Nucleus structure Flashcards
(37 cards)
What is heterochromatin and euchromatin
Heterochromatin and euchromatin are two major categories of chromatin higher order structure. Heterochromatin has condensed chromatin structure and is inactive for transcription, while euchromatin has loose chromatin structure and active for transcription.
Inside of the nucleus structure
Inside of the nucleus is not uniform and there is a system; a geography or a pattern within a nucleus
The size of the nucleus can be anywhere between 5microns to 20 microns (a micron being 10^-6)
What is a nucleolus
A sub region of a nucleus and has its own structure and its own definite regions (nucleolar organising center; pars fibrosis)
A nucleus may have one or more nucleoli.
What is a hetero chromatin
Regions of the chromosomes that has become extremely compacted- so dark that it appears dark in an electron microscope. Because they are so dense, electrons cannot get through them. These dense compacted regions of chromosomes normally indicate that these regions are inactive- they are not being actively used in transcription.
The nuclear pores allows the interior of the nucleus to communicate with the rest of the cell; because it carries out its own functions, it needs ingredients to do so. For this, the nuclear pores are important as this allows the flow of materials in and out.
Overview of the nucleus
The nucleus takes up most of the space within the eukaryotic cell
Nucleus needs to replicate too so goes through nuclear division (through mitosis) followed by a separation of the cells (cytokinesis)
The interior of the nucleus with all the material inside is called the nucleoplasm
The nucleoplasm communicates with the cytosol (rest of the cell) through nuclear pores (that lies within double layer nuclear membrane (nuclear envelope))
The space between the double layered nuclear membrane is called the peri nuclear space. This whole nuclear envelope is supported by a scaffolding/framework that lies within the nucleus, underneath the nuclear envelope. This is called the nuclear lamina.
When we look within the structure of a nucleus, we will find heterochromatin, euchromatin and nucleolus.
What drives the nucleus
One of the main driving forces of the nucleus is make RNA; transcribing DNA into RNA. To do that, the nucleus has to import proteins (enzymes that enable this to happen). The nucleotides has to also be imported from which the nucleus is going to build the RNA. And also once it has made the RNA, it has to send the RNA back out to the cytoplasm for it to be translated.
How does transcription and translation occur in eukaryotic cells and also in prokaryotic cells
These processes are decoupled. DNA is transcribed into RNA within the nucleus and the RNA is translated in the cytoplasm- there is a geographical difference between them.
Unlike prokaryotes, where these processes are coupled.
What happens to the nuclear envelope and the RER?
It branches off to the rough endoplasmic reticulum. The peri nuclear space is contiguous to the RER; meaning that they share the same borders and the interiors are connected.
What do you call the inside of a membrane sac or a layered membrane?
The lumen
So, another name for the lumen of the nuclear envelope is the peri nuclear space.
It is about 20-40nm across
(Nm being 10^-9)
What is a nuclear pore
Not completely open; is gated
Nuclear lamina- what are lamins
Nuclear lamina is a mesh of fibres that support the nuclear envelope; this allows the nucleus to have a shape.
Similar function to cytoskeleton.
Nuclear lamina is composed by a type of fibre proteins called lamins. These belong to the class of fibres known as the intermediate filaments and are formed by polymerised sub-units.
Some of the intermediate filaments form part of the cytoskeleton.
Lamins are a special type of intermediate filament that form a scaffold under the nuclear envelope.
DNA can attach themselves to the lamins as well as the envelope. This provides a scaffold to which the nuclear envelope can attach and give shape to the nucleus and probably is a place where we can attach all our chromosomes in the inside.
Nuclear lamina- monomeric units
Lamins are monomeric units and they can hybridise/ polymerise with each other to make long fibres (long, stretchy fibrous protein). So, we can polymerise them to form the mesh of fibres to provide the scaffolding but we can also depolymerise them to the monomeric units (which breaks down the scaffolding). This results in the nuclear envelope breaking down.
Lamins and mitosis
In mitosis, we need to depolymerise the lamins to allow the nuclear envelope to fall apart and then reform at the end of the mitosis.
This polymerisation and depolymerisation of the lamins (of these fibres) is controlled by a process called phosphorylation (a type of post-translational modification).
This is special to eukaryotic cells- they can modify their proteins after the proteins have been made.
What are types of modifications that can be made to proteins once they are made
And what are the enzymes that help this are called
One of them is phosphorylation- this is where a phosphate group is added to the protein. This phosphate group can also be taken off- can be dephosphorylated. There are enzymes that add phosphates called kinases and the enzymes that remove the phosphate groups can called phosphotases.
Quite often the act of phosphorylation acts as a switch on the protein- switches it between two stages; the active or deactive stage.
This is very common in eukaryotic cells rather than prokaryotic cells
How to polymerise and depolymerise lamins.
The polymerisation of these lamins to form these big fibres is controlled by this act of phosphorylation. When you phosphorylate lamins, the depolymerise. So, when you add a phosphate group to the lamins, the whole fibres fall apart. When you remove the phosphate, they reassemble.
Lamin sub-units
Even we call them as monomeric, they exist as dimeric- two proteins wrapped around each other (like a rope). Proteins have a N-terminus and a C-terminus.
How do lamin sub-units form a molecular structure
Then a dimer can become tetramer- two dimers polymerised (stuck together) but not completely aligned together horizontally- rather one is slightly off. The tetramer is slightly skewed- its shape allow another tetramer or a dimer to attach itself to it. This allows a filament to be rapidly made composed of these tetramers.
These filaments are then twisted around each other like a rope and then these can make really long strong molecular structures. The organisation of these tetramers into lamin filaments occurs when the lamins are dephosphorylated. If the lamins are phosphorylated, those dimers would fall apart.
Summarised functions of the nuclear lamina
Is a mesh of fibres that scaffolds the nuclear envelope and allows the nucleus to have a shape. This can occur because the nuclear lamin is attached to proteins in the nuclear envelope.
Chromosomes also seem to be attached to the nuclear envelope, perhaps via the nuclear lamins. Regions of chromosomes are defined by their binding to the scaffold are called tags.
What are nuclear pores
The interior of the nucleus (the nucleoplasm) communicates with the cytosol via protein bounded nuclear pores. Allowing the passing of important raw materials that enables transcription of DNA to RNA and replication of DNA to occur
Nuclear pores allow free diffusion of small molecules (e.g magnesium ion) but larger molecules must be targeted and actively transported.
Each pore has 8 or 9 separate channels that allow diffusion of small molecules between the nucleoplasm and the cytoplasm.
Why can’t every molecule pass in and out of the nuclear pore
There is a filter shaped like a gate (called spoke) that sort of hooks itself onto the ends of the lumen of the nuclear envelope (peri nuclear space). It is attached to a nuclear basket and also other components attached to it.
This spoke ensures that small molecules can pass through and large molecules can be allowed to pass through if needed.
Bigger molecules such as proteins or RNA need to be imported or exported.
Transport through the nuclear pores
Small molecules can easily diffuse through the channels in the nuclear pores but larger molecules must be actively targeted and transported.
The DNA is trancribed (made into RNA) in the nucleus, but the RNA is translated (made into protein) in the cytoplasm.
Therefore the RNA must be exported out and the proteins (e.g RNA polymerase that transcribes DNA to RNA) must be imported back into the nucleus.
There many instances where the proteins needed in the nucleus are made out in the cytoplasm.
Proteins that need to imported into the nucleus have nuclear localisation signals (NLS).
In eukaryotic cells, signals are quite common.
Nuclear localisation signals- the 3 types
Those like the NLS of the SV40 protein
Those like the bi-partite NLS of CBTF^122.
Those like the NLS of the yeast protein Mata-2.
All of these types of NLS are composed of basic residues (amino acids) and have similar modes of action requiring interactions with proteins known as Importins.
What is a localisational signal
Is a region normally at the beginning (doesn’t have to be) of a protein (peptide sequence) which doesn’t take part in the folding and activity of the protein. It contains information about where the protein should be taken. So, it is not part of the important sequence where the protein folds into the correct shape or for it to have an active site.
If the NLS is not in the beginning of the peotide sequence, it is normally in the middle.
What so importins do
Importins can recognise the peptide sequence in the NLS. Importins carry the protein to the nuclear pore and allow it to be imported.
