Section 12-13 Flashcards
(113 cards)
1
Q
What is the most common input of the TCA cycle?
A
acetyl-CoA
2
Q
What does beta-oxidation of fat yeild?
A
Acetyl-CoA
3
Q
Which AAs yeild acetyl-CoA?
A
4
Q
The conversion of pyruvate to acetyl-CoA is an example of what?
A
Oxidative decarboxylation
5
Q
What are biproducts of the pyruvate –> acetyl-CoA reaction?
A
NADH & CO2
6
Q
Where does the NADH go after its production from the pyruvate–>acetyl-CoA reaction?
A
ETC
7
Q
What is the scientific name of vitamin B5?
A
Pantotheinc acid
8
Q
What are the 3 main parts of a CoA molecule?
A
ADP moiety, pantothenic acid (vitamin B5), beta-mercaptoethylamine
9
Q
What is special about beta-mercaptoethylamine
A
It has a reactive thiol group (–SH) which attaches to other molecules. Ex: Acetyl-CoA
10
Q
What is the pyruvate dehydrogenase complex?
A
A cluster of multiple copies of 3 enzymes
11
Q
What 3 enzymes exist in the Pyruvate Dehydrogenase complex?
A
E1: pyruvate dehydrogenase
E2: dihydrolipoyl transacetylase
E3: dihydrolipoyl dehydrogenase
12
Q
How many copies of the 3 enzymes exist in the bovine kidney Pyruvate Dehydrogenase complex?
A
60
13
Q
What are the two co-substrates (coenzymes) in the PDC?
A
CoA-SH and NAD
14
Q
What are the 3 prosthetic groups in the Pyruvate Dehydrogenase complex? Where can they be found?
A
- Thiamine pyrophosphate (TPP) —- E1
- Lipoate —- E2
- FAD — E3
Found permanently attached to one of each enzyme respectively
15
Q
Where can vitamin B be found throughout the pyruvate dehydrogenase complex?
A
- TPP = thiamine (B1)
- FAD = riboflavin (B2)
- NAD = niacin (B3)
- CoA = pantothenate (B5)
Vitamin deficiency affects TCA cycle!!!
16
Q
What part of the pyruvate molecule is transfered to CoA-SH?
A
The acetyl group
17
Q
What happens at E1 (pyruvate dehydrogenase) of the pyruvate dehydrogenase complex? What is the 1st C removed as? What is the remaining 2C attached to TPP called?
A
Pyruvate (3C) attaches to TPP.
The 1st C is removed as CO2 (decarboxylation)
Hydroxyethyl TPP
18
Q
E2: what is lipoate permanently attached to? What is the name if this compound?
A
Lysine.
Lyopyllysine
19
Q
What 3 forms does lipoate exist in?
A
Reduced form: SH
Oxidized form: H’s removed
Acetylated form: acetyl group transfered from pyruvate
20
Q
How many intermediates does the TCA cycle have? How many enzymes?
A
9 intermediates
8 enzymes
21
Q
How many carbons does acetyl-CoA donate to oxaloacetate? How long is the C-chain of oxaloacetate?
What happens to these C atoms? At what steps?
A
acetyl-CoA donates 2C to oxaloacetate (4C compound).
The 2C atoms are eventually converted to CO2 (step 3 & 4)
22
Q
What is step 1 of the TCA cycle?
A
acetyl-CoA + oxaloacetate –> citrate.
Enzyme: citrate synthase.
Condensation reaction - H2O put in, this removes CoA
23
Q
How does citrate regulate PFK-1?
ACC? (from FA synthesis)
A
Citrate inhibits PFK-1 and AAC
24
Q
What is step 2 of the TCA cycle?
How many steps is this reaction? What is removed in the 1st step? What is added in the second step?
A
Citrate –> Isocitrate.
Enzyme: aconitase
2 step reaction - H2O removed, then added
25
How many carboxyl groups do citrate and isocitrate have? What cycle are they a part of?
3 carboxyl groups
tricarboxylic acid cycle
26
What is step 3 of the TCA cycle?
What type of reaction is this?
How many steps is this reaction?
Step 1:
Step 2:
Step 3:
Isocitrate --> alpha-ketogluterate.
Enzyme: isocitrate dehydrogenase. 2 isoforms -> mitochondrial isoform is NAD dependent
3 steps
Step 1: Isocitrate is oxidized by NAD+ or NADP+. (1st NADH formed)
Step 2: 1st CO2 removed (decarboxylation)
Step 3: rearrangement of enol intermediate
27
What is step 4 of the TCA cycle? Enzyme? What is produced here as biproducts?
What is the alpha-ketogluterate dehydrogenase complex similar to?
alpha-ketogluterate --> succinyl-CoA
Enzyme: alpha-ketogluterate dehydrogenase complex
2nd CO2 produced
2nd NADH produced
Similar to: PDC (E3 is the same, E1/E2 are similar)
28
What is step 5 of the TCA cycle?
Enzyme? How many isoforms does enzyme have?
Which enzyme interconverts GDP and ADP?
What is other biproduct?
Succinyl-CoA --> succinate
Enzyme: succinyl-CoA syTHETASE/THASE (2 isoforms. One uses GDP, other uses ADP)
Synthetase: when no energy molecule involved
Syhthase: when ATP involved
nucleoside diphosphate kinase. GTP + ADP --> GDP + ATP
Substrate level phosphorilation - GTP/ATP produced
CoA cleaved out for recycling
29
What is step 6 of the TCA cycle? Enzyme?
What type of reaction is this?
What is produced?
Where do the H ions come from?
Succinate --> fumarate
Enzyme: succinate dehydrogenase
Dehydrogenation reaction
FADH2
H ions come from substrate itself, not free-floating H's)
30
Where is the succinate dehydrogenase enzyme located? As opposed to what location?
The only enzyme located in the inner wall of the mitochondrial membrane (as opposed to the free floating matrix)
31
What is step 7 of the TCA cycle? Enzyme?
What type of reaction is this? How many steps? What are the steps? What is the transition state called?
Fumarate --> malate
Enzyme: fumarase
Hydration reaction. 2 steps:
1. hydroxyl group added
[Carbanion transition state]
2. free floating H added
32
What is step 8 of the TCA cycle? Enzyme?
What type of reaction is this?
What is made here?
Malate --> oxaloacetate
Enzyme: malate dehydrogenase (mitochondrial isoform)
Dehydrogenation
3rd NADH made
33
What are the biproducts of the crebs cycle? via 1 acetyl-CoA
Acetyl-CoA = 2 CO2 + 3 NADH + 1 FADH2 + 1 GTP(ATP)
34
What is the overall purpose of the TCA cycle?
Convert the 2-C's in acetyl-CoA to CO2
35
What does amphibolic mean?
a biochemical pathway that involves both catabolism and anabolism
TCA cycle is the hub of MANY reactions
36
What other reactions can citrate be used for other than the TCA cycle?
Used in sterols for FA synthesis
37
What other reactions can alpha-ketogluterate be used for other than the TCA cycle?
AA metabolism: converted to glutamate with addition of amino group. From there, can become (-->glutamine, proline, arginine) or (->purines)
38
What other reactions can succinyl-CoA be used for other than the TCA cycle?
Porphyrins, heme
39
What other reactions can oxaloacetate be used for other than the TCA cycle?
-->PEP-->gluconeogenesis
or
-->PEP-->serine, glycine, cystein, phenylalanine, tyrosine, tryptophan
or
->aspartate/arginine--> pyrimidines
40
How are the intermediates that leave the TCA cycle for other reactions brought back?
Anaplerotic reactions -
41
How many TCA cycle reactions are regulated?
4
42
Which reactions of the TCA cycle are irreversible?
1,3,4 (points of regulation)
43
Which 4 enzymes of the TCA cycle are regulated?
Pyruvate dehydrogenase complex, citrate synthase, isocitrate dehydrogenase, alpha-ketoglutarate dehydrogenase complex.
44
What inhibits the pyruvate dehydrogenase complex? Activates it?
Inhibits: ATP, acetyl-CoA, NADH, fatty acids
Activates: AMP, CoA, NAD(+),Ca(2+)
45
What inhibits citrate synthase? Activates it?
Inhibits: NADH, succinyl-CoA, citrate, ATP
Activates: ADP
46
What inhibits isocitrate dehydrogenase? Activates it?
Inhibits: ATP
Activates: ADP, Ca(2+)
47
What inhibits the alpha-ketoglutarate dehydrogenase complex? Activates it?
Inhibits: succinyl-CoA, NADH
Activates: Ca(2+)
48
Do FAs contribute to gluconeogenesis? Why is this a trick question?
No. But...odd number of C's in FAs, cleaved into acetyl-CoA by succinate, converted to oxaloacetate, may contribute to gluconeogenesis
49
The mitochondria is the site of what?
Oxidative phosphorylation
50
Oxidative phosphorilation involves the reduction of _____ to ____ using what?
O2 to H2O using electrons donated from NADH & FADH2
51
How many protein are in the mitochondria? How many have unknown functions?
1100
300
52
What is the outer membrane of the mitochondria permeable to?
Small molecules and ions
53
What is the inner membrane impermeable to?
Most small molecules and ions, including H(+)
54
What does the inner membrane of the mitochondria contain?
Respiratory electron carriers (Complex I-IV), ATP synthase, ADP-ATP translocase
55
What does the matrix of the mitochondria contain?
Pyruvate dehydrogenase complex, TCA cycle, FA beta-oxidation enzymes, AA oxidation enzymes, DNA&ribosomes, ATP/ADP/Mg(2+),Ca(2+), K(+)
56
What is another name for ubiquinone?
coenzyme-Q
57
How many electrons does ubiquinone have? semiquinone? ubiquinol?
Ubiquinone: 0
Semiquinone: 1
Ubiquinol: 2
58
What characteristics of coenzyme-Q allow it to be a mobile electron carrier?
small and hydrophobic
59
What complexes does coenzyme-Q transfer electrons from and to?
1 and 2 --> 3
60
How many types of cytochromes are there? Which one is mobile?
3 (a,b,c)
Cytochrome C is mobile
61
What structure is inside of cytochromes?
heme
62
How many electrons can cytochrome c carry at a time?
1
63
How are the electrons from NADH and FADH2 that come from the TCA cycle transferred into the complexes?
Iron-sulfur proteins
64
What are the iron-sulfur complexes always connected to in iron sulfur proteins?
Cystein residues of the protein
65
What type of centers aid the transfer of electrons from NADH and FADH2 to the Fe-S protiens?
FAD (Flavin MonoNucleotide), FMN (Flavin adinosine diphosphate)
66
What complex is FMN found in? What is the path of the electrons?
Complex 1
NADH-->FMN-->Fe-S-->Q
67
What complex is FAD found in? What is the path of electrons in complex 2?
2,3,4
Complex 2: FADH2-->FAD--> Fe-S-->QH2
68
Where are the 5 places that electrons come from in the form of NADH to the ETC?
1. B-oxidation: 1 NADH/cycle
2. Glycolysis: 2 NADH
3. Pyruvate and acetyl-CoA: 1 NADH
4. TCA: 3 NADH
5. AA oxidation to Pyruvate, Acetyl-CoA, Fumerate, alpha-ketogluterate, succenyl-CoA (AA catabolism creates NADH as electron donors for complex 1!)
69
What is another expression for the inter membrane space and the matrix relative to their charge due to the ETC?
Intermembrane space: P side
Matrix: N side
70
How many protons are pumped from the matrix to the intermembrane space at complex 1?
4H+
71
Which of the 4 complexes in the ETC is the largest? How many subunits does it have?
Complex 1.
43 subunits
72
What enzyme is complex 2? Where else is this enzyme found? What is the role of this enzyme?
Succinate dehydrogenase. TCA cycle.
Converts Succinate to Fumarate creating FADH2
73
How many proteins are pumped out at complex 2?
zero
74
What acts as a cofactor in complex 2?
FAD
75
How many protons are pumped out in complex 3?
4
76
Flow of electrons through complex 3?
QH2-->Fe-S-->Cytochrome-c
77
What is the net equation of complex 3?
QH2 + 2 cyt c (oxidized) + 2H+(n-side) --> Q + 2 cyt c (reduced) + 4H+(p-side)
78
What happens at complex 4?
electrons from cytochrome c are transfered to O2, reducing O2 to H2O
79
How many proteins are critical to electron flow in complex 4?
3
subunits 1,2,3
80
Electron transfer through complex 4 begins with what electron carrier?
cyt c
81
What is the electron flow through complex 4?
2 cytochrome c's each donate an electron to CuA. The electrons then pass through heme-a to the Fe-Cu center: heme a3 and CuB. O2 binds to heme-a3(receives 2 electrons) and 2 more electrons come in from cytochromes ---- creates 2 molecules of water
82
What is a respirasome?
functional combinations of 2 or more different electron-transfer complexes
83
What complexes forms respirasomes?
Complex 1 -- 3 -- 4
Complex 2 -- 3 -- 4
84
What is the net equation of the complex 1-3-4 respirasome?
1 NADH + 11H+(n-side) + 1/2 O2 = NAD+ + 10 H+(p-side) + H2O
85
What is the net equation of the complex 2-3-4 respirasome?
FADH2 + 6H+(n-side) + 1/2 O2 = FAD + 6H+(p-side) + H2O
86
Does NADH or FADH2 produce more electromagnetic gradient?
NADH
87
What 4 things is the electrochemical gradient of the ETC created by?
1. Active transport of protons across membrane (Complex 1,4)
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 O2 (complex 4)
88
What are the two functional units of ATP Synthase?
F0, F1
89
Where is F0 located? What is it's function?
Bound to membrane
Transports protons down the gradient & transfers energy to F1
90
Where is F1 located? What is it's function?
Matrix
Catalyzes the hydrolysis of ATP
91
How many binding sites does the F1 complex have? What subunits is each binding site made up of? Which of these binding sites does ATP bind to?
3.
No all different.
Each binding site has an alpha & beta subunit.
ATP -- Beta subunit
92
What are the 3 different types of beta confirmations with ATP that occur at the beta subunit of the F0 complex of ATPase
1. Tight: Beta-ATP
2. Loose: Beta-ADP
3. Very loose: Beta-emty
93
How does the proton motive force affect rotation of the FO subunit of ATPase?
It causes rotation of the central gamma shaft
Gamma shaft = rotational catalyst
94
How many protons does ATPase require to rotate the gamma shaft? How many does it require to phosphorylate ADP with a Pi?
3H+
1H+
95
Why is it that 2.5 ATP are made for every NADH brought to ETC?
NADH causes 10H+ to be pumped out, divided by 4 H+ needed to produce 1ATP.
96
Why is it that 1.5 ATP are made for every FADH2 brought to ETC?
FADH2 causes 6 H+ to be pumped out, divided by 4 H+ needed to produce 1 ATP.
97
What does the malate aspartate shuttle do?
It transports "reducing equivalents" from cytosolic NADH into the mitochondrial matrix
98
What 1st happens once NADH from the cytoplasm enters the intermembrane space of the mitochondria through porins?
Where does malate go once it has been formed?
What does malate do once it is inside the matrix?
What happens to the newly formed NADH in the matrix?
NADH+H(+) passes two H+'s/electrons to oxaloacetate --> malate
Malate now crosses the inner membrane via the malate-alpha-ketogluterate transporter.
Malate gives NAD+ two hydrogens --> NADH.
The new NADH goes to the ETC?
99
Because oxaloacetate can not pass through the inner membrane, what is it converted to? Which crosses the inner membrane and back into the intermembrane space via what transporter?
Oxaloacetate + glutamate = Aspartate
Glutamate-aspartate transporter
100
How is aspartate converted to oxaloacetate in the intermembrane space?
Aspartate + alpha-ketoglutarate
101
In what parts of the body is the Malate-Aspartate shuttle used?
liver, kidney, heart
102
In what parts of the body is the Glycerol 3-phosphate shuttle used?
Skeletal muscle and brain
103
What is the mechanism of the glycerol-3-phosphate shuttle?
Dihydroxyacetone phosphate accepts 2 reducing equivalents from NADH (via cytosolic G3P dehydrogenase) --> G3P.
G3P then passes its 2 reducing equivalents to mitochondrial G3P dehydrogenase in the form of FADH2.
mitochondrial G3P dehydrogenase the passes the 2 reducing equivalents in the form of FADH2 to ubiquinone which then travels through inner membrane to complex 3
104
How much ATP does glucose yeild?
30-32
105
How many ATP's does glycolysis yeild when it uses the malate-aspartate shuttle? The G3P shuttle?
5
3
106
What happens when the mass action ratio: [ATP]/[ADP][Pi] is high?
This means that ATP production is high/enough, this inhibits formation of ATP at various levels of oxidative phosphorilation
107
How fast is ATP synthesized in cells?
As fast as it is utilized
108
What protein is expressed in brown adipose tissue next to the ETC and ATPase? What is another name for this protein?
Uncoupling protein UCP1
aka. thermogenin
109
What is the function of the uncoupling protein in adipose tissue? What does this allow?
It provides a path for protons to return to the matrix bypassing ATP synthase - this net movement generates heat without any ATP outcome (the energy conserved by H+ pumping is dissipated as heat)
Allows babies (and some adults) to maintain body tempurature
110
What is steroidogenesis?
The formation of steroids
111
What group of enzymes catalyze Steroidogenesis?
Mitochondrial cytochrome P450 oxygenases
112
Steroidogenesis is dependent on what? What is the final electron acceptor? What is it reduced to?
NADH dependent
O2 = final electron acceptor
O2 is reduced to water
113
What is apoptosis?
the death of cells that occurs as a normal and controlled part of an organism's growth or development.
