The Amino Acids

II. Acid-Base Characteristics

The Rosy Maple Moth

(Dryocampa rubicunda)

non-ionized form of amino acid

does not exist in appreciable amounts

H2N C C
OH
H

R
+

fully ionized form of amino acid

-major form at physio pH (6.8-7.2)

H3N C C
O
H
note all amino acids
have ionized carboxyl
group above pH 2
and ionized amino
group below
pH 9-10

Before we talk about the ionization of amino acids

lets review the concept of pKa and the acid dissociation constant

Because Ka values vary over a wide range, they are expressed using a log scale:

pKa = -log10Ka

The lower the pKa the stronger the acid.

The dissociation of a weak acid can be represented by the following equation:

HA

H+

conjugate base of HA

weak acid

Ka

A-

[H+][A-]

where Ka is the acid dissociation constant. The larger

the Ka, the stronger the acid.

[HA]

in terms of an actual acid, acetic acid

we could write

H+
weak acid, acetic acid
(CH3COOH)

conjugate base, acetate ion

(CH3COO- )

or
CH3COOH

H+

CH3COO-

CH3COOH
Ka

[H+][CH3OO-]
[CH3COOH]

H+

CH3COO-

1.76 x 10-5

so Ka is the acid dissociation constant and indicates the extant to which an

acid is dissociated in an aqueous medium when at equilibrium.
Lets put this number another way - the percent of the acetic acid molecules
that are dissociated when at equilibrium:

we can solve for the concentrations of the dissociated products in a 0.1 M solution:

Ka

1.76 x 10-5

1.76 x 10-5

[H+][CH3COO-]

[CH3COOH]

[H+] [CH3COO-]
[CH3COOH]

x2
0.1 M

x = 1.33 x 10-3 M = [CH3COO-]

1.33 x 10-3 M
% dissociation =
0.1 M
CH3COOH

H+

= 0.0133 x 100
+

CH3COO-

= 1.33 %

so, the pKa is just a value that indicates the extent to which an acid dissociates
in aqueous solution at equilibrium
the lower the pKa, the more dissociation and the stronger the acid

H+

weak acid, acetic acid

(CH3COOH)

weak acid, formic acid

(HCOOH)

pKa =4.76

conjugate base, acetate ion

(CH3COO- )

H+

conjugate base, formate ion

(HCOO- )

pKa =3.75

+ H+

conjugate base, acetate ion

(CH3COO- )

H+

incorrect

correct

+ H+

pKa =4.76

acetate ion

formate ion

H+

pKa =3.75

pKa =4.76

conjugate base, acetate ion

(CH3COO- )

conjugate base, formate ion

(HCOO- )

pKa =3.75

H+

weak acid, acetic acid

(CH3COOH)

conjugate base, acetate ion

(CH3COO- )

H+

weak acid, formic acid

(HCOOH)

ethanol
(CH3CH2OH )

pKa =4.76

pKa =3.75

conjugate base, formate ion

(HCOO- )

H+

conjugate base, ethoxide ion

(CH3CH2O- )

pKa =15

non-ionized form of amino acid

does not exist in appreciable amounts

H2N C C
OH
H

R
+

fully ionized form of amino acid

-major form at physio pH (6.8-7.2)

H3N C C
O
H
note all amino acids
have ionized carboxyl
group above pH 2
and ionized amino
group below
pH 9-10

pKa 2.21 9.15 --

pKa 2.20 9.11 10.07

end of pKa review

The Ionization of Amino acids

All amino acids possess two ionizable groups, the amino group and the carboxyl
group.
seven of the amino acids also possess ionizable side chains as well.
the ionization of these groups follow simple acid-base chemistry rules
since amino acids (and proteins) are most relevant at physiological pH (6.8-7.4)
we are most interested in their ionic states around this pH
the ionic state of an amino acid influences its reactivity and its ability to participate
in chemical reactions

non-ionized form of amino acid

does not exist in appreciable amounts

H2N C C
OH
H

R
+

fully ionized form of amino acid

-major form at physio pH

H3N C C
O
H
note all amino acids
have ionized carboxyl
group above pH 2
and ionized amino
group below
pH 9-10

recall,
that for any acid, say, the amino acid alanine:

NH3CHCH3COOH
Ka

H+ + NH3CHCH3COO-

[H+][NH3CHCH3COO-]
[NH3CHCH3COOH]

and

pKa = -log10Ka

CH3

H2N C C
OH
H
O
C
OH

CH3

H3N C C
O
H
pKa = 2.3

O
C

at pH < pKa the protonated form (weak acid) predominates

at pH > pKa, the ionized (conjugate base) form predominates
since physiological pH is 7, the carboxylate group is always
unprotonated
when the pH = pKa, both forms have equal concentrations

Verification using the Henderson-Hasselbalch equation

When the environmental pH is equal to the pKa:

pH = pKa + log [COO ]

[COOH]
-]
[COO
2.3 = 2.3 + log
[COOH]
-]
[COO
0 = log
[COOH]
100 = [COO ]
[COOH]
-]
[COO
1 =
[COOH]

solve for the ratio of

conjugate base/weak acid
by taking antilog of 0
thus when pH = pKa, the
concentrations of both
species are equal

Practice Questions (Solutions will be posted on D2L).

1.

When the pH = pKa of the ionization of the carboxyl group on an amino acid,
the protonated and unprotonated forms of the carboxyl group are at
equal concentrations in a population of amino acid molecules.

Calculate the ratio of protonated to unprotonated carboxyl groups (pKa 2.3)

when the environmental pH is pH 1.0 (i.e less than the pKa).
Calculate the ratio at pH 5.

We can do the same thing for the amino group on alanine

CH3

H2N C C
OH
H
+NH
3

CH3

H3N C C
O
H
pKa = 9.7

NH2

at pH < pKa the protonated form predominates

at pH > pka, the unprotonated form predominates
since physiological pH is 7, the amino group is always
protonated and this gives it a positive charge
when the pH = pKa, both forms have equal concentrations

The changing ionic (charge) state of an amino acid as pH increases

4. At pH above 9.7, the amino

group loses its proton.

3. At physiological pH, both

groups are ionized.

1. At pH less than 2.3

both groups are protonated
since pH is below both their
pKas.

2. When pH = pKa (2.3), protonated

and non-protonated carboxyl
groups at equal concentrations.

so, at any pH between 2.3 and 9.7 (which includes physiological pH range of 6.8-7.4)
both the amino and carboxylate groups are ionized

notice this graph introduces

a new quantity, pI
pI means isoelectric point
pI for an amino acid is
the pH at which the
predominant form of the
amino acid is neutral.
i.e no net charge

so, the pI is the pH at which the amino acid carries no net charge (is neutral)
Calculating the Isoelectric point (pI) for the amino acid alanine:

pI =

pI =

(pK1 + pK2)

2
(2.3 + 9.7)

pI = 6

2
therefore, alanine is a neutral
chemical at pH of 6

All amino acids possess ionizable amino and carboxyl groups, but seven of the
amino acids also have ionizable side chains as well.

Predict the form of the side chain at physiological pH (pH 6.8-7.4)

pH > pKa
pH < pKa

pH < pKa

pH > pKa
pH < pKa
pH < pKa
Remember:

pH < pKa group is protonated

pH > pKa group is unprotonated

Calculating the pI for amino acids with ionizable side chains is straight-forward
but a little different than for amino acids without ionizable side chains.

Consider the negatively charged amino acid glutamate

Glutamate:

2.19

4.25

9.67

9.67

pKacarboxyl = 2.19
pKaamino = 9.67
pKasidechain = 4.25

Notice that the calculation of pI

always involves the pKas that
bracket the neutral charge

4.25
2.19

Notice that at pH above its

pI, glutamate is predominantly
negatively charged

Nelson p85

(pK1 + pK2)
pI =

(2.19 + 4.25)
=

= 3.22

Consider the positively charged amino acid lysine

Lysine:
2.18

10.79

8.95

10.79

pKacarboxyl = 2.18
pKaamino = 8.95
pKasidechain = 10.79

8.95

2.18

Notice that at pH below its

pI, lysine is predominantly
positively charged

Nelson p85

(pK2 + pK3)
pI =

(10.79 + 8.95)
=

= 9.87

Practice Questions (Solutions will be posted on D2L).

2. Given the above data, calculate the pI for the amino acid isoleucine.
3. Calculate the pI for the amino acid tyrosine.

Proteins are of course long polymers of amino acids

To understand the structure and function of proteins, we need to understand
the structure and function of amino acids.

the pentapeptide Tyrosine-Glycine-Glycine-Phenylalanine-Leucine

Essential vs non-essential amino acids for humans

Essential in this context means required in diet
-all amino acids are actually essential for life

Essential

Non-essential

Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

Cysteine
Alanine
Serine
Tyrosine
Proline
Glutamate
Aspartate
Arginine
Glutamine
Asparagine
Glycine

Structure of
glucose

CHNOPS