General Interview Questions - Protein Folding & Targeting

Where in the cell does protein synthesis and folding occur?

What are the physical factors that drive the folding of polypeptides?
Why are chaperones often necessary for protein folding?
Consider both a prokaryotic and a eukaryotic cell, where can a protein end up?
What specifies the location of a protein?
Probes: lots of vocabulary (see below) to draw out answers. 
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General importance
1. In aqueous solution, polypeptides will fold to minimize the interactions between their hydrophobic R-groups with water.
2. Generally this leads to a compact globular, rather than an extended, structure.
3. Generally, the native (functional) state of a protein is the state of lowest free energy.
4. Chaperones facilitate the process by which a polypeptide folds into its native state, primarily by unfolding incorrectly folded polypeptides.
5. Chaperones recognize incorrectly folded polypeptides by the fact that they have display hydrophobic R-groups on their surface.
6. Some chaperones catalyze proline-peptide bond isomerization or break cysteine disulfide bonds, thereby facilitating correct polypeptide folding.
7. Some chaperones can mediate the assembly of multipolypeptide proteins by binding and stabilizing polypeptides prior to their assembly with the 'final' partners.
8. The process of protein folding begins as the newly synthesized polypeptide emerges from the ribosomal tunnel; before that folding is sterically suppressed.
9. H-bonds that form between the -C=O and -NH groups of the peptide bond are responsible for the common secondary structural motifs of proteins, alpha-helices and beta-sheets.
10. In an alpha-helix, the R-groups of the amino acid residues point outward, perpendicular to the helix axis. In a beta-sheet, the R-groups alternate in pointing above and below the plane of the sheet.
11. The synthesis of all polypeptide begins in the cytoplasm. For many proteins that are inserted into the plasma (or internal cellular membranes), translation is regulated by specific signals.
12. Polypeptides and proteins are targeted to specific cellular compartments but signals encoded in their structure. In some cases these signals are cleaved away once the polypeptide reaches its target.

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