Containment: From Lipids To Membranes Flashcards
How long ago did membranes exist ?
BEFORE the RNA world
Why is it likely that membranes existed much earlier than the RNA world
Because you need to contain molecules within an area to sustain life (prevent diffusion of components)
Why does it make sense that membranes existed earlier than the RNA world?
Because their formation is a natural phenomenon
Amphipathic
Has both hydrophobic and hydrophilic parts
Hydrophobic tail
C and H
Bonds not polarised because similar electronegativities
What makes the Hydrophilic head polar?
Head contains oxygen so makes head group polar
Oxygen is highly electronegative
Fatty acids in water form
Micelles
What is the hydrophobic effect?
In water fatty acids spontaneously form micelles
Example of how fatty acids could be produce abiotically
Fatty acids could be produced in geysers, catalyses by minerals
Explain how abiotic cells (division) can occur naturally?
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’
What are the three main types of lipids in the current cell membrane?
Phosphoglycerates
Spingholipids
(Both types of phospholipid)
Hopanoids and cholesterol
What do Phospholipids make up? And why phospholipids specifically?
Lipid bilayers
Because they have thicker hydrophobic tails
What effect do the aliphatic, non polar, hydrophobic tails have?
makes them more linear, thicker tail so by nature they are able to form more stable membranes (don’t form micelles)
Phosphoglycerides
Phosphate
Glycerol
Two fatty acids
Glycerol linkers ester bonds
X
X
What kind of linkers to sphingolipids have
Sphingosine linkers
Where is the slide bond in sphingosines?
Amino group links to a fatty acid chain
What is a sphingolioid made up of?
Sphingosine
Fatty acid
Phosphate
How do the phosphate and Sphingosine connect in a spingolipid?
The OH on the sphingolipid makes an ester bond with the phosphate
What sort of variation can you get in phospholipids?
Different tail lengths
Different tail saturation
Variation in head groups
In phospholipids what do longer tails do?
Increase membrane thickness
Decrease membrane fluidity
What are unsaturated fatty acids?
One of the tails contains one or more C=C
What are the two types of double bonds in lipids?
Trans (rare)
Cis (common - makes a kink)
What do double bond in one of the tails of a fatty acid do and how do they do it?
They increase membrane fluidity because the double bond means that they take up more space
Unsaturated lipids …
Increase membrane fluidity
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
Importance of variation of head groups in phospholipids
Plays a role in protein-membrane interactions, signalling and recognition.
What type of ring system lipid are in prokaryotes ?
Hopanoids - A pentacyclic compound (5 rings)
What type of ring system lipid are in eukaryotes?
Cholesterol - a tetracycline compound (a steroid)
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
What do Hopanoids and cholesterol do?
Intercalate into the bilayer and increase membrane stiffness
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)
Two ways lipids can move in a membrane
Lateral
Transverse
Lateral movement of lipids
Move within one bilayer (leaflet)
Relatively fast
What is transverse movement of lipid
Move from one leaflet to the other leaflet (to the other side of the membrane)
What is transverse also called
Flip flop
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)
What are flippases
Proteins that catalyse flip-flop of specific lipids to create asymmetrical of the lipids in the leaflets
3 classes of proteins in or on membranes
Integral membrane proteins
Peripheral membrane proteins
Membrane anchored proteins
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)
X
X
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
What is a hydropathy index
Scan from N terminus to C terminus of a protein and plot where hydrophobic residues (amino acids)
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
How do peripheral membrane proteins associate with the membrane lipids and proteins ?
Polar interactions
How can peripheral membrane proteins be extracted to study them separately?
High salt concentrations which disturbs polar interactions
Two classes of membrane anchor proteins
Extracellular
Cytoplasmic
What are the three main classes of cytoplasmic membrane anchored proteins?
(And what are they)
S-acylation
N-myristoylation
Prenylation
PROTEIN LIPIDATIONS
S-acylation
What type of modification
Reversible or irreversible
Occurs on what residues?
PTM
Reversible
Occurs on cysteine residues
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
Where does N-myristoylation occur
Only occurs on the N terminal glycine residue (on the amino group)
Two ways N-myristoylation can happen
- Protein cleaved in cytoplasm, produces glycine at the end, enzymes that therefore add myristoylate, causes the protein to move to the membrane
- Can happen cotranslationally: methionine is first AA but then it’s removed during translation, if there is then a glycine then this becomes myristoylated.
N-myristoylation
What type of modification
Reversible or irreversible
Occurs on what residues?
PTM and co translational
Irreversible
On N terminal glycine
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
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
Two kinds of Prenylation
Farnesyl (if X is A/C/M/S/Q)
Geranylgeranyl (if X is E/L)
Two main extra cellular protein lipidations (membrane anchored proteins)
Lipoprotein (in prokaryotes) GPI anchor (in eukaryotes)
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
What does GPI anchor stand for?
Glycosyl-phosphatidyl-inositol
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
What type of movements do lipids do that proteins DO NOT?
Flip-flop (transverse the membrane)
X something about important in mainting if vesicles bud off and asymmetrity maintained ???
X
Proteins are asymmetrical and don’t flip
X
Outside
Glycosylation Disulphide bridges (stabilise protein)
Cytoplasm
Phosphorylation (done by misses in the cytoplasm)
PTMs are different …
Inside and outside of the membrane
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 ????
What are lipid rafts/nanodomains?
Local, robust, dynamic membrane regions with different lipid and protein composition
What might we find in lipid rafts/nanodomains?
Lipoproteins
GPI anchored proteins
Receptors
3 main things that can pass though membrane
- Gases
- Hydrophobic molecules
- Small polar molecules
2 main things that cannot pass through membrane
- Large polar molecules
2. Charged molecules
Passive transport is from a
High to low concentration
Renier says WITH the electrochemical gradient
Two types of passive transport
Channels
Transporters - bind molecules, undergo conformational change, release molecule on other side
Passive channels are
Two things
- Selective for specific molecules
2. Regulated (ligand/voltage gated)
Active transport is …
From low to high concentration
Renier says AGAINST the electrochemical gradient
Three ways to get energy for active transport
Light
ATP hydrolysis
Electrochemical gradient of a different molecule
Two types of coupled transport that occurs involving electrochemical gradients (for getting energy for active transport)
Symporter cotransporter
Antiporter exchange
Membrane proteins have
A signal peptide (at the N terminus)
a transmembrane region
Cytoplasmic proteins have
No signal peptide or TMD
Secreted proteins have
A signal peptide (at the N terminus)
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
What does SignalP software do?
Predicts where signal peptides occur in amino acid sequence
7 steps of protein translocation (synthesis of secreted proteins)
- Hydrophobic signal peptide emerges from the ribosome after translation
- Signal recognition particle (SRP) binds SP and blocks rest of translation
- SRP binds to SRP receptor on the membrane (prokaryotes = plasma membrane, eukaryotes = rough ER membrane)
- Signal peptide enters protein translocation which is in the membrane
- 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)
- Signal peptide se cleaves after the signal peptide (so we never see the SP on the protein)
- Once stop codon is reached the ribosome dissociates after completing translation
What type of process is protein translocation
Co translational (happens during translation)
Signal Recognition Particle (SRP) structure
Ribonucleoprotein complex (RNA world relic)
Translational pause domain (part that blocks translation)
Hinge
SP binding protein
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
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)
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
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