BIOCHEM: Control exam 2 tasks

I have no idea if these are correct, but i hope if it isn't, someone would be kind enough to correct it for me. thnxz ^^

1. explain why the velocity of TCA cycle is elevated in hard muscle work. Write the chemical equations of the reactions, rate which is increased in this situation. What is the mechanism of this phenomenon?

The velocity of TCA cycle is elevated in hardwork of muscle due to the decrease in ATP/ADP radical ratio that regulates the allosteric inhibition of isocitrate dehydrogenase. This increases the velocity that the 3rd reaction [the slowest] would move. As a consequence, NAD's convertion into NADH2 would increase and the NADH2 would then be used in the oxidative phosphorylation process and be converted to free protons in the mitochondrial matrix. The protons would then be taken in by ATP synthase into the inner mitochondrial membrane and changes ADP into ATP.

*draw isocitrate --> ketoglutarate
*draw atp synthase

2. oxygen does not take part in TCA cycle immediately, but the cycle is known to be aerobic. Explain why it is inhibited in the absence of oxygen.

acetyl CoA + 3 NAD + FAD + ADP + HPO₄^-2 ---------------> 2 CO₂ + CoA + 3 NADH⁺ + FADH⁺ + ATP

as shown, it doesn't require oxygen. Thus, the answer does not lie within the TCA cycle itself. The TCA cycle has kinetic association with the respiratory chain. The produced NADH and FADH would require to enter the oxydative phosphorylation chain. There it requires oxygen.

Within complex IV of the respiratory chain, also known as cytochrome C oxidase, protons are transfered by cytochrome C into the enzyme and is received by copper.
1st.
2nd.
route of electrons are cyt c --> Cu A --> Fe[heme a] --> Fe[heme a3] --> Cu B --> O2 molecule --> H2O

3. In an experiment, Acetyl CoA was added to a homogenate containing all enzymes of the TCA cycle and the mitochondrial respiratory chain. What will be the measurement of quantitative content of oxaloacetate and acetyl CoA demonstrate before and after the incubation?
a) did the increase in level of oxaloacetate occur?
YES.
b) did the content of acetyl CoA change? what metabolic transformations of acetyl CoA proceed in the TCA cycle?
Yes. Acetyl CoA broke into Acetate part and joined with the oxaloacetate of TCA cycle to for citrate with catalysation of enzyme citrate synthase.

4. A patient's low energy state was developed after his severe disease. A doctor recoommended to the patient to use B group vitamins. Explain the reason for this recommendation.
5. A disorder of the process of oxidative phosphorylation is possible in deficiency of B group vitamins. Explain the mechanism of this disorder. Write the overal equation of the pyruvate oxidative phosphorylation. Fill the table:

Vit B is important here due to its constituents vit B1 thymine, Vit B2 aka riboflavin,Vit B3 aka niacin and Vit B5 aka pantothenic acid being the precursors of the TPP,FAD, NAD and CoA respectively. The inability to produce these coenzymes will cause a distruption in the whole chain of processes.

TPP – is the 1^st enzyme of the pyruvate DH complex. The lack of it would result inability to form acetyl-CoA.

FAD – is important for the change of succinate into fumarate by enzyme succinyl dehydrogenase.

NAD- is an important coenzyme that transports protons from TCA cycle to the respiratory chain.

CoA- is very important indeed for the binding of acetyl during the pyruvate à Acetyl CoA process. Furthermore, it plays a significantly important role in the binding to succinyl CoA.

FMN- in addition, vit B2 also is the precursor of FMN which is a main prosthetic group of NAD DH of complex 1 ETC.

Thus, this makes Vitamin B deficiency one factor of low energy state and also register it as a very important attribute of our body metabolism.s.

6. In an experiment, the respiration of an isoated mitochondria was registered. Malate was used as the substrate oxidized. Can a mitochondria oxidise malate if:
a) rotenone is added into the incubation medium?
oxidation of malate will slow down because the proton acceptor that removes H+ from malate will be unable to recycle itself. The usage of rotenone would block the activity of NAD DH enzyme of the ETC. Thus, NADH is unable to be oxidised back to NAD. The accumulation of NADH2 will increase the [NADH2]/[NAD] ratio. Which then regulates the cycle by allosteric inhibition of DH.

b) succinate is added together with rotenone?
no idea

7. How can cell energy potential influence the TCA cycle rate? Describe the experimental data to prove your conclusion. Write the TCA cycle reaactions regulated by the cell energy potential.
Energy potential means [ADP]/[ATP] ratio.
[ADP]/[ATP] ratio inhibits DH allosterically. Thus reduces rates of malonate DH, isocitrate DH, and alpha keto glutarate DH.
*draw the reactions that the DH enzymes catalyses.

8. Succinate was used as a substrate in experiment of skeletal muscle tissue respiration in vitro. The addition of malonate into the incubation medium stopped oxygen consumption and one of the TCA cycle intermediate was accumulated as a result of that addition.
Answer the questions :
a) what is the reason for respiration stopping?
Due to succinate being used in the experiment. It points out to us that complex 2 aka succinate DH is the main proton acceptor enzyme here. Thus,when malonate inhibits complex 2. There is no transfer of protons and electrons. Thus, respiration stops.
b) is it possible to remove the inhibition induced by malonate? Inhibition by malonate is possible to be reversible by adding alot of succinate.
c) if your answer is "yes", describe the pathway of the malate inhibition removal.
???

9. The action of antimycine A and rotenone on the experimental animals was researched. It was demonstrated that both these substances are very toxic for animals. Using the application sites of antimycine A nad rotenone in the ETC enzymes,explain:
a) what are the reasons for their toxicity
that they are both inhibitors of ETC. rotenone is for 1st complex, amyticine is for 3rd complex.
b) which of these substances is more toxic? prove it.
antimycine is more toxic due to its restriction of a more vital pathway. which will result the P:O level depleting to 1. Rotenone is also dangerous and will restrict the oxidation of NADH. But complex 2 is able to cover up better for it. It would have a P:O of 2. Antimycine restriction can be lightened by VitC oxidation at complex 4. producing P/O : 1.

10. in normal state, the value of body temperateure is higher than the temperature of the enviroment (36.6C against 20C). Explain what the temperature difference is due to. What is the role of mitochondria in this phenomenon.

Homeostasis. In this phenomenon, mitochondria goes into respiratory oxidation instead of phosphorylative oxidation. Instead of ATP being produced, the protons will diffuse back into matrix, and result in enery in terms of heat being produced instead of storage of energy into ATP.

11. The use of 2,4-dinitrolphenol for treatment of obesity for a long time lead to some negative results such as muscle weakness, body temperature increased, sometimes even lethal outcome took placed.
a) what application of 2,4-dinitrophenol was based on?
2,4-dinitrophenol is lipid soluble and worked to translocated protons on higher side of conc. gradient to the lower. This application in the mitochondria is that it translocates protons from the intermembrane space to the matrix where it originally came from. This would reduce the high electrochemical potential at a quick rate. Thus, allowing the oxidation of fatty acids in the TCA to occur very fast due to the lesser energy needed to translocate protons past the inner mitochondrial membrane.

b) what are the reasons for the side effect of 2,4-dinitrophenol?
As a result 2,4-dinitrophenol, respiratory oxidation occuring and generates heat, ATP synthethase does not work and result in weakness due to lack of ATP.

12. alpha ketoglutarate was used as a substrate oxidized in the experiment with mitochonria isolated from the animal. Oxigen and inorganic phosphate consumption were measured. these data were used for the calculation of P:O ratio values. Create a scheme of proton and electron transport along the ETC frm alpha ketogluatrate to oxigen and predict the max. thoretical value of P:O ratio.
max P:O is 3. coz NADH is the product.
*draw the TCA with ETC?

13. if the conc of ADP in cell increases the rate of TCA cycle wil increase too quite fast. The elevation of the activity of the enzyme leads to acceleration of the cycle as a whole? what is the mech of activating effects of ADP excess.
the [ADP]/[ATP] ratio allosterically binds and moves the TCA cycle by isocitrate DH. Higher more ADP faster the cycle will proceed.

14. Increase in ATP and NADH concentration is known to lead to a decrease in TCA cycle velocity. Which TCA enzymes activity depends on ATP and NADH2 concentration?
The oxidoreductases : dehydrogenases.
What is the mechanism of ATP and NADH2 inhibitory action?
allosteric binding to the DHs.

15. when isolated mitochondria are used for studying oxidative phosphorylation, the entire cytochrome C is added to into the incubation medium containing a buffer solution, oxidised substrate, ADP and inorganic phosphate. Explian why cytochrome is needed for this reaction and why can it be taken from any source?
Cytochrome C can be taken from any source due to its solubility. It is water soluble and can be found not only within the mitochondria's inter membrane space but also within the cytoplasm. Cytochrome C functions to transport only 1 electron from the 3rd complex of ETC to the 4th complex where it will accumulate and once there is 4 electrons available, it will bind with 1 molecule of oxygen to form water.

16. suppose mitochondria can oxidize succinate in the presence of rotenone? Explain your assumption.
rotenone is inhibitor of 1st complex. 2nd complex isnt influenced. but P:o lvl drops to 2.

17. newborn children and dormant animals have got this peculiar adipose tissue - brown adipose tissue, located on their neck and back. Adults haven't got this tissue. this tissue contains alot of mitochondria, that is why its brwon coloured. P/O ratio in brown adipose tissue is less than 1. What is the physiological significance of brown adipose tissu?
--- too lazy to find now.

18. A patient consulted a doctor because of his weigh loss, subfebrile temperature and high irritability. The patient was found to have thyroid gland hyperfunction. Expain the reasons for observed symptoms.
thyroid gland produces thryrosin which is a uncoupler. General uncoupler action results in the increase of TCA cycle velocity with no ATP synthesis but high oxidative respiration which results high body temperatures.

19. most substrates in body are oxidized by NAD-dependant DH. the exception is succinate DH. This enzyme contain FAD as the proton and electron acceptor. Guess wh FAD is more convenient acceptor than NAD for succinate, when redox potential for NADH2/NAD+ = -0.32V, FADH2/FAD+ = +0.05V and for fumarate/succinate = +0.03

As we know, the respiratory chain proceeds due to increasing redox potential.
It begins from a -0.32V at NADH oxidation and ends at +0.82V at reduction of oxygen to water.
Thus, the electron transfer goes from:

succinate[+0.03] ----> FAD[+0.05]--->finally oxigen at[+0.82] THIS IS CORRECT.



succinate[+0.03]----->NAD[-0.32]------> finally oxygen at [+0.82] THIS IS NOT POSSIBLE.



20. A woman suffered from sleeplessness. The doctor prescribed her a sopofic drug - aminobarbital. The woman had taken the drug for a long time. As a result, she suffered from fatigue and acute muscular weakness. Can you explain the reasons and mechanisms for the complications?
aminobarbital is a inhibitor for the 1st complex NADH DH. The weakness as a result of this drug is due to insufficient ATP which is inable to be generated without the 1st complex of the ETC.

21. a man had been rescued from a burning house. He wasn't burned and didnt get any injuries, but was in an unconsious state. Due to resuscitation, the patient's life was saved. What is the reason for the severe condition of the saved man? what action was taken by the doctor?
He suffered from CO intoxication. It inhibits the 3rd complex of the respiratory chain, resulting a P:O = 1 situation.
The doctor could then increase the administration of oxygen to win back the haemoglobins that is competitively inhibited by CO.