biochem lecture 5 pt 1 Flashcards
(253 cards)
1
Q
common intermediate example
A
acetyl CoA
2
Q
what do we have a often in catabolic pathways
A
convergence of diff catabolic processes that converge at a common intermediate
3
Q
what does common intermediate represent
A
common currency that can be used to make ATP
4
Q
what diff pathways will converge at level of acetyl CoA
A
glycolysis, oxidation of fatty acids, degradation of AAs
5
Q
basically what does this mean
A
divergent energy sources, but converge thru formation of common intermediate acetyl CoA
6
Q
why is acetyl coA important
A
these two carbon fragments can all be used or oxidized via the TCA cycle regardless of whether they come from glucose or fatty acids etc
7
Q
what is importance of acetyl CoA
A
reducing power; can extract e- from Carbons, and transfer to electron carriers like NAD and FADH
8
Q
where does most of reducing power in cell respiration come from
A
TCA cycle
9
Q
what are three stages
A
partial oxidation via glycolysis of glucose into pyruvate, pyruvate into acetyl CoA by PDH complex, and other 2 Cs from pyruvate will be oxidized in oxidative decarboxylation step
10
Q
what happens to pyruvate in TCA cycle
A
complete oxidation of 3 Cs
11
Q
what happens to all 3 carbons in pyruvate in TCA cycle
A
released as waste in form of CO2
12
Q
describe TCA
A
amphibolic
13
Q
amphibolic
A
plays a role in catabolism and anabolism
14
Q
what is TCA a central pathway for
A
recovering E from several metabolic fuels
15
Q
what can TCA intermediates serve as
A
precursors for biosynthetic pathways
16
Q
what is advantage of a cycle
A
you can have intermediates that are generated, and siphoned off into other pathways
17
Q
why do we have cycles instead of linear pathways
A
intermediates can be directed out of cycle to other pathways, or can have things going into pathways to continue cycle
18
Q
anapleurotic reactions
A
rxns that replenish intermediates depleted by other rxns
19
Q
what can some intermediates in TCA cycle be used for
A
biosynthesis of fats, amino acids, components of heme or porphyrin ring structure (succinyl CoA)
20
Q
what do cytochromes found in ETC have
A
protoporphyrin ring structures, heme-like structures
21
Q
where are some gluconeogenesis precursors derived from
A
TCA cycle (like oxaloacetate)
22
Q
what is TCA cycle important for
A
both catabolic and anabolic processes
23
Q
how are intermediates maintained
A
anaplerotic rxns
24
Q
anapleurotic reactions
A
rxns that replenish intermediates that have been depleted by other reactions, maintain levels
25
why is replenishment reactions important
if we have lowering of oxaloacetate (end product of TCA), it reduces level of flow/flux thru pathway, inhibits overall flow
26
what is having replenishment rxns necessary for
maintaining flux/flow thru the cycle
27
important precursors in gluconeogenesis
malate --> Oxaloacetate --> glucose
28
important precursors in lipid biosynthesis
citrate --> oxaloacetate + acetyl coA --> lipids
29
precursors in porphyrin biosynthesis
succinyl CoA
30
what pathways use TCA cycle intermediates
gluconeogenesis, lipid biosynthesis, AA biosynthesis, porphyrin biosynthesis
31
what is succinyl coA important for
heme production
32
where does TCA cycle take place
mitochondrial matrix
33
where does glycolysis take place
cytosol/cytoplasm
34
describe mitochondria
double membrane organelle, has microcomparments
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describe outer membrane of mitochondria
permeable to small things (less than 5 kD)
36
describe inner membrane of mitochondria
impermeable; only permeable to O2, H2O, CO2
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what does other stuff require in mitochondria
transport proteins
38
describe structure of mitochondria
folded inner mitochondrial membranes, cristae
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what is importance of cristae or folded membrane
can increase internal surface area
40
what happens in inner mitochondrial membrane
its where components of ETC and ATP synthase reside
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what does increased SA mean
you can localize more copies of ETC and ATP synthesizing components
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endosymbiosis theory
mitochondria arose from symbiotic relationship b/w bacteria and eukaryotic cell (bacteria had cushy environment, cell could harvest its ATP)
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which is more permeable, inner or outer membrane
outer membrane
44
why is relative impermeability of inner membrane important
for when we talk about ATP synthesis, and establishing a proton gradient across inner membrane
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what is required for shuttling things into and out of mitochondria
transport mechanisms
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where is glycolysis
cytoplasm
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where is TCA cycle and ATP synthesis
mitochondria
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so what happens if pyruvates generated in glycolysis need to undergo complete oxidation in TCA cycle
need to be transported to mitochondria
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big picture of TCA cycle; first step
pyruvate from glycolysis is split to acetyl CoA
50
what does first overall big picture step (pyruvate --> acetyl CoA ) generate
1 NADH, 1 CO2
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what is second big picture step
acetyl Coa + oxaloacetate --> citrate
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what happens to citrate
enters cycle
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what is 3rd big picture step
one 2 carbon acetyl group of citrate is oxidized
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how many steps in it
8 steps; 2 CO2, 3 NADH, 1 FADH2, 1 GTP/ATP
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what is generated at the end of TCA cycle
oxaloacetate
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what do pyruvates derived from glycolysis undergo
preparative step or activation
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does pyruvate itself enter TCA cycle?
nope, needs to be converted to acetyl CoA
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how are pyruvates converted to aectyl coa
pyruvate dehydrogenase complex
59
what enters the TCA cycle
acetyl CoA
60
what do we generate in this prep step
1 NADH, first CO2 thats produced (from converting pyruvate to acetyl coa)
61
what are nadh/fadh2
money in the bank, reduced electron carriers that can be cashed in the ETC and used to generate ATP
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what happens after acetyl coa is amde
2 carbon fragments joined to coenzyme A (acetyl CoA) combine w/ oxaloacetate --> citrate
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what is oxaloacetate
end product of TCA cycle
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what is starting point of TCA
citrate
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what kind of rxn involved in formation of citrate
condensation reaction (where you combine 2 carbon acetyl units from acetyl CoA w/ oxaloacetate)
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what happens for each acetyl CoA that enters cycle
8 rxns overall
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how many CO2s do we generate
2 CO2s per turn of the cycle
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how many oxidative decarboxylation steps
2 oxidative decarboxylation steps
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how many carbons from acetyl CoA will be completely oxidized
w carbons
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what do we generate per cycle
3 NADH, 1 FADH2, 1 GTP/ATP
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what is important for cycle to continue
regeneration of oxaloacetate
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how many pyruvates per glucose do we generate in glycolysis
2
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so how many acetyl CoAs
2; (2*2 = 4 carbon acetyl units)
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how many turns of cycle for complete oxidation of a single glucose molecule
2 turns
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so how much do we produce per glucose
6 NADHs, 2 FADH2s, 2 GTP/ATPs, 4 CO2s per glucose, every 2 turns of cycle
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what is prep step
production of acetyl coA from pyruvate
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why is prep step necessary
allows for oxidation of carbons in TC cycle
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what does coenzyme A have
reactive thiol group
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what happens when thiol group is linked to two carbon acetyl units from pyruvate
thioester linkage
80
what is acetyl coa an example of
high energy intermediate
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what happens when thioester bond in acetyl coA is cleaved in first step of TCA cycle
2 carbon acetyl unit is gonna be transferred to oxaloacetate (to form citrate), and free E is released
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what is free E released from cleavage of thioster bond used for
to form citrate from acetyl coa. + oxaloacetate
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basically what does hydrolysis of thioester bond of high E intermediate acetyl coA used for
provides E needed to carry out first step in TCA cycle
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basically what is preparation
generation of acetyl CoA from pyruvate
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what does coenzyme A receive
2 carbons (in form of acetyl group)
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where does coenzyme A receive 2 Cs from
pyruvate
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what linkage is formed in prep step
thioester linkage (acetyl CoA)
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what energy complex takes pyruvate from glycolysis to produce acetyl CoA
pyruvate dehydrogenase complex
89
what is pyruvate dehydrogenase complex
massive complex, multi sub unit, many components
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what coenzymes does pyruvate dehydrogenase complex utilize
coenzyme A, NAD, FAD, TPP, lipoic acid. etc
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what else is generated in prep step (pyruvate --> acetyl CoA)
NADH and CO2 (first co2 produced)
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how many rxns in prep phase
5 sequential rxns; oxidative decarboxylation
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what is oxidative decarboxylation
where you generate CO2 thru a series of redox rxns that take place in this enzyme complex
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what does pyruvate dehydrogenase have
multiple copies of these 3 enzymes
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what 3 enzyme/subunits are in pyruvate dehydrogenase complex
pyruvate dehydrogenase (E1), dihydrolipoyl transacetylase (E2), dihydrolipoyl dehydrogenase (E3)
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E1
pyruvate dehydrogenase
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E2
dihydrolipoyl transacetylase
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E3
dihydrolipoyl dehydrogenase
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how many copies of E1, E2, E3
multipleeee
100
what is PDH complex an example of
substrate channeling
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what is substrate channeling
series of sequential rxns that hand off intermediates to each other
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what happens to the intermediates in substrate channeling
we never lose them, they are effectively trapped
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how are the intermediates trapped
thru formation of covalent intermediates within enzyme complex
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what does substrate channeling allow for
more efficient catalysis; cuz intermediates are tethered to coenzymes in enzyme complex
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what is step 1
E1 carries out oxidative decarboxylation step
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what is released in step 1
CO2; 1 carbon from carboxyl group of pyruvate is released
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what happens to the remaining 2 carbon fragment in pyruvate
transferred to a coenzyme TPPP
108
what is TPP formed
hydroxyethyl TPP
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what is hydroxyethyl TPP tethered to
TPP coenzyme
110
what does E1 complex do
hands off acetate unit to next coenzyme (lipoic acid)
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what is the next coenzyme
lipoic acid
112
what is lipoic acid here called
lipoyllysine
113
why lipoyllysine
cuz its tethered to a specific lysine in E2 complex
114
where does 2 carbon fragment from hydroxyethyl TPP go
transferred to acyl lipoyllysine
115
what is lipoic acid basically like
a long arm, like arm of crane as it rotates
116
where does lipoic acid rotate
in E2 subunit
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what is acetate tethered to
acetate is tethered to partially oxidized lipoyllysine
118
what does the tethered acetate undergo
partial reduction; one of 2 sulfurs is reduced to thiol
119
when is this partial reduction happening
in process of transferring acetate from TPP from E1 to lipoic acid in E2
120
what is step 3
E2 subunit is gonna transfer acetate group to a molecule of coenzyme A
121
what mediates the actual synthesis of acetyl CoA
E2
122
what does E2 do
generates acetyl CoA which can go into TCA cycle
123
so are we done after E2?
nope
124
why aren't we done
once we've transferred this 2 carbon acetate unit to generate acetyl CoA in step 3, we are left w/ a fully reduced form of lipoyllysine
125
what is CoA-SH
reduced form of coenzyme A
126
what is lipoyllysine
cofactor that's attached to a lysine within E2 polypeptide
127
why is having the two thiol/SH groups here a problem
cuz in order for E2 to accept another 2 carbon fragment from hydroxyethyl TPP of E1, it needs to be in fully oxidized form
128
what is fully oxidized form of lipoyllysine
disulfide bridge form
129
what does lipoyllysine start out as
fully oxidized form; disulfide bridge
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what are steps 4 and 5 important in
regeneration of fully oxidized lipoyllysine of E2
131
where does E3 come into play
in regenerating oxidized lipoyllysine
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what would happen without reoxidation of lipoyllysine
E1 can't transfer the two carbon fragment to lipoyllysine to generate another acetyl CoA; everything would stop
133
what does E3 do in order to generate oxidized lipoyllysine from the reduced form here
sets up sequential redox reactions in steps 4 and 5
134
what does step 4 involve
FAD: reduced lipoyllysine is gonna transfer 2 Hs (2 electrons) to FAD
135
why is step 4 a win-win
we regenreate oxidized lipoyllysine (needed to keep stuff going) and also generate some reducing power in form of FADH/FADH2
136
what happens if we generate reduced FAd/FADH2
we need a pool of oxidized FAD to keep E3's regeneration step going
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what is step 5
a second redox step in which FADH2 is reoxidized
138
what else is produced in step 5
we generate reduced NAD so NADH
139
why is E3 subunit important
cuz it regenerates oxidized lipoyllysine and oxidized FAD (so that E2 can carry out regeneration)
140
how do we reoxidize FADH2 to FAD
by setting it up w/ another redox rxn involving NAD (NADH)
141
why is it not enough to have first 3 steps
cuz its not enough to just produce acetyl CoA; E2 subunit needs to reset itself
142
why is E3 so important
cuz its gonna regenerate oxidized form of lipoic acid to keep things going
143
what is E1
pyruvate dehydrogenase
144
what does E1 do
forms hydroxyethyl TPP intermediate
145
basically what does E1 do (how does it form hydroxyethyl TPP intermediate)
uses TPP as a cofactor, attacks the carbonyl C2 of pyruvate (releases CO2), and TPP is bound to hydroxyethyl group --> hydroxyethyl TPP
146
what is lipoic acid
cofactor that is covalently tethered to specific lysine residue of E2
147
what for form of lipoic acid is involved
oxidized form of lipoic acid
148
what is lipoic acid involved in
in transfer of acetate (2 carbon) units from hydroxyethyl TPP intermediate to lipoic acid
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what form of lipoic acid is gonna be used in synthesis of acetyl CoA
hemi/partially reduced / acetylated form
150
what form of lipoic acid are we left with
reduced form
151
what has to happen to the reduced form of lipoic acid
has to be re-oxidized (by steps 4 and 5, E3 subunit)
152
basically what is E3, steps 4 and 5 all about
getting lipoyllysine back to fully oxidized form so it can accept another acetate unit from hydroxyethyl TPP intermediate from E1
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what's involved w/ E2
lipoamide side chain extends to E1. transfers hydroxyethyl from TPP to dihydrolipoamide. partial reduction creates acetyl group, second reduction transfers acetyl group to CoA
154
how is acetyl CoA generated
coenzyme A receives 2 Cs from pyruvate in form of acetyl group
155
what linkage does acetyl CoA have
high E thioester linkage
156
what do we need to regenerate after we generate acetyl CoA
oxidized lipoic acid to keep things going, so it can accept more pyruvate
157
what does E3 do basically
resets the system
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what's up w/ E3
catalyzes regeneration of disulfide/oxidized form of lipoamide. uses bound cofactor FAD (reduced to FADH2). NAD+ oxidizes FADH2 to regenerate FAD. NAD becomes reduced (NADH_
159
what happens after E3
PDH enzyme complex is regenerated. NADH is made
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what is PDH complex tethered by
lipoamide arm
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what happens to intermediates in PDH
intermediates never leave complex
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what is stage 2 of TCA
oxidation of acetyl CoA
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what is one of major waste products generated in TCA
CO2
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how else is acetyl CoA made
fatty acid oxidation, amino acid degradation
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how many steps in stage 2
8 steps
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what are products of stage 2
3 NADH, 1 FADH2, 1 GTP/ATP (per cycle; multiply by 2 to get per glucose unit)
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what are byproducts of stage 2
H2O, CO2
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common intermediate acetyl coA
whether it comes from pyruvate (like we discussed), or from oxidation/degradation of fatty acids or AAs, it can be fed into the TCA cycle
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first step of TCA
combo of acetyl CoA (2 carbon fragment) w/ oxaloacetate (end product) --> citrate
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how many steps in TCA cycle
8 steps
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what happens in steps 3 and 4
sequential oxidative carboxylation --> CO2 generated in steps 3 and 4 AND NAD reduced to NADH
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how can acetyl CoA be derived rom fatty acids
beta oxidation
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what is major source of E
fatty acids
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per molecule who gives more E
fatty acids
175
but what is preferred E source for organsims
glcuose; faster and easily obtained
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step 1 of TCA
formation of citrate from acetyl CoA and oxaloacerate
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what enzyme for step 1
citrate synthase
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what kinda rxn in step 1
condensation
179
what C of acetyl group is joined to what of OAA
methyl C of acetyl group is attached to carbonyl C of oxaloacetate
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what happens to free CoA-SH (reduced); that's not used in condensation rxn
goes back to PDH complex
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what is step 2 of TCA
formation of isocitrate from citrate
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what enzyme in step 2
aconitase
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describe step 2
citrate --> cis-aconitate --> isocitrate (2 rounds of aconitase)
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what intermediate formed in step 2
cis-aconitate C2-C3 double bond intermediate
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how many steps in step 2
2 steps
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what is step 3
oxidation of isocitrate
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what do we get in step 3
isocitrate --> a-ketoglutarate
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what kinda rxn is step 3
a 3-step oxidative decarboxylation
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what enzyme in step 3
isocitrate dehydrogenase
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describe step 3
isocitrate --> oxalosuccinate --> a-ketoglutarate
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what does initial oxidation of isocitrate do in step 3
oxalosuccinate intermediate; produces first NADH
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what does decarboxylation give in step 3
oxalosuccinate --> alpha-ketoglutarate; CO2 is produced
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what ion in enzyme active site stabilizes intermediates in step 3
manganese
194
what is step 4
oxidation of a-ketoglutarate
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what kinda rxn is step 4
another oxidative decarboxylation
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what enzyme in step 4
a-ketoglutarate dehydrogenase complex
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what is a-ketoglutarate dehydrogenase complex similar to
PDH complex
198
what happens in step 4
a-ketoglutarate --> succinyl CoA
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what else is produced in step 4
Co2, NADH
200
similarities b/w PDH and enzyme in step 4
same cofactors (TPP, FAD, NAD)
201
differences b/w PDH and enzyme in step 4
produces succinyl CoA instead of acetyl CoA; AND produces second NADH and Co2
202
describe energy of succinyl coA
high energy
203
what is step 5
succinyl CoA --> succinate
204
what enzyme in step 5
succinyl CoA synthetase
205
what else is produced in step 5
produces GTP or ATP as well as CoASH
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what kinda rxn is step 5
substrate level phosphorylation
207
what do u need to look for anytime u have substrate level phosphorylation rxn
high E intermediate (succinyl CoA)
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what does whether GTP or ATP is produced depend on
S-CoA-synth isozyme
209
what drives ATP/GTP formation in step 5
free E released in breakage of thioester bond
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what is step 6
oxidation of succinate
211
describe step 6
succinate --> fumarate
212
what enzyme in step 6
succinate dehydrogenase
213
what else is generated in step 6
FADH2 (reduced FAD)
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where is FADH2 generated
step 6
215
what is FAD bound to
covalently bound to enzyme along w/ iron-sulfur centers
216
where do electrons flow in step 6
from FAD - iron/sulfur - ETC
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what does this electron flow ultimately lead to
ATP production (ox/phos)
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where is succinate dehydrogenase
embedded in inner mitochondrial membrane
219
what is complex 2 of ETC
succinate dehdyrogenase
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what is succinate dehydrogenase
complex 2 of ETC
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what is step 7 of eTC
hydratino of fumarate
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what enzyme for step 7
fumarase
223
what happens in step 7
fumarate --> malate
224
how do we go from fumarate to malate (what is added)
H2O added across fumarate double bond
225
what kinda fumarate does this work with
only trans, notcis
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what is step 8 of TCA
oxidation of malate
227
what enzyme in step 8
malate dehydrogenase
228
what happens in step 8
L-Malate --> dehydrogenase
229
what else is produced in step 8
3rd NADH (malate kicks it out)
230
what happens w/o oxaloacetate
we can't keep cycle going
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why is malate important
regenerates OAA for another cycle of TCA
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where is TCA regulated
3 exergonic steps / rate limiting steps
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what 3 steps is TCA regulated
citrate synthase (1st step), isocitrate dehydrogenase, a-ketoglutarate dehdyrogenase
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what does it mean if a rxn is exergonic
mostly one directional pathway/step
235
are exergonic rxns forward or reverse
mainly forward
236
why are exergonic steps-rate limiting
if you deplete [ ] or have lower levels of substrates, used up rapidly, need to keep replenishing to keep it going
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what inhibits/activates the above enzyme
when you have high concentrations of intermediates (citrate, succinyl CoA, NADH), serves as feedback inhibitors of citrate synthase and dehydrogenases
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what determines whether the cell is under catabolic mode or anabolic mode [AKA which pathways are operational]
E state of cell
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what are indicators of energy state of the cell
specific intermediates and reduced electron carriers
240
what does high [ ] of intermediates like citrate or succinyl CoA mean
we have a lot of NADH, so reducing power, so high E
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what are indicators of low E
lower amounts of reduced e- carriers, more NAD+, more AMP/ADP
242
what do we have in muscles
calcium
243
what is calcium
important activator of isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase
244
what is the point
you can turn pathways on or off at exergonic steps
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describe these exergonic steps
unidirectional, favorable steps
246
what happens if you shut down reversible steps
might block potentially reversible/opposing steps that occur in anabolic processes
247
how can we most effectively control the amount of flux/flow in a pathway
at these unidirectional, exergonic, rate limiting steps
248
indicators of high/low E staet
ATP, NADH, acetyl-COA, ADP, NAD+, coA, calcium
249
what compounds are inhibitory
ATP, NADH, acetyl coA
250
what compounds are stimulatory
ADP, NAD+, CoA, Calcium
251
what do these inhibitory compounds serve as
feedback inhibitors of catabolic steps; indicators of high E state
252
what kinds of compounds are stimulatory
stuff that indicates low E state
253
key regulatory points in TCA
citrate synthase, isocitrate dehydrogenase, a-ketoglutarate dehydrogenase
