Okay, we're ready to start. Welcome back. Hope you had a nice weekend. And I hope you also had some time to review some of the material that we've been discussing in this course. As you're going to see, every lecture we cover a lot of ground.
So it is important that you stay, you keep the pace of studying. Don't wait until it's time for the test to start learning everything because it's going to, the material will accumulate. So I have this question here just for you to see how much you remember about what we talked about last time when we were talking about the building blocks of DNA and RNA.
And here's an example of a kind of question that you might see on a test. It says the structure on the right is an example of what? Nucleoside, deoxynucleoside, deoxynucleoside monophosphate.
Phosphate, nucleoside deoxyphosphate, and nucleoside monophosphate. What does it look like to you? Anybody want to? Yes, we have one hand right here.
Which one? E? E as in excellent. Okay.
So the answer given was E here. How many think it could be E? Let me see your hands. Okay, that is the correct answer. Nucleoside monophosphate.
Remember that we said that the names of nucleotides are the name of the nucleoside, which is the sugar and the base, and then however number of phosphates you have. And this is not a deoxynucleoside because it has a hydroxyl group and the two prime carbon position. That should have been the clue.
Okay, so... And some of you may be confused with the term nucleotide. You know, nucleotide is just a general term that we use to refer to all of the nucleosides, mono, di, or triphosphates.
As long as the nucleoside has a phosphate, one, two, or three, it's generally referred to as a nucleotide. It's a general terminology for that. But more specifically, nucleoside, monophosphate in this case. Okay, it's the same structure, the same figure.
A different question. How would you call this nucleoside monophosphate? Yeah, back there. Diaz and David, UMP?
We have UMP on the table. How many think it could be UMP? Let me see your hands.
Okay. All right. UMP is correct.
So those of you who are still thinking about it, it means that you need to review, right? And I hope that you got the answer without looking for information, but it came out of your head. What you need to know to answer this question is number one, what is the base? And number two, what is the sugar, right? So the sugar we already know it's a ribose and because it has a hydroxyl group at the two prime carbon position.
And the base is uracil. Remember that uracil and thymine are the two pyrimidines that have two carbonyl groups, right? And the difference between those two is that thymine also has a methyl group attached to this carbon number five here, but uracil does not. So UMP or uridine monophosphate. Okay.
So I could give you the symbols or I could give you the full name, uridine monophosphate. Either way, you should be able to recognize the correct answer. Okay. So this gives you an idea of how you need to be studying for the test.
All right. So I need to tell you that the nucleoside triphosphates or NTPs. or dNTPs, if they're the deoxynucleoside triphosphates, those are the building blocks.
I should say the precursor molecules that are used to make chains of DNA or RNA. The enzymes, DNA polymerase or RNA polymerase, whichever enzyme we're talking about, they make use of nucleoside triphosphates. And then they incorporate them into a strand or a chain.
And we're going to see that reaction later on. So we need nucleoside or deoxynucleoside triphosphates as precursors. The other thing I want to tell you about nucleoside triphosphates, specifically ATP and GTP, is that cells have evolved to recognize these molecules as energy-rich molecules, right?
And... Of course, other nucleoside triphosphates are also energy rich, but these are the two favorite ones that are used in the cells as sources of energy to allow the cells to carry out different metabolic reactions that require energy. And the reason for this is that there is a lot of energy stored in the phospho and hydride bonds that link together these phosphate groups.
OK. And so this gives you a qualitative feel for the different levels of energy that are stored in those bonds. OK, so here you have the first phosphate that we're going to call the alpha phosphate, the one that is attached to the fipron carbon.
The next one is the beta phosphate and the next one is the gamma phosphate. So between the gamma and the beta phosphate, that phospho and hydride bond is a very high energy rich bond. And then the next one between the beta and the alpha is also high in energy, but less so than the first one.
And then the next one, the phosphoester bond between the alpha phosphate and the fipron carbon also has some energy stored into it. But it would be the one that has the least of the three. There's a lot of energy in these bonds because it takes a lot of energy to create them in the first place.
Because... And notice that these phosphate groups have a lot of negative charge associated with them. These oxygens are negatively charged. So they don't like to be put next to each other because the same charges tend to repulse themselves. So when those negative charges are put close to each other, they really want to pull apart, right?
A force of repulsion. So in order to keep them bound there, you need to put energy into those bonds. And that's why they have a lot of energy stored in them.
And so the cells can then use the strategy of cleaving one or two of those phosphoenhydride bonds to release that energy and then use some of it to carry out chemical reactions. So ATP is the most widely used nucleoside triphosphate in many chemical reactions. But also you're going to see examples where GTP is also a great source of energy.
So this is a dual use of these molecules. On the one hand, they act as precursors to build molecules of RNA, but they also act as sources of energy for the cell. So you can imagine that there are very large quantities of these nucleoside triphosphates in the cell. Okay, so now we're going to go ahead and...
assemble these nucleotides together into a chain. And here we have a chain of two nucleoside triphosphates joined together. So we have the smallest chain here just consisting of two building blocks.
And is this a chain of DNA or RNA? Oh. Okay, it is DNA, DNA, right? DNA. First, because you see that thymine is one of the bases.
That's one clue. These are the bases. And also, but the one that I wanted you to see is that this is a deoxyribose that is being used here, right? Because it lacks the oxygen.
But you will see that when the building blocks are joined together, you no longer have three phosphates. Two of those phosphates, the beta and the gamma phosphates, are cleaved off. in the process of joining together two nucleotides. And in fact, the energy that is released by cleaning up those phosphates is used by the enzyme to carry out this reaction of joining together these nucleotides. Notice that the nucleotides are joined together by a special linkage involving a phosphate.
And this linkage from this C C3, three prime carbon from one nucleotide all the way out to the five prime carbon of the other nucleotide over here is... called a three prime to five prime phosphodiester bond. That's the name of that linkage.
And you can see why. That linkage joins together the three prime carbon of one nucleotide up here to the five prime carbon of the other nucleotide over here. It involves a phosphorus or a phosphate group, and it has two ester bonds because there's one ester bond here between this phosphorus and that carbon, three prime, and another one between this. phosphorus and the five prime carbon.
So the term di means two. So you have two ester bonds, three prime to five prime phosphodiester bonds. So that's the key linkage that keeps that strand intact.
It joins one nucleotide with the next. Notice also that as we look at this very simple strand of DNA, we create what's called a backbone structure of the chain. And the backbone structure is made up of phosphates and sugars, phosphates and sugars. And that's a very repetitive structure. The backbone structure just consists of one phosphate and one sugar, one phosphate, one sugar, and so forth.
We can have hundreds and thousands or tens of thousands of these nucleotides joined together, and the backbone structure will look the same all along the molecule. What's going to be different is... the base that is attached to each of the sugars, right?
So that is why when we want to designate the sequence of DNA, we just simply use the letters T, G, C, A, T, because that is the part of the nucleotide that differs at each position, and it is the component of each nucleotide that renders the specific chemical properties of that nucleotide. Notice that they're not part of the backbone structure. These bases, instead, they are kind of stemming out, ready to react chemically with something else.
Okay, so I talked about the sugar phosphate backbone. The other thing I want you to notice is that the two ends of this chain, and even though it consists of only two nucleotides, this is a chain that has different ends. On one end, what you see, this is called the 5'end, because at this end, the 5'carbon that is joined to a phosphate is freely exposed. It's not participating in linking chemically to another nucleotide.
It's just freely exposed. And so that's why we call it the 5'end. Notice that here at this end, in this nucleotide, the 3'carbon is joining another nucleotide.
So it's buried within the backbone structure of the molecule. But if you go all the way to the other end, we refer this to the three prime end, because here it's going to be the three prime carbon that is joined to the hydroxyl group that is freely available at this end. It is not participating in a linkage, in a phosphodiester linkage that is joining another nucleotide. Okay, so... From now on, when you look at a structure of DNA or RNA, I want you to train your eyes to look at each end and determine what is the five prime end and what is the three prime end, okay?
Because that is important for us to understand the structure of that molecule, okay? So those ends are different. Okay, so here's a more simplistic designation of a chain of DNA. It only has six nucleotides here. You can see, again, appreciate the backbone structure of this chain that is made up of phosphates and sugars.
And you can appreciate also that the bases are not part of the backbone, but are stemming out of the sugar, ready to interact with something else. And also you can appreciate that this is the 5'end because here you have the 5'carbons sticking out of the sugar that is attached to the phosphate, freely accessible. And on the other hand what you have is the 3'carbon, right, freely accessible. They're not showing the OH group here but there is an OH group attached to the 3'carbon. This is another way that we can designate a chain of DNA or it could be RNA.
We use the same kind of symbol. This is a shorthand notation for it. And for some students, it can be a little bit confusing because the sugars in this structure are not designated as ring structures the way they really are.
But the symbol that is used is more of a line. So you have a vertical line here that represents the sugar. And it's only illustrating the key of the structure. parts of this sugar where the one prime carbon would be way at the top here that is attached to the base.
In the middle of that line, you have the three prime carbon participating in a phosphodiester bond. And then at the bottom of the line, you have the five prime carbon. Okay.
So that's what this, how you interpret this. And again, it's showing, it's illustrating the sugar phosphate backbone, but it's usually used to emphasize the the phosphate groups, you know, what's going on with the phosphate groups, if there's cleavage of that phosphate group, where is that cleavage taking place, etc. This kind of a representation makes it easier to illustrate that.
Okay, so DNA has primary structure and it has secondary structure and it has super secondary structure. We're going to talk more about that later. But the primary structure refers to the sequence of nucleotides in a chain.
So once we have nucleotides joined together, we're talking about primary structure of DNA. And it is that primary structure of DNA that makes up the genetic information, right? That specific sequence of nucleotides is what determines the genetic information. If you alter that primary structure...
You can also alter the genetic information, and that can lead to mutations, the production of proteins, for instance, that have a different structure, maybe non-functional or maybe having a different function. We'll talk more about that later in the course. But I can designate this primary structure right here as a sequence of letters, A, G, T, A, C, G, right?
So when you see... a sequence of letters, in your mind you should think of this molecule right here, right? And notice that I haven't labeled the 5'N and 3'N.
So we should label it. That would be the correct way of designating this sequence of letters. But if you ever encounter a sequence of letters that don't have the 5'N and 3'N labeled, you should assume that the left side is the 5'N. and the right side is the 3'end.
Because by convention, geneticists write the sequence of a single chain of DNA from the 5'end on the left to the 3'end on the right. So I'm just going to go ahead and label it like this. But sometimes you'll see the sequence labeled the other way, where the 3'is labeled on the left and 5'on the right. That's okay too.
But what I want to emphasize is that if I were to write the same sequence, A, G, T, A, C, G, and I put the 3 prime on this side and the 5 prime on the right side, that is an entirely different molecule, okay, than this one right here. Chemically, they are different, even though it has same sequence backwards. So you need to pay attention to that.
Okay, so now the secondary structure of DNA is that structure that we're very familiar with, where you have two strands of DNA wound together in a helical fashion. We're going to look at that structure a little bit more closely. And it was due to the work of James Watson and Francis Crick.
They were the ones, the first, to propose a model for the DNA structure that ended up being correct. And so they won the Nobel Prize for solving, essentially, the structure of DNA. And because of their work, we could now better understand the function of DNA once we understood the structure. But, you know, even though they got most of the recognition for solving the structure of DNA, they didn't solve it on their own. They based their work on scientific knowledge that was already available.
In some cases, because they would go to conferences, to meetings, and they would hear other people trying to solve questions about DNA. And they took notes and they used all of that to solve their structure. One of the most important pieces of information that they used was that shown by Chargaff and his group.
In the years 1949 to 1953, Chargaff published a series of papers where he showed he was a chemist. So he was trying to analyze the composition of DNA. And being a good chemist, he would isolate, you know, the different nucleotides, the A, the T, the C, and the G.
And something, an interesting observation popped up. And that is that although every organism had different quantities of these nucleotides that were constant in different organisms, what he did find was the amount of A nucleotides was proportional to the amount of T's. and that the amount of C nucleotides was proportional to the amount of Gs. And so this was very interesting and that was constant in pretty much all the organisms that he studied.
So here you see some examples, Ocstymus and spleen, yeast, birds, humans. He took different cell samples and analyzed their DNA and you can see here that the molar proportions of As and Ts were very close to each other. here and here, here and here, here and here, etc. And that the molar proportions of G's and C's, look down here, very similar 28, 26, 14, 13, sometimes varying a little bit more, but I guess within experimental error, he concluded that they still remain proportional.
When he looked at the percentages of G's plus C, that varied from organism to organism. They have different uh percentages of when you compare the the amount of g's and c's relative to the total nucleotides you can see that in different organisms those percentages vary however the proportions of g's to to um g's to t to c's were maintained and so here you see even more work that came after that because this was very interesting uh follow-up work uh continued to show the same trend in different organisms so i'm not gonna walk you through all of this, all of these numbers, but you can see that the proportions of A's and T's are similar in different organisms and that of G's and C's as well. If you took the ratio of A's to T's, of course, the ratio was very close to one because their proportions are similar. And the ratio of G's to C's is also close to one. And in fact, I mean, you would predict this mathematically that then it must be true that if you take the proportions of A plus G, all of the purines, you add them all up and divide them by the sum of all of the pyrimidines, then the proportions also are still one or close to one.
That is that there is a proportional amount of purines to pyrimidines. But if you try to do other kinds of ratios, like sum up all of the A's and T's, and get the ratio of that to the sum of G's and C's, then now those ratios don't necessarily fall near one. In fact, they're all over the place. That's because the percentages of G's plus C's vary from organism to organism. But the main points are summarized up here, that the amounts of A's are proportional to T's and the amount of C's proportional to G's.
And so this was a key observation that Watson and Crick was taken into account and they were playing with molecular models to try to figure out what is it about that proportion? How can you get G's and C's to interact with each other? Because they reason that if the proportion of G's to C's was similar, then maybe in that molecule, G's must somehow interact with C's and that A's must interact with T's.
And so they came up with the idea that these bases pair up very specifically by hydrogen bonds, and that between A's and T's you would form two hydrogen bonds, and between G's and C's you can form three hydrogen bonds. And so this became part of what became known as the specific base pairing rules that Watson and Crick developed. And so that this this base pairing between A and T and G and C was necessary.
to provide this complementarity between the two strands of DNA. This is how then two strands are going to be interacting. When you have an A and one strand, you have to have a T and the other to pair up.
A C and one strand will pair up with a G and the other one, etc. Yes? Is the ratio of A's and G's similar to the ratio of C's?
Yes, because so if you add them up, A's and G's are the purines. Yes. And C's and T's are the pyrimidines.
And so if you add them both together, that ratio is still going to be similar. Figure out that like the A's combine together and not like A's. Okay. So how do they figure out that? that A's and T's are the ones that are binding together and the G's and C's.
Again, they came back, they got it from Chargov's rules because they found that A's were proportional to T's and C's proportional to G's. Okay. A's were not proportional to C's. Okay.
So what I want to do is take a closer look at the base pairing rules and how they came up with this. the number of hydrogen bonds that are formed between different base pairs. So here you have the molecule of adenine. You should recognize this molecule already.
It's a two ring structure. It has an amino group at the six carbon position right here, attached to that six carbon position. This is the nitrogen at position one, the carbon at position two. And the first thing I want to mention, and this is just review from chemistry. that nitrogen and oxygen are the two atoms that are widely present in biological molecules that are highly electronegative.
So there's this concept of electronegativity. And what do we mean by that? What we mean is that oxygen and nitrogen, when they form a covalent bond with any other molecule, yeah, any other atom, I'm sorry, that covalent bond is formed by the sharing of a pair of electrons between the two atoms.
But because nitrogen and oxygen are among the two most highly electronegative atoms, they will draw those electrons closer to itself, more tightly than the other atom, okay? So, for instance, nitrogen right here is covalently bound to hydrogen. And nitrogen is much more electronegative than hydrogen.
So there's a pair of electrons right there in that covalent bond that is shared between the two atoms. But those electrons are drawn more closer to the nitrogen because nitrogen pulls those electrons to itself with greater force. When that happens, there are partial charges that are formed. Nitrogen, because it pulls the electrons, which are negatively charged towards itself a little bit more, nitrogen becomes partially negatively charged.
And then that leaves this hydrogen that kind of has to release those electrons away from it a little bit, acquires a partial positive charge. And we call them partial and we use this symbol right here, delta symbol, to designate a partial charge. We say partial because the electrons are not fully given away, okay? They're still holding on to it.
So hydrogen, which has a partial positive charge, now has the ability to interact electrostatically with another atom that has a partial negative charge, okay? And this is how hydrogen bonds are formed. This nitrogen right here has a partial negative charge because it pulls Notice that it has covalent bonds with this carbon and with this carbon.
And notice that carbon, hydrogen, and sulfur are examples of atoms that have similar electronegativity, but they are much less than those of nitrogen and oxygen. So this nitrogen is going to pull these electrons toward itself more tightly, as well as these electrons over here toward itself. So it acquires partial negative charge. So I'm drawing these arrows right there to show you the direction of the pooling of those electrons toward the more electronegative atom. And so when you understand that, you can then understand how these hydrogen bonds are formed.
Here you have thiamine over here. And notice that thiamine has this carboxyl group. Again, you have an oxygen here. That oxygen is going to have a partial negative charge for the reasons I just explained.
And so this negative charge will be attractive to this positive charge on this hydrogen over here. And that force of attraction that involves a hydrogen that is positively charged is called a hydrogen bond. OK, so when you have a partially positively charged hydrogen interacting with another partial negatively charged atom, such as oxygen or nitrogen, that's called a hydrogen bond.
So here again, you form and that's the bond is illustrated by this dotted line. So this is different from the chemical bond. We're not sharing a pair of electrons here. It's simply a force of attraction because charges of opposite signs attract each other. Kind of like magnets, right?
Little magnets. Think of that. So here, over here, we have another force of attraction forming another hydrogen bond because here we have a partially positively charged hydrogen attached to this nitrogen.
And this nitrogen we said is partially negatively charged. So. two hydrogen bonds.
What about this hydrogen right here? Would this hydrogen form a hydrogen bond? I'm talking about this hydrogen at position two.
Oh, I'm seeing some people saying no. Someone who said no, can you explain why not? Yes.
That's correct. That's correct. This hydrogen is attached to this carbon and they have similar levels of electronegativity.
So this covalent bond is having a pair of electrons that is more or less equally shared. So now there's no partial charges for it. So one take home message, just because you see a hydrogen doesn't mean that it will form a hydrogen bond. OK, you have to check what is it attached to.
If it's attached to a nitrogen or an oxygen, yes, it's going to have partial positive charge. And that is the reason why you don't form a third hydrogen bond right here, down here, because this oxygen has a partial negative charge. It would be able to form a hydrogen bond if there was a partial positive charge there, but it can't.
So only two hydrogen bonds right there. That's what Watson and Crick figured out. Again, this is just showing the arrows of the direction of the pool of electrons where there's a highly electronegative atom. And basically, oh, I already asked that question.
Basically, the two atoms that you need to be concerned about are oxygen and nitrogen. Whenever you see oxygen and nitrogen, beware, there could be polarity form. We call that polarity when there's this distribution of partial charges. So two hydrogen bonds are formed between adenine and thymine.
And now down here, we see the base pairing between guanine and cytosine. And you can see that three hydrogen bonds are formed. That's represented by the three dotted lines.
And you can see why. Here's a partial negative charge up here. It matches or complements a partial positive charge over here.
Here's a partial positively charged hydrogen. that happens to be in the right space at the right distance from this nitrogen that has a partial negative charge. So there's a match and again here there's another match between a partial negative charge and a partial positive charge. So you have perfect matches of three complementary groups and so you form three hydrogen bonds.
So this interaction is of course going to be stronger than the interaction between A's and T's because you have three hydrogen bonds holding that base pair. together. It takes more energy to break apart a GC base pair than it does to break apart an AT base pair.
Now, I want you to think about these groups that form these partial charges that are going to participate in hydrogen bonding. We need to identify them as hydrogen bond donors. or hydrogen bond acceptors. You need a hydrogen bond donor to match a hydrogen bond acceptor so that you form a hydrogen bond.
Okay. The donor is the group that carries the hydrogen that is going to form the hydrogen bond. So this NH2 group is referred to as a hydrogen bond donor group. Okay. And then the acceptor is the other group.
The one that receives that hydrogen, so to speak, is the one that does not have the hydrogen. Instead, it has the partial negative charge. That's the acceptor. So I want you to think of these groups as hydrogen bond donors, hydrogen bond acceptors, because when you form base pairs, you need a hydrogen bond donor to match a hydrogen bond acceptor, so you form the hydrogen bond. So notice that the guanine, starting from top to bottom and this edge of the base, it has at the top an acceptor, hydrogen bond acceptor, a hydrogen bond donor, and a hydrogen bond donor.
ADD, acceptor, donor, donor. And that matches the opposite over here. Here you have a DAA, donor, acceptor, and acceptor. Okay, so it matches very nicely.
And the same applies up here, donor and acceptors. So I want you to train yourself to think of base pairs that way. So when we talk about base pair complementarity, We're really talking about two ideas.
The first one is what we talked about just now, and that is the specific base pairing that occurs between guanine and cytosine and between adenine and thymine. You need that specific base pairing for the complementarity between two strands of DNA so that they can associate in a very specific manner. Now, those of you who may have been looking at these bases a little bit more deeply, you may have noticed that... hey, if I take a thymine and a cytosine, or let's say, yeah, if I take two pyrimidines, or if I take two purines, and I try to turn them around to see if I can make base pairings, you can. On paper, you can pair them up, and they can form, they should be able to form hydrogen bonds.
You can put two purines or two pyrimidines. So why don't you form them in the molecule of DNA? The reason for that has to do with... what we call geometric complementarity. And that is, if you think of this figure right here, this is representing two strands of DNA.
The dotted line is representing the sugar phosphate backbone structure of each of the two strands. And here you have the bases inside the structure trying to form base pairs. And so you will notice that if you try to base pair two purines within the context of the structure of DNA, There's not enough space in there between the two strands.
And so they will collide. This would be too bulky. And if you try to do that, it's going to cause the DNA strands on both sides to kind of bulge out. And that is a very unfavorable kind of situation. So DNA does not like that.
It doesn't prefer to pair two purines. If you try to pair two pyrimidines, you have the opposite problems. They're too far apart. You need them to come close enough to each other in space so that the hydrogen bonds can form. If you just like magnets, if you take magnets and pull them out a little bit too far, you no longer have a force of attraction.
So that's what's happening here. So the best scenario, the optimal scenario is where you have one purine on one strand and a pyrimidine on the other. OK, as long as you have purine, pyrimidine, purine, pyrimidine, base pairing, we're good. Okay, so rule number one is that because of geometrical complementarity, you need to base pair a purine with a pyrimidine.
And then rule number two is that the hydrogen bonding will specifically happen between the A purine and the T pyrimidine and between the G purine and the C pyrimidine. Notice also that when you have two strands of DNA paired up in this way, Those strands have opposite directions. We say that they are anti-parallel.
One strand is going in the 5'to 3'from top to bottom, shown here. The other one is 3'to 5'from top to bottom, shown here. So they are kind of flipped around, and we say that they are anti-parallel. Watson and Crick also required more information than this to solve their structure.
So they had the basis that they can pair up, but they still needed more information about the structure. And Rosalind Franklin was an excellent researcher. She was a chemical physicist and she was trying to solve the structure of DNA herself, too. And she worked in the same institute that Watson and Crick were working in at the time. And she was using the method of X-ray crystallography.
to try to solve the structure of DNA. And that would have been the real scientific, right, correct way to get to the structure. And she was working with DNA fibers. She had isolated fibers of DNA, and she was trying to understand this structure using this method. Now the method of X-ray crystallography is a complicated one.
People study PhDs just to learn how to use this method and apply it. It's quite complicated. You need a lot of algorithms to solve the structure.
But the basic principle behind this method is that the researcher shines an x-ray beam through a sample containing the molecule that you want to analyze, in this case DNA. Here it says that you have a crystal. Crystals were later used because there were better samples of these molecules. But in those days, they were using fibers of DNA.
So it turns out that the X-ray beam has a small enough wavelength that it can hit and collide onto electrons on the molecule that you're analyzing. When the X-ray, you know, most of the X-ray beams are just going to go right through the molecule without hitting anything. But when they do hit an electron on the molecule, it causes the beam to scatter. And that scatter is illustrated here that can be picked up on a photographic plate.
And then the investigator is able to analyze that scattering pattern. And that scattering pattern gives him quite a bit of information about those electron targets. The angle of the scattering of those beams gives them information about the relative distance between those. electron targets that you're hitting and also the intensity of that beam gives them information about the relative size of that target.
So after analyzing many samples in many different directions and all of them gathering all this information they can begin to build slowly the structure of this molecule. And one of these scattering results that she was able to obtain was one that looks like this very famously. having an X-like shape of different signals of X-ray scattering. Now, at the time, she already understood that this meant that the DNA had to have a helical shape because another scientist called Linus Pauling, who was trying to use this same method to solve the structure of different proteins, he found that proteins that have an alpha helical structure also show an X-ray scattering pattern having an X-like pattern just like this. And so he was talking about this and how this X-like pattern showed to him that this molecule had a helical structure.
Watson and Crick didn't know this, and they were desperate to find out any information that Rosalind can give them, but Rosalind didn't want anything to do with them. I mean, they were they didn't get along. They were constantly fighting. Rosalind felt that Watson and Crick weren't weren't real scientists. They weren't they were just playing with molecular models.
She was the one who was trying to solve this the smart way. And so they were always in animosity and she would not show them at all her data. OK. And so we've been we've learned through history that that what happened and.
maybe unfortunately or unfortunately, however you want to look at it. I think more unfortunately, the director of the Institute managed to get the keys to her lab when she wasn't around. And they actually went into her lab to start to look at her x-ray film diffraction patterns.
And they saw this one. And once they saw this one, because they had heard the work from Linus Pauling too, they didn't know anything about x-ray crystallography, but they knew that that x-ray pattern having an X pattern meant that the structure had to be helical. And so with that, they went back and they worked at their modeling and working with a helical structure.
And that's how they came up with their model at the end. Unfortunately, they didn't acknowledge Rosalind Franklin. And this, it was only after she died, because she died some years later, she was actually recognized.
And so today we try to make that effort and always recognizing her as well, because without her work, they wouldn't have been able to solve this structure. These are unfortunate things that happen in science. But we're grateful for the knowledge of this structure because once we understood this structure, we were able to then better understand the function of DNA.
And so here is a representation of their structure. Here they are taking a picture illustrating. their structure and their molecular models. It was very rudimentary, the one that we're using. But once again, they figured out that the two DNA strands had to be anti-parallel.
One of them goes five prime to three prime from top to bottom, and the other one goes in the other direction. So this is just a ribbon model representation of the structure where this outer ribbon is representing the sugar phosphate backbone, which is kind of repetitive all the way along. And then the bases are represented right here in the center of the DNA molecule, base pairing G's with C's and A's with T's. Notice that the base pairs are interacting in a perpendicular direction relative to the direction of the helical structure.
They're perpendicular to it and they are in the middle of the DNA. And that's one of the things that was stalling Rosalind in solving the structure. Because although she knew that the structure was helical, she was thinking that those bases had to be facing outside.
She was trying to figure out a model where the bases were facing outside because that's how she understood those bases could have chemical properties that could interact with other things. But Watson and Crick were thinking, no, those bases have to be somehow interacting with each other. And so they put them in the center of the molecule.
And, you know, one of the things that Rosalind also found from her X-ray diffraction pattern was that there was a repetitive target, electron target, that was 3.4 angstroms apart. She didn't know what that was yet, but something was repeating helically 3.4 angstroms apart. So Watson and Crick noticed that in their structure, every base pair was separated by. 3.4 angstroms. Okay.
So from one base pair to the next 3.4 angstrom. In their structure, they found that the helix, once they put it together, one full turn of the helix, if you start right here and do one complete turn, you would have a total of 10 base pairs in that one full turn. That meant then that the vertical distance of one full turn of DNA, if you start here and then here, would have to be 10 times 3.4 angstroms.
because 10 bass pairs, right? Or 34 angstroms. The other thing that they noticed in the structure was that there were these indentations or grooves that were formed along the length of the helix. One of them was wider than the other one. So they called this one the major groove, and then the other indentation, the minor groove.
Okay. This turned out to be an interesting finding as we're going to see. later. The width of this helix was found to be 20 angstroms. So why are we saying all of these?
Because these findings from these parameters that they measured from this molecular model end up being quite correct. Further studies of the DNA structure, they made some modifications, very slight, but pretty much this was very close to the correct model. Over here, you see a little bit more detail on a section of the helix where you have the sugar phosphates on the outside and the bases, base pairing on the inside. And they, it has been found that there are two forces that keep this, the two strands stably bound together.
One of them, one of those forces come from the base pairing, right? All of that base pairing between the bases are provide the energy to keep those two strands together. But another kind of force that plays an important role is called base stacking forces. And that is that these bases that are, you know, one over the other, even though they're turning along the length, they're kind of stacked up over each other. And so there's plenty of van der Waals type of interactions that is taking place between successive bases there, and that is contributing to the stability of the structure.
And then finally down here you have... more detail of each of the nucleotides so that you can appreciate how each of the nucleotides are aligned along each of the strands and base pairing with each other.