Quality Control Of Proteins Flashcards
What is the basic structure of any protein?
Made up of polypeptide chains
Made up of a combination of amino acids from a choice of 20 AAs
Each protein has a unique AA order
Polypeptide chains have a N terminus (amino group) and a C terminus (carboxyl group)
What gives a protein its complexity and functionality?
A polypeptide chain will have a polypeptide backbone from which different side chains can project
This confers unique properties
What are the four protein structures?
Primary
Secondary
Tertiary
Quaternary
Describe the primary protein structure
The simple unique structure of a protein
Describe the secondary protein structure
Coiling or bending of the polypeptide chain into an alpha helix or a beta pleated sheet
They can exist separately or jointly in a protein
Describe the tertiary structure of a protein
The folding back and forth upon itself and held together by disulphide bridges and hydrogen bonds
This adds stability to the protein
Describe the quaternary structure of a protein
Complex molecule formed by the interaction of two or more polypeptide chains with various subunits
What way does a protein fold to be energetically favourable?
It’s unique 3D conformation where it buries most of its hydrophobic residues in an interior core
What is the definition of an abnormal protein?
A misfolded protein:
When a protein has a sizeable exposed patch of hydrophobic amino acids on its surface
What reasons are there for abnormal misfolded proteins?
Failed to fold properly after it left the ribosome an accident caused it to unfold
Failed to find its partner subunit on a larger protein complex
When do protein fold?
Some proteins start folding at the N terminal once it leaves the ribosome
Sometimes most of the folding process is complete by the time the C terminal is released
Describe the molten globule stage
This is the dynamic and flexible state where some protein begin adding side chains and adjustments can be made
What are molecular chaperones?
Proteins that interact, stabilise or help a nonnative protein to acquire its native conformation
Required for most proteins to fold
What do molecular chaperons do?
Specifically recognise incorrect/ off pathway proteins by their exposure of hydrophobic surfaces
Bind hydrophobic surfaces of healthy proteins to their own hydrophobic surfaces
Do molecular chaperones remain a part of the final folded protein?
No they are not part of the final functional unit
Why does protein degradation happen to maintain homeostasis?
To remove
Incorrectly synthesised proteins
Damaged proteins
Cell cycle specific proteins
Signalling proteins no longer needed
What are the two major protein degradation pathways?
Selective
Non selective (lysosomes)
What are the two types of selective pathway in protein degradation?
Unfolded protein response (UPR) - rER
Ubiquitin proteosome system (UPS)
What are the two processes that lead non functional proteins to lysosomes?
Autophagy
Endocytosis
Describe what happens during autophagy
A membrane is formed around the targeted region of the non functioning cell
Next it fuses with a lysosome for degradation
Describe what happens during Endocytosis
The plasma membrane forms a pocket
Then it pinches off into the cell to form a vesicle inside the endosome that will then fuse with the lysosome for degradation
What is the unfolded protein response?
A signalling pathway that is initiated when there is an accumulation of misfolded proteins in the endoplasmic reticulum
Why is the unfolded protein response in the ER triggered?
When there is not enough chaperone capacity to fold proteins properly there are more misfolded abnormal proteins
A signal is then sent to bring the cell back to homeostatic function
What does the unfolded protein response in the ER do?
Halts gene expression and protein translation
Produces more chaperones
Enhances ER-associated degradation pathway (ERAD)
What is the ER-associated degradation pathway?
The retranslocation of misfolded proteins to the cytosol where they are marked for degradation
Is the unfolded protein response of the ER effective?
Despite UPR many proteins transported from ER into the cytosol fail to fold properly (>80%)
In prolonged stress the UPR commits the cell to apoptosis
What are the transmembrane receptors with parallel signally pathways to the nucleus?
IRE1
PERK
ATF6
What does PERK do?
Stops protein synthesis by phosphorylating (inactivating) translation factors restraining mRNA
What is IRE1?
A transmembrane kinase that activates a phosphorylation cascade that signal to the nucleus to initiate transcription of rough ER chaperone proteins
How does ATF6 operated during the unfolded protein response?
It undergoes proteolytic cleavage where the cytosolic portion signals to the nucleus to initiate transcription of rER chaperone proteins
What are heat shock proteins?
Molecular chaperones
They are produced when there is an accumulation of misfolded proteins
When are heat shock proteins triggered?
When the increase in misfolded proteins is due to an increase in temperature
Name two heat shock proteins
Hsp60
Hsp70
What does hsp70 do?
First hsp70 must bind to ATP
Then it will bind to the misformed protein
(ATP-ADP)
Causes a conformational change in the protein
Hsp70 uses many cycles of ATP hydrolysis to fold polypeptide chains properly
Does Hsp70 work alone?
It is often aided by hsp40
It will act before the protein leaves the ribosome
What is hsp60?
It is a form of chaperone
Exists in a barrel complex
(It will act later in protein synthesis
How does hsp60 work?
Hydrophobic regions of misfolded proteins are captured by the complex
ATP and protein cap added
The protein is now in an ‘isolation chamber’
ATP hydrolysis causes the complex to weaken and reform
When ready ATP binding causes the protein to be ejected and recaptured until
ATP hydrolysis eventually allows protein to be correctly folded
When is the unbiquitin proteasome system enacted?
When attempts to refold the protein through other pathways fail
What are the first three steps to the ubiquitin prtoeasome degradation system?
Recognition of an abnormal hydrophobic patch on the protein surface
Marks the protein for destruction
Delivers it to the proteasome for destruction
Describe the proteasome system
ATP dependent protease
Constitutes 1% of a cells total protein
Present in the cytosol, nucleus and ER
Consists of a central hollow cylinder and multiple protein subunits
Some subunits will have active sites facing inwards
Threads the target protein through the proteasome core
What are some of the functions of ubiquitin within the cell?
Cell cycle
Regulated cell proliferation / differentiation
Organelle biogenesis
Apoptosis
Quality control
What does monoubiquitylation tag a protein for?
The addition of a single ubiquitin molecule to a protein
Tagged for histone regulation
What does multiubuitylation tag for?
Several ubiquitin molecules added to a protein separately
Tags for Endocytosis
What does polyubuitylation tag for?
A chain of ubiquitin molecules added to a protein
Tagged for Proteasomal degradation and DNA repair
What are the steps of (poly)ubiquitylation?
Ubiquitin is activated by ubiquitin-activating enzyme (E1)
E1 attaches to ubiquitin (ATP dependent)
Passes activated ubiquitin to ubiquitin-conjugating enzymes (E2)
E2 transports ubiquitin to ubiquitin ligases (E3)
E3 binds to degrons in the target protein
E2 forms a polyubiquitin chain linked to a lysine of the target protein
What are degrons?
Specific degradation signals
How does the proteasome recognise which proteins are to be destroyed?
The polyubiquitin chains is what the proteasome will recognise as being the ‘tag’
