Carbohydrates 6/22/2013 1:16:00 PM
Monosaccharides: simple sugars with a carbonyl group. Aldehyde or ketone;
most are polar.
D-glyceraldehyde is a 3C sugar with an aldehyde and a CH2OH on the end.
Triose: 3C sugar, such as dihydroxyacetone (ketose)
Ketoses are numbered relative to the position of the ketose
The aldehyde and ketone carbonyl undergo nucleophilic attack by the –OH
group to form pyran or furan rings. Hemiacetals or hemiketals.
Hemiacetal: the reaction of an aldehyde with HOR’ leads to the
Carbon having a chiral centre.
Mutarotation: attack of the carbonyl by –OH in the structure.
Alpha: the new OH group is on the opposite side as the CH2OH. OH
is axial and below the plane of the ring.
Beta: same side. The OH is equatorial and above the plane of the
Anomer: identical except for the position of the OH at the new chiral centre.
In order for something to be a reducing sugar, the free hydroxyl must be
adjacent to the O molecule within the ring.
Condensation reaction: releasing H2O to form a glycosidic bond. Happens in
Sucrose = glucose + fructose
Lactose = galactose + glucose
Cellubiose = glucose x 2, but with a B-1, 4 linkage
Maltose = glucose x 2, but with an A-1, 4 AND a B-1, 4 linkage.
Maltase: cleaves the A-1, 4 glycosidic bond in maltose. NOT beta
Lactase: cleaves the B-1, 4 glycosidic bond between galactose and glucose
Sucrase: cleaves the A-1, B-2 glycosidic bond between glucose and fructose.
Glycogen: branched polymer of A-1, 4 and A-1, 6 linkages with only 1
Amylose: unbranched glucose units with A-1, 4 linkages
Amylopectin: linear A-1, 4 chains with A-1, 6 branch points every 30
A-amylase: digests glycogen, amylose, and amylopectin. Acts at random
locations to give maltose and maltotriose.
B-amylase: hydrolyzes 2 glucose units at a time, producing maltose, from
the non-reducing ends. Not found in mammals.
No enzyme to break down cellulose. Unbranced glucose joined by B-1, 4 linkages. Forms a pleated sheet
of intermolecular H bonds
Glycosyltransferase: enzyme that links sugars together.
UDP-glucose is a high energy intermediate
Allows glucose to be attached to an acceptor sugar
Heparin and blood clotting: a pentasaccharide sequence in heparin binds
antithrombin, which can then bind factor Xa (clotting) or thrombin (no
clotting). Phospholipids and Biological Membranes 6/22/2013 1:16:00 PM
Lipids within the membrane:
Phospholipids: FA chains, head group, glycerol or sphingosine
Glycolipids: FA chains and cerebroside plus sugars
FFA are hydrocarbons
Unsaturated FA have double bonds
Palmitic acid: 16:0
Stearic acid: 18:0
Linoleic acid: 18:2
Alpha-linolenic acid: 18:3
Cis bonds are very present in membranes – less packing and more fluidity.
The Tm depends on FA length and degree of saturation (fully
saturated has a higher Tm than unsaturated)
Stearic acid has a higher Tm than palmitic acid (longer chain)
18:1 has a lower Tm than 18:0 because of unsaturation
Esterification: lose an OH on FA tail to form an ester with a glycerol
Each gram of glycogen binds 2g of water
3 units fat: 1 unit glycogen
In an equal amount of fat and glycogen, there is 6x more energy in
2 FA:glycerol, + Pi and OH = phosphoglyceride
Sphingolipids: 18:1 amide bond
Pi group always on C3 of glycerol
Common alcohol additives to phosphoglyceride include:
Neutral phospholipids inlcude:
Phosphatidylethanolamine, which has an NH3+
Phosphatidylcholine, with an N+ and 3 CH3
Negatively charged phospholipids include: Phosphatidylserine
Will be found in the inner leaflet
Sphingolipids include sphingosine and sphingomyelin
Sphingomyelin adds a choline group
Glycolipids usually have a cerebroside backbone with the addition of a sugar
unit, usually glucose or galactose.
Phospholipase activity: can remove FA heads or groups from phospholipids
PLA2 cleaves the C2 of phosphatidylcholine (now called 1-
PLA1 cleaves C1 2-acylphosphatidylcholine
PLC cleaves between the phosphate and glycerol to give DAG and
PLD cleaves on the other side to give choline and phosphatidate
Cholesterol modulates fluidity because it doesn’t pack well. The OH group
interacts with the heads.
Phosphatidylcholine and sphingomyelin usually face the ECM
Glycophorin A: transmembrane A-helix that can dimerize
Bacteriorhodopsin: 7 Tm helices, uses light E to transport protons out of the
cell for ATP synthesis
Prostaglandin H2 Synthase-1: catalyzes conversion of arachidonic acid into
prostaglandin H2 Metabolism and Glycolysis 6/22/2013 1:16:00 PM
∆G=∆G’ + RT ln Keq
Keq = products/reactants
If Keq >1, ∆G’ is -, and rxn is favourable and exergonic
If Keq <1, ∆G’ is +, and rxn is unfavourable and endergonic
If Keq =1, ∆G’ is O, and rxn can proceed in either direction
Add ∆G’s together to get the overall ∆G.
Hydrolysis of ATP Phosphates:
ATP + H2O ADP + Pi = -31 KJ/mol
ATP + H2O AMP + Ppi = -46 KJ/mol
ADP + H2O AMP + Pi = -36 KJ/mol
AMP + H2O Adenosine + Pi = -14 KJ/mol
Ppi + H2O 2 Pi = -34 KJ/mol
Need to regenerate ATP:
ADP + Pi ATP = +31 KJ/mol
ATP + H2O AMP + Ppi = -46 KJ/mol
Ppi + H2O 2 Pi = -34 KJ/mol (together, -80)
Coupled with creation of ATP, net is -49 KJ/mol
Energy use in the cell:
The creatine kinase reaction is reversible under physiological pH. Keq =1
As ATP in the muscle is depleted, more ATP can be made by using
phosphocreatine. Creatine kinase allows phosphocreatine to support ATP
levels and contraction briefly. Glucose will enter the muscle through Glut-4
when phosphocreatine levels fall.
1. Hexokinase phosphorylates glucose in the cytoplasm through ATP
glucose-6-phosphate + ADP + H. ∆G’=-16.7 KJ/mol 2. Phosphoglucose isomerase converts glucose-6-phosphate into fructose-
6-phosphate by moving the carbonyl from C1 to C2. ∆G’ =1.67 KJ/mol.
3. PFK-1 and ATP transfer a P onto F-6-P on C1, to form Fructose-1,6-
Bisphosphoglycerate + ADP + H. ∆G’ = -14 KJ/mol. PFK-1 is inhibited
allosterically by ATP, citrate, and activated by AMP. High AMP + low ATP
+ high Frc-2,6-BP = activation of PFK-1. High ATP and citrate = PFK-1
4. Aldolase lyase puts F-1,6-BP into 2 sugar isomers DHAP and
glyceraldehyde-3-phosphate. ∆G’ = + 24
5. Triose phosphate isomerase interconverts DHAP and glycerol-3-
phosphate. ∆G’=+7.6. So, for every molecule of F-1,6-BP, you get 2
molecules of glyceraldehyde-3-phosphate
6. Glyceraldehyde-3-phosphate + NAD + Pi (through GA3P-
dehydrogenase) 1,3-Bisphosphoglycerate + NADH + H+ (all x2).
Produces a high energy substrate, NADH
7.Phosphoglycerate kinase transfers a P from 1,3-BPG to ADP. 2x 1,3-
BPG + PGK + 2ADP 2ATP + 2 3-phosphoglycerate
8. Phosphoglycerate mutase relocates P from 3-PG from C3 to C2 to form
9. Enolase removes a water from 2-phosphoglycerate to form
phosphoenolpyruvate. ∆G=+1.8. Remember, this produces 2
10. Pyruvate kinase dephosphorylates phosphoenolpyruvate to form 2
molecules of pyruvate + ATP. Pyruvate kinase is allosterically activated by
AMP, frc-1,6-BP, and inhibited by ATP and alanine.
When there is low blood glucose, pyruvate kinase is inhibited by
Total: 2x pyruvate, 2x ATP, 2x NADH, and 2x H2O. ∆G=-72.3
**Note: PFK1 converts fructose-6-phosphate into fructose-1,6-bisphosphate,
and PFK2 converts fructose-6-phosphate into fructose-2,6-bisphosphate.
This product plays a role in the regulation of glycolysis by activating PFK1 in
a feed forward control model. Glucose + 2Pi +2ADP + 2NAD+ 2 pyruvate + 2ATP + 2NADH + 2H +
2H2O Mitochondrial Bioenergetics 6/22/2013 1:16:00 PM
FA, pyruvate, and AAs enter the MTC to start the CAC
PDC and CAC are in the matric, ETC and ATP synthesis occur in the inner
Pyruvate Dehydrogenase Complex:
Pyruvate + CoA + NAD+ Acetyl CoA + CO2 + NADH
E1: pyruvate dehydrogenase
E3: dihydrolipoamide dehydrogenase
Step 1: E1. Pyruvate dehydrogenase:
Pyruvate interacts with TPP, which is bound to E1. Decarboxylation
of TPP hydroxyethyl TPP. Part of pyruvate now bound to TPP and
Step 2: E2. Dihydrolipotransacetylase
Has a cofactor called lipoic acid inside. Has a disulfide bond in its
ring structure. Allows for easy reduction of sulfur groups. Thioester
bonds able to form between CoA and lipoic acid.
Acetyl group (hydroxyethyl) transferred to one of the sulfurs on
lipoic acid. Forms one reduced sulfur and the other sulfur will be
attached to the acetyl group through a Thioester bond. Same bond
that forms in acetyl CoA, now just need to transfer that to CoA-SH
Lipoamide group (attached via lysine residue on E2) swings over to
CoA to let CoA interact and form acetyl CoA. SH on CoA takes the
sulfur bond from the acetyl group. Now we have acetyl CoA, no
longer bound to the enzyme anymore.
Lipoic acid group is now completely reduced (SH and SH) Can no
longer react with HE-TPP. Need to regenerate disulfide bond.
Conveniently, there is an FAD bound to E3
Step 3: E3. dihydrolipodehydrogenase Hydrogens from lipoic acid transferred onto FAD to make FADH2
Now we’ve regenerated our disulfide
Now we’re stuck with FADH2 that is bound to the enzyme
Need to regenerate FAD
NAD+ in the cell oxidizes FADH2 back to FAD and form NADH +
H+. That can now float off into solution
NET: 1 NADH per pyruvate
PDC Covalent Modification:
Active PDC can be phosphorylated on E1 by PDC kinase, using an
Phosphatase dephosphorylates E1 using water.
Increased Acetyl CoA inhibits E2
Increased NADH inhibits E3
Increased ATP inhibits PDC
Muscle at rest:
NADH will inhibit E3, Acetyl CoA will inhibit E2, and ATP will inhibit
PDC. They do this by activating PDC kinase, which inactivates PDC
Muscle while running:
Pyruvate will stimulate PDC, as will ADP. They do this by inhibiting
Ca2+ also stimulates PDC phosphatase, which dephosphorylates
PDC, rendering it active.
Citric Acid Cycle:
2 oxidative decarboxylation reactions produce 2 NADH and release
Net is 1 FADH2, 3 NADH, and 1 GTP. Uses 2 H2Os
1. Citrate synthase
OAA and acetyl CoA can join to make a thioester bond to make
citryl CoA, which is then hydrolyzed by H2O to make citrate.
Can be inhibited by ATP or NADH
citrate is hydrolyzed to cis-aconitate by aconitase
The OH is moved to C2, and a double bond and H2O is lost 3. Isocitrate dehydrogenase reaction:
Isocitrate + NAD+ alpha-KG + CO2 + NADH
4. Alpha-KG dehydrogenase
Alpha-KG + NAD+ + CoA succinyl CoA + CO2 + NADH
Inhibited by NADH, succinyl CoA, and ATP
CoA transferred to alpha-KG
Stimulated by Ca2+
5. Succinyl CoA synthetase
Succinyl CoA + Pi + GDP succinate + CoA + GTP
Hydrolysis of acetyl CoA is coupled with phosphorylation of GDP
6. Succinate dehydrogenase reaction
succinate + FAD fumarate + FADH2
Straight to ETC
Fumarate + H2O Malate
8. Malate dehydrogenase
Malate + NAD+ OAA + NADH
Control of the CAC: 3 enzymes are controlled.
ATP, Acetyl CoA, and NADH all inhibit the entire PDC
Citrate synthase: Inhibited by ATP and NADH, stimulated by ADP
Isocitrate dehydrogenase: inhibited by ATP and NADH, stimulated
Alpha-KG dehydrogenase: inhibited by ATP, succinyl CoA, and
NADH, stimulated by Ca2+
Standard reduction potential: a molecule’s tendency to be reduced or
oxidized. +ve: able to accept electrons, -ve: able to donate electrons. NAD+
has a negative potential.
The Electron Transport Chain:
Starting off with 10 NADH and 2 FADH2
NADH gets oxidized to NAD+ + H + 2e (oxidation is losing
A H consists of a proton and an electron Electrons transferred to a series of transition molecules. Higher to
lower energy states means it is releasing energy.
At the end, 2e + 2H+ + 0.5O2 H2O (reduction of oxygen to
The energy created is used to pump protons across the
mitochondria into the outer membrane through the transport
proteins spanning the membrane.
By the time water is formed, the H protons have been pumped into
the outer membrane
The only byproduct of the oxidation of NADH is water, ATP not
The greater concentration of H in the outer membrane causes a
proton gradient to form.
H wants to get back into the matrix, where ATP is formed.
H goes back into the matrix via ATP synthase, because cristae is
impermeable to protons.
As they enter the ATP synthase, causes structure to spin. An ADP
molecule attaches to part of the protein (F1).
As inner axle turns, it turns F1 as well. Squeezes the ADP and
phosphate together to form ATP.
Electron donors: NADH and succinate, glycerol-3-phosphate and
Electron carriers: Coenzyme Q and cytochrome
Complex 1: e donated by NADH
Complex 2: e donated by succinate (from Kreb’s) in the form of
FADH2 and glycerol-3-phosphate in the form of FADH2, and fatty
acyl CoA donates in the form of FADH2 (First step in beta-oxidation)
During glycolysis, the NADH produced generates dihdroxyacetone
phosphate, which is converted to glycerol-3-phosphate. NOTE: NADH is
worth 1.5 ATP in this step!!!!
Reduction potential increases as we move down the ETC
Coenzyme Q: no electrons
CoQH2: fully reduced
o Moves 2 e at a time, similar to NADH
o Lipid soluble, can move through the cell membrane
o Accepts electrons from complex 1 and 2 Iron-sulfur centres: Fe-S. Inside complexes. Move electrons one at
a time. Seen in complexes 1 and 2.
Cytochromes: move electrons one at a time. Found in complexes 3
4 protons yield 1 ATP – complex 1 pumps 4 out from 1 NADH
Complex 1: NADH dehydrogenase – 4 H+
Receives electrons from NADH (2 electrons)
Gives electrons to CoQ CoQH2
Protons then pumped out
Complex 2: succinate dehydrogenase
Receives electrons from NADH via succinate
Gives electrons to CoQ
Complex 3: cytochrome BC1 – 4 H+
Receives electrons from CoQH2
Gives electrons to cytochrome C
CoQH2 donates an electron to CoQ and one to cytochrome C
CoQ then leaves, and a new CoQH2 comes in to start the process
Complex 4: cytochrome oxidase – 2 H+
Receives electrons from cytochrome c. Cu+ Cu2+
Gives electrons to O2 (final electron acceptor)
1 NADH 1 H2O 2 H+ from complex 4. Also leaves 0.5 O2. So if
2 NADH go through, you’ll make a full O2
Proton-motive force: building up a high proton gradient in the
intermembrane space to do work son
Electron transport is coupled to ATP synthesis; neither reaction can occur
without the other
If you add cyanide (electron transport blocker), it not only blocks electron
transport but also ATP synthesis.
Adding oligomycin (electron transport blocker) does the same thing. But DNP
(an uncoupler), when added, can allow electron transport to occur without
3 protons pump through for 1 ATP
3 beta subunits and 3 alpha subunits
The F0 portion is the membrane, F1 in matrix Proton motive force also moves substrates of ATP inside the matrix
(ADP and phosphate) and product out
There are no negative inhibitors of the ETC! Just turned down by a lack of
Rotenone and amytal inhibit electron flow from FeS to CoQ in complex 1,
thereby blocking 10 H+. But, electrons in FADH2 can evade this block, only
Antimycin A blocks complex 3. Use of reduced cytochrome C will allow
Cyanide, azide, and CO all inhibit complex 4. ATP Synthesis and Metabolic Regulation 6/22/2013 1:16:00 PM
Adding succinate increases O2 consumption and ATP synthesis
Adding cyanide blocks complex 4, no more O2 consumed and no more ATP
Oligomycin inhibits ATP synthesis
DNP is an uncoupler – rescues O2 consumption
Uncouplers: acidic molecules that can accept H and are hydrophobic.
Transports H+ across the membrane. Doesn’t inhibit anything, just brings
H+ back into the MTC. Allows O2 to be consumed.
MTC with leaky membranes will not synthesize ATP
Stress promotes leaky MTC membranes
Swelling and shrinking of MTC can also affect ATP synthesis
ATP synthase is reversible, membrane bound, and reliant on H+ gradient
If you inject O2, pH drops because of H+ pumped out
Lower pH increases synthesis
Can be reversed by ATP hydrolysis
ATP synthase can be used to drive H transport via ATP hydrolysis
Detergents can break down the membrane and obliterate the H gradient
Inhibits ATP synthesis
But electron transport could probably still occur
P/O ratios: phosphates added to ADP/reduced O2. Dependent on ATP
Cytosolic NADH: 1.5 ATP
Water formation in oxidative phosphorylation:
In ATP synthesis:
o ADP + Pi ATP + H2O
o NADH + H + O NAD+ + H2O
o FADH2 + O FAD + H2O
Therefore, 2.5 H2O/2.5 ATP from NADH
1.5 H2O from FADH2
+ 1 H2O formed in the last step of ETC
ATP/H2O generation for one molecule of glucose:
2 ATP are used in the formation of glucose-6-phosphate and
2 x 2 ATP directly produced from glyceraldehyde-3-phosphate
2 x 1 NADH from glyceraldehyde 3-phosphate 2 x 1 H2O produced by enolase
Total: 2 ATP net, 2 cytoplasmic NADH, 2 H2O
2 x 1 NADH
2 x 3 NADH
2 x 1 GTP
2 x 2 H2O consumed
2 x 1 FADH2
Total: 6 NADH, 2 ATP, 4 H2O, 2 FADH2
ETC + ATP Synthase:
8 x 2.5 NADH: 20 ATP
2 x 1.5 FADH2: 3 ATP
2 x 1.5 cytosolic NADH: 3 ATP
12 x 1 H2O formed by each NADH and FADH2 oxidized from
Total: 26 ATP, 12 H2O
26 x 1 H2O per ATP produced from ATP synthase
New Total: 26 ATP, 38 H2O
Grand Total: 30 ATP, 36 H2O
Degradation of Palmitic Acid:
-2 ATP for activation
7 x 1 NADH
7 x 1 FADH2
7 x -1 H2O
-1 H2O at the end
Total: -2 ATP, 7 NADH, 7 FADH2, -8 H2O
8 x 3 NADH
8 x 1 FADH2
8 x 2 H2O
8 x 1 GTP
Total: 24 NADH, 8 FADH2, 16 H2O, 8 ATP
ETC + ATPS: 31 x 2.5 NADH = 77.5
15 x 1.5 FADH2 = 22.5
46 x 1 H2O per NADH/FADH2
Total: 100 ATP, 46 H2O
100 H2O per ATP
Grand total: 106 ATP, 122 H2O
G protein signalling from epinephrine or glucagon (low blood glucose)
Hormones bind to membrane proteins
Alpha-GTP released and attaches to adenylyl cyclase
Makes cAMP from ATP
Phosphodiesterase can inhibit cAMP
cAMP binds to regulatory subunits to release catalytic subunits of
PKA to activate it.
PKA phosphorylates protein targets
Glycogen phosphorylase: removes a glucose from glycogen by
phosphorylating C1. Occurs on the non-reducing ends. Creates glucose-1-
phosphate and glycogen with n-1 residues. Glucose-1-phosphate can then
go to muscle or liver. Occurs in low glucose states.
Under stress or exercise, adrenaline/epinephrine levels rise, and