Protein folding diagrams

Question 1

Overall context of amino acid

Answer 1

size… what other amino acids are involved…

Question 2

protein folding possibilities

Answer 2

they are limited, they fold by a series of conformational adjustments. (rapidly and reverisbly forming secondary structures)

Question 3

what are the steps of protein folding

Answer 3

1. Rapid and reversible formation of local secondary structures
2. Domain formation via cooperative aggregation with a few intermediates
3. formation of the molten globule, followed by adjustments in the domain conformations. Native tertiary structure begins to appear.
4. Series of complex motions gives rigid core packing and excludes remaining H2O to give final protein

Question 4

Molten globule

Answer 4

blob not completely defined.
- compact
- partially folded
- continuation of an intermediate state
- no defined tertiary structure for the side chain (because side chain can still move around)

Question 5

Rigid core

Answer 5

• non polar amino acids, excluding water to the active site, away from non polar stuff
• efficiently packed with R groups in “relaxed” conformations even though many intramolecular interactions occur between side chains

Question 6

why are relaxed conformations packed into protein cores

Answer 6

to be able to move a little bit but not a ton, avoid breaking

Question 7

Why do helices and sheets occur often

Answer 7

they are space efficient and have low steric strain

Question 8

Why do proteins fold with a series of conformational adjustments?

Answer 8

to reduce free energy (release free energy… lower in free energy, more stable) lower and achieve native status, although the folding pathways are rough and some hcan get lost long the way

Question 9

Folding landscape diagram

Answer 9

Energy funnel is rough, proteins can get lost or caught up in a misfolded state. Need a protein to fix that problem

Question 10

Chaperones

Answer 10

• trap misfolded protein
• use free energy of atp hydrolysis to release better folded protein/subunit
• folding accessory protein

Question 11

how is the hydrophobic effect used to find misfolded proteins

Answer 11

theyre hydrophobic surface is on the outside