BIOC405 EXAM 3 QUESTIONS AND ANSWERS WITH
COMPLETE SOLUTIONS VERIFIED
Where do each of the 5 reactions of pyruvate dehydrogenase occur (E1, 2, or 3?)
Step 1: E1
Step 2: E1 and E2
Step 3: E2
Step 4: E2 and E3
Step 5: E3
What does pyruvate dehydrogenase do?
Catalyzes the oxidative decarboxylation reaction that sets up acetyl-CoA for the citric
acid cycle. It takes two carbons from pyruvate and sticks 'em onto CoA, creating acetyl-
CoA.
What differs about the fate of pyruvate under hypoxic conditions?
Under normal conditions, pyruvate dehydrogenase takes 2 carbons from pyruvate and
gives them to acetyl-CoA to get it started in the citric acid cycle for aerobic respiration
(oxidative phosphorylation).
In hypoxic conditions (e.g., exercising muscle, cells without mitochondria, anaerobic
organisms), pyruvate instead goes through cytosolic fermentation in order to regenerate
NAD+ for glycolysis.
Where do you find pyruvate dehydrogenase?
The mitochondrial matrix (within the inner membrane)
,How does pyruvate get into the mitochondria?
The outer membrane is pretty permeable, but pyruvate must go through a membrane
transport protein called MPC to get through the mitochondria's inner membrane
What are cristae?
The folds in the inner membrane of mitochondria. They maximize the surface area of
the membrane to increase area for ATP generation.
What is the structure of mitochondria like within the cell?
Mitochondria form networks within the cell that can move, fuse, break apart, etc.
depending on what the cell needs at any given moment.
*yellow in the image is the mitochondrial network
What cells lack mitochondria?
- Cells in the lens of the eye—mitochondria would scatter light and prevent it from hitting
the retina.
- Red blood cells—mitochondria would consume the O2 that RBCs carry.
- Bacteria—they don't have membrane-bound organelles, so no mitochondria.
What is the overall reaction for pyruvate dehydrogenase?
Two carbons from pyruvate go to acetyl-CoA (remaining one expelled as CO2)
Electrons from pyruvate go to NADH
What is decarboxylation?
The removal of a carbon into CO2 as a waste product. One CO2 is expelled per
pyruvate.
,Is the pyruvate-->acetyl-CoA reaction catalyzed by pyruvate dehydrogenase
favorable or unfavorable?
Highly favorable:
ΔG° = -33.5kJ/mol
Describe the structure of pyruvate dehydrogenase
It's made up of three enzymes:
E1 (pyruvate dehydrogenase): tetramers that wrap the exterior of the core
E2 (dihydrolipamide transacetylase): icosahedral or octahedral (differs by species) core
with swinging arms of lipoyl domains connected by flexible linkers
E3 (dihydrolipamide dehydrogenase): dimers that sit in the pores of E2
What purpose do each of the cofactors serve in the pyruvate dehydrogenase
reaction?
What are the 5 cofactors that aid the pyruvate dehydrogenase reaction?
1. Thiamine pyrophosphate (TPP) (vitamin B1)
2. Lipoic acid/lipoamide
3. Coenzyme A (vitamin B5)
4. Flavin adenine dinucleotide (vitamin B2)
5. NAD+ (vitamin B3)
What are the 5 reactions of the pyruvate dehydrogenase complex?
Describe step 1 of the pyruvate dehydrogenase complex reaction
E1 (pyruvate dehydrogenase), using TPP (thiamine pyrophosphatase) as a cofactor,
decarboxylates pyruvate (breaks off COO-, which is expelled as CO2) and binds it to
TPP, creating hydroxyethyl-TPP
, Step 1 needs a cofactor because pyruvate is an α-keto acid, which, because of the way
it's set up, has nowhere for the electrons to go when the COO- group is broken off. TPP
(non-covalently) binds to E1 and acts as an electron sink, stabilizing the hydroxyethyl
intermediate.
Describe step 2 of the pyruvate dehydrogenase complex reaction.
E2 (dihydrolipamine transacetylase) transfers two carbons from pyruvate onto the
lipoamide cofactor as an acetyl group, creating acetyl-dihydrolipoamide.
E2 has a lipoic acid bound to a lysine (creating the lipoamide), which creates a flexible
swinging arm with a reactive disulfide. The swinging arm reaches out to E1 to grab the
two carbons from pyruvate (which, after step one, are bound to TPP) and attach them to
the distal sulfur via a high-energy thioester bond, creating acetyl-dihydrolipoamide.
Describe step 3 of the pyruvate dehydrogenase complex reaction.
E2 transfers the acetyl-group from acetyl-dihydrolipoamide (bound to E2) to coenzyme
A (CoA) (not bound to E2), creating acetyl-CoA. The two electrons from pyruvate
remain on dihydrolipoamide (E2)
What are the differences between FAD/FADH2 and NAD+/NADH
- FAD/FADH2 is insoluble and is only found tightly bound to proteins
- NAD+ accepts 2e- and an H+ in the form of a hydride ion (H-) in one go. FAD accepts
2H+ and 2e-, but they go to different places on the molecule sequentially.
Describe steps 4 and 5 of the pyruvate dehydrogenase complex reaction.
E3 has an active disulfide bond that pulls 2e- off dihydrolipoamide, regenerating the
lipoamide cofactor (restoring its disulfide bond)
COMPLETE SOLUTIONS VERIFIED
Where do each of the 5 reactions of pyruvate dehydrogenase occur (E1, 2, or 3?)
Step 1: E1
Step 2: E1 and E2
Step 3: E2
Step 4: E2 and E3
Step 5: E3
What does pyruvate dehydrogenase do?
Catalyzes the oxidative decarboxylation reaction that sets up acetyl-CoA for the citric
acid cycle. It takes two carbons from pyruvate and sticks 'em onto CoA, creating acetyl-
CoA.
What differs about the fate of pyruvate under hypoxic conditions?
Under normal conditions, pyruvate dehydrogenase takes 2 carbons from pyruvate and
gives them to acetyl-CoA to get it started in the citric acid cycle for aerobic respiration
(oxidative phosphorylation).
In hypoxic conditions (e.g., exercising muscle, cells without mitochondria, anaerobic
organisms), pyruvate instead goes through cytosolic fermentation in order to regenerate
NAD+ for glycolysis.
Where do you find pyruvate dehydrogenase?
The mitochondrial matrix (within the inner membrane)
,How does pyruvate get into the mitochondria?
The outer membrane is pretty permeable, but pyruvate must go through a membrane
transport protein called MPC to get through the mitochondria's inner membrane
What are cristae?
The folds in the inner membrane of mitochondria. They maximize the surface area of
the membrane to increase area for ATP generation.
What is the structure of mitochondria like within the cell?
Mitochondria form networks within the cell that can move, fuse, break apart, etc.
depending on what the cell needs at any given moment.
*yellow in the image is the mitochondrial network
What cells lack mitochondria?
- Cells in the lens of the eye—mitochondria would scatter light and prevent it from hitting
the retina.
- Red blood cells—mitochondria would consume the O2 that RBCs carry.
- Bacteria—they don't have membrane-bound organelles, so no mitochondria.
What is the overall reaction for pyruvate dehydrogenase?
Two carbons from pyruvate go to acetyl-CoA (remaining one expelled as CO2)
Electrons from pyruvate go to NADH
What is decarboxylation?
The removal of a carbon into CO2 as a waste product. One CO2 is expelled per
pyruvate.
,Is the pyruvate-->acetyl-CoA reaction catalyzed by pyruvate dehydrogenase
favorable or unfavorable?
Highly favorable:
ΔG° = -33.5kJ/mol
Describe the structure of pyruvate dehydrogenase
It's made up of three enzymes:
E1 (pyruvate dehydrogenase): tetramers that wrap the exterior of the core
E2 (dihydrolipamide transacetylase): icosahedral or octahedral (differs by species) core
with swinging arms of lipoyl domains connected by flexible linkers
E3 (dihydrolipamide dehydrogenase): dimers that sit in the pores of E2
What purpose do each of the cofactors serve in the pyruvate dehydrogenase
reaction?
What are the 5 cofactors that aid the pyruvate dehydrogenase reaction?
1. Thiamine pyrophosphate (TPP) (vitamin B1)
2. Lipoic acid/lipoamide
3. Coenzyme A (vitamin B5)
4. Flavin adenine dinucleotide (vitamin B2)
5. NAD+ (vitamin B3)
What are the 5 reactions of the pyruvate dehydrogenase complex?
Describe step 1 of the pyruvate dehydrogenase complex reaction
E1 (pyruvate dehydrogenase), using TPP (thiamine pyrophosphatase) as a cofactor,
decarboxylates pyruvate (breaks off COO-, which is expelled as CO2) and binds it to
TPP, creating hydroxyethyl-TPP
, Step 1 needs a cofactor because pyruvate is an α-keto acid, which, because of the way
it's set up, has nowhere for the electrons to go when the COO- group is broken off. TPP
(non-covalently) binds to E1 and acts as an electron sink, stabilizing the hydroxyethyl
intermediate.
Describe step 2 of the pyruvate dehydrogenase complex reaction.
E2 (dihydrolipamine transacetylase) transfers two carbons from pyruvate onto the
lipoamide cofactor as an acetyl group, creating acetyl-dihydrolipoamide.
E2 has a lipoic acid bound to a lysine (creating the lipoamide), which creates a flexible
swinging arm with a reactive disulfide. The swinging arm reaches out to E1 to grab the
two carbons from pyruvate (which, after step one, are bound to TPP) and attach them to
the distal sulfur via a high-energy thioester bond, creating acetyl-dihydrolipoamide.
Describe step 3 of the pyruvate dehydrogenase complex reaction.
E2 transfers the acetyl-group from acetyl-dihydrolipoamide (bound to E2) to coenzyme
A (CoA) (not bound to E2), creating acetyl-CoA. The two electrons from pyruvate
remain on dihydrolipoamide (E2)
What are the differences between FAD/FADH2 and NAD+/NADH
- FAD/FADH2 is insoluble and is only found tightly bound to proteins
- NAD+ accepts 2e- and an H+ in the form of a hydride ion (H-) in one go. FAD accepts
2H+ and 2e-, but they go to different places on the molecule sequentially.
Describe steps 4 and 5 of the pyruvate dehydrogenase complex reaction.
E3 has an active disulfide bond that pulls 2e- off dihydrolipoamide, regenerating the
lipoamide cofactor (restoring its disulfide bond)
