pyruvate dehydrogenase complex
-an enzymatic activity that converts pyruvate from glycolysis into acetyl-CoA for citric acid cycle
-occurs in higher cells (oxidative decarboxylation) and yeast cells (non-oxidative decarboxylation)
pyruvate dehydrogenase complex located where?
what does it require?
-mitochondrion
-require pyruvate to be transported from cytoplasm to mitochondrion
the 3 units of pyruvate dehydrogenase complex
-E1 pyruvate decarboxylase
-E2 Dihyrolipoamide transacetylase
-E3 Dihyrolimpoamide dehydrogenase
the 5 coenzymes of pyruvate dehydrogenase complex
1.Thiamine pyrophosphate (TPP)
2.Lipoamide
3.NAD
4.FAD
5.Coenzyme A (CoASH or CoA)
what is the relationship between the mechanism of the pyruvate dehydrogenase complex and the alpha-keto-glutarase complex of the citric acid cycle?
both involve the oxidation of alpha-keto acids
what can yeast do with decarboxylation of pyruvate that humans can't?
-yeast can decarboxylate without oxidation
purpose of E1 pyruvate decarboxylase
-decarboxylate pyruvate (kicks out CO2) (goes from 3 carbon pyruvate to 2 carbon acetyl)
-part of oxidation
purpose of E2 Dihyrolipoamide transacetylase
-part of oxidation (kicks off 1 pair of electrons)
-transfers acetyl group to CoA
purpose of E3 Dihyrolimpoamide dehydrogenase
-attaches electrons to electron carrier NADH
-regenerates original enzyme
The fate of pyruvate through pyruvate dehydrogenase complex in aerobic organism.
1. pyruvate is decarboxylated at E1 site, then binds to TPP to prevent highly reactive 2 carbon intermediate from reacting
2.E1 oxidation and transfer of 2 carbon intermediate is passed to lipoamide molecules, E2 (lipoamide is first electron carrier and r
3 major steps of pyruvates conversion to Acetyl-CoA
1.decarboxylation
2.oxidation
3.formation of acetyl-CoA
The fate of pyruvate through pyruvate dehydrogenase complex in yeast
1. pyruvate is decarboxylated at E1 site, then binds to TPP to prevent highly reactive 2 carbon intermediate from reacting
2. acetealdahyde is formed with gain or loss of electrons
3. acetealdahyde is fermented into ethanol
HOWEVER
when oxygen is present,
The majority of oxidation occurs here-
-consequences?
-structure?
-mitochondria
-constant oxidation can damage mitochondria
-contain outer membrane (fairly permeable), inner membrane (only permeable to H2O,CO2, and CO), and inner liquid matrix, inner membrane infoldings called cristae
where does citric acid cycle occur?
in what cells?
what is the input and output?
-mitochondrial matrix
-in almost every cell
-2 carbons are added via acetyl-CoA and 2 carbons are expelled as CO2 (the 2 carbons from the acetyl-CoA in the beginning do not get oxidized into CO2 until the beginning of the second time through the cycle)
What are the electron carriers in the citric acid cycle?
-what are all the products of the cycle?
-in what amounts for 1 acetyl-CoA?
-in what amounts for 1 glucose?
-what about CO2?
-NAD+ (NADH) and FAD (FADH2)
-NADH, FADH, GTP
-3 NADH, 1 FADH, 1 GTP
-6 NADH, 2 FADH, 2 GTP (2 acetyl-CoA for 1 glucose)
-CO2 is released as a byproduct is not a product of the cycle
The 2 main parts of the citric acid cyle
1.release of CO2
2.Conversion to oxaloacetate
1st rxn of citric acid cycle
enzyme?
substrate?
product?
process?
favorable?
1st rxn of citric acid cycle
-citrate synthase
-acetyl-CoA and oxaloacetate
-citrate (5 carbon)
-citrate synthase catalyzes joining of acetyl group to oxaloacetate
-very favorable due to breaking of thioester bond in acetyl-CoA, helps pull forward unfavor
2nd rxn of citric acid cycle
enzyme?
substrate?
product?
process?
inhibition?
2nd rxn of citric acid cycle
-aconitase
-citrate
-isocitrate (5 carbon)
-aconitase catalyzes rearrangement of citrate into isocitrate
-aconitase inhibited by fluorocitrate, fluoroacitate is a poison which is used by citrate synthase in step 1 to make fluo
3rd rxn of citric acid cycle
enzyme?
substrate?
product?
process?
favorable?
3rd rxn of citric acid cycle
-isocitrate dehydrogenase
-isocitrate
-alpha ketoglutarate (a-kg) (5 carbon), NADH, CO2
-isocitrate dehydrogenase catalyzes decarboxylation of isocitrate (1st oxidation)
-product strongly favored
4th rxn of citric acid cycle
enzyme?
substrate?
product?
process?
favorable?
4th rxn of citric acid cycle
-a-kg dehydrogenase complex
-a-kg (important intermediate because involved in anaplerotic rxns related to transamination)
-succinyl-CoA (4 carbon), NADH, CO2
-same process as conversion of pyruvate to acetyl-CoA with same 5 en
5th rxn of citric acid cycle
enzyme?
substrate?
product?
process?
5th rxn of citric acid cycle
-succinyl-CoA synthetase (named for reverse reaction)
-succinyl-CoA, Pi, GDP
-Succinate (4 carbon), CoA, GTP
-succinyl-CoA synthetase catalyzes only substrate level phosphorylation in citric acid cycle (GDP to GTP), high energ
6th rxn of citric acid cycle
enzyme?
substrate?
product?
process?
favorable?
6th rxn of citric acid cycle
-succinate dehydrogenase
-succinate (intermediate in production of heme) and FAD
-fumarate (trans double bond,4 carbon) and FADH2
-succinate dehydrogenase linked to FAD electron carrier takes electrons and protons (3rd oxidati
7th rxn of citric acid cycle
enzyme?
substrate?
product?
process?
7th rxn of citric acid cycle
-fumurase
-fumurate
-L-malate (4 carbon)
-fumurase adds water across double bond of fumurate and yields L-malate
8th rxn of citric acid cycle
enzyme?
substrate?
product?
process?
favorable?
8th rxn of citric acid cycle
-malate dehydrogenase
-L-malate
-Oxaloacetate (4 carbon) and NADH
-malate dehydrogenase oxidizes hydroxyl of L-malate(4th and final oxidation)
-very unfavorable +delta G, rare oxidation that is not energetically favorable, pul
how is citric acid cycle regulated?
-allosterically in several places, but more importantly by the amount of NAD+ and FAD that is available
-NAD+ and FAD are essential for the citric acid cycle and the pyruvate dehydrogenase complex
-this is related to metabolic control
What is ATP output of citric acid cycle?
glycolysis under anaerobic conditions?
-if all NADHs and FADH2s are converted to ATP then between 30-38
-2
-citric acid cycle is very efficient at producing energy
How is oxygen a limiting reagent for the citric acid cycle?
If NADH is high (low NAD+) and oxygen is low, then NADH cant be converted back to NAD+, which stops the cycle because NAD+ is required for 3 reactions in the cycle (citric acid cycle cannot sidestep the lack of oxygen like fermentation in glycolysis)
-opt
affect of arsenite and mercury on pyruvate dehydrogenase and a-kg dehydrogenase?
treatment?
-compounds react to sulfur in lipoamide of E3 and bind to them (preventing restoration of enzyme)
-treat lipoamide with BAL, which extracts arsenite because BAL also contains sulfur to which arsenite binds
anaplerotic reactions
ex's
how do they feed eachother?
-reactions that 'fill up' the intermediates of metabolism needed for multiple purposes
-oxaloacetate can be converted into aspartic acid or glucose
-succinyl CoA can be used in porphyrins, heme, chlorophyll
-citrate can be used in fatty acids, sterols
-a-
oxaloacetate in other metabolic pathways
-can be converted to glucose via gluconeogenesis
-can be converted to aspartate via transamination
-can be converted to citric via citric acid cycle
-a-kg also important anaplerotic intermediate
glyoxylate cycle
-why unique?
-made up of what?
-benefits?
-pathway related to citric acid cycle occurring only in plants and bacteria
-requires two additional enzymes not found in animals
-isocitrate lyase (cleaves isocitrate to glyoxylate and succinate, both of which can ultimately be made into malate) and mala
glyoxylate cycle steps
products?
1.formation of citrate
2.formation of isocitrate
3.formation of a.glyoxylate and b.succinate
4a.formation of malate
4b.formation of fumurate then formation of malate
5. formation of oxaloacetate
-results in 2 oxaloacetates
glyoxylate cycle only occurs in plants and yeast because...
they are the only organisms containing the enzymes isocitrate lyase and malate synthase
which group of steps are bypassed in the glyoxolate cycle? consequences?
decarboxylation
produces less NADH than citric acid cycle
what is a consideration for whether or not an organism runs the glyoxolate or citric acid cycle?
the energy state
if energy is high then it will run the glyoxolate cycle
if energy is low then it will run the citric acid cycle
what can't animals do because they can't run the glyoxolate cycle? how does this relate to obesity in plants and animals?
can't make net amounts of glucose from acetyl-CoA
plants can turn acetyl-CoA into either glucose or fatty acids
humans can basically only turn acetyl-CoA into fatty acids
what makes up a membrane
-a lipid bilayer and other molecules (cholesterol,proteins,glycoproteins,glycolipids)
what are the two main categories of molecules in a lipid bilayer
glycerophospholipids and sphingolipids
glycerophospholipids are made up of what? how are the fatty acids arranged? what is most common in nature?
-gycerol, phosphate, one or more fatty acids
-either saturated (no double bonds) or unsaturated (one or more double bonds)
-double bonds in nature almost always in cis configuration (result is bend shape for fatty acid)
relationship between glycerophospholipids and fats
-they both have glycerol backbone and two fatty acids
-glycerophospholipids have a phosphate on position 3 of the glycerol
how are phosphoglycerides named?
phosphotidyl-X where X is the name of the molecule attached to the phosphate
what is phosphatidic acid? Important intermediate in the synthesis of what?
-glycerophospholipid with no molecule attached to the phosphate in 3rd position
-phosphatidyl lipids and fats
sphingolipids are related to which glycerophospholipids?
related to glycerophospholipids based on sphingosine
What is sphingomyelin?
-component of myelin sheath of nerve cells
and membranes of other nerves and brain tissue
cerebroside
sphingolipids containing a single sugar
ganglioside
sphingolipid containing complex carbohydrate moiety
steroids
lipids not derived from fatty acids
In animals, steroids is derived from what?
cholesterol
where is cholesterol found? what is its purpose?
-in the membrane of cells
-to maintain stability of the membrane
what percent of the dry weight of the brain is made up of cholesterol
14%, it is very prominent
how are the poles of a lipid bilayer oriented? why? what about fatty acids?
-polar exterior facing water and non-polar interior
-provides a barrier to both polar and non-polar substances
-in contrast, fatty acids aggregate into a micelle
4 types of membrane proteins
1. integral (protein projects through both sides of the membrane, contain both hydrophobic and hydrophilic portions)
2.peripheral (protein projects into only one side of the membrane)
3. anchored (protein linked to a molecule, like a fatty acid, embedded
ease of removing integral,peripheral, and associated membrane proteins from the membrane
integral proteins are difficult to remove, but peripheral and associated membrane proteins are not
what are the 2 purposes of a cell membrane
-to provide a barrier between cell and external environment
-provide a barrier to passage of many molecules, including possible food
bacteriorhodopsin
integral membrane protein that uses light,chemisty, and mechanics to move protons across membrane barrier
liposomes? purpose? how?
-artificially assembled lipid bilayers containing compounds
-way of getting compounds into cells that are not easily transported across the cell via other means
-liposome fuses with a cell membrane and the contents are delivered into the cell
what unique feature of membrane-spanning proteins can be used to identify the amino acid sequence of a protein and predict if it is a membrane protein
they contain alternating regions of non-polar membrane crossing regions interrupted by polar short sections joining them
prostoglandins
molecules associated with numerous physiological phenomena such as uterine contraction and pain
prostoglandins are derived from what? how? can they be inhibited (how)?
-made from arachidonic acid
-in a reaction catalyzed by the peripheral membrane protein Prostaglandin Synthase (cyclooxygenase or COX enzyme)
-can be inhibited by NSAIDS like aspirin and ibuprofin
How can and why do NSAIDS cause stomach irritation?
there are different COX enzymes throughout the body, some play critical roles in the synthesis of intestinal tissue. If they are inhibited then irritation can result (more likely in people who take high or regular doses as a result of illness such as rheu
COX-2 enzymes are found where? why were they found? what was the result?
-in joints
-to create medications that inhibit joint pain
-many had to be recalled due to side effect of damaging heart tissue
membranes that retain fluidity at lower temperatures are characterized by...
shorter, more unsaturated fatty acids
membranes that do not retain fluidity at lower temperatures are characterized by...
longer, saturated fatty acids
fish membranes are made up of what kind of fatty acids? why?
-unsaturated and polyunsaturated fatty acids
-membranes have to remain fluid at fairly low temperatures
Tm
the midpoint of the conversion between the solid and fluid state of a membrane
How does cholesterol affect the Tm of a membrane?
it doesn't change the Tm but does widen the range of the transition temperature between solid and fluid state
name of fluidity model for membranes
fluid mosaic model
What does NA/K ATPase do?
what type is it?
what type of transport mechanism?
How?
Why?
-transports three sodiums out of the cell and two potassiums in for each cycle
-P type
-electrogenic (antiport, because moves molecules in opposite directions)
-hydrolysis of ATP drives the process
-movement of NA and K molecules is critical for maintaini
cholesterol enters cells how? how is this a different form of transport?
-enters cells via LDLs that attach to a receptor on the cell's surface, entire LDL w/cholesterol is brought into the cell via endocytosis
-the molecule is not moving into the cell through a specific protein receptor
what is a pump? what does it do? when are they electroneutral or electrogenic?
-the protein component of an active transport system
-if it moves two molecules in the same direction it is a symport, if it moves two molecules in opposite directions across the membrane it is an antiport
-it is electroneutral if the action does not resu
is ATP the only energy source for active transport
NO
glucose transporter in blood cells is an example of what kind of transport
-passive,glucose just diffuses into the cells
-other glucose transporters in cells are active
phosphoaspartate
the covalent intermediate used in P-type ATP-using transport systems
mechanism for Ca/ATPase pump?
what type of transport?
-Ca binds then ATP binds
-phosphate from ATP transfers to protein to make phosphorylaspartate
-conformational change occurs moving Ca ions across membrane
-hydrolysis of phosphate from aspartic side chain of protein
-second conformational change to origin
2 examples of active transport that don't require ATP
What are they referred to as?
why?
-lactose permease (lactose is carried into the cell using proton gradient,higher outside) electrical gradient
-Na/glucose pump (uses tendency of Na to move from outside to inside of cell as driving force) concentration gradient
-secondary transporters
-th
Digitoxigenin (from foxglove) what is it used for? how does it work?
-treating congestive heart failure
-in small amounts it inhibits Na/K ATPase which reduces the sodium gradient and ultimately reduces the export of calcium from heart cells (which stimulate muscle contraction) via the Na/Ca pump (which uses the sodium gra
P-type ATPases
p-type means they have an intermediate covalent bond between aspartatic acid and phosphate
ABC transporters? example? how do they work?
-another class of transporter proteins that use ATP to move molecules
-Multidrug Resistance Protein, which is involved in the resistance of cancer cells to chemotherapy drugs
-1.bind the compound, 2.conformational change allowing ATP to bind
3. protein ev
How do nerve cells use the Na/K gradient to transmit signals?
1. opening Na gates, allowing Na to diffuse into the cell (raising internal voltage because of influx of positive ions)
2. opening of K gates, allowing K to diffuse out of the cell
3. results in overcompensation, K gates close and region recovers to norma
how does the nerve signal move?
before initial influx of Na can be pumped out it diffuses down to next Na gate changing the voltage and causing it to open, triggering the chain of events from the first gate, ultimately this continues until arriving at the end of the axon
how nerve signals move between cells?
-the 'wave' of sodium arrives at the end of the cell causing synaptic vesicles to fuse with the end of the nerve cell and release their contents into the synaptic cleft
-neurotransmitters interact with receptors on next cells postsynaptic membrane and sim
for Na/K gates, how does energy relate to what molecules move through the gate
-when the desolvation energy is less than the resolvation energy (energy realized by moving through the channel) then the movement is favored
-for K gates the movement of K is favored because they fit perfectly, but Na is too small and bounces around with
tetrodotoxin
neurotoxin that inhibits the action of nerve cells by blocking Na gates, found in pufferfish
what are the two mechanisms that channels use for specificity
physical shape and energy
mitochondria are the site of what two major processes
electron transport and oxidative phosphorylation
how are electrons transported to the mithochondria
they are carried to the electron transport system by NADH and FADH2
cristae (infoldings of inner mitochondrial membrane) contain what?
the complexes of electron transport and are where oxidative phosphorylation occurs
Complex I
electrons from NADH enter the electron transport system here
Complex II
electrons from FADH2 enter the electron transport system here
inner mitochondrial membranes are impermeable to protons (T or F)
TRUE
coenzyme Q
-it accepts a pairs of electrons from either complex I or complex II in the electron transport system and passes them SINGLY to complex III
-serves as traffic cop for electrons
sequence of electrons passing from coenzyme Q
Coenzyme Q to
Complex III to
Cytochrome c (small protein like coenzyme Q) to
Complex IV to
oxygen (to form water)
what is the terminal electron acceptor in the electron transport system
oxygen, it is also a limiting compound that can back up the chain (ex. during periods of heavy exercise)
Which complexes pump protons out of the mitochondrial matrix and into the intermembrane space?
complexes I,III, and IV
Why can't you make NAD without oxygen?
because without oxygen electrons cannot be removed from the end of the electron transport chain which in the beginning removes electrons from NADH, therefore all the NAD's are carrying electrons as NADH and have no where to move them
flavins? where are they found?
-compounds that can transport electrons
-found along with iron-sulfur proteins in complex I
cytochromes? where are they found?
-proteins with heme groups (containing iron atoms Fe+2 or Fe+3)
-found in complex III and IV
-along with copper atoms (Cu+1 or Cu+2)bound by cysteine or histidine in complex IV
examples of compounds that block action of complex I
-rotenone (insectiside)
-amytal
examples of compounds that block complex III
-Antimycin A
examples of compounds that block compound IV
-cyanide, azide, CO
-most lethal as there is no way around for electrons
Q cycle? what are the steps?
-movement of electrons through complex III
-
1.CoQ (containing both QH2 and Q) and cytochrome c bind complex III
2. (from QH2)1 electron goes to Q and 1 electron goes to cytochrome c, both protons get pumped out
3. cytochrome C and now Q leave, Q- still i
what issue can arise during electron transfer in complex IV? what enzyme can help solve the issue?
-electron transfer happens 1 electron at a time so electron flow can be interrupted, if this happens reactive oxygen species can be produced
-enzymes like superoxide dismutase and catalase help to deactivate superoxides
What are steps of electron transfer in complex IV?
1. 1st electron goes to copper and 2nd goes to iron
2.oxygen binds to iron and then form a bridge between the iron and copper atoms
3.3rd electron added to oxygen allows proton from matrix to bind, cleaving bond
4.4th electron reduces oxygen on iron, prot
Superoxide dismutase (SOD)? how does it work?
-enzyme that deactivates superoxides
-1.oxidized SOD takes electron from O2- (making O2) and becomes reduced
2.SOD gives extra electron to superoxide(O2-) and two protons to make H2O2 (hydrogen peroxide) which is converted to oxygen and water by catalase
Complex 5?
ATP synthase, creates ATP via oxidative phosphorylation powered by the movement of protons back into the mitochondrial matrix
what are the two essential functions of electron transport? how are they related?
1.pump protons out of the mitochondrial matrix
2.reoxidize NADH and FADH2 to NAD and FAD
-tightly coupled in healthy cells
chemiosmotic hypothesis? what are the three key aspects? proposed by who?
-explains how mitochondria make ATP in oxidative phosphorylation
1.intact inner mitochondrial membrane
2.electron transport makes proton gradient
3.ATP made by movement of protons back into matrix
-Peter Mitchell
what is required in order for electron transport and oxidative phosphorylation to remain coupled?
intact mitochondrial membrane
what are the 3 sites of ATP synthase and what are their functions?
L(loose)-holds ADP and Pi
O(open)-releases created ATP
T(tight)-combines ADP and pi into ATP
What are the conversions of the three sites of ATP sythanse? which direction does the complex rotate?
L goes to T
O goes to L
T goes to O
** LOT TLO
where are uncoupling proteins found? why, what do they do?
-brown fat
-intentionally poke holes in mitochondrial membranes of certain cells to stimulate the generation of heat around nerve cells to ensure rapid transmission of signals
what are the two side effects of having holes in the mitchondrial membranes?
1.generation of heat
2.inability to make ATP (burning of glucose and fat)
what happens to the citric acid cycle when there are holes in the mitochondrial membrane
it runs faster because NADH is rapidly converted back to NAD
where is NAD needed?
citric acid cycle
where is ADP needed?
complex V
What is the effect of 2,4 DNP on NAD? why?
NAD goes up because there is no uphill gradient when pumping protons back across membrane to slow the conversion form NADH to NAD
how does ADP make it into the mitochondrian?
via the ATP/ADP translocase (antiport moving ATP out and ADP in)
How does NADH make it into mitochondrial matrix?
-there is no protein to bring NADH in
-electrons use shuttles instead
-insects use G3P/DHAP shuttle to move electrons from NADH to FAD in complex 2 (making FADH2)
-mammals use malate/aspartate system which converts oxaloacete to malate (carries electrons)
what is the precursor to CDP-diacylglycerol?
phosphatidic acid
CDP-diaclglycerol? how is it made?
-the precursor to many glycerophospholipids
-CTP combines with phosphatidic acid to make it(high energy intermediate) and pyrophosphate
phosphatidyl serine, ethanolamine, and choline can all be made from what?
CDP-diaclglycerol
-phosphatidyl choline requires methyl group donation from SAM, leaving S-Adenosyl-homocysteine
how can phosphatidyl choline and phosphatidyl ethanolamine be made without phosphatidic acid biosynthesis?
by using CDP activated intermediates attached to the diacylglycerol form of the phosphotidyl group
how are sphingolipids synthesized?
-palmitoyl-CoA and serine and the addition of a fatty acid to the amine group makes a ceramide, then sugars are added to make either a cerebroside or ganglioside
ceramide
a class of sphingolipids
tay-sachs and other neural disorders are linked to what?
deficiencies in enzymes that degrade sphingolipids (specifically cerbrosides and gangliosides)
cholesterol can be synthesized totally from what?
acetyl-CoA
if steroids are derived from cholesterol then what compounds do they include?
steroid hormones, vitamin D, bile acids and more
isoprenes(isoprenoids) is how many carbons? what are made from isoprene units?
5
-steroids,vitamin A and E
HMG-CoA reductase? what does it do? how is it regulated?
-most important enzyme in cholesterol synthesis
-converts HMG-CoA to mevalonate and is primary regulator of making cholesterol
-feedback inhibition
isopentenyl pyrophosphate and dimethylallyl pyrophosphate are made up of what? where do they come from?
-acetyl-CoA
-mevalonate, which comes from HMB-CoA (isoprene synthesis overlaps with ketone body synthesis)
isopentenyl pyrophosphate and dimethyallyl pyrophosphate yield what?
10 carbon geranyl pyrophosphate
geranyl pyrophosphate and isopentenyl pyrophosphate yield what?
15 carbon farnesyl pyrophosphate
two farnesyl pyrophosphates yield what?
30 carbon squalene
squalene manipulation yields what?
lanosterol
how many steps between lanosterol and cholesterol?
19
what is cholesterol's relationship to bile salts?
bile salts (glycocholate and taurocholate for ex.) are made from cholesterol
How does SREBP regulate HMG-CoA reductase production?
1.when cholesterol levels dip, SREBP-ER moves to golgi
2.serine protease cleaves SREB-G, freeing MD regions
3. MD regions migrate to metalloprotease which clips D from M
3.D travels to nucleus and binds promoter region in front of HMG-CoA reductase and ot
what is SREBP?
steroid response element binding protein , it controlls where or not HMG-CoA reductase is made