1

AMINO ACIDS
AMINO ACIDS
are the structural units (monomers) that make
up proteins
R C COO
-
H
NH
3
+

Stereochemistry
Classification
Properties: reactions
NH
3
+
H
COO
-
R
`
H
3
+
N
H
COO
-
R
Enantiomers: identical chemical and physical properties but one:
the rotation oI the polarized light
Stereochemistry of amino acids
Nomenclature of stereoisomers
COO
-
C
+
H
3
N H
R
L-Amino acid D-Amino acid
COO
-
C H NH
3
+
R
Chemically identical/ Physically almost identical
Biologically different! Biologically different!
L-Amino acid D-Amino acid
Stryer 5
th
ed.
2
CLASSIFICATION OF
AMINO ACIDS
20 standard amino acids
Properties of their R groups
Nonpolar, aliphatic R groups
H
Glycine(Gly; G)
CH
3
Alanine (Ala; A)
CH
Valine (Val; V)
CH
3
CH
3
CH
Leucine (Leu; L)
CH
3
CH
3
CH
2
Isoleucine (Ile; I)
CH
Proline (Pro; P)
HN
COOH
CH
3
CH
3
CH
2
Methionine (Met; M)
CH
2
S CH
3
CH
2
Aromatic R groups
CH
2
Phenylalanine
(Phe; F)
CH
2
Tyrosine
(Tyr; Y)
OH
CH
2
Tryptophan
(Trp; W)
NH
Polar, uncharged R groups
Serine (Ser; S) Threonine (Thr; T) Cysteine (Cys; C)
Asparagine (Asn; N)
OH
CH CH
3
Glutamine (Gln; Q)
CH
2
OH
CH
2
SH
CH
2
C
O
NH
2
CH
2
C
O
NH
2
CH
2
Negatively charged {acid) R groups
CH
2
Aspartate (Asp; D)
CH
2
COO
-
CH
2
COO
-
Glutamate (Glu; E)
Positively charged {basic) R groups
Lysine (Lys; K)
Arginine (Arg; R)
CH
2
CH
2
NH
3
+
CH
2
CH
2
NH
2
+
CH
2
CH
2
C NH CH
2
NH
2
Histidine (His; H)
HN NH
+
CH
2
3
Lehninger 4
th
ed.
Non standard amino acids
Modifications of standard residues
already incorporated into a protein
Amino acids that are not constituents of
proteins
Cystine
4-Hydroxyproline
5-Hydroxylysine
Phosphoserine, desmosine, 6-N-metyl-lysine,
-carboxyglutamate, etc
SH
SH
S
S
HN
COOH
OH
CH
2
CH
2
NH
3
+
CH
2
CH
NH
3
+
CH
-
OOC
OH
Ornithine
Citruline
L-Homoserine
-Alanine
.
CH
2
CH
2
NH
3
+
NH
3
+
CH
-
OOC CH
2
CH
2
CH
2
NH
3
+
CH
-
OOC CH
2
O
C NH NH
2
CH
2
OH
NH
3
+
CH
-
OOC CH
2
CH
2
CH
2
-
OOC NH
3
+
Amino acid derivatives
Histamine
GABA
Dopamine
Thyroxine, S-adenosylmethionine, etc
CH
2
CH
2
NH
3
+
HO
HO
CH
2
NH
3
+
CH
2
-
OOC CH
2
HN NH
+
CH
2
CH
2
+
H
3
N
Properties of the
amino acids
Absorption spectrum
Reactions
Acid-base properties
4
Stryer 5
th
ed.
Chemical reactions of
amino acids
Characteristics of their functional groups
They can be used for:
- detection
- quantification
- identification
- synthesis of polypeptides
Reactions of the -carboxyl group
Formation of an ester
Formation of an amide
Reduction to alcohol
OH
O
C R + R` HO O R`
O
C R
OH
O
C R + R` H
2
N N R`
O
C R
H
OH
O
C R + reductant OH
H
C R
Reactions of the -amino group
Formation of an amide
OH
O
C R + R` H
2
N N R`
O
C R
H
Reactions of the R group
-COOH y -NH
2
groups: the same as -COOH and
-NH
2
Reactions of specific groups (thiol, tyrosine -OH,
indole group, guanidinium group, etc)
Reaction of the sulfhydryl group (-SH)
Cysteine oxidation
SH
Disulfide bond
S Cys Cys + S Cys HS Cys
5
Acid-base properties of
amino acids
Brnsted and Lowry 1heory:
Acid. hvdrogen ion donor
Base. hvdrogen ion acceptor
pK -log K
If K
a
is large (pK low), the acid is largelv dissociated so
the acid is 'quite strong`
If K
a
is small (pK high), verv little of the acid is dissociated
so the acid is 'quite weak`
AH A
-
H

K
[A
-
] [H

]
[AH]
Brnsted and Lowry 1heory:
Acid. hvdrogen ion donor
Base. hvdrogen ion acceptor
AH is an acid
A
-
is its confugated base
AH A
-
H

K
[A
-
] [H

]
[AH]
Acids and bases in Biochemistry
Carboxyl group (-COOH)
Sulfhydryl group (-SH)
Hydroxyl group (-OH)
Amino group (-NH
2
)
pH
pH is an easy way to express how acidic or basic a
solution is
The pH in a solution is equal to the negative logarithm of
the concentration of hydronium ions (H
3
O
+
)
pH = -log [H
+
]
[H
+
] = 10
-pH
Acidic and basic solutions are defined by their pH value:
Acidic solution: pH is less than 7
Basic solution: pH is higher than 7
Neutral solution: pH is equal to 7
6
pH = -log [H
+
]
CH
3
COOH
Acetic acid Acetate
CH
3
COO
-
+ H
+
K
a

[Ac
-
j [H
+
j
[AcHj
pH pK
a
+ log
[Ac
-
j
[AcHj
If: pH pK
a
1 [Ac
-
j [AcHj
pH < pK
a
< 1 [Ac
-
j < [AcHj
pH > pK
a
> 1 [Ac
-
j > [AcHj
[Ac
-
j
[AcHj
[Ac
-
j
[AcHj
[Ac
-
j
[AcHj
| Acid |
| Base |
log pK pH
a
+ =
Henderson-Hasselbalch Equation
M
o
l
a
r

f
r
a
c
t
i
o
n
0.5
1
AcH Ac
-
pK
a
= 4.7
pH
CH
3
COOH CH
3
COO
-
+ H
+
NH
3
+
CH R COOH
(+1) (0)
Dipolar ion or
Zwitterion
(-1)
K
1
NH
3
+
CH R COO
-
K
2
NH
2
CH R COO
-
Glycine
Stryer 5
th
ed.
7
NH
3
+
CH R COOH
(+1) (0)
K
1
NH
3
+
CH R COO
-
K
1

[j [H
+
j
[+1j
pH pK
1
+ log
[j
[+1j
If: pH pK
1
1 [j [+1j
pH < pK
1
< 1 [j < [+1j
pH > pK
1
> 1 [j > [+1j
[j
[+1j
[j
[+1j
[j
[+1j
(0)
NH
3
+
CH R COO
-
K
2
NH
2
CH R COO
-
(-1)
K
2

[-1j [H
+
j
[j
pH pK
2
+ log
[-1j
[j
If: pH pK
2
1 [-1j [j
pH < pK
2
< 1 [-1j < [j
pH > pK
2
> 1 [-1j > [j
[-1j
[j
[-1j
[j
[-1j
[j
M
o
l
a
r

f
r
a
c
t
i
o
n

o
f

g
l
y
c
i
n
e
0.5
pK
1
2.4 pI 6.1
1
(+)
(0)
(-)
pK
2
9.8 pH
Isoelectric point
pI
pK
1
pK
2
2
Stryer 5
th
ed. Stryer 5
th
ed.
8
NH
3
+
CH COOH
(+2)
pK
1
(CH
2
)
4
NH
3
+
2.2
NH
3
+
CH COO
-
(+1)
pK
2
(CH
2
)
4
NH
3
+
9.2
NH
2
CH COO
-
(0)
pK
R
(CH
2
)
4
NH
3
+
10.8
NH
2
CH COO
-
(-1)
(CH
2
)
4
NH
2
Lysine
NH
3
+
CH COOH
(+1)
pK
1
CH
COOH
2
NH
3
+
CH COO
-
(0)
pK
R
CH
COOH
3.9
NH
3
+
CH COO
-
(-1)
pK
2
CH
COO
-
10
NH
2
CH COO
-
(-2)
CH
COO
-
Aspartate
When acids and bases are mixed they neutralize
each other
AcH + OH
-
Ac
-
+ H
2
O
Neutralization reaction
Ac
-
+ H
+
AcH + H
2
O
If an acid is added:
Ac
-
+ H
+
AcH + H
2
O
AcH Ac
-
Buffer solutions
AcH + OH
-
Ac
-
+ H
2
O
If a base is added:
A solution consisting of a mixture of a weak acid and its
conjugate base is a buffer solution
Blood is a buffer solution
The normal pH in human blood is 7.4
To maintain this pH, our body uses three main systems:
Carbonate buffer: H
2
CO
3
/ HCO
3
-
Phosphate buffer: H
2
PO
4
-
/ HPO
4
2-
Proteins