BC basic - from big bang

1
Hydride, Hydrogen and Proton
hydride
-
Hydrogen atom
Juang RH (2004) BCbasics
2
Proton Is Adsorbed or Desorbed
Proton abundant and small, affects the charge of
a molecule
lone pair electrons
pKa
H
pKa
Ampholyte contains both positive and negative
groups on its molecule
Juang RH (2004) BCbasics
3
Acidic environment
Neutral environment
Alkaline environment
NH2 H
COOH
5.5
0
1
-1
Isoelectric point
Juang RH (2004) BCbasics
4
Amino Acids Have Buffering Effect
pH
pK2
?
pI
Isoelectric point
?
pK1
OH ?
Juang RH (2004) BCbasics
5
Environment pH vs Protein Charge
Buffer pH
Isoelectric point, pI

-
0
-
Net Charge of a Protein
Juang RH (2004) BCbasics
6
pKa of Amino Acid Residues
Residues on amino acids can release or accept
protons
pKa 1.82.4
pKa 3.94.3
pKa 6.0
pKa 8.3
pKa 10
pKa 8.811
pKa 1012.5
Smaller pKa releases proton easier
Only His has the residue with a neutral pKa
(imidazole)
pKa of a carboxylic or amino groups is lower than
pKa of the R residues
Juang RH (2004) BCbasics
7
pKa of Amino Acids
Amino acids -COOH -NH2 -R Gly G 2.34 9.60 Ala A
2.34 9.69 Val V 2.32 9.62 Leu L 2.36 9.68 Ile I
2.36 9.68 Ser S 2.21 9.15 Thr T 2.63 10.4 Met
M 2.28 9.21 Phe F 1.83 9.13 Trp W 2.38 9.39 Asn
N 2.02 8.80 Gln Q 2.17 9.13 Pro P 1.99 10.6 As
p D 2.09 9.82 3.86 Glu E 2.19 9.67 4.25 His H 1.82
9.17 6.0 Cys C 1.71 10.8 8.33 Tyr Y 2.20 9.11 10.
07 Lys K 2.18 8.95 10.53 Arg R 2.17 9.04 12.48
two pKa
pK2
pI
pK1
three pKa
pK3
?
pK2
?
pI ?
pK1
Juang RH (2004) BCbasics
8
Aspartic acid
first
1
Isoelectric point is the average of the two pKa
flanking the zero net-charged form
pK1 2.1
second
0
3.0
Isoelectric point
pK2 3.9
-1
third
pK3 9.8
-2
OH
Juang RH (2004) BCbasics