call these pyrimidines. These particular, these two on the right, these two purines, this one up here this is adenine, and we talk about how they pair in the overview video on DNA. This one right over here is adenine, this nitrogenous base. This one over here is guanine. That is guanine. And then over here, over here, this single ring nitrogenous base which makes it a pyrimidine, this is thymine. This right over here is thymine. This is thymine and then last but not least if we're talking about DNA, when we go into RNA, we're also gonna talk about uracil. But when we talk about DNA this one over here is cytosine. Cytosine. You could see the way it's structured. The thymine is attracted to adenine. It bonds with adenine and cytosine bonds with guanine. How are they bonding? Well, the way that these nitrogenous bases form the rungs of the ladder, how they want they're drawn to each other, this is our good old friend hydrogen bonds. This all comes out of the fact, that nitrogen is quite electronegative. 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 at 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. The partial negative charge of this oxygen is going to be attracted to the partial positive charge of this hydrogen, and so you're going to have a hydrogen bond. That's then going to happen between this hydrogen which is going... Its electrons are being hogged by this nitrogen and this nitrogen with who, which itself hogs electrons. That forms a hydrogen bond. And then down here you have a hydrogen that has a partially positive charge because its 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. 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 the overview video of DNA.