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Hydride, Hydrogen and Proton
hydride
1s
-
-
Proton
+
+
-
-
+
-
Hydrogen atom
1
H
1.008
Juang RH (2004) BCbasics
Proton Is Adsorbed or Desorbed
Proton： abundant and small, affects the charge of a molecule
lone pair
electrons
Amino
High pKa Low
N H
H+
H+
N H
H
H
Low pKa High
Carboxylic
C
O H
O
O
C
O
H+
Ampholyte contains both positive and negative groups on its molecule
Juang RH (2004) BCbasics
Acidic environment
Neutral environment
Alkaline environment
pK2 ~ 9
NH2 H+
R-C-H
COOH
NH2 H+
R-C-H
COOpK1 ~ 2
+1
NH2
R-C-H
COO-
5.5
0
Isoelectric point
-1
Juang RH (2004) BCbasics
Amino Acids Have Buffering Effect
pH 12
★
pK2
Isoelectric point =
pI
9
NH2 H+
6
H-C-R
COO-
3
★
pK1 + pK2
2
pK1
0
[OH] →
Juang RH (2004) BCbasics
Environment pH vs Protein Charge
Buffer pH
10
9
8
7
Isoelectric point,
pI
+
6
5
4
3
0
-
-
Net Charge of a Protein
Juang RH (2004) BCbasics
pKa of Amino Acid Residues
Residues on amino acids can release or accept protons
a -COOH
R -COOH
His -Imidazole·H+
Cys -SH
Tyr -OH
a -NH3+
R -NH3+
a -COOR -COO-
+ H+ pKa = 1.8~2.4
+ H+ pKa = 3.9~4.3
His -Imidazole + H+ pKa = 6.0
+ H+ pKa = 8.3
Cys -S+ H+ pKa = 10
Tyr -Oa -NH2
R -NH2
+ H+ pKa = 8.8~11
+ H+ pKa = 10~12.5
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
pKa of Amino Acids
Amino acids
-COOH -NH2
Gly
Ala
Val
Leu
Ile
Ser
Thr
Met
Phe
Trp
Asn
Gln
Pro
Asp
Glu
His
Cys
Tyr
Lys
Arg
2.34
2.34
2.32
2.36
2.36
2.21
2.63
2.28
1.83
2.38
2.02
2.17
1.99
2.09
2.19
1.82
1.71
2.20
2.18
2.17
G
A
V
L
I
S
T
M
F
W
N
Q
P
D
E
H
C
Y
K
R
9.60
9.69
9.62
9.68
9.68
9.15
10.4
9.21
9.13
9.39
8.80
9.13
10.6
9.82
9.67
9.17
10.8
9.11
8.95
9.04
-R
pH
two pKa
pK2
pI
pK1
pK1 + pK2
2
three pKa
pK3
3.86
4.25
6.0
8.33
10.07
10.53
12.48
pK2
pK1
?
?
pI ?
[OH-]
Juang RH (2004) BCbasics
H
first
HOOC-CH2-C-COOH
NH3+
+1
pK1 = 2.1
H
second
HOOC-CH2-C-COO-
Aspartic acid
Isoelectric point is the average
of the two pKa flanking the
zero net-charged form
2.1 + 3.9
= 3.0
2
Isoelectric point
0
NH3+
pK2 = 3.9
H
-OOC-CH -C-COO2
-1
NH3+ third
pK3 = 9.8
H
-OOC-CH -C-COO2
NH2
-2
-2
pK3
-1
pK2
pK1
0
+1
[OH]
Juang RH (2004) BCbasics