Chirality & PKA
A carbon with four different substituents is called this.
A chiral center (stereocenter / asymmetric carbon).
The process by which a polypeptide acquires its correct 3-D biologically active native state.
Protein folding.
PDI stands for this enzyme, which fixes mis-paired disulfide bonds.
Protein Disulfide Isomerase.
Ubiquitin is a small protein of this many amino acid residues.
76 residues.
Which statement about the molten globule is correct?
A) Globular proteins in cytoplasm
B) An intermediate in the folding pathway
C) Always has incorrect disulfide bonds
D) Refers to transmembrane proteins
B) An intermediate in the folding pathway
Only this optical form of amino acids is used by the ribosome for protein synthesis.
L-amino acids.
This paradox shows proteins can't fold by randomly sampling every conformation.
Levinthal's paradox.
PPIs speed up this slow isomerization involving one specific residue.
Cis–trans isomerization of Xaa-Pro (proline) peptide bonds.
Ubiquitin attaches to this residue of the target protein via an isopeptide (amide) bond.
A lysine residue.
What makes a protein absorb light at 280 nm?
A) Tyrosine and asparagine
B) Histidine and lysine
C) Tryptophan and tyrosine
D) Phosphorylated Ser and Thr
C) Tryptophan and tyrosine
This amino acid's side chain has a pKa near 6.5, letting it bind or release protons near physiological pH.
Histidine.
A compact intermediate with native-like secondary structure but poorly defined tertiary structure.
The molten globule state.
This chaperone acts early, binding ~7 hydrophobic residues as the protein leaves the ribosome.
Hsp70.
E1, E2, E3 in order do these three jobs.
E1 = activating (ATP, thioester); E2 = conjugating (carries Ub on its Cys); E3 = ligase (transfers Ub to substrate lysine, picks the target).
In Anfinsen's ribonuclease experiment, the roles of urea and β-mercaptoethanol were:
A) Urea denatures; βME re-natures
B) Urea reduces S–S; βME denatures
C) Urea solubilizes; βME denatures
D) Urea denatures; βME reduces disulfide bond
D) Urea denatures; βME reduces disulfide bond
In the R/S system with the lowest-priority group pointing away, priority running highest→lowest in this direction means S.
Counter-clockwise (clockwise = R).
This folding model: local regions adopt favored structures, form a mobile native-like nucleus, then condense.
The nucleation-condensation model.
Why are correct disulfide bonds resistant to PDI while incorrect ones are the preferred substrate?
Correct bonds are buried in the hydrophobic core (inaccessible); incorrect ones are exposed on the surface.
A K48-linked polyubiquitin chain sends the tagged protein here.
The proteasome, for degradation to amino acids.
Best method to purify a His-tagged protein:
A) Anion exchange
B) Gel filtration
C) Affinity chromatography with a metal-ion column
D) SDS-PAGE
C) Affinity chromatography with a metal-ion column
For aspartic acid (pKa 2.09, 9.82, 3.86), you average these two values to get the pI.
(2.09 + 3.86)/2 — the two lowest, flanking the net-neutral species.
On the folding funnel, the top, the bottom, and the 'bumps' inside each represent these three things.
Top = all unfolded conformations; bottom = native structure; bumps = kinetic traps / intermediates that hinder folding.
This barrel-shaped chaperone caps with GroES, enlarges its chamber with ATP, and ejects the protein after ~15 s.
Hsp60 / the GroEL–GroES chaperonin system.
Of E1/E2/E3, this class is most numerous (500–1000 in mammals) because of this key job.
E3 ligases — they identify the specific protein substrates for ubiquitination.
A 110 kDa protein, Asp/Glu-rich and Lys/Arg/His-poor, sits where on a 2-D gel?
A) Top right
B) Top left
C) Bottom right
D) Bottom left
A) Top right