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Lipid Metabolism
Andy Howard
Introductory Biochemistry
15 April 2008
15 April 2008
Making and Breaking Lipids
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Lipid biosynthesis is a significant route to
the creation of energy-storage molecules,
membrane components, and hormones;
Lipid catabolism is a critical energyproducing pathway, and we also need to
understand degradation of functional
lipids
… but first, a few final slides about plants!
Lipid Metabolism
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15 April 2008
What we’ll discuss
End of plant stuff
 Lipid anabolism

 Fatty

acid synthesis
 Making fats and
phospholipids

 Eicosanoids
 Ether lipids

 Sphingolipids
 Isoprenoids & steroids
Lipid Metabolism
Fatty acid oxidation
 Sequence
of reactions
for saturated FAs
 Unsaturations
 Energetics
Phospholipid
degradation
Steroid and other
degradative systems
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15 April 2008
Crassulacean acid
metabolism
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Leaf cells open to CO2 uptake lose a
lot of water during the day
(high evaporation rate)
Solution: assimilate carbon at night
Reactions are as in C4 pathway;
cellular specialization and enzyme
regulation are different
Lipid Metabolism
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15 April 2008
Stomata and vacuoles
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Stomata (spaces between cells that
can open to allow access for
respiration) near mesophylls open only
at night, enabling PEP carboxylation to
oxalacetate and then reduction to
malate
Malate stored in central vacuole, then
released during the day when the
stomata are closed
Lipid Metabolism
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15 April 2008
CAM: day and night
University of Newcastle, Plant Physiology program
Lipid Metabolism
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15 April 2008
iClicker quiz question 1

Oxidation of a 2ncarbon fatty acid yields
(n-1) QH2,
(n-1) NADH, and n
acetyl CoA. Initiating
the process costs 2
ATPs. Assume we can
get 10 ATP per acetyl
CoA. How much ATP
can we get from
oxidizing palmitate?
Lipid Metabolism
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(a) 104 ATP
(b) 106 ATP
(c ) 108 ATP
(d) 112 ATP
(e) Undeterminable
given the data
supplied
p. 7 of 85
15 April 2008
Answer to 1st question
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Palmitate is a C16 carboxylic acid.
Therefore in the conditions of the
problem, 2n = 16, n = 8, n-1 = 7.
Thus we get 7 QH2, 7 NADH,
8 acetyl CoA produced by its oxidation
Thus we get 7*2.5 + 7 * 1.5 + 8 * 10 =
17.5 + 10.5 + 80 = 108 ATP produced
Starting the process costs 2 ATP, so the
net result is 106 ATP gained
Lipid Metabolism
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15 April 2008
iClicker quiz question 2
Why would you not expect to find crassulacean
acid metabolism in tropical plants?
 (a) Tropical plants do not photosynthesize.
 (b) Tropical plants cannot develop the stomata
that close off the chloroplast-containing cavities
 (c) Water conservation is less critical in areas of
high rainfall
 (d) The waxy coating required to close off the
leaves’ access to O2 would dissolve in the high
humidity and high temperature of the tropics
 (e) None of the above
Lipid Metabolism
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Answer: (c)

The primary significance of CAM is
conservation of water in regions of low
humidity, where evaporation rates are
high and water is scarce. Neither of these
conditions pertains in the tropics.
Lipid Metabolism
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Control of CAM
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PEP carboxylase inhibited by
malate and low pH
That prevents activity during
daylight, which would lead to futile
cycling and competition for CO2
between PEP carboxylase and
RuBisCO
Lipid Metabolism
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15 April 2008
Compartmentation in bacteria
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In photosynthetic bacteria,
RuBisCO is concentrated in protein
microcompartment called a
carboxysome
Active carbonic anhydrase there:
catalyzes HCO3-  OH- + CO2
That tends to keep the CO2 / O2
ratio high
Lipid Metabolism
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Lipids:
What we won’t cover
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Special Cases
Locations for synthesis
Regulation by hormones
Absorption and mobilization
Ketone bodies
Lipid Metabolism
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Lipid Anabolism

Malonyl CoA
Generally the starting point for building
up lipids are acetyl CoA and malonyl
CoA, and their variants acetyl ACP and
malonyl ACP
 Fatty
acids
 Steroids

These are energy-requiring reactions:
the compounds we’re making are
reduced
Lipid Metabolism
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Overview (cf.
fig. 16.1)

Acetoacetyl ACP
Bacteria:
acetyl CoA + malonyl ACP 
acetoacetyl ACP + CO2 + CoASH

Eukaryotes:
CoA + ACP 
acetyl ACP + CoASH
 Acetyl ACP + malonyl ACP  acetoacetyl
ACP + CO2 + ACP
 acetyl
Lipid Metabolism
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Making
malonyl
CoA
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PDB 1w96 (biotin
carboxylase domain)
183 kDa trimer
yeast
Acetyl CoA incorporates
an extra methylene via
acetyl CoA carboxylase
Biotin- and ATPdependent enzyme;
similar to pyruvate
carboxylase
Lipid Metabolism
1uyr (carboxyltransferase domain)
162 kDa dimer; yeast
15 April 2008
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Making
malonyl ACP
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Malonyl CoA:ACP
transacylase
transfers the malonate group
from coenzyme A to the acyl
carrier protein
Ferredoxin-like protein
Similar enzyme converts acetyl
CoA to acetyl ACP
Lipid Metabolism
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PDB 1NM2
35 kDa
monomer
Streptomyces
coelicolor
15 April 2008
Acyl carrier
protein itself
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Acts as a template on
which acyl chain
elongation can occur
Simple protein: 83
amino acids, mostly
helical
This is actually an
NMR structure
Lipid Metabolism
PDB 1OR5
9.1 kDa monomer
Streptomyces
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Initiation reaction
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We want to start with a four-carbon unit attached
to acyl carrier protein
We get that by condensing acetyl CoA or acetyl
ACP with malonyl ACP with ketoacyl ACP
synthase (KAS) to form acetoacetyl ACP
Intermediate has KAS covalently attached to
both substrates
Decarboxylation of enzyme-bound intermediates
leads to 4-carbon unit attached to ACP
3+21+4
Lipid Metabolism
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Is this typical? Yes!
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We’ve carboxylated acetyl CoA to
make malonyl ACP and then
decarboxylated the product of
malonyl ACP with acetyl CoA /
ACP
This provides a favorable freeenergy change (at the expense of
ATP) for the overall reaction
Similar approach happens in
gluconeogenesis
(pyruvate  oxaloacetate  PEP)
Lipid Metabolism
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Ketoacyl ACP
synthase
PDB 1HNJ
70 kDa dimer;
monomer shown
E.coli
15 April 2008
Elongations in FA
synthesis: overview
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Acetoacetyl ACP: starting point for elongations
Pattern in each elongation is
reduction  dehydration  reduction,
resulting in a saturated product
Reenter pathway by condensing with malonyl ACP
Elongated product plays the same role that acetyl
CoA or acetyl ACP plays in the initial -ketoacyl ACP
synthase reaction: C2n + C3 -> CO2 + C2n+2
Lipid Metabolism
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1st step: reduce
ketone  sec-alcohol
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Enzyme:3-ketoacyl
ACP reductase
Ketone reacts with NADPH
+ H+ to produce sec-alcohol + NADP
D-isomer of sec-alcohol always forms;
by contrast, during degradation,
L-isomer forms
Enzyme is typical NAD(P)-dependent
oxidoreductase
Lipid Metabolism
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PDB 2C07
125 kDa
tetramer;
Monomer shown
Plasmodium
falciparum
15 April 2008
2nd step: alcohol
to enoyl ACP
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3-hydroxyacyl ACP dehydratase
Eliminates water at beta, alpha
postions to produce
PDB 1DCI
182 kDa hexamer
trans-2-enoyl ACP:
trimer shown
R–CHOH–CH2-CO-S-ACP 
Rat mitochondria
R–CH=CH–CO-S-ACP + H2O
Note that this is a derivative of a
trans-fatty acid; but it’s complexed to ACP!
This form is primarily helical;
there is an alternative found in Aeromonas that is an
alpha-beta roll structure
Lipid Metabolism
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3rd step:
enoyl CoA to
saturated ACP
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PDB 2Z6I
Enzyme: enoyl-ACP reductase
73 kDa dimer
Leaves behind fully saturated FA
Streptococcus
complexed to acyl carrier protein:
pneumoniae
R–CH=CH–CO-S-ACP 
R–CH2CH2CO-S-ACP
This can then condense with malonyl ACP with
decarboxylation to form longer beta-ketoacyl ACP:
Rn-ACP + malonyl-CoA 
-keto-Rn+2-ACP + CO2 + CoASH
Enzyme is FMN-dependent
Lipid Metabolism
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How does this end?
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Generally starts at C4 and
goes to C16 or C18.
Condensing enzyme won’t fit
longer FAs
Completed fatty acid is
cleaved from ACP by action
of a thioesterase
with a 3-layer Rossmann
fold
Lipid Metabolism
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Palmitoyl
thioesterase I
PDB 1EI9
31 kDa monomer
bovine
15 April 2008
The overall reaction
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Acetyl CoA + 7 Malonyl CoA + 14NADPH +
14 H+  14 NADP + Palmitate + 7CO2 +
8HS-CoA + 6H2O
In bacteria we have separate enzymes:
a type II fatty acid synthesis system
In animals we have a type I FA synthesis
system: a large, multi-functional enzyme
including the phosphopantatheine group by
which the ACP attaches
Lipid Metabolism
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iClicker question
What advantage, if any, might be associated with
type I fatty acid synthesis systems?
 (a) None
 (b) Reactants remain associated with the
enzymatic complex, reducing diffusive
inefficiencies
 (c) Lowered probability of undesirable reductions
of metabolites
 (d) Lowered probability of undesirable oxidations
of metabolites
 (e) improved solubility of products
Lipid Metabolism
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Answer: (b)
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If the enzyme doesn’t have to find the
substrate at the beginning of each
reaction, things will proceed more readily.
Lipid Metabolism
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Activating
fatty acids
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Activate stearate or palmitate
via acyl CoA synthetase:
R–COO- + CoASH + ATP 
PDB 1BS0
R–CO–SCoA + AMP + PPi
42 kDa monomer
As usual, PPi hydrolysis drives
E.coli
the reaction to the right
PLP-dependent reaction
Bacteria have one acyl CoA synthetase
Mammals: four isozymes for different FA
lengths (small, medium, long, very long)
Lipid Metabolism
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Extending and
unsaturating fatty acids
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There are applications for FAs with more than
18 carbons and FAs with >=1 cis double bonds
Elongases and desaturases exist to handle
these needs (fig. 16.7)
Desaturase adds a cis-double bond; if the FA
already has unsaturations, the new one is
added three carbons closer to the carboxyl
Elongases condense FA with malonyl CoA;
decarboxylation means we add two carbons
Lipid Metabolism
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Bacterial
Desaturases
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Acyl ACP desaturases in
bacteria simply add a cis
double bond in place of the
normal trans double bond at
the second phase of
elongation; the cis double
bond thus created remains
during subsequent rounds
Ferritin-like structure
Lipid Metabolism
PDB 1ZA0;
30 kDa monomer
Mycobacterium
tuberculosis
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15 April 2008
Eukaryotic
Desaturases
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Desaturases like stearoyl ACP
desaturase in eukaryotes act
on the completed saturated
fatty acyl CoA species
Enzyme is ferritin-like or RNRlike
Mammals can’t synthesize
linoleate and they need it, so it
has to be part of the diet
Lipid Metabolism
PDB 1OQ9
80 kDa dimer
monomer shown
castor bean
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Making arachidonate
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We can convert dietary linoleate to
archidonyl CoA via desaturation and
elongations (fig. 16.7)
The fact that the new double bonds start
3 carbons away from the previous one
means they’re not conjugated
Lipid Metabolism
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Phosphatidates
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Phosphatidates are
intermediates in
making triacylglycerol
&
glycerophospholipids
Fatty acyl groups
esterifying 1 and 2
positions of glycerol,
phosphate esterifying
3 position
Lipid Metabolism
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Making
phosphatidates
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Glycerol-3-phosphate
acyltransferase transfers acyl
CoA to 1 position of glycerol3-phosphate; prefers
saturated chains
1-acylglycerol-3-phosphate
acyl transferase transfers
acyl CoA to 2 position of
resulting molecule; prefers
unsaturated chains
Lipid Metabolism
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PDB 1IUQ
40 kDa monomer
Cucurbita
15 April 2008
Making triacylglycerols
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Phosphatidate phosphatase gets rid
of the phosphate at the 3 position by
hydrolysis to make 1,2-diacylglycerol
 A bit
counterintuitive in making
phospholipids: why get rid of the
phosphate when you’re going to put a
phosphorylated compound back at 3
position?
 But the groups you add already have
phosphate on them
Lipid Metabolism
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Further steps in making
triacylglycerols
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Diacylglycerol acyltransferase catalyzes
reaction between 1,2-diacylglycerol and
acyl CoA to form triacylglycerol
See fig. 16.9, left-hand side
Lipid Metabolism
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Making phospholipids from
1,2-diacylglycerol
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1,2-diacylglycerol reacts with CDPcholine to form phosphatidylcholine with
liberation of cytidine monophosphate
1,2-diacylglycerol reacts with CDPethanolamine to form
phosphatidylethanolamine
 this
can be methylated 3 times to make
phosphatidylcholine
 S-adenosylmethionine is the methyl donor in
that case
Lipid Metabolism
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CDPethanolamine
How do we get
CDP-alcohols?
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Easy:
CTP + alcohol phosphate 
CDP-alcohol + PPi
As usual, reaction is driven to the right by
hydrolysis of PPi
Enzymes are CTP:phosphoethanolamine
cytidylyltransferase and
CTP:phosphocholine cytidylyltransferase
Lipid Metabolism
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Making acidic
phospholipids
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Phosphatidate activated to CDPdiacylglycerol as catalyzed by
CTP:phosphatidate cytidylyltransferase with
release of PPi (see previous reactions)
This can react with serine or inositol to form
the relevant phospholipids; see fig. 16.10.
This route to phosphatidylserine is found
only in bacteria
Lipid Metabolism
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Phosphatidylserine
Lipid Metabolism
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Phosphatidylinositol
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Phosphatidylinositol is made by this CDPdiacylglycerol pathway in bacteria and
eukaryotes
Lipid Metabolism
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Making phosphatidylserine
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Alternative approach to phosphatidylserine
found in eukaryotes:
make phosphatidylethanolamine, then
phosphatidylethanolamine:serine
transferase swaps serine for ethanolamine
When we do it that way, we can recover
phosphatidylethanolamine back by a
decarboxylation (or another exchange)
Ethanolamine is just serine without COO- !
Lipid Metabolism
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Where does this happen?
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Mostly in the endoplasmic reticulum in
eukaryotes
Biosynthesis enzymes are membrane
bound but have their active sites facing
the cytosol so they can pick up the watersoluble metabolites from which they can
build up phospholipids and other lipids
Lipid Metabolism
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Making eicosanoids

Classes of eicosanoids:
 Prostaglandins
and thromboxanes
 Leukotrienes
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Remember that we make arachidonate
from linoleoyl CoA; eiconsanoids made
from arachidonate
Reactions involve formation of oxygencontaining rings; thus the enzymes are
cyclooxygenases
Lipid Metabolism
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What eiconsanoids do
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They’re like hormones, but they act very
locally: within µm of the cell in which
they’re produced
Involved in platelet aggregation, blood
clots, constriction of smooth muscles
Mediate pain sensitivity, inflammation,
swelling
Therefore enzymes that interconvert
them are significant drug targets!
Lipid Metabolism
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15 April 2008
Prostaglandin H2
Synthesizing
prostaglandins
PDB 2OYU
 Prostaglandin H synthase (PGHS) 132 kDa dimer
binds on inner surface of ER
Monomer shown
sheep
 Cyclooxygenase activity makes a

hydroperoxide; this is converted to
PGH2
PGH2 gets converted to other
prostaglandins, prostacyclin,
thromboxane A2 (fig. 16.12)
Lipid Metabolism
p. 47 of 85
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How aspirin works
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Aspirin blocks irreversibly inhibits the
COX activity of PGHS by transferring an
acetyl group to an active-site Ser
That blocks eiconsanoid production,
which reduces swelling and pain
But there are side effects because some
PGHS isozymes are necessary
Lipid Metabolism
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Cyclooxygenase inhibition
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Cox-1 is constitutive and regulates secretion of
mucin in the stomach
Cox-2 is inducible and promotes inflammation,
pain, fever
Aspirin inhibits both: the mucin-secretion
inhibition means that causes bleeding or ulcers in
the stomach lining
Other nonsteroidal anti-inflammatories (NSAIDs)
besides aspirin compete with arachidonate rather
than binding covalently to COX-1 and COX-2
Lipid Metabolism
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Could we find a
COX-2 inhibitor?
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This would eliminate the stomach
irritation that aspirin causes
Some structure-based inhibitors have
been developed
They work as expected; but
They also increase risk of cardiovascular
disease
Prof. Prancan (Rush U) discussed these
issues in his February 2007 colloquium
Lipid Metabolism
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15 April 2008
Leukotrienes
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Lipoxygenases convert
arachidonate to these
compounds, which contain 3
conjugated double bonds
These compounds interact
with GPCRs
Involved in inflammatory and
allergic reactions
Also involved in the
pathophysiology of asthma
Lipid Metabolism
Leukotriene B4
p. 51 of 85
PDB 2P0M
146 kDa dimer
rabbit
15 April 2008
Synthesis of
ether lipids
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Remember: these are
lipids with ether linkages instead of acyl linkages
Begins with dihydroxyacetone phosphate
Acyltransferase acylates DHAP C-1
1-alkyl-DHAP synthase swaps an alcohol for the
acyl group at C-1
Keto group at C2 of DHAP is reduced to an
alcohol (NADPH-dependent reaction)
Lipid Metabolism
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Ether lipids,
continued
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1-alkylglycerophosphate acyltransferase adds
another acyl group at C-2
Dephosphorylated at C-3 (as with phospholipids
… take the P off, put it back on …)
Phosphocholine or other phosphate-based ligand
added at C-3
Plasmalogens earn a double bond between the
two carbons adjacent to the ether oxygen on C-1
Lipid Metabolism
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15 April 2008
ceramide
Sphingolipid
synthesis
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These are based formally
on sphingosine, a C18
unsaturated amino alcohol (fig.16.14)
Condense serine with palmitoyl CoA to make 3ketosphinganine and CO2
NADPH-reduce this to sphinganine
Acetylate the amine group to make Nacylsphinganine
Beta-unsaturate the palmitoyl group to make
ceramide, the basis for all other sphingolipids
Lipid Metabolism
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15 April 2008
ceramide
Sphingolipid
synthesis
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These are based formally
on sphingosine, a C18
unsaturated amino alcohol (fig.16.14)
Condense serine with palmitoyl CoA to make 3ketosphinganine and CO2
NADPH-reduce this to sphinganine
Acetylate the amine group to make Nacylsphinganine
Beta-unsaturate the palmitoyl group to make
ceramide, the basis for all other sphingolipids
Lipid Metabolism
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15 April 2008
ceramide
Sphingolipid
synthesis
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These are based formally
on sphingosine, a C18
unsaturated amino alcohol (fig.16.14)
Condense serine with palmitoyl CoA to make 3ketosphinganine and CO2
NADPH-reduce this to sphinganine
Acetylate the amine group to make Nacylsphinganine
Beta-unsaturate the palmitoyl group to make
ceramide, the basis for all other sphingolipids
Lipid Metabolism
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15 April 2008
spingomyelin
Other
sphingolipids
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React ceramide with phosphatidylcholine;
products are sphingomyelin and 1,2diacylglycerol
React ceramide with UDP-galactose to
form a galactocerebroside
Additional UDP-sugars or CMP-N-acetylneuraminic acid can be added
Lipid Metabolism
p. 57 of 85
15 April 2008
Steroid
synthesis:
overview
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Cholesterol is important on its own & as a
precursor of steroid hormones, bile salts
Derived formally from isoprene
Isoprenoid synthesis based on
mevalonate &
isopentenyl
diphosphate
Lipid Metabolism
p. 58 of 85
15 April 2008
Making HMG-CoA
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Condense 3 molecules of acetyl CoA:
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2 acetyl CoA  acetoacetyl CoA + CoASH;
catalyzed by acetoacetyl CoA synthase
Acetoacetyl CoA + acetyl CoA + H2O 
3-hydroxy-3-methylglutaryl CoA + CoASH + H+
catalyzed by HMG CoA synthase
These are important intermediates: precursor to
steroids and ketone bodies
Not the committed step toward isoprenoids
because we can also make ketone bodies from
HMG-CoA
Lipid Metabolism
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15 April 2008
iClicker quiz question
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Creation of new C-C bonds requires
energy. Where is it coming from in these
condensations?
(a) enzymatic catalysis
(b) hydrolysis of ATP
(c) hydrolysis of thioether bonds
(d) hydrolysis of thioester bonds
(e) none of the above
Lipid Metabolism
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Answer: (d)
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(a) no. Enzymatic catalysis doesn’t
change thermodynamics: it changes
kinetics
(b) no. There’s no ATP involved.
(c) no. These acyl CoA molecules
contain thioester linkages
(d) yes. Hydrolysis of thioester linkages
yields substantial amounts of free energy
Lipid Metabolism
p. 61 of 85
15 April 2008
HMGCoA to
mevalonate
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PDB 1DQA
PDB 1DQA
205 kDa tetramer
205 kDa
Human
tetramer
human
HMGCoA reductase is
the first committed step
on pathway toward
isoprenoids
HMGCoA + 2NADPH +
2H+  mevalonate +
2NADP+ + CoASH
Many drug-discovery
projects involve
inhibition of this enzyme
Lipid Metabolism
p. 62 of 85
15 April 2008
Mevalonate to isopentenyl
diphosphate
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Two successive ATP-dependent kinase steps
convert mevalonate to mevalonate 5diphosphate
ATP-dependent decarboxylation yields
isopentenyl diphosphate
This is an isoprene-donating group involved in
making non-steroidal isoprenoid compounds as
well as steroids
Lipid Metabolism
p. 63 of 85
15 April 2008
Mevalonate kinase
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Converts mevalonate to
mevalonate 5-phosphate
Secondary control point in
isoprenoid synthetic pathway
Human diseases associated
with abnormalities
 Mevalonic
aciduria
 Hyperimmunoglobulinemia
(Periodic fever syndrome)
Lipid Metabolism
p. 64 of 85
PDB 2HFS
73 kDa
dimer;
monomer
shown
Leishmania
major
15 April 2008
Isopentenyl
diphosphate to
squalene




Isomerized to dimethylallyl diphosphate
That condenses with another molecule of IPDP
to make geranyl diphosphate (C10)
Another condensation with IPDP (with the same
enzyme) makes farnesyl diphosphate (C15)
Two farnesyl diP fuse head-to-head to make
squalene (C30, no heteroatoms)
Lipid Metabolism
p. 65 of 85
15 April 2008
Geranyl diphosphate &
farnesyl diphosphate
Geranyl
diphosphate:
C10
Farnesyl
diphosphate:
C15
Lipid Metabolism
p. 66 of 85
15 April 2008
Squalene

Made via head-to-head synthesis from 2
molecules of farnesyl diphosphate
Squalene: C30
Lipid Metabolism
p. 67 of 85
15 April 2008
lanosterol
Squalene to
cholesterol



Several messy steps move
the double bonds around
replace double bonds with
ring closures  lanosterol
Eliminate 3 methyls, move
one double bond, remove
another double bond, and
voila: cholesterol
Lipid Metabolism
lanosterol synthase;
converts 2,3oxidosqualene to
lanosterol
PDB 1W6K
81 kDa monomer
human
p. 68 of 85
15 April 2008
What happens to cholesterol?




Inserted into membranes
Assembled into lipoproteins
Derivatized to make bile salts
Modified into hormones
Lipid Metabolism
p. 69 of 85
15 April 2008
Other isoprenoids




Generally made from isopentenyl
pyrophosphate
Pathways to isopentenyl pyroP are
ancient: used in bacteria
Pathways to steroids comparatively
recent
Cholesterol essential in animal
membranes; plants have other sterols
like campesterol (24-methyl-cholesterol)
Lipid Metabolism
p. 70 of 85
15 April 2008
Lipid catabolism


We’ve been focusing on making lipids
Now we’ll look at how they’re broken
down
 As
energy sources
 In recycling lipid components that have
functional or structural significance
Lipid Metabolism
p. 71 of 85
15 April 2008
Fatty acid (beta) oxidation

Degradation proceeds 2 C at a time
somewhat like synthesis
 Called -oxidation because in each round the form
that gets shortened is a -ketoacyl CoA





Activated form is acyl CoA, not acyl ACP
Product is n molecules of acetyl CoA from a
2n-carbon fatty acid
Yields n-1 NADH and n-1 QH2
Occurs in the mitochondrion or peroxisome,
whereas synthesis occurs in the cytosol
Lipid Metabolism
p. 72 of 85
15 April 2008
Reactions in -oxidation

Proceeds through cycle n times for a 2ncarbon fatty acid
Diagram
courtesy
Richard
Paselk,
Humboldt
State U.
Lipid Metabolism
p. 73 of 85
15 April 2008
Acyl-CoA
dehydrogenase


Converts fatty acid
saturated at C2,3 to
trans-2-Enoyl CoA:
—CH2—CH2—COSCoA
Several isozymes for
various sizes of FAs
Lipid Metabolism
medium-chain acyl CoA
dehydrogenase
PDB 3MDE
169kDa tetramer;
dimer shown
Pig liver
p. 74 of 85
15 April 2008
ElectronTransferring
Flavoprotein (ETF)




Here, it converts FADH2
created by acyl-CoA
dehydrogenase back to FAD
via Fe-S protein
Rossmann-fold protein
Plays role in other redox
reactions
Ultimate acceptor is Q, which
can be re-oxidized in the ETS
Lipid Metabolism
p. 75 of 85
PDB 1EFV
63 kDa
heterodimer
human
15 April 2008
Hydration step




Enzyme is 2-enoyl CoA
dehydratase
- roll protein
onverts enoyl CoA to L-3hydroxyacyl CoA
Remember this is the opposite
stereochemistry relative to
synthetic intermediate
Lipid Metabolism
p. 76 of 85
PDB structure
1S9C:
dehydratase
domain of
human
multifunctional
enzyme
15 April 2008
Second
oxidative step



Enzyme is L-3-hydroxyacylCoA dehydrogenase
NADH is reduced product
NADH can be used in
biosynthesis (via shuttles) or
oxidized in the ETS
Rossmann-fold protein
Lipid Metabolism
dehydrogenase
domain of
multifunctional
enzyme
PDB 1E6W
114 kDa tetramer
rat
p. 77 of 85
15 April 2008
Thiolysis




HS-CoA attacks C3carbonyl and cleaves off
acetyl CoA, resulting in
shortening by two carbons
Enzyme is 3-ketoacyl-CoA
thiolase
Similar to acetoacyl-CoA
thiolase found in
isopentenyl diP pathway
Substrate can go through
another round
Lipid Metabolism
p. 78 of 85
PDB 1QFL
171 kDa
tetramer
Zooglea
15 April 2008
Formal similarity




… between FA oxidation steps 1-3 and
middle reactions of TCA cycle:
–CH2CH2– oxidized to trans-CH=CH—:
like succinate to fumarate
Trans-ene hydrated to L-CHOH-CH2—:
like fumarate to L-malate
Alcohol oxidized to ketone:
like L-malate to oxalacetate
Lipid Metabolism
p. 79 of 85
15 April 2008
Peroxisomal
-oxidation

Very common






in many non-mammalian
eukaryotes it’s the only kind
In mammals this handles odd cases;
mitochondria are the primary oxidizers
PDB 1IS2
Initial reaction doesn’t produce QH2:
145 kDa
it produces hydrogen peroxide as the other
dimer
product besides trans-2-enoyl CoA
rat liver
Reaction catalyzed by acyl-CoA oxidase
Peroxisomes don’t have ETS so the reducing
equivalents used in other ways
Compartmentation keeps H2O2 away from ETS
Lipid Metabolism
p. 80 of 85
15 April 2008