11: Membranes

Lipids, which are nonpolar, aggregate together to minimize its interactions with water. At the same time, these interactions are driven by the hydrophobic effect.

In aqueous solution, lipid aggregates form micelles, bilayers, or vesicles.

Micelles are small spherical aggregates of amphipathic molecules. Their hydrophilic head groups form the exterior of the sphere and the hydrophobic acyl side chains make up the interior.

Formation of micelles is favored when the surface area of the lipids' head groups are higher than their side chains.

For example, free fatty acids and SDS form micelles.

Bilayers are the linear, two dimensional arrangement of two lipid "leaflets," whose hydrophobic portions interact via the hydrophobic effect, with their hydrophilic heads pointing outwards toward the aqueous solution.

Formation of bilayers are favored when the surface area of the lipids' head groups are similar with their side chains.

For example, glycerophospholipids and sphingolipids form bilayers.

Vesicles are bilayers that have folded in on themselves, due to the unstable nature of the bilayer's ends. This forms a large "bubble," similar to that of a micelles, but vesicles contain an aqueous compartment on the inside.

Formation of vesicles is favorable when bilayers form, because bilayers are inherently unstable due to the interaction of hydrophobic chains interacting with water at the ends.

Homogenous bilayers are ~3nm thick, but most bilayers are not homogenous; they contain many integral and associated proteins.

With proteins included, these heterogenous membranes are more realistically around 5nm-8nm thick.

Homogenous: 3nm Heterogenous: 5nm-8nm

They are flexible, self-repairing, and selectively permeable.

Biological membranes have many associated proteins that are fluid within the membrane, meaning they are pretty free to move around. Lipids are also able to transverse the membranes as well. This is all done while maintaining the selective permeability of the membrane.

The mitochondria, nucleus, and chloroplast.

The golgi apparatus, The endoplasmic reticulum The lysosome

Plasma membranes are enriched with: cholesterol and sphingolipids.

Mitochondrial membranes are enriched with: phosphatidylglycerol and cardiolipin.

The endoplasmic reticulum

Synthesis: endoplasmic reticulum vesicle (taxi) --> cis golgi cis golgi (undergoes modifications) --> trans golgi trans golgi --> vesicle (taxi) to membrane

phosphatidylcholine

sphingolipids and cholesterol

phosphatidylserine, phosphatidylethanolamine, and phosphatidylinositol

phosphatidylcholine and sphingomyelin

Lipid transfer proteins offer another route of lipid transport from their site of synthesis to their membrane.

LTPs are proteins that have water-soluble exteriors with a hydrophobic "pocket" on the interior that binds lipids.

It carries one type of lipid TO the membrane and carries another type FROM the membrane.

Post translational modifications within the endoplasmic reticulum/golgi apparatus. ex. glycosylation ex. addition of lipid anchors

Ser, Asn, and Thr

IMPs are proteins that are firmly embedded within the bilayer and can only be removed with detergents or organic solvents that disrupt the bilayer's hydrophobic interactions itself.

PMPs are proteins that associate with the hydrophilic surface of bilayers and can be removed using mild treatments that disrupt hydrogen bonds.

Amphitropic proteins associate reversibly with the membrane.

-topic refers to how many times a protein's hydrophobic portion spans a leaflet of the membrane. Monotopic proteins penetrate only one LEAFLET of the membrane (half of the membrane). Bitopic proteins span two leaflets (the membrane once). Polytopic proteins span the membrane many times.

Bacteriorhodopsin spans the bilayer 7 times.

Each span has about 20 residues, each forming alpha-helices across the membrane.

20%-30% of proteins are integral.

This is based off of the fact that all integral proteins have AT LEAST one amino acid sequence of 20 consecutive nonpolar residues. Then, genomic sequencing is just used to figure out how many proteins are produced.

This is a measure of how hydrophobic/hydrophilic each residue is. It denotes the free energy of transfer of a residue into an aqueous environment. Thus, hydrophobic residues will be positive on the index because it requires energy to put them into an aqueous environment. Likewise, hydrophilic residues will be negative on the index because it is energetically favorable to put them in water.

This index is used to plot known sequences of proteins to determine whether or not they could be integral.

alpha-helices and beta-barrels. They are both favored for the same reason: maximization of intrachain hydrogen bonding and the hydrophobic effect.

Porins are beta-barrel structured integral proteins that allow certain polar solutes to move across the lipid bilayer more easily.

The positive inside rule is a generalization of residue locations within membranes: Lys and Arg (positively charged residues) occur most often at the cytoplasmic face of plasma membranes.

Lo state occurs below physiological temperatures. Lipid movement is heavily constrained.

Ld state occurs above physiological temperatures. Lipid movement is characterized by free lateral movement of lipids about the membrane and rotation of bonds.

Physiological conditions are characterized by an intermediate between Ld and Lo states. There is moderate lateral and rotational movement of lipids in the bilayers.

Long-chain saturated fatty acids: favor Lo because they pack together very well.

Short-chain/unsaturated fatty acids: favor Ld because they are more mobile/have kinks that prevent ordering.

Sterols: bring disorder to FA favoring order, and bring order to FA favoring disorder; sterols are a mediator of fluidity.

Flippases are enzymes that catalyze the "flip" of membrane lipids from the outside-leaflet to the inside-leaflet. They work by providing a path that is more energetically favorable for the lipid to move.

They require ATP.

Flippase: F L i (destination i-nside) P

The opposite of flippases.

Floppases are enzymes that catalyze the "flop" of membrane lipids from the inside-leaflet to the outside-leaflet. They work by providing a path that is more energetically favorable for the lipid to move.

They require ATP.

Floppase: F L o (destination o-utside) P

Scramblases are unique in that they do NOT require ATP. They are enzymes that rearrange lipids in either direction (out->in or in->out), based on their concentration gradients.

While ATP-independent, some still require Ca2+ ions to function.

FRAP and single-particle tracking

Head groups are tagged with fluorescent proteins for a large portion of the lipid bilayer, then a small portion is irradiated, (bleached) and microscopy is used and the rate of that portion recovering its full fluorescence is measured.

Single lipid molecules are tagged and tracked on a very short time scale.

Form aggregates with other nearby proteins, and/or anchor themselves to a specific spot on the membrane.

Sphingolipids and cholesterol aggregate together and cause the membrane to be a bit thicker where they cluster. There is a very low concentration of phospholipids.

Rafts: cholesterol-sphingolipid raft on a "sea" of phospholipids. They are stabilized by the hydrophobic effect, and thus proteins with longer hydrophobic sequences are more favored to reside in these rafts.

Like before, proteins that are highly hydrophobic prefer to reside on rafts.

Caveolae are "little caves" that cover up to half of a plasma membrane. They are caused by specialized rafts from cholesterol-rich regions of the membrane. Caveolae functions relate to membrane trafficking and signal transduction.

BAR domains and septins

BAR domains are a superfamily of proteins that have concave-curved domains. They are positively charged on the inside of their concave surface and bind to the negatively charged PIP2 and PIP3 surface of membranes, causing the membrane to curve outwards.

BAR domains are comprised of coiled coils that form long, thin dimers, as well as their characteristic concave surface. Some BAR proteins have alpha-helix wedges at their ends that insert themselves into the sides of the membrane, both anchoring themselves and forcing the membrane to curve.

BAR domains also are capable of polymerizing and stabilizing the induced curvature.

Septins are a family of GTP-binding proteins that have an amphipathic helix at its edges that inserts itself, similarly to BAR proteins, into the sides of a membrane, inducing curvature.

Fusion proteins mediate membrane fusion. They ensure:

1. Recognition of membrane segments

2. Proximity of membrane segments

3. Local disruption of membrane

4. Proper hemifusion and fusion of membrane leaflets.

5. That fusion happens as a result of signaling.

SNARE = Snap-receptor, a class of fusion proteins that mediates membrane fusion, esp. in cases of endo/exo-cytosis.

v-SNAREs and t-SNARES bind each other, forming long thin helices that work together to zip themselves up, pulling two membranes together at the same time.

Integrins, selectins, and cadherins.

Integrins are surface-associated proteins that integrate extracellular and intercellular information by binding signals and exchanging the information across the membrane.

Selectins are extracellular proteins that bind specific polysaccharides onto nearby cell surfaces, only in the presence of Ca2+.

Cadherins are plasma membrane proteins that bind other cadherins on adjacent cells.