Introduction to Biochemistry - Quiz 3.4.5

I failed this one - it is obvious that when sugar resources are low. It is not so obvious that we can still use the citric acid cycle to do biosynthesis because the citric acid cycle itself create biosynthesis pre-cursors and there is anapleroic reactions to replenish them. However, the glyoxylate cycle is important when microorganism is invading the host. In that case, the host is depleted with the sugar and the microorganism will need the glyoxylate cycle.

To summarize, the answer is

When sugar resources are low, and
During invasion of a host

Plants make use of the glyoxylate cycle during seed germination. and cease it when they are full grown therefore plants will not be affected by inhibitors.

By upregulating isocitrate lyase enzyme to overcome the normal levels of itaconic acid, and
By degrading the itaconic acid.

They become succinate and glyoxylate, glyoxylate can combine with another acetyl group to form malate with malate synthase, the succinate will simply go through the citric acid cycle as usual.

Note that we need to give a reason that is "NOT" true. The answer is:

The inhibition of ICL also inhibits the citric acid cycle of the microorganism and helps further to eradicate the pathogen.

This is simply not true, the ICL is not used in the citric acid cycle at all.

Introduction to Biochemistry - Quiz 3.4.4

The major goal of citric acid cycle is to produce the electron donors for the oxidative phosphorylation step, which means

To produce NADH
To produce FADH2

That's what I answered for the first time and I get partial credits, so I make another trial. I was thinking about it could be the production of GTP, after all it is for the energy.

But I learn a lesson here, citric acid cycle is also used to make precursors for bio synthesis of fatty acids and amino acids.

It is Fatty acids, Amino acids and pyruvate.

The problem is that pyruvate to acetyl coenzyme A released a lot of energy and is essentially irreversible, so there is no hope there. But once it enters the cycle, we cannot escape from the fate that two carbons will be decarboxylated away through the decarboxylation. So while it is possible to get glucose out of the oxaloacetate, the glucose is not made from the acetyl coenzyme A because there is no net conversion of acetate to oxaloacetate.

Iso-citrate to alpha-ketoglutarate and alpha-ketoglutarate to succinyl-coA.
This two oxidative decarboxylation tooks the carbons away.

A single turn in the glyoxylate cycle consume one and produce two oxaloacetate molecules, so it is a net production one one oxaloacetate molecule. To produce two oxaloacetate molecules and therefore 2 PEP molecules, we need two full turns.

Bacteria upregulate the glyoxylate cycle and down regulate the citric acid cycle.

I got this all wrong :(

I thought if the bacteria is feeding on pyruvate, there is no glucose around and it must build glucose, but that was false. Pyruvate itself can be an entry point to gluconeogenesis, therefore the cell can do citric acid cycle.

Once we decided it is the citric acid cycle, the rest follows:

Down regulate glyoxylate cycle
Down regulate gluconeogenesis
Up regulate citric acid cycle
Down regulate isocitrate lyase
Down regulate malate synthase
Unregulated citrate synthase
Upregulate phosphatase of AceK

Note: AceK can be used to phosphatase (i.e. remote the phosphate group) of the isocitrate dehydrogenase, that allows the citric acid cycle to move forward.

Introduction to Biochemistry - Quiz 3.4.3

This is obvious, $ O_2 $ and FAD are not product of the citric acid cycle.

To regenerate citric acid cycle intermediates, they are often used for biosynthesis of other molecules and the citric acid cycle would stop without them replenished.

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.