1. Chapter 12
Intracellular Compartments and Protein Sorting

2. How all of the 10,000~20,000 kinds of proteins go to the right destination?

3. Intracellular compartments in eukaryotic cells
The nucleus and the cytosol
All organelles that function in the secretory and endocytic pathways
Mitochondria
Plastids

4. Three fundamentally different ways of protein translocation

5. Two types of protein sorting signals

6. Nucleus Cytosol transport

7. Nuclear Cytosol transport
Signal sequences are rich in the positively charged amino acids (R, K)
Nuclear proteins can be transported through the pore complex in folded conformation
GTP is required (Ran GTPase)
Signal sequences often are not cleaved off after transport.

8. Nuclear pore complex
Containing FG-repeats serve as binding sites for the import receptors

9. Nuclear localization signals are rich in the positively charged amino acids

10. Nuclear import receptors

11. p.674

15. Protein transport into Mitochondria and Chloroplast

16. Mitochondria and chloroplast protein import
Signal sequences are amphipathic a helix consisted of positively charged and uncharged amino acids.
Proteins are transported through TOM, TIM and OXA complexes
ATP hydrolysis and H+ gradient drive mitochondrial and chloroplast protein import
Most of the time, signal sequences are cleaved after transport.

17. ATP hydrolysis and electrochemical H+ gradient are used to drive protein import into mitochondria

18. Signal sequences are amphipathic a helix

26. Thylakoid protein targeting

27. Perxisome protein targeting
Perxisomes are different from mitochondria and chloroplasts.

28. Peroxisome Functions Peroxisomes are sites for b oxidation.
In animals, b oxidation happens in both mitochondria and peroxisomes.
In yeast and plant cells, b oxidation happens in peroxisomes exclusively.
Animal peroxisome is important in catalyzing the first reactions of plasminogens synthesis.

29. plasminogen

30. Plant peroxisome
Peroxisomes in leaves are important for photorespiration.
Peroxisomes in germinating seed are essential for converting fatty acids into sugars (glyoxysome).

31. Peroxisome protein targeting
Signal sequences are either 3 amino acids (SKL) sequences located at the C terminus or some (uncharacterized) sequences near N terminus.
Import mechanisms are poorly understood.
At least 23 peroxins are involved in recognition and docking of peroxisomal proteins.
ATP is also required for peroxisome protein targeting.

32. ER protein targeting
SRP (signal-recognition particle) and SRP receptor guide proteins with ER signal sequence to ER.
Proteins are transferred across the ER membrane through a translocator Sec61 complex co-translationally.
Signal sequences has eight or more nonpolar amino acids at its center (p. 667).
Signal sequence is removed from most soluble proteins after translocation.

33. SRP (signal-recognition particle)
Large hydrophobic pocket lined by methionines

34. Protein synthesis is paused

35. Signal sequence in the growing polypeptide chain binds to a specific site inside the pore to open it.

36. Sec61 complex

43. Glycosylation N-linked oligosaccharide : ER
O-linked oligosaccharide : Golgi (mechanism unknown)

44. Glycosylation and protein folding
Oligosaccharyl transferase will transfer oligosaccharide to the target asparagine as soon as that amino acid has emerged into the ER lumen during protein translocation.

47. Nucleus
cytosol
ER lumen