Basic Properties of DNA Secondary Structure At this point we now have a good picture of the chemical structure of the DNA molecule, now we need to begin placing it in the context of the cell. A typical eukaryotic chromosome contains from 1 to 20 cm of DNA. However, during metaphase of mitosis and meiosis, this DNA is packaged in a chromosome with a length of only 1 to 10 um. How is this amazing density achieved inside the cell? Highly dense secondary structure: eukaryotic chromosomal DNA of length 1-20cm is packed into chromosome of length 1 to 10um. DNA is packed into a dense and regular struture called chromatin. There are three levels of packaging: nucleosomes, 30nm fibers, and loops of fibers. Highly compact structure of packaged DNA inhibits transcription, DNA must be unpacked in order to be expressed.

Chromatin DNA in the cell exists packed into a dense and regular structure called chromatin. Chromatin is composed of DNA, proteins, and a small amount of RNA. The proteins found in chromatin largely consist of histones, a basic protein which is positively charged at neutral pH, and nonhistone chromosomal proteins which are largely acidic at neutral pH. Chromatin is the name for the in vivo form of the genetic material. Chromatin is composed of DNA, proteins, and a small amount of RNA. Histones are the most important type of protein found associated with chromatin.

Histones and the Nucleosome

Nucleosome Structure Histones have been highly conserved in all eukaryotes. There are five major histone types, called H1, H2a, H2b, H3, and H4, and which exist in specific molar ratios within the chromatin. Histones bind together with the DNA to form the basic structural subunit of chromatin, small ellipsoidal beads called nucleosomes which are around 11nm in diameter and 6nm high. Each nucleosome contains 146 nucleotide pairs which wrap around the histon protein complex 1 and 3/4 turns. The nucleosome complexes give the DNA molecula a packaging ratio of 6. Histones are highly conserved structural proteins found in all eukaryotes Histone modifications can affect gene expression. Histones bind with DNA to form the basic subunti of DNA secondary structure, the nucleosome.

Further Packaging: 30nm Fibers and Loops Secondary packaging: nucleosome beads coil into a helical structure called the 30nm fiber. Tertiary packaging: 30nm fibers are further organized into loop, scaffolds, and domains. Beyond the nucleosome, there are two more levels of structural packaging. The second level of packing is the coiling of the nucleosome beads into a helical structure called the 30 nm fiber that is found in both interphase chromatin and mitotic chromosomes. This structure increases the packing ratio to about 40. The final packaging occurs when the fiber is organized in loops, scaffolds and domains that give a final packing ratio of about 1000 in interphase chromosomes and about 10,000 in mitotic chromosomes. One important note is that DNA is not always packed into the super-dense chromosome structures evident during mitotic and meiotic replication. During interphase, or the general not-currently-reproducing phase of the cell where most of a cell's work is done, the chromatin, while still highly dense, is about 1/10 as dense as during cellular replication. This is important because it is believed that the highly-dense chromatic structure of DNA sterically inhibits transcription and thus gene expression. In order for genes to be expressed the chromatin structure must be relaxed so that the transcriptional proteins can gain access to the DNA molecule.