Biochemistry - from lipids to membranes

Did cell membranes (most likely) exist before or after the RNA world

Before the RNA world - to prevent diffusion of the components

What are membranes made of

Amphipathic lipids. Hydrophilic head and hydrophobic tail.

Activity of amphipatic lipids in water

Spontaneously form micelles, vesicles, and membranes - due to polar nature

Three types of membrane lipids

Phospholipids split into phosphoglycerates and sphingolipids

And hopanoids (in prokaryotes) / steroids (in eukaryotes)

Features of the two types of phospholipids

Phosphoglycerates - consist of phosphate, glycerol, and two fatty acids. Have glycerol linkers

Sphingolipids - consist of phosphate, sphingosine, one fatty acid. Have sphingosine linkers

Possible variation in the phospholipids and why

Tail length - longer tails increase membrane thickness, and decrease fluidity

Saturation - greater/fewer double bonds, cis double bonds cause kinks (trans ones don’t)

Head groups - have different roles in signalling, recognition, protein-membrane interactions

Features of hopanoids / steroids

Flat, hydrophobic molecules

Intercalate into bilayer and increase membrane stiffness (e.g. cholesterol)

How can lipids be stored

In lipid droplets, surrounded by a phospholipid monolayer w/ proteins

Three types of membrane proteins

Integral, peripheral, and membrane-anchored

Feature of integral proteins

Embedded in the phospholipid bilayer, connected to both sides

Carry hydrophobic domains

Features of peripheral proteins

Only connected to the periphery of the bilayer

Associate with membrane lipids and proteins through polar interactions

Can be extracted at high salt conc. as this disrupts the polar bonds

Two-types of membrane-anchored proteins

Cytoplasmic and extracellular

Features of cytoplasmic membrane-anchored proteins

Cytoplasmic membrane-anchored protein are embedded through 3 main PTM lipidations:

• S-acylation (on cysteine, PTM, reversible)

• N-myristylation (on N-terminal glycine, irreversible)

• prenylation (on cysteine in C-terminal CaaX motif, irreversible)

Features of extracellular membrane-anchored proteins

Extracellular membrane-anchored proteins are able to be embedded either:

• in prokaryotes as a lipoprotein (PTM, stable, lipid added to N-terminal cysteine)

• in eukaryotes end sequence of protein replaced by GPI anchor (co-translational, stable, C-terminal glycosyl-phosphatidyl-inositol)

How can lipids move in the membrane

Lateral diffusion - easy, around 1micrometer / second

Transverse diffusion - move from one side of the bilayer to the other using flippases. Harder and energetically unfavourable as polar head must pass through non-polar environment.

How can proteins move in the membrane

Only lateral diffusion

Some are immobile due to attachment to matrices, filaments etc.

Proteins cannot flip-flop/move transversely due to much more extensive hydrophilic regions

What causes /maintains asymmetry in the membrane of lipids, proteins and PTMs

Asymmetry of lipids maintained by flippases and transverse diffusion

PTMs asymmetric as they differ on the inside and outside of the membrane

What are nano-domains / lipid rafts

Certain areas have certain molecules clustered together

E.g. lipids with similar properties, proteins with specific properties like longer transmembrane sections

Creates local and dynamic regions with different lipid/protein concentrations

What does movement across the membrane depend on

Size and polarity of particles

Two types of transport across the membrane

Passive diffusion - same direction as electrochemical gradient (caused by diff. in molecules outside and inside cell); can be through channel or transporter (selective for specific molecules)

Active diffusion - against direction of electrochemical gradient; requires energy from either light, metabolism, electrochemical gradient itself, or combination

Co-transporters and exchanges allow for coupled transport

What is protein translocation controlled by

Signal peptide - secretion signal on protein sequence.

Proteins that remain in the cytoplasm do not have SP

Proteins that embed in membrane have both the SP and a transmembrane domain

Features and role of signal peptide (SP)

Amphipathic alpha helix - 1-5 positive residues and 7-15 hydrophobic residues, so core hydrophobic section

Role to transport ribosome and protein attached to translocator, where the protein or some parts of it can be translocated to other side

Steps of the SP controlling translocation

1. Protein translated at ribosome, and hydrophobic part of the SP emerges from the ribosome

2. Signal recognition particle (SRP) binds to SP and temporarily blocks translation

3. SRP binds to SRP receptor on membrane (of the ER in euks or plasma membrane in proks), in doing so anchors ribosome to membrane

4. SP enters the protein translocator, causing SRP and ribosome to dissociate

5. Translocation continues and the protein passes through the membrane, following the SP through the translocator

6. Signal peptidase cleaves protein after the SP

How do trans-membrane domains lead to transmembrane proteins

Are also hydrophobic alpha helixes

Act as ‘stop’ and ‘start’ signals to the translocator

Can produce membrane embedded proteins, and proteins with multiple passes through the membrane