Cell Biology - Outcome 2 Flashcards
Protein Processing and Degradation
where do all protein begin synthesis?
on free ribosomes
what does the signal peptide sequence determine?
the fate of this protein being synthesised at the ribosome
what is the signal peptide sequence composed of?
approximately 20 amino acids and its location within the growing polypeptide
what are the two terminals on a polypeptide chain and what are they composed of?
amino acid terminal (n-terminal)
- NH3+
carbonyl terminal (c-terminal)
-COO-
what is another determining factor of the fate of the protein?
whether the protein is being synthesised on a free ribosome or on a ribosome attached to the ER (‘bound’ ribosome)
what determines whether or not the ribosome will dock at the ER membrane and become a ‘bound’ ribosome
the protein that the ribosome is synthesising
what happens if no signal peptide is detected on the protein?
the free ribosome completes the synthesis and the protein is released into the cytoplasm
what happens if the protein has an organelle specific signal sequence?
it will be targeted to the organelle for import
eg. the nucleus, mitochondria, chloroplasts and peroxisomes
what pathway is entered if the ribosome synthesising the protein becomes a ‘bound’ ribosome and attaches to the the RER?
the secretory pathway
what happens if the protein being synthesised has a signal peptide at the n-terminal?
- protein synthesis will be halted
- ribosome synthesising the protein will be moved to the membrane of the RER by the signal recognition particle (SRP)
what is the function of the signal recognition particle (SRP)?
- scans the cytoplasm and looks for an ER n-terminal signal sequence
- binds to signal sequence and then pulls protein (and ribosome its attached to) to membrane of RER and ‘docks’ the ribosome to membrane of the RER
what is the transmembrane channel that SRP brings the protein to and what happens?
brings protein to a translocon and protein synthesis continues
what happens to the synthesising protein if it is hydrophilic in nature?
the protein will enter the lumen of the ER
what happens once the protein is inside the lumen of the RER?
- the signal sequence is cleaved off by an enzyme called signal peptidase
- the protein will then be folded into its functional conformation, and may also get post-translationally modified
what happens to a protein that is destined to be an ER protein and it requires no further modifications?
it will remain in the lumen of the ER
what happens to the protein if it does require further modifications?
it will proceed to the Golgi apparatus via a RER vesicle
where do proteins that have a highly hydrophobic. central region remain/ where do they go and what are they capable of?
- in the bilayer of the ER membrane or be sent to another organelle membrane via RER or Golgi vesicle
- capable of diffusing laterally along the ER membrane.
what is the fate of newly synthesised proteins that have hydrophobic central regions?
to be transmembrane proteins which serve as:
- channels
- pumps
- enzymes
- receptors
in the cell membrane and in organelle membranes
where may hydrophobic proteins be sent to?
- a lysosome
- to be secreted out of the cell, out into surrounding extracellular fluid, picked up by bloodstream and transported to its target tissue
what does it mean for a protein to be GLYCOSYLATED?
a sugar group will be added (aids cellular location)
what does it mean for a protein to be CLEAVED?
parts of the protein will be cut off/ bonds in the protein will be broken
(may activate protein to become functional)
what does it mean for a protein to be PHOSHORYLATED?
a phosphate group will be added (may activate protein)
what happens if a protein is destined to be a membrane protein?
the vesicle will fuse with the cell membrane and the protein will insert
what happens if a protein is destined to be a protein in another part of the body?
- the vesicle will use with the membrane and be secreted out into the surrounding extracellular fluid
- picked up by bloodstream and transported to its target tissue
what happens if a protein is destined to be a protein in an organelle?
the vesicle will fuse with the specific organelle membrane and the protein will insert
what happens if a protein is destined to be used by a lysosome/needs to be degraded?
vesicle will fuse with the lysosomal cell membrane and the protein will insert
why may a protein only be short-lived in a cell due to regulatory processes?
to allow control of a signalling/metabolic pathway
what happens to newly synthesised proteins in the lumen of the RER?
a quality control check is carried out on them
what type of proteins are rejected when being checked in the lumen of the RER?
any proteins that are found to be incorrectly formed or incorrectly folded
what are abnormal proteins targeted for?
degradation
what are the 3 processes of degradation and removal of proteins?
- ubiquitination
- lysosomes
- autophagy
what is involved in the ubiquitination process?
- it uses a molecule of ubiquitin to ‘tag’ obsolete proteins for destruction
it involves 3 main enzymes:
- ubiquitin activating enzyme (E1)
- ubiquitin conjugating enzyme (E2)
- ubiquitin ligase (E3)
what does the ubiquitin activating enzyme (E1) do?
activates the ubiquitin molecule in the presence of ATP
what does the ubiquitin conjugating enzyme (E2) do?
it covalently links the ubiquitin molecule to itself (E2)
what does ubiquitin ligase (E3) do?
it ligates the ubiquitin molecule to the target molecule (ie. protein)
what is monoubiquitination?
where a tag of only one ubiquitin molecule is sufficient to tag the protein and completes one cycle of the tagging process
what is polyubiquitination?
where a protein is tagged with many ubiquitin molecules hence multiple cycles of the process occurs adding a ubiquitin molecule during each cycle
how many of E1, E2 and E3 enzymes do mammalian genomes encode approximately?
- 12 E1 enzymes
- 30-40 E2 enzymes
- hundreds of E3 enzymes
what does the variation of enzymes (E1, E2 and E3) suggest?
a wide variety of protein targets with different regulatory mechanisms for each one
what do lysosomes account for cellular protein degradation?
10-20%
what does the ubiquitination process account for all cellular protein degradation?
80-90%
what are lysosomes?
special vesicles derived from the Golgi apparatus
what is the function of lysosomes?
to degrade damaged or unwanted macromolecules back down to macromolecules
what are macromolecules?
- proteins
- nucleic acids
- lipids
- complex carbohydrates
what are micromolecules?
- amino acids
- simple sugars
describe the full process for when macromolecules are targeted for degradation.
- macromolecules that are targeted for degradation are packaged into vesicles by the Golgi.
- Golgi then fuses with the lysosome and delivers its contents (macromolecules) into interior of lysosome.
- hydrolytic enzymes (eg. lipases, proteases, nucleases) and an acidic environment (pH 2) inside the lysosome degrade the macromolecules to micromolecules
- lysosome then transports micromolecules out into the cytosol for re-use.
what is autophagy?
a self-destruction process where the cell removes dysfunctional organelles
what are the 4 stages of autophagy?
- induction
- formation
- docking and fusion
- breakdown
describe what happens during induction
double membrane starts to ‘cup’ around organelle
describe what happens during formation
organelle completely surrounded. autophagosome is formed
describe what happens during docking and fusion
autophagosome fuses with lysosome
describe what happens during breakdown
organelle and phagosome membrane are digested by the lysosome
when may autophagy occur and give an example
- may occur at times of cellular stress and low energy states
- during starvation molecules are broken down to be put back into the cycle to generate energy for proteins for survival
