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16 Cards in this Set

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What was Antinsen's folding experiment? Why doesn't it work in an actual cell?

Antisen's folding experiment showed that even after applying a denaturant, once you remove the denaturant, the protein will refold itself. However, the temperature of a cell is not 4 degrees like the experiment and in the cell we have an issue of overcrowding. Physical conditions are not suitable.

How does a protein surpass unfavorable conditions and fold?

Cell conditions would actually promote aggregation, so we have MOLECULAR CHAPERONES!

What do chaperones bind to?

1: Bind weakly to unfolded proteins (maybe as they are in the process of folding)




2: Bind to nascent chains




3: Bind to misfolded proteins

Steps of a chaperone folding process

1: Burst phase (0-5ms): collapse of hydrophobic core; building secondary structures


2: Intermediate (5-100ms): domains form, recognizable tertiary structure; both folded and unfolded characteristics


3: Attainment of native structure (100ms to minutes): RATE LIMITING STEP; repack hydrophobic side chains; stabilize structure

Chaperonin Structure

Lid (7 subunits) + 2 stack barrel (7 subunits each)




Inside structure is completely hydrophilic (water) which is what would push the hydrophobic core together`

Why is the inside chamber beneficial for protein folding?

1: Hydrophilic Core




2: Protein is sequestered and alone! Can't bind to anything else or do anything besides folding

How is ATP associated with protein folding?

ATP hydrolysis needs to take place --> causes a conformational in the large subunits of the barrel --> lid dissociates --> folded protein can emerge into the cytosol

Heat Shock Factor (Hsf)

Transcription factor involved in activating TXN of chaperonins




Inactive state bound to chaperonins in cytosol




When there is stress on the cell, we want to end normal TLN but we want to increase TLN of Heat Shock Proteins (Hsp)

Proteasome structure

26S = 20S core/active site + 19S regulatory cap

What is the proteasome core?

ACTIVE SITES!!




alpha and beta subunits --> alpha rings form tunnel that gives access to the channel

What is the function of the proteasome regulatory cap?

1: Recognize and bind UBQ substrates


2: de-UBQ them


3: Prepare for proteolysis and present to catalytic core

Ubiquitin and Ubiquitinylation

substrate that covalently links to polypeptides to signal for degradation




FOUR IS THE MAGIC TARGET NUMBER OF UBQs!!

What are the enzymes involved in Ubiquitinylation and what are the steps?

E1: activating enzyme which activates the carboxy terminus of Ubq by ATP rxn (Ubq-AMP)




E2: Conjugating enzyme --> accepts Ubq from E1 and transfers it to a prtein via E3 Ligase action




E3 also specifies substrate selection

What does Quality Control refer to?

1: Correct folding of proteins




2: Correct targeting and subsequent degradation of misfolded proteins in the Ubq/Proteasome pathway

Protein Aggregation

Occurs when misfolded proteins overhwlem the Ubq/Proteasome pathway




1: amorphous assemblies held by hydrophobic interactions




2: ordered assemblies of amyloid fibers (extremely stable conformation of stacked beta-sheets)

Name the diseases involved in protein aggregates

1: Alzheimer's - stable stacked beta sheets; extracellular amyloids of AB peptide cleaved from APP (Alz. Precursor Protein)




2: Parkinson's Disease: alpha-synuclein aggregates




3: Huntington's: poly-Q stretch




4: Prion diseases: transmissible amyloids = contagious! attack brain; CJD