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Advanced Cell Biology > Lecture 12 - Intracellular compartments and protein sorting > Flashcards

Lecture 12 - Intracellular compartments and protein sorting Flashcards

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1
Q

Advantages of sub cellular compartments

A

Allows different ‘factories’ within the cell

Incompatible metabolic processes can go on next to each other

e.g. pH, ion concentration

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2
Q

Sub cellular compartmentalisation has driven

A

Evolution

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3
Q

Organelles have (4)

A
  1. Specific protein and lipid composition
  2. Specific structure
  3. Specific number
  4. Specific arrangement
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4
Q

Organelle number is up or downregulated depending on (2)

A

The environment

The metabolic needs of the cell

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5
Q

The Golgi can fragment during cell division

A

Into two structures to be distributed to mother and daughter cells

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6
Q

Membrane contacts allow

A

Communication between organelles and cells

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7
Q

Tether proteins

A

Aid membrane fusion

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8
Q

Exchange factors

A

Involved in cell signalling pathways

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9
Q

An animal cell contains

A

10 billion protein molecules

10,000 different kinds

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10
Q

Almost all proteins are synthesised in the

A

Cytoplasm

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11
Q

Most proteins need to be transported

A

To the correct location to be functional

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12
Q

Phospholipid bilayers allow

A

The formation of compartments

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13
Q

Structure of a phospholipid

A
  1. Hydrophobic tails

2. Hydrophilic head

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14
Q

Structure of the hydrophobic tail of a phospholipid

Non Polar

A

One straight hydrocarbon tail

One bent hydrocarbon tail - a cis C=C double bond

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15
Q

Structure of the hydrophilic head of a phospholipid

Polar

A

Hydrophobic tails are bonded to a Glycerol
Glycerol is bonded to a Phosphate
Phosphate is bonded to a variable residue
e.g. choline, ethanolamine

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16
Q

Phospholipids are amphipathic/amphiphilic

A

Containing both polar and non polar parts

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17
Q

Lipophilic

A

Fat loving, non polar, fatty acid

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18
Q

The variable residue bonded to the polar head group of a phospholipid provides

A

Different properties

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19
Q

All lipid molecules in the cell are

A

Amphipathic

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20
Q

The C=C ‘kink’ in the phospholipid tail allows for

A

Membrane fluidity

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21
Q

The length of the phospholipid tail also allows for

A

More electrostatic interactions between other phospholipids (more fluidity)

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22
Q

Cholesterol

A

Helps maintain membrane fluidity and flexibility

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23
Q

Structure of cholesterol

A

Polar head group attached to
Rigid steroid rings attached to
Non polar hydrocarbon tail

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24
Q

Cholesterol stabilises membranes

A

By interacting with fatty acids (slipping inbetween) the phospholipids

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25
Q

Without cholesterol in the membranes what would happen? (2)

A

When temperatures are increased the membranes could burst

When temperatures are decreased phospholipids could crystallise

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26
Q

Cholesterol has an important role in

A

Permeability and mobility of membranes

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27
Q

Micelle

A

Lipid molecules that arrange themselves in a spherical form in aqueous solutions in a single layer

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28
Q

Vesicle

A

A large structure consisting of liquid enclosed by a lipid bilayer

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29
Q

The two fatty acid tails in a phospholipid cause it to form a

A

Bilayer

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30
Q

Why do phospholipids form enclosed compartments?

A

Exposure of hydrocarbon tails is energetically unfavourable

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31
Q

A phospholipid with a single tail will form

A

Micelles (single layer)

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32
Q

Lipid molecules in a bilayer will diffuse laterally at around

A

2um/sec (very dynamic)

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33
Q

Phospholipid translocators

A

Enzymes that catalyse the rapid ‘flip flop’ of phospholipids from one side of the bilayer to the other

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34
Q

Interactions between lipids and proteins in the bilayer

A

Form micro domains
Influences membrane and protein properties
e.g. Signalling processes, micro domain formation

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35
Q

Micro domains + cholesterol are called

A

Rafts

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36
Q

Rafts

A

‘Swim’ in the lipid bilayer

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37
Q

What do rafts do?

A

Islands for signalling

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38
Q

How do cells move proteins between compartments? (3)

A
  1. Gated transport
  2. Transmembrane transport
  3. Vesicular transport
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39
Q

A type of organelle transport that has selective gates that actively transport large molecules and diffuse small molecules is?

A

Gated transport

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40
Q

Example of gated transport

A

Transport into the nucleus

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41
Q

A type of organelle transport that unwinds and pulls specific proteins through the membrane

A

Transmembrane transport

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42
Q

Example of transmembrane transport

A

Transport in mitochondria, plastids, peroxisomes, ER

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43
Q

A type of organelle transport that has membrane enclosed vesicles, that fuse with the membrane of another organelle to release cargo

A

Vesicular transport

44
Q

Example of vesicular transport

A

ER, Golgi, secretory vesicles, lysosomes, late endosomes, early endosomes

45
Q

Each of the transport systems has

A

Particular proteins associated with it

46
Q

Proteins are made in

A

The cytosol on ribosomes

47
Q

Proteins are transported to specific places depending on their

A

‘Labels’ (sorting signals)

48
Q

Sorting signals are

A

Amino acid ‘labels’ at the end of a polypeptide that tell them where to go
They have specific physio-chemical properties

49
Q

Signal peptidases

A

Remove the sorting signal after transport

50
Q

Some signals are

A

Spaced out along the protein, coming together to form a 3d ‘signal patch’

51
Q

Recognition based on protein-protein interactions forms the basis of

A

Most cellular processes

52
Q

Positively charged amino acids in a protein can be a signal for

A

Nuclear import

53
Q

Signals can be for

A

Import or Export

54
Q

Sorting signals are usually at the

A

N terminus

55
Q

Which end of a protein exits the ribosome first?

A

N terminus

56
Q

Signals are usually at the beginning of a protein (N terminus)

A

Because the folding is inhibited otherwise the signal will be folded into the structure

57
Q

How can you identify sorting signals? (4)

A
  1. Identify minimal sequences that are responsible for targeting a specific protein
  2. Fuse that sequence to a reporter gene (GFP)
  3. Mutate single amino acids within the sequence
  4. This will determine which amino acids are integral to targeting (as the protein will remain in the cytoplasm and not be transported)
58
Q

Gated transport into the nucleus is through

A

Nuclear pores

59
Q

Structure of a nuclear pore

A

30 proteins make a ‘basket’

Only 5 types of proteins:

  1. Annular subunits (central)
  2. Lumenal subunits (TM)
  3. Ring subunits (faces)
  4. Fibrils (FG repeats)
  5. Nuclear basket
60
Q

Unstructured proteins inside a nuclear pore form a tangled network that

A

Resists movement

61
Q

Molecules less than 5kDa can move

A

Freely through a nuclear pore

62
Q

Molecules greater than 60kDa

A

Need to be actively transported

63
Q

Fibrils

A

Seal the pore

Grab proteins that should go into the nucleus

64
Q

What is transported in and out of the nucleus?

A 
mRNA (out)
Transcription Factors (in)
Ribosomal proteins (in)
65
Q

Transcription Factors

A

Proteins which activate gene expression and bind to specific promotor regions

66
Q

In one second

A

1000 proteins pass through a pore

67
Q

Ribosomal proteins are transported IN because

A

rRNA is inside the nucleus

Too complex a process for the cytoplasm

68
Q

The ribosomal subunits are transported

A

Out of the nucleus

69
Q

NLSs

A

Nuclear localisation signals

70
Q

NLSs can be located

A

Anywhere on the protein

71
Q

NLSs are

A

Positively charged residues

72
Q

Only one protein in a complex needs to have a NLSs for

A

All subunits to be transported

73
Q

Nuclear import receptors

A

Recognise NLSs directly or indirectly

‘S’ shaped with a pocket to bind cargo

74
Q

Karyopherins, Importins

A

Another name for nuclear import receptors

75
Q

Nuclear import adaptor proteins

A

Receptor is binding another protein (an adaptor) that bind the protein

76
Q

Ran

A

Small GTPase - molecular switch with two states, active (GTP cound) inactive (GDP bound)

77
Q

GAPs

A

GTPase activating proteins
Switch Ran OFF
By increasing rate of GTP hydrolysis

78
Q

GEFs

A

Guanine nucleotide exchange factors
Turn Ran ON
By increasing rate of GDP-GTP exchange

79
Q

Ran-GEF is found in

A

The nucleus

80
Q

Ran-GAP is found in

A

The cytosol

81
Q

Karyopherins in the cytosol

A

Do NOT bind Ran-GDP

Therefore cytosolic Karyopherins are free to bind cargo

82
Q

Karyopherins in the nucleus

A

DO bind Ran-GTP

Causing a confromational change in the Karyopherin that releases the cargo

83
Q

Karyopherins that get transported back into the cytosol

A

Ran-GTP is hydrolysed by GAP and Karyopherin is released to allow more cargo to bind

84
Q

Ran-GDP is transported

A

Back into the nucleus via its own nuclear transport receptor and converted back to Ran-GTP by GEF

85
Q

Nuclear export occurs when

A

Specific proteins interact with Karyopherins in a Ran-GTP specific manner

86
Q

Nuclear import and export is regulated by a

A

Molecular switch

Ran-GTPase

87
Q

Transmembrane transport into the mitochondria is special because

A

It has a double membrane

Proteins can be in the outer membrane, the intermembrane space, the matrix, or the inner membrane

88
Q

Mitochondria in live cells look like

A

Spaghetti or worms

Interconnected networks, highly dynamic, fusing and dividing all the time

89
Q

Proteins to be imported into the mitochondria are

A

Synthesised in the ribosomes, but not folded

90
Q

Chaperones

A

Are proteins that bind and block folding

91
Q

Signals that determine entry into the mitochondria matrix

A

Form amphiphilic alpha helices with positively charged clusters on one side

92
Q

Mitochondrial entry signals are recognised by

A

Protein translocator complexes TOM and TIM

93
Q

TOM

A

Translocator outer mitochondrial membrane complex

94
Q

TIM

A

Translocator inner mitochondrial membrane complex

95
Q

TOM transports proteins across the outer mitochondrial membrane by

A

Binding to the signal sequence and hydrolysing ATP

This causes dissociation of Chaperones

96
Q

Hsp60 and 70

A

Family of chaperone proteins in the matrix of mitochondria that fold proteins

97
Q

TIM transports proteins across the inner mitochondrial membrane by

A

Binding to the signal sequence and using the inner membrane potential to drive the positively charged residues into the matrix

98
Q

Signal sequences directed to the mitochondria are

A

Positively charged

99
Q

Once the protein is inside the matrix it is immediately bound by

A

Hsp70 (chaperone protein)

100
Q

ATP hydrolysis releases

A

Hsp70 from the polypeptide

101
Q

Hsp60

A

Folds the protein in the matrix once Hsp70 has been released

102
Q

Inner mitochondrial membrane proteins have either:

A
  1. A hydrophobic region region following the positively charged signal sequence - this stops TIM23 from translocating the protein through to the matrix
  2. A second signal sequence facilitating transport back from the matrix to the inter membrane space via the OXA translocator
  3. Metabolite transporters are pulled through TOM as a loop, and bound by intermembrane chaperones. These guide the transporters to a second TIM complex (TIM22) which inserts them into the membrane
103
Q

Intermembrane space proteins either

A
  1. Have a sequence that stops TIM23 moving the protein into the maxtrix or cytosol (so remains in the space)
  2. Get transported through OXA and then have the signal cleaved by a specific peptidase
104
Q

Method to study the mechanism of protein translocation (4)

A

In vitro radiolabelled translated protein incubated with and without purified organelles:

  1. Centrifuged proteins that have gone into the organelle will pellet with the organelle, proteins which have not will be in the supernatant
  2. SDS page analysis will show proteins which have had sequence cleaved (lower MW so will travel faster through the gel)
  3. Incubate organelles with proteases, proteins that have not been translocated will be degraded
  4. Genetics: yeast cells have histidine in the cytoplasm, can artifically add a ER targeting sequence to HisDH, so cell will not generate histidine and cells die. Mutating the His gene will allow the mutant cells to live. Mutated protein must be involved in translocation
105
Q

Chloroplast transport is similar to mitochondrial transport but requires

A

An additional step

Different topological problems

106
Q

In chloroplasts

A

A second hydrophobic sequence is unmasked after the first is cleaved in the stroma

107
Q

Chloroplasts use

A

Energy from GTP and ATP to get photosystem proteins across a double membrane
Then a H+ gradient across the thylakoid membrane

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