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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
Unsaturated lipids …
Increase membrane fluidity
26
What kind of variation in head groups of phospholipids can you have?
Variation in what is on the phosphate ``` Glycerol Choline Ethanolamine Serine Glucose Inositol ```
27
Importance of variation of head groups in phospholipids
Plays a role in protein-membrane interactions, signalling and recognition.
28
What type of ring system lipid are in prokaryotes ?
Hopanoids - A pentacyclic compound (5 rings)
29
What type of ring system lipid are in eukaryotes?
Cholesterol - a tetracycline compound (a steroid)
30
Describe the general structure of Hopanoids and cholesterol inside the membrane (3 things)
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
31
What do Hopanoids and cholesterol do?
Intercalate into the bilayer and increase membrane stiffness
32
Where are Triglycerates (fats and oils) stored and why?
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)
33
Two ways lipids can move in a membrane
Lateral | Transverse
34
Lateral movement of lipids
Move within one bilayer (leaflet) | Relatively fast
35
What is transverse movement of lipid
Move from one leaflet to the other leaflet (to the other side of the membrane)
36
What is transverse also called
Flip flop
37
What could make it hard for a lipid to do transverse movement and why?
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
What are flippases
Proteins that catalyse flip-flop of specific lipids to create asymmetrical of the lipids in the leaflets
39
3 classes of proteins in or on membranes
Integral membrane proteins Peripheral membrane proteins Membrane anchored proteins
40
Integral membrane proteins 3 types + example
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
X
X
42
How can we predict transmembrane domains?
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
What is a hydropathy index
Scan from N terminus to C terminus of a protein and plot where hydrophobic residues (amino acids)
44
What does the hydropathy index graph of bacteriorhodopsin show?
you see 7 regions that are more hydrophobic and these represent the 7 alpha helices that are in the its membrane
45
How do peripheral membrane proteins associate with the membrane lipids and proteins ?
Polar interactions
46
How can peripheral membrane proteins be extracted to study them separately?
High salt concentrations which disturbs polar interactions
47
Two classes of membrane anchor proteins
Extracellular Cytoplasmic
48
What are the three main classes of cytoplasmic membrane anchored proteins? (And what are they)
S-acylation N-myristoylation Prenylation PROTEIN LIPIDATIONS
49
S-acylation What type of modification Reversible or irreversible Occurs on what residues?
PTM Reversible Occurs on cysteine residues
50
What happens in S Acylation/s-palmitoylation
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
Where does N-myristoylation occur
Only occurs on the N terminal glycine residue (on the amino group)
52
Two ways N-myristoylation can happen
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
N-myristoylation What type of modification Reversible or irreversible Occurs on what residues?
PTM and co translational Irreversible On N terminal glycine
54
Prenylation What type of modification Reversible or irreversible Occurs on what residues?
PTM irreversible On cysteine in C terminal end where there is a CaaX motif
55
What is a CaaX motif?
``` 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
Two kinds of Prenylation
Farnesyl (if X is A/C/M/S/Q) | Geranylgeranyl (if X is E/L)
57
Two main extra cellular protein lipidations (membrane anchored proteins)
``` Lipoprotein (in prokaryotes) GPI anchor (in eukaryotes) ```
58
Lipoprotein What type of modification Occurs on what residues? What is added?
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
What does GPI anchor stand for?
Glycosyl-phosphatidyl-inositol
60
``` GPI anchor  What type of modification? Where does it occur? What does it consist of? + what are the lipid tails linked to? ```
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
What type of movements do lipids do that proteins DO NOT?
Flip-flop (transverse the membrane)
62
X something about important in mainting if vesicles bud off and asymmetrity maintained ???
X
63
Proteins are asymmetrical and don’t flip
X
64
Outside
``` Glycosylation Disulphide bridges (stabilise protein) ```
65
Cytoplasm
Phosphorylation (done by misses in the cytoplasm)
66
PTMs are different …
Inside and outside of the membrane
67
Lipid rafts/nanodomains 30 mins 55secs XXXX
Proteins with a longer transmembrane helix tend to partition in lipid rafts because that part of the membrane is thicker ????
68
What are lipid rafts/nanodomains?
Local, robust, dynamic membrane regions with different lipid and protein composition
69
What might we find in lipid rafts/nanodomains?
Lipoproteins GPI anchored proteins Receptors
70
3 main things that can pass though membrane
1. Gases 2. Hydrophobic molecules 3. Small polar molecules
71
2 main things that cannot pass through membrane
1. Large polar molecules | 2. Charged molecules
72
Passive transport is from a
High to low concentration | Renier says WITH the electrochemical gradient
73
Two types of passive transport
Channels | Transporters - bind molecules, undergo conformational change, release molecule on other side
74
Passive channels are | Two things
1. Selective for specific molecules | 2. Regulated (ligand/voltage gated)
75
Active transport is …
From low to high concentration | Renier says AGAINST the electrochemical gradient
76
Three ways to get energy for active transport
Light ATP hydrolysis Electrochemical gradient of a different molecule
77
Two types of coupled transport that occurs involving electrochemical gradients (for getting energy for active transport)
Symporter cotransporter Antiporter exchange
78
Membrane proteins have
A signal peptide (at the N terminus) a transmembrane region
79
Cytoplasmic proteins have
No signal peptide or TMD
80
Secreted proteins have
A signal peptide (at the N terminus)
81
Properties of a signal peptide
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
What does SignalP software do?
Predicts where signal peptides occur in amino acid sequence
83
7 steps of protein translocation (synthesis of secreted proteins)
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) 6. Signal peptide se cleaves after the signal peptide (so we never see the SP on the protein) 7. Once stop codon is reached the ribosome dissociates after completing translation
84
What type of process is protein translocation
Co translational (happens during translation)
85
Signal Recognition Particle (SRP) structure
Ribonucleoprotein complex (RNA world relic) Translational pause domain (part that blocks translation) Hinge SP binding protein
86
Explain the synthesis of transmembrane proteins
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
Where are the termini of a membrane protein ?
Protein with the N terminus on one side of the membrane and the C terminus on the other side (cytoplasmic)
88
What would the resulting membrane protein look like if it’s sequence has multiple TMDs?
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 (See handmade flashcards)

Building a phenotype - lectures (36 decks)

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