Term
| Explain the effect on the electron density map for regions of random coil structure. |
|
Definition
| Random coil structures will not show up on electron density maps or they will be slightly altered to show ideal geometry. |
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Term
| How is crystal structure resolution influenced by protein dynamics? |
|
Definition
| Must be in folded state because irregular structure and random coil do not diffract x-rays. |
|
|
Term
| What is the Levinthal Paradox? |
|
Definition
| The time it takes a protein to randomly fold would be t=10n/1013 seconds where n=# of amino acids. |
|
|
Term
| What is a folding funnel? |
|
Definition
| The "well" inthe free energy diagram where the native folded protein exists. |
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Term
When a protein starts to fold, its polypeptide has a very large/small conformational
entropy? |
|
Definition
| Very large conformational entropy. |
|
|
Term
| Describe the process of protein folding? |
|
Definition
fast hydrophobic collapse corresponds to secondary structure formation, then slower
tertiary packing and finding native arrangement of electrostatic interactions |
|
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Term
| Why do unfolded proteins bind to PDI? |
|
Definition
| The hydrophobic sections are attracted nonpolar patches on the chaperone. |
|
|
Term
| Why do (re)-folded proteins not get unfolded by PDI |
|
Definition
| No nonpolar surface bits. |
|
|
Term
| Describe the basice disulfide exchange mechanism. |
|
Definition
free sulfhydryl lone electron pair attacks a
disulfide bond |
|
|
Term
| What is the purpose of the ring in GroEL/ES? |
|
Definition
| Binds substrate and and ATP and then expands and stretches the substrate to physcially unfold it. |
|
|
Term
| What is the purpose of ATP in the GroEL/ES? |
|
Definition
| Hydrolize to make folding thermodynamically favorable. |
|
|
Term
| What does the term amyloid refer to? |
|
Definition
| Insoluble protein aggregates associated with Alzheimer's and Prion disease. |
|
|
Term
| What disease are prions responsible for? |
|
Definition
|
|
Term
| What conformational change to prions undergo? |
|
Definition
A more α-helical soluble form to a more β-sheet insoluble
form |
|
|
Term
| How does salt affect protein stability? |
|
Definition
Increases electrostatic interactions on the surface. Should stabilize folded protein, but not by much. |
|
|
Term
| How does pH affect protein stability? |
|
Definition
| pH should not affect folded protein stability and stabilize interactions. |
|
|
Term
When would you use ion exchange chromatography?
|
|
Definition
| When separating out molecules or proteins of different charges at a certain pH. |
|
|
Term
| When would you use gel filtration? |
|
Definition
| When separating out proteins of different molecular weights. |
|
|
Term
| When would you use gel filtration? |
|
Definition
| When separating out molecules of different sizes. |
|
|
Term
| When would you use affinity chromatography? |
|
Definition
| When the molecule has a binding affinity that can be taken advantage of. |
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