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15 April 2008 Lipid Metabolism p. 2 of 85
Making and Breaking Lipids Lipid biosynthesis is a significant route to
the creation of energy-storage molecules, membrane components, and hormones;
Lipid catabolism is a critical energy-producing pathway, and we also need to understand degradation of functional lipids
… but first, a few final slides about plants!
15 April 2008 Lipid Metabolism p. 3 of 85
What we’ll discuss End of plant stuff Lipid anabolism
Fatty acid synthesisMaking fats and
phospholipidsEicosanoidsEther lipidsSphingolipids Isoprenoids & steroids
Fatty acid oxidation Sequence of reactions
for saturated FAs Unsaturations Energetics
Phospholipid degradation
Steroid and other degradative systems
15 April 2008 Lipid Metabolism p. 4 of 85
Crassulacean acid metabolism
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
15 April 2008 Lipid Metabolism p. 5 of 85
Stomata and vacuoles 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
15 April 2008 Lipid Metabolism p. 6 of 85
CAM: day and night
University of Newcastle, Plant Physiology program
15 April 2008 Lipid Metabolism p. 7 of 85
iClicker quiz question 1 Oxidation of a 2n-
carbon 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?
(a) 104 ATP (b) 106 ATP (c ) 108 ATP (d) 112 ATP (e) Undeterminable
given the data supplied
15 April 2008 Lipid Metabolism p. 8 of 85
Answer to 1st question 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
15 April 2008 Lipid Metabolism p. 9 of 85
iClicker quiz question 2Why 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
15 April 2008 Lipid Metabolism p. 10 of 85
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.
15 April 2008 Lipid Metabolism p. 11 of 85
Control of CAM 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
15 April 2008 Lipid Metabolism p. 12 of 85
Compartmentation in bacteria 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
15 April 2008 Lipid Metabolism p. 13 of 85
Lipids:What we won’t cover
Special Cases Locations for synthesis Regulation by hormones Absorption and mobilization Ketone bodies
15 April 2008 Lipid Metabolism p. 14 of 85
Lipid Anabolism 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
Malonyl CoA
15 April 2008 Lipid Metabolism p. 15 of 85
Overview (cf. fig. 16.1)
Bacteria:acetyl CoA + malonyl ACP acetoacetyl ACP + CO2 + CoASH
Eukaryotes:acetyl CoA + ACP
acetyl ACP + CoASHAcetyl ACP + malonyl ACP acetoacetyl
ACP + CO2 + ACP
Acetoacetyl ACP
15 April 2008 Lipid Metabolism p. 16 of 85
Making malonyl CoA
Acetyl CoA incorporates an extra methylene via acetyl CoA carboxylase
Biotin- and ATP-dependent enzyme; similar to pyruvate carboxylase
PDB 1w96 (biotin carboxylase domain)183 kDa trimeryeast
1uyr (carboxyl-transferase domain)162 kDa dimer; yeast
15 April 2008 Lipid Metabolism p. 17 of 85
Making malonyl ACP
Malonyl CoA:ACPtransacylasetransfers the malonate group from coenzyme A to the acyl carrier protein
Ferredoxin-like protein Similar enzyme converts acetyl
CoA to acetyl ACP
PDB 1NM235 kDa monomerStreptomyces coelicolor
15 April 2008 Lipid Metabolism p. 18 of 85
Acyl carrier protein itself
Acts as a template on which acyl chain elongation can occur
Simple protein: 83 amino acids, mostly helical
This is actually an NMR structure
PDB 1OR59.1 kDa monomerStreptomyces
15 April 2008 Lipid Metabolism p. 19 of 85
Initiation reaction
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 ACP3 + 2 1 + 4
15 April 2008 Lipid Metabolism p. 20 of 85
Is this typical? Yes! 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 free-energy change (at the expense of ATP) for the overall reaction
Similar approach happens in gluconeogenesis(pyruvate oxaloacetate PEP)
Ketoacyl ACP synthasePDB 1HNJ70 kDa dimer;monomer shownE.coli
15 April 2008 Lipid Metabolism p. 21 of 85
Elongations in FA synthesis: overview 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
15 April 2008 Lipid Metabolism p. 22 of 85
1st step: reduce ketone sec-alcohol
Enzyme:3-ketoacylACP 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
PDB 2C07125 kDa tetramer; Monomer shownPlasmodium falciparum
15 April 2008 Lipid Metabolism p. 23 of 85
2nd step: alcohol to enoyl ACP
3-hydroxyacyl ACP dehydratase Eliminates water at beta, alpha
postions to producetrans-2-enoyl ACP:R–CHOH–CH2-CO-S-ACP R–CH=CH–CO-S-ACP + H2O
Note that this is a derivative of atrans-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
PDB 1DCI182 kDa hexamertrimer shownRat mitochondria
15 April 2008 Lipid Metabolism p. 24 of 85
3rd step:enoyl CoA to saturated ACP
Enzyme: enoyl-ACP reductase Leaves behind fully saturated FA
complexed to acyl carrier protein: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
PDB 2Z6I73 kDa dimerStreptococcus pneumoniae
15 April 2008 Lipid Metabolism p. 25 of 85
How does this end? 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 thioesterasewith a 3-layer Rossmann fold
Palmitoyl thioesterase IPDB 1EI931 kDa monomerbovine
15 April 2008 Lipid Metabolism p. 26 of 85
The overall reaction 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
15 April 2008 Lipid Metabolism p. 27 of 85
iClicker questionWhat 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
15 April 2008 Lipid Metabolism p. 28 of 85
Answer: (b)
If the enzyme doesn’t have to find the substrate at the beginning of each reaction, things will proceed more readily.
15 April 2008 Lipid Metabolism p. 29 of 85
Activating fatty acids
Activate stearate or palmitatevia acyl CoA synthetase:
R–COO- + CoASH + ATP R–CO–SCoA + AMP + PPi
As usual, PPi hydrolysis drivesthe 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)
PDB 1BS042 kDa monomerE.coli
15 April 2008 Lipid Metabolism p. 30 of 85
Extending and unsaturating fatty acids
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
15 April 2008 Lipid Metabolism p. 31 of 85
Bacterial Desaturases
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
PDB 1ZA0;30 kDa monomerMycobacteriumtuberculosis
15 April 2008 Lipid Metabolism p. 32 of 85
Eukaryotic Desaturases
Desaturases like stearoyl ACP desaturase in eukaryotes act on the completed saturated fatty acyl CoA species
Enzyme is ferritin-like or RNR-like
Mammals can’t synthesize linoleate and they need it, so it has to be part of the diet
PDB 1OQ980 kDa dimermonomer showncastor bean
15 April 2008 Lipid Metabolism p. 33 of 85
Making arachidonate 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
15 April 2008 Lipid Metabolism p. 34 of 85
Phosphatidates
Phosphatidates are intermediates in making triacylglycerol & glycerophospholipids
Fatty acyl groups esterifying 1 and 2 positions of glycerol, phosphate esterifying 3 position
15 April 2008 Lipid Metabolism p. 35 of 85
Making phosphatidates
Glycerol-3-phosphate acyltransferase transfers acyl CoA to 1 position of glycerol-3-phosphate; prefers saturated chains
1-acylglycerol-3-phosphate acyl transferase transfers acyl CoA to 2 position of resulting molecule; prefers unsaturated chains
PDB 1IUQ40 kDa monomer
Cucurbita
15 April 2008 Lipid Metabolism p. 36 of 85
Making triacylglycerols 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
15 April 2008 Lipid Metabolism p. 37 of 85
Further steps in making triacylglycerols Diacylglycerol acyltransferase catalyzes
reaction between 1,2-diacylglycerol and acyl CoA to form triacylglycerol
See fig. 16.9, left-hand side
15 April 2008 Lipid Metabolism p. 38 of 85
Making phospholipids from 1,2-diacylglycerol
1,2-diacylglycerol reacts with CDP-choline to form phosphatidylcholine with liberation of cytidine monophosphate
1,2-diacylglycerol reacts with CDP-ethanolamine to form phosphatidylethanolamine this can be methylated 3 times to make
phosphatidylcholine S-adenosylmethionine is the methyl donor in
that case
15 April 2008 Lipid Metabolism p. 39 of 85
How do we get CDP-alcohols?
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
CDP-ethanolamine
15 April 2008 Lipid Metabolism p. 40 of 85
Making acidic phospholipids
Phosphatidate activated to CDP-diacylglycerol 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
15 April 2008 Lipid Metabolism p. 42 of 85
Phosphatidylinositol Phosphatidylinositol is made by this CDP-
diacylglycerol pathway in bacteria and eukaryotes
15 April 2008 Lipid Metabolism p. 43 of 85
Making phosphatidylserine
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- !
15 April 2008 Lipid Metabolism p. 44 of 85
Where does this happen?
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 water-soluble metabolites from which they can build up phospholipids and other lipids
15 April 2008 Lipid Metabolism p. 45 of 85
Making eicosanoids
Classes of eicosanoids: Prostaglandins and thromboxanes Leukotrienes
Remember that we make arachidonate from linoleoyl CoA; eiconsanoids made from arachidonate
Reactions involve formation of oxygen-containing rings; thus the enzymes are cyclooxygenases
15 April 2008 Lipid Metabolism p. 46 of 85
What eiconsanoids do 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!
15 April 2008 Lipid Metabolism p. 47 of 85
Synthesizing prostaglandins
Prostaglandin H synthase (PGHS) binds on inner surface of ER
Cyclooxygenase activity makes a hydroperoxide; this is converted to PGH2
PGH2 gets converted to other prostaglandins, prostacyclin, thromboxane A2 (fig. 16.12)
Prostaglandin H2
PDB 2OYU132 kDa dimerMonomer shownsheep
15 April 2008 Lipid Metabolism p. 48 of 85
How aspirin works
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
15 April 2008 Lipid Metabolism p. 49 of 85
Cyclooxygenase inhibition 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
15 April 2008 Lipid Metabolism p. 50 of 85
Could we find a COX-2 inhibitor?
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
15 April 2008 Lipid Metabolism p. 51 of 85
Leukotrienes 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
Leukotriene B4
PDB 2P0M146 kDa dimerrabbit
15 April 2008 Lipid Metabolism p. 52 of 85
Synthesis of ether lipids
Remember: these arelipids 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)
15 April 2008 Lipid Metabolism p. 53 of 85
Ether lipids, continued
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
15 April 2008 Lipid Metabolism p. 54 of 85
Sphingolipid synthesis
These are based formally on sphingosine, a C18unsaturated amino alcohol (fig.16.14)
Condense serine with palmitoyl CoA to make 3-ketosphinganine and CO2
NADPH-reduce this to sphinganine Acetylate the amine group to make N-
acylsphinganine Beta-unsaturate the palmitoyl group to make
ceramide, the basis for all other sphingolipids
ceramide
15 April 2008 Lipid Metabolism p. 55 of 85
Sphingolipid synthesis
These are based formally on sphingosine, a C18unsaturated amino alcohol (fig.16.14)
Condense serine with palmitoyl CoA to make 3-ketosphinganine and CO2
NADPH-reduce this to sphinganine Acetylate the amine group to make N-
acylsphinganine Beta-unsaturate the palmitoyl group to make
ceramide, the basis for all other sphingolipids
ceramide
15 April 2008 Lipid Metabolism p. 56 of 85
Sphingolipid synthesis
These are based formally on sphingosine, a C18unsaturated amino alcohol (fig.16.14)
Condense serine with palmitoyl CoA to make 3-ketosphinganine and CO2
NADPH-reduce this to sphinganine Acetylate the amine group to make N-
acylsphinganine Beta-unsaturate the palmitoyl group to make
ceramide, the basis for all other sphingolipids
ceramide
15 April 2008 Lipid Metabolism p. 57 of 85
Other sphingolipids
React ceramide with phosphatidylcholine;products are sphingomyelin and 1,2-diacylglycerol
React ceramide with UDP-galactose to form a galactocerebroside
Additional UDP-sugars or CMP-N-acetyl-neuraminic acid can be added
spingomyelin
15 April 2008 Lipid Metabolism p. 58 of 85
Steroid synthesis: overview
Cholesterol is important on its own & as a precursor of steroid hormones, bile salts
Derived formally from isoprene Isoprenoid synthesis based on
mevalonate &isopentenyldiphosphate
15 April 2008 Lipid Metabolism p. 59 of 85
Making HMG-CoA Condense 3 molecules of acetyl CoA:
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
15 April 2008 Lipid Metabolism p. 60 of 85
iClicker quiz question 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
15 April 2008 Lipid Metabolism p. 61 of 85
Answer: (d)
(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
15 April 2008 Lipid Metabolism p. 62 of 85
HMGCoA tomevalonate
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
PDB 1DQA205 kDa tetramerHuman
PDB 1DQA205 kDa tetramerhuman
15 April 2008 Lipid Metabolism p. 63 of 85
Mevalonate to isopentenyl diphosphate Two successive ATP-dependent kinase steps
convert mevalonate to mevalonate 5-diphosphate
ATP-dependent decarboxylation yields isopentenyl diphosphate
This is an isoprene-donating group involved in making non-steroidal isoprenoid compounds as well as steroids
15 April 2008 Lipid Metabolism p. 64 of 85
Mevalonate kinase Converts mevalonate to
mevalonate 5-phosphate Secondary control point in
isoprenoid synthetic pathway Human diseases associated
with abnormalities Mevalonic aciduria Hyperimmunoglobulinemia
(Periodic fever syndrome)
PDB 2HFS73 kDa dimer;monomer shownLeishmania major
15 April 2008 Lipid Metabolism p. 65 of 85
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)
15 April 2008 Lipid Metabolism p. 66 of 85
Geranyl diphosphate & farnesyl diphosphate
Geranyl diphosphate:C10
Farnesyl diphosphate:C15
15 April 2008 Lipid Metabolism p. 67 of 85
Squalene Made via head-to-head synthesis from 2
molecules of farnesyl diphosphate
Squalene: C30
15 April 2008 Lipid Metabolism p. 68 of 85
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
lanosterol
lanosterol synthase; converts 2,3-oxidosqualene to lanosterolPDB 1W6K81 kDa monomerhuman
15 April 2008 Lipid Metabolism p. 69 of 85
What happens to cholesterol?
Inserted into membranes Assembled into lipoproteins Derivatized to make bile salts Modified into hormones
15 April 2008 Lipid Metabolism p. 70 of 85
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)
15 April 2008 Lipid Metabolism p. 71 of 85
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
15 April 2008 Lipid Metabolism p. 72 of 85
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
15 April 2008 Lipid Metabolism p. 73 of 85
Reactions in -oxidation Proceeds through cycle n times for a 2n-
carbon fatty acid
Diagram courtesy Richard Paselk, Humboldt State U.
15 April 2008 Lipid Metabolism p. 74 of 85
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
medium-chain acyl CoA dehydrogenasePDB 3MDE169kDa tetramer;dimer shownPig liver
15 April 2008 Lipid Metabolism p. 75 of 85
Electron-Transferring 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
PDB 1EFV63 kDa heterodimerhuman
15 April 2008 Lipid Metabolism p. 76 of 85
Hydration step
Enzyme is 2-enoyl CoA dehydratase
- roll protein onverts enoyl CoA to L-3-
hydroxyacyl CoA Remember this is the opposite
stereochemistry relative to synthetic intermediate
PDB structure 1S9C: dehydratase domain of human multifunctional enzyme
15 April 2008 Lipid Metabolism p. 77 of 85
Second oxidative step
Enzyme is L-3-hydroxyacyl-CoA dehydrogenase
NADH is reduced product NADH can be used in
biosynthesis (via shuttles) or oxidized in the ETSRossmann-fold protein
dehydrogenase domain of multifunctional enzymePDB 1E6W114 kDa tetramerrat
15 April 2008 Lipid Metabolism p. 78 of 85
Thiolysis HS-CoA attacks C3-
carbonyl 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
PDB 1QFL171 kDa tetramerZooglea
15 April 2008 Lipid Metabolism p. 79 of 85
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
15 April 2008 Lipid Metabolism p. 80 of 85
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 Initial reaction doesn’t produce QH2:
it produces hydrogen peroxide as the other product besides trans2enoyl CoA
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
PDB 1IS2145 kDa dimerrat liver