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Extra resources for Physics of biomolecules and cells
The total human genome is about 109 bp, requiring about 109 /200 nucleosomes. The total amount of DNA elastic energy stored in the nucleus is about 108 kB T . That is serious energy. In the ﬁgure below , you see what some of this energy does when you decondense the chromatin by chemical treatment: it causes a DNA explosion! F. Bruinsma: Physics of Protein-DNA Interaction “bruinsma” 2002/8/8 page 43 ✐ 43 Fig. 21. Decondensed Chromatin (from Ref. ). This bending energy cost must be compensated by some form of attractive interaction between the core and the DNA.
The mRNA strands are exported through gateways in the nuclear membrane called “nuclear pores”. Unlike bacteria, only a certain part of the genome is accessible for transcription, depending on cell type. Diﬀerentiation of eukaryotic cells takes place by the progressive “silencing” of certain genes and enhanced expression of other genes. After bacterial gene expression had been clariﬁed, it was expected that gene expression of animal and plant cells quickly would be understood as well, so it was a great disappointment when it was found that eukaryotic gene transcription was far more complex.
There is a C2 rotation symmetry. This symmetry is a characteristic of many prokaryote repressor proteins. The DNA operator sequence has a corresponding (approximate) rotation symmetry. Simple repressor proteins like cro address the DNA with “reading heads”. A reading head is an α-helix that can be inserted into the major or minor groove of the DNA double helix (usually the major groove). The second panel is a cartoon of the cro repressor/DNA complex showing the α-helices of the protein. There are two reading heads ✐ ✐ ✐ ✐ ✐ ✐ ✐ 22 “bruinsma” 2002/8/8 page 22 ✐ Physics of Bio-Molecules and Cells Fig.