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By Dudoit S., Speed T. P.

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17 Structure of a typical terminator. The regions marked with arrows are complementary, and so can anneal together resulting in the formation of a stem-loop structure. more stable than the DNA–DNA pairing. The size of the bubble is limited, however, by topological constraints. The helix has to be unwound to some extent to allow the strands to separate, which causes stress in the molecule, since the two strands can only be separated by increasing the winding on either side. The larger the unwound region, the greater the stress.

14 Mechanism of excision repair. Endonuclease cleavage removes a portion of the damaged strand. The gap is filled in by DNA polymerase I; the 5 to 3 exonuclease action of DNA polymerase I allows it to remove more DNA and replace it. Finally, the sugar-phosphate backbone is resealed by DNA ligase. 14. The process is initiated by an endonuclease (a complex enzyme, coded for by genes known as uvrA, uvrB and uvrC, since mutations in these genes cause reduced ultraviolet resistance). This enzyme cuts the DNA strand on either side of the damage, which exposes a 3 OH group; this can be used as a primer by DNA polymerase I to replace the short region of DNA between the nicked sites (15–20 bases long).

The formation of a biologically active product involves several further steps. First of all, the protein has to fold correctly. There are three conformational levels, in addition to the primary structure (which is the amino acid sequence itself). 23), which are stabilized by non-covalent interactions (such as hydrogen bonds). Different regions of the protein will adopt different secondary structures, separated by turns or less defined loops. 24). This conformation is stabilized by non-covalent interactions, and also by covalent disulphide bridges between cysteine residues.

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