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Molecular Biology > Protein Sorting > Flashcards

Protein Sorting Flashcards

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1
Q

What is an outer boundary of cells, bilayer

-Protective barrier, has transporters, signaling

A

Plasma Membrane

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2
Q

What organelle contains the genome

-Principle site for DNA and RNA synthesis

A

Nucleus

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3
Q

What consists of cytosol and cytoplasmic organelles

-Intermediary metabolism

A

Cytoplasm

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4
Q

What organelle has ribosomes attached to it, no ribosomes attached to it

A

Rough ER and Smooth ER

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5
Q

What contains stacks of disc-like compartments and is responsible for post-translational changes on proteins and lipids, trafficking

A

Golgi Apparatus

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6
Q

What is are the primary functions of the mitochondria

A

Make ATP
signaling
cell differentiation
cell death

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7
Q

What contain digestive enzymes that degrade organelles and biomolecules

A

Lysosomes

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8
Q

Describe peroxisomes

A

Small vesicular compartments that contain enzymes used in oxidation reactions

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9
Q

What three topological categories are cells divided into

A
  1. Nucleus and cytosol
  2. Organelles in secretory and endocytic pathways (ER, Golgi, endosomes, lysosomes)
  3. Mitochondria
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10
Q

What is responsible for allowing the lumen of the different cellular compartments to communicate with each other and with the cell exterior

A

budding and fusion

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11
Q

What type of transport is between the nucleus and cytosol through nuclear pore complexes

A

Gated transport

active transport and free diffusion

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12
Q

What type of transport is associated with protein translocators that directly transport specific proteins from cytosol across an organelle membrane

A

Transmembrane Transport

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13
Q

What type of transport is associated with membrane-enclosed transport intermediates and move proteins between various compartments via vesicles

A

Vesicular Transport

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14
Q

What do sorting signals play an important role in

A

Protein transfer/transport to various compartments

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15
Q

Sorting signals are made up of?

A

stretch of amino acids, typically 15-60 residues long

-may be localized on N or C terminus or with protein sequence

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16
Q

What form signal patches?

A

Multiple scattered sequences in proteins

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17
Q

What enzyme can remove signal after protein reaches final destination

A

Signal peptidase

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18
Q

What are signal sequences recognized by?

A

Complementary receptors

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19
Q

Give some properties of nuclear transport

A

Gated, bidirectional, and selective

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20
Q

Proteins that are needed by the nucleus are imported from where

A

cytoplasm, where they are synthesized

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21
Q

Where are tRNA and mRNA exported after they are synthesized in the nucleus

A

cytosol

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22
Q

What are perforated nuclear envelopes in eukaryotes referred to as

A

Nuclear Pore Complexes (NPCs)

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23
Q

Give some properties of Nuclear Pore Complexes

A
  1. Composed of 30 different proteins or nucleoporins
  2. Arranged in octagonal symmetry with one or more aqueous pores
  3. Transport molecules in both directions
  4. passive diffusion of small molecules and facilitated transport
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24
Q

In Nuclear Pore complexes what facilitates transport

A

binding of particles to fibrils extending from NPC

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25
Q

What signal is responsible for directing molecules to the nucleus

A

Nuclear localization signals (NLSs)

-type of sorting signal

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26
Q

What are some properties of Nuclear localization signals

A
  1. Short sequences rich in positively charged amino acids (lysine and arginine)
  2. Located on many different sites on proteins
    - forms loops or patches on surface
  3. Result in selective import of proteins into nucleus
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27
Q

What types of receptors recognize nuclear localization signals

A

nuclear import receptors (NIRs)

28
Q

List some features of Nuclear import receptors

A
  1. soluble cytosolic proteins

2. bind to NLS on protein and to NPC proteins present on fibrils that extend into cytoplasm

29
Q

Nuclear pore complexes have ________ repeats which serve as binding sites for import receptors

A

Phenylalanine glycine

30
Q

How do receptors plus cargo traverse the Nuclear pore complex

A

By binding, dissociating, and re-binding to adjacent Phenylalanine glycine repeats

31
Q

Nuclear export relies on what types of signals

A

Nuclear export signals on molecules that need to go out of the nucleus

32
Q

Although Nuclear export receptors are similar to nuclear import receptors, what is the key difference

A

Import receptors bring cargo into nucleus and export receptors bring cargo from nucleus to cytoplasm

33
Q

What drives nuclear transport in the appropriate direction

A

Gradient of Ran conformational states

34
Q

What binds to complex of import receptor and cargo to cause the release of the cargo

A

Ran-GTP

35
Q

In the cytoplasm what hydrolyzes Ran-GTP

A

Ran-GAP

-this leads to the release of the receptor from Ran-GDP and allows it to be ready for another cycle

36
Q

List some key features of shuttling proteins

A
  1. Some contain both Nuclear localization signal and Nuclear export signal
  2. shuttle back an forth between nucleus and cytosol
  3. Rate of import is greater than rate of export
37
Q

Gene regulatory proteins are tightly controlled by what two signals

A

Nuclear localization signal and nuclear export signal being turned on and off
-mechanism include being phosphorylated, proteolysis, and binding to inhibitory molecules

38
Q

What types of protein are encoded in nuclear DNA

A

Mitochondrial proteins

39
Q

The movement of proteins across outer and/or inner mitochondrial membranes is referred to as

A

Translocation

40
Q

What directs protein to correct compartments in the mitochondria

A

Signal sequences

-N-terminal and internal signal sequences

41
Q

Describe mitochondrial signal sequences

A
  1. Form amphiphilic alpha helix
  2. positively charged cluster on one end and are hydrophobic at the other end
  3. Specific receptor proteins recognize this configuration
  4. protein translocators mediate translocation
42
Q

What does Translocase of the outer membrane (TOM) do

A
  1. Required for import of all nucleus encoded proteins and inserts them in the outer membrane
43
Q

Where can you find Translocase of the inner membrane (TIM)

A

Present in both inner and outer membrane

44
Q

There are two TIM complexes, name them and list what they do

A
  1. TIM 22-mediates insertion of a specific subclass of proteins (ATP,ADP and Pi transporter)
  2. TIM 23-transports soluble protein into matrix and helps insert membrane proteins in inner membrane
45
Q

TOM and TIM complexes have two components, what are they

A
  1. Receptors for mitochondrial precursor proteins

2. Translocation signlas

46
Q

The Sorting and Assembly Machinery or SAM complex is responsible for what

A

Translocates and insets/fold beta barrel proteins in the outer membrane`

47
Q

What does the OXA complex do

A

Mediates the insertion of proteins that are synthesized in the mitochondria

48
Q

What keeps precursor proteins unfolded

A

Interactions with chaperone proteins (Cytosolic Hsp 70 family)

49
Q

List come of the key steps in protein import into the mitochondrial matrix

A
  1. import receptors of TOM bind signal sequence of incoming protein
  2. chaperones are stripped off and unfolded protein is fed, sequence signal first, into translocation channel
  3. TOM transport protein across outer membrane to inner membrane space
  4. Protein binds to TIM and moves through channel to matrix
  5. Signal sequence is cleaved off by peptidase
50
Q

Mitochondrial Hsp70 is bound to _____ on the matrix side

A

TIM 23

51
Q

Transport through TIM depends on what

A

membrane potential

52
Q

Hsp 70 releases protein in an ____

A

ATP dependent step

53
Q

Hsp 60 helps in folding of imported protein using ___

A

ATP

54
Q

Key steps of import of proteins into outer membrane of mitochondria

A
  1. Pass through TOM complex and enter inter-membrane space
  2. Bind to chaperone proteins
  3. Then bind to SAM complex in outer membrane
  4. SAM inserts and folds them in outer membrane
55
Q

List some key features of ER

A
  1. Network or branching tubules and sacs
  2. ER membrane continuous with nuclear membrane
  3. plays a central role in protein and lipid synthesis
56
Q

List some key features of ER signal sequences

A
  1. Vary in aa sequence

2. Have 8 or more non-polar aa’s at its center

57
Q

What two components guide ER signal sequences to the ER membrane

A
  1. Signal recognition particle (SRP)

2. SRP receptor

58
Q

List some key features of Signal Recognition Particles

A
  1. made of 6 different polypeptides bound to single RNA molecule
  2. cycles between ER membrane and cytosol and binds to the ER signal sequence
  3. Rod shaped with large hydrophobic pocket lined with methionines
59
Q

SRP wraps around large ribosomal subunit and binds at these two places

A
  1. ER signal sequence of emerging protein

2. Elongation factor binding site

60
Q

SRP-ribosome complex binds to what receptor present in ER membrane

A

SRP receptor

61
Q

Once SRP and receptor are released the protein is translocated across what membrane

A

ER membrane

62
Q

Describe the translocator present in the ER

A
  1. Has water filled pore
  2. Core is made of Sec61 complex
  3. 3 subunits with largest surrounding central pore
  4. Pore is gated by short helix
63
Q

List some key steps in protein translocation across ER

A
  1. SRP binds to ER signal sequence
  2. Signal sequence triggers opening of translocator
  3. signal sequence interacts with specific site w/in pore, called start-transfer signal
  4. Signal peptidase cleaves off signal
64
Q

Integration of membrane proteins require what

A

That some portions of protein pass through membrane and others do not

65
Q

What region in polypeptide stops transfer process before entire polypeptide is translocated

A

hydrophobic region, called stop transfer signal

66
Q

In multiple TM proteins what determines topology of the protein

A

Several combinations of start-transfer and stop-transfer

Molecular Biology (2 decks)

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