Chapter 10, Part 2: Structure of Prokaryotic and Eukaryotic Chromosomes
Prokaryotes
E. coli has around 3,000 genes on a single double-stranded circular molecule.
Once thought to be "naked" DNA when compared to the well dressed mitotic chromosomes of eukaryotes, prokaryotes in fact do wear clothes, albeit a loincloth. Simple basic amino acids are found to be associated with the bacterial chromosome.
The chromosome is also called a nucleoid; it lacks a membrane enclosure.
Supercoiling and associated basic proteins influence the folding of the DNA molecule .
Diploids have two complete sets of chromosomes, except for the sex chromosomes in one of the sexes.
Eukaryotes also have many more genes, eleven times as many. See Figure 9.17.
The genes are packaged onto more than one chromosome, 46 in the case of humans.
The uncompacted length of DNA of each E. coli is 1mm; humans have 2 meters of DNA in each cell.
How do you get 2 meters of DNA into a cell that is typically only 6 um wide and 2 um deep?
The same way you get a mile of fishing string on a real.
You wind it around something.
The chromosomes that you are familiar with from textbook photos and diagrams are actually mitotic or meiotic chromosomes.
During interphase, the chromosomes are not visible.
The DNA of each chromosome is a single linear molecule, which is consistent with what is referred to as the anemone model.
Some of the DNA make up the genes, most of the DNA does not.
Some evidence for the genes being on the chromosomes came from lamp brush chromosomes, found in amphibian eggs during the long pro phase. See Figure 9.20.
We already covered the evidence provided by "The Fly Guy" Morgans mapping studies.
More evidence came from autoradiographs of a Hydrocephaly DNA molecules, which showed assembly of RAN within the nucleus upon the DNA.
The DNA and associated proteins are called chromatin.
Some of the protein components have been characterized and are well understood.
The histones are. Other non-histone chromosomal proteins have been studied; many are yet to be discovered. See Figure 9.18.
Almost every discussion on histones includes a statement about how they are extremely conserved between plants and animals . This means there is little difference in their amino acid sequences found between those of distantly related species.
This fact is often used to support an argument about the importance of these proteins.
It really is more of a measurement of the necessity for maintaining a certain structure.
Being that DNA must wrap around these histones, and these histone core particles are composed of subunits that snap together (they are referred to as separate proteins in the literature, but are non-functional when separate from each other), it makes sense that little structural change would be tolerated.
Histones are rich in basic amino acids, which makes sense because DNA is an acid. See Figure 9.19.
Arginine, lysine and glutamine are such basic amino acids.
There are five major types of histones: H1, H2a, H2b, H3 and H4.
All but H1 are found in pairs together to form a core particle.
What is a nucleosome? The definition I prefer for nucleosome is "The arrangement of DNA and histone protein forming regular spherical structures in eukaryotic chromatin".
Therefor all but H1 form an octomeric association of proteins, which when DNA wraps around it, forms a nucleosome.
It looks like a bead on a string.
Three Levels of Packaging
Beads on a string: The DNA is wound around histones to form a nucleosome.
There is additional structure and packaging that is not yet understood.
There is some evidence for a central axis scaffolding protein complex, which is thought to be required for the amount of packaging found in the highly compact chromosomes like mitotic chromosomes.
Centromere: A Closer Look
This can be defined as a region of a chromosome where the spindle fibers attach during M phase.
Interestingly, this region does not replicate during S phase as does all the other regions of DNA of the chromosomes. See Figure 9.29.
In yeast, there is a specific sequence, which has been studied completely, that accommodates just one fiber (microtubule).
In more complex eukaryotes, there are repeated sequences, some which are important to spindle fiber attachment, while other sequences have no known function.
In yeast the centromeric region is called the CEN region. See Figure 9.30.
The functional or essential part is about 110 to 120 nucleotide base pairs in length.
Scientists have cloned these out of yeast and with cloned telomeric sequences and an origin of replication, they have made Yeast Artificial Chromosomes called YACs.
Telomeres: A Closer Look
We shall learn later that there is a real problem replicating the DNA at the end of the chromosomes, regardless.
Prokaryotes have avoided this issue by not having an end; their molecules are circular.
Eukaryotes have addressed this issue by using a specialized mechanism for replicating these ends.
Therefore, there are distinct ends to the chromosomes called telomeres.
In humans, it is a repeated sequence of 5'TTAGGC3'.
It might be that another characteristic of the telomeric end of the chromosome is to seal it, making degradation by enzymes less likely. See Figure 9.31.
Repetitive DNA in Eukaryotes
Another classification for DNA found in eukaryotic cells relates to the number of copies of a certain sequence that exist in a cell. (This is when that sequence exists at a rate that substantially exceeds what would be expected by random chance.)
The DNA will be classified as unique or single-copy DNA if there are 1 to 10 copies per genome;
moderately repetitive DNA if 10 to 100000 copies;
highly repetitive if more than 100000 copies.
A simple method for determining this uses a technique called rehybridization kinetics. See Figure 9.32 and 9.33.
In a nutshell, when you heat DNA it becomes single-stranded because the hydrogen bonds are too weak to hold the double-strands together.
When you cool it, it becomes double-stranded again. However, the rate it becomes double-stranded upon cooling depends on the concentration of the complementary fragments.
The concentration of highly repeated DNA would be far greater than the other two classes, and so would come together first.
A lot of the human genome is taken up by highly repetitive and moderately repetitive DNA; but why?
Some call it junk DNA. Some think some of it is a remnant of a viruses, now a transposons, that spread throughout the genome of one of our ancestors.
Some believe that the dinosaurs became extinct because of the accumulation of such junk DNA.
Maybe humans have a time-bomb ticking in their genomes. But, then again, it just might be time for "geneticists to the rescue!".