Lecture 2: energy metabolism

Question 1

For what processes is energy metabolism needed?

Answer 1

E.g. for biosynthesis, transport, movement

Question 2

What molecules in our diet are broken down and used for energy consuming processes?

Answer 2

Carbohydrates, lipids and proteins.

Question 3

What are currencies of energy? Also name two examples.

Answer 3

Energy derived from diet molecules are used for energy consuming processes and therefore need to be ‘stored’ in some way. ATP and ion motive forces across the membrane are examples of energy currencies.

Question 4

Why is ATP a currency of energy?

Answer 4

ATP is needed for storage and transport of energy. It contains 3 phosphate molecules. When ATP is hydrolysed, the bond between P2 and P3 is broken down. The release of P3 yields ADP and energy.

Question 5

What are ion or proton motive forces? And what’s the difference?

Answer 5

Ion/proton motive forces arise when there’s a ion/proton gradient. Molecules are then transported to the side of the membrane with the lowest concentration of these molecules. Since the membrane is ion tight, you need an ion channel or transporter.
Proton motive forces are used by bacteria, mitochondria and chloroplasts and ion (sodium) motive forces are used in eukaryotes.

Question 6

Can bacteria also use ion (sodium) motive forces?

Answer 6

Yes

Question 7

How is energy obtained from nutrients?

Answer 7

Through breakdown of nutrients through substrate level phosphorylation (glycolysis), citric acid cycle (TCA) and oxidative phosphorylation.

Question 8

Answer following questions about glycolysis:

1. What molecule is mainly used and what new molecule is generated?
2. What intermediary molecule is generated before pyruvate is generated?
3. How much ATP is needed and how much ATP is generated?
4. Where does glycolysis occur in a bacterial cell and where in a eukaryotic cell?

Answer 8

1. Glucose (carbohydrate) is used, pyruvate is generated
2. Glucose is split into 2 molecules of glyceraldehyde-3-phosphate
3. Demand of 2 ATP, yielding 4 ATP
4. Cytosol

Question 9

What happens in the citric acid cycle? And what enzyme is specifically important?

Answer 9

Pyruvate is metabolised into acetyl CoA with the help of the enzyme pyruvate dehydrogenase. The TCA cycle also yields NADH and GTP (needed for oxidative phosphorylation).

Question 10

Where does the citric acid cycle occur in bacteria and eukaryotes?

Answer 10

In the bacterial cytosol or the mitochronial matrix

Question 11

Why does it make sense that the TCA cycle occurs in the matrix of mitochondria?

Answer 11

In the TCA cycle NADH is generated. NADH is needed in oxidative phosphorylation that also occurs in the mitochondrium.

Question 12

For what is NADH used during oxidative phosphorylation?

Answer 12

The outer membrane of mitochondria aren’t ion tight, while the inner membrane is. NADH is used here by enzymes that are located in the inner membrane of the mitochondria during of oxidative phosphorylation.

Question 13

Explain how oxidative phosphorylation works.

Answer 13

NADH or FADH2 is used by enzymes that are located in the respiratory chain of oxidative phosphorylation. Here, a proton is transported from the inner membrane to the intermembrane space, which creates a proton motive force. Electrons are transported through the respiratory chain to generate H2O from 1/2O2. ATP synthase then uses the proton motive force to generate ATP, where a proton is transported back into the matrix.

Question 14

In general 1/2O2 is used with the help of electrons to generate H2O. Can other molecules than 1/2O2 be used to generate H2O?

Answer 14

Bacteria can also use nitrogen to from H2O.

Question 15

Why is oxidative phosphorylation more efficient, but also slower compared to glycolysis? What does this mean if there’s high or low concentration of sugar?

Answer 15

Oxidative phosphorylation yields 30 ATP, glycolysis only yields 2 ATP. But the enzymatic rate of enzymes in oxidative phosphorylation is much lower compared to glycolysis.
For a high concentration of suger glycolysis is used, since it is much quicker. For a low concentration of suger, oxidative phosphorylation is used.

Question 16

Bacteria can withstand and adapt to different conditions. This means that they can also adapt the way they produce ATP. How?

Answer 16

In conditions with low oxygen, ATP synthase can alter its function. Instead of transporting protons to the inside of the matrix, protons are transported to the outside of the matrix. This also creates a proton motive force, without the need of oxygen.

Question 17

Eukaryotes use sodium motive forces. How does this work?

Answer 17

Sodium (Na+) is transported to the outside of the cell with the use of energy derived from ATP.

Question 18

How does complex I of the respiratory chain look like and what is its function?

Answer 18

Complex I consists of two subunits, one is integrated in the membrane and the other is connected to the membrane. Its function is to oxidize NADH.

Question 19

The current treatment against tuberculosis is composed of 4 antibiotics. Name them and their target.

Answer 19

• Frontline drugs isoniazid (1) and ethambutol (2), they interfere with the cel envelope.
• Rifampin (3) inhibits RNA polymerase and thus transcription.
• Pyrazinamide (4) interferes with multiple bacterial pathways.

Question 20

Why is resistance likely for the current treatment of antibiotics?

Answer 20

Because the treatment only has a small range of targets.

Question 21

Bedaquiline (BDQ) is a promising new antibiotic. What does it do?

Answer 21

It inhibits ATP synthase.

Question 22

Why can we consider bedaquiline as a good antibiotic?

Answer 22

A good antibiotic can target bacteria that can adapt to different environments. Bedaquiline kills bacteria in different environments (low pH, low nutrients, low oxygen, replicating/dormant etc.).

Question 23

How does bedaquiline cause bacterial death (bactericidal)?

Answer 23

• ATP level decrease
• delta pH decrease
• ATP synthase-dependent uncoupling
• H+/K+ antiporter

Question 24

Just look at other targets and drug candidates that are known against M. tuberculosis.

Answer 24

Ok

Question 25

Research has been performed to investigate how important ATP is in synaptic functions like endo- and exocytosis. What two things were found when ATP was visualized in synapses?

Answer 25

1. ATP is rapidly divided between boutons (axon terminals)
2. A mutation in metabolism of neurons results in a decrease in ATP levels in the synapses.

Question 26

What is the relationship between cancer and the metabolism of cells?

Answer 26

Under normal and healthy conditions, oxidative phosphorylation is used to produce ATP. However, cancer cells often reside in hypoxic environments. Therefore they use the Warburg effect to produce ATP. Here glucose is rapidly taken up, which causes the production of lactate. So cancer cells don’t make use of oxidative phosphorylation.

Question 27

How does the warburg effect arise or what factors are responsible for enhanced glycolysis rates?

Answer 27

Tumor cells produce a special isoform of pyruvate kinase, therefore glycolysis is enhanced. (It’s possible that there’s also downregulation of oxidative phosphorylation.

Question 28

What gene is probably downregulated/mutated in cancer?

Answer 28

p53, this gene(-product) is involved in regulation of mitochondrial respiration. p53 is often mutated in cancers, which probably causes decreased oxidative phosphorylation.

Question 29

So what are three results found in mouse models that support the relationship between mutated p53 and ATP production?

Answer 29

Disrupted p53 in mice result in lower oxygen consumption and higher percentage of glycolysis. It also causes a decrease in levels of the protein SCO2.

Question 30

What’s the function of the protein SCO2?

Answer 30

SCO2 is important for assembly of complex IV (cytochrome C oxidase) in the respiratory chain. So when p53 is disrupted, SCO2 is too.