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Chapter 31: Problem 7

(Integrates with Chapter \(30 .\) ) In what ways are the mechanisms of action of EF-Tu/EF-Ts and DnaK/GrpE similar? What mechanistic functions do the ribosome A-site and DnaJ have in common?

Short Answer

Expert verified
EF-Tu/EF-Ts and DnaK/GrpE share a similar cyclical mechanism of action which is dependent on the hydrolysis of GTP or ATP for the binding and release of molecules. The ribosome A-site and DnaJ act as 'gatekeepers', ensuring the correct and accurate synthesis and folding of proteins.

Step by step solution

01

Understanding the function of EF-Tu/EF-Ts and DnaK/GrpE

To start with, EF-Tu, or elongation factor thermo unstable, coupled with EF-Ts, or elongation factor thermo stable, are responsible for the accurate selection and binding of the aminoacyl-tRNA to the ribosome during protein synthesis. DnaK and its co-chaperone GrpE, on the other hand, assist in protein folding and help stabilise proteins under stressful conditions, such as heat shock.
02

Comparing the mechanisms of action

Despite their distinct roles, EF-Tu/EF-Ts and DnaK/GrpE share a similar mechanism of action. Both interactions depend on cycles of binding and release using energy derived from the hydrolysis of GTP (for EF-Tu/EF-Ts) or ATP (for DnaK/GrpE). EF-Tu, after the hydrolysis of GTP, is released from the aminoacyl-tRNA and replaced by EF-Ts. Similarly, DnaK, upon the hydrolysis of ATP, releases the protein substrate, with GrpE facilitating the exchange of ADP to ATP, thus resetting the cycle.
03

Understanding the function of ribosome A-site and DnaJ

The ribosome A-site, or the aminoacyl site, is where each new amino acid is added during protein synthesis. DnaJ acts as a co-chaperone to DnaK and binds to unfolded or partially folded proteins to target them for folding or refolding by DnaK.
04

Comparing the mechanistic functions

Both the ribosome A-site and DnaJ have similar functions in ensuring the accuracy and correctness of protein synthesis. They both act as 'gatekeepers', with the A-site monitoring the accuracy of the codon-anticodon pairing of the tRNA and mRNA, and DnaJ recognising and binding to misfolded proteins to prevent the formation of incorrect structures.

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Most popular questions from this chapter

Not only is the Sec61p translocon complex essential for translocation of proteins into the ER lumen, it also mediates the incorporation of integral membrane proteins into the ER membrane. The mechanism for integration is triggered by stop-transfer signals that cause a pause in translocation. Figure 31.5 shows the translocon as a closed cylinder spanning the membrane. Suggest a mechanism for lateral transfer of an integral membrane protein from the protein-conducting channel of the translocon into the hydrophobic phase of the ER membrane.

Many multidomain proteins apparently do not require chaperones to attain the fully folded conformations. Suggest a rational scenario for chaperonc- independent folding of such proteins.

Fluorescence resonance energy transfer (FRET) is a spectroscopic technique that can be used to provide certain details of the conformation of biomolecules. Look up FRET on the Web or in an introductory text on FRET uses in biochemistry, and explain how FRET could be used to observe conformational changes in proteins bound to chaperonins such as GroEL. A good article on FRET in protein folding and dynamics can be found here: Haas, E., 2005. The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements. ChemPhysChem \(6: 858-870 .\) Studies of GroEL using FRET analysis include the following: Sharma, S., et al., 2008. Monitoring protein conformation along the pathway of chaperonin-assisted folding. Cell \(133: 142-153\); and \(\mathrm{Lin}, \mathrm{Z},\) et al. \(, 2008 .\) GroEL stimulates protein folding through forced unfolding. Nature Structural and Molecular Biology \(15: 303-311\)

(Integrates with Chapter 30 .) Human rhodanese \((33 \mathrm{kD})\) consists of 296 amino acid residues. Approximately how many ATP equivalents are consumed in the synthesis of the rhodanese polypeptide chain from its constituent amino acids and the folding of this chain into an active tertiary structure?

A common post-translational modification is removal of the universal N-terminal methionine in many proteins by Met-aminopeptidase. How might Met removal affect the half-life of the protein?
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