8 LC Concepts in Molecular Biology 17.10.2022
Autophagy and quality control 1
Autophagy means self eating, and the eating part occurs in lysosomes.
→lysosomes, how are they generated?
Lysosomes are very important cell organelle because they are very special by chemical compositions,
where are fit hydrolases and almost every macromolecule can be degraded there. Generally they enzymes
are matured from the golgy apparatus, and enzymes that end up in the lysosomes are actually trafficked to
the golgy apparatus and from there to the late endosomes and then finally endosomes.
Hydrolasys referring to this class of enzymes, they can
be:
- Nucleases
- Proteses
- Glycosidases
- Lipases
- Phosphatases
- Sulfatases
- Phospholipases
The lysosomes are aciditc with a pH about 5.0 and usually
they have enzymatic activityonly at a pH below 7; that’s
why this enzymes can be trafficked trhough the
endoplasmic reticulum and the golgy apparatus to the
lysosomes because they are catalytically inactive at
neutral pH.
Lysosomes are also a really important control center for cellular signaling, because they can contribute to
the sensing of a neutral status of the cell. Because the lysosome degrades a lot of material, that’s either
delivered form in or out the cell, chopping it into its individual building blocks which (aa, sugars…) can be
transported back crossing them into the cytoplasm. Therefore, the activity of this transporters cvan be
sensed by the cell and tell the cell how much nutrients are avaibleble. There is one signaling complex,
mTORC1, which is composed of multiple subunits:
→ its key sub-unit is the torc kinase (target of ripamasine TOR), whose activity its required for cell
growth and protein synthesis. This mTORC kinase complex is targeted to the lysosome’s membrane
by rather complicated cascade of molecular events that lead to activation and membrane
nuclearization of small gtp binding proteins.
The nucleotide binding status can very exactly controlled; they are controlled upstream by molecules, by
gaps and gaps that can either allow this gtpases to bind gtp or gdp, and the activity of thiese gaps and gaps
is ultimately controlled by the availability of aminoacids for ex.
TORC will be active when it’s targeted to the membrane, and when it’s inactive it actually falls off the
lysosome’s membrane, being solved in the cytoplasm and inactive.
- Its activity is required, for example, for protein synthesis.
,8 LC Concepts in Molecular Biology 17.10.2022
TORC activity depends on:
- the amount of aminoamides available, also of membrane cholesterol; this leads to active
RagGTPases.
- Availability of nutrients and growth factors
- TORC also needs Rheb GTPaes to be anchored in the membrane, that because when growth factors
are available
- TORC is a coincidence detector, recognizes Rheb on the membrane and the presence of these
RagGTPases, and if it’s target to the membrane can be active. If either one is missing Torc will fall of
and will be inactive.
The lysosome membrane its scuffled to couple metabolic signaling to the sensing of availability of amino
acids and also cholesterol.
➢ Hydrolases
These hydrolases are also synthesized into the ER, and are transported further to the golgi apparatus and
then they get a very crutiall signal, the mannose 6-phosphate M6P. That’s linked to N-linked
oligosaccharides. (this oligo saccaharosides are attached already in the ER, so cotranslationally, and one of
its terminus obtains the M6P). The signal that serves to recognize for lysosomes hydrolazes is depicted
here and is called signal patch.
In the golgi there are enzymes called phosphor trasferases which recognized the signal patch, and will use
a sugar that’s present in the golgy apparatus and ultimately aattach a M6P to one of its terminus ending
oligosaccharides, and then the hydrolase is released.
, 8 LC Concepts in Molecular Biology 17.10.2022
In this case a 3D linear signal patch is recognized and can be distributed over the entire popli-peptide
chain, but after the fold is together in one area of the molecule. In the tras-golgi, after the protein has
been made, a hydrolase obtains its mono-6phosphate signal and it’s recognized by a receptor in the
apparatus and targeted to late endosomes and finally lysosomes. The adaptors for general function in this,
are GGAs which have to link the receptor to the clathrine machinery, required for vescicle formation.
The M6P receptor recognmizes the M6P on the hydrolase and you also have these GGAs that recognizes
the receptor and also other small gtp binding proteins arf when its bound to the membrane (in it’s GTP
bound state), willing to recruit then clathrin (a vescicle formation) that will then contain m6p receptors and
its trafficked to lisosomes.
When it’s trafficked to lysosomes, in late endosomes, the pH is lower then 7 and the receptor loses its
affinity for M6P and then the hydrolase willl disassociate and end up in the earlly endosome (then it
matures to late endosome and then finally lisosome) and the receptor is trasported back into the golgy
apparatus. The trasport back also accurs by a special code that is a retromer.
The retromer binds a membrane and deforms the membrane into long tubes; this is functionally important
because the cell wants to recycle back membrane rather than luminal content; if you have tubinal
mambrane then ypu have different surface to volume ratinal the sferical vescicles. Ypu have then a lot of
mamebrane and very little volume,
Autophagy and quality control 1
Autophagy means self eating, and the eating part occurs in lysosomes.
→lysosomes, how are they generated?
Lysosomes are very important cell organelle because they are very special by chemical compositions,
where are fit hydrolases and almost every macromolecule can be degraded there. Generally they enzymes
are matured from the golgy apparatus, and enzymes that end up in the lysosomes are actually trafficked to
the golgy apparatus and from there to the late endosomes and then finally endosomes.
Hydrolasys referring to this class of enzymes, they can
be:
- Nucleases
- Proteses
- Glycosidases
- Lipases
- Phosphatases
- Sulfatases
- Phospholipases
The lysosomes are aciditc with a pH about 5.0 and usually
they have enzymatic activityonly at a pH below 7; that’s
why this enzymes can be trafficked trhough the
endoplasmic reticulum and the golgy apparatus to the
lysosomes because they are catalytically inactive at
neutral pH.
Lysosomes are also a really important control center for cellular signaling, because they can contribute to
the sensing of a neutral status of the cell. Because the lysosome degrades a lot of material, that’s either
delivered form in or out the cell, chopping it into its individual building blocks which (aa, sugars…) can be
transported back crossing them into the cytoplasm. Therefore, the activity of this transporters cvan be
sensed by the cell and tell the cell how much nutrients are avaibleble. There is one signaling complex,
mTORC1, which is composed of multiple subunits:
→ its key sub-unit is the torc kinase (target of ripamasine TOR), whose activity its required for cell
growth and protein synthesis. This mTORC kinase complex is targeted to the lysosome’s membrane
by rather complicated cascade of molecular events that lead to activation and membrane
nuclearization of small gtp binding proteins.
The nucleotide binding status can very exactly controlled; they are controlled upstream by molecules, by
gaps and gaps that can either allow this gtpases to bind gtp or gdp, and the activity of thiese gaps and gaps
is ultimately controlled by the availability of aminoacids for ex.
TORC will be active when it’s targeted to the membrane, and when it’s inactive it actually falls off the
lysosome’s membrane, being solved in the cytoplasm and inactive.
- Its activity is required, for example, for protein synthesis.
,8 LC Concepts in Molecular Biology 17.10.2022
TORC activity depends on:
- the amount of aminoamides available, also of membrane cholesterol; this leads to active
RagGTPases.
- Availability of nutrients and growth factors
- TORC also needs Rheb GTPaes to be anchored in the membrane, that because when growth factors
are available
- TORC is a coincidence detector, recognizes Rheb on the membrane and the presence of these
RagGTPases, and if it’s target to the membrane can be active. If either one is missing Torc will fall of
and will be inactive.
The lysosome membrane its scuffled to couple metabolic signaling to the sensing of availability of amino
acids and also cholesterol.
➢ Hydrolases
These hydrolases are also synthesized into the ER, and are transported further to the golgi apparatus and
then they get a very crutiall signal, the mannose 6-phosphate M6P. That’s linked to N-linked
oligosaccharides. (this oligo saccaharosides are attached already in the ER, so cotranslationally, and one of
its terminus obtains the M6P). The signal that serves to recognize for lysosomes hydrolazes is depicted
here and is called signal patch.
In the golgi there are enzymes called phosphor trasferases which recognized the signal patch, and will use
a sugar that’s present in the golgy apparatus and ultimately aattach a M6P to one of its terminus ending
oligosaccharides, and then the hydrolase is released.
, 8 LC Concepts in Molecular Biology 17.10.2022
In this case a 3D linear signal patch is recognized and can be distributed over the entire popli-peptide
chain, but after the fold is together in one area of the molecule. In the tras-golgi, after the protein has
been made, a hydrolase obtains its mono-6phosphate signal and it’s recognized by a receptor in the
apparatus and targeted to late endosomes and finally lysosomes. The adaptors for general function in this,
are GGAs which have to link the receptor to the clathrine machinery, required for vescicle formation.
The M6P receptor recognmizes the M6P on the hydrolase and you also have these GGAs that recognizes
the receptor and also other small gtp binding proteins arf when its bound to the membrane (in it’s GTP
bound state), willing to recruit then clathrin (a vescicle formation) that will then contain m6p receptors and
its trafficked to lisosomes.
When it’s trafficked to lysosomes, in late endosomes, the pH is lower then 7 and the receptor loses its
affinity for M6P and then the hydrolase willl disassociate and end up in the earlly endosome (then it
matures to late endosome and then finally lisosome) and the receptor is trasported back into the golgy
apparatus. The trasport back also accurs by a special code that is a retromer.
The retromer binds a membrane and deforms the membrane into long tubes; this is functionally important
because the cell wants to recycle back membrane rather than luminal content; if you have tubinal
mambrane then ypu have different surface to volume ratinal the sferical vescicles. Ypu have then a lot of
mamebrane and very little volume,
