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Wednesday, October 18, 2017

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.


Wednesday, October 4, 2017

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:

Ferric iron
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.

Tuesday, October 3, 2017

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.

Friday, September 29, 2017

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.