| Question | Answer |
| Keq | =Ka= [H+][A-]/[HA] |
| pKa | = -log(Ka) |
| pH | = -log[H+]
= pKa + log([deprotonated]/[protonated]) |
| inflection point | where pH=pKa |
| buffer | weak acid + conjugate base |
| dE | = Ef - Ei
= Q + W |
| H | = E + PV |
| dG | = dH - TdS
= dGo + RTln([p]/[r]) |
| R (constant) | 0.008314kJ/mol*K |
| avg wt. of an aa | 110Da |
| Ramachandran Plot | shows most likely orientation |
| amino acid structure bonds | 1: covalent peptide bonds
2: backbone H-bonds
3: interactions of aa sc w/ eachother and backbone atoms
4: weak non-covalent interactions |
| alpha helix | rise/residue=1.5A
rise/turn=5.4A
residues/turn=3.6
right-handed
i to i+4 C=O- - -H-N hydrogen bond |
| beta sheet | antiparallel: one chain -->, other chain <--; straight bonds
parallel: both chains -->; diagonal bonds |
| side chain interactions w/ alpha helices | adjacent
i to i+3 or i to i+4
pseudo 7 repeat |
| alpha keratin | dimer of a-helices
high Cys content -- disulfide bonds
7-residue repeats where a & d are nonpolar
coiled coil |
| silk fibroin | antiparellel B-sheets arranged parallel
alternating sequence:Gly-X-Gly, X=Ala, Ser
all Gly on one side and X on other |
| collagen | basic unit= tropocollagen, 3 left-handed chains interwoven --> right-handed superhelical twist
33% Gly, also some unusual aa's (face center)
Pro permits sharp turns
covalent x-links between Lys and His
diseases: Ehlers-Danlos & brittle bone |
| globular proteins | hydrophilic surface, hydrophobic interior
generally all a-helices xor B-sheets
supersecondary structures or motifs |
| domains | functionslly independent |
