Chapter 10: Membranes Flashcards
what is a (cell) membrane?
a double layer of lipids and proteins that surrounds/encloses a cell.
how does Dr. Shimko describe a membrane bilayer?
as a 3D sheet that extends all the way around a cell or organelle and creates an exterior and interior to the cell or organelle
what 2 reasons does Dr Shimko give for why membranes are so important?
- they provide separation/barrier between the exterior and interior (of a cell)
- they prevent the movement of charged/polar species from one side of the membrane to the other
what is a (membrane) leaflet?
what you call each lipid layer in a membrane
why can we describe (membrane) lipid bilayers as ‘ideally’ amphipathic?
when/if the bilayers have equal amounts of polar and non-polar regions
the exp from the slides showed a bilayers whose polar region was the exact same length (in Angstroms) as its non-polar region
what is a liposome?
a membrane bilayer that extends out to a large size and encloses a large space
what is a liposome also called?
vesicle
how are vesicles/liposomes useful for (polar) drug delivery?
You can put your (polar) drug into a vesicle and it will fuse with the cell’s membrane, create an opening, and release the vesicle contents into the interior of the cell.
why do phospholipids (spontaneously) form a bilayer?
hydrophobic effect?
to maximize favorable interactions between hydrophobic regions (tails and other tails) and polar regions (polar head groups and aqueous environment)
to minimize unfavorable interactions (between hydrophobic tails and polar/aqueous environment and between polar heads and hydrophobic tails)
what comprises a biological membrane?
phospholipids, sterols (cholesterols), glycolipids, sphingolipids, glycosphingolipids, proteins etc
What are 3 types of protein structures found embedded in biological membranes?
integral member proteins
peripheral proteins
proteins with covalently linked tails
Are all membranes in your body the same?
No
The composition varies based on the type of cell, AND based on which leaflet you’re examining (the external/extracellular, leaflet vs the internal/intracellular leaflet)
Do you still need to know about sphingolipids?
yes
How can you separate a membrane leaflet?
cool the membrane to its solid state and pull them apart while they’re rigid
how does asymmetry (in composition) impact lipids’ ability to move from one leaflet to the other?
it makes it such that the lipids can’t move from one leaflet to another without help
why is it thermodynamically UNfavored for a phospholipid to move from the external membrane leaflet to the internal membrane leaflet (or vice versa)
this movement requires the polar/hydrophilic head to pass through a region of hydrophobic tails
what is transverse diffusion?
what you call it when a phospholipid moves from one membrane leaflet to the other
what is lateral diffusion?
what you call it when a phospholipid moves around within the leaflet it’s already in
which is faster: transverse diffusion or lateral diffusion?
lateral. Transverse rarely occurs and requires enzymes to occur with any kind of appreciable speed
What kind of diffusion does flippase enzyme do?
transverse diffusion from the external membrane leaflet to the internal membrane leaflet
Are flippase and flopase enzymes specific?
yes
they only bind to specific phospholipids
What kind of diffusion does floppase enzyme do?
transverse diffusion from the INTERNAL membrane leaflet to the EXTERNAL membrane leaflet
What kind of diffusion does scramblase enzyme do?
simultaneous diffusion of two phospholipids (where one is defusing from the outer to the inner membrane leaflet while the other is moving in the opposite direction)
are flippse, floppase, and scramblase enzymes considered catalysts?
Yes
what is the difference between ‘integral’ membrane proteins and ‘peripheral’ membrane proteins?
integral membrane proteins are so closely associated with the membrane structure that they cannot be moved/removed without disrupting the membrane itself
peripheral membrane proteins are associated with the membrane but can be removed from the membrane (with detergents or pH changes, etc) without disrupting the membrane; association with the membrane is weaker than with integral proteins
what is a transmembrane protein?
the type of integral protein that spans the (entire) membrane
do transmembrane proteins have to have a specific structure, size, solubility, location, directionality, etc in order to be functional?
yes
what two 2o structures are commonly found in transmembrane proteins?
alpha helix and beta sheets, especially beta barrels
what is a hydropathy plot?
A hydropathy plot, is a graph showing the distribution of hydrophobic amino acids over the length of a peptide sequence, which is used to predict the position of transmembrane domains within a protein
The hydropathy plot displays the hydrophobic and hydrophilic tendencies of an amino acid sequence.
why can some transverse proteins’ polar amino acids exist in the hydrophobic region of the membrane?
bc they exist in oppositely charged pairs that neutralize each other
which two amino acids are often found at the interface of polar head groups and hydrophobic tails in a transverse membrane protein?
Tyr
Trp
what are 3 secondary structures can be observed in transmembrane (integral) proteins?
alpha helix
beta sheet (especially beta barrel)
complex
do/can transmembrane (integral) proteins start being integrated into membranes while they’re still forming?
yes, they need the lipids (and their hydrophobicity/hydrophilicity) in order for them to fold
why are alpha helices so effective as transmembrane (integral) proteins?
They have hydrophobic regions that can embed themselves favorably into the hydrophobic part of the membrane, and hydrophilic regions that can embed themselves favorably into the hydrophilic part of the membrane
when integrating into a membrane, is it more ideal for an alpha helix to be mostly hydrophobic or mostly hydrophilic?
hydrophobic
how many residues are usually observed in a transmembrane protein that has an alpha helix structure?
20 residues
what 3 things can hydropathy plots help you learn about unknown transmembrane proteins?
polarity, solubility, folding behavior, etc
on a hydropathy plot, does a tall spike represent a very hydrophobic amino acid region, or a very hydrophilic one?
hydrophobic. The y axis shows you hydrophobicity and The higher you go, the more hydrophobic you are.
what does the x axis on a hydropathy plot show you?
the section of amino acid being examined (N terminus is on the left and C terminus is on the right)
why is hydropathy plotting useful in examining transmembrane proteins?
it tells/shows you which regions of the amino acid chain are hydrophobic enough to be found embedded in the membrane
what is distinctive about the hydropathy plot produced by a beta barrel transmembrane protein?
because the structure has alternating hydrophobic and hydrophilic sheet sides, the graph alternates/oscilates between polar and not polar regions
You don’t see aggregated regions of polar and non polar like you would on an alpha helix graph
why are beta barrels so effective as transmembrane (integral) proteins?
they have alternating polar and non-polar residues (where all the polar residues are facing the same direction/on the same face and all the NON polar regions are facing the other direction/on the other face)
This means that one face can interact favorable with the polar part of a membrane while the other face interacts favorable with the NON polar part of the membrane
do transmembrane beta barrels have their hydrophobic face in the core or in the outside face?
on the outside
this is opposite of what we observe with regular, free, soluble beta barrels (which have their non-polar regions arranged as a hydrophobic core)
what 4 amino acids are commonly found in the polar head part of the membrane?
Lys, Arg, Glu, Asp (because they are charged at phyisiological pH)
what did Dr . Shimko call it when two oppositely charged amino acids can exist in the non-polar part of a cell membrane?
he called it a salt bridge
what is a chemical gradient?
an imbalance (of a substance) inside and outside of a cell that the cell uses to manage the potential energy it needs to drive thermodynamically UNfavorable processes)
are biological organisms generally at equilibrium with the outside environment?
no (not while we’re alive)
why do chemical gradients occur in cells? In other words, why aren’t imbalances rectified automatically through osmosis?
The thermodynamic barrier (for moving charged/polar species across the non-polar cell membrane) is too high for this to occur without help
are membranes selectively permeable barriers?
yes
what two factors impact the likelihood of a species passing through a membrane?
size and polarity
which molecules can pass through cell membrane without help?
hydrophobic ones
and net neutral gases (O2 and CO2)
can water diffuse through a cell membrane?
not very well
what does a permeability coefficient tell you?
A quantitative measure of the rate at which a molecule can cross a membrane such as a lipid bilayer; expressed in units of cm/s and equal to the diffusion coefficient divided by the width of the membrane.
what are (membrane) transporters and what 5 types of substrates do they interact with?
transmembrane proteins that assist in the movement of ions, peptides, small molecules, lipids and macromolecules across a biological membrane.
what does it mean to be a selectively permeable barrier?
it means that molecules/species need assistance in order to cross the barrier
what is the main phenomena that directs movement across a membrane?
extracellular and intercellular concentrations of the substance being moved
what is simple diffusion?
what you call it when a (small, non-polar or weakly polar) substance moves through a membrane without assistance, by traveling right through the lipids in the lipid bilayer
why are small, non-polar or weakly polar substances able to move through a membrane without assistance (via simple diffusion)?
the thermodynamic barrier to this is very small
being neutral, these species do not upset the polar heads or the non-polar tails in the membraine
what is the difference between ‘facilitated transport’ ‘facilitated diffusion’, and ‘passive diffusion’?
nothing. They are just listed with different names in the slides
what is the difference between ‘active transport’ and ‘passive transport’?
active transport moves molecules AGAINST their gradient (towards the higher concentration)
passive transport moves molecules DOWN their gradient (towards the lower concentration)
What kind of carriers do active transporters use: active carriers or passive carriers?
active carriers
What kind of carriers do passive transporters use: active carriers or passive carriers?
passive carriers
which type of molecule movement is thermodynamically favored: down the gradient or against the gradient?
down the gradient
Why are membrane transporters considered catalysts?
they lower the activation energy barrier for polar molecules to cross the membrane
what are 2 reasons the energy barrier is so high for moving polar species across the membrane?
- they have to shed their water shell before crossing
2. they have to overcome the unfavorable interactions with the hydrophobic tails in the membrane
how do membrane transporters act as catalysts to reduce the energy barrier for polar species crossing the membrane?
they cannot reduce the energy required to remove the species’ water shell, but they can shield the species from the hydrophilic interactions on the way from the outside of the cell to the inside of the cell.
what are the three types of membrane transporters?
uniport
symport
antiport
what is the difference between simple diffusion and facilitated diffusion?
in simple diffusion, the molecules pass directly through the lipids in the lipid bilayer
in facilitated diffusion, the molecules travel through pores or carriers that are integrated into the lipid bilayer
what are the two types of protein transporters used in facilitate diffusion?
channels (pores)
carriers
what is the difference between a channel protein transporter and a carrier protein transporter?
channels/pores are open on both ends simultaneously
carriers can only be open on one end at a time
what’s the difference between uniport, symport, and antiport transporters?
uniport can move once substance in one direction at a time
symport can move two substances in the same direction at a time (and both must be present in order for either to move across the membrane)
antiport can move two substances in opposite directions at a time
if channels/pore are open on both ends all the time, how do they have selectivity/regulation?
they have ‘filters’ inside the shaft of the protein
exp. aquaporin
how is aquaporin and example of a selective/regulated channel/pore?
it’s inner shaft is lined with a bunch of significantly non-polar amino acids and 2 Asparagines
the non-polar amino acids usher non-polar molecules down the shaft.
The Asparagine’s aren’t polar enough to attract polar or charged species such as H+
how to molecules enter the cell through carriers when the carriers are only open on one end?
the molecule triggers a conformation change in the carrier via induced fit. Shape change closes the extracellular end of the carrier around the molecule, and opens the intercellular end so the molecule can flow through the carrier into the cell
Do carriers ever have filters like how channels do?
Yes. Carriers can have a potassium selectivity filter where the inner shaft of the carrier is lined with carbonyls that attracts/is coordinated by K+. This triggers the carrier’s conformation change.
Doesn’t work with Na+ bc Na+ is too small to coordinate all of the carbonyls/maximize favorable interactions in order to trigger the conformation change
what is the difference between primary active transport and secondary active transport?
primary consumes ATP in order to move molecules against their gradient and conserve the resulting potential energy that gets trapped in the high concentration
secondary ‘couple’ molecules traveling against their gradient with molecules moving down their gradient in order to move the first molecule without investing any energy
what are 3 examples of how cell scan obtain the energy needed for primary active transport?
- get it from ATP hydrolysis
- get it from photons
- get it from redox rxns
why do specific structure, size, solubility, location, directionality, etc matter to transmembrane proteins (in order to be functional)?
protein’s polar regions must exist near polar regions of the membrane and vice versa
what will happen to a transmembrane protein that gets integrated into the membrane in the wrong position?
it will not be functional
