Introduction to Biochemistry - Quiz 3.4.2

Glycolysis occurs in the cytosol, while the oxidative decarboxylation of pyruvate occurs in the mitochondria, and the citric acid cycle occurs in the mitochondria.

NAD+ is in E3
Coenzyme-A is in E2
Lipoate is in E2
FAD is in E3
TPP is in E1

The key is that pyruvate to acetyl-CoA is irreversible, so there is no way we can get back pyruvate or sugar.

Incorporation into fatty acids
Complete oxidation to form carbon dioxide.

This question is "tricky" - there is more than 1 unit for certain steps, it is clear in the problem but I still missed it.

Decarboxylation happens in E1, where pyruvate attaches to TPP.
Oxidation happens in E1 and E2, where the molecule linked to lipoamide with a thioester bond.
Transfer happens in E2, where the molecule is now attached to CoA instead.
Regeneration happens in E2 and E3, the lipoamide now forms the disulfide bond.

PDH is allosterically activated by its substrates and
PDH is allosterically inhibited by its product.
This is simply the Le Chatelier's principle.

The pyrudehydrogenase kinase phosphorylate PDH, so when pyrudehydrogenase is activated, the PDH is deactivated and we generate less energy.

NADH ATP and Acetyl-CoA are products of the PDH, so they should deactivate PDH.
Pyruvate is product of PDH, so it should inhibit PDH.
At low energy state, ADP accumulates, to it should inhibit PDH
Calcium does not impact PDH.

PDH is the gateway into the citric acid cycle, so it is tightly regulated.

Thioester bond cannot be stabilized by resonance structure, therefore it is less stable and has a high free energy of hydrolysis. We need to have this high free energy state to form Acetyl-CoA, which also have a thioester bond.

Introduction to Biochemistry - Quiz 3.4.1

Process 1 is glycolysis - breaking down of glucose into pyruvate.
Process 2 is fermentation - generating energy without using oxygen
Process 3 is citric acid cycle - building up a high energy reduced NADH AND FADH2.
Process 4 is oxidative phosphorylation - building ATP using the high energy reduced molecules.

Note that only the reduced form (i.e. NAD+ and FAD) are electron acceptors. NADH and FADH2 are electron donors.

Water

Introduction to Biochemistry - End of session 3.3 assessment

I failed this one, with a careless mistake. Notice the word "regenerate", therefore the answer is obviously NAD+ and ATP.

ATP synthesis is coupled to redox reactions with an ion gradient.

This is really just checking the numbers in the video, the order is as follow:

Oxygen
Nitrate
Ferric iron
Sulfate
Carbon dioxide

All of the statements above are correct, and all of them have impact. It boils down to which one is most substantial.

Here are the correct answers:

Nitrate is a major limiting nutrient for plants.
Denitrifying bacteria remove nitrate from the soil.

All we need to do is to list them in oxidation state order:

Nitrate -> Nitrite -> Nitric Oxide -> Nitrous Oxide -> Dinitrogen

Introduction to Biochemistry - Quiz 3.3.3

There is a high diversity between tissues and within tissues.

To reinforce epithelial tight junctions.

Introduction to Biochemistry - Quiz 3.3.2

ATP synthesis is coupled to redox reaction with an ion gradient. This looks remarkably similar.

The final electron acceptor is not oxygen.

The availability of electron acceptors and fuel sources in the environment are the key factors to influence population of bacteria.

• Denitrifying bateria consumed the nitrate in the soil. 
• Plants are not growing as good as it was. 
• Farmer compensates with nitrate fertilizers (Economic impact)
• These fertilizers get washed to the ocean
• Phytoplankton grows much more than it was, consuming more oxygen. 
• Fishes die because of the lack of oxygen. (Environment impact) 

Protons are pumped from the cytoplasm to the periplasm by the action of complexes I and III.
Protons are consumed in the cytoplasm during reduction steps of denitrification.

6 oxygen atoms and 12 hydrogen atoms make 6 molecules of water, this is easy :)

Introduction to Biochemistry - Quiz 3.3.1

Water - obviously, the carbon don't just go away by themselves. The product of fermentation must have some carbon in it.

NAD+ is required for glycolysis.

Acetyl-CoA is the common intermediate.