DNA Structure

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One of the most famous discoveries in Biology is the structure of DNA. Heck even elementary school kids can tell you that DNA is a double helix. But, how many people know that one of the guys responsible, James Watson did it in part as a chance to meet women? He was a young guy and goofy looking. He figured if he could become famous by discovering the structure of DNA, success with women would follow.

So if you want to be successful with whatever gender it is you want to be successful with, you better pay attention to today’s lesson.

Now what I’m going to do is I’m going to begin by going through the nucleotides, the little building blocks of DNA. Then I’ll continue by describing how those building blocks get joined together, and then wrapped into that double helix. Last, I’ll finish off by going through the numbers, the dimensions of DNA.

What are nucleotides? Nucleotides are the building blocks of DNA. Now, interestingly enough, Watson and Crick, or Francis Crick who Watson’s partner, they were using a textbook that had the wrong structure for the nucleotides. Because the structures of nucleotides were known long before the structure of DNA was discovered. That mistake in that textbook, slowed them down a lot until finally, a Biochemistry friend of them pointed out what the mistake was. So I’m going to do my best to avoid those mistakes.

So let’s take a look at the basic structure of a nucleotide. Now a nucleotide has three components. It has a Phosphate group here, attached to a 5-carbon sugar, often that’s called a Pentose for five. A 5-Carbon sugar here. Here we have what’s called a Nitrogenous base. Let’s go closer in on the Pentose sugar that’s in DNAs nucleotides.

The 5-carbon sugar in DNA, which is Deoxyribonucleic acid,, as you might be able to guess, it’s Deoxyribose so.

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So we see here its got5 carbons 1, 2, 3, 4, 5. Now to make it easier to refer to the different parts of the sugar, scientists have actually decided, let’s start with the ring. The one thing that’s different, is oxygen. So let’s make that like 12 on a clock, and we’ll go clockwise. So this is Carbon number 1, Carbon number 2, Carbon number 3, Carbon number 4. And the one carbon that’s after the ring up here, is carbon number 5.

Now for reasons that I don’t quite get, scientists said let’s not call it Carbon number 1, let’s just call it 1 prime, 2 prime, 3 prime, 4 prime, 5 prime. If you’re going to write this, you put a little apostrophe next to the number. So it would be 5’. To make this even less clattered, I left off the apostrophes, because it’s just annoying me.

This is Deoxyribose in DNA. You may have heard of that other nucleic acid called RNA. Well, what’s the difference in DNA and RNA? Let’s take a quick look at the sugar.

We can see here Deoxyribose has the same basic structure. But if you take a look here is ribose, here is Deoxyribose. What’s the difference? Chop off this oxygen, that’s Deoxyribose. We deoxygenated it.

Here we have 5 carbons with Oxygen on each Carbon, here is Oxygen, here is an Oxygen, here is an Oxygen, here is an Oxygen, and there is an Oxygen. Every Carbon here has an oxygen except for Carbon number two.

Let’s go back and take a look at how we assemble the nucleotide around our Deoxyribose. So here we see our various carbons, off of Carbon number 5, that’s where we attach phosphate group. So the 5'-carbon has the phosphate group. A lot of times we’ll just refer to it as the 5' Phosphate. Where does that Nitrogenous base go? Let’s hook it up to Carbon number 1.

So if we take a look, we can see the Nitrogenous space here is attached to that first Carbon, or the 1' Carbon. So when I start talking about how DNA is put together, I’m going to start using these 3', and 5' nomenclatures.

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So now I’ve talked about base, and Nitrogenous base is just a polysyllabic way of saying it’s a base. It donates OH groups or absorbs Hydrogen ions that has a lot of Nitrogen in it. There’s four kinds of Nitrogenous bases. So let’s take a look at those four different kinds of nucleotides that they create.

They're Thymine, Cytosine, Adenine and Guanine. You can see how they’re all attached to the 5-Carbon sugar with their Phosphate groups over there. Let’s zoom in on the Nitrogenous bases.

Hopefully you saw pretty quickly that there is some significant differences. Two of them; Thymine and Cytosine, have single rings with other stuff arranged around it, while Adenine and Guanine have two of these rings structures with other stuff around it. It’s not important for you to memorize the things around here, just know that Cytosine and Thymine, because they’re one ring structures, they’re classified as Pyrimidines. While Adenine and Guanine, with their two rings, they’re classified as Purines.

Now how can you remember that? The simplest way; take a look at the word Pyrimidine. What do you notice? A 'y'. Look at Thymine, what do you see? A 'y'. Look at Cytosine what do you see? A 'y'. Look at Purine, no ys, Adenine no ys, Guanine no ys. So it’s 'y', y not. If a three year old can keep track of y and y not, you should too. So Pyrimidines have ys, Purines don’t. That’s the easiest way to remember.

Now that we know how individual nucleotides are put together, let’s see how they get assembled to form that very famous double helix structure. So if we take a look, here is one nucleotide. Remember 5 refers to the 5'-Carbon that the Phosphate’s attached to. 3 refers to the 3'Carbon down here. What happens is that, this Phosphate joins up to the OH group here on the 3'-Carbon.

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That OH group falls off. Often in this Phosphate we may have Hydrogens attached to it, so we pull off an OH and H, that’s forming water. This is why it’s called dehydration, we're removing two Hydrogens and Oxygen here. We’re removing water. This is called dehydration synthesis.

So we’re joining this 5'-Phosphate to that one's 3'-Carbon. It’s like doing that conga line. Here is the 5 fingers, and somebody comes up and puts their 5 fingers onto my shoulders. Where my hands are these Phosphate, the next one’s putting his 5 prime fingers on my shoulders which are my 3 prime end.

Now, what if I wanted to add another one? Well, I just do that right here. Here I see the next nucleotide comes in, joining its 5'-Carbon to this 3'-Carbon here. So what I’m doing is I’m creating one long strand with the Phosphates and Sugars, forming the backbone with the Nitrogenous bases sticking off like this.

But we know that DNA is not a single Helix like RNA is. Instead it forms a double helix. So let’s take a look at that other strand. What happens is that I get one sugar Phosphate backbone on this side, the other sugar Phosphate backbone on that side with the bases pointing at each other.

Now, there is something wrong with this one. What’s wrong? It’s upside down. Why did that happen? That is the key inside that James Watson came up with. He had been sitting around playing with models. That was one of the things that was unusual about what James Watson did. He skipped straight to using the models and he said data is just confusing. Let’s build a model, see if it works and then see if the data matches it.

So to give credit where credit is due, he did come up with some new ways of helping address these problems. What he realized is that, when he turned one of his model of Cytosine upside down and put it up to bind with the Guanine, it wound up being the exact same width as in Thymine turned upside down and joined to an Adenine. So what we’ll see is that, with one strand you have your Phosphate on the 5'-Carbon up here, 3'-Carbon down there.

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With the other strand, it's oriented in exactly the opposite direction. Now scientists don’t like just to say exactly opposite direction, they’ll call this anti-parallel. Because you remember from Geometry two lines that are going in the same direction and never touch, are parallel. Well, this is kind of like that, but because there’s orientation, they’re anti-parallel. So you’ll have one strand with the 3' end down here. The other one with the 5' end up there. This one has 3' up, 5'down.

The bases point towards each other in the inside of the double helix. A lot of times if they’re doing an essay on DNA structure, talk about how it forms like a ladder, a spiralling ladder, when we do the helix twist, with the sugar Phosphate backbone forming the sides of the ladder, and the Nitrogenous bases forming the ranks.

Now you’ll notice these dash lines, those represent Hydrogen bonds; the weak attractions between slightly positive and slightly negative portions of the bases here. You’ll see that Adenine forms two Hydrogen bonds to Thymine. Guanine forms three hydrogen bonds to Cytosine. This is called the Base Pairing rules; Adenine to Thymine, Guanine to Cytosine. That was an idea first come up by Erwin Chargaff and its called Chargaff’s Rules.

We see here with Guanine to Cytosine is 3 Hydrogen bonds, regions of DNA that have lots of Gs and Cs, will actually be held together. The same distance, but it’s a little bit harder to get them to separate, because there’s more Hydrogen bonding going on there, as opposed to regions where there is lots of Adenines and Thymines, which has a slightly weaker attraction.

So this is how we form the ladder shape, but why does it twist up? Well, let’s take a look at a physical model. Here we see a very simple model of a DNA molecule. Here are my Nitrogenous bases. This happens to be Guanine, this is Cytosine. Here we see an Adenine and Thymine and so on, and so forth.

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In this model, these metal rivets represent the sugars, while this part here represents the Phosphate. I’ve labelled it 3' here, 5' there. Now remember, Phosphates have a strong negative charge. What do negative charges do to other negative charges? They repel. So what’s going to happen is that, this Phosphate here is going to try to repel this Phosphate here, which will repel that Phosphate there, and that one there. They’re going to try to get away from each other, but they're held to each other. So they can’t move this way, but what they can do, is move in three dimensions.

Remember, molecules are not flat, they’re in three dimensions. So what happens is that, they start try to squirm away from each other, tightening up until, what’s this shape? It’s a helix. Now if they tighten up too much, then this one starts getting close to that one, so they will get to a certain point, where it’s most stable. And that’s like this. That’s how a DNA structure or a DNA molecule looks.

An interesting side note about the discovery of DNA dimensions is that, a lot of the data came from the work of a woman by the name Doctor Rosalind Franklin. Now for a variety of reasons, Watson and Franklin didn’t get along. So Rosalind Franklin wasn’t ready or willing to share her data with Watson. Now it turned out that her major collaborator, or the person whose lab she was working under, was Maurice Wilkins. She also did not get along with him.

Now while Franklin didn’t want to share her data with Watson, James Watson was friends with Maurice Wilkins. And at one when he was talking to Maurice, and complaining about Rosalind’s unwillingness to share data, Maurice Wilkins showed this picture to James Watson. It was from this picture that he was able to actually figure out the structure of DNA. Now let’s take a look at what that was.

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So if you look at this picture, if we follow one complete twist of one strand here in this double helix, how many nucleotides is it? Well, let’s count it. You’ll see 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 nucleotides per twist. That’s what we see here; 10 nucleotides, and I’ve abbreviated nucleotide nt, because it’s too long to write. So here we have 10 nucleotides per complete twist. One complete twist is 3.4 nanometers in length. That means that one base along the single strand is 0.34 nanometers. So if we have 10 nucleotides per twist, that’s 3.4 nanometers.

Then what’s the width? It’s always 2 nanometers. That again was Watson’s big insight. That if you add an Adenine plus a Thymine, remember Adenine is one of those Purines. It’s got two rings. Thymine is a Pyrimidine, it’s got one ring. 2 plus 1 is 3. And a Guanine plus a Cytosine. Guanine remember is 2 rings, Cytosine is a ring, so that’s again a total of three rings. It turns out that combination gives you a consistent width of 2 nanometers. That’s it.

That’s the dimensions of DNA. That’s what you’ll want to vomit up in the middle of an essay on DNA structure. They’re probably not going to ask that on the multiple choice, but anything on DNA structure, if you can remember those numbers there, you’re going to get one or two more points.

Now remember on an essay, a total possible score of 10 is your maximum. The average score is somewhere between 2 to 4. So just remembering these numbers can get you 50 percent all the way to an average score.

Now you know that DNA is made out of nucleotides with a 5'-Phosphate, and 5-Carbon sugar and one of 4 possible Nitrogenous bases; Adenine, Guanine, Cytosine, and Thymine. You know that they arrange themselves with a 5'-Phosphate of 1 joining to the 3'-Phosphate of the other. They form a long strand. The other strand is oriented in the exact opposite or anti-parallel direction.

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Then that twists up into the double helix. You know that the double helix is itself 2 nanometers wide, with a new twist forming every 10 base pairs making one complete twist, 3.4 nanometers long. You also know that the two strands are held together by Hydrogen bonds between the Adenine and Thymine on one side, Guanine and Cytosine as well.

Now one last question to ask yourself, why was Watson so very certain that his discovery of the structure of DNA would help him meet women? Well, it turns out that, I don’t want to give it away, but his discovery and Crick’s of course, helped lead to the discovery of how DNA copies itself. And also gave us clues that helped us to figure out how our genes are actually coded in the DNA molecule.