1. Chapter 12
Intracellular Compartments and Protein Sorting
張學偉 助理教授

2. The compartmentalization of cells

3. All eucaryotic cells have the same basic set of membrane-enclosed organelles

4. The major intracellular compartments of an animal cells.
Cytoplasma = cytosol + cytoplasmic organelles

8. The topological relationships of membrane-enclosed organelles can be interpreted in terms of their evolutionary origins

13. Protein can move between compartments in different ways

14. Sorting signal
by signal sequences

15. Vesical transport

16. Signal sequences and signal patches direct proteins to the correct cellular address

17. Sorting signal (signal sequences) recognize by sorting receptors
Cut by signal peptidases
Sorting signal (signal sequences) recognize by sorting receptors

18. Red +
Green  -
Yellow Hydrophobic
Blue  hydroxylated
N-terminal signal
C-terminal signal

22. The transport of molecules between the nucleus and the cytosol

24. Nuclear pore complexes perforate the nuclear envelope

25. Composed by more than 50 different proteins
called nucleoporins.

28. 26nm
15nm
9nm
size

29. Nuclear localization signals (NLS) direct nuclear proteins to the nucleus

31. Nuclear pore transport (large aqueous pore) is
Colloidal gold spheres coated
with peptides containing NLS
Nuclear pore transport
(large aqueous pore) is
fundmental different from
organelle transport
(lipid bilayer).

32. Nuclear import receptors bind nuclear localization signals and nucleoporins

33. FG-repeat (Phe-Gly) serve as binding sites for the import receptors.
Nuclear import do not always
bind to nuclear proteins directly.
Soluble
cytosolic
protein
FG-repeat (Phe-Gly) serve as binding sites for the import receptors.

34. Nuclear export works like nuclear import, but in reverse
Nuclear export signals & nuclear export receptor
& nuclear transport receptor (karypherins)
tRNA or 5S RNA: nuclei cytosol
NLS-particle: cytosol nuclei

35. The Ran GTPase drives directional transport through nuclear pore complexes

36. Ran = GTPase
GAP = GTPase-activing protein
GEF = Guanine exchange factor

37. Bidirectional model

40. Transport between the nucleus and cytosol can be regulated by controlling access to the transport machinery
Always in & out, shuttling

41. Ventral side
Dorsol protein
The control fly embryo development by nuclear transport

43. The nucleus envelope is disassembled during mitosis

44. Lamina (whole structure) & lamins (protein subunit)

46. The transport of proteins into mitochondria and chloroplasts

48. Newly mito & chloropl are produced by the growth of
preexisting organelle.
Their growth depends mainly on the cytosolic protein import

49. Translocation into the mitochondrial matrix depends on a signal sequence and protein translocators

50. Red = +
Yellow = nonpolar
On different side
Amphipathic a helix

51. translocase Transport to matrix Insert to inner memb. For protein syn
Require for import all
nucleus-encoded
mitochondria protein
Transport to matrix
Insert to inner memb.
For protein syn
In mito

52. Interacting protein: eg Charperone protein  hsp70 family
All Interacting protein help to prevent aggregation before
engaging with TOM complex in outer mito membrane.
Mitchondrial precursor proteins are imported as unfolded polypeptide chains

53. Mitochondrial precursor proteins are imported into the matrix at contact sites that join the inner and outer membranes

55. Protein import by mitochondria

56. ATP hydrolysis and a H+ gradient are used to drive protein import into mitochondria

57. Charperone protein also function as translocator
Freely permeable to ions and metabolites
but not to most protein
pulling
Charperone protein also function as translocator

58. Repeated cycles of ATP hydrolysis by mitochondrial Hsp70 complete the import process.
Hsp 60 provide chamber for unfolded polypeptide chain
facilitates folding (chapter 6)

61. Protein transport into the inner mitochondrial membrane and the intermembrane space required two signal sequences

64. Two signal sequences are required to direct proteins to the thylakoid membrane in chloroplasts
Resemble in mitochondria

67. peroxisomes

69. Peroxisomes use molecular oxygen and hydrogen peroxide to perform oxidative reactions

70. Catalase: 2H2O2 2H2O + O2
Urate oxidase: RH2 + O2 R + H2O2
Animal:
b-oxidation occur at both mitochondria & perixosome.
Plant & yeast:
b-oxidation occur only at perixosome.

71. Plasmalogen
the most abundant protein in myelin.
deficient result in neurological disease.
Animal Perxisome catalyze the first step for plasmalogen biosyn

72. Glyoxylate cycle

73. A short signal sequence directs the import of proteins into peroxisomes

74. Most peroxisomal membrane proteins are made in the cytosol
Peroxins:
-at least 23 distinct proteins for driving ATP hydrolysis
-deficent result in Zellweger syndrome.
Most peroxisomal membrane proteins
are made in the cytosol
 insert into preexisting peroxisomes.

75. The endoplasmic reticulum

77. Membrane-bound ribosomes define the rough ER

79. Many ribosomes bind to a single mRNA

81. ER capture 2 type of protein:
Cotranslatioal transport?
Posttranslational transport?
ER capture 2 type of protein:
transmembrane protein & water-sol protein

82. In mammalian cells Compared to page 697 p690 Protein import to ER
 Cotranslational process
(chaperone are not required to keep protein unfolded)
Protein import to mitochondria, chloroplasts, nuclei, peroxisomes
 Postranslational process
(chaperone needed for unfolding)

83. Smooth ER abundant in some specialized cells

84. Lipid metabolism (cholestersol)
Detoxification by cytochrome p450
Sequester Ca+2 from cytosol (SR)
Autophagocytosis & phenobarital

85. Rough and smooth regions of ER can be separated by centrifugation

87. Cell-free system

88. Signal sequences were first discovered in proteins imported into the rough ER

90. A signal-recognition particle (SRP) directs ER signal sequences to a specific receptor in the rough ER membrane

92. ER & SRP for import

94. The polypeptide chain passes through an aqueous pore in the translocator

97. Translocation across the ER membrane does not always require ongoing polypeptide chain elongation

98. p693
rare

99. Protein that are
are first released into cytosol (bind to hsp to prevent folding)
ATPase
c/o sealing the pore
Binding protein
(hsp70-like
chaperone protein)
yeast

100. The ER sequence is removed from most soluble proteins after translocation

101. Start-transfer signal

102. In single-pass transmembrane proteins, a single internal ER signal sequence remains in the lipid bilayer as a membrane-spanning of a helix

105. Combinations of start-transfer and stop-transfer signals determine the topology of multipass transmembrane proteins

108. hydrophobicity

109. Translocated polypeptide chains fold and assemble in the lumen of the rough ER
Important ER resident proteins:
PDI (protein disulfide isomerase; produce -s-s-)
BiP chaperone protein (prevent aggregate & help to keep in ER)

110. Most (Soluble & membrane-bounded) proteins synthesized in the RER are glycosylated by the addition of a common N-linked oligosaccharide
Very few protein in cytosol is glycosylated.

111. O-linked oligosaccharide are found in Golgi.
N-linked oligosaccharide
- are by far the most common oligosaccharides
found in glycoprotein. (RER)
are recognized by 2 ER charperon protein
(calnexin & calreticulin)
O-linked oligosaccharide are found in Golgi.

114. Oligosaccharides are used as tags to mark the state of protein folding

116. Improperly folded proteins are exported from the ER and degraded in the cytosol

117. Retrotranslocation
(dislocation)
deglycosylation

118. Misfolded proteins in the ER activate an unfolded protein response

120. Some membrane proteins acquire a covalently attached glycosylphosphatidylinositol (GPI) anchor

121. Segregate protein from other membrane protein

122. Most membrane lipid bilayers are assembled in the ER

127. Phospholipid exchange proteins help to transport phospholipids from the ER to mitochondria and peroxisomes

129. Chapter 12 practice Roadmap of protein traffic
Signal sequences & organelle targeting
Organelle epigenetic control
Nuclear pore complex & nuclear import/export & its receptor/signal
The control of nuclear import during T-cell activation
Protein translocation process in mitochondrial membrane: TOM, TIM, OXA
Relationship among import of mitochondrial precursor proteins, role of energy,its hsp70.
Translocation of a precursor protein into the thylakoid space of chloroplasts.
Peroxisomal enzymes & reactions, import mechanism distinct from mitochondria & chloroplast or unique character of peroxisome
SER, RER preparation, SRP, ribosome and RER protein transport
Cotranslation & postranlation translocation in bacteria, archea, and eucaryotes
Hydrophobicity of membrane protein and transmembrane domain
Process and role of protein N-link glycosylation in RER
Membrane lipid bilayer assembly in ER: using example of phosphatidylcholine synthesis
Phospholipid transport from ER to other organelles and comparison of ER and plasma
membrane