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BIO230 Midterm > Week 5 > Flashcards

Week 5 Flashcards

1
Q

What are some animal-specific cell characteristics?

A
  • extracellular matrix
  • lysosome
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2
Q

What are some plant-specific cell characteristics?

A
  • chloroplast
  • vacuole (2 types, storage and similar to animal lysosome)
  • cell wall
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3
Q

What are some standard organelles found in both plant and animal cells?

A
  • nucleus
  • ER
  • Golgi
  • peroxisome
  • mitochondria
  • plasma membrane
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4
Q

What are some movement of proteins?

A
  • within cell from different compartments
  • out of the cell
  • in cell
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5
Q

Where is protein synthesis initiated?

A

on ribosomes in the cytosol and must be sorted to the correct location

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6
Q

What is the post-translational process in protein sorting?

A

sorting of proteins that are fully synthesized in the cytosol before being directed to their final destinations

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7
Q

How are mitochondrial proteins imported during the post-translational process?

A
  • imported as unfolded polypeptide chains
  • contain a mitochondrial signal sequence that directs them to the translocators (TOM and TIM complexes)
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8
Q

What is the co-translational process in protein sorting?

A

the simultaneous synthesis and translocation of proteins into the Endoplasmic Reticulum (ER) as ribosomes are translating them

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9
Q

What are the main mechanisms of protein transport?

A
  1. Gated Transport - Movement between the cytosol and the nucleus
  2. Transmembrane Transport - Proteins are transported across membranes through translocators (often unfolded).
  3. Vesicular Transport - Vesicles move protein between compartments
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10
Q

What is gated transport?

A

the movement of proteins between the cytosol and the nucleus through the Nuclear Pore Complex (NPC)

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11
Q

What is the role of the Nuclear Pore Complex (NPC)?

A

facilitates the selective transport of macromolecules (like proteins and RNA), allowing small molecules to diffuse freely (<5,000 daltons).

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12
Q

What are the main types of nuclear transport?

A
  1. Nuclear Import: cytosol into the nucleus.
  2. Nuclear Export: nucleus to the cytosol.
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13
Q

What is the Nuclear Pore Complex made up of?

A

nucleoporins (a lot of proteins make it up)

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14
Q

What is a Nuclear Localization Signal (NLS)?

A

a specific amino acid sequence rich in lysine (Lys) and arginine (Arg) that directs the transport of cargo proteins into the nucleus by binding to nuclear import receptors

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15
Q

How do nuclear import receptors function?

A
  • bind to nuclear localization signal
  • binds to nucleoporins in nuclear pore complex
  • transports proteins into the nucleus
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16
Q

How do nuclear export receptors function?

A

bind to a Nuclear Export Signal (NES) on cargo proteins and facilitate their transport from the nucleus to the cytosol

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17
Q

What is a Nuclear Export Signal (NES)?

A

a specific amino acid sequence that directs the transport of cargo proteins into the cytosol by binding to nuclear export receptors

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18
Q

What is the role of Ran GTPase in nuclear transport?

A
  • critical for both nuclear import and export
  • exists in two forms:
    1. Ran-GTP (high concentration in the nucleus)
    2. Ran-GDP (high concentration in the cytosol).
    Ran-GTP binding promotes cargo release during import, while GTP hydrolysis facilitates cargo release during export.
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19
Q

What is the role of Ran-GAP?

A

(GTPase-Activating Protein): Stimulates GTP hydrolysis by Ran in the cytosol, promoting the conversion of Ran-GTP to Ran-GDP in the cytosol.

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20
Q

What is the role of Ran-GEF?

A

Promotes the exchange of GDP for GTP by Ran in the nucleus, maintaining a high concentration of Ran-GTP.

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21
Q

What are the cycles of Ran GTPase?

A

cycles between GDP-bound and GTP-bound

High (Ran-GTP) nucleus, low (Ran-GTP) cytosol

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22
Q

How does Ran GTPase move between the nucleus and cytosol?

A
  1. Ran-GTP: to cytosol
    - with nuclear import/ export receptors
  2. Ran-GDP: to nucleus
    - transported by NTF2 (nuclear transport factor 2)
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23
Q

What is the mechanism of nuclear import?

A
  1. Nuclear import receptor binds cargo in the cytosol.
  2. The receptor-cargo complex moves to the nucleus.
  3. Ran-GTP binds to the receptor in the nucleus, causing cargo release.
  4. The empty receptor + Ran-GTP returns to the cytosol.
  5. Ran-binding proteins and Ran-GAP promote GTP hydrolysis, releasing the import receptor.
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24
Q

What is the mechanism of nuclear export?

A
  1. Nuclear export receptor binds to Ran-GTP and cargo in the nucleus.
  2. The receptor-cargo-Ran-GTP complex moves to the cytosol.
  3. Ran-binding protein and Ran-GAP promotes GTP hydrolysis, resulting in cargo and export receptor release.
  4. The empty receptor returns to the nucleus.
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25
Q

How can nuclear import and export be regulated?

A

the presence of signaling molecules (e.g., calcium ions) that affect the exposure of NLS and NES, thereby influencing the transport of proteins like NFAT in T-cells.

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26
Q

What triggers the nuclear import of NFAT?

A
  1. High calcium levels in cytosol trigger the nuclear import of NFAT
  2. When calcium levels rise, NFAT becomes dephosphorylated,
  3. its Nuclear Localization Signal (NLS) is exposed
  4. Brought into the nucleus and activation of gene transcription
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27
Q

What happens to NFAT in resting T-cells?

A

NFAT is phosphorylated and retains a Nuclear Export Signal (NES), which prevents it from entering the nucleus

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28
Q

How does NFAT exit the nucleus?

A
  • exits the nucleus when calcium levels are low in the nucleus
  • leading to its phosphorylation, which exposes the NES
  • allows it to bind to export receptors for transport back to the cytosol
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29
Q

What experimental approach can be used to study NFAT transport?

A
  • expressing an NFAT-GFP fusion protein in T-cells
  • add a calcium ionophore to increase intracellular calcium
  • monitor the fluorescence to visualize NFAT’s nuclear import
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30
Q

What is transmembrane transport?

A

the movement of proteins across cellular membranes(ER, mitochondria, plastids, and peroxisomes)

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31
Q

What are the key features of transmembrane transport?

A
  • Proteins are usually unfolded during transport.
  • Requires protein translocators.
  • Involves specific signal sequences for targeting.
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32
Q

What are the main characteristics of proteins that are sorted to mitochondria and chloroplasts?

A

they have their own genome and ribosomes but most proteins are nuclear-encoded
- translated in the cytosol
- imported into organelles
- post-translational sorting
- proteins unfolded

33
Q

How to mitochondrial and chloroplast proteins stay unfolded in the cytosol?

A

by association with hsp70 chaperones

34
Q

What type of signal sequence is required for mitochondrial protein import?

A

an N-terminal amphipathic α-helix signal sequence for import into the mitochondrial matrix

35
Q

What are the main protein translocators involved in mitochondrial protein import?

A
  • Translocase of the Outer Membrane (TOM) Complex
    -Translocase of the Inner Membrane (TIM23) Complex
36
Q

How do precursor proteins interact with the TOM complex?

A

Precursor proteins with a mitochondrial signal sequence bind to receptors on the TOM complex, allowing them to be translocated across the outer membrane into the intermembrane space

37
Q

What is the role of the TIM23 complex in mitochondrial import?

A

facilitates the translocation of proteins from the intermembrane space into the mitochondrial matrix, allowing the protein to pass through the inner membrane

38
Q

What happens to the mitochondrial signal sequence after the protein is imported into the matrix?

A

signal sequence is cleaved off by a signal peptidase once the protein has successfully entered the mitochondrial matrix

39
Q

What is the energy requirement for mitochondrial protein import?

A

the electrochemical gradient across the inner mitochondrial membrane and ATP hydrolysis

40
Q

What type of signal sequence is required for chloroplast protein import?

A

an N-terminal amphipathic α-helix signal sequence that directs them to the chloroplast

41
Q

What are the protein translocators involved in chloroplast import?

A
  • TOC complex(Translocon of the Outer Chloroplast membrane)
  • TIC (Translocon of the Inner Chloroplast membrane) complex
42
Q

What happens to the signal sequence after a protein is imported into the chloroplast?

A

cleaved off once the protein is inside the chloroplast.

43
Q

What additional signal is required for proteins targeted to the thylakoids within the chloroplast?

A

have a hydrophobic thylakoid signal sequence that directs them to the correct location

44
Q

What are the steps involved in protein import to the chloroplast?

A
  1. Protein synthesis occurs in the cytosol with an N-terminal signal sequence.
  2. The protein is recognized by the TOC complex on the outer membrane.
  3. The protein translocates through the TOC and TIC complexes into the stroma.
  4. The signal sequence is cleaved, and the protein folds into its active form.
45
Q

What is the primary signal for sorting proteins to peroxisomes?

A

the peroxisomal targeting signal (PTS), which is typically a sequence of three amino acids at the C-terminus (SKL)

46
Q

Are proteins folded or unfolded when transported to peroxisomes?

A

folded

47
Q

What role do receptors play in the transport of proteins to peroxisomes?

A

Soluble receptors bind to the peroxisomal targeting signal (PTS) of the precursor protein and facilitate its docking to the translocator complex on the peroxisomal membrane

48
Q

How is the translocator complex involved in peroxisome protein import?

A
  • The translocator complex is a large protein complex that facilitates the transport of the folded precursor protein across the peroxisomal membrane
  • It binds to the receptor, allowing the protein to be transported into the peroxisome.
49
Q

What happens to the receptor after the protein is transported into the peroxisome?

A

remains on the outside of the peroxisome after the protein is transported in

50
Q

What is the primary function of the Endoplasmic Reticulum (ER) in protein sorting?

A
  • responsible for the synthesis and modifications of proteins, as well as the synthesis of lipids
  • Proteins sorted to the ER have an ER signal sequence.
51
Q

How are proteins sorted to the ER?

A
  • by transmembrane transport
  • they are further sorted by vesicular transport to other compartments or the cell surface
52
Q

What kinds of proteins have ER signal sequences?

A

proteins sorted to the ER:
- soluble proteins
- transmembrane proteins
- proteins destined for Golgi, secretion, lysosomes

53
Q

What are the major steps in the protein sorting process to the ER?

A
  1. mRNA is translated by ribosomes in the cytosol.
  2. The ER signal sequence emerges and binds to the SRP.
  3. The SRP-ribosome complex is directed to the ER membrane.
  4. The ribosome binds to the translocon, and the protein is translocated into the ER lumen.
  5. The signal sequence is cleaved, and the protein is properly folded and modified.
54
Q

What is the function of the Signal Recognition Particle (SRP) and the SRP receptor?

A
  • The SRP binds to the ER signal sequence and the ribosome, directing the complex to the ER membrane where it binds to the SRP receptor, facilitating the transfer of the ribosome to the translocator channel.
55
Q

How does SRP interact with the ribosome?

A
  • Initially, SRP has a low affinity for the ribosome.
  • When the ribosome synthesizes the ER signal sequence, the affinity increases, allowing SRP to bind tightly to the ribosome and the signal sequence.
56
Q

What happens after SRP binds to the ribosome and the ER signal sequence?

A
  • SRP-ribosome complex is directed to the ER membrane
  • it binds to the SRP receptor
  • facilitated by GTP binding and hydrolysis
  • promotes the release of the SRP and the ribosome onto the translocator
57
Q

What is the function of the translocator in the ER?

A
  • a gated channel that allows the polypeptide chain to pass through into the ER lumen
  • prevents the diffusion of ions and small molecules during the process.
58
Q

What is the mechanism of transport for soluble proteins into the ER?

A
  • The ER signal sequence (N-terminal start-transfer sequence) emerges first during translation
  • binds to the SRP, which then directs the ribosome to the ER membrane.
  • The polypeptide chain passes through a gated channel in the translocator
  • the signal sequence is cleaved by signal peptidase
  • ER signal sequence laterally diffuses into the lipid bilayer
  • protein is released into the ER
59
Q

How do single-pass and multi-pass transmembrane proteins differ in their sorting?

A

Single-pass transmembrane proteins: a single start-transfer sequence that is cleaved
Multi-pass transmembrane proteins: multiple start-transfer and stop-transfer sequences that determine their orientation in the membrane

60
Q

What determines the orientation of transmembrane proteins in the ER?

A

the amino acids flanking the internal start-transfer sequence; positively charged amino acids tend to face the cytosolic side

61
Q

What are single-pass transmembrane proteins?

A

proteins that span the membrane only once
- 3 types of insertions

62
Q

What are the steps involved in the first type of single-pass transmembrane protein?

A
  • The ER signal sequence is recognized as a start-transfer sequence at the N-terminal
    -the protein is fed through until it hits the transmembrane domain
  • the TM domain is a stop-transfer signal
  • signal peptidase cleaves the start-transfer sequence and it laterally diffuses
63
Q

What are the steps involved in the second type of single-pass transmembrane protein?

A
  • the transmembrane domain is an internal start-transfer sequence (not cleaved), which is recognized by translocator
  • protein is fed through until the protein comes out the other side
  • either the N or C terminus will be on the cytosolic side (pos)
64
Q

What are multi-pass transmembrane proteins?

A

proteins that span the lipid bilayer multiple times

65
Q

How are multi-pass transmembrane proteins inserted into the membrane?

A

through a series of start-transfer and stop-transfer sequences that dictate their orientation and the number of transmembrane segments

66
Q

What is the role of hydrophobic sequences in multi-pass transmembrane proteins?

A

act as signals for the translocator to insert the protein into the membrane and determine the orientation

67
Q

What is the simplest example of a multipass transmembrane protein?

A
  • 1 TM domain: internal start transfer sequence
  • 2 TM domain: stop-transfer sequence
  • C and N terminus are on cytosolic side
68
Q

Can you give an example of a multi-pass transmembrane protein?

A

Rhodopsin
- 1 TM: start-transfer (+) amino acid, cytosolic (C is in cytosol)
- 2 TM: start-transfer
- 3 TM: stop-transfer
- 4 TM: start-transfer
- N (-) is on lumen

69
Q

What are ER targeting sequences and stop-transfer sequences?

A
  • specific hydrophobic sequences
  • predicted by stretches of hydrophobic amino acids
70
Q

What are the main types of membrane proteins?

A
  1. Integral (including transmembrane)
  2. Lipid-anchored
  3. Peripheral
71
Q

What are integral membrane proteins?

A
  • proteins that are embedded within the lipid bilayer of the membrane
  • can span the membrane (transmembrane proteins) or be partially embedded
72
Q

What are lipid-anchored proteins?

A

proteins that are covalently attached to lipid molecules, allowing them to associate with the membrane without spanning it

73
Q

What are peripheral membrane proteins?

A

proteins that are not embedded in the lipid bilayer but are associated with the membrane surface, often through interactions with integral proteins or lipid head groups

74
Q

What is a GPI-anchored protein?

A

a type of lipid-anchored protein that are attached to the membrane via a (GPI) anchor, allowing them to be located on the extracellular surface of the membrane.

75
Q

Where are transmembrane proteins typically glycosylated?

A

on their extracellular face, which is important for cell recognition and signaling

76
Q

What is the role of the C-terminal hydrophobic domain in GPI-anchored proteins?

A
  • crucial for its attachment to the GPI anchor
  • hydrophobic region allows the protein to be embedded in the membrane.
77
Q

How is the GPI anchor formed?

A
  • The GPI anchor is performed in the membrane
  • The target protein is transferred to the GPI anchor by an enzyme located in the endoplasmic reticulum (ER)
78
Q

Where do GPI-anchored proteins end up after synthesis?

A

the luminal side of the ER and can then be transported to the cell exterior surface

BIO230 Midterm (6 decks)

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