Introduction to Biochemistry - End of session 3.1, 3.2 assessment

Glucose, 2 ATP, 2 Inorganic phosphate, 2 NAD+, 2 ADP are reactants
2 Water molecule, 2 Pyruvate, 4 ATP, 2 Protons H+ and 2 NADH are products.

First, glucose is phosphorylated into Glucose-6-Phosphate
Second, Glucose-6-Phosphate is isomerized into Frutose-6-Phosphate
Third, Frutose-6-Phosphate is further phosphorylated into Frutose-1,6-Bisphosphate
Fourth, the unstable Frutose-1,6-Bisphosphate is broken down into Dihydroxylacetonephosphate and Glyeraldehyde-3-Phosphate.
Fifth, the Dihydroxylacetonephosphate is isomerized into Glyeraldehyde-3-Phosphate

A pyruvate is a ketone and a carboxylate acid, with hydrogen disassociated in physiological pH.

It is too expensive to create PEP, therefore
It would not be replenished, because few phosphate groups have a higher free energy of hydrolysis in the cell.

In glycolysis, glucose is broken down to two molecule of pyruvate. In aerobic organism, this molecule can be completely oxidized to form carbon dioxide, but without oxygen, In baker's yeast, ethanol is formed. This is necessary to regenerate NAD+ that is expended during glycolysis.

They need to be very small to squeeze through capillaries.
By eliminating their mitochondria, they do not use oxygen for oxidative phosphorylation.

Glycolysis culminates in the production of pyruvate, which is converted to lactate and exported to the bloodstream, where is enters the liver and is converted to glucose, which can be exported back into the bloodstream.

I thought it is 6-phosphogluconate, but the answer is NADPH, they are both in the pathway of removing reactive oxygen species.

I googled a bit, reactive oxygen species are really bad thing like peroxides. So glutathione is really good stuff :)

With one glucose, normally it consume 2 ATP and generate 4 ATP, with a single glyceraldehyde-3-phosphate entered the shunt and skipped 1 ATP production, it generates 3 ATP now. So the net gain in ATP is 1 ATP.

The binding of one oxygen molecule to a hemoglobin subunit increases the affinity of other subunits for oxygen. That explain why affinity increase as the binding goes.

This is just reading graph, curve A is lung and curve B is vein. The answers are 90 and 50.

Increased 2,3 BPG decreases oxygen binding, therefore
Decreased 2,3 BPG increase oxygen binding, reduce oxygen release to tissue.

At high altitude, the tissue needs more oxygen, therefore it will correspond to increased 2,3 BPG.

Therefore the first answer is Moving from Quito (~2800 meters above sea level) to New Orleans (~0 meters above sea level)

The not so obvious are the others:

If one receive oxygen therapy, one has a lot of oxygen in the blood. The tissue do not need that much, so the person would have decreased 2,3 BPG level so that the oxygen stays with hemoglobin.

If one has a chronic lung illness, one has less oxygen. The tissue needs more oxygen, the reverse happen.

If one do aerobic exercise training, one's tissue need more oxygen, the reverse happens.

Therefore the second answer is "Receiving long term oxygen therapy due to chronic lung disease, such as emphysema"

Introduction to Biochemistry - Quiz 3.2.2

In the R state, hemoglobin has a higher affinity for oxygen, while in the T state, hemoglobin has a lower affinity for oxygen.

The answers are 15 and 60, this is just reading curves. Note that the question ask for the "release" of it, so it is 100 minus the read value.

Curve A has a higher affinity, Curve B has a lower affinity.
Lung has higher affinity, vein has lower affinity.
Presence of 2,3 BPG has a lower affinity.

Therefore the answer is:

Curve A represents oxygen binding in the lung, while curve B represents oxygen binding in the veins.

The easy way to remember this is lung blows out carbon dioxide, drive the carbonic acid to disassociate, driving up the pH - and at the lungs, we have higher affinity.

The curve labeled curve A likely represents hemoglobin binding at a higher pH, and the affinity for oxygen is higher than hemoglobin's affinity for oxygen at pH 7.4.

The curve labeled curve B likely represents hemoglobin binding at a lower pH, and the affinity for oxygen is lower than hemoglobin's affinity for oxygen at pH 7.4.

• Lactic acid decrease the affinity of hemoglobin for oxygen. (Because of reduced pH)
  
• Carbon dioxide decrease the affinity of hemoglobin for oxygen (Because additional carbon dioxide drives the formation of carbonic acid, driving down pH)
  
• 2, 3 bisphosphoglycerate decrease the affinity of hemoglobin for oxygen (Because 2,3 BPG occupies the binding site with hydrogen bond and salt bridges, making T state more stable)

The behavior allows for relatively large change in oxygen delivery by relatively little change in oxygen partial pressure. That in turns make it possible to reach homeostasis faster.

Introduction to Biochemistry - Quiz 3.2.1

They lack mitochondria - mitochondria is where cellular aerobic respiration take place. Without it, a cell cannot do aerobic respiration.

It regenerates glucose from lactate generated anaerobically in red blood cells and muscle.

NADH did it, NADH is a strong electron donor.

NADPH did it.

I am always confused with this "reason" type of question. Unless someone is designing it and has a reason of doing so, there reason isn't a reason, it is just what nature did.

That's said, if we interpret the question is "What make "NADH transfer electrons to iron" a necessarily step", then it is a sensible question.

The answers are:

To regenerate NAD+ needed to drive glycolysis forward, and
To maintain hemoglobin-bound iron in its reduced (Fe2+) state.

Introduction to Biochemistry - Quiz 3.1.2

In order for ATP to be useful, it has to be that

ATP is readily synthesized from higher-energy molecule by substrate level phosphorylation, and
ATP phosphorylates many other molecules that have a lower free energy of hydrolysis.

The first is obviously, we need to be able to create ATP.
The second means it has to be high energy enough to drive many other reactions.

They are catalyzed by the same enzyme, and they share some of the same product and reactant. Note that if they share all of the same product and reactants, they are basically the same reaction, not coupled.

The first enzyme is pyruvatedecarboxylase, the next is alcohol dehydrogenase.

It is easy to remember because the first reaction is the removal of the carboxylate group from the pyruvate.

The final step of lactate fermentation. The input is pyruvate, and the output is lactate. Lactate is the reduction of the ketone group to an hydroxyl group. It is easy to remember because lactate is lactic acid, the carboxylate group stays.

To regenerate NAD+ to support continued glycolysis.

Introduction to Biochemistry - Quiz 3.1.1

During the preparatory, or energy investment phase of glycolysis, 2 ATP are hydrolyzed per molecule of glucose. During the payoff phase, 4 ATP are synthesized per molecule of glucose. The net yield is 2 ATP molecule per glucose.

The pyrurate is drawn in the question above - note that it is both a ketone and a carboxylate.

Phosphoenolpyruvate is unstable and has higher potential to transfer its phosphoryl group to ADP than 2-phosphoglycerate do.

This is a drag-n-drop question, the answers are shown above in the question.

The molecule is glucose-6-phosphate. It is formed by the action of the first enzyme in glycolysis, called hexokinase.