Bioenergetics 1

Question 1

What are the 3 major enzymes of respiration?

Answer 1

NADH dehydrogenase, cytochrome bc1, cytochrome c oxidase. (aa3-type oxidase) Oxygen = reduced to water which generates ATP.

Question 2

In short, what is the electron transfer pathway?

Answer 2

NADH dehydrogenase -> quinone -> quinole -> cytochrome bc-1 complex -> soluble cyt c -> aa3-type oxidase -> ATP synthase

Question 3

Where does the NADH come from that nadh dehydrogenase uses?

Answer 3

TCA cycle (most of it. Rest is electrons from sugar turn NAD into NADH. only small fraction.)

Question 4

How many electrons come from one NADH molecule?

Answer 4

2 electrons

Question 5

how many proton pumps are opened up bc of electron transfer in nadh dehydrogenase?

Answer 5

4

Question 6

Is the pumping mechanism of NADH dehydr the same as cyt-bc1?

Answer 6

No . Cyt bc-1 complex is also a (free energy transducing) proton pumping enzyme but the mechanism is different.

Question 7

How much water does a half and a whole oxygen molecule give? How many electrons are needed?

Answer 7

Half O2 molecule (O) needs 2 electrons -> 1 H2O molecule.

Whole O2 molecule (2O) needs 4 electrons -> 2 H2O molecules.

Question 8

How many protons does ATPase need in order to make one ATP?

Answer 8

3, Protons make the subunits switch.

Question 9

Why do people think the ancestors of our mitochondria are prokaryotic cells?

Answer 9

Bc they have similar respiratory enzymes. Core is basically the same of those enzymes and structure-function relationships are comparable. Extended with the observation that chloroplasts and cyanobacteria have many types of similarity as well.

Question 10

What is a big difference between mitochondria in the host cell vs in the bacterium?

Answer 10

Big difference between 2 systems: mitochondria are secured in the host cells, not many environmental changes as opposed to bacteria.

Question 11

Overview of substrate level- and oxidative phosphorylation in prokaryotes?

Answer 11

Glucose -> glycolyis -> pyruvate -> citric acid cycle -> CO2.

Substrate level Phosphorylation: O2 + NADH -> NAD+ + H2O
and ATP

Oxidative phosph = more ATP

Question 12

Wat is de totale opbrengst van glycolyse -> pyruvaat?

Answer 12

omdat je 2 ATP invest en er 4 uit krijgt, is totale opbrengst 2 ATP + 2 NADH

Question 13

What enzyme oxidizes pyruvate? What is the yield?

Answer 13

Pyruvate dehydrogenase (PDH), which has NADH as cofactor. Pyruvate -> Acetyl CoA. 3 subunit enzyme. Net yield 2 pyruvate -> 2 AcetylCoA = 2NADH

Question 14

Then, citric acid cycle for further oxidation of acetyl-CoA to CO2. What is the net yield per 2 acetyl-CoA to 4 CO2?

Answer 14

2 ATP + 6 NADH + 2 FADH2

Question 15

So, total yield of Glycolysis, PDH, Citric acid cycle? (catabolism of glucose -> 6CO2)?

Answer 15

4 ATP, 10 NADH, 2DADH2

Question 16

For every 2 electrons that move in the NADH dehydr, how many protons are pumped from inside to outside?

Answer 16

4. No matter where they come from, redox free energy of electron transfer gives rise to the pumping always!!

Question 17

How many protons do 2 electrons give rise to in the cyt-bc 1 complex?

Answer 17

every 2 electrons give 2 protons.

Question 18

What is the fixed stoichiometry during transfer of 2 electrons from 1 NADH to oxygen?

Answer 18

4+2+4 = 10 protons

Question 19

As said earlier, catabolism of glucose to 6 CO2 total net yield = 10 NADH. Then how many protons is the total yield?

Answer 19

10 * 10 = 100

Question 20

Why is oxidation of 2 electrons from FADH2 different?

Answer 20

Follows a different route. Only proton pumping during complex 3 (cyt bc-1) and 4 (cyt c oxidase). Gives rise to 6 H+ . With 2NADH2 that makes 12 H+.

Question 21

So we had 10 NADH molecules which gave rise to 10 * 10 = 100 protons. However, there was also 2 FADH2. What is then the total proton movement over the membrane?

Answer 21

100 + 6protons *2 FADH2 = 112 protons

Question 22

How many ATP’s does that yield?

Answer 22

112/3 = 37,33
Net yield by oxidative phosphorylation = 37,33 ATP per 1 glucose molecule. There was also some substrate phosphorylation, yielding 4 ATP. Total net yield during catabolism of 1 molecule glucose to 6 co2 = 41,33 molecules of ATP.

Question 23

What is more efficient, mitochondrial or bacterial ATP production? Why is mitochondrial atp yield 31 ATP versus 41,33 atp?

Answer 23

Bacterial. Bc cost of uptake NADH, Pi and ADP/ATP exchange = 10,33 ATP.

Question 24

Bacteria have an adaptive response to radical formation. It will change the make-up of its respiratory network. We cant do that as we only have 3 enzymes. What quinol oxidase can they synthesize and what advantage does that give?

Answer 24

It prevents over reduction and oxidative stress. Ba3-type oxidase, receives electrons from quinol directly (NADH dehydr is skipped, gets it from succinate), which is faster.

Question 25

What does the cbb3-type oxidase do?

Answer 25

It is used to respire at low oxygen tension (very high affinity for oxygen). Km very low.

Question 26

Why is nitrate reduction ;ess efficient than aerobic reduction?

Answer 26

1) Less electrogenic enzymes available -> lower PMF
2) Shorter pathway @ electrogenic enzyme NAR: lower free energy transduction, electrons received from quinol -> lower PMF
3) Other problem: Dangerous way of living as it produces toxic intermediates: nitrite and nitric oxide (NO)

Question 27

What are signals to induce nitrate reduction pathways?

Answer 27

Low oxygen AND nitrite are signals to induce such pathways.