During the transition to the open complex, the conformation of both the RNA polymerase and the DNA change. 

1) 90° bend in the DNA, which allows the template strand to approach the active site of the enzyme; 

2) strand opening of the promoter DNA between -11 and +3 with respect to the transcription start site; 

3) the promoter DNA scrunches into the active channel forming the transcription bubble; and 

4) closing of the jaws of the enzyme to encircle the section of the promoter downstream section of the transcription start site.

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#Id: 8754

#Unit 1. Molecules and their Interaction Relevant to Biology

The mammalian protein p53 also have both structured and unstructured segments. With its unstructured region at the carboxyl terminus four different proteins.

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#Unit 1. Molecules and their Interaction Relevant to Biology

Thermodynamic measurements indicate that native proteins are only marginally stable under physiological conditions. The free energy required to denature them is ∼0.4 kJ ∙ mol−1 per amino acid residue.

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#Unit 1. Molecules and their Interaction Relevant to Biology

Protein stability is the net balance of forces, which determine whether a protein will be in its native folded conformation or a denatured state.

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#Unit 1. Molecules and their Interaction Relevant to Biology

A fully folded 100-residue protein is only about 40 kJ ∙ mol−1 more stable than its unfolded form (for comparison, the energy required to break a typical hydrogen bond is ∼20 kJ ∙ mol−1).

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#Id: 8758

#Unit 1. Molecules and their Interaction Relevant to Biology

The combined hydrophobic and hydrophilic tendencies of individual amino acid residues in proteins can be expressed as hydropathies. The greater a side chain’s hydropathy, the more likely it is to occupy the interior of a protein.

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#Unit 1. Molecules and their Interaction Relevant to Biology

Hydrogen bonds, which are central features of protein structures, make only minor contributions to protein stability.