Lectures 17-18: Regulation of TCA + Ox. phos. Flashcards
1
Q
5 pathways of carbohydrates from diet
A
- glycolysis
- gluconeogenesis
- glycogenesis
- glycogenolysis
- pentose phosphate pathway
2
Q
4 pathways of fats from diet
A
- b-oxidation
- FA synthesis
- TG synthesis
- Cholesterol synthesis
3
Q
5 pathways of proteins from diet + 1 extra
A
- transamination
- urea cycle
- aa catabolism
- aa synthesis
- synthesis of aa derivatives
+ nucleic acid synthesis
4
Q
what is cellular respiration?
- 3 stages
A
- process by which pyruvate produced by glycolysis is further oxidized to H2O and CO2 (cells consume O2 and produce CO2)
1. acetyl CoA production/oxidation of fuels to acetyl-CoA
2. acetyl CoA oxidation/oxidation of acetyl groups to Co2 in the citric acid cycle
3. electron transfer chain and oxidative phosphorylation
5
Q
generally:
- stage 1 of cellular respiration –> 3 things into what? + generates (3)
- stage 2: 1 thing into 2 things + generates (3)
- stage 3: 2 things into 1 thing + generates what?
A
- aa, fatty acids and glucose –> acetyl-coA
+ generates ATP, NADH and FADH2 - acetyl-coa into NADH and FADH2 through citric acid cycle
+ generates NADH, FADH2 and 1 GTP/ATP - NADH and FADH2 into ATP through respiratory/electron transfer chain
+ generates vast majority of ATP from catabolism
6
Q
where does each stage of cellular respiration happen?
A
- glycolysis –> cytoplasm
- TCA cycle –> mitochondrial matrix
- oxidative phosphorylation –>inner mitochondrial membrane
7
Q
3 sources of acetyl-coa?
A
- b oxidation of fat
- amino acids (leucine, thronine, etc.)
- glycolysis yields pyruvate
8
Q
pyruvate is the intermediate that links what 2?
A
- 2 central catabolic pathways
- glycolysis and TCA cycle
9
Q
citric acid cycle is a hub of metabolism: with ________ pathways leading in and ________ pathways leading out
A
- catabolic leading in
- anabolic leading out
10
Q
3 fates of pyruvate from glycolysis?
A
- enters mitochondria to be oxidized by citric acid cycle to generate energy
- after its conversion to acetyl-CoA, may be used as starting material for synthesis of FA and sterols
- precursor for synthesis of amino acids
11
Q
pyruvate to acetyl-coA is what kind of reaction?
- reversible or irreversible?
- explain what happens
- what is generated?
- transfer of e- from _______ to _______ generates __-__ ATP
A
- oxidative decarboxylation
- irreversible
- carboxyl group is removed from pyruvate, forming CO2 and 2 remaining carbons becomes acetyl group of acetyl-CoA
- NADH generated –> enters respiratory chain as e- donor
- NADH to oxygen generates 2-5 ATP
12
Q
what enzyme complex catalyzes pyruvate to acetyl-coa?
- which 5 cofactors are needed? which one not derived from vitamins?
A
- pyruvate dehydrogenase complex (E1 + E2 + E3)
- CoA-SH, NAD+, lipoate, TPP, FAD
- lipate not derived from vitamins
13
Q
pyruvate dehydrogenase (PDH) complex:
- cluster of multiple copies of what?
- describe E1, E2 and E3 –> name + cofactors
A
- multiple copies of 3 enzymes (60 copies in bovine PDC)
- E1 = pyruvate dehydrogenase –> bound cofactor TPP
- E2 = dihydrolipoyl transacetylase –> covalently bound lipoyl group of lipoate
- E3 = dihydrolipoyl dehydrogenase –> cofactors FAD and NAD
14
Q
pyruvate to acetyl-coa
- do intermediates leave the enzyme surface?
- what is that called?
- which cofactors remain bound to their enzyme?
A
- no! never leave enzyme surface
- substrate channeling
- thiamine pyrophosphate (TPP), lipoate and FAD
15
Q
which steps of pyruvate to acetyl-coa catalyzed by which enzyme?
A
E1 –> step 1 and 2:
1. pyruvate + TPP –> release CO2
2. hydroxyethyl TPP tnrasfers 2e- to acyl lipoyllysine
E2 –> step 3:
3. acyl lipoylysine reduced + CoA-SH replaces SH group to form acetyl-CoA, releasing reduced lipoyllysine
E3 –> steps 4 and 5
4. FAD to FADH2 (reduced)
5. FADH2 transfers e- to NAD+ to form NADH + H+
16
Q
citric acid cycle:
- how many intermediates?
- how many enzymes/steps?
- 5 general steps
A
- 9 intermediates
- 8 enzymes/steps
1. acetyl-coA donates 2C to oxaloacetate (4C) forming citrate (6C)
2. citrate transformed to isocitrate (6C)
3. isocitrate dehydrogenated with loss of Co2 to form a-ketoglutarate (5C)
4. a-ketoglutarate loses CO2 and yields 4C succinate
5. succinate converted in 3 steps into 4C oxaloacetate –> ready for another cycle
17
Q
4 net by-products of citric acid cycle
A
- 2 CO2 (isocitrate to a-ketoglutarate + a ketoglutarate to succinyl coA)
- 3 NADH (same reactions that produce CO2 + malate to oxaloacetate)
- 1 FADH2 (succinate to fumarate)
- 1 ATP/GTP (succinyl-CoA to succinate)
18
Q
do carbons of acetyl-coa contribute to CO2 production?
A
No
19
Q
TCA cycle can serve both ________ and ________ pathways –> is __________
A
- catabolic and anabolic
- is amphibolic
20
Q
reactions that replenish intermediates are called what?
- 4 examples
A
- anaplerotic
1. pyruvate + HCO3 + ATP –> oxaloacetate (through pyruvate carboxylase)
2. phosphoenolpyruvate + CO2 + GDP –> oxaloacetate + GTP (PEP carboxykinase)
3. phosphoenolpyruvate + HCO3 –> oxaloacetate (PEP carboxylase)
4. pyruvate + HCO3- + NADPH –> malate + NADP+ (malic enzyme)
21
Q
regulation of TCA cycle:
- enzymes of which reactions are regulated?
- cycle is activated by what?
- cycle is inhibited by what?
- PDH is phorphorylated on which enzyme = __________
- what does succinyl-CoA inhibit?
- what activates TCA cycle?
A
- of irreversible reactions
- substrate (acetyl-CoA)
- inhibited by product accumulation
- on E1 enzyme = inactivation of complex
- succinyl-CoA inhibits citrate synthase (acetyl-Coa –> citrate) and a-ketoglutarate dehydrogenase complex (a-ketoglutarate –> succinyl-coa) to regulate a-ketoglutarate for aa metabolism
- Ca2+
22
Q
what activates vs inhibits pyruvate dehydrogenase complex? (catalyzes what reactions)
A
- pyruvate to aceyl-coa
- inhibits: ATP, Acetyl-CoA, NADH, Fatty acids
activates: AMP, CoA, NAD+, Ca2+
23
Q
what activates vs inhibits citrate synthase? (catalyzes what reactions)
A
- acetyl-coa to citrate
- inhibits: NADH, succinyl-CoA, citrate, ATP
- activates: ADP
24
Q
what activates vs inhibits isocitrate dehydrogenase? (catalyzes what reactions)
A
- isocitrate –> a-ketoglutarate
- inhibits: ATP
- activates: Ca2+ + ADP
25
what activates vs inhibits a-ketoglutarate dehydrogenase complex? (catalyzes what reactions)
- a-ketoglutarate --> succinyl-CoA
- inhibits: succinyl-CoA, NADH
- activates: Ca2+
26
carbs, lipids and aa are _________ fuels
reduced
27
electrons are transferred to cofactors ____ OR ____
NAD or FAD
28
oxidative phosphorylation occurs in ________ and involves huge ________ ________ embedded in _______ ________ ________
- mitochondria
- protein complexes
- embedded in inner mitochondrial membrane (contains components of respiratory chain and ATP synthase)
29
energy from _____ and _______ is used for ATP synthesis
- these 2 molecules are _______ ______ ________
- NADH and FADH2
- reduced electron carriers
30
oxidative phosphorylation involves oxidation/reduction of ____ to _____ using ______ donated from ______ and ________
- reduction of O2 to H2O using electrons donated from NADH and FADH2
31
3 membrane-bound electron carriers?
1. __________ --> + 1 e- VS + 2e- + transfers e- from where to where?
2. ________ --> 3 types
3. ______ _______ proteins --> contains how many of each atoms?
1. ubiquinone/coenzyme Q (fully oxidized) = mobile electron carrier
- QH --> semiquinone radical
- QH2 --> ubiquinol (fully reduced)
- transfers e- from complex I/II to complex iv
2. cytochrome --> type a, b or c
3. iron sulfur proteins --> 1, 2 or 4 iron associated with sulfur
2.
32
overview of oxidative phosphorylation:
- complex I and II
- complex III
- complex iv
1 and 2: catalyze electron transfer to ubiquinone from 2 different electron donors: NADH (complex I) and succinate/FADH (complex II)
3. carries electrons form reduced ubiquinone to cytochrome c
4. completes sequence by transferring electrons from cytochrome c to O2
33
5 sources of NADH
1. b-oxidation (1 NADH per cycle)
2. glycolysis (2 NADH)
3. pyruvate to acetyl-CoA (1 NADH)
4. TCA (3 NADH)
5. amino acid oxidation to pyruvate, acetyl-coA, fumarate, a-ketoglutarate, succinyl-CoA
34
4 paths of electrons to ubiquinone
1. (complex I) NADH --> flavin mononucleotide (FMN) --> iron-sulfur protein (Fe-S) --> Q --> QH2
2. (complex II) Succinate --> Flavin adinosine diphosphate (FAD) --> Fe-S --> QH2
3. (glycerol 3-phosphate dehydrogenase) glycerol 3-phosphate (cytosolic) --> FAD --> QH2
4. Fatty-acyl CoA --> FAD (of acyl-coA dehydrogenase) --> FAD (ETF) --> Fe-S, FAD (ETF:Q oxidoreductase) --> QH2
35
complex I:
- size? shape?
- ____ subunits encoded by (2) types of genes
- name?
- 2 processes
- largest of 4 complexes. L shaped (1 arm embedded in intermembrane + one arm inside matrix)
- 45 subunits encoded by nuclear and mitochondrial genes
- NADH-quinone oxidoreductase
1. transfer of 2 e- from NADH to ubiquinone (through FMN, Fe-S and Q)
2. pumping 4 H+ from matrix (negative) to intermembrane space (+)
36
net equation of complex I
NADH + Q + 5 H+(N) --> NAD+ + QH2 + 4 H+ (P)
37
which side of membrane is negative vs positive?
- intermembrane space = positive
- matrix = negative
38
complex II:
- name?
- 4 subunits --> roles? + binding site for what?
- 2 roles?
- pumps H+?
- succinate dehydrogenase
- a and b --> extend to matrix --> have iron-S proteins --> bound to FAD (co-factor) + binding site for succinate
- c and d have heme --> binding site for ubiquinone
ROLES:
1. converts succinate to fumarate in TCA cycle
2. capture and donate e- in electron transport chain (AKA reduces ubiquinone (Q) to QH2 (Ubiquinol)
- NO proton pumping
39
Complex III:
- 3 functional units?
- 2 pathways/steps/roles?
- cytochrome b = a dimer: cavern where ubiquinone can move from matrix to intermembrane space
- cytochorme C1
- iron-sulfur center
1. transfers electron from ubiquinol to cytochrome C --> QH2 oxidized --> 1 e- passes through Fe-S --> heme C1 --> cyt C AND QH2 --> 1 e- to heme b --> Q --> becomes °Q- --> becomes QH2 (ish)
2. releases 4 protons to intermembrane space --> 2 QH2 each release 2 protons
40
reactions of stage 1 and 2 + net equation of complex III
stage 1:
QH2 + Q + cyt c (oxidized) --> Q + °Q- + 2 H+ (P) + cyt c (reduced)
stage 2:
QH2 + °Q- + 2H+ (N) + cyt c (oxidized) --> Q + 2H+ (P) + QH2 + cyt c (reduced)
net equation:
QH2 + 2 cyt c (oxidized) + 2 H+ (N) --> Q + 4 H+ (P) + 2 cyt c (reduced)
41
complex IV:
- name?
- 3 subunits
- 2 roles?
- cytochrome oxidase
- Subunit 1 = 2 hemes + 1 copper ion
- subunit 2: copper ion
- subunit 3: heme a1
1. transfer electron from cytochrome c to O2 (4 e- bc 4 cyt c) (cyt c --> copper ion --> heme a --> heme a3 --> copper ion B --> O2 --> forming H2O in matrix
2. transports 2 protons to outside per electron pair (4 H+ in total) (uses energy from O2 to H2O)
42
what is a respirasome?
2 examples
functional combinations of many complexes/electron carriers
1. complex 1, 3 and 4
2. complex 2, 3 and 4
43
net equation for respirasome of complex 1, 3 and 4
What + _____ H+ + 0.5 O2 —> ?
1 NADH + 11 H+ (N) + 1/2 O2 --> NAD+ + 10 H+(P) + H2O
44
net equation for respirasome of complex 2, 3 and 4
1 FADH2 + 6 H+ (N) + 1/2 O2 --> FAD + 6 H+ (P) + H2O
45
does NADH or FADH2 produce more electrochemical gradient?
NADH
10 H+ vs 6 H+
46
proton motive force comes from (2)?
- role?
1. chemical potential (delta pH) --> inside alkaline
2. electrical potential --> inside negative
- drive protons back into matrix which provide E to synthesize ATP
47
electrochemical proton gradient created by (3)
1. active transport of protons (complex 1 and 4)
2. release of protons into intermembrane space --> oxidation of QH2 (complex 3)
3. chemical removal of protons from the matrix --. reduction of Q (complex 1, 2, 3) and Oxygen (complex 4)
48
is the inner mitochondrial membrane permeable to H+?
- How can H+ reenter matrix?
- no! impermeable
- leave matrix through complexes
- reenter matrix through Fo (pump/channel)
49
is the inner mitochondrial membrane permeable to NADH?
- how does NADH travel to matrix/intermembrane space? (2 ways depending on where?)
impermeable!
- in most cells --> malate aspartate shuttle (NAD+ on intermembrane space vs NADH on matrix side)
- in skeletal muscle and brain --> glycerol 3-phosphate shuttle
50
what is the ATP yield of glucose (glycolysis, pyruvate oxidation, TCA)?
glycolysis: 5 (or 7)
pyruvate oxidation: 5
TCA cycle: 20
TOTAL: 30 or 32
51
how many ATP do NADH and FADH2 yield?
- NADH: 2.5 ATP
- FADH2: 1.5 ATP
52
what is the ATP yield of palmitate (b-oxidation, TCA cycle)?
beta oxidation: 28
TCA cycle: 80
TOTAL: 108 ATP!
53
how is oxidative phosphorylation regulated?
- mass action ratio [ATP]/([ADP][Pi]) --> increase ATP/NADH or decrease ADP/AMP/NAD --> low rate of everything (glycolysis, TCA, ox phos)
54
ATP is synthesized as fast as ?
as fast as it is utilized!
