Closed complexes

The roles of the Pharmaceutical Industry and the FDA, and the relationships between them, have evolved considerably since the 1962 effectiveness amendments to the FD C Act, and today the two parties are engaged in a close, complex, generally supportive - if sometimes fractious -relationship. There is no doubt that the achievements of these two parties, both individually and together, have been spectacular - even historic -as their effectiveness and safety standards have been embraced by the whole world. Indeed, these standards are now recognised as a landmark in post-enlightenment science, as well as a forerunner of the current philosophy of evidence-based medicine. 

Fig. 1.27. Two-step mechanism of transcription initiation. The binding of a procaryotic RNA polymerase to its promoter can be subdivided into two steps. In the first step the RNA polymerase binds to the closed promoter with low affinity. The closed complex isomerizes in a second step to an open complex in which the promoter is partially unwound. Detailed consideration reveals that further steps can be distinguished. These are not shown here for simplicity reasons.

The pathway of transcription initiation is becoming much better defined (Fig. 26-6a). It consists of two major parts, binding and initiation, each with multiple steps. First, the polymerase binds to the promoter, forming, in succession, a closed complex (in which the bound DNA is intact) and an open complex (in which the bound DNA is intact and partially unwound near the... 

Diverse Functions of TFIIH In eukaryotes, the repair of damaged DNA (see Table 25-5) is more efficient within genes that are actively being transcribed than for other damaged DNA, and the template strand is repaired somewhat more efficiently than the nontemplate strand. These remarkable observations are explained by the alternative roles of the TFIIH subunits. Not only does TFIIH participate in the formation of the closed complex during assembly of a transcription complex (as described above), but some of its subunits are also essential components of the separate nucleotide-excision repair complex (see Fig. 25-24). 

A satisfactory mathematical model for initiation of transcription supposes that the polymerase and DNA bind reversibly to form a complex with formation constant Kf. This initial specific polymerase-promoter complex is referred to as a closed complex because it is thought that the bases in the DNA chain are all still paired. It is postulated that in a rate-determining step the closed complex is converted into an open complex, which is ready to initiate mRNA synthesis (Eq. 28-1).26 67 In the open complex the hydrogen bonds... 

Self-Assembly of Closed Complexes by Hydrogen Bonding... 

As a DNA polymerase incorporates a dNTP, a conformational change from an open to a closed complex occurs. The importance of H-bonding interactions and geometric shape of the nucleobases has been examined for the stability of the closed form of the polymerase. This has been studied using the incorporation of the TTP isostere derived from difluorotoluene opposite dA, and the 5 -C-nucleoside triphosphate derivative of pyrene opposite an abasic site. 

In a first approximation, the formation of a transcription-competent complex can be described according to a two-step mechanism (Fig. 1.17). The initial binding of the RNA polymerase to the promotor leads to the formation of a closed complex in which the RNA polymerase is only weaWy bound. Isomerization of the closed complex transforms it intoa transcription-competent open state. In the open complex, the RNA polymerase is tightly bound, and the DNA is partially unwound at the transcription start site. 

Polymerase binds to promoter sequence In duplex DNA. "Closed complex"... 

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