Download LECT05 amino acids

Amino Acids
• Colorless, crystalline, water soluble
substances
• Distinguishing features are a -COOH
group and a -NH3 group attached to the
same carbon
• R group gives individuality
• R group varies from a simple H to a
complex phenyl ring
• Classification reflects structural feature
or property of R groups
Classification
Non-Polar
glycine
alanine
valine
leucine
isoleucine
methionine
proline
phenylalanine
tryptophan
Polar but Uncharged
serine
threonine
asparagine
glutamine
tyrosine
cysteine
Polar charged (+)
lysine
arginine
histidine
Polar charged (-)
aspartic acid
glutamic acid
Charges on Amino Acids
R
H
a
pKa = 2
C-COOH
N:
H
H
pKa = 9.5
a
R
See Tutorial
“Ionization” on
Web
H
C-COO
+N
H
H
H
Zwitterion
(Rhymes with “bitter ion”)
GLYCINE
Alanine
Serine
COO H C - CH
CH23OH
H
NH3
Stereochemistry
Carboxyl group up
Chiral center
COO-
H3N *C
Amine group
left
R
H
L-amino acid
When R=H, no chiral center
Take Home: All amino acids that occur in proteins are of the
L configuration
Chirality or “handedness”
4 Different Substituents
+
H3 N
COO
C H
R
L
R
D
Mirror Image
L
L
H
COO
+
C NH3
D
Chiral Center
Mirror Image
Not Reproduced
No Chiral Center
Mirror Image
Reproduced
CHARGE ON AMINO ACIDS DEPENDS ON
pH OF SOLUTION
+ COOH
H3N C H
CH3
+ COO
H3N C H
CH3
+1
0
COO
H2N C H
CH3
-1
Conjugate
Conjugate
pH 1-2
pH 3-8
pH 9-12
Amino Acid
Glycine
Alanine
Valine
Leucine
Isoleucine
Serine
Threonine
Methionine
Phenylalanine
Tryptophan
Asparagine
Glutamine
Proline
Cysteine
Histidine
Aspartic acid
Glutamic acid
Tyrosine
Lysine
Arginine
Abbreviations
Gly
Ala
Val
Leu
Ile
Ser
Thr
Met
Phe
Trp
Asn
Gln
Pro
Cys
His
Asp
Glu
Tyr
Lys
Arg
G
A
V
L
I
S
T
M
F
W
N
Q
P
C
H
D
E
Y
L
R
pK1
pK2
2.34
2.34
2.32
2.36
2.36
2.21
2.63
2.28
1.83
2.83
2.02
2.17
1.99
1.71
1.82
2.09
2.19
2.2
2.18
2.17
9.6
9.69
9.62
9.6
9.6
9.15
10.43
9.21
9.13
9.39
8.8
9.13
10.6
10.78
9.17
9.82
9.67
9.11
8.95
9.04
2.20
9.52
pK3
8.33
6.0
3.86
4.25
10.07
10.79
12.48
Table 1: Approximate pK values for Ionizable Groups in Amino Acids
Group
a-carboxyl
a-amino
-carboxyl
-carboxyl
imidazole N
thiol SH
phenolic OH
-amino
guanidinium N
Amino Acid
Approx. pK
All
All
Aspartic acid
Glutamic acid
Histidine
Cysteine
Tyrosine
Lysine
Arginine
2.0
9.5
4.0
4.0
6.0
8.5
10.5
10.5
12.5
estimate charges on the molecule for a given pH.
Know these values
Biochemical Strategies
p. 32
Titration Curve for an Amino Acid
pK2=9.5
COOH
H-N-C-H
H
H
+H
pK1=2
+
Glycine
To draw a titration
curve, (1) determine
number of dissociable
groups, (2) place pK
values in center
of range (3) draw
curve.
H3N-
9.5
-COOH
H2N-
pH
+
H3N-
-COOH
2.0
-COO-
0
0.5
1.0
1.5
Equivalents OH-
2.0
+ COOH + COO
H3N-C-H
H3N-C-H
+ COO + COO
H3N-C-H H3N-C-H
+ COO
H3N-C-H
-
COOH2N-C-H
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
CH2
COOH
COOH
COOH
COO-
COO-
COO-
pK3 = 9.5
8
+ COOH
H3N-C-H
pK2 = 4.0
pH
pK1 = 2.0
CH2
4
CH2
COOH
2
0
See Strategies
p. 33
L-Glutamate
1.0
2.0
Equivalents of OH-
3.0
Isoelectric Points (pI) of Amino Acids
1. pH at neutral charge (note the word “pH” in the definition)
2.
pI =
pK1 + pK2
2
pI
pK1
pK2
pK1 + pK2
2
Simple Amino Acid
pI for an Amino Acid with a Charged R Group
3
+ COOH
H3N C H
CH2
COOH
pK = 9.5
1
2
pK = 2
Rule: Always use the
2 pKs that border the
“0” charged species
pK = 4
8
?
pH
6
4
+1
?
2
pK1
pK2
pK3
0
-1
-2
Isoelectric Point of Lysine
pI = about 10
COO H
+
12
H3N-C-H
10
CH2
CH2
CH2
CH2
H3N +
pH 7 = +1
pH 1= +2
pK3= 10.5
8
pK2= 9.5
6
4
pK1= 2
2
+2
+1
-1
0
Lysine is a basic amino acid
pI = pK2 + pK3
2
=
9.5 + 10.5
2
= 10
See Strategies, p 35
Table 2: Classification of Amino Acids based on R group Features
Aromatic
Phenylalanine
Tyrosine
Tryptophan
Hydroxy
Serine
Threonine
Sulfur
Cysteine
Cystine
Methionine
Basic
Amide
Lysine
Histidine
Arginine
Asparagine
Glutamine
Hydrophobic
Acidic
Leucine
Isoleucine
Valine
Aspartic acid
Glutamic acid
Non-polar
Polar noncharged
Charged
acidic
Charged
basic
+
CH2
CH2
CH2
NH
H2N=C
NH2
Guanidino
L-Arginine
CH2
HN
NH
+
Imidazole
L-Histidine
COO
+
H3N C H
H
Glycine
CH2
CH2
S
CH3
Thioether
L-Methionine
CH2
CH2
COOL-Glutamate
CH3
CH2
L-Alanine
H3C
CH3
Isopropyl
L-Valine
CH2
Phenyl
L-Phenylalanine
CH2OH
L-Serine
CH2SH
L-Cysteine
COO
+
H3N C H
CH2
CH2
COO-
N
H
L-Proline
CH2
Secondary amine
*
H-C-OH
CH3
L-Threonine
N
H
CH2
CH2
H3N+
L-Lysine
Indole ring
L-Tryptophan
See Tutorial on
Amino Acid
Structures on
Web
A = Alanine
C = Cysteine
D = Aspartic acid
K= Lysine
L = Leucine
M = Methionine
T = Threonine
V = Valine
W = Tryptophan
E = Glutamic acid
F = Phenylalanine
G = Glycine
N = Asparagine
P = Proline
Q = Glutamine
Y = Tyrosine
H = Histidine
I = Isoleucine
R = Arginine
S = Serine