SMV EXPERIMENTAL CELL BIOLOGY I
The basics of cell biology
Cell biology
Cells are the basic unit of life. They come in different shapes and sizes, but they all share
common properties: membrane-enclosed unit of life, metabolism, growth and division, and
response to environmental signals, internal and external communication.
Typical questions asked in cell biology are:
- What happens in-/outside a cell?
- Which factors are involved?
- Why does it happen? (which cause/consequence)
- Where does it happen in the cell?
- Can we modify/manipulate cellular processes?
Basic features of the cell
All cells contain DNA, proteins and metabolites (molecules produced or altered by the cell).
The interplay between these factors are very important.
We have two main types of cells:
- Prokaryotic cell: typically they are small, single cells and no membrane enclosed sub
compartments. They are also biochemically flexible.
- Eukaryotic cell: larger cells, many multicellular and they have membrane enclosed
compartments: nucleus, endoplasmic reticulum, golgi, mitochondria, lysosomes,
transport vesicles and some have chloroplasts.
Nucleus: DNA synthesis, transcription, RNA synthesis. Surrounded by phospholipid
membranes, they have nuclear pores which make exchange/transport possible.
Nucleolus: ribosome/RNA synthesis, but also is involved in protein quality control.
ER: protein modification and transport. Is also closely connected to protein synthesis, the
first station for secreted proteins. A new found addition: mitochondrial fission is initiated by
the ER, so it helps the division of the mitochondria.
Golgi: membrane system, further modifies proteins, in particular glycosylation and sorts and
transports proteins in transport vesicles where they should be directed to. Has a cis- and
trans- side.
Mitochondria: energy metabolism and fatty acid oxidation. Produces ATP and the citric acid
cycle happens here, the key cycle of metabolism.
Lysosome: small organelle, hydrolytic enzymes for mainly degradation processes, but also
for signalling and secretion. Involved in a very important process called autophagy, which
means degradation of larger parts of the cell.
Transport vesicles: transport between compartments, crucial for distribution of material and
information. Key transport means in eukaryotic cells and are closely related to the ER/Golgi.
They are directed to cells with specific proteins.
Cytoskeleton: much more dynamic than we thought. Involved in structuring the cells, cell
movement and transport within the cell. Components: microtubuli, keratin and actin.
,Chloroplasts: only in photosynthetic organisms. They capture energy from sunlight and
produce ATP.
Cytosol: water-based gel, is very crowded. Concentration of metabolites is higher if the
volume is smaller, which means metabolism is also higher.
,Energy metabolism
Cells need energy for activities, for example biosynthesis, transport and for movement.
Energy has to be provided by breakdown of molecules in the diet: carbohydrates, lipids and
proteins. The cells have to link the energy consuming processes to the energy sources. This
is done by the following energy currencies:
- ATP: a small molecule with three phosphate groups. The release of the third Pi group
yields ADP and energy. It is used for endergonic reactions.
- Ion motive forces: ion gradients across biomembranes. These can also drive
endergonic reactions. The two most popular ion motive forces are proton motor force
(bacteria, mitochondria, chloroplasts) and sodium motive force (plasma membranes
in eukaryotes).
Energy from nutrients
Energy from nutrients can be converted into ATP or ion motor force via these pathways:
- Glycolysis: glucose is broken down into pyruvate. Pyruvate will now be converted into
Acetyl CoA. A critical feature is that you need to invest 2 ATP to get this pathway
started, and eventually it will yield 4 ATP. Netto ATP is 2. This pathway happens in
the cytosol of the cells and also yields NADH, which can later be used as a substrate
in oxidative phosphorylation.
- Citric acid cycle (TCA cycle): acetyl CoA will enter this central metabolic cycle. Yields
1 GTP (equivalent to ATP), NADH and FADH2 (both substrates to oxidative
phosphorylation). Located in the cytosol and mitochondrial matrix.
- Oxidative phosphorylation: happens in the matrix of mitochondria, the inner
membrane is ionized the outer membrane is not. NADH is used by enzymes of the
respiratory chain. In this chain protons are transported across the inner membrane by
enzyme complexes I-IV, which builds proton motor force. Electrons are transported
across the chain which gives the energy to transport the protons and makes water at
the end of the chain. The energy of the proton motive force can be used by ATP
synthase to make ATP. This chain is very efficient, yields way more ATP, but is
slower than glycolysis because the enzymatic rates are low. The rates can fluctuate
(if there is a lot of sugar around etc). In some organisms ATP synthase can be
reversed and can create proton motive force, for example in a low oxygen
environment.
, The sodium motor force is mainly used in eukaryotic cells. Sodium needs to be pumped out
of the cell to establish sodium motor force, this can be done by using the energy of ATP.
Biomedical impact metabolism
- Drugs acting on ATP production as promising antibiotics against tuberculosis.
- Glucose uptake, metabolism as target for drugs against sleeping sickness.
- Energy metabolism as important feature in diabetes.
- Respiratory chain in cancer.
- Role of ATP levels in synapse?
- Central role in apoptosis/aging?
ATP production as a drug target. This strategy works very nicely to combat bacteria in
tuberculosis, which is caused by Mycobacterium tuberculosis. Tuberculosis is treated with a
cocktail of at least 4 antibiotics. If the target range is small, resistance is likely. So we need
to develop new antibiotics with new targets and reduce the duration of the treatment.
Newly found BDQ prevents growth of mycobacterium tuberculosis. The mechanism of action
has to do with ATP synthase. It inhibits ATP synthase in a dose response related way. Drug
combination with other antibiotics is important. There is still ongoing research for synergy
with several other antibiotics, they enhance each other effects. BDQ also kills bacteria in
different environments, how does it do this and how does it kill? The mechanism of how
most antibiotics kill is not exactly clear.
Other parts of the respiratory chain can be used as targets for antibiotica. Mycobacteria have
more compounds in their chain than humans. This strategy works very nicely against
tuberculosis, but also works in other pathogenic bacteria.
Role of ATP levels in synapse, are the mitochondria critical for synapse energy
requirements? And which mechanisms are more ATP dependent? We found that ATP is
rapidly dispersed between different boutons. Also that neurons with energy metabolism
mutation have lower synaptic ATP levels which inhibits synaptic vesicle cycling.
Mitochondria and cancer
Oxidative phosphorylation is used for ATP synthesis, but many cell types are dependent on
glycolysis for ATP production, This can often be cancer cells because they exist in a hypoxic
environment (Warburg effect). Glycolysis can work better in cancer cells due to isoform of
pyruvate or downregulation of oxidative phosphorylation, due to relation between p53 and
mitochondrial respiration. p53 is responsible for the DNA remaining intact. Disrupted p53 in
mice cause:
- Lower oxygen consumption and a higher percentage of glycolysis.
- Decreased levels of SCO2, which mimics the disruption of p53. However,
overproduction of SOC2 does rescue oxygen consumption. SCO2 is a key protein for
biosynthesis of cytochrome oxidase.
The basics of cell biology
Cell biology
Cells are the basic unit of life. They come in different shapes and sizes, but they all share
common properties: membrane-enclosed unit of life, metabolism, growth and division, and
response to environmental signals, internal and external communication.
Typical questions asked in cell biology are:
- What happens in-/outside a cell?
- Which factors are involved?
- Why does it happen? (which cause/consequence)
- Where does it happen in the cell?
- Can we modify/manipulate cellular processes?
Basic features of the cell
All cells contain DNA, proteins and metabolites (molecules produced or altered by the cell).
The interplay between these factors are very important.
We have two main types of cells:
- Prokaryotic cell: typically they are small, single cells and no membrane enclosed sub
compartments. They are also biochemically flexible.
- Eukaryotic cell: larger cells, many multicellular and they have membrane enclosed
compartments: nucleus, endoplasmic reticulum, golgi, mitochondria, lysosomes,
transport vesicles and some have chloroplasts.
Nucleus: DNA synthesis, transcription, RNA synthesis. Surrounded by phospholipid
membranes, they have nuclear pores which make exchange/transport possible.
Nucleolus: ribosome/RNA synthesis, but also is involved in protein quality control.
ER: protein modification and transport. Is also closely connected to protein synthesis, the
first station for secreted proteins. A new found addition: mitochondrial fission is initiated by
the ER, so it helps the division of the mitochondria.
Golgi: membrane system, further modifies proteins, in particular glycosylation and sorts and
transports proteins in transport vesicles where they should be directed to. Has a cis- and
trans- side.
Mitochondria: energy metabolism and fatty acid oxidation. Produces ATP and the citric acid
cycle happens here, the key cycle of metabolism.
Lysosome: small organelle, hydrolytic enzymes for mainly degradation processes, but also
for signalling and secretion. Involved in a very important process called autophagy, which
means degradation of larger parts of the cell.
Transport vesicles: transport between compartments, crucial for distribution of material and
information. Key transport means in eukaryotic cells and are closely related to the ER/Golgi.
They are directed to cells with specific proteins.
Cytoskeleton: much more dynamic than we thought. Involved in structuring the cells, cell
movement and transport within the cell. Components: microtubuli, keratin and actin.
,Chloroplasts: only in photosynthetic organisms. They capture energy from sunlight and
produce ATP.
Cytosol: water-based gel, is very crowded. Concentration of metabolites is higher if the
volume is smaller, which means metabolism is also higher.
,Energy metabolism
Cells need energy for activities, for example biosynthesis, transport and for movement.
Energy has to be provided by breakdown of molecules in the diet: carbohydrates, lipids and
proteins. The cells have to link the energy consuming processes to the energy sources. This
is done by the following energy currencies:
- ATP: a small molecule with three phosphate groups. The release of the third Pi group
yields ADP and energy. It is used for endergonic reactions.
- Ion motive forces: ion gradients across biomembranes. These can also drive
endergonic reactions. The two most popular ion motive forces are proton motor force
(bacteria, mitochondria, chloroplasts) and sodium motive force (plasma membranes
in eukaryotes).
Energy from nutrients
Energy from nutrients can be converted into ATP or ion motor force via these pathways:
- Glycolysis: glucose is broken down into pyruvate. Pyruvate will now be converted into
Acetyl CoA. A critical feature is that you need to invest 2 ATP to get this pathway
started, and eventually it will yield 4 ATP. Netto ATP is 2. This pathway happens in
the cytosol of the cells and also yields NADH, which can later be used as a substrate
in oxidative phosphorylation.
- Citric acid cycle (TCA cycle): acetyl CoA will enter this central metabolic cycle. Yields
1 GTP (equivalent to ATP), NADH and FADH2 (both substrates to oxidative
phosphorylation). Located in the cytosol and mitochondrial matrix.
- Oxidative phosphorylation: happens in the matrix of mitochondria, the inner
membrane is ionized the outer membrane is not. NADH is used by enzymes of the
respiratory chain. In this chain protons are transported across the inner membrane by
enzyme complexes I-IV, which builds proton motor force. Electrons are transported
across the chain which gives the energy to transport the protons and makes water at
the end of the chain. The energy of the proton motive force can be used by ATP
synthase to make ATP. This chain is very efficient, yields way more ATP, but is
slower than glycolysis because the enzymatic rates are low. The rates can fluctuate
(if there is a lot of sugar around etc). In some organisms ATP synthase can be
reversed and can create proton motive force, for example in a low oxygen
environment.
, The sodium motor force is mainly used in eukaryotic cells. Sodium needs to be pumped out
of the cell to establish sodium motor force, this can be done by using the energy of ATP.
Biomedical impact metabolism
- Drugs acting on ATP production as promising antibiotics against tuberculosis.
- Glucose uptake, metabolism as target for drugs against sleeping sickness.
- Energy metabolism as important feature in diabetes.
- Respiratory chain in cancer.
- Role of ATP levels in synapse?
- Central role in apoptosis/aging?
ATP production as a drug target. This strategy works very nicely to combat bacteria in
tuberculosis, which is caused by Mycobacterium tuberculosis. Tuberculosis is treated with a
cocktail of at least 4 antibiotics. If the target range is small, resistance is likely. So we need
to develop new antibiotics with new targets and reduce the duration of the treatment.
Newly found BDQ prevents growth of mycobacterium tuberculosis. The mechanism of action
has to do with ATP synthase. It inhibits ATP synthase in a dose response related way. Drug
combination with other antibiotics is important. There is still ongoing research for synergy
with several other antibiotics, they enhance each other effects. BDQ also kills bacteria in
different environments, how does it do this and how does it kill? The mechanism of how
most antibiotics kill is not exactly clear.
Other parts of the respiratory chain can be used as targets for antibiotica. Mycobacteria have
more compounds in their chain than humans. This strategy works very nicely against
tuberculosis, but also works in other pathogenic bacteria.
Role of ATP levels in synapse, are the mitochondria critical for synapse energy
requirements? And which mechanisms are more ATP dependent? We found that ATP is
rapidly dispersed between different boutons. Also that neurons with energy metabolism
mutation have lower synaptic ATP levels which inhibits synaptic vesicle cycling.
Mitochondria and cancer
Oxidative phosphorylation is used for ATP synthesis, but many cell types are dependent on
glycolysis for ATP production, This can often be cancer cells because they exist in a hypoxic
environment (Warburg effect). Glycolysis can work better in cancer cells due to isoform of
pyruvate or downregulation of oxidative phosphorylation, due to relation between p53 and
mitochondrial respiration. p53 is responsible for the DNA remaining intact. Disrupted p53 in
mice cause:
- Lower oxygen consumption and a higher percentage of glycolysis.
- Decreased levels of SCO2, which mimics the disruption of p53. However,
overproduction of SOC2 does rescue oxygen consumption. SCO2 is a key protein for
biosynthesis of cytochrome oxidase.
