12 LC Concepts in Molecular Biology 24.10.2022
CELL COMPARTMENTALIZATION AND PHASE SEPARATION
How is the densely packed cellular
space organized to enable control over
complex biochemical reactions in space
and time?
In cells we do have compartments,
such as the largest one: ER the
endoplasmic reticulum, a classic form
of membrane bound organelle which is
fully formed by a bilayer membrane.
ER has different compartments and we
infer these differences because these
compartments have different shapes:
- Smooth ER
- Rough ER, with ribosomes.
- Nucleus and ER are treated as different entities, yet the nucleus that is the vessel for protecting and
transmitting the genome is nothing but actually and extension of the ER.
What are the functions of the ER?
In the ER there is translation going on, as ribosomes are bound to the membrane and they insert
transmembrane proteins into the ER membrane that can go to the er or to other membranes, and it also es
the power house for lipids synthesis (vast majority of lipids are made in the er by specialized proteins
residing in the er); other function is genome protection, duplication and transition. so basically
everything that happens to the nucleus, that we associate with nucleus function, the dogma of molecular
biology from dna via rna to protein, is happening in the nucleus and this is also a compartmentalized
function that the ER is supporting.
In order to create such a complicated structure, the cell has to accomplish many different task, from
creating the material, keeping it in shape (there are proteins responsible for it), and for. ex. if you want to
pass the membrane (after creating compartments separated by membranes) you need channels. The main
transport channels in the ER are the traslocon, the channel to which ribosomes attach and inject newly
synthesized transmembrane proteins, and the other major and biggest channel in the cell is the nuclear
pore complex, which creates the gate between the cytoplasm and the nucleoplasm allowing bidirectional
transport of macromolecules.
That’s how we have classicly thought about compartments and how compartments can give rise to
different functions. This is one example, there are others such as golgi and mitochondria.
Now there is a new type of thinking about compartmentalization that is focused on membrane-less
compartments so compartments that don’t have classically a double bilayer membrane and use
different mechanisms to diversify and specialize biochemistry.
Will be discussed with the following goals:
, 12 LC Concepts in Molecular Biology 24.10.2022
Liquid phase behaviors of droplet condensates
We can see here that if you look at the nucleus, the outside structures P granules attached to the aoutter
side of the nucleus exhibit a very peculiar behavior like droplets that are stretched out, collapse, and go to
the surface of the nucleus. These organelles which don’t have a membrane, there was none known, they
have sort of a honey like behavior as they are put under force.
An other example is shown in nucleoli, the site of ribosome biogenesis, and spherical nucleoli from
Xenopus laevis, frog, they can actually coalesce and fuse into a larger sphere. the nucleoli does not have
a membrane too and exhibits this liquid-like behavior from initially 2 spherical shape, sphericity is lost
when the two interact, and then they expand back into a spherical shape that has increased volume.
An other example, where we don’t really know what it is composed of, in a more advanced stage of phase
separation and even induced experimentally there are liquid-like structures developed , that have the
ability to fuse and also form spherical compartments. (in drosophila oocyte).
These processes of phase-separation as it is called is chemical at different scales. And when you deal with
this there are different words for the same thing: some talk about condensates, others coacervates, we will
call the whole process liquid-liquid phase separation or LLPS, and the droplets will be called condensates,
because there is a condensation process that leads to their emergence.
Liquidity or liquid-like behavior can be studied with fluorescence after photobleaching FRAT, for ex here
when you have a liquid droplet or condensate, after photobleaching in in the middle over time there is a
certain recovery of molecules into the droplets. This can occur either from the outside ( the replacement of
molecules from the outside) or simply by reorganization in the inside of such a condensate.
molecules within a liquid phase exhibit dynamic reorganization
(picture following)
CELL COMPARTMENTALIZATION AND PHASE SEPARATION
How is the densely packed cellular
space organized to enable control over
complex biochemical reactions in space
and time?
In cells we do have compartments,
such as the largest one: ER the
endoplasmic reticulum, a classic form
of membrane bound organelle which is
fully formed by a bilayer membrane.
ER has different compartments and we
infer these differences because these
compartments have different shapes:
- Smooth ER
- Rough ER, with ribosomes.
- Nucleus and ER are treated as different entities, yet the nucleus that is the vessel for protecting and
transmitting the genome is nothing but actually and extension of the ER.
What are the functions of the ER?
In the ER there is translation going on, as ribosomes are bound to the membrane and they insert
transmembrane proteins into the ER membrane that can go to the er or to other membranes, and it also es
the power house for lipids synthesis (vast majority of lipids are made in the er by specialized proteins
residing in the er); other function is genome protection, duplication and transition. so basically
everything that happens to the nucleus, that we associate with nucleus function, the dogma of molecular
biology from dna via rna to protein, is happening in the nucleus and this is also a compartmentalized
function that the ER is supporting.
In order to create such a complicated structure, the cell has to accomplish many different task, from
creating the material, keeping it in shape (there are proteins responsible for it), and for. ex. if you want to
pass the membrane (after creating compartments separated by membranes) you need channels. The main
transport channels in the ER are the traslocon, the channel to which ribosomes attach and inject newly
synthesized transmembrane proteins, and the other major and biggest channel in the cell is the nuclear
pore complex, which creates the gate between the cytoplasm and the nucleoplasm allowing bidirectional
transport of macromolecules.
That’s how we have classicly thought about compartments and how compartments can give rise to
different functions. This is one example, there are others such as golgi and mitochondria.
Now there is a new type of thinking about compartmentalization that is focused on membrane-less
compartments so compartments that don’t have classically a double bilayer membrane and use
different mechanisms to diversify and specialize biochemistry.
Will be discussed with the following goals:
, 12 LC Concepts in Molecular Biology 24.10.2022
Liquid phase behaviors of droplet condensates
We can see here that if you look at the nucleus, the outside structures P granules attached to the aoutter
side of the nucleus exhibit a very peculiar behavior like droplets that are stretched out, collapse, and go to
the surface of the nucleus. These organelles which don’t have a membrane, there was none known, they
have sort of a honey like behavior as they are put under force.
An other example is shown in nucleoli, the site of ribosome biogenesis, and spherical nucleoli from
Xenopus laevis, frog, they can actually coalesce and fuse into a larger sphere. the nucleoli does not have
a membrane too and exhibits this liquid-like behavior from initially 2 spherical shape, sphericity is lost
when the two interact, and then they expand back into a spherical shape that has increased volume.
An other example, where we don’t really know what it is composed of, in a more advanced stage of phase
separation and even induced experimentally there are liquid-like structures developed , that have the
ability to fuse and also form spherical compartments. (in drosophila oocyte).
These processes of phase-separation as it is called is chemical at different scales. And when you deal with
this there are different words for the same thing: some talk about condensates, others coacervates, we will
call the whole process liquid-liquid phase separation or LLPS, and the droplets will be called condensates,
because there is a condensation process that leads to their emergence.
Liquidity or liquid-like behavior can be studied with fluorescence after photobleaching FRAT, for ex here
when you have a liquid droplet or condensate, after photobleaching in in the middle over time there is a
certain recovery of molecules into the droplets. This can occur either from the outside ( the replacement of
molecules from the outside) or simply by reorganization in the inside of such a condensate.
molecules within a liquid phase exhibit dynamic reorganization
(picture following)
