Faculty of Biochemistry and Molecular Medicine
Biomolecules for Biochemists (8 op)
740147P Biomolecules for Bioscientists (8 op)
740148P Biomolecules (5 op)
740143P
LIPIDS
Docent Tuomo Glumoff
LIPIDS
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lectures
Answers to problems will be given at the lectures and they will also be available in NOPPA after the lectures.
- lipids have many functions:
• fats insulate heat and serve as energy storage
• form membranes
• some are vitamins or hormones or other signal molecules
• enzyme cofactors, electron carriers
• light-absorbing pigments, protein anchors to membranes
• emulsifiers
- lipids are not polymers, but often associate through noncovalent forces
- hydrophilic and hydrophobic parts = amphipathic
FATTY ACIDS
COOH
- simplest lipids are fatty acids
• carboxylic acids with a hydrocarbon side chain
• straight chain vs. branched chain
• saturated = contain only single bonds
• unsaturated = contain double bond(s)
• configuration about the double bond usually cis
• mostly even number of carbons
COOH
COOH
COOH
-
- fatty acids are in anionic form at physiological pH:
RCOOH
pKa ≈ 4.5
+
RCOO + H
- naming and abbreviating fatty acids: number of carbons, double bonds (their position and configuration)
 see table on page 35
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- fatty acid carbon numbering starts from the carboxy end; however if ω-naming system used, then:
- w- (omega) fatty acids: the position of the double bond(s) counted from the methyl end group, e.g. w-3, w-6
- essential: mammals cannot make double bonds between D9 and the methyl end
- abundant in some plant seeds and fish oils
COOH
fatty acids with double bond(s) in this
region must be obtained from food
fatty acids with double bond(s) in this
region can be synthesized in the body
- chain length and degree of saturation affects solubility, packing and melting temperature
- cis-double bond makes a bend to the fatty acid tail
PROBLEM 1. What is one apparent influence to
the physical properties of a fatty acid upon
introduction of double bond(s)?
- in cells not much free fatty acids exist, but most are parts of more complex lipids
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TRIACYLGLYCEROLS ≈ FATS
- fatty acyl esters of glycerol
- efficient energy stores
- may contain different fatty acids
- in animals fat stored in adipose cells
- fats and oils are mixtures of triacylglycerols; fat is solid, oil is liquid
at room temperature
- 3 major functions of fat:
• energy production  get ATP to drive metabolic processes
• heat production (alternative for ATP production)
• thermal insulation (layers of fat cells under the skin)
- 2 advantages of storing energy in the form of fat rather than carbohydrate:
• fat is less oxidized than carbohydrate, so, fat has more energy-releasing capacity left
• fat is tightly packed and need no water, which would increases the weight to carry
- composition and naming system
Molecules in 3D for example from here:
www.biotopics.co.uk
classification of lipids
Numbering begins from the carboxylic end!
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PROBLEM 2. Draw the structure or abbreviate the following fatty acids: (NOTE: some may be hypothetical –
taken here just for the sake of practicing)
a) 18:2tD5,8
b) 22:4cD3,9,12,20
c)
O
OH
SOAPS AND DETERGENTS
- saponification: fat + alkali (NaOH, KOH)  soap
- fatty acids are released and form sodium or potassium salts
- detergents are synthetic molecules that often have better defined chemical and physical properties than soaps
- detergents can be used to denaturate proteins or extract and solubilize membrane proteins (mimic the membrane
environment and mask the hydrophobic surface of the membrane protein)
O
O
SDS, sodium dodecyl sulfate
S
O
Triton X-100
PROBLEM 3. Chemistry of cleaning: Why do many cleansing
agents used to remove stains or spots are basic by pH
and what is the practical advantage of this?
WAXES
- a long-chain fatty acid ester + a long-chain alcohol = wax
- the head group is left only weakly hydrophilic  waxes
are insoluble
- used as protective coatings by both animals and plants
-
+
O Na
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LIPID CONSTITUENTS OF BIOLOGICAL MEMBRANES
- cell membranes contain a variety of different lipids that also affect the structure and function of the membranes
i) GLYCEROPHOSPHOLIPIDS (phosphoglycerides)
- phosphate-containing head group
- derivatives of glycerol-3-phosphate
glycerol backbone
- major group of lipids in most biological
membranes
- R1 & R2 derived from fatty acids
- R3 possess great variance
ii) GLYCOGLYCEROLIPIDS
- built on non-phosphorylated glycerol
- sugar at R3
- monogalactosyl diglyceride abundant in chloroplast membranes
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-
sphingomyelin is part of membraneous structure
that surrounds and insulates nerve axons
- sphingolipids at cell surfaces mediate biological recognition:
• extracellular molecules
• cell-cell contacts
• blood group antigens
- ganglioside is a soluble
lipid due to many
carbohydrate units
iv) CHOLESTEROL
- a steroid
- rigid structure due to all-chair conformation of the cyclohexane rings
- content up to ca. 25% in some membranes
- disrupts regularity in the membrane  can regulate membrane
stiffness and permeability
- without cholesterol
the flexibility of the
membrane could
change too rapidly
as a response to
changes in
environment
- cholesterol helps
membranes to
adapt better and so
membranes do not
break
- stiff (jäykkä) – breaks more easily
- cholesterol adds flexibility to the
membrane structure; not as stiff
Despite knowing much of the membrane and membrane lipids:
 why so many different types of lipids in biological
membranes - no clear understanding as yet
example of lipid function in tissues:
lung surfactant (keuhkosurfaktantti)
i.e. why do we need to know about lipids...
- major lipid component of the surfactant is dipalmitoyl
phosphatidylcholine, DPPC
- alveoli cells are coated
with DPPC
- DPPC is tightly packed, since fatty acids
in DPPC are saturated
- tight packing of DPPC resists collapse of the
alveolar space when breathing out
- when not collapsed, also less energy is
needed in expanding the alveolar space
when breathing in
- defect in the surfactant causes diseases associated with breathing
difficulties
 knowing about lipid structure-function (biochemistry)
makes it possible to understand physiology and disease
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Blood group antigens.
ref. Carbohydrate lectures!
A case: how will a snake venom kill you?
Phosphatidylserine is a glycerophospholipid that contains the amino acid serine as the R3 group, and two myristic
acids as the groups R1 and R2. Many snake venoms contain the enzyme phospholipase A2 that can remove the
R2 fatty acid in a reaction involving a water molecule. What remains is lysolecithin, which is more amphiphilic and
can act as a detergent that disrupts the red blood cell membranes causing hemolysis.
a) Draw the molecular formula of phosphatidylserine
b) Draw also the molecular formula of lysolecithin.
(will be done at the lecture)
- membranes of different cells or cell organelles differ in their lipid composition
LIPIDS THAT FUNCTION AS SIGNAL MOLECULES
- steroid hormones and many vitamins are derived from cholesterol
 Steroid metabolism: Aineenvaihdunta II course
EICOSANOIDS
- eicosi = 20
- oxygenated derivatives of C20 polyunsaturated fatty acids; synthesized in the body from arachidonic acid
- carry messages to nearby cells
- various physiological regulation functions, like blood flow to organs, smooth-muscle contraction, body temperature
- many cause inflammation and pain  aspirin (acetylsalicylic acid) kills pain by inhibiting prostaglandin synthesis
PROBLEM 4.
Is arachidonic acid an
essential lipid? Why?
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AGGREGATION OF LIPIDS AND STRUCTURE OF BIOLOGICAL MEMBRANES
- at the air-water interface lipids cover twice the area of the membrane made of them
- membrane monolayers, bilayers and micelles
- micelles – bilayers – liposomes
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- detergents easily form micelles
- CMC = critical micelle concentration
e.g. SDS 8.2 mM
Mw=288; Mw (micelle)=18.000
63 monomers/micelle
- liposomes are spherical vesicles
containing an aqueous inner
compartment surrounded by a lipid
bilayer
- may form inside cells or can be made
experimentally
SUMMARY
- synthesis of new lipid bilayer is not well understood
• adding lipids to increase size of membrane
• different membranes have different composition of lipids and proteins
• transfer of newly synthesized membrane?
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- fluid
mosaic model describes the arrangement of lipid and protein within the membrane
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what now follows is a trial to combine structural features of both lipids and proteins in order to understand
biological membrane structure and function  fluid mosaic model
(we have to jump a little bit away from lipids every now and then)
- there are integral as well as peripheral membrane proteins: either penetrating the membrane or just associated with it
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- lateral movement of lipids fast
- transverse diffusion slow; helped by enzyme flippase
fast
slow
fast
fast
- biological membrane may exist in an ordered gel phase or as
disordered liquid crystal (fluid) or in a transition state having
characteristics of both
- affected by composition, temperature
 change in temperature compensated by change of lipid
composition to maintain fluidicity
- different membrane lipids, including cholesterol, pack well
together to form the membrane
- lipid side chains affect membrane packing and thus the
physical properties of the membrane
- head groups add functionality to the membrane
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- notice that the percentage of total saturated fatty acids in cells increases and unsaturated decreases as a
function of increased environmental temperature.
Proteins as part of membrane structure:
- different types of integral membrane proteins, I to VI
- transmembrane domain can also be built of b-sheets (e.g. porins)
- lipid anchoring (type V) is also considered a type of its own (next page)
a porin channel that forms
a “hole” in the membrane
90o
Characteristics of membrane proteins:
- topology of an integral membrane protein can be
predicted from its sequence (despite shortage of
experimentally determined structures of that type of
proteins)
- continuous sequence of >20 hydrophobic residues
indicates a membrane-spanning a-helix
- hydropathy plot
- aromatic amino acids often found at the lipid-water
interface
-
lipid-anchoring is possible both for integral and
peripheral membrane proteins:
• prenylation
• fatty acylation
• GPI-link
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outside
phospholipid
sugars
protein
inside
GPI anchor
lipid and protein composition varies between membranes of different cells/cell organelles
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- membrane bilayer is also asymmetric: lipid and protein composition varies between different sides of the bilayer
- lipids and proteins may also be laterally organized into domains that cover different parts of a cell
• certain proteins associate to form aggregates
• specific protein-lipid interactions  certain proteins and certain lipids are found together
lipid rafts
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- divalent metal ions ligate certain lipids with negative head groups
- glycosphingolipids and cholesterol form rafts that associate with certain proteins
lipid raft
- many membrane proteins are glycosylated (=glycoproteins)
Basic concept: protein and glycan are synthesized separately and then attached to each other
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Example: the ebola virus infection mechanism employs specific interaction with components in the lipid rafts
i.e. lipid raft is a target for the virus
- one of the virus membrane proteins contains a sequence (called ”fusion peptide”) including a tryptophan and
a phenylalanine (1)
- the fusion peptide makes a strong interaction with cholesterol molecules in the membrane
- virus uses this interaction to integrate its membrane into the endocytotic membrane to release the genetic material into
the cytoplasm (2)
- cells with less cholesterol in their membrane are less prone to ebola virus infection
1
2
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• membrane of the same cell may also have a different lipid
and protein composition on different sides of the cell,
for example apical and basolateral sides of epithelial cells
- certain membrane proteins associate with cytoskeleton  form distinct localizations
- human erythrocyre membrane as an example of studying a membrane structure:
• peripheral membrane proteins (on the cytoplasmic side) removed by change in pH or ionic strength
• integral membrane proteins removed by a non-ionic detergent Triton X-100
• cytoskeleton-forming proteins are revealed; most notable are spectrin and actin (next page)
actin structure
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electron micrograph of erythrocyte membrane skeleton
spectrin structure
- examples of plasma membrane composition and functionality (below and next page)
Pathogen infections
Toxins
Leukocyte rolling
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FUNCTIONS ASSOCIATED WITH BIOLOGICAL MEMBRANES
- barrier against the outside
- selective intake and excretion of substances  membrane transport
- cell-cell and other recognition
- fusion and separation events
Membrane transport:
- passive diffusion through
the membrane
- permeability depends on
the molecule
Membrane transport:
- facilitated diffusion through pores/channels
- facilitated transport by carrier molecules
- driving force either ion gradient or coupled to
ATP production
•Energy needed when diffusion goes
against the concentration gradient
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- rate of diffusion varies
red = ”open”
blue = ”closed”
substrate
- conformational change of proteins is
an important issue very often related to
protein function, like binding of
substrate (enzymes) or other
substances (receptors, protein-protein
interactions, etc.)
- an example of triose phosphate
isomerase, where one loop moves ca.
10 Å to give way for substrate to bind
Vesicle fusion:
- coated vesicles are a transport means for
newly synthesized and secreted proteins
- both for soluble and integral membrane proteins
- endocytosis (transport in), exocytosis (transport out)
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- caveolae form via association of caveolin proteins,
which are asymmetrically positioned in the membrane
- make it possible for membrane to curve and finally
form a vesicle
- so called SNARE proteins insert into both membranes,
bind to each other, and anchor the vesicle to the target
membrane
- in this way mediate the membrane fusion
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- physiological phenomena involving membrane fusion
http://www.chem.qmul.ac.uk/iupac/lipid/
IUPAC-IUB Commission on Biochemical Nomenclature (CBN)
Nomenclature of Lipids
Fahy et al., A comprehensive classification system for lipids
Journal of Lipid Research 46, 839-861 (2005)
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RECAP QUESTIONS
PROBLEM 5. When we classify a certain compound as a ”lipid”, we do so using a different rationale
compared to e.g. classifying another compound as a ”nucleic acid” or a ”protein”. What is the difference?
PROBLEM 6. Thickness of biological membranes is 5 to 8 nm (50 to 80 Å) with the lipid bilayer part ca. 3 to 5
nm. The carbon-carbon bond length is about 1.5 Å. Estimate the length of a palmitate molecule (consider a
fully extended form). If two molecules of palmitate were placed end to end, like in a lipid bilayer, how would
their total length compare with the thickness of a lipid bilayer and a biological membrane (i.e. can our
understanding of the membrane structure be correct)?
PROBLEM 7. Liposomes can be prepared by suspending a suitable lipid in water and sonicating. Any
chemicals dissolved in water may then trap inside liposomes. Liposomes may also fuse with cell membranes;
each type of liposome with a cell membrane that contains same or similar lipids. What possible practical use
could this phenomenon offer?
(example)
Glycine trapped
in phospholipid
vesicles
Sonication
(”sonic disruption”)