Packaging of DNA: Study with Video Lessons, Practice Problems & Examples

DNA packaging is essential for fitting approximately 2 meters of DNA into a cell, typically 5 to 8 micrometers in diameter. The primary structure is the nucleosome, consisting of DNA wrapped around histone proteins, forming a 10-nanometer fiber. This further condenses into a 30-nanometer chromatin fiber and DNA looping, which organizes DNA into larger structures. Ultimately, chromosomes, highly condensed forms of chromatin, facilitate cell division. Key features include centromeres, kinetochores, and telomeres, which protect DNA integrity and assist in chromosome movement during mitosis and meiosis.

DNA Packaging Overview

Hi, in this video, we're going to be talking about DNA packaging. So why do we need to talk about DNA packaging and why does this happen? Well, it does it because the packaging of DNA is necessary in order to fit the DNA into or within the confines of the cell. So there's so much DNA; each cell contains around two meters of it. And that's a huge problem because our cells are considerably smaller than two meters. They're usually an average of 5 to 8 micrometers in diameter. So how do you actually fit two meters of DNA into such a very small amount? Well, you have to package it, and so there are a few different packaging levels that we're going to talk about. Here below, you can see the nucleosome which is here, the 30 nanometer fiber which is here, some looping which is here, and then finally the chromosome which is here, which is number five. And so we're going to go through each one of these packaging levels in order to determine how they form and what they actually do to package all of the DNA into a cell. So let's move on.

Nucleosome

So the first packaging level that we're going to talk about is the nuclear zone. The nuclear zone consists of DNA and histone proteins. It was discovered by Dean, who wished you wish and labor one. I'm not even going to attempt it. You don't need to know these names. Are you really going to be tested on them? Just sort of know that these people exist. Somebody discovered it. What they did was a really interesting experiment where they took DNA isolated from cells and they put in enzymes that chop up DNA. What they found is that the DNA wasn't just chopped entirely to pieces, but instead it was chopped into these sort of repetitive 200 base pair fragments. So, they were like, well, why is the DNA being chopped into 200 base pair fragments when, if it was entirely exposed, it should just be cut all to pieces. And so they hypothesized that the DNA was cut into 200 base pair fragments because it was being protected by something, and what it's being protected by are histone proteins.

What are histone proteins? They are a major class of proteins that are bound to DNA to form a nuclear zone. There are actually five classes of these proteins. They're not given very creative names. Here they are: H1, H2A, H2B, H3, H4. They are classified based on the ratio of lysine to arginine present on the protein. So, we have DNA, we have these five classes of histone proteins. How do these all come together to create a nucleosome?

How they do this is that there are eight histone proteins per nucleosome core. You have two H2A and two H2B, and they are bound together to form dimers. You also have another pair of two H3s and two H4s that are combined to form a nucleosome core. So there are eight proteins here. You have your four here because you have two pairs, and your four here which you have two pairs. And because these are positively charged proteins because of their lysine and arginine, the negatively charged DNA easily wraps around them. Now you have this setup so that takes care of four of the classes but obviously not the fifth. So, the fifth class is an H1 histone and that acts as a linker histone connecting them together. Each one of these nucleosomes is about 10 nanometers long. In a nucleosome, there's going to be 147 base pairs of DNA wrapped around it, and it'll wrap 1.67 times around the histone core. Like I said, you don't need to know those numbers, just sort of if you're thinking about what the nucleosome is, how big it is? Well, it's 147 base pairs. If we're going to look at the nucleosome here, you have your DNA, this is your double helix, and you can see that the DNA, which is here in red is easily wrapping around this nucleosome core. So this is going to have your eight histone proteins. It's not really shown here. But if I were to draw the H1 histone, which is a linker, it would be kind of in the middle here, working to link these nucleosomes which is each one of these is a nucleosome, together. So this is the very first packaging level of DNA, from the double helix to the nucleosome. And then you get this sort of nucleosome string. So now, let's move on.

Complex DNA Packaging

Okay. So now, I'm going to talk about the next two levels of DNA packaging, which are the chromatin fiber and DNA looping. You'll see here that I don't have a lot of information in this section, especially compared to the previous section on the nucleosome. The reason is that not much is known about these. We know they exist. We have some images of them, but how they form and what are all of these components and why they form this way is not really known. So, I'm just going to give you the very basic information that is known and show you an image of what this looks like.

The first thing is the formation of the chromatin fiber. We have our nucleosomes; remember, those are kind of the "beads on a string." They are packaged into what facilitates this 30nm fiber creation, which is the H1 histone protein. Remember, this is the linker histone protein. It connects adjacent nucleosomes and is required for the 30nm fiber formation. These are generally packaged in zigzags around a double helix. So if I were to show you this image, you're going to be looking at the chromatin fiber here, 3a and 3b. What you can see is that there is a sort of zigzag formation. You can't really draw on it, but if you were to look at this, you're going to see these zigzag formations of these nucleosomes connecting together. This forms this kind of snake-like fiber that is eventually formed into 30nm long fibers.

Now, if we're moving on to DNA looping, that's going to be your images over here. Let me back out of the way so you can see it better. Each loop contains around 50,000 to 100,000 base pairs. We're dealing with much larger structures now. These structures are maintained by non-histone proteins, or proteins that are not histones, that attach the DNA to this protein scaffold that allows them to form these really unique structures. I mean, look at this: this structure here, and this one here. These are kind of weird, and we actually don't have good images of what this looks like in real life. So, the models, you can imagine, look very weird, but it also looks weird inside the cell. This DNA looping condenses the DNA even further than 30nm, so that it can be packaged into the cell. So, now, let's move on.

Chromosomes

Hello, everyone. In this lesson, we are going to be talking about DNA packaging, specifically how chromosomes are made and how we utilize chromosomes in our cells. Now, it's obvious that DNA is gigantic. These huge strings of nucleic acids, and we're going to have to package our DNA in some form, so it's just not crazy all over the place. So we all kind of understand what chromosomes are, but here we're going to go into a little bit more detail. So chromosomes are Chromatin that is packaged in a particular way. So remember, chromatin, we learned, is going to be the DNA, nucleic acids, all those bases, plus the proteins associated with them, things like nucleosomes and histones, and It's going to include RNA that is also associated with the DNA. This is going to be chromatin. And chromatin is going to be packed into the form of a chromosome, and this is going to have thousands and thousands of genes in each chromosome for that particular organism. And chromosomes are going to exist in 2 unique states, 2 distinct states. And these are going to be the interphase Chromosome State and the metaphase chromosome state. So basically, the differences between these two states is going to be the density of compaction. How compacted, how tightly wound is the DNA? Is it loose? Is it tightly wound? That's going to be the difference here. So interphase chromosomes are referring to when the cell is in interphase, and this means that it's not actively dividing at the moment. So these are actually going to be less condensed DNA threads, less condensed chromatin. And they're going to occupy the nucleus and it's going to be kind of just like loose threading of the DNA. It's not going to be terribly condensed. This is one of the loosest forms that DNA is in. And because it's so loose, you can't really see interphase chromosomes under the microscope. They really can't see where individual chromosomes are whatsoever. So it's very loose and it's not condensed at all. Now, whenever the cell decides that it's going to go into cellular division, be it mitosis or meiosis, then we're going to get metaphase chromosomes. And metaphase chromosomes are created from the interphase chromosomes and basically just condensing them down as much as we can. So metaphase chromosomes are going to be more condensed. These are going to be the stereotypical x structures that you guys can will see down here in just a second. These are going to be the stereotypical x structures that we think of whenever we think of chromosomes, and they can be seen under a microscope during cellular division. These are very highly condensed forms of chromosomes. Now, why would we want them to be very highly condensed? Well, remember, I said this is happening when the cell is dividing And if the DNA is very tightly condensed into its own chromosomes, it's much easier to move. It's much easier to separate the chromosomes than if they're all tangled and loose together in the interphase chromosome state. So that's why your cells greatly condense down the chromosomes into that nice tightly packaged metaphase chromosome. Now, chromosomes are going to have some very important structural features that we're going to talk about as well. So chromosomes contain centromeres, kinetochores, and telomeres in addition to all of the genes that are in your chromosomes. So first, we're going to talk about a centromere. The centromere is going to be the region where two sister chromatids meet, and it's going to hold the sister chromatids together. Centromeres are specialized regions and generally consist of large sequences of repetitive satellite DNA. So it's very repetitive in that area and its main job is just to allow for those sister chromatids to attach to one another and it allows kinetochore proteins to attach. So, what is a kinetochore? The kinetochore is going to be a protein structure assembled on the centromere and the mitotic spindles or the microtubules attach to the kinetochore. I know it's a lot of layers here, but they're all very important. These are very important structures for cellular division because they allow those chromatids to be separated and they allow chromosomes to be moved around. Now, we also have another special structure called the telomere. The telomere is utilized to ensure chromosomal integrity. Telomeres are repetitive DNA sequences, but they're at the end of a chromosome, and they're utilized to protect the chromosome from degradation, protect it from deteriorating. Because every time a chromosome replicates, some of the ends of the chromosome are lost whenever the chromosome is replicated. So we put repetitive kind of nonsense DNA at ends of our chromosomes that it doesn't matter if it gets lost whenever the cell replicates. This is the DNA most highly repeated in telomeres. Over time, the job of the telomere is to protect the coding DNA, the important DNA. Now, let's go down and we're going to talk about Karyotypes. Karyotypes, this is an example of a karyotype here. A karyotype is an ordered display of a full set of an organism's chromosomes. And karyotypes are commonly done for humans and you're going to see that in diploid organisms like humans, this is a human karyotype here. So this is a Human Karyotype, you're going to have homologous pairs. So we are diploid organisms, which means we have 2 sets of chromosomes, which I'm just going to write chromosomes. We have 2 sets of chromosomes so there are 2 of each chromosome and these are called homologous pairs. So you're going to find homologous pairs in all of the chromosomes except for the male Y chromosome, which does not have a homologous pair. Females, the X chromosomes do have homologous pairs, but in males the Y chromosome does not have a homologous pair. Other than that, you're going to see all these paired chromosomes as you can see in this image. So remember that human beings have 23 unique chromosomes, but 46 in total. And you can see all 46 here, but they're paired up because there's 2 of each chromosome or 23 unique different chromosomes. Okay, everyone. I hope that was helpful. Now, let's go on to our next topic.

Conservation of DNA Packaging

Okay. So now we're going to talk about the conservation of DNA packaging. We have all these really complex ways that DNA is packaged in order to fit it into the cell. However, that doesn't necessarily mean that every cell does it the same way. In organisms throughout the world, the packaging of DNA is highly conserved. So, it is done very similarly across organisms. How does this happen? This happens because histone proteins are extremely conserved. For instance, you don't necessarily need to know this number, but the H3 histone protein of sea urchin and calf thymus differs by only one amino acid. So, you can imagine the differences that exist between a sea urchin and a calf thymus are huge, but the H3 histone protein has only changed by one amino acid.

Now, it's not to say that there are only these five histone proteins. There are actually histone variants that we're going to talk about in future lessons, and they are usually extremely important but have only one function. So, as the H2A, H2B, H3, H4, H1 histamine that we talked about in the formation of the nucleosome are super conserved. However, there are variants that have popped up. Instead of forming the nucleosome, they actually have very unique and specific functions in different organisms.

One example of this is the centromeric H3. This is a histone protein that exists only at centromeres and has a very specific function in assembling kinetochore proteins.

Just to take a second to look at some of the conservation, here you have different animals on the side. This is looking at the histone protein H1. You can see that if you look at the amino acid sequence, which is what this is, amino acid sequence. Sometimes they refer to amino acids as amino acid residues. You can see that looking through all these organisms, it's extremely similar. There are some variations, but even within these variations, most of them are the same. Therefore, they're extremely conserved proteins, which makes DNA packaging extremely conserved as well. So now, let's move on.

Unusual Chromatin Structures

Okay. So in this video, we're going to be talking about unusual chromosome structures. I've talked to you a lot about the packaging of DNA and how that's normally done in organisms. But in a few organisms, there are unique chromosomes that I'm just going to mention to you just so you know that not everything is perfect in the world of cell biology. Certain organisms contain unique eukaryotic chromosome structures. One of these is going to be called polytene chromosomes, and they're found in Drosophila, which, if you remember, are fruit flies. How these form is instead of separating during division, which is what happens during most forms of division, they actually link together. So, kind of the exact opposite of what should happen during division. When this happens, they actually have this unique banding that you can just visualize under a scope. We don't really know what causes this banding, why some of them are darker and some of them lighter. But it's thought that most of this banding, the darker and lighter, is caused by different condensations. So the darker the band, the more condensed. We can see an example of polytene chromosomes here. These are these sort of very long chromosomes that you can see that have been linked together, and they have these bands, which you can actually visualize some up close, and they think that the darker version is more condensed DNA whereas the lighter portion of it is less condensed. This is one sort of unusual chromosome structure that occurs on Earth.

Another structure is called a lampbrush chromosome, and this is generally found in various oocytes or ovarian cells, but not really observed in mammals, just sort of other types of animal ovarian cells. These are interesting because they are the largest chromosomes known. So, these chromosomes, you don't actually need special, really intense microscopes to see; you can just see them with a normal light microscope that you probably have in your biology labs. So that's kind of a unique feature. And so, those are polytene and lampbrush, two sort of unique chromosome structures that exist and that are important to know about in the study of cell biology. So now let's move on.

Which of the following histone proteins do not form dimers that make up the nucleosome core?

• A. H2A
• B. H2B
• C. H3
• D. H4
• E. H1

How many histone proteins are found within the nucleosome core?

• A. 2
• B. 4
• C. 8
• D. 9

Interphase chromosomes are more condensed than other forms of chromosomes?

• A. True
• B. False

Here’s what students ask on this topic:

Why is DNA packaging necessary in cells?

DNA packaging is essential because each cell contains approximately 2 meters of DNA, which must fit into a cell typically 5 to 8 micrometers in diameter. Without efficient packaging, the DNA would not fit within the confines of the cell. The packaging process involves multiple levels, starting with the nucleosome, where DNA wraps around histone proteins, forming a 10-nanometer fiber. This further condenses into a 30-nanometer chromatin fiber and DNA looping, which organizes DNA into larger structures. Ultimately, chromosomes, highly condensed forms of chromatin, facilitate cell division and ensure the DNA is compact and organized within the cell.

What are nucleosomes and how do they contribute to DNA packaging?

Nucleosomes are the fundamental units of DNA packaging, consisting of DNA wrapped around histone proteins. Each nucleosome contains eight histone proteins (two each of H2A, H2B, H3, and H4) forming a core, around which 147 base pairs of DNA wrap 1.67 times. The H1 histone acts as a linker, connecting adjacent nucleosomes. This structure forms a 10-nanometer fiber, resembling beads on a string, which further condenses into higher-order structures. Nucleosomes play a crucial role in compacting DNA to fit within the cell nucleus and regulate gene expression by controlling DNA accessibility.

What is the difference between interphase and metaphase chromosomes?

Interphase chromosomes exist when the cell is not actively dividing and are less condensed, forming loose DNA threads within the nucleus. This loose structure makes individual chromosomes difficult to see under a microscope. In contrast, metaphase chromosomes are highly condensed and form the stereotypical X-shaped structures visible during cell division (mitosis or meiosis). This high level of condensation facilitates the efficient separation and movement of chromosomes during cell division, ensuring accurate distribution of genetic material to daughter cells.

How do histone proteins contribute to the conservation of DNA packaging across different organisms?

Histone proteins are highly conserved across different organisms, meaning their structure and function have remained relatively unchanged through evolution. For example, the H3 histone protein of sea urchins and calf thymus differs by only one amino acid. This conservation ensures that the fundamental mechanism of DNA packaging is similar across diverse species. Histone variants also exist, performing specific functions in different organisms, but the core histones (H2A, H2B, H3, H4, and H1) involved in nucleosome formation are remarkably conserved, maintaining the integrity and efficiency of DNA packaging.

What are telomeres and what role do they play in chromosome structure?

Telomeres are repetitive DNA sequences located at the ends of linear chromosomes. They protect the chromosome from degradation and prevent the loss of important genetic information during DNA replication. Each time a cell divides, a small portion of the telomere is lost, but this does not affect the coding regions of the DNA. Telomeres ensure chromosomal integrity and stability, playing a crucial role in cellular aging and the prevention of genomic instability, which can lead to diseases such as cancer.