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Building a phenotype - lectures > Containment: From Lipids To Membranes > Flashcards

Containment: From Lipids To Membranes Flashcards

1
Q

How long ago did membranes exist ?

A

BEFORE the RNA world

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2
Q

Why is it likely that membranes existed much earlier than the RNA world

A

Because you need to contain molecules within an area to sustain life (prevent diffusion of components)

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3
Q

Why does it make sense that membranes existed earlier than the RNA world?

A

Because their formation is a natural phenomenon

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4
Q

Amphipathic

A

Has both hydrophobic and hydrophilic parts

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5
Q

Hydrophobic tail

A

C and H

Bonds not polarised because similar electronegativities

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6
Q

What makes the Hydrophilic head polar?

A

Head contains oxygen so makes head group polar

Oxygen is highly electronegative

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7
Q

Fatty acids in water form

A

Micelles

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8
Q

What is the hydrophobic effect?

A

In water fatty acids spontaneously form micelles

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9
Q

Example of how fatty acids could be produce abiotically

A

Fatty acids could be produced in geysers, catalyses by minerals

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10
Q

Explain how abiotic cells (division) can occur naturally?

A

Fatty acids assemble in micelles, vesicles and membranes

Vesicles with more content cause increase in osmotic pressure (when solute concentration outside cell is lower than in the cell) so it expands

Large vesicles tend to breakup in ‘abiotic cell division’

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11
Q

What are the three main types of lipids in the current cell membrane?

A

Phosphoglycerates
Spingholipids
(Both types of phospholipid)

Hopanoids and cholesterol

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12
Q

What do Phospholipids make up? And why phospholipids specifically?

A

Lipid bilayers

Because they have thicker hydrophobic tails

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13
Q

What effect do the aliphatic, non polar, hydrophobic tails have?

A

makes them more linear, thicker tail so by nature they are able to form more stable membranes (don’t form micelles)

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14
Q

Phosphoglycerides

A

Phosphate
Glycerol
Two fatty acids
Glycerol linkers ester bonds

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15
Q

X

A

X

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16
Q

What kind of linkers to sphingolipids have

A

Sphingosine linkers

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17
Q

Where is the slide bond in sphingosines?

A

Amino group links to a fatty acid chain

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18
Q

What is a sphingolioid made up of?

A

Sphingosine
Fatty acid
Phosphate

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19
Q

How do the phosphate and Sphingosine connect in a spingolipid?

A

The OH on the sphingolipid makes an ester bond with the phosphate

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20
Q

What sort of variation can you get in phospholipids?

A

Different tail lengths

Different tail saturation

Variation in head groups

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21
Q

In phospholipids what do longer tails do?

A

Increase membrane thickness

Decrease membrane fluidity

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22
Q

What are unsaturated fatty acids?

A

One of the tails contains one or more C=C

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23
Q

What are the two types of double bonds in lipids?

A

Trans (rare)

Cis (common - makes a kink)

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24
Q

What do double bond in one of the tails of a fatty acid do and how do they do it?

A

They increase membrane fluidity because the double bond means that they take up more space

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25
Q

Unsaturated lipids …

A

Increase membrane fluidity

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26
Q

What kind of variation in head groups of phospholipids can you have?

A

Variation in what is on the phosphate

Glycerol 
Choline
Ethanolamine 
Serine
Glucose
Inositol
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27
Q

Importance of variation of head groups in phospholipids

A

Plays a role in protein-membrane interactions, signalling and recognition.

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28
Q

What type of ring system lipid are in prokaryotes ?

A

Hopanoids - A pentacyclic compound (5 rings)

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29
Q

What type of ring system lipid are in eukaryotes?

A

Cholesterol - a tetracycline compound (a steroid)

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30
Q

Describe the general structure of Hopanoids and cholesterol inside the membrane (3 things)

A

Mostly hydrophobic

Has a small hydroxyl group which sticks out at the surface of the membrane

Rest of the ring structure is inside the membrane - intercalates into the bilayer and increases membrane stiffness

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31
Q

What do Hopanoids and cholesterol do?

A

Intercalate into the bilayer and increase membrane stiffness

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32
Q

Where are Triglycerates (fats and oils) stored and why?

A

Inside lipid droplets or inside the two bolsters of a membrane

Because they can be in between the hydrophobic tails (the fats and oils are hydrophobic)

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33
Q

Two ways lipids can move in a membrane

A

Lateral

Transverse

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34
Q

Lateral movement of lipids

A

Move within one bilayer (leaflet)

Relatively fast

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35
Q

What is transverse movement of lipid

A

Move from one leaflet to the other leaflet (to the other side of the membrane)

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36
Q

What is transverse also called

A

Flip flop

37
Q

What could make it hard for a lipid to do transverse movement and why?

A

If lipid has a big head groups it’s harder for it to do transverse movement (cos would have to go through the hydrophilic middle of the bilayer)

38
Q

What are flippases

A

Proteins that catalyse flip-flop of specific lipids to create asymmetrical of the lipids in the leaflets

39
Q

3 classes of proteins in or on membranes

A

Integral membrane proteins
Peripheral membrane proteins
Membrane anchored proteins

40
Q

Integral membrane proteins

3 types + example

A

Alpha helix (eg. Receptors have this structure)

Helical bundle - multiple alpha helices (eg. Transporters, enzymes, receptors)

Beta barrel - makes a pire in the membrane (eg. Transporters)

41
Q

X

A

X

42
Q

How can we predict transmembrane domains?

A

Scan from N terminus to C terminus of a protein and plot where hydrophobic residues (amino acids) are (hydropathy index)

Pick out regions that are more hydrophobic than other regions

However many regions this is gives an indication of how many transmembrane domains there are

43
Q

What is a hydropathy index

A

Scan from N terminus to C terminus of a protein and plot where hydrophobic residues (amino acids)

44
Q

What does the hydropathy index graph of bacteriorhodopsin show?

A

you see 7 regions that are more hydrophobic and these represent the 7 alpha helices that are in the its membrane

45
Q

How do peripheral membrane proteins associate with the membrane lipids and proteins ?

A

Polar interactions

46
Q

How can peripheral membrane proteins be extracted to study them separately?

A

High salt concentrations which disturbs polar interactions

47
Q

Two classes of membrane anchor proteins

A

Extracellular

Cytoplasmic

48
Q

What are the three main classes of cytoplasmic membrane anchored proteins?

(And what are they)

A

S-acylation
N-myristoylation
Prenylation

PROTEIN LIPIDATIONS

49
Q

S-acylation

What type of modification
Reversible or irreversible
Occurs on what residues?

A

PTM
Reversible
Occurs on cysteine residues

50
Q

What happens in S Acylation/s-palmitoylation

A

Lipid tail added via thioester bond onto the sulfur of the cystein in the protein

= protein now associated with the membrane

Enzymes that add and removed the lipid tail so can regulate whether or not to make the protein associated or not associated with the membrane

51
Q

Where does N-myristoylation occur

A

Only occurs on the N terminal glycine residue (on the amino group)

52
Q

Two ways N-myristoylation can happen

A
  1. Protein cleaved in cytoplasm, produces glycine at the end, enzymes that therefore add myristoylate, causes the protein to move to the membrane
  2. Can happen cotranslationally: methionine is first AA but then it’s removed during translation, if there is then a glycine then this becomes myristoylated.
53
Q

N-myristoylation

What type of modification
Reversible or irreversible
Occurs on what residues?

A

PTM and co translational
Irreversible
On N terminal glycine

54
Q

Prenylation

What type of modification
Reversible or irreversible
Occurs on what residues?

A

PTM
irreversible
On cysteine in C terminal end where there is a CaaX motif

55
Q

What is a CaaX motif?

A 
C = cysteine 
a = aliphatic residue 
X = the last residue

So Prenylation only occurs if it’s a cysteine then two aliphatic residues and then the final residue AND this occurs at the C terminus

56
Q

Two kinds of Prenylation

A

Farnesyl (if X is A/C/M/S/Q)

Geranylgeranyl (if X is E/L)

57
Q

Two main extra cellular protein lipidations (membrane anchored proteins)

A 
Lipoprotein (in prokaryotes)
GPI anchor (in eukaryotes)
58
Q

Lipoprotein

What type of modification
Occurs on what residues?
What is added?

A

PTM
On N terminal cysteine residue
Adds a complex with three lipid tails, two tails link to the sulfur in the cysteine, one tail linked to N terminus of protein

59
Q

What does GPI anchor stand for?

A

Glycosyl-phosphatidyl-inositol

60
Q 
GPI anchor

What type of modification?
Where does it occur? 
What does it consist of? + what are the lipid tails linked to?
A

Cotranslational process (modification is added after the protein is made BUT signal recognised as soon as protein emerges from ribosome)
C terminus of protein
Several sugars, Last sugar is inositol, Three lipid tails: one linked to inositol and the other two linked to the phosphoglycerate

61
Q

What type of movements do lipids do that proteins DO NOT?

A

Flip-flop (transverse the membrane)

62
Q

X something about important in mainting if vesicles bud off and asymmetrity maintained ???

A

X

63
Q

Proteins are asymmetrical and don’t flip

A

X

64
Q

Outside

A 
Glycosylation
Disulphide bridges (stabilise protein)
65
Q

Cytoplasm

A

Phosphorylation (done by misses in the cytoplasm)

66
Q

PTMs are different …

A

Inside and outside of the membrane

67
Q

Lipid rafts/nanodomains

30 mins 55secs XXXX

A

Proteins with a longer transmembrane helix tend to partition in lipid rafts because that part of the membrane is thicker ????

68
Q

What are lipid rafts/nanodomains?

A

Local, robust, dynamic membrane regions with different lipid and protein composition

69
Q

What might we find in lipid rafts/nanodomains?

A

Lipoproteins
GPI anchored proteins
Receptors

70
Q

3 main things that can pass though membrane

A
  1. Gases
  2. Hydrophobic molecules
  3. Small polar molecules
71
Q

2 main things that cannot pass through membrane

A
  1. Large polar molecules

2. Charged molecules

72
Q

Passive transport is from a

A

High to low concentration

Renier says WITH the electrochemical gradient

73
Q

Two types of passive transport

A

Channels

Transporters - bind molecules, undergo conformational change, release molecule on other side

74
Q

Passive channels are

Two things

A
  1. Selective for specific molecules

2. Regulated (ligand/voltage gated)

75
Q

Active transport is …

A

From low to high concentration

Renier says AGAINST the electrochemical gradient

76
Q

Three ways to get energy for active transport

A

Light
ATP hydrolysis
Electrochemical gradient of a different molecule

77
Q

Two types of coupled transport that occurs involving electrochemical gradients (for getting energy for active transport)

A

Symporter cotransporter

Antiporter exchange

78
Q

Membrane proteins have

A

A signal peptide (at the N terminus)

a transmembrane region

79
Q

Cytoplasmic proteins have

A

No signal peptide or TMD

80
Q

Secreted proteins have

A

A signal peptide (at the N terminus)

81
Q

Properties of a signal peptide

A

N terminal amino acid is MET

7-15 hydrophobic residues (that make an amphipathic helix)

3-7 uncharged residues in an AxA pattern

1-6 acidic residues

82
Q

What does SignalP software do?

A

Predicts where signal peptides occur in amino acid sequence

83
Q

7 steps of protein translocation (synthesis of secreted proteins)

A
  1. Hydrophobic signal peptide emerges from the ribosome after translation
  2. Signal recognition particle (SRP) binds SP and blocks rest of translation
  3. SRP binds to SRP receptor on the membrane (prokaryotes = plasma membrane, eukaryotes = rough ER membrane)
  4. Signal peptide enters protein translocation which is in the membrane
  5. When this happens it signals SRP and receptor to dissociate and TRANSLATION CONTINUES

(So now when the protein is release it’s released into the lumen of the ER/extracellular space)

  1. Signal peptide se cleaves after the signal peptide (so we never see the SP on the protein)
  2. Once stop codon is reached the ribosome dissociates after completing translation
84
Q

What type of process is protein translocation

A

Co translational (happens during translation)

85
Q

Signal Recognition Particle (SRP) structure

A

Ribonucleoprotein complex (RNA world relic)

Translational pause domain (part that blocks translation)
Hinge
SP binding protein

86
Q

Explain the synthesis of transmembrane proteins

A

Same process as protein translocation however if there is a TMD then the presence of a second hydrophobic alpha helix sends a STOP signal to the translocator.

Ribosome dissociates from translocator, still continues translation but that part of the protein stays in the cytoplasm

87
Q

Where are the termini of a membrane protein ?

A

Protein with the N terminus on one side of the membrane and the C terminus on the other side (cytoplasmic)

88
Q

What would the resulting membrane protein look like if it’s sequence has multiple TMDs?

A

Signal peptide = start signal (takes it to membrane)

2nd hydrophobic alpha helix = stop signal to translator so protein translation continues in cell not outside membrane

3rd hydrophobic alpha helix = sends start signal to translocator and tells it to go back into membrane so protein is translated and passed back outside membrane

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Building a phenotype - lectures (36 decks)

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