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46 Cards in this Set
- Front
- Back
Aromatic AAs (3)
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Phe F
Trp W Tyr Y |
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Negatively charged AAs (2)
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Asp D
Glu E |
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Positively charged AAs (3)
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Arg R
Lys K His H |
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Polar uncharged AAs (5)
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Asn N
Gln Q Ser S Thr T Cys C |
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Nonpolar aliphatic (7)
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Ala A
Gly G Val V Leu L Ile I Pro P Met M |
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D
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Asp
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E
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Glu
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R
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Arg
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K
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Lys
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H
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His
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N
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Asn
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Q
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Gln
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S
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Ser
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T
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Thr
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C
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Cys
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A
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Ala
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G
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Gly
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V
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Val
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L
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Leu
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I
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Ile
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P
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Pro
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F
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Phe
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M
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Met
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W
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Trp
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Y
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Tyr
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Imidazole
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Indole
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amide
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guanidine
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Henderson-Hasselbalch Equation
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|
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Disulfide bond breakage
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by oxidation or reduction
Mercaptoethanol Dithiothreitol (DTT) heating does not break disulfide bonds |
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β-turns
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usually between antiparallel β-sheet segments
most use Proline as second member from n-terminal to bend chain: _ - Pro _ - _ |
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β-sheets
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adjacent sheets require small R-groups
can be parallel or antiparallel |
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α-helix
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1 turn = 5.4Å, 3.6 AA residues
G and P unfavorable in a helix net dipole along axis, δ+ at N-term - 4 AAs at either end not fully H-bonded - + charged AAs found at N-term - - charged AAs found at C-term R groups interact with other Rs 3 or 4 AAs away Bulkiness of adjacent AAs affects stability of helix |
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Histidine
His H |
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Relationship of S, G, and H
and units |
ΔG = ΔH - TΔS
ΔG, ΔH in J/mol ΔS in J/(mol * K) |
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ΔG°, ΔS°, K°eq etc.
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Standard constants:
298 K, all reactants at 1M which implies that pH = 1 |
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ΔG'°, ΔS'°, K'°eq etc.
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Transformed standard constants:
pH = 7 (ΔG'°, ΔS'° etc. are constants, ΔG, ΔS, etc. depend on conditions) |
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Biochemical simplifying conventions
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pH = 7
if H2O, H+, and/or Mg2+ are reactants or products, concentrations not included in equations (incorporated into transformed constants etc.) |
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relationship between K'eq and ΔG'°
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ΔG'° = -RT ln K'eq
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Relationship between ΔG'° and ΔG
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ΔG = ΔG'° + RT ln Q
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Q (not glutamine)
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mass action ratio
for wA + xB <=> yC + zD Q= ([A]^w [B]^x) / ([C]^y [D]^z) |
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Acid and base net charges when pH is less than or greater than pKA?
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Acid protonated below pH = pKA, charge = 0
Acid deprotonated above pH = pKA, charge = -1 Base protonated below pH = pKA, charge = +1 Base deprotonated above pH = pKA, charge = 0 |
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Nernst equation
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E = E° + (RT/nF) ln ([e-acceptor]/[e-donor]
= E° + 0.026V / n ..... |
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Free-energy change from reduction potentials
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ΔG'° = -nF ΔE'°
ΔG = -nF ΔE |
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Standard Reduction Potential
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E° = relative affinity of electron acceptor
electrons move from lower to higher E°; acceptor has higher E° ΔE'° = E'° of electron acceptor - E'° of electron donor |