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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#Unit 3. Fundamental Processes

Most mRNAs decay stochastically (like the decay of radioactive isotopes), and as a result mRNA stability is usually expressed as a half- life (t½).

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#Unit 3. Fundamental Processes

Method for determining mRNA half-lives.

RNA polymerase II transcription is shut down, either by a drug or a temperature shift in strains with a temperature sensitive mutation in a Pol II gene. The levels of specific mRNAs are determined by northern blot or RT-PCR at various times following shutdown.

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#Unit 3. Fundamental Processes

In E. coli the typical mRNA half-life is about 3 minutes, but half-lives of individual mRNAs may be as short as 20 seconds or as long as 90 minutes.  In budding yeast, mRNA half-lives range from 3 to 100 minutes, whereas in metazoans, half-lives range from minutes to hours, and in rare cases, even days.

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#Unit 3. Fundamental Processes

Degradation of bacterial mRNAs is initiated by removal of a pyrophosphate from the 5’ terminus. The monophosphorylated form stimulates the catalytic activity of an endonuclease RNase E

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#Unit 3. Fundamental Processes

PNPase a 3’ to 5’ exonucleases in E. coli, are unable to progress through double-stranded regions. Thus, the stem-loop structure at the 3’ end of many bacterial mRNAs protects the mRNA from direct 3’ attack.

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#Unit 3. Fundamental Processes

RNase E and PNPase, along with a helicase and another accessory enzyme, form a multiprotein complex called the degradosome.