Lecture 8: Intracellular Compartments and Protein Sorting Flashcards Preview

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Flashcards in Lecture 8: Intracellular Compartments and Protein Sorting Deck (80):
1

3 features of cellular compartmentalization?

-segregation of metabolic function -organelle-specific environments -membrane surfaces

2

Segregation of metabolic function

-glycolosis in cytoplasm -Krebs cycle in mitochondria

3

Organelle-specific environments

-redox potential in ER -changing PH in ER -acidic PH of lysosomes -glycosylation reactions in the ER and golgi

4

Membrane surfaces

-lipid synthesis -PH gradients and ATP production

5

What are the three types of transport between compartments?

-gated transport -transmembrane transport -vesicular transport

6

Identify the type of transport in red

Q image thumb

gated transport

7

Identify the type of transport in blue

Q image thumb

Transmembrane transport

8

Identify the type of transport in green

Q image thumb

vesicular transport

9

How does a protein “know” where to go? 

Specific elements of a protein, mostly primary amino acid sequence, direct protein traffic 

– Signal sequences 

– Signal patches 

10

What signal sequence is this?

Q image thumb

import into nucleus

11

What signal sequence is this?

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Return to ER

12

What signal sequence is this?

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Import into mitochondria

13

What signal sequence is this?

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Import into plasmid

14

What signal sequence is this?

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import into peroxisomes

15

What signal sequence is this?

Q image thumb

Import into ER

16

What signal sequence is this?

Q image thumb

Return to ER

17

Gated transport occurs___

from the cytoplasm to the nucleus

18

The nuclear envelope is directly connected to the ___

ER

19

Nuclear pore complex

>125 MegaDaltons 

>30 proteins (nucleoporins) 

~3,000-4,000 NPCs per nucleus 

20

• Molecules less than ____ Da freely diffuse through the NPC

5,000

21

 Protein between _____ Da diffuse through more slowly proportional to their size 

20-60,000

22

Proteins greater than ___ Da require help to enter

60,000

23

How do “big” proteins enter and exit the nucleus?

• They use a regulated (gated) pathway that relies on specific import signals or nuclear localization signals 

24

• Nuclear localization signals (NLSs) bind to...

specific receptor proteins that direct import into the nucleus through the NPC 

25

The nuclear localization signal (NLS) was identified by systematically deleting or modifying sequences in _____

SV40 T-antigen 

26

A change as small as ___ can disrupt the activity of an NLS 

one amino acid

27

Functionality as an NLS is ___ its location within the polypeptide 

independent of

28

___ bind NLSs and nucleoporins

Nuclear import receptors

29

Nuclear import receptors are a family of related protein called ____ or ____

importins or karyopherins

30

These protein bind “cargo” via the NLS in the cytosol and then bind to the NPC 

nuclear import receptors (importins)

31

• Specific nucleoporins form tentacle-like fibril composed of amino acid repeats ___

-FG (Phenylalanine-Glycine) 

-Importins bind to these FG repeats 

32

Different families of import receptors recognize different ____

NLSs (nuclear localization signals)

A image thumb
33

Some cargos require an ___ that contains the NLS

adapter protein

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34

• Nucleocytoplasmic transport is ____

bidirectional 

35

• Large molecules like _____ must exit the nucleus and enter the cytoplasm through the NPC 

new ribosomal subunits and RNA molecules

36

• Nuclear export is very similar to import, but topologically reversed.... 

-Depends on nuclear export signals (NES) 

-Depends on export receptors (exportins/ karyopherins) 

37

Ran GTPase

A small G-protein that provides energy and directionality to nucleocytoplasmic transport 

38

Like all small G-proteins, ___ is a molecular switch that changes activity based on a bound ____ 

Ran, nucleotide

39

• The gradient of the two conformational forms of Ran drive ____ in the appropriate direction 

nuclear transport

40

The Ran GTPase cycle

A image thumb
41

How Ran provides directionality

A image thumb
42

RanGTP cargo displacement

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43

Ran-GTP and cargo binding to an import receptor is...

mutually exclusive

44

The nuclear envelope disassembles during mitosis 

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45

The ER network composed of sheets and tubules is regulated by ___ 

fusion and fission

46

Posttranslational transmembrane transport

• Mitochondria

• Chloroplasts

• Peroxisomes

47

Mitochondrial function

  • Energy (ATP) production by oxidative phosphorylation
  • Intermediary metabolism (TCA cycle) 
  • Lipid metabolism

 – Catabolism (beta-oxidation)

 – Synthesis 

48

While mitochondria contain DNA and protein synthesis machinery, the majority of mitochondrial proteins are _____ encoded genes that are postranslationally imported

nuclear

49

___ and ____ regulate mitochondrial shape

Fusion and fission

50

Mitochondrial matrix targeting sequence 

• 20-50 amino acids 

• Rich in hydrophobic, positively charged basic (R,K) and hydroxylated (S,T) amino acids 

• Tend to lack acidic residues (D,E) 

• Form amphipathic alphahelices 

• Cleaved off the mature protein by a matrix protease 

51

Translocation into the mitochondrial matrix depends on ____

a signal sequence and protein translocators

52

In mitochondrial protein imports, precursor proteins are imported as ____

unfolded polypeptide chains 

53

Proteins are imported into the matrix at ___ that join the inner and outer membrane 

contact sites

54

___ and ____ are used to drive import into mitochondria

ATP hydrolysis and a proton gradient

55

Repeated cycles of ATP hydrolysis by ___ complete the import process 

mHSP70

56

Transport to the inner membrane and inner membrane space requires ___ signals 

two

57

• Translocase of the Outer Membrane (TOM) 

  • Required for the import of all nuclear encoded genes 
  • Helps insert membrane proteins into the outer membrane

58

Sorting and Assembly Machine (SAM) complex 

– Helps insert and fold beta-barrel proteins

59

What does TIM stand for?

• Translocase of the Inner Membrane (TIM) 

60

TIM23 complex

• Spans both membranes 

• Mediates translocation of proteins in to the matrix space and inner membrane proteins 

61

TIM22 complex 

 Mediates the insertion of a subclass of inner membrane proteins 

62

OXA complex 

• Mediates the insertion of inner membrane proteins synthesized in the mitochondrial matrix 

63

Protein translocators in the mitochondrial membrane 

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64

Which protein translocaters are in the outer mitochondrial membrane?

-TOM complex

-SAM complex

65

Which protein translocaters are in the inner mitochondrial membrane?

-TIM22 complex

-TIM23 complex

-OXA complex

66

The negative membrane potential helps “attract” the_____ charged mitochindrial targeting signal 

 positively

67

The integration of Porins (Beta-barrel proteins) into the outer mitochondrial membrane is accomplished by what protein translocators?

TOM and SAM

68

Protein import into the mitochondrial matrix is accomplished by which two translocators?

TOM and TIM23

69

How are proteins targeted to the inner mitochondrial membrane?

TOM/TIM23 path but with a stop transfer sequence

OR

TOM/TIM23 path and OXA complex

70

How are proteins targeted to the inner membrane space of the mitochondria?

TOM/TIM23/OXA then protease cleaves the second signal sequence

OR
TOM/TIM23 and stop transfer sequence, protease cleaves stop transfer sequence

71

How do you target to the inner membrane space through the outer membrane?

TOM complex, then protein oxidized by Mia40

72

What are the two complexes responsible for protein import into the stroma of the chloroplast?

TIC (inner membrane)

TOC (outer membrane)

73

What are the four ways to translocate into the thylakoid space?

Sec pathway

SRP-like pathway

TAT pathway

spontaneous insertion

74

Peroxisomal Functions 

• House oxidative enzymes 

– Oxidases produce peroxide (H202), hence the name peroxisome 

– Contains catalase to degrade H202 

• Lipid metabolism 

– fatty acids beta oxidation 

• Exclusively peroxisomal in yeast and plants 

• Shared with mitochondria in animal 

75

_____ do not contain DNA and all proteins are imported posttranslationally 

peroxisomes

76

At least ___ peroxisomal targeting sequences (PTS) are known for matrix proteins 

two

77

____ import is fundamentally different from other organelles since fully-folded proteins can be imported 

peroxisome

78

___ is a specific protein that catalyzes protein import into peroxisomes

Pex19

79

___ genes or ___, are proteins responsible for the generation and maintenance of peroxisomes

Pex genes or peroxins

80