lecture 9 - the amino acids ii _ acid-base characteristics

8/18/2019 Lecture 9 - The Amino Acids II _ Acid-Base Characteristics

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The Amino Acids

II. Acid-Base Characteristics

The Rosy Maple Moth(Dryocampa rubicunda)


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H3N – C – C

O

O-H

R

–

–+

H2N – C – C

O

OHH

R

–

–

non-ionized form of amino acid

does not exist in appreciable amounts

fully ionized form of amino acid

-major form at physio pH (6.8-7.2)

note all amino acids

have ionized carboxyl

group above pH 2

and ionized aminogroup below

pH 9-10


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Before we talk about the ionization of amino acids

lets review the concept of pKa and the acid dissociation constant


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

pKa = -log10KaThe lower the pKa the stronger the acid.

[HA] Ka

[A-] [H+]

=where Ka is the acid dissociation constant. The larger

the Ka, the stronger the acid.

HA A-H+ +

weak acid conjugate base of HA

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

in terms of an actual acid, acetic acid

we could write


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H+ +

weak acid, acetic acid

(CH3COOH)

conjugate base, acetate ion

(CH3COO- )

-

CH3COOH CH3COO-H+ +

or

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[CH3COOH]

Ka [CH3OO

-]

[H+

]= 1.76 x 10-5=

CH3COOH CH3COO-H+ +

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

acid is dissociated in an aqueous medium when at equilibrium.

Let’s put this number another way - the percent of the acetic acid molecules

that are dissociated when at equilibrium:


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[CH3COOH] K

a

[CH3COO-] [H+]

=1.76 x 10-5

=

[CH3COOH]

[H+]1.76 x 10-5 =

0.1 M

x2

=

x = 1.33 x 10-3 M =

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

[CH3COO-]

[CH3COO-]

% dissociation = 1.33 x 10-3

M

0.1 M = 0.0133 x 100 = 1.33 %

CH3COOH CH3COO-H+ +


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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)


(CH3COO- )

-

H+ +

weak acid, formic acid

(HCOOH)

conjugate base, formate ion

(HCOO- )

- H H

pKa =4.76

pKa =3.75

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(CH3COO- )

- H+ +

H+ + incorrect

correct


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-

H H+

+

H+ +

acetate ion

formate ion

δ+ δ-

pKa =4.76

pKa =3.75


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(CH3COO- )

-


(HCOO- )

- H

pKa =4.76

pKa =3.75

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H+ +

weak acid, acetic acid(CH3COOH)

conjugate base, acetate ion(CH3COO- )

-

H+ +

weak acid, formic acid

(HCOOH)


(HCOO- )

- H H

pKa =4.76

pKa =3.75

H+ +

HH

HH

- pKa =15

conjugate base, ethoxide ion(CH3CH2O- )

ethanol(CH3CH2OH )

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H3N – C – C

O

O-H

R

–

–+

H2N – C – C

O

OHH

R

–

–




-major form at physio pH (6.8-7.2)



group above pH 2


pH 9-10


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pKa 2.21 9.15 -- pKa 2.20 9.11 10.07


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end of pKa review


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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 participatein chemical reactions

f ll i i d f f i id


17/33

H3N – C – C

O

O-H

R

–

–+

H2N – C – C

O

OHH

R

–

–




-major form at physio pH



group above pH 2


pH 9-10


18/33

recall,

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

NH3CHCH3COOH H+ + NH3CHCH3COO-

and

[NH3CHCH3COOH]

Ka [NH3CHCH3COO-][H

+

]=

pKa = -log10Ka


19/33

H3N – C – C

O

O-H

CH3

–

–+

H2N – C – C

O

OHH

CH3

–

–

– C

O

OH – C

O

O-

pKa = 2.3

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

at pH > pKa, the ionized (conjugate base) form predominatessince physiological pH is 7, the carboxylate group is always

unprotonated

when the pH = pKa, both forms have equal concentrations

Veri ication using t e Hen erson Hasse a c equation


20/33

pH = pKa[COOH]

[COO-]

+ log

Veri ication using t e Hen erson-Hasse a c equation

When the environmental pH is equal to the pKa:

2.3 = 2.3

[COOH]

[COO-]

+ log

0 =[COOH]

[COO-]

log

100 =[COOH]

[COO-]

solve for the ratio of

conjugate base/weak acidby taking antilog of 0

1 =[COOH]

[COO-]

thus when pH = pKa, the

concentrations of both

species are equal


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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.


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

H3N – C – C

O

O-H

CH3

–

–+

H2N – C – C

O

OHH

CH3

–

–

+NH3 – pKa = 9.7

NH2 –

at pH < pKa the protonated form predominates

at pH > pka, the unprotonated form predominatessince 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


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1. At pH less than 2.3

both groups are protonated

since pH is below both their

pKa’s.

2. When pH = pKa (2.3), protonated

and non-protonated carboxyl

groups at equal concentrations.

3. At physiological pH, both

groups are ionized.

4. At pH above 9.7, the amino

group loses its proton.

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

( )


24/33

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


25/33

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 =2

(pK1 + pK2)

pI =2

(2.3 + 9.7)

pI = 6therefore, alanine is a neutral

chemical at pH of 6


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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)


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

Remember: pH < pKa → group is protonated

pH > pKa → group is unprotonated

pH > pKa

pH > pKa

pH < pKa

pH < pKa

pH < pKa

pH < pKa


28/33

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.

C id th ti l h d i id l t t


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Consider the negatively charged amino acid glutamate

pI =2

(pK1 + pK2)

=2

(2.19 + 4.25)

= 3.22

Nelson p85

2.19

4.25

4.252.19

9.67

9.67

Notice that the calculation of pIalways involves the pKa’s that

bracket the neutral charge

Glutamate:

pKacarboxyl = 2.19pKaamino = 9.67

pKasidechain = 4.25

Notice that at pH above its

pI, glutamate is predominantly

negatively charged

Consider the positively charged amino acid lysine


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2.18

8.95

10.79

10.798.952.18

Nelson p85

Lysine:

pKacarboxyl = 2.18

pKaamino = 8.95

pKasidechain = 10.79

pI =

2

(pK2 + pK3)

=

2

(10.79 + 8.95)

= 9.87

Consider the positively charged amino acid lysine

Notice that at pH below its

pI, lysine is predominantlypositively charged

Practice Questions (Solutions will be posted on D2L)


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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.


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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


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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 Cysteine

Isoleucine AlanineLeucine Serine

Lysine Tyrosine

Methionine Proline

Phenylalanine Glutamate

Threonine Aspartate

Tryptophan Arginine

Valine Glutamine

Asparagine

Glycine

Structure of

glucose

CHNOPS

lecture 9 - the amino acids ii _ acid-base characteristics

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