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
Non-Polar Polar but Uncharged Polar charged (+)
glycinealaninevalineleucineisoleucinemethionineprolinephenylalaninetryptophan
serinethreonineasparagineglutaminetyrosinecysteine
lysineargininehistidine
Polar charged (-)
aspartic acidglutamic acid
Classification
Charges on Amino Acids
COOHC-
H
R
Zwitterion(Rhymes with “bitter ion”)
pKa = 2
pKa = 9.5
N:
H H
R C-
COO
N
H
+H
H
H
See Tutorial “Ionization” on
Web
See Tutorial “Ionization” on
Web
GLYCINE
H C -
NH3
COO -
HCH3
Alanine
CH2OH
Serine
Stereochemistry
COO-
CH3N H
R
L-amino acid*
Amine group left
Chiral center
Take Home: All amino acids that occur in proteins are of the L configuration
Carboxyl group up
When R=H, no chiral center
Chirality or “handedness”
4 Different Substituents
L L D
COO
H3N HC+
R
COO
H C
R
NH3
+
L D
Mirror Image
Mirror ImageReproduced
Mirror ImageNot Reproduced
Chiral Center No Chiral Center
CHARGE ON AMINO ACIDS DEPENDS ON
pH OF SOLUTION
COOHCCH3
H3N H+ COO
CCH3
H3N H+ COO
CCH3
H2N H
+ 1 0 -1
Conjugate Conjugate
pH 1-2 pH 3-8 pH 9-12
Glycine Gly G 2.34 9.6Alanine Ala A 2.34 9.69Valine Val V 2.32 9.62Leucine Leu L 2.36 9.6Isoleucine Ile I 2.36 9.6Serine Ser S 2.21 9.15Threonine Thr T 2.63 10.43Methionine Met M 2.28 9.21Phenylalanine Phe F 1.83 9.13Tryptophan Trp W 2.83 9.39Asparagine Asn N 2.02 8.8Glutamine Gln Q 2.17 9.13Proline Pro P 1.99 10.6Cysteine Cys C 1.71 10.78 8.33Histidine His H 1.82 9.17 6.0Aspartic acid Asp D 2.09 9.82 3.86Glutamic acid Glu E 2.19 9.67 4.25Tyrosine Tyr Y 2.2 9.11 10.07Lysine Lys L 2.18 8.95 10.79Arginine Arg R 2.17 9.04 12.48
2.20 9.52
Amino Acid Abbreviations pK1 pK2 pK3
Table 1: Approximate pK values for Ionizable Groups in Amino Acids
Group Amino Acid Approx. pK
-carboxyl All 2.0-amino All 9.5-carboxyl Aspartic acid 4.0-carboxyl Glutamic acid 4.0imidazole N Histidine 6.0thiol SH Cysteine 8.5phenolic OH Tyrosine 10.5-amino Lysine 10.5guanidinium N Arginine 12.5
estimate charges on the molecule for a given pH.
Know these values
Biochemical Strategies p. 32
Titration Curve for an Amino Acid
pK1=2pK2=9.5
pH
0 1.0 1.5 2.00.5
2.0
9.5 -COOH
Equivalents OH-
Glycine
-COOH
-COO-
H3N-+
H2N-
H3N-+
To draw a titrationcurve, (1) determinenumber of dissociable groups, (2) place pK values in centerof range (3) draw curve.
COOHH-N-C-H
H
H
H
+
pH
pK3 = 9.5
pK2 = 4.0pK1 = 2.0
0 1.0 2.0 3.0
2
4
8
Equivalents of OH-See Strategies p. 33
-HCOOHC
CH2
CH2
COOH
H3N-+
-HCOO-
C
CH2
CH2
COOH
H3N-+
-HCOO-
C
CH2
CH2
COOH
H3N-+
-HCOO-
C
CH2
CH2
COO-
H3N-+
-HCOO-
C
CH2
CH2
COO-
H3N-+
-HCOO-
C
CH2
CH2
COO-
H2N-
-HCOOHC
CH2
CH2
COOH
H3N-+
L-Glutamate
Isoelectric Points
1. pH at neutral charge (note the word “pH” in the definition)
(pI) of Amino Acids
2. pI = pK1 + pK2
2
pK1
pK2
Simple Amino Acid
pI
pK1 + pK2
2
pI for an Amino Acid with a Charged R Group
COOHC
CH2
COOH
H3N H+
1 pK = 2
2 pK = 4 3
pK = 9.5
2
4
6
8
pH
pK1pK2pK3
?
?
0 -1 -2
+1
Rule: Always use the 2 pKs that border the “0” charged species
COOC-HH3N-
+
CH2
CH2
CH2
CH2
H3N+
pH 7 = +1
H
pH 1= +2
2
4
6
8
10
12
+2 +1 0 -1
pI = about 10
pK1= 2
pK2= 9.5
pK3= 10.5
pI = pK2 + pK3
2=
9.5 + 10.5
2= 10
Lysine is a basic amino acid
Isoelectric Point of Lysine
Table 2: Classification of Amino Acids based on R group Features
Aromatic Sulfur Basic Amide
Phenylalanine Cysteine Lysine AsparagineTyrosine Cystine Histidine GlutamineTryptophan Methionine Arginine
Hydroxy Hydrophobic Acidic
Serine Leucine Aspartic acidThreonine Isoleucine Glutamic acid
Valine
See Strategies, p 35See Strategies, p 35
Non-polar
Polar non-charged
Charged acidic
Charged basic
CH2NN
CH2
HH
Imidazole
+
PhenylL-HistidineL-Phenylalanine
CH2
CH3H3CIsopropyl
L-Valine
Thioether
L-Methionine
SCH3
CH2
CH2
CH2
CH2
CH2
NHH2N=C
NH2
+
GuanidinoL-Arginine
CH2OHL-Serine
CH2SH
L-Cysteine
CH2CH2COO-
L-Glutamate
HGlycine
CH3
L-AlanineCCOO-
H3N H+
NCOO-
H
L-ProlineSecondary amine
L-Tryptophan
Indole ring
NH
CH2
CH2
CH2
CH2
CH2
H3N+
L-Lysine
L-Threonine
H-C-OH
CH3
*
CCOO-
H3N H+
See Tutorial on Amino Acid Structures on Web
See Tutorial on Amino Acid Structures on Web
A = AlanineC = CysteineD = Aspartic acid
E = Glutamic acidF = PhenylalanineG = Glycine
H = HistidineI = Isoleucine
K= LysineL = LeucineM = Methionine
P = ProlineQ = Glutamine
N = Asparagine
R = ArginineS = Serine
T = ThreonineV = ValineW = Tryptophan
Y = Tyrosine
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