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BIO 344 > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

What cell is composed of a single intracellular compartment?

A

*bacteria (prokaryote)

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2
Q

What cell is divided into functionally distinct, membrane enclosed organelles?

A

*eukaryotes

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3
Q

What contains the genome?

A

*nucleus

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4
Q

What does the Golgi apparatus do?

A

*receives lipids and proteins from ER and ships them to other parts of the cell

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5
Q

What do lysozomes do?

A

*contain digestive enzymes that degrade old of malfunctioning organells

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6
Q

What do endosomes do?

A

*sorting compartment of the cell

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7
Q

What do peroxisomes do?

A

*small vesicular compartments that contain enzymes used in various oxidation reactions

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8
Q

What contain their own genomes?

A

*mitochondria and plastids

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9
Q

What are the four distinct families for the evolutionary scheme groups for intracellular compartments?

A
  • nucleus and cytosol are topologically continuous
  • all organelles that function in the secretory and endocytic pathways
  • the mitochondria
  • the plastids (only in plants)
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10
Q

What does the transport of protein synthesis depend on?

A

*aa sequence

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11
Q

Proteins that lack sorting signals go to where?

A

*cytosol

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12
Q

Proteins that have sorting signal go to where?

A

*nucleus, ER, mitochondria, plastids, peroxisomes

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13
Q

What are the 3 mechanisms of protein translocation?

A
  • gated transport
  • transmembrane transport
  • vesicular transport
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14
Q

What mechanism is when proteins move between the cytosol and the nucleus?

A

*gated transport

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15
Q

What acts as a selective gate for gated transport?

A

*nuclear pore complex

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16
Q

What mechanism is the transport of specific proteins across a membrane from the cytosol into a space that is topologically distinct?

A

*transmembrane

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17
Q

What does the protein have to do to get through the translocator?

A

*unfold to snake through

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18
Q

What mechanism is the membrane enclosed transport intermediates ferry proteins from one compartment to another?

A

*vesicular

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19
Q

In what mechanism does the cargo get discharged into a second compartment by fusing with the membrane enclosing that compartment?

A

*vesicular

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20
Q

What mechanism can only move proteins only between compartments that are topologically equivalent?

A

*vesicular

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21
Q

Protein transfer is usually guided by what?

A

*sorting signals in the protein

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22
Q

What are sorting signals recognized by?

A

*sorting receptors

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23
Q

What terminus are signal sequences on?

A

*N-terminus

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24
Q

What removes signal sequences once sorting is complete?

A

*signal peptidases

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25
Q

What is a multiple internal aa stretches that form specific 3D structure on surface?

A

*signal patch

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26
Q

What is the signal sequence for import into the nucleus?

A

*Lys-lys-lys-arg-lys

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27
Q

What is the signal sequence for import into peroxisomes?

A

*ser-lys-leu

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28
Q

What is the signal sequence for return to the ER?

A

*lys-asp-glu-leu

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29
Q

Why are signal sequences important?

A

*they are both necessary and sufficient for protein targeting

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30
Q

Signal sequences of all proteins are what?

A

*interchangeable

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31
Q

What are sorting receptors?

A
  • recognize classes of proteins

* reused

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32
Q

What possesses ribosomes that engage in protein synthesis?

A

*outer nuclear membrane

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33
Q

What contains proteins that are anchoring sites for chromatin and nuclear lamina?

A

*inner nuclear membrane

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34
Q

What encloses the DNA and defines the nuclear compartment?

A

*nuclear envelope

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35
Q

What is where proteins are made and transported to the perinuclear space?

A

*ER membrane

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36
Q

What are some proteins that are transported from the cytosol to the nuclear compartment?

A

*histones, DNA and RNA poly, RNA-processing proteins

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37
Q

What are some proteins that are transported from the nuclear compartment to the cytosol?

A

*tRNA and mRNA

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38
Q

Water soluble molecules do what?

A

*diffuse freely between nucleus and cytosol

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39
Q

60,000 Dalton molecules do what?

A

*use passive diffusion

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40
Q

How do DNA and RNA polys get into the nucleus?

A

*active transport

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41
Q

What contains transmembrane proteins that anchor?

A

*luminal subunit

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42
Q

What blocks passive diffusion of large macro molecules?

A

*nuclear basket

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43
Q

What is the reason that the NPC is selective?

A

*arises from the presence of sorting signals

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44
Q

How is NPC transport different than other transports?

A
  • occurs through large aqueous pore
  • fully folded nuclear proteins can be transported
  • ribosomal subunits pass as assembled particles
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45
Q

What is NLS?

A

*almost anywhere in aa sequence

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46
Q

What do nuclear import receptors bind to?

A

*NLS and NPC proteins

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47
Q

Nuclear import and export requires what?

A

*energy (utilizes GTP hydrolysis)

48
Q

What are the 2 conformational states of Ran?

A

*GTP and GDP

49
Q

What ran regulatory protein is on the cytosolic side?

A

*GAP

50
Q

What ran specific regulatory protein is on the nuclear side?

A

*GEF

51
Q

What controls cargo loading and unloading?

A

*Ran-GTP

52
Q

What contain their own DNA, ribosomes and other protein synthesis and is a double membrane bound?

A

*mitochondria and chloroplasts

53
Q

How do you make new mitochondria and chloroplasts?

A
  • results from growth of preexisting organelles

* growth depends mainly on import of proteins from the cytosol

54
Q

What is the target for matrix for mitochondrial proteins?

A

*N-terminal signal sequence

55
Q

What is the target for other compartments for mitochondrial proteins?

A

*internal sequence that is not removed

56
Q

Signal sequence for Mitochondrial import can form what?

A

*amphiphilic alpha helix

57
Q

What is alpha helix recognized by?

A

*receptor proteins, not specific sequence

58
Q

What are some multi-subunit protein translocators?

A
  • TOM complex
  • TIM
  • SAM
  • OXA
59
Q

What does TOM do?

A

*trnslocates proteins across outer membrane

60
Q

Where are beta barrels transported to?

A

*SAM complex

61
Q

What does TIM 23 do?

A

*transport some soluble proteins into the matrix and helps to insert transmembrane proteins into the inner membrane

62
Q

What does TIM 22 do?

A

*mediates the insertion of a subclass of inner membrane proteins

63
Q

What does OXA do?

A

*mediates the insertion of those inner membrane proteins that are synthesized within mitochondria

64
Q

What gradient does the thylakoid membrane in chloroplast use to direct proteins?

A

*H+ gradient across their thylakoid membrane, not inner membrane

65
Q

What are the four routes to translocate protein into the thylakoid space?

A
  • sec path
  • SRP like path
  • TAT path
  • spontaneous insertion
66
Q

What do peroxisomes posses?

A

*single membrane

67
Q

Where are the amino acids sequence located at in peroxisomes?

A

*C-terminus

68
Q

What do peroxin do?

A

*import proteins

69
Q

What powers peroxins?

A

*ATP hydrolysis

70
Q

What membrane constitutes more than half of the total membrane?

A

*endoplasmic reticulum

71
Q

Why does the ER have ribosomes?

A

*for translocation across the ER membrane usually occurs during translation (co-translationally)

72
Q

What is the site of production of all the transmembrane proteins and lipids for most of the cell’s organelles?

A

*ER membrane

73
Q

What are the two types of proteins the ER captures from the cytosol?

A
  • transmembrane

* water soluble

74
Q

Which proteins are only partly translocated across the ER membrane and become embedded in it?

A

*transmembrane

75
Q

Which proteins are fully translocated across the ER membrane and are released into the lumen?

A

*water soluble proteins

76
Q

ER signal sequences are directed where?

A

*ER (SRP and SRP receptor)

77
Q

Improperly folded proteins are exported from the ER and degraded in what?

A

*cytosol

78
Q

What do proteins need to do if they are translocated?

A

*need to be retrotranslocated

79
Q

Translocated polypeptide chains fold and assemble in what?

A

*the lumen of the rough ER

80
Q

ER resident proteins that are in the lumen contain an ER retention signal where?

A

*4 aa at C terminus

81
Q

Most proteins synthesized in the rough ER are what?

A

*glycosylated (about half are)

82
Q

Most of the soluble and membrane bound proteins that are made in the ER are what?

A

*glycoproteins

83
Q

Oligosaccharides are used for what?

A

*as tags to mark the state of protein folding

84
Q

What degrades the protein into an amino acid?

A

*proteasome

85
Q

The ER assembles what?

A

*most lipid bilayers

86
Q

Phospholipid synthesis occurs exclusively in the cytosolic leaflet of the ER membrane. Why?

A

*first thing they encounter

87
Q

What does scramblase do?

A
  • flips phospholipids for us between the two leaflets

* ensure symmetric growth

88
Q

What does flippases do?

A
  • flip phospholipids (maintain highly asymmetric composition)
  • contributes to membrane potential
89
Q

How do cells respond quickly to the world around it?

A

*continually adjust the composition of their plasma membrane (add and remove cell surface proteins embedded in the membrane, exo and endocytosis)

90
Q

What is exocytosis?

A

*vesicle membrane becomes part of plasma membrane

91
Q

What do transport vesicles continually do?

A

*bud off from one membrane and fuse with another

92
Q

What are some membrane traffic pathways?

A
  • biosynthetic-secretory pathway
  • endocytic pathway
  • retrograde retrieval pathway
93
Q

What is endocytic pathway?

A

*leads inward from the plasma membrane

94
Q

What is biosynthetic secretory pathway?

A

*going outward from the ER to Golgi

95
Q

What is retrograde retrieval pathway?

A

*backflow of secreted components (move back to donor compartment)

96
Q

What is vesicular transport?

A

*between 10+ chemically distinct membrane enclosed compartments

97
Q

How are the unique characteristics of the compartments maintained?

A

*by retrograde retrieval processes (adjust membrane), have pumps (adjust lumen components)

98
Q

What are coated vesicles?

A

*variety of cage proteins

99
Q

What are the two functions of protein coat?

A
  • concentrates specific membrane proteins in a specialized patch
  • coat molds the forming vesicle
100
Q

Three types of coats?

A
  • clathrin
  • COPI
  • COPII
101
Q

What does clathrin do?

A

*mediate transport from the Golgi apparatus and from the plasma membrane

102
Q

What does COPI and COPII do?

A

*mediate transport from the ER and from the Golgi cisternae

103
Q

What does triskelions do?

A

*spontaneously form basket like substance

104
Q

Phosphoinositides mark what?

A

*organelles and membrane domains

105
Q

What makes up less than 10% of total phospholipids in the membrane?

A

*phosphoinositides

106
Q

Different PIPs show the cells what?

A

*where to send things back to (due to phophoralytation at 3,4, or 5 group)

107
Q

Local production of PIPs plays a major part of what?

A

*regulating assembly of clathrin coats

108
Q

What controls the assembly of clathrin coats?

A

*Coat recruitment GTPases (use energy to recruit proteins)

109
Q

Where are coat recruitment GTPases usually found in high concentrations at?

A

*in the cytosol in an inactive, GDP bound state

110
Q

In order for GDP to become active what has to happen?

A

*sat GEF has to mediate this, helix pops out and inserts itself into the cytosolic leaflet of membrane

111
Q

Monomeric GTPases control what?

A

*coat assembly

112
Q

In its GTP bound state, the Sar1 protein exposes what?

A

*an amphiphilic helix

113
Q

Sar1 bound to GTP recruits what?

A

*sec 23 and 24 (adapter proteins), bind cargo, cop II coat forms

114
Q

What is sec 13/31?

A

*dimers

115
Q

What does sec 13/31 associate with to form what?

A

*sec 23 and 24 to form a protein cage

116
Q

What does a protein cage do?

A

*function as energy to pull in vesicle and pinch it off at membrane

117
Q

What does GDP have to be switched to in order to become active?

A

*GTP

BIO 344 (3 decks)

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