Quality Control Of Proteins

Question 1

Quality control begins in the ….

Answer 1

ER

Question 2

Genetic information ->

Answer 2

Functional proteins by transcription, translation, folding

Question 3

Linear amino-acid chain ->

Answer 3

Unique functional structure
Folding intermediates, hydrophobic domains, aggregation prone

Question 4

Describe the 4 structures of proteins

Answer 4

1. Primary: The unique sequence of amino acids in the protein.
2. Secondary : Coiling or bending of the polypeptide into an alpha helix or a beta pleated sheet. They can exist separately or jointly in a protein
3. Tertiary: The folding back of a molecule upon itself and held together by disulfide bridges and hydrogen bonds. This adds to the proteins stability
4. Quaternary: Complex molecule formed by the interaction of 2 or more polypeptide chains with various subunits

Question 5

Protein folding leaves what in the core

Answer 5

Hydrophobic residues in an terror core

Question 6

Burying hydrophobic residues in the interior core is…

Answer 6

Energetically favourable as it is the conformation of lowest free energy

Question 7

If a protein ……….. on he surface it means it is …..

Answer 7

If a protein has a sizeable exposed patch of hydrophobic amino acids on its surface it is misfolded (abnormal)

Question 8

What could cause a protein to be misfolded?

Answer 8

Failed to fold properly after it left the ribosome
An accident causes it to unfold
Failed to find its partner subunit on a larger protein complex

Question 9

Misfolded proteins form…

Answer 9

Aggregates which are dangerous to the cell

Question 10

what minimises the damage of misfolded proteins

Answer 10

Elaborate mechanisms that recognise the hydrophobic patches on proteins and minimise the damage they cause

Question 11

Describe protein folding

Answer 11

Some protein folding begins immediately s the protein chain emerges from the ribosome, starting from the N-terminal end
As it emerges it forms a compact structure that contains most of the final secondary features in roughly the right conformation
For some protein domains this dynamic and flexible state called a molten globule is the starting point in which many side chain adjustments occur it takes several minutes to synthesise a protein of average size
For some proteins much of the folding process is complete by the time the ribosomes release the C-terminal end of the protein

Question 12

most proteins require what to fold

Answer 12

Molecular chaperones

Question 13

What are molecular chaperones?

Answer 13

Proteins that interact, stabilise or help a nonnative protein to acquire its native conformation

Question 14

describe molecular chaperones

Answer 14

Not present in the final functional structure
Chaperones optimise the efficiency of folding
Without chaperones proteins may follow the wrong pathway and could aggregate
Specifically recognise incorrect off pathway proteins by their exposure of hydrophobic surfaces
Chaperones bind the hydrophobic surfaces of normal proteins to their own hydrophobic surfaces

Question 15

In order to maintain homeostasis, the cell needs to remove:

Answer 15

Incorrectly synthesised proteins (errors in amino acid sequence)
Damaged proteins (oxidative damage)
Cell-cycle specific proteins
Signalling proteins no longer required

Question 16

What are the two major protein degradation pathways

Answer 16

Non selective (lysosomes)
Selective (unfolded protein response; ubiquitin proteosome system)

Question 17

Where are misfolded or nonfunctional proteins directed to

Answer 17

The lysosome by autophagy or endocytosis

Question 18

Describe autophagy

Answer 18

Membrane is formed around a targeted region of the cell fuses with the lysosome for degradation

Question 19

Describe endocytosis

Answer 19

Plasma membrane forms a pocket, pinches off into the cell to form a vesicle inside the endosome that fuses with the lysosome for degradation

Question 20

The amount of machinery =

Answer 20

volume of proteins that needs to be produced

Question 21

Describe the unfolded protein response in the ER

Answer 21

A signalling pathway initiates with an accumulation of misfolded proteins in the ER triggers the unfolded protein response
With not enough chaperone capacity to fold proteins properly, a signal is transmitted across the membrane which brings cells back to a homeostatic state
Halts gene expression ad protein translation
Produces more molecular machinery for protein folding (chaperones)
Enhances ER-associated degradation pathway (ERAD)
Despite UPR many proteins transported from the ER into the cytosol fail to fold properly
In prolonged stress, the UPR commits the cell to apoptosis

Question 22

What is ERAD

Answer 22

ER-associated degradation pathway
Retranslocation of misfolded proteins to the cytosol where they are marked for degradation

Question 23

Describe IRE1, PERK and ATF6

Answer 23

Transmembrane receptors with parallel signalling pathways to the nucleus

Question 24

Describe PERK

Answer 24

Stops protein synthesis by phosphorylating (inactivating) translation factors restraining mRNA

Question 25

What is IRE1

Answer 25

A transmembrane kinase that activates a phosphorylation cascade signals to the nucleus to initiate transcription of rER chaperone proteins

Question 26

ATF6 undergoes…

Answer 26

Proteolytic cleavage where the cytosolic portion signals to the nucleus to initiate transcription of rER chaperone proteins

Question 27

Accumulation of misfolded proteins triggers…

Answer 27

The heat shock response

Question 28

What are heat shock proteins

Answer 28

Molecular chaperones
Hsp60 and Hsp70 work with subset of other proteins to aid folding

Question 29

Increase in temp =

Answer 29

Increased risk of misfolding proteins =. More hsp synthesis

Question 30

Describe Hsp70

Answer 30

Acts before protein leaves ribosome
Often helped by HSP40
ATP bound Hsp70 binds to protein and ATP-ADP
Causes conformational change in the protein
HSP70 uses many cycles of ATP hydrolysis to fold polypeptide chains properly

Question 31

Describe HSP60

Answer 31

Exists as a barrel complex - acts later in protein synthesis
Hydrophobic regions of misfolded proteins captured by complex
ATP and protein cap added
In isolation chamber, ATP hydrolysis causes the complex to weaken and reform
When ready, ATP biding causes protein to be ejected and recaptured until repeated ATP hydrolysis eventually allows protein to be correctly folded
Chaperonin

Question 32

When attempts to re fold a protein fails…..

Answer 32

A Proteolytic pathway destroys the protein

Question 33

Describe the Proteolytic pathway

Answer 33

Begins with recognition of an abnormal hydrophobic patch on the protein surface
Mark the protein for destruction and delivers it for destruction to the proteosome

Question 34

Describe the proteosome system

Answer 34

ATP dependent protease
Constitutes 1% of a cells total protein
Present in cytosol, nucleus and ER
Consists of a central hollo cylinder and multiple protein subunits
Some subunits proteases with active sisters facing inwards
Target protein threaded through proteosome core

Question 35

Function of ubiquitin

Answer 35

Cell cycle, regulated cell proliferation, differentiation organelle biogenesis, apoptosis, quality control of proteins

Question 36

Describe ubiquitiylation

Answer 36

The targeting of proteins by ubiquitin is a highly regulated
Ubiquitin is activated by ubiquitin-activating enzyme (E1).
E1 attaches to ubiquitin (ATP-dependent)
Passes activated ubiquitin to ubiquitin-conjugating (E2) enzymes
E2 transports ubiquitin to ubiquitin ligases (E3)
E3 binds to specific degradation signals (degrons) in the target/misfolded protein
E2 forms a polyubuiquitin chain linked to a lysine of the target protein
This polyubuiquitin chain will then be recognised by a specific receptor in the proteasome

Question 37

Summary

Answer 37

In the final steps of protein synthesis molecular chaperones prevent protein aggregation
Chaperones compete with a quality control mechanism
Both compete to bind proteins with abnormally exposed hydrophobic patches
Ubiquitin is covalently added to a misfolded protein by ubiquitin ligase and the resulting polyubiquitin chain is recognised by the proteasome for destruction
Abnormally folded proteins can aggregate to cause destructive human diseases