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46 Cards in this Set

  • Front
  • Back
Aromatic AAs (3)
Phe F
Trp W
Tyr Y
Negatively charged AAs (2)
Asp D
Glu E
Positively charged AAs (3)
Arg R
Lys K
His H
Polar uncharged AAs (5)
Asn N
Gln Q
Ser S
Thr T
Cys C
Nonpolar aliphatic (7)
Ala A
Gly G
Val V
Leu L
Ile I
Pro P
Met M
D
Asp
E
Glu
R
Arg
K
Lys
H
His
N
Asn
Q
Gln
S
Ser
T
Thr
C
Cys
A
Ala
G
Gly
V
Val
L
Leu
I
Ile
P
Pro
F
Phe
M
Met
W
Trp
Y
Tyr
Imidazole
Indole
amide
guanidine
Henderson-Hasselbalch Equation
Disulfide bond breakage
by oxidation or reduction
Mercaptoethanol
Dithiothreitol (DTT)


heating does not break disulfide bonds
β-turns
usually between antiparallel β-sheet segments

most use Proline as second member from n-terminal to bend chain:

_ - Pro _ - _
β-sheets
adjacent sheets require small R-groups

can be parallel or antiparallel
α-helix
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
Histidine
His
H
Relationship of S, G, and H

and units
ΔG = ΔH - TΔS

ΔG, ΔH in J/mol
ΔS in J/(mol * K)
ΔG°, ΔS°, K°eq etc.
Standard constants:

298 K, all reactants at 1M which implies that pH = 1
ΔG'°, ΔS'°, K'°eq etc.
Transformed standard constants:

pH = 7

(ΔG'°, ΔS'° etc. are constants, ΔG, ΔS, etc. depend on conditions)
Biochemical simplifying conventions
pH = 7

if H2O, H+, and/or Mg2+ are reactants or products, concentrations not included in equations (incorporated into transformed constants etc.)
relationship between K'eq and ΔG'°
ΔG'° = -RT ln K'eq
Relationship between ΔG'° and ΔG
ΔG = ΔG'° + RT ln Q
Q (not glutamine)
mass action ratio

for wA + xB <=> yC + zD

Q= ([A]^w [B]^x) / ([C]^y [D]^z)
Acid and base net charges when pH is less than or greater than pKA?
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
Nernst equation
E = E° + (RT/nF) ln ([e-acceptor]/[e-donor]

= E° + 0.026V / n .....
Free-energy change from reduction potentials
ΔG'° = -nF ΔE'°

ΔG = -nF ΔE
Standard Reduction Potential
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