Lipids & Membranes
Lipids
Lipids are non-polar (hydrophobic) compounds,
soluble in organic solvents.
Most membrane lipids are amphipathic, having a
non-polar end and a polar end.
Fatty acids, the simplest lipids, consist of a
hydrocarbon chain with a carboxylic acid at one end.
an 16-C fatty acid: CH3(CH2)14-COONon-polar
polar
O

Abbreviated notation

a C

3
1 O
for a 16-C fatty acid
4
2
with one cis double
bond between carbons
fatty acid with a cis-9
9 &10 is 16:1 cis  9.
double bond
Some examples:
14:0 myristic acid
16:0 palmitic acid
18:0 stearic acid
18:1 cis9 oleic acid
18:2 cis9,12 linoleic acid
18:3 cis  9,12,15 a-linonenic acid
20:4 cis  5,8,11,14 arachidonic acid
20:5 cis  5,8,11,14,17 eicosapentaenoic acid

Double bonds in
fatty acids are
usually have the
cis configuration.
4

a
3
2
O
C
1
O
fatty acid with a cis-9
double bond
Most naturally occurring fatty acids have an even number
of carbon atoms.
There is free rotation about C-C bonds in a fatty acid,
except at a double bond. Each cis double bond causes a
kink in the chain. Rotation about other C-C bonds would
permit a more linear structure than shown above, but with
a kink.
Glycerophospholipids
Glycerophospholipids
(phosphoglycerides), are common
constituents of cellular membranes.
They have a glycerol backbone.
Hydroxyls at C1 & C2 are esterified
to fatty acids.
An ester forms
when a hydroxyl
reacts with a
carboxylic acid,
with loss of H2O.
CH2OH
H
C
OH
CH2OH
glycerol
Formation of an ester:
O
R'OH + HO-C-R"
O
R'-O-C-R'' + H2O
Phosphatidate
O
O
R1
C
H2C
O
O
CH
H2C
C
R2
O
O
phosphatidate
P
O
O
The simplest glycerophospholipid is phosphatidate, in
which fatty acids are esterified to hydroxyls on C1 & C2,
while the C3 hydroxyl is esterified to Pi.
O
O
R1
C
H2C
O
O
CH
H2C
C
R2
O
O
P
O
X
O
glycerophospholipid
In most glycerophospholipids (phosphoglycerides), Pi is
in turn esterified to OH of a polar head group (X), e.g.:
serine, choline, ethanolamine, glycerol, or inositol.
The 2 fatty acids tend to be non-identical. They may differ
in length and/or the presence/absence of double bonds.
O
O
R1
C
H2C
O
O
CH
H2C
C
R2
O
O
P
O
CH3
O
CH2
CH2
+
N CH3
CH3
phosphatidylcholine
Phosphatidylcholine, with choline as polar head
group, is an example of a glycerophospholipid. It
is a common membrane lipid.
O
O
R1
C
H2 C
O
O
CH
H2 C
C
R2
O
O
P
O
O
H
OH
OH
H
OH
phosphatidylinositol
OH
H
H
H
H
OH
Phosphatidylinositol, with inositol as polar head group,
is another example of a glycerophospholipid.
In addition to being a membrane lipid, phosphatidyl
inositol has roles in cell signaling.
Glycerophospholipid
Each glycerophospholipid
includes
 a polar region: glycerol,
carbonyl of fatty acids, Pi,
& polar head group (X)
 2 non-polar hydrocarbon
tails of fatty acids (R1, R2).
Such an amphipathic lipid
is often represented as at right.
O
O
R1
C
H2C
O
O
C
CH
H2C
R2
O
O
P
O
O
glycerophospholipid
polar
"kink" due to
double bond
non-polar
X
OH
Sphingolipids are derivatives of the
lipid sphingosine, which has a long
hydrocarbon tail, and a polar domain
that includes an amino group.
H2C
OH
H
C
CH
H3N+
CH
HC
(CH2 )12
OH
H2C
O
OH
H
C
CH
NH
CH
C
R
ceramide
HC
(CH2 )12
CH3
sphingosine
CH3
The amino group of sphingosine can
form an amide bond with a fatty acid
carboxyl to yield a ceramide.
Ceramides usually include a polar
head group, esterified to the terminal
OH of the sphingosine.
CH3
H3C
+
N
O
H2
C
H2
C
O
CH3
Sphingomyelin, a
ceramide with a
phosphocholine or
phosphethanolamine
head group, is a
common constituent
of plasma membranes
P
O
O
phosphocholine
H2C
sphingosine
O
fatty acid
OH
H
C
CH
NH CH
C
R
Sphingomyelin
Sphingomelin, with a phosphocholine head group, is
similar in size and shape to the glycerophospholipid
phosphatidyl choline.
HC
(CH2 )12
CH3
Polar head groups of sphingolipids (ceramides):
Sphingolipid
Polar head group
sphingomyelin
phosphocholine or
phosphoethanolamine
cerebroside
a monosaccharide such as glucose
or galactose
ganglioside
a complex oligosaccharide,
including the acidic sugar sialic acid
Gangliosides, which have complex oligosaccharide head
groups, are often found in the outer leaflet of the plasma
membrane bilayer, with sugar chains extending out from
the cell surface.
Cholesterol
HO
Cholesterol
Cholesterol has a rigid ring system and a short branched
hydrocarbon tail. It is largely hydrophobic, but has one
polar group, a hydroxyl, making it amphipathic.
Cholesterol is found in membranes, and is the precursor
for synthesis of steroid hormones and vitamin D.
Monolayer at
air/water interface
Bilayer
Spherical Micelle
Amphipathic lipids form complexes in which polar
regions are in contact with water and hydrophobic regions
away from water. Depending on the lipid and its
concentration, possible molecular arrangements include:
 A monolayer at an air/water interface.
 Various micelle structures. A spherical micelle is a
stable configuration for amphipathic lipids with a
conical shape, such as fatty acids.
 A bilayer. This is the most stable configuration for
amphipathic lipids with a cyllindrical shape, e.g.,
phospholipids.
Membrane fluidity:
The interior of a lipid bilayer
is normally highly fluid.
liquid crystal
crystal
In the liquid crystal state, hydrocarbon chains of
phospholipids are disordered and in constant motion.
At low temperature, bilayer phospholipids may undergo
transition to a crystalline state in which fatty acid tails are
fully extended, packing is highly ordered, & van der Waals
interactions are maximal.
Kinks in fatty acid chains, due to cis double bonds,
interfere with packing of lipids in the crystalline state.
Thus double bonds inhibit transition to the crystalline state,
& lower the phase transition temperature.
Cholesterol inserts into bilayer
membranes with its OH adjacent to
polar phospholipid head-groups, and its
hydrophobic ring system adjacent to
fatty acid chains of phospholipids.
Being slightly shorter than a
phospholipid, cholesterol extends not
quite to the center of the bilayer.
Cholesterol
in membrane
Cholesterol inhibits transition from liquid crystal to
crystalline state, because the rigid cholesterol ring
interferes with close packing of phospholipid fatty acid
tails. However the rigid cholesterol makes the membrane
somewhat less fluid.
There are 2 strategies by which phase changes of
membrane lipids are avoided:
 Cholesterol is abundant in membranes, such as
plasma membranes, that include many lipids with
long-chain saturated fatty acids. Cholesterol blocks
transition to the crystalline state.
 Membranes that lack cholesterol, e.g., mitochondrial
inner membrane, consist mainly of phospholipids
whose fatty acids include one or more double bonds.
The double bonds lower the melting point to below
physiological temperature.
Cellular membranes contain a mixture of lipids.
 The fatty acid moiety of sphingolipids tends to be
saturated.
 Glycerophospholipids often include at least one fatty
acid that is kinked due to one or more double bonds.
Sphingolipids tend to separate into sphingolipid-rich
membrane microdomains, called lipid rafts.
This has been attributed to the close packing of
sphingolipids, with their fully saturated hydrocarbon tails.
peripheral
Membrane
proteins
 peripheral
 integral
 having a lipid
anchor
lipid
anchor
lipid bilayer
integral
Membrane
Proteins
Peripheral proteins are on the membrane surface. They
are water-soluble, with mostly hydrophilic surfaces.
Many peripheral proteins adhere to exposed domains of
integral proteins, e.g., by ionic & H-bond interactions.
They often can be dislodged by high salt concentrations,
change of pH, and/or chelators that bind divalent cations.
Some cytosolic proteins temporarily bind to membranes,
via domains that recognize and bind to particular lipids
that transiently exist in the membrane. For example:
Pleckstrin homology domains (PH) bind phosphorylated
derivatives of phosphatidylinositol. A PH domain has a
unique  sandwich structure (2 orthogonal  sheets
capped at one end by an amphipathic a helix).
Many signal proteins include PH domains, that promote
their binding to the cytosolic surface of the plasma
membrane, where they cooperate in signal cascades.
Kinases that transfer Pi to the inositol moiety of
phosphatidylinositol, creating ligands for PH domains,
are themselves regulated by signal pathways.
O
O
R1
C
H2C
O
O
C
CH
H2C
R2
O
O
P
O
O
phosphatidylinositol3-phosphate
OH
2
H
H
1
6
OH
H
2
H
OPO 3
3
H
4
OH
5
H
OH
FYVE domains bind to a particular phosphatidylinositol
derivative, phosphatidylinositol-3-phosphate.
FYVE domains include specific structural motifs in which
zinc ions are bound by Cys & His residues.
O
O
R1
C
H2C
O
O
C
R2
CH
H2C
OH
diacylglycerol
C1 domains recognize and bind to diacylglycerol, which
is generated by signal-activated cleavage of a
phosphorylated derivative of phosphatidylinositol.
C1 domains are named for a domain in an enzyme
Protein Kinase C, that is activated by diacylglycerol.
C1 domains are similar in structure to FYVE domains.
peripheral
Integral proteins
have domains that
extend into the
hydrocarbon core
of the membrane.
Often they span
the bilayer.
lipid
anchor
lipid bilayer
integral
Membrane
Proteins
Structural & spectroscopic data indicate that a layer of
relatively immobilized lipid surrounds the transmembrane
portion of an integral protein.
Hydrocarbon tails of lipids at the protein-lipid interface
assume conformations that allow them to fill in surface
irregularities of protein domains exposed to the bilayer.
Integral proteins
can be removed
from membranes
only by treatment
with detergents,
amphipathic
molecules that break
up the lipid bilayer.
membrane
detergent
solubilization
polar
non-polar
Protein with
bound detergent
Hydrophobic domains of detergents substitute for lipids in
coating hydrophobic surfaces of integral proteins. This
allows the proteins to dissolve in water.
Without detergents, purified integral proteins tend to
aggregate, as their hydrophobic surfaces come together,
to minimize contact with water.
CH3
CH3
H3C
C
CH
CH2
CH2
C
CH3
CH
CH2
CH2 C
CH
CH2
S
Protein
farnesyl residue linked to protein via cysteine S
Some proteins have a covalently attached lipid anchor,
that inserts into the bilayer. Examples:
 fatty acid (myristic or palmitic acid)
 isoprenoid (e.g., farnesyl)
 GPI (glycosylphosphatidylinositol, a glycolipid).
Such an anchor may allow reversible membrane
association. Release may occur via:
 a conformational change that causes the attached
lipid to be retracted into (buried within) the protein, or
 hydrolytic cleavage of the lipid (GPI).
Lateral Mobility
The Fluid Mosaic Model of membrane structure
emphasizes the highly fluid character of the bilayer core
and the ability of integral proteins and lipids to rapidly
diffuse within the plane of the membrane.
Lateral mobility of a membrane lipid is depicted above.
Lateral diffusion of membrane lipids and proteins (within
the plane of the membrane) is assayed by FRAP:
Fluorescence Recovery After Photobleaching.
FRAP technique: A membrane lipid or protein is tagged
with a fluorescent dye. Proteins may be labeled with
fluorescent antibodies.
A laser bleaches (destroys fluorescence of) label in a
region of membrane. Fluorescence recovers as
undamaged label diffuses into the region.
Generally lipids diffuse faster than proteins, which are
larger. Protein diffusion may be constrained by proteinprotein interactions, e.g. association with cytoskeleton.
Flip-flop of lipids (from one
half of a bilayer to the other)
is very slow. Flip-flop would
require the polar head group
of a lipid to traverse the
hydrophobic membrane core.
Flip Flop
Flippase enzymes catalyze flip-flop in membranes where
lipid synthesis occurs. Otherwise, flip-flop of lipids is rare.
The 2 leaflets of a bilayer tend to differ in lipid
composition.
Flip-flop of integral proteins does not occur. All copies
of a given type of integral protein have the same
orientation relative to the 2 sides of the bilayer membrane.
Transmembrane topology
Transmembrane topology of membrane proteins is
studied with membrane-impermeant probes, added
on one side of a membrane:
 Protease enzymes (Degradation would indicate
surface exposure of a protein segment.)
 Monoclonal antibodies raised to peptides equivalent
to a segment of the protein sequence (Binding would
indicate surface exposure of that protein segment.)
 Enzymes that attach labels to particular amino acids
or sugars (Labeling would indicated surface exposure.)
Membrane protein structure:
Integral proteins are difficult to crystallize. Fewer
integral proteins than soluble proteins have had their
structure solved at atomic resolution.
The most common structural motif in integral proteins is
a membrane-spanning a-helix, consisting largely of
hydrophobic amino acids.
R-groups of a transmembrane a-helix would contact the
hydrophobic membrane core.
Aliphatic residues predominate in lipid-exposed protein
domains toward the middle of the bilayer.
Tyr & Trp are common closer to the membrane surface.
The polar character of the Trp amide & the Tyr OH, in
addition to their hydrophobic ring structures, may make
them ideally suited for localization at the polar/apolar
interface.
Lys & Arg are often found in transmembrane segments,
just outside the partly polar aromatics. Their positively
charged groups, at the ends of aliphatic side chains, may
extend outward to interact with polar lipid head groups.
membrane
Cytochrome oxidase dimer
(PDB file 1OCC)
An example of an integral protein whose intra-membrane
domains consist mainly of transmembrane a-helices is
cytochrome oxidase. Explore with Chime the a-helix
colored green at the far left in this view.
Porin -barrel
A family of bacterial outer
envelope channel proteins
called porins have instead
 barrel structures.
Porin Monomer
At right is shown one
channel of a trimeric
channel complex.
The  barrel consists of
 sheet rolled up to form
a cylindrical pore.
PDB 1AOS
 polar R group
 non-polar R group
In a -sheet, amino acid R-groups alternately point above
& below the sheet. Much of porin primary structure
consists of alternating polar & non-polar amino acids.
Polar residues line the aqueous lumen of the channel.
Non-polar residues are in contact with membrane lipids.
Explore an example of a bacterial porin with Chime.
Hydropathy plots
A 20-amino acid a-helix just spans a lipid bilayer.
Hydropathy plots are used to search for 20-amino
acid stretches of hydrophobic amino acids in a protein
for which a crystal structure is not available.
Putative hydrophobic transmembrane a-helices have
been identified this way in many membrane proteins.
Protein topology studies are used to test the predicted
transmembrane localization of protein domains.
Hydropathy plots alone are not conclusive.
Simplified helical wheel diagram of four
a-helices lining the lumen of an ion channel.
A “helical
wheel” looks
down the axis
of an a-helix,
projecting sidechains onto a
plane.
Polar amino acid R-group
Non-polar amino acid R-group
An a-helix lining a water-filled channel might have polar
amino acid R-groups facing the lumen, & non-polar Rgroups facing lipids or other hydrophobic a-helices.
Such mixed polarity would prevent detection by a
hydropathy plot.