IV. Cell biology | 69. Characteristics of the metabolome of subcellular organelles; maintenance of the internal milieu of subcellular organelles

Question 1

I. Basics
1. What is Metabolome?

Answer 1

total number of metabolites present within an organ, tissue or cell

Question 2

II. Internal milieu of subcellular organelles
1. What are the 6 Internal milieu of subcellular organelles?

Answer 2

1. Lysosomes
2. Peroxisomes
3. Mitochondria
4. Endoplasmic reticulum
5. Nucleus
6. Cytosol

Question 3

II. Internal milieu of subcellular organelles
2A. What are the features of lysosomes?

Answer 3

• Have an acidic pH (= 4,7), maintained by a H+-pump (ATPase) pumping protons into the lysosome and thereby decreasing the pH
• V-type ATPases in the membrane hydrolyzes ATP to pump protons inside (keeps pH stable)
• Signal sequence of proteins: sugar with a phosphate group

Question 4

II. Internal milieu of subcellular organelles
2B. What is the signal sequence of protein of lysosomes?

Answer 4

Signal sequence of proteins: sugar with a phosphate group

Question 5

II. Internal milieu of subcellular organelles
3A What is the role of perixosomes?

Answer 5

• Used in the reduction of organic substrates, a
  process usually creating H2O2 which is eliminated
  by catalase (it is a peroxidase)
• It allows for a closed off compartment where
  reactive species can be quickly eliminated
• Performs oxidative breakdown reactions, lipid
  synthesis + metabolism, detoxification and production from oxygen radicals
  +) Beta-oxidation of very long chain FA (VLCFA)
  +) Alpha-oxidation of branched chain FA (BCFA)

Question 6

II. Internal milieu of subcellular organelles
3B. What is the structure of perixosomes?

Answer 6

Single lipid membrane. Gets most of its proteins
from selective transport from the cytosol

Question 7

II. Internal milieu of subcellular organelles
3C. What are 2 types of oxidation in Peroxisomes?

Answer 7

Performs oxidative breakdown reactions, lipid
synthesis + metabolism, detoxification and production from oxygen radicals
- Beta-oxidation of very long chain FA (VLCFA)
- Alpha-oxidation of branched chain FA (BCFA)

Question 8

II. Internal milieu of subcellular organelles
3D. What does peroxisome contain?

Answer 8

Contains enzymes and chemicals dangerous for cytoplasm
=> for the production + degradation of H2O2

Question 9

II. Internal milieu of subcellular organelles
3E. What is the signal sequence of peroxisomes?

Answer 9

(1) C-terminal tripeptide (PTS1) recognized by Pex5 (a cytosolic receptor)
(2) N-terminal nonapeptide (PTS2) recognized by Pex7/18

Question 10

II. Internal milieu of subcellular organelles
4A. Describe the structure of mitochondria?

Answer 10

• Composed a double lipid membrane
• Has 2 compartments: intermembrane space (oxidative phosphorylation) and the matrix (Krebs cycle)
• Intermembrane space contains large amount of protons, which create a
  strong electrochemical gradient between this space and the matrix => the proton gradient is maintained by complexes of the respiratory chain and the ATP synthase

Question 11

II. Internal milieu of subcellular organelles
4B. What is the primary function of the mitochondria?

Answer 11

The primary function of the mitochondria is the synthesis of energy in the form of ATP required for proper functioning of all cell organelles

Question 12

II. Internal milieu of subcellular organelles
4C. What are the translocators in mitochondria?

Answer 12

• Translocators in the outer membrane: TOM (uses ATP) and SAM (follows + integrates TM proteins)
• Translocators in the inner membrane: TIM 23 (uses ATP) and TIM 22 + OXA (folds + inserts TM proteins)

Question 13

II. Internal milieu of subcellular organelles
4D. What is Mitochondrial hsp70?

Answer 13

Mitochondrial hsp70
=> translocates protein into matrix

Question 14

II. Internal milieu of subcellular organelles
4E. What is the role of porins?

Answer 14

The outer membrane has porins, so it is the inner membrane which forms a barrier for the protein transport
- Of the approximately 1500 mitochondrial proteins, only 10 are synthesized in the mitochondria
- Mitochondrial proteins will stay there once translocated inside. If there is a leak in the mitochondrial membrane, it can be a sign of apoptosis

Question 15

II. Internal milieu of subcellular organelles
4F. What is the signal sequence of mitochondria?

Answer 15

amphipathic alpha-helix

Question 16

II. Internal milieu of subcellular organelles
5A. What are the features of ER

Answer 16

• Main site of Ca2+-storage => is regulated by various transport such as the IP3- transporter which opens in response to binding IP3 (gated ion channel), or by ACTIVE
  transport
• It also need to have its own pool of reductive intermediates, because the ER is less
  reductive than the cytosol. This allows the formation of certain peptide tertiary structures that would not be able to form in the cytosol (disulfide bonds), or in biotransformation reactions which also require NADPH
• Translocators pull nascent proteins inside, such as the sec61, after it is bound to the SRP-receptor

Question 17

II. Internal milieu of subcellular organelles
5B. Why does ER need to have its own pool of reductive intermediates?

Answer 17

It also need to have its own pool of reductive intermediates, because the ER is less
reductive than the cytosol. This allows the formation of certain peptide tertiary structures that would not be able to form in the cytosol (disulfide bonds), or in biotransformation reactions which also require NADPH

Question 18

II. Internal milieu of subcellular organelles
6. What are the features of nucleus?

Answer 18

• The nuclear pore complex in the double membrane of the nucleus is responsible for
  all the transportations into and out of the cell
• It allows free diffusion of ions, water and small molecules
• Bigger molecules require an NLS signal to be transported by an importin/exportin
  and Ran-GDP/GTP

Question 19

II. Internal milieu of subcellular organelles
7A. What are the features of cytosol?

Answer 19

• Is a reductive environment, which is mainly regulated by special reducing enzymes
• These regulate the redox balance in the cytosol by keeping reactive oxygen species (ROS) at very low levels

Question 20

II. Internal milieu of subcellular organelles
7B. What is the role of glutathione in cytosol?

Answer 20

One of the enzyme is called glutathione, which is important in minimizing oxidative stress and maintaining the reducing environment of the cytosol. The balance between these two molecules appears to be key for the cytosolic redox homeostasis

Question 21

II. Internal milieu of subcellular organelles
7C. Why does the cytosol need to be reductive?

Answer 21

• The cytosol needs to be reductive in order to create a good redox gradient between the cytosol and mitochondrion.
• Since the mitochondrion is oxidative (it uses C to create CO2 in the citric acid cycle), the cytosol needs to be reductive, in order to provide the reduced cofactors for the respiratory chain which aids maintenance of the proton-gradient in the mitochondria, and thereby allows ATP synthesis to occur

Question 22

II. Internal milieu of subcellular organelles
8. What are oxidation and reduction?

Answer 22

• Oxidation = gain oxygen / loss of hydrogen
• Reduction = loss of oxygen / gain of hydrogen