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Describe the behavior of lipids within aqueous solution.
What three structures do they tend to form?
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.
Describe a micelle's structure. When is formation of a micelle favorable? Give an example of molecules that form micelles.
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.
Describe a bilayer's structure. When is formation of a bilayer favorable? Give an example of molecules that form bilayers.
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.
Describe a vesicle's structure. When is formation of a vesicle favorable?
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.
How thick is a homogenous membrane bilayer? What about when membrane proteins are included?
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
What are three key features of membranes?
They are flexible, self-repairing, and selectively permeable.
Describe what the term "fluid mosaic" refers to.
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.
What three organelles have a double membrane?
The mitochondria, nucleus, and chloroplast.
What organelles are involved/related to the "endomembrane" system of cells?
The golgi apparatus, The endoplasmic reticulum The lysosome
Plasma membranes are enriched with what types of lipids?
Plasma membranes are enriched with: cholesterol and sphingolipids.
Mitochondrial membranes are enriched with what types of lipids?
Mitochondrial membranes are enriched with: phosphatidylglycerol and cardiolipin.
Where are membrane lipids and proteins synthesized?
The endoplasmic reticulum
What is the route that membrane lipids and proteins take from synthesis to their destination at a membrane?
Synthesis: endoplasmic reticulum vesicle (taxi) --> cis golgi cis golgi (undergoes modifications) --> trans golgi trans golgi --> vesicle (taxi) to membrane
What type of lipid comprises a large portion of the lumenal (inner) leaflet of the golgi apparatus?
phosphatidylcholine
What type of lipid comprises a large portion of the outer leaflet of the golgi apparatus?
sphingolipids and cholesterol
What type of lipid comprises a large portion of the lumenal (inner) leaflet of the plasma membrane?
phosphatidylserine, phosphatidylethanolamine, and phosphatidylinositol
What type of lipid comprises a large portion of the outer leaflet of the plasma membrane?
phosphatidylcholine and sphingomyelin
What are lipid-transfer proteins? (What are their function?) (What structural features do they have that allow them to transport lipids?)
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.
What does it mean for a lipid-transfer protein to be bispecific?
It carries one type of lipid TO the membrane and carries another type FROM the membrane.
Describe modifications that proteins undergo on their way to their membrane, and give a few examples
Post translational modifications within the endoplasmic reticulum/golgi apparatus. ex. glycosylation ex. addition of lipid anchors
When a protein is post-translationally modified with glycosylation, which residues are most often points of attachment for oligosaccharides?
Ser, Asn, and Thr
What is an integral membrane protein? How can they be removed from the membrane?
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.
What is an peripheral membrane protein? How can they be removed from the membrane?
PMPs are proteins that associate with the hydrophilic surface of bilayers and can be removed using mild treatments that disrupt hydrogen bonds.
What are amphitropic proteins?
Amphitropic proteins associate reversibly with the membrane.
Describe the terms monotopic, bitopic, and polytopic.
-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.
How many times does bacteriorhodopsin span the lipid bilayer?
How many residues per span, and what secondary structure does each span form?
Bacteriorhodopsin spans the bilayer 7 times.
Each span has about 20 residues, each forming alpha-helices across the membrane.
About what percent of all proteins in many organisms are integral proteins?
How did we figure this out?
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.
What is the hydropathy index?
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.
What structural motifs are favored within integral proteins in a bilayer? Why?
alpha-helices and beta-barrels. They are both favored for the same reason: maximization of intrachain hydrogen bonding and the hydrophobic effect.
What are porins?
Porins are beta-barrel structured integral proteins that allow certain polar solutes to move across the lipid bilayer more easily.
What is the positive-inside rule?
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.
Describe the "Liquid-ordered" state of a lipid bilayer.
Lo state occurs below physiological temperatures. Lipid movement is heavily constrained.
Describe the "Liquid-disordered" state of a lipid bilayer.
Ld state occurs above physiological temperatures. Lipid movement is characterized by free lateral movement of lipids about the membrane and rotation of bonds.
What state are lipid bilayers typically found it at physiological conditions?
Physiological conditions are characterized by an intermediate between Ld and Lo states. There is moderate lateral and rotational movement of lipids in the bilayers.
What lipid components determine the movement within a membrane?
Specifically describe the effect of sterols within membranes.
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.
Describe the function of a flippase.
What does it do How does it do it Does it require ATP?
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
Describe the function of a floppase.
What does it do How does it do it Does it require ATP?
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
Describe the function of a scramblase.
What does it do How does it do it Does it require ATP?
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.
What are two experimental methods used to "track" lipid movement across a membrane
FRAP and single-particle tracking
Describe the "rate of fluorescence recovery after photobleaching" (FRAP) process
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.
Describe the single-particle tracking method.
Single lipid molecules are tagged and tracked on a very short time scale.
The membrane is a fluid mosaic. But what do integral proteins tend to do to maintain their positions relative to one another?
Form aggregates with other nearby proteins, and/or anchor themselves to a specific spot on the membrane.
Describe what raft microdomains are on a 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.
What proteins tend to associate on these rafts?
Like before, proteins that are highly hydrophobic prefer to reside on rafts.
What are caveolae? Describe its function, Describe its effect on a cell membrane, Describe related lipids and proteins.
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.
Name two types of proteins that induce membrane curvature.
BAR domains and septins
Describe BAR domains. What is their function? What are their characteristic molecular features?
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.
Describe septins. What is their function? What are their characteristic molecular features?
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.
What do fusion proteins do? (5)
Fusion proteins mediate membrane fusion. They ensure:
Recognition of membrane segments
Proximity of membrane segments
Local disruption of membrane
Proper hemifusion and fusion of membrane leaflets.
That fusion happens as a result of signaling.
Describe the function of SNAREs.
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.
Name three types of protein associated with membrane-surface-adhesion.
Integrins, selectins, and cadherins.
What is an integrin?
Integrins are surface-associated proteins that integrate extracellular and intercellular information by binding signals and exchanging the information across the membrane.
What is a selectin?
Selectins are extracellular proteins that bind specific polysaccharides onto nearby cell surfaces, only in the presence of Ca2+.
What is a cadherin?
Cadherins are plasma membrane proteins that bind other cadherins on adjacent cells.
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