20 free response questions

Need a calculator
Average will be 2 hours, budget 3
Graphing calculator will be allowed
Average will be 80% ish
No models needed

General knowledge
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Phi and psi angles for beta sheets and alpha helix
Know the areas/regions, not specific angles.

Difference between motif and domain

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motif can be beta alpha beta

o Most is three secondary structures
Domains tend to be larger.
o Domain is the smallest unit of folding of a protein that is stable.

Protein structure: What determines structure and folding?

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The partial double bond of the peptide bond is the most determining feature
Hydrophobic interactions tend to contribute most to folding (burying the
hydrophobic amino acids).

Crystallization: What determines favorability of protein folding?

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Review the crystallization question about alanine substitution

o Entropy effects tend to be greatest.

Crystallization: Things that we need for crystal formation

1. Protein 10mg/mL
2. pH pI 5.5 then pH 6.5-7.5 (pH above or below the pI, depending). We want
all the peptides in the same charge state
3. PEG (water bonds to PEG, large hydration sphere, so water is away from
the protein surface which makes the protein interact with itself).
4. Additives:
a. Things like ligands
b. Di or poly valent cations
c. Nano-bodies stabilize proteins in solution
d. Detergents are excellent for membrane proteins because it
increases solubility.
5. Salt