Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 432


Spring 2009

Lecture Notes: 2 March

© R. Paselk 2006


DNA Structure and Folding

Chromosomes, etc.

Let's look at how DNA is arranged in cells and viral particles. One of the problems facing organisms is how to pack the very long DNA molecule into the small volume of a cell.

Let's start with the simpler system of the T-even phages as represented by T2 in text Figure 24-1 (p 923) in the text. Note the huge amount of DNA which has been relaesed from the polyhedral head. For the related T4 phage the 168,889 bp DNA molecule is 60,800 nm in length and packs into a 210 nm long polyhedral head.

Similarly impressive packing is seen in E. coli which has a 1.7 mm long, 4,639,221 bp circular chromosome packaged into a "corner" of the 0.002 mm long bacterial cell. (micrograph, text Figure 24-4, p 926 and diagrammatically, text Figure 24-3, p 926-7)

Another even more complex packing is seen in eukaryote cells. (chromosome micrograph, text Figure 24-5a, p 927) As an example human cells have a total length of DNA per chromosome set (chromosome micrograph, text Figure 24-5b, p 927) of about 2 m (3.2 x 109 bp), giving a total length of DNA in an adult of about 2 x 1014 m (0.02 light years).

So what's in all of this DNA? Let's look at Table 24-2 in the text (p 928). In particular we want to note the relationship of the number of "genes" vs. the amount of DNA.

Note that in going from E. coli and Homo sapiens the number of base pairs is increased by a factor of nearly 700 while the number of genes increases only by a factor of 7-8.

So what is different?

The Supercoiling of DNA

DNA in vivo is supercoiled in various ways. Supercoiling allows DNA to take up a more compact form, and is a necessary consequence of replication and transcription.

So what is supercoiling? Supercoiling means that the helix is itself wrapped into a higher level coil, it is super-twisted or has super-helicity.

We will discuss supercoiling in terms of topology, the study of properties of geometric forms, and the transformations that leave them invarient in certain properties (e.g. a tea cup and a donut are topologically the same in that they have a single surface penetrated by a single hole).

Super helix topology. The topology of the DNA helix/supehelix can be described by a simple equation:

L = T + W


So let's look at DNA in terms of topology. The best information is from viruses and plasmids - both are small enough to work with in whole form.

Bacteria, plasmids, mitochondria and viruses usually have circular DNA, or in the case of viruses, the DNA becomes circularized after injection into the host.

Pathway Diagrams

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Last modified 2 March 2009