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BIOC 341 > Lecture 8: Intracellular Compartments and Protein Sorting > Flashcards

Lecture 8: Intracellular Compartments and Protein Sorting Flashcards

1
Q

3 features of cellular compartmentalization?

A

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

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2
Q

Segregation of metabolic function

A

-glycolosis in cytoplasm -Krebs cycle in mitochondria

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3
Q

Organelle-specific environments

A

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

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4
Q

Membrane surfaces

A

-lipid synthesis -PH gradients and ATP production

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5
Q

What are the three types of transport between compartments?

A

-gated transport -transmembrane transport -vesicular transport

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6
Q

Identify the type of transport in red

A

gated transport

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7
Q

Identify the type of transport in blue

A

Transmembrane transport

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8
Q

Identify the type of transport in green

A

vesicular transport

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9
Q

How does a protein “know” where to go?

A

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

– Signal sequences

– Signal patches

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10
Q

What signal sequence is this?

A

import into nucleus

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11
Q

What signal sequence is this?

A

Return to ER

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12
Q

What signal sequence is this?

A

Import into mitochondria

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13
Q

What signal sequence is this?

A

Import into plasmid

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14
Q

What signal sequence is this?

A

import into peroxisomes

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15
Q

What signal sequence is this?

A

Import into ER

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16
Q

What signal sequence is this?

A

Return to ER

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17
Q

Gated transport occurs___

A

from the cytoplasm to the nucleus

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18
Q

The nuclear envelope is directly connected to the ___

A

ER

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19
Q

Nuclear pore complex

A

>125 MegaDaltons

>30 proteins (nucleoporins)

~3,000-4,000 NPCs per nucleus

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20
Q

• Molecules less than ____ Da freely diffuse through the NPC

A

5,000

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21
Q

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

A

20-60,000

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22
Q

Proteins greater than ___ Da require help to enter

A

60,000

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23
Q

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

A

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

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24
Q

• Nuclear localization signals (NLSs) bind to…

A

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

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25
Q

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

A

SV40 T-antigen

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26
Q

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

A

one amino acid

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27
Q

Functionality as an NLS is ___ its location within the polypeptide

A

independent of

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28
Q

___ bind NLSs and nucleoporins

A

Nuclear import receptors

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29
Q

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

A

importins or karyopherins

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30
Q

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

A

nuclear import receptors (importins)

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31
Q

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

A
  • FG (Phenylalanine-Glycine)
  • Importins bind to these FG repeats
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32
Q

Different families of import receptors recognize different ____

A

NLSs (nuclear localization signals)

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33
Q

Some cargos require an ___ that contains the NLS

A

adapter protein

34
Q

• Nucleocytoplasmic transport is ____

A

bidirectional

35
Q

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

A

new ribosomal subunits and RNA molecules

36
Q

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

A
  • Depends on nuclear export signals (NES)
  • Depends on export receptors (exportins/ karyopherins)
37
Q

Ran GTPase

A

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

38
Q

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

A

Ran, nucleotide

39
Q

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

A

nuclear transport

40
Q

The Ran GTPase cycle

A
41
Q

How Ran provides directionality

A
42
Q

RanGTP cargo displacement

A
43
Q

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

A

mutually exclusive

44
Q

The nuclear envelope disassembles during mitosis

A
45
Q

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

A

fusion and fission

46
Q

Posttranslational transmembrane transport

A
  • Mitochondria
  • Chloroplasts
  • Peroxisomes
47
Q

Mitochondrial function

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

– Catabolism (beta-oxidation)

– Synthesis

48
Q

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

A

nuclear

49
Q

___ and ____ regulate mitochondrial shape

A

Fusion and fission

50
Q

Mitochondrial matrix targeting sequence

A
  • 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
Q

Translocation into the mitochondrial matrix depends on ____

A

a signal sequence and protein translocators

52
Q

In mitochondrial protein imports, precursor proteins are imported as ____

A

unfolded polypeptide chains

53
Q

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

A

contact sites

54
Q

___ and ____ are used to drive import into mitochondria

A

ATP hydrolysis and a proton gradient

55
Q

Repeated cycles of ATP hydrolysis by ___ complete the import process

A

mHSP70

56
Q

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

A

two

57
Q

• Translocase of the Outer Membrane (TOM)

A
  • Required for the import of all nuclear encoded genes
  • Helps insert membrane proteins into the outer membrane
58
Q

Sorting and Assembly Machine (SAM) complex

A

– Helps insert and fold beta-barrel proteins

59
Q

What does TIM stand for?

A

• Translocase of the Inner Membrane (TIM)

60
Q

TIM23 complex

A

• Spans both membranes

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

61
Q

TIM22 complex

A

Mediates the insertion of a subclass of inner membrane proteins

62
Q

OXA complex

A

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

63
Q

Protein translocators in the mitochondrial membrane

A
64
Q

Which protein translocaters are in the outer mitochondrial membrane?

A
  • TOM complex
  • SAM complex
65
Q

Which protein translocaters are in the inner mitochondrial membrane?

A
  • TIM22 complex
  • TIM23 complex
  • OXA complex
66
Q

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

A

positively

67
Q

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

A

TOM and SAM

68
Q

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

A

TOM and TIM23

69
Q

How are proteins targeted to the inner mitochondrial membrane?

A

TOM/TIM23 path but with a stop transfer sequence

OR

TOM/TIM23 path and OXA complex

70
Q

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

A

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

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

71
Q

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

A

TOM complex, then protein oxidized by Mia40

72
Q

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

A

TIC (inner membrane)

TOC (outer membrane)

73
Q

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

A

Sec pathway

SRP-like pathway

TAT pathway

spontaneous insertion

74
Q

Peroxisomal Functions

A

• 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
Q

_____ do not contain DNA and all proteins are imported posttranslationally

A

peroxisomes

76
Q

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

A

two

77
Q

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

A

peroxisome

78
Q

___ is a specific protein that catalyzes protein import into peroxisomes

A

Pex19

79
Q

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

A

Pex genes or peroxins

80
Q
A

BIOC 341 (24 decks)

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