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UVic BIOL 360 - Fall 2019 > Compartments and Protein Sorting (ch 12) > Flashcards

Compartments and Protein Sorting (ch 12) Flashcards

1
Q

At what stage of protein translation does the signal recognition particle (SRP) recognize the emerging protein?

A

The SRP goes partially into the ribosome tunnel to scan the protein before it even emerges.

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2
Q

What are the 4 distinct intracellular compartment families?

A
  1. Nucleus + cytosol
  2. All secretory+endocytic organelles
  3. Mitochondria
  4. Plastids
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3
Q

What are the 3 distinct protein transport pathways?

A
  1. Gated Transport (cytosol>nucleus)
  2. Transmembrane transport (>ER)
  3. Vesicular transport (secretory transport)
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4
Q

What is the purpose of a protein signal sequence?

A

An “address” for proteins. Can be hydrophilic/phobic, polar/non-polar, -ve/+ve charge. Just something recognizable.

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5
Q

In folded protein, signal sequence is on ______. In unfolded protein, signal sequence is on ______.

A

Folded: protein surface
Unfolded: N-terminus

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6
Q

Does most protein transport occur while the protein is folded or unfolded?

A

Unfolded.

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7
Q

What end of the protein enters the ER initially? What about if the protein has to re-enter the ER after leaving?

A

Enter initially: N-terminus

Re-enter: C-terminus

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8
Q

Where would you expect to find shorter proteins? What about longer ones?

A

Shorter: in cytosol, lost signal sequence
Longer: in transit to other locations

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9
Q

What is transported into the nucleus through the nuclear pore complexes?

A

Only mRNA and transcription factors.

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10
Q

At what rate are molecules transported into and out of the nucleus?

A

~500 molecules per second!

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11
Q

How does the nuclear membrane bend around the nuclear pore complexes?

A

With the help of membrane ring proteins and nuclear basket proteins which distort the membrane.

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12
Q

How many different proteins make up a nuclear pore complex?

A

~30 different proteins.

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13
Q

How are large molecules excluded from the nucleus by the nuclear pore complexes?

A

Because of the channel nucleoporins which project into the opening and filter away large molecules but allow small ones to pass.

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14
Q

What is the function of nuclear import receptors?

A

To enable the movement of cargo proteins into the nucleus when directly bound to the receptor or indirectly through an adaptor protein.

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15
Q

Does changing one amino acid on a nuclear localization signal affect the import of a protein?

A

It can. Sometimes resulting in aggregation and no transport.

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16
Q

How do nuclear import receptors carry cargo through the nuclear pore complex?

A

By attaching to FG repeats on nucleoporins and “hopping” through the channel.

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17
Q

How is a monomeric GTPase activated? By what?

A

Guanine exchange factor (GEF) replaces GDP on inactive GTPase with GTP to activate.

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18
Q

How is a monomeric GTPase inactivated? By what?

A

GTPase activating protein (GAP) removes a phosphate from GTPase-bound GTP, converting it to GDP and inactivating the GTPase.

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19
Q

What is the name for the monomeric GTPase involved in transport across the nuclear pore?

A

Ran-GTP and Ran-GDP depending on localization and activation status.

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20
Q

What mechanism imposes transport directionality through the nuclear pore?

A

The activation/inactivation of Ran-GDP/GTP.

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21
Q

How is Ran-GDP activated as it enters the nucleus? By what?

A

Ran-GEF replaces Ran-bound GDP with GTP, activating Ran.

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22
Q

How is Ran-GTP deactivated as it exits the nucleus? By what?

A

Ran-GAP converts Ran-bound GTP to GDP, deactivating Ran.

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23
Q

How does Ran-GTP assist nuclear import receptors to transport proteins into the nucleus?

A

Ran-GTP replaces cargo protein by binding to nuclear import protein, releasing the cargo into the nucleus. The import protein with bound Ran-GTP then exits the nucleus.

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24
Q

How does Ran-GTP assist nuclear export receptors to transport proteins out of the nucleus?

A

Binds to export receptor in nucleus, causing it to pick up the cargo protein and take it out of the nucleus. Ran-GDP and cargo both release once in the cytosol.

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25
Q

How does mRNA export differ from Ran-driven protein export through the nuclear pores?

A

mRNA export is driven by ATP rather than Ran-GTP.

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26
Q

How is transport through the nuclear pore complex regulated?

A

By limiting access to transport machinery and turning import/export signals on/off via phosphorylation.

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27
Q

What is SREBP? What about SCAP?

A

SREBP: sterol response element binding protein
SCAP: SREBP cleavage activating protein

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28
Q

What 2 proteins are involved in feedback regulation of cholesterol synthesis via the nuclear pore complex?

A
  1. SREBP

2. SCAP

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29
Q

Do cargo proteins always just pass smoothly through the nuclear pore complex?

A

No. Many cargo proteins circulate in the pore for a while before passing through or even being rejected.

30
Q

Is Ran absolutely required for transport through the nuclear pore complex? What effect does it have?

A

No. But it makes import much more effective (50% vs 0.01%).

31
Q

Are proteins transported into the nucleus folded or unfolded? Where would the nuclear localization signal be present?

A

Proteins are transported in their folded conformation with the nuclear localization signal exposed.

32
Q

What 2 spaces exist in the mitochondria?

A
  1. Intermembrane space

2. Matrix space

33
Q

What 3 spaces exist in the chloroplast?

A
  1. Intermembrane space
  2. Stroma (matrix space)
  3. Thylakoid space
34
Q

Can mitochondria be generated by the cell? How are they replicated?

A

No. They must arise from mitochondrial DNA contained within existing mitochondria.

35
Q

How many types of proteins are provided to a new mitochondria by the nucleus? How many are provided by another mitochondria?

A

~1000 from the nucleus, 13 from mitochondrial DNA.

36
Q

Where are mitochondrial precursor proteins synthesized? When are they translocated into the mitochondria?

A

Fully synthesized in the cytosol. Translocated into the mitochondria post-translationally.

37
Q

What is an example of a signal sequence for import and localization to a mitochondrial subcompartment?

A

Cytochrome oxidase subunit IV.

38
Q

What is the function of a TOM complex in the mitochondria membrane?

A

Translocase on outer mitochondrial membrane, identifies linear proteins.

39
Q

What is the function of a SAM complex in the mitochondria membrane?

A

Sorting and assembly machine, folds linear proteins imported by TOM into β-barrels.

40
Q

What is the function of a TIM22 complex in the mitochondria membrane?

A

Translocase on inner mitochondrial membrane, inserts proteins into inner membrane.

41
Q

What is the function of a TIM23 complex in the mitochondria membrane?

A

Translocase on inner mitochondrial membrane, moves proteins into matrix space.

42
Q

What is the function of an OXA complex in the mitochondria membrane?

A

Cytochrome oxidase activity, inserts proteins into inner membrane.

43
Q

In what conformation are proteins transported into the mitochondria? What assists this?

A

Unfolded and bound to chaperones to prevent folding.

44
Q

What mechanism drives protein import into the mitochondria?

A

Active transport from ATP hydrolysis or membrane potential.

45
Q

What other mitochondrial process assists the import of protons by creating an electrochemical gradient?

A

Oxidative phosphorylation (produces ATP).

46
Q

Do all eukaryotes have mitochondria?

A

Nope!

47
Q

In bacteria, the SAM complex in the mitochondria is replaced by the ___ complex on the outer bacterial membrane.

A

BAM complex.

48
Q

What must occur following import before a mitochondrial protein can be activated?

A

Cleavage of the signal sequence.

49
Q

What is the purpose of a “stop-transfer” sequence in a mitochondrial protein?

A

Allows protein to stop partway through the inner (or outer) membrane because of hydrophobic interactions.

50
Q

How does protein translocation into chloroplast differ from translocation into mitochondria?

A

TOM complex replaced by TOC complex, TIM complex replaced by TIC complex.

51
Q

What is Mia40? What is its role in the mitochondria?

A

Mitochondrial intermembrane space assemby. Folds proteins once imported into the intermembrane space.

52
Q

What are the 3 main functions of the endoplasmic reticulum?

A
  1. Lipid biosynthesis
  2. Protein biosynthesis of transmembrane proteins
  3. Ca2+ storage
53
Q

How can the ER be isolated? What else occurs during this process?

A

Centrifugation will break up the ER into rough and smooth microsomes which can be separated by density in a tube with a sucrose gradient.

54
Q

What 2 main ways can proteins be translocated?

A
  1. Co-translationally

2. Post-translationally

55
Q

How does translocation of proteins occur in the ER? Why?

A

Co-translationally. Proteins are not fully made in the cytosol and must be finished in rough ER ribosomes.

56
Q

Why do proteins being translocated into the ER not need chaperone proteins?

A

Folding is not possible because translocation is done co-translationally and identification occurs before the protein is exposed out of the ribosome channel.

57
Q

Describe the structure of a signal recognition particle in the ER.

A

6 proteins connected by an SRP RNA molecule.

58
Q

What 4 steps outline the function of a signal recognition particle in the ER?

A
  1. Recognition (of new protein + binding)
  2. Targeting (of membrane protein translocator)
  3. Release (of ribosome onto protein translocator)
  4. Recycling (of SRP to next ribosome)
59
Q

What 2 ER proteins can recognize an ER signal sequence?

A
  1. Signal recognition particle

2. Protein translocator

60
Q

In what 2 ways can a protein translocator in the ER open?

A
  1. Pore for hydrophilic portions

2. Opens laterally for hydrophobic portions

61
Q

On a hydrophobicity plot, how can we tell the number of transmembrane domains in a transmembrane protein?

A

By counting the number of peaks.

62
Q

Are proteins targeted for translocation always recognized by their N-terminus sequence?

A

No. Some proteins are recognized by their C-terminus, in which case the normal membrane localization is reversed and the C-terminus can be anchored.

63
Q

What 2 events constitute the “dual recognition” of proteins by the ER?

A
  1. SRP recognizes protein in the cytosol

2. Protein translocator recognizes protein during binding

64
Q

Why is “dual recognition” of proteins by the ER important?

A

It ensures that inappropriate proteins do not enter the ER lumen.

65
Q

Where in the cell are signal recognition particles (SRPs) mainly found?

A

In and around the rough endoplasmic reticulum (ER).

66
Q

If a protein is engineered to have two different localization signals, which determines its destination?

A

The one closest to the N-terminus or which will be read first.

67
Q

Where is a protein sent if it has no localization signal or ER retention signal?

A

To the cytosol, where it will eventually be picked up and degraded.

68
Q

What are some examples which support the theory that mitochondria and chloroplasts are engulfed prokaryotes?

A
  1. Neither can be made from scratch by the cell
  2. Distinct transmembrane transport methods
  3. Have their own ribosomes
  4. Have their own DNA
69
Q

Transmembrane proteins have start-transfer and stop-transfer sequences. In a recombinant experiment, you change the order of those sequences. What happens to the integration of that recombinant protein into the membrane?

A

It integrates normally in the same way as the wild-type protein.

70
Q

Excitatory neurotransmitters ___ channels which results in a ___ charge on the cytosolic side of the cell. Inhibitory neurotransmitters ___ channels which results in a ___ charge on the cytosolic side of the cell.

A

Opens sodium. Positive. Opens potassium of chlorine. Negative.

71
Q

In what case are proteins transported from the ER to the cytosol via the retrotranslocation pathway?

A

When a protein has failed to fold properly in the ER it is moved to the cytosol and degraded via a proteosome.

UVic BIOL 360 - Fall 2019 (10 decks)

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