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Biochemistry (Chapter 3- Acid-Base Chemistry)

Presentation · March 2016

DOI: 10.13140/RG.2.1.3091.9447

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 Biochemistry
Chapter 3- Acid-Base Chemistry
Hikmet Geçkil, Professor
Department of Molecular Biology and Genetics
Inonu University
 pH, pKa, pI, Acids & Bases

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 2

• Measurement of pH is one of the most
important and frequently used procedures in
biochemistry.

• The pH affects the structure and activity of

biological macromolecules;
– For example, the catalytic activity of enzymes is
strongly dependent on pH
– Measurements of the pH of blood and urine are
commonly used in medical diagnoses.

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 3

• pH term was introduced in 1909 by Sorensen.
• pH is defined as the negative log of the hydrogen ion
concentration (i.e., [H⁺]).
pH= -log [H⁺]
• The pH scale is logarithmic and is a convenient way of
showing [H⁺]. e.g., for 0.0000001 M [H⁺] is simply equal to 7.0
in pH scale.

• Remember! 1 pH unit difference corresponds to 10 fold

difference in [H⁺], while 2 and 3 pH unit difference
correspond to 100 and 1000 times difference in [H⁺],
respectively.

• Thus, pH 4 is ten times more acidic than pH 5 and 100 times

more acidic than pH 6.

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 4

• pKa is the negative log of the dissociation
constant, which is a measure of strength of an
acid or base .

• When pKa = pH, there is equal concentration of

acid and its conjugate base (e.g., acetic acid=
acetate).

• pKa of an acid group is defined as the pH at

which the protonated and unprotonated
species are present in equal concentrations.

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 5

• pKa of amino acid side chains play an important
role in defining the pH-dependent characteristics of
a protein.
– e.g. The pH-dependent activity of enzymes and the pH-
dependence of protein stability are determined by the
pKa values of amino acid side chain .

• Most drugs are either weak acids or weak bases.

– Aspirin is a weak acid with a pK 3.5. Thus, this drug will
be protonated (COOH) and uncharged in the stomach
which has a pH around 2.0. Uncharged drugs easily cross
the cell membranes and shows their effects (e.g., in the
case of acpirin, acetylating target proteins and
enzymes).

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 6

• If pH values < pKa, the compound is protonated

• If pH values > pKa, the compound is deprotonated

• Let’s give acetic acid (CH3COOH) which has pKa 4.76 as the
examle:

• At pH<4.76, it is mostly found in CH3COOH form (i.e., acetic

acid)

• At pH> 4.76, it is mostly found in CH3COO- form (i.e., acetate)

• At pH= 4.76, the concentration of CH3COOH is equal to

CH3COO- (Buffer)

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 7

• The quantitative relationship between the pH of
the solution and the concentration of a weak
acid and its conjugate base is described by :

Henderson -Hasselbalch equation

pH= pKa+log (A-)/ (HA)

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 8

 Henderson-Hasselbalch Equation

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 9

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 10
 Buffers stabilize pH

Buffers (pKa 1pH)

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 11

• A reaction between CO2 and H2O forms carbonic acid, a weak acid
that dissociates into carbonate and bicarbonate ions:

CO2 + H2O = H2CO3 = H+ + HCO3- = 2H+ + CO32-

• If H+ is added to a carbonic acid (H2CO3) solution, it reacts with

bicarbonate (CO32-) and carbonate (HCO3-), which drives the
reaction to the left.

• If OH- is added, it removes H+ from solution, which pulls the

reaction to the right.

• Because carbonic acid is able to remove both excess H+ and excess

OH- from aqueous solution, it is a buffer, or a substance that
minimizes changes in pH.

• Weak acids and weak bases act as buffers in aqueous solution.

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 12

pH buffering in organisms

• Many enzymes are exquisitely sensitive to pH,

and pH gradients across intracellular
compartments are necessary for various cellular
functions.

• Thus, intracellular pH is carefully regulated.

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 13

pH buffering in organisms

• Many enzymes
are exquisitely
sensitive to
pH, and pH
gradients
across
intracellular
compartments
are necessary
for various
cellular
functions.

• Thus,
intracellular
pH is carefully
regulated. The cytosol and each intracellular compartment in a eukaryotic
cell have a characteristic pH.

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 14

 Carbonic anhydrase increases the speed of buffering by increasing
the rate of conversion between carbon dioxide and carbonic acid.
Two different forms of carbonic anhydrase (abbreviated CA) are
shown: CA2 and CA12.
Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 15
 Physiological Buffers

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 16

• Since protonation-deprotonation are responsible for the
charges on biomacromolecules which maintain their
solubility in water, their solubility is often lowest at their
isoelectric point pI, the pH value at which the molecule
has no net charge.

• Separation of plasma proteins by charge is done in this

manner.

• When pH is kept higher then the isoelectric pH (pI), the

proteins will have negative charge and so the proteins
will move towards the positive electrode.

• Vice versa, the proteins will move towards the negative

electrode.

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 17

Titration curves

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 18

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 19
 Some pH problems

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 20

Biochemistry/Hikmet Geckil Chapter 3: Acid-Base Chemistry 21
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