BIOCHEMISTRY DISCUSSION 8
Leahh
33TheStructureofInformationalMacromolecules-DNAandRNA.pptxBiochemistry: A Short Course Fourth Edition CHAPTER 33 The Structure of Informational Macromolecules: DNA and RNA
Tymoczko • Berg • Gatto • Stryer
© 2019 W. H. Freeman and Company.
Created by Brett Barbaro
Created by Brett Barbaro
All right - so up until now, we've studied three of the four major types of biomolecules. We've studied proteins, carbohydrates, and lipids - and now, we are going to study the fourth type which is nucleic acids, which are what make up DNA and RNA, which are important informational macromolecules in the cell.
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James Watson
Francis Crick
Watson and Crick - Discoverers of DNA’s Structure
Created by Brett Barbaro
You may be familiar with this picture, James Watson and Francis Crick. These guys discovered the structure of DNA back in 1953. Francis Crick also went on to make notable contributions to the decoding of DNA, including the formulation of the central dogma of molecular biology, which is that information flows from DNA to RNA to protein.
Image: https://gvonkapherr.wordpress.com/2015/03/16/formidable-women-rosalind-franklin-1920-1958/
Rosalind Franklin
The x-ray image that elucidated DNA’s structure
A great explanation of the x-ray image can be found at:
https://www.dnalc.org/view/15014-Franklin-s-X-ray-diffraction-explanation-of-X-ray-pattern-.html
Rosalind Franklin & The Discovery of DNA’s Structure
Created by Brett Barbaro
Rosalind Franklin is another figure that was involved in the discovery of the structure of DNA. She actually is the one that generated the x-ray image seen on the right, which is what finally gave them the clue that the DNA structure was helical. When Watson and Crick saw that, they knew that DNA was helical, and then they worked out the structure from there. Watson and Crick actually got the Nobel Prize for the work with DNA, but Rosalind Franklin was conspicuously passed over. Apparently she and Watson did not get along very well.
Chapter 33: Outline
33.1 A Nucleic Acid Consists of Bases Linked to a Sugar–Phosphate Backbone
33.2 Nucleic Acid Strands Can Form a Double-Helical Structure
33.3 DNA Double Helices Can Adopt Multiple Forms
33.4 Eukaryotic DNA Is Associated with Specific Proteins
33.5 RNA Can Adopt Elaborate Structures
Created by Brett Barbaro
So we'll start out our studies of DNA by looking at the nucleic acids and how they form long chains. And then we will talk about how these long chains combine to make the double helix that you see in DNA. And we'll also explore some other forms of DNA double helices that exist. We will talk about how DNA is packaged, and the proteins that it associates with. And then finally we're going to talk about RNA and its ability to fold into complex three dimensional structures.
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DNA
DNA, the genetic information that is passed from one generation to the next, is composed of four nucleotides with the bases A, G, C, and T.
DNA forms a double helix of two separate strands with complementary sequences.
During replication, the two strands unwind, each serving as a template for a new daughter double helix.
Created by Brett Barbaro
All right, so the very basic stuff of DNA: There are four basic nucleotides that DNA is made out of, containing the bases adenine, guanine, cytosine, and thymine. And those have the abbreviations A, G, C, T. So we'll see a lot of those letters in the next eight chapters here.
DNA forms a double helix that has two strands that have complementary sequences. And when you unwind these two strands, you can build new strands on each of the original strands.
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Diagram of DNA Replication
Created by Brett Barbaro
Figure 33.1 DNA replication. Each strand of one double helix (shown in blue) acts as a template for the synthesis of a new complementary strand (shown in red).
Here's a diagram showing how that occurs, sort of. You start with the original parent molecule on the top. It splits and forms two daughter molecules, and the blue strands of the daughter molecules are the same molecules that were in the original parent. The red strands are new DNA molecules that have been synthesized complementary to the original parent molecule strands. And it's this specific feature of DNA that makes it able to replicate such that when a cell divides, each daughter cell is able to receive a full copy of the DNA.
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Section 33.1 A Nucleic Acid Consists of Bases Linked to a Sugar-Phosphate Backbone
Learning objective 1: List the components of nucleic acids.
Nucleic acids are long, linear polymers constructed from four types of monomers.
Each monomer consists of a sugar, a phosphate, and a base.
The sequence of the bases is the information content of the nucleic acid.
Created by Brett Barbaro
Figure 33.2 The polymeric structure of nucleic acids.
All right - so we'll talk about DNA, nucleic acids in general, as polymers of four different types of monomers. And these monomers are identical except for the base portion. Each one contains a sugar, a phosphate, and a base. And the sequence of the bases is where the information is held.
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DNA and RNA Differ in the Sugar Component and One of the Bases
The sugar component of deoxyribonucleic acid (DNA) is deoxyribose, a ribose in which the 2’-hydroxyl is replaced with a hydrogen.
Ribonucleic acid (RNA) contains the sugar ribose.
Atoms in sugar units are numbered with primes to distinguish them from atoms in bases.
Created by Brett Barbaro
Figure 33.3 Ribose and deoxyribose. Atoms in sugar units are numbered with primes to distinguish them from atoms in bases.
Now, DNA and RNA differ primarily in the sugar component. And the sugar component of DNA is deoxyribose, whereas the sugar component of RNA is simply ribose. And deoxyribose is the same as ribose, but with the 2' oxygen removed (so it's “deoxy”). Now, if you look at the structure of these two, you'll see that ribose has more oxygens on it. Well, that actually makes it a little bit less stable. Remember that oxygen is reactive, and so deoxyribose is more stable than ribose, and therefore, that’s why it’s better for long term storage of information in DNA. We also notice that these carbon atoms are numbered with a prime ('). That's to distinguish them from other atoms in DNA. So if you hear about 4' carbon, you know that's in the sugar part.
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Structures of the Backbones of DNA and RNA
The backbones of DNA and RNA consist of the sugars linked by phosphodiester bridges between the 3’-hydroxyl of one sugar and the 5’-hydroxyl of an adjacent sugar.
Bases are attached to carbon atom 1’ in the sugar.
Created by Brett Barbaro
Figure 33.4 Backbones of DNA and RNA. The backbones of the nucleic acids are formed by 3-to-5 phosphodiester linkages. A sugar unit is highlighted in red and a phosphate group in blue.
All right - so the units of DNA and RNA are connected. Starting up at the top, you can see the 5' oxygen and then you can see down to the 3' oxygen, which is attached to a phosphate group, and then the phosphate group is attached to the 5' oxygen of the next base {unit}. And the bases are attached to the 1' carbon atom in the sugar. Just like amino acids have an amino terminus and an acid terminus, DNA molecules have a 5' end and a 3' end, so they are also directional.
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Diagram of Purines and Pyrimidines
Two of the bases are purines (adenine and guanine), and two are pyrimidines [cytosine and thymine (DNA) or uracil (RNA)].
Created by Brett Barbaro
Figure 33.5 Purines and pyrimidines. Atoms within bases are numbered without primes. Uracil is present in RNA instead of thymine.
Taking a look at our bases here, we've got basically two different kinds. There's purines and pyrimidines. Purines, such as adenine and guanine...contain two rings. Pyrimidine, cytosine, uracil, and thymine contain a single ring. And they’re numbered as you can see on the left.
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Nucleotides Are the Monomeric Units of Nucleic Acids
A base bound to a sugar is called a nucleoside. The nucleosides of DNA are deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine. By convention, deoxythymidine, which rarely occurs in RNA, is simply called thymidine.
The nucleosides of RNA are adenosine, guanosine, cytidine, and uridine.
In all cases, the C-1’ of the sugar is attached to the N-9 of the purine or the N-1 of the pyrimidine.
A nucleotide is a nucleoside with one or more phosphoryl groups attached.
Nucleoside triphosphates are the building blocks of DNA and RNA.
Created by Brett Barbaro
When the base is bound to a sugar, just the base and the sugar, that's called a nucleoSIDE. So the nucleosides of DNA would be deoxyadenosine, deoxyguanosine, deoxycytidine, and deoxythymidine. (I said deoxyadeno-SIGN; it could be adeno-SEEN – I think both pronunciations are OK.) By convention, as they say, deoxythymidine is usually just called thymidine. But I've personally found that it doesn't matter very much what you talk about/which words you use, because the context in which you use them is what usually determines what their meaning is. It's usually not a problem to distinguish between them.
Nucleosides of RNA are adenosine, guanosine, cytidine, and uridine.
And if you attach a phosphoryl group to any of these on the 5' or the 3' end, they become nucleoTIDES.
So a nucleoSIDE triphosphate is a nucleoTIDE. And we’re quite familiar with nucleoside triphosphates, such as ATP. Adenine triphosphate, or adenosine triphosphate. {I make that mistake a LOT!}
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Diagram of the β-Glycosidic Linkage in a Nucleoside
Created by Brett Barbaro
Figure 33.6 -Glycosidic linkage in a nucleoside.
The bases are attached to the riboses with a β-glycosidic linkage. We discussed those many chapters ago. It just means that it sticks up out of the plane.
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Structures of Nucleosides 5’-ATP and 3’-dGMP
Created by Brett Barbaro
Figure 33.7 Nucleotides adenosine 5-triphosphate (5-ATP) and deoxyguanosine 3-monophosphate (3-dGMP).
And here is a diagram of our good old friend ATP. This is called 5'-ATP in this case, because the phosphates are attached to the 5' carbon of the ribose.
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DNA Molecules Are Very Long and Have Directionality
Nucleic acid chains are presented by abbreviations such as pApGpCpT and pAGCT, or more simply AGCT.
Nucleic acid chains have directionality in that the two ends are different. One end has a free 5’-OH group or a 5’-OH group attached to a phosphoryl group and one end has a free hydroxyl attached to the 3’ carbon of the sugar.
Nucleic acid chains are written in the 5’-to-3’ direction.
DNA molecules can be extremely long, some consisting of more than 1 billion nucleotides in length.
DID YOU KNOW?
Most human cells have 6 billion base pairs of information. All 6 billion base pairs would be 3.6 m in length if all of the molecules were laid end to end. Human beings are composed of approximately 10 trillion cells. If all of this DNA were strung end to end, it would reach to the Sun and back about 65 times.
This is single-stranded. Another way to think about it is if you laid all the double-stranded DNA in a cell end-to-end, it would be about as tall as you are. If you bundled all of the DNA in the body together, it would be a rod about 6mm in diameter, so about the size of a 6-foot pencil.
Created by Brett Barbaro
Now, it says here that "DNA molecules are very long and have directionality." Well they don't have to be very long. I mean, you can have two different nucleotides attached together and call it DNA, but they CAN be {and usually are} extremely long. They are often written just as a string of letters, like AGCTGACTGCGCAT... blah, blah, blah. It says here, you can sometimes see them written pApGpCpT or pAGCT; I suppose that's true, but not very common, though - it's usually just a string of letters.
As I mentioned before, the nucleic acids have a directionality and we always write them from the 5' to 3' direction. That's also the way in which they are synthesized inside the cell, so that's convenient and makes a lot of sense.
Now, DNA molecules can be more than a BILLION nucleotides in length. And that's a lot. We talked about how big a billion is. And that's for a single molecule; I mean, that's kind of extraordinary.
In each cell that we have is probably about six billion base pairs of information. That's divided up into 23 chromosomes. But if you took each one of these molecules inside your cell and laid them end to end, it would be about 3.6 meters long, which is quite extraordinary for something which is compacted into the nucleus of a cell.
Human beings have about ten trillion cells, so if you stuck all of the DNA, single-stranded DNA molecules end to end, it would reach to the Sun and back about 65 times, which is just mind-blowing.
A little bit more reasonable and perhaps relatable idea, is that if you were to take the double-stranded DNA in your cell and lay it end to end, it would be about as tall as you are, about 6 feet.
And then if you were to take all of the DNA in all of your cells and bundle it together, it would be a 6 foot rod about 6mm in diameter, so about the diameter of a pencil. And that is all of the DNA in your body. You can make a rough comparison at this point, imagining your body as a single cell, and that {6-foot pencil of} DNA is the DNA which is inside that cell. That's about the ratio of the amount of DNA {to the size of} a cell.
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Diagram of the Structure of a DNA Chain
Created by Brett Barbaro
Figure 33.8 The structure of a DNA chain. The chain has a 5 end, which is usually attached to a phosphoryl group, and a 3 end, which is usually a free hydroxyl group.
Here’s another representation of the DNA clearly showing the linkage between nucleotides and the 5’ to 3’ orientation.
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Electron Micrograph of Part of the E. coli Genome
Created by Brett Barbaro
Figure 33.9 An electron micrograph of part of the E. coli genome. The E. coli was lysed, extruding the DNA. [Dr. Gopal Murti/Science Photo Library/Photo Researchers.]
And here is an electron micrograph of actual DNA. The center part there was an E. coli cell that was lysed, which means that it was broken open, and all of the DNA inside spread out and that’s what you see - these lines that are strewn all over the place.
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http://www.nature.com/scitable/topicpage/genome-packaging-in-prokaryotes-the-circular-chromosome-9113#
Ecoli genome
vs.
Ecoli
Size of the Ecoli genome vs the size of an ecoli organism
Created by Brett Barbaro
Now, I didn’t feel like that last image showed you all of the DNA, so for comparison we have here a complete set of the DNA. You have your E. coli on the left and that is the relative size of all of the DNA spread out. And if you look closely, you will see that there are a lot of little squiggles and turns and twists of the DNA, and that’s the supercoiling which we will talk about in a second.
http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure1.1-reduced.jpg
E. coli molecule illustration
Created by Brett Barbaro
Now, here’s an illustration of E. coli ,with all of the DNA inside, and also a clear view of the flagellae, pili and internal molecules and the membrane.
http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure4.2-reduced.jpg
Closer look at E. coli
Created by Brett Barbaro
Here is a little more close up view of that. And up in the right you can see the highlighted section. We are going to zoom in on that for the next bit to take a closer look at the DNA.
http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure4.1-reduced.jpg
DNA and elements within E. coli
Created by Brett Barbaro
So here, we can see an illustration of the DNA in the lower left. And you can see it interacting with a number of proteins, and it’s all bound together in the center of the E. coli, in what’s called a nucleoid {since it’s a prokaryote, it doesn’t have a nucleus}. You can get a great view of a lot of the other proteins and elements of the E. coli from this illustration as well.
http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure4.6-reduced.jpg
Illustration of unwound E. coli DNA
Created by Brett Barbaro
And finally, we’re just going to focus here on the DNA. You can see in certain parts it’s unwound. In certain parts it is bound to certain proteins that bend it at an angle. Sometimes it’s bound with proteins to keep it single stranded. It’s replicating. There’s a number of activities going on in this picture, but we’ll get into more detail on that later.
http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure4.3-reduced.jpg
Biochemicals in E. coli illustration
Created by Brett Barbaro
And here is another close up exploded view of this organism. And what we are looking at here is a few select proteins in blue. I wish I could tell you what they are, but I don’t know {see http://onlinelibrary.wiley.com/doi/10.1002/bmb.20345/full to explore further!}. The purple is RNA though, and that is winding around. And you also see a number of small molecules in orange. Those might be ATP or glucose or other members of the glycolytic pathway that we’ve studied. You can see red dots in there. And if you look at how the water molecules...well, you see first of all the blue water molecules which are all over the place. This gives you some idea of how densely packed everything is. If you look at the red dots, you’ll see that the blue molecules are oriented toward the red dots with the oxygens facing in. From that, I will guess that that is sodium. And you also see green dots with the hydrogen side of the water molecules pointing towards them - that would probably be chloride. Sodium chloride, sodium and chlorine, are very important ions for all life basically. You will also see amongst all of these things, small yellow bits, those would be phosphates - there’s a diphosphate there in the middle. So this is what it actually looks like, or might actually look like, at this level.
The DNA contained within Paris japonica dwarfs all other plant and animal genomes that have been analyzed so far. It is 50 times longer than the human genome. Photo: CLIVE NICHOLS
http://www.telegraph.co.uk/news/science/science-news/8196572/Worlds-largest-genome-belongs-to-slow-growing-mountain-flower.html
Genome Size and Complexity
Created by Brett Barbaro
Now getting back to DNA - having a lot of DNA does not necessarily mean anything. It doesn’t mean that you’re more complicated or important, necessarily. This plant here, the Paris japonica, has about 50 times more DNA in its cells than humans. So if having a lot of DNA makes you more complicated, then these flowers are a great deal more complicated than we are.
http://phenomena.nationalgeographic.com/2013/02/06/you-have-46-chromsomes-this-pond-creature-has-15600/
Oxytricha trifallax has 15600 chromosomes
Chromosome Number and Complexity
Created by Brett Barbaro
A similar thing goes for the number of chromosomes. We have 46 chromosomes, but this organism has 15,600 chromosomes. So having a lot more chromosomes does not necessarily make you anything in particular. I wouldn’t venture to guess even how many chromosomes a banana might have, or a mouse. I do know that fruit flies have 4 pairs of chromosomes, or 8 chromosomes total, but I only know that because I worked with fruit flies for a long time. What I do know is that we have 23 pairs of chromosomes, and that appears to be suitable for our needs.
Section 33.2 Nucleic Acid Strands Can Form a Double-Helical Structure
General features of DNA are as follows:
DNA molecules consist of two chains of opposite directionality—one strand runs in the 5’-to-3’ direction and the other in the 3’-to-5’ direction– intertwined to form a right-handed double helix.
The sugar–phosphate backbones are on the outside of the helix, whereas the bases are inside the helix.
The bases are nearly perpendicular to the axis of the helix with adjacent bases separated by 3.4 Å.
The helix is approximately 20 Å wide.
Created by Brett Barbaro
Figure 33.11 A skeletal representation of the double helix illustrates the helix properties. (A) Side view. Adjacent bases are separated by 3.4 Å. The structure repeats along the helical axis (vertical) at intervals of 34 Å, which corresponds to 10 nucleotides on each strand. (B) Axial view. Looking down the helix axis reveals a rotation of about 36° per base and shows that the bases are stacked one on top of another. [Drawn by Adam Steinberg.]
So let’s talk a little bit about the double helical structure of DNA. You can see in the diagram there, on the right, that there’s two chains that are involved in the helical structure, and these are two separate molecules. They run antiparallel to each other, which means that if you start at the 5’ end of one, it will be associated with the 3’ end of the other one. So the strands are complementary, not identical. The sugar phosphates are on the outside of the helix, and the bases are on the inside. And if you think about it, that makes a lot of sense because the sugars and phosphates are highly hydrophilic, and also the phosphates have negative charges which repel each other, and that tends to push the phosphates to the outsides of the helix. There’s about 3.4 angstroms from base to base, or 34 angstroms for a repeating turn, approximately 10.4 bases per turn. The bases in this form of DNA are all nearly perpendicular to the axis, and the overall width of the DNA is about 20 angstroms. I say DNA, rather than molecule, because DNA is actually two molecules. And if you divide a full turn, 360 degrees, by 10 bases, you actually get close to 36 degrees for each base rotation.
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http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure2.4-reduced.jpg
Illustration of DNA and RNA
Created by Brett Barbaro
This is a slightly better diagram I think, because it I think shows you a little bit more clearly what this molecule would look like. And you have the double stranded portions on the bottom, and single stranded on the top. And this would be a DNA double helix on the left, and an RNA double helix on the right. You can see how the bases stick into the center of the molecules and the phosphate groups run along the outside.
The Double Helix Is Stabilized by Hydrogen Bonds and the Hydrophobic Effect
Adenine always forms hydrogen bonds with thymine, whereas guanine forms hydrogen bonds with cytosine.
The helix is stabilized by hydrogen bonds between base pairs as well as by hydrophobic interactions and van der Waals forces, called stacking forces, between adjacent bases.
Created by Brett Barbaro
Figure 33.12 Structures of the base pairs proposed by Watson and Crick.
Now this is the important thing about DNA, which is that the bases are complementary to each other. Guanine pairs with cytosine, and adenine pairs with thymine. These are hydrogen bonds that are formed between the bases, and those hydrogen bonds help keep the strands together. But most importantly, when you’re trying to synthesize a new strand of DNA, if you have a single strand and you encounter a cytosine, you know that the next thing you need to add is a guanine to pair with that.
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http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure2.5-reduced.jpg
DNA Base Pairing Illustration
Created by Brett Barbaro
Now, adenine and thymine each have two hydrogens that are available for hydrogen bonding, and you can see on the top here where those are and how they orient to each other. And then guanine and cytosine have three hydrogen bonds between them. Now, it’s because of their shape and charge structure that adenine won’t pair with guanine or cytosine. None of these bases will pair with anything other than the one that is intended for them. So they have very strong shape and charge complementarity and specificity.
An Axial View of DNA
Created by Brett Barbaro
Figure 33.13 An axial view of DNA. Base pairs are stacked nearly one on top of another in the double helix. The stacked bases interact with van der Waals forces. Such stacking forces help stabilize the double helix.
There are also interactions that occur between the stacked bases along the center of the DNA, and those are van der Waals interactions and not charge complementary interactions.
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http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure2.6-reduced.jpg
Illustrations of Various Nucleic Acid Forms
Created by Brett Barbaro
And here are some diagrams/illustrations of these nucleic acids in various forms. You’ll see DNA on the left with a single stranded RNA on the bottom (that’s the messenger RNA). Transfer RNA is a molecule that is important in protein synthesis and that consists of a single RNA molecule folded up into a complex three-dimensional structure. On the right is the ribosome small unit, which is a large complex of both proteins and RNA, in which the RNA has a number of catalytic functions.
The Strands of the Double Helix Can Be Reversibly Separated
During replication or transcription, the two strands of the DNA double helix must be separated.
In the laboratory, DNA strands can be separated by heating a solution of DNA, a process called denaturation or melting. The temperature at which half of the DNA molecules are denatured is called the melting temperature (Tm).
Upon cooling, the two strands can bind to each other to re-form the double helix, a process called annealing.
Created by Brett Barbaro
Now remember that the strands of DNA are complementary to each other, and so if you pull them apart they will tend to zip back up into the same configuration. This is made use of in the laboratory - by heating DNA you can separate the strands, and that’s called denaturation (or also melting). And then when you cool them, the strands will actually find each other again and recreate the same double-helical form, and that process is called reannealing.
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Section 33.3 DNA Double Helices Can Adopt Multiple Forms
In the cell, the most commonly seen form of the DNA double helix is called the B form or the Watson–Crick helix.
The double helix can also exist in an A form, which is shorter and wider than the B form with the bases at an angle rather than perpendicular to the helix axis.
RNA double helices and RNA–DNA hybrid helices, structures observed in transcription and RNA processing, adopt a double-helical form very similar to that of A-DNA.
Created by Brett Barbaro
Figure 33.17 B-form and A-form DNA. Models of 10 base pairs of B-form and A-form DNA depict their right-handed helical structures. Notice that the A-form helix is shorter than the B-form helix and that the base pairs are tilted rather than perpendicular with respect to the helix axis. [Drawn by Adam Steinberg, after 1BNA.pdb and 1DNZ.pdb.]
So there are multiple forms of DNA. We normally see the B form, which is the one that was found by Watson and Crick, and you can see that on the side - it looks very familiar. But there is also an A form in which the center of the DNA is actually kind of hollowed out, and that is actually a conformation that is more often taken by RNA or RNA-DNA hybrids, which exist as well. And, of course, you can imagine - if the B form is stable and the A form is stable, there must also be transitional states between those to get from the B form to the A form.
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http://mgl.scripps.edu/people/goodsell/books/MoL2figures/Figure2.4-reduced.jpg
Illustration of DNA and RNA
Created by Brett Barbaro
Back to this diagram - on the left you see the DNA double helix, and on the right you see the RNA double helix. And you can tell that they are a little bit different. The DNA double helix is a little bit narrower and the grooves are a little bit wider. And on the RNA double helix you can see the oxygens - you see the three starred oxygens there in the middle of the diagram? Those are pointing out more toward the exterior of the RNA. And furthermore, the bases are angled a little bit more steeply with regard to the axis.
Z-DNA Is a Left-Handed Double Helix in Which Backbone Phosphoryl Groups Zigzag
The double helix can also form Z-DNA. Z-DNA is left-handed, and the backbone is zigzagged, accounting for the name “Z-DNA.”
Created by Brett Barbaro
Figure 33.18 Z-DNA. DNA can adopt an alternative conformation under some conditions. This conformation is called Z-DNA because the phosphoryl groups zigzag along the backbone. [Drawn by Adam Steinberg, after 131D.pdb.]
And that is not all! We have also discovered a form of DNA called the “Z form” of DNA - and this could also be an RNA form - and this is extremely different. So this is a left handed helix, which means it’s kind of twirling in the opposite direction of the A and the B forms of DNA. And it’s an interesting thing, we don’t actually know why it does this or what the biological role is for Z DNA, but we do know that there are proteins that do specifically bind to Z DNA, and therefore they must have some sort of function. Now if this can exist, and A and B can exist, you must be able to imagine that there are a whole bunch of other configurations that it will transit through. And that’s an important thing to know - DNA is flexible and dynamic, not a static form like you might imagine. It’s always bending and changing.
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Table 33.1 Comparison of A-, B-, and Z-DNA
Created by Brett Barbaro
This is just a number of facts and comparisons between the helix types that you can look up in your textbook and figure out what they mean.
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The Major and Minor Grooves Are Lined by Sequence-Specific Hydrogen-Bonding Groups
DNA in the B form has a major groove and a minor groove.
The presence of the grooves allows access to the hydrogen-bonding capabilities of the exposed bases.
Created by Brett Barbaro
Figure 33.20 Major and minor grooves in B-DNA. Notice the presence of the major groove (depicted in orange) and the narrower minor groove (depicted in yellow). The carbon atoms of the backbone are shown in white. [Drawn by Adam Steinberg.]
Another feature of DNA that we will talk about is the major groove and the minor groove. The major groove is the wider groove, and the minor groove is the backside of that, which is a little bit narrower. And you can see that, in the major groove especially, the bases are exposed so that they can interact with other molecules.
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The Major and Minor Grooves Are Lined by Sequence-Specific Hydrogen-Bonding Groups
The hydrogen bonding capability provides a means of sequence-specific interactions between DNA and the molecules with which it must interact with in the processes of replication and transcription.
Created by Brett Barbaro
Figure 33.19 Major- and minor-groove sides. Because the two glycosidic bonds are not diametrically opposite each other, each base pair has a larger side that defines the major groove and a smaller side that defines the minor groove. The grooves are lined by potential hydrogen-bond donors (blue) and acceptors (red).
Another feature of DNA that we will talk about is the major groove and the minor groove. The major groove is the wider groove, and the minor groove is the backside of that, which is a little bit narrower. And you can see that, in the major groove especially, the bases are exposed so that they can interact with other molecules.
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http://www.rcsb.org/pdb/101/motm.do?momID=23
Major and Minor Groove Face Illustration
Created by Brett Barbaro
Base pairing in the DNA double helix, showing hydrogen bond acceptors (A) and donors (D), and the different sizes of methyl groups and hydrogen atoms (large and small stars). Additional 'extragenetic' information is read from the surfaces that are left exposed in the double helix - this extragenetic information is used by proteins to read the genetic code in DNA without unwinding the double helix.
This illustration shows a little more clearly what those faces look like. On the left, you can see the major groove at the top in green, and the minor groove in the bottom in blue. There is an adenine and thymine pair and there is a guanine-cytosine pair. The A on the left stands for acceptor of a hydrogen bond, and D stands for a donor of a hydrogen bond. You can see on the upper right, the adenine-thymine presents an acceptor, a donor, and then another acceptor, and then a large methyl hydrophobic group, presenting a unique structure that can be recognized by proteins. On the other side, in the minor groove, you have two acceptors which are separated by a small hydrophobic group, which is another unique shape. On the guanine and cytosine pair, we see an acceptor, an acceptor, a donor, and a small hydrophobic group, and on the minor groove, we see an acceptor, a donor, and an acceptor. These features will combine and change based on the sequence of the DNA, presenting a basically two-dimensional surface that has a combination of shapes and charges that will be complementary to very specific proteins.
Double-Stranded DNA Can Wrap Around Itself to Form Supercoiled Structures
In order to fit inside a cell, the DNA molecule must be compacted. In E. coli, the DNA double helix is a circular molecule that is twisted into a superhelix by the process of supercoiling.
The unwound DNA and the supercoiled form are topological isomers of each other.
Linear DNA molecules can also form superhelices when packaged into chromosomes.
Created by Brett Barbaro
So we’ve talked about all of the DNA that fits inside your nucleus (or cell for bacteria, which doesn’t have a nucleus - just inside the nucleoid body). But in order to make that work, you have to fold it up. And DNA is folded up in very specific ways. One of the ways that you can take DNA and compact it is by twisting it into what’s called a superhelix. You have the helix of the DNA, and then you can make a helix of that helix, and that’s called the process of supercoiling. It doesn’t involve changing the sequence at all, but it does involve changing the shape.
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Electron Micrographs of Circular DNA from Mitochondria
Relaxed
Supercoiled
Created by Brett Barbaro
Figure 33.21 Electron micrographs of circular DNA from mitochondria. (A) Relaxed form. (B) Supercoiled form. [Courtesy of Dr. David Clayton.]
You can see here on the left - on the top is the relaxed form of a DNA. (This is a circular DNA like you would find in E. coli.) And then on the bottom you can see a supercoiled form where it’s all wound up.
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Diagram of Supercoiling in DNA
Created by Brett Barbaro
Figure 33.22 Supercoiling in DNA. Partial unwinding of a circular molecule of DNA allows supercoiling. [Information from W. Saenger, Principles of Nucleic Acid Structure (Springer, 1984), p. 452.]
This supercoiling is achieved by introducing twists in the DNA. And you may have experienced this when twisting a string. You might recall, string is actually a coiled bundle of fibers and if you twist the ends of a string, then it will tend to twist up into a supercoiled structure. Well, very similarly like this, if you introduce a twist or untwist into a circular {or straight} DNA, it will naturally fall into a supercoiled structure.
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Section 33.4 Eukaryotic DNA Is Associated with Specific Proteins
Learning objective 2: Describe how DNA is packaged to fit inside the cell.
There are 3.6 meters of DNA in a human cell, packaged into 46 chromosomes.
Supercoiling accounts for some of the compaction of the DNA, but further compaction occurs by binding certain proteins to the DNA.
This video shows how it’s done, and includes some awesome images of cell division:
How DNA is Packaged (Advanced) - www.youtube.com/watch?v=gbSIBhFwQ4s.mp4
Created by Brett Barbaro
Ok - so there’s a lot more DNA in a human cell than there is in E. coli. And although there may be some supercoiling taking place, we use a much more complicated method for compacting our DNA and organizing it. And I’ve got a video at the bottom which will show you better than any combination of words and pictures I think, how this all happens. So I will ask you to take a look at that video, I think you can click the link (www.youtube.com/watch?v=gbSIBhFwQ4s.mp4) and then we’ll come back and we can discuss the individual stages of this process.
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Nucleosomes Are Complexes of DNA and Histones
Chromatin is the entire complex of a cell’s DNA and its associated proteins.
Histones are highly basic proteins that are components of chromatin.
Two copies each of histones H2A, H2B, H3, H4 and 200 bp of DNA compose a nucleosome.
Nucleosomes are joined by linker DNA, to which histone H1 binds, so that the histone-DNA complex has the appearance of beads on a string.
Created by Brett Barbaro
So all of the DNA and the associated proteins - and there are a lot more associated proteins than are shown in that video - all of that together is called chromatin. And that chromatin is visible in the microscope because it’s so much stuff glommed together. But the first stage of organizing the DNA is wrapping it around histones. And the histones are very basic proteins, that means that they are very highly positively charged. And that makes sense, because a DNA is very negatively charged because of all the phosphates, and so the histones naturally associate with the DNA. And then they associate specifically with each other to create the little balls of protein and DNA that is called a nucleosome. There is a little bit of DNA between each linked nucleosome, which is called linker DNA, and that gives it all the appearance of beads on a string.
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Electron Micrograph of Chromatin Structure
Created by Brett Barbaro
Figure 33.24 Chromatin structure. An electron micrograph of chromatin showing its “beads on a string” character. [©Don. W. Fawcett/Science Source.]
This is an electron micrograph of DNA with the nucleosomes attached and the characteristic beads on a string appearance. You can see that the distances between the nucleosomes are not completely uniform, but they are all pretty close to the same length.
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Diagram of Linked Core Particles
Created by Brett Barbaro
Figure 33.25 Linked core particles. Core particles are joined to one another by linker DNA. [Information from D. L. Nelson and M. M. Cox, Lehninger Principles of Biochemistry, 5th ed. (W. H. Freeman and Company, 2008), p. 963.]
This illustration will just show you a little bit more clearly perhaps how this works. The DNA actually wraps twice around each nucleosome core particle.
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Eukaryotic DNA Is Wrapped Around Histones to Form Nucleosomes
The eight histones of the core particle are arranged as an octamer composed of (H3)2(H4)2 tetramer and a pair of (H2A–H2B) dimers.
DNA wraps around the outside of an the octamer.
Nucleosomes themselves are arranged in 30-nm fibers in which the nucleosomes could be arranged into two interwound left-handed helical stacks, with the linker DNA crossing the interior of the fiber. Further folding generates the chromosome.
Created by Brett Barbaro
The nucleosome is actually a complex of 8 histones in each core particle. And that is 2 H3 histones, 2 H4 histones and then 2 H2A and 2 H2B histones in dimeric form, and the DNA gets wrapped around the outside of that.
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Diagram of a Nucleosome Core Particle
Created by Brett Barbaro
Figure 33.26 A nucleosome core particle. Schematic representations of a core of eight histone proteins surrounded by DNA. (A) A view showing the DNA wrapping around the histone core. (B) A view related to that in part A by a 90-degree rotation.
This diagram shows 4 of the {histone} particles inside of the {nucleosome}, with the DNA wrapped around it. But clearly seen in this diagram is the amino terminal tails of the histones. And those stick out and interact with DNA, but are also extremely important for control of gene expression. Those amino terminal tails can be modified by various proteins which change the structure of the histone, sometimes breaking it apart and thus exposing the DNA so that it can be transcribed or replicated. And other times, the modifications prevent the histones from breaking apart, thus repressing the transcription of genes.
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Diagram of Higher-Order Chromatin Structure
Created by Brett Barbaro
Figure 33.27 Higher-order chromatin structure. (A) A proposed model for chromatin in which the nucleosomes are packed into two interwound left-handed helical stacks. (B) The paths of two helical stacks are illustrated. [Information from F. Song et al. Science 344:376–380, 2014 (Figure 1D, p. 377).]
As you saw in the video, these histones are able to stack up on top of each other and form a helical structure, which is another layer of organization of the DNA. And then these chromatin fibers are also able to wrap up into higher level structures, super supercoils, which are able to pack in more tight ways.
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Diagram of the Compaction of DNA into a Eukaryotic Chromosome
Created by Brett Barbaro
Figure 33.28 The compaction of DNA into a eukaryotic chromosome. [Information from H. Lodish, A. Berk, P. Matsudaria, C. A. Kaiser, M. Krieger, M. P. Scott, S. L. Zipursky, and J. Darnell, Molecular Cell Biology, 5th ed. (W. H. Freeman and Company, 2004), p. 406.]
So this is just an interesting diagram showing the whole process - from naked DNA at the bottom, to the beads on a string that you see when it interacts with a nucleosome, to the 360 angstrom fiber, and finally to larger and larger folding, leading to the formation of the chromosome, which is its final form before a cell divides.
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Section 33.5 RNA Can Adopt Elaborate Structures
A common structural motif seen in nucleic acids, most notably RNA, is the stem-loop, which occurs when complementary sequences in the same strand form a double helix.
Created by Brett Barbaro
Figure 33.30 Stem-loop structures. A stem-loop structure can be formed from single-stranded DNA or from RNA.
All right, so now we have talked about packaging the DNA. We are going to move onto the subject of RNA. And this is actually kind of true of DNA as well, but RNA is much more dynamic in the cell, so when we talk about these elaborate structures that are formed, they’ll usually be in RNA. So one of these structures that we can see is called a stem loop. And this is one thing that you can see in DNA sometimes. You will remember, when complementary sequences are peeled apart or melted, when you bring them back together they will tend to form a double helix again. And so there can be complementary sequences in a single strand of DNA or RNA, and those can find each other and form double helices within a single strand. And one of those structures is a stem loop, which you see here. These are adjacent and “palindromic” sections of the nucleic acids that complement each other, and therefore come together. And you can’t see the helical structure {in this diagram}, but whenever any nucleic acid comes together, you will normally find it in some sort of helix.
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Section 33.5 RNA Can Adopt Elaborate Structures
Non-Watson–Crick base pairs occur frequently in RNA.
More elaborate structures may form, often stabilized by Mg2+ ions.
Created by Brett Barbaro
Figure 33.31 The complex structure of an RNA molecule. A single-stranded RNA molecule can fold back on itself to form a complex structure. (A) The nucleotide sequence showing Watson–Crick base pairs and other nonstandard base pairings in stem-loop structures. (B) The three-dimensional structure and one important long-range interaction between three bases. In the three-dimensional structure to the left, cytidine nucleotides are shown in blue, adenosine in red, guanosine in black, and uridine in green. In the blown-up view, hydrogen bonds within the Watson–Crick base pair are shown as dashed black lines; additional hydrogen bonds are shown as dashed green lines.
This is an interesting example of probably an RNA structure that is a single strand folded up upon itself - and you can see a great deal of complementarity between the parts of the RNA. In fact, it seems to make one large helix on the left, and one large helix on the right. And there are little loops and bits that come out that makes it more flexible, so this molecule would have a very complex three dimensional shape. Another thing to note is that, in this structure, there’s three nucleotides that are highlighted here, with a little box around them, that interact together in a three-nucleotide structure. This is called “non-Watson-Crick base pairing”, and it does occur in these complex RNAs a lot. These structures can also interact with other molecules and ions like zinc or magnesium in order to keep them stable.
And here is an example of the triple-base structure that we saw in the last diagram. And if you look closely, you can see that there is extensive hydrogen bonding between that 2’ hydroxyl group on the ribose. And, if you remember, that 2’ hydroxyl group does not exist on deoxyribose, so that’s one of the reasons that RNA can participate in more hydrogen bonding and create more stable three dimensional structures than DNA.
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