7 LC Concepts of Molecular Biology 13.10.2022
Proteolytic Degradation
➢ How do vertebrates form and function with only 20.000 protein-coding genes?
We need to increase the number of functional proteins and entities
that we have in the cell, in part this is done by differential splicing.
Most transcription genes in mamalians system get spliced into 5
different variants, increasing it by 5. Other things, is to also add a
dynamic to this because we are also changing environments and we
need to deal with this.
So we need do adap to different enviroments and entities.
Thinking about the central dogma in biology, it would take a very long time to get this dynamic and initiate
synthesis de novo → it is too slow to mediate cellular dynamic.
The trick to get all of this dynamic is post translational modifications, such as:
- Phosphorylation
- Post translation modification, can lead to different complex formation, different catalization in the
cell, activation and inactivation, as well as send the signal to degrade the protein by proteosome.
Even though we have 20k to 25k genes, that automatically our functional proteome is probably over
million protein species because of this alternative splicing as post translational modifications.
➢ Ubiquitine
This is itself a small protein of 8.5kDa kilo Dalton in molecular mass, extremely conserved from yeast to
human cells (except for on aam).
,7 LC Concepts of Molecular Biology 13.10.2022
- The c-terminus is G76, so in total there are 76 amminoacids; in all species c-ter has this extremely
conserved 6 amm c-term tail of lucine-arginine-lucine-arginine-glicine-glicine. Because it is a protein
itself, it also has many modification sites where other ubiquitines can be put on.
How does this post translation modification work?
Any Lys that is in this protein can in principle be a target site for covalent conjugation of ubiquitine through
its the c-terminus to lead Lys with an isopeptide bond.
If you think about proteins in the cell, they are well structured and it’s not really all Lys but just the
exposed one, but it’s very difficult to predict will Lys in a protein will be ubiquitinated. There is no strong
motive that will determine it, but the enzymes will regognize the site where they’ll put the modification.
There are three classes of enzymes that will make sure that you can pu this post translation modification
on:
- Writers
- Readers
- Erasers
For ex. kinase being the writers, phosphates being
erasers and certain domains like phosphor
recognition domain like sh2 in proteins.
There is this cascate of E1, E2, E3 enzymes that
will generate the cascade to write the ubiquitine
code on to proteins; in early eukaryotes ancestors there were single genes of this encoding for single
proteins and nopw if we look at how this is currently in mammalian situation is that ubiquitine is basically
the only protein that is extremely conserved to humans; but is very different is the number of proteins that
we have in writers, readers and erasers. So the modification itself is not what changes but just how we use
it is massively diversified in evolution.
, 7 LC Concepts of Molecular Biology 13.10.2022
How this conjugation works?
The situation is basically what drawn in the image, however ubiquitine can form different bonds on
substrates and this is very active on going work because its very difficult to detect experimentally.
Yet, it’s not still clear what function this bonds with different subtrate biologically mean. The one that is
clear is Thioester Bond, a covalent bond on Cystines that forms with enzymes that have a sulfate on the
side chain.
Proteolytic Degradation
➢ How do vertebrates form and function with only 20.000 protein-coding genes?
We need to increase the number of functional proteins and entities
that we have in the cell, in part this is done by differential splicing.
Most transcription genes in mamalians system get spliced into 5
different variants, increasing it by 5. Other things, is to also add a
dynamic to this because we are also changing environments and we
need to deal with this.
So we need do adap to different enviroments and entities.
Thinking about the central dogma in biology, it would take a very long time to get this dynamic and initiate
synthesis de novo → it is too slow to mediate cellular dynamic.
The trick to get all of this dynamic is post translational modifications, such as:
- Phosphorylation
- Post translation modification, can lead to different complex formation, different catalization in the
cell, activation and inactivation, as well as send the signal to degrade the protein by proteosome.
Even though we have 20k to 25k genes, that automatically our functional proteome is probably over
million protein species because of this alternative splicing as post translational modifications.
➢ Ubiquitine
This is itself a small protein of 8.5kDa kilo Dalton in molecular mass, extremely conserved from yeast to
human cells (except for on aam).
,7 LC Concepts of Molecular Biology 13.10.2022
- The c-terminus is G76, so in total there are 76 amminoacids; in all species c-ter has this extremely
conserved 6 amm c-term tail of lucine-arginine-lucine-arginine-glicine-glicine. Because it is a protein
itself, it also has many modification sites where other ubiquitines can be put on.
How does this post translation modification work?
Any Lys that is in this protein can in principle be a target site for covalent conjugation of ubiquitine through
its the c-terminus to lead Lys with an isopeptide bond.
If you think about proteins in the cell, they are well structured and it’s not really all Lys but just the
exposed one, but it’s very difficult to predict will Lys in a protein will be ubiquitinated. There is no strong
motive that will determine it, but the enzymes will regognize the site where they’ll put the modification.
There are three classes of enzymes that will make sure that you can pu this post translation modification
on:
- Writers
- Readers
- Erasers
For ex. kinase being the writers, phosphates being
erasers and certain domains like phosphor
recognition domain like sh2 in proteins.
There is this cascate of E1, E2, E3 enzymes that
will generate the cascade to write the ubiquitine
code on to proteins; in early eukaryotes ancestors there were single genes of this encoding for single
proteins and nopw if we look at how this is currently in mammalian situation is that ubiquitine is basically
the only protein that is extremely conserved to humans; but is very different is the number of proteins that
we have in writers, readers and erasers. So the modification itself is not what changes but just how we use
it is massively diversified in evolution.
, 7 LC Concepts of Molecular Biology 13.10.2022
How this conjugation works?
The situation is basically what drawn in the image, however ubiquitine can form different bonds on
substrates and this is very active on going work because its very difficult to detect experimentally.
Yet, it’s not still clear what function this bonds with different subtrate biologically mean. The one that is
clear is Thioester Bond, a covalent bond on Cystines that forms with enzymes that have a sulfate on the
side chain.
