LifeScience I Week 1 Topic 2

MEDICAL
BIOCHEMISTRY
WATER DIPOLAR MOLECULE AND ITS
TETRAHEDRAL ARRANGEMENT
Water Molecules Exhibit a Slight but
Important Tendency to Dissociate
Ionization of Water
H2O ↔ H+ + OH¯
K = [H+][OH¯] / [H2O] (1)
K = 1.8 x 10-16
1 M of water weights 18 g, then 1 L (1000g) contains 1000g/18g= 55,56 M/L.

1 liter H2O contains 55.56 moles H2O
Rearranging constant values in equation (1) leads to equation (2)
K[H2O] = [H+][OH¯] (2)

K[H2O] = KW
KW = K[H2O] = 1.8 x 10-16 x 55.56 = 1 x 10-14
KW = [H+][OH¯] = 1 x 10-14
Ion Product of Water
Kw= K x [H2O]
Kw= 1,8x10-16 M/L x 55,56 M/L
Kw= 1 x10-14 M/L
In pure water the concentration of H+ equals OH- .
+ -
Kw= [H] [OH]
-7 2
Kw= (1 x10 ) M/L
+
If [H] > 1 x10-7 acidic reaction
+
If [H] < 1 x10-7 basic reaction
pH is Negative log of the Hydrogen Ion Concentration
pH = – log [H+] (3)
pH = – log [1 x 10-7] = – (– 7) = 7
If pH = 7 neutral reaction
If pH < 7 acidic reaction
If pH > 7 basic reaction
If we know pH of any solution, we can calculate M of [H+] using equation (3)

[H+] = 10 -pH
Amino Acids Can Act as Acids or Bases
Stronger Acid, higher Ka , l o w e r p Ka
Weaker Acid, lower Ka, h i g h e r p Ka
Conjugate base / Conjugate acid

MONOCARBOXYLIC ACIDS
DICARBOXYLIC ACIDS
Acids dissolved in water contribute with proton (doner )
Bases dissolved in water consume proton (acceptor)
Stronger Acid, higher Ka , l o w e r p Ka
Weaker Acid, lower Ka, h i g h e r p Ka
The Henderson-
Hasselbalch Equation
Describes the Behaviour
of Weak Acids & Buffers
Henderson-Hasselbalch equation
+ -
HA ↔ H + A - (conjugated base)
[A]
pH = pKa + log
[HA] (acid)
-
When acid is exactly half neutralized, [A] = [HA]
Under these conditions,
-
[A] 1
pH = pKa + log = pKa + log = pKa + 0
[HA] 1
Therefore, at half-neutralization, pH = pKa
The Henderson-Hasselbalch equation also allows us to (1) calculate pKa, given

pH and the molar ratio of proton donor and acceptor; (2) calculate pH, given pKa
and the molar ratio of proton donor and acceptor; and (3) calculate the molar ratio
of proton donor and acceptor, given pH and pKa.
The pH Scale Designates the H+
and OH- Concentrations
The value of 7 for the pH of a precisely
neutral solution is not an arbitrarily. It is
derived from the absolute value of the ion
product of water at 25C°, which by convenient
coincidence is a round number. Solutions
having a pH greater than 7 are alkaline or
basic; the concentration of OH- is greater
than that of H+. Conversely, solutions having
a pH less than 7 are acidic.
Keep in mind that the pH scale is logarithmic,
not arithmetic. To say that two solutions differ
in pH by 1 pH unit means that one solution
has ten times the H+ concentration of the
other, but it does not tell us the absolute
magnitude of the difference.
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.
The pH of the blood plasma of people with severe, uncontrolled
diabetes, for example, is often below the normal value of 7.4; this
condition is called acidosis. In certain other diseases the pH of the
blood is higher than normal, a condition known as alkalosis.
Extreme acidosis or alkalosis can be life-threatening.
Titration Curves Reveal the pKa of
Weak Acids
Titration is used to determine the amount

of an acid in a given solution. A measured
volume of the acid is titrated with a
solution of a strong base, usually sodium
hydroxide (NaOH), of known
concentration. The NaOH is added in
small increments until the acid is
consumed (neutralized), as determined
with an indicator dye or a pH meter. A plot
of pH against the amount of NaOH added
(a titration curve), reveals the pKa of the
weak acid. Consider the titration of a 0.1
M solution of acetic acid
with 0.1 M NaOH at 25C°.
Buffering against pH Changes in Biological Systems
Almost every biological process is pH-dependent; a small change in pH produces a

large change in the rate of the process. This is true not only for the many reactions in
which the H1 ion is a direct participant, but also for those reactions in which there is
no apparent role for H+ ions. The enzymes that catalyze cellular reactions, and many
of the molecules on which they act, contain ionizable groups with characteristic pKa
values.
Cells and organisms maintain a specific and constant cytosolic pH, usually near pH
7, keeping biomolecules in their optimal ionic state. In multicellular organisms, the pH
of extracellular fluids is also tightly regulated. Constancy of pH is achieved primarily
by biological buffers: mixtures of weak acids and their conjugate bases.
AMINO ACIDS CAN ACT AS ACIDS OR BASES
Residues encompassing the Active Site of
Enzyme Matter
General Relationship between charge
Properties of Amino Acids and Proteins and pH
• At the pH less than pI, the molecule is positively charged, whereas at pH

greater than pI, the molecule is negatively charged
• As proteins are complex polyelectrolytes that contain many ionizable

groups that regulate zwitterion form, calculation of protein pKa value
utilizing Henderson-Hasselbalch relationship is difficult. Accordingly, pI
values are experimentally measured by determining the pH value at
which the protein does not move in an electric field
Proteins; Enzymes Act as General Acid and/or Base
• The enzymes can add (general acid) or remove (general base) protons
from a substrate changing its charge
• The removal of a proton makes a group more nucleophilic (necleophile is

a group that will attack a positive center. e.g. OH- is more nucleophilic
than a water and ionized cysteine is more nucleophilic than is the ionized
sulfur atom
• The advantage of the enzymes using general acid and general base
catalysis is that at physiological neutral pH, thay can catalyse a reaction
even though the concentration of OH- and H+ is very low
pH Alters a Reaction by Affecting General Acid/Base
• Nearly all enzymes involve general acid/base catalysis, and it is not

unexpected that reaction rates would be affected by pH.
For example, some enzymes require a histidine imidazole in its

base form for catalytic activity. If the pKa of this histidine is 6.0, at pH 6.0
one-half of the enzyme molecules are in the active base (imidazole) form
and one-half of the enzyme molecules are in the inactive acid (imidazolium)
form. Accordingly, the enzyme exhibits 50% of its potential activity.
Whearas, At pH 7.0, the ratio of [imidazole]/[imidazolium] is 10:1 and the
enzyme exhibits 10/(10 + 1) X 100 = 91 % of its maximum potential activity.
• Thus a change in pH has a dramatic effect on the enzyme's activity.

LITERATURE
Robert K. Murray-Harper’s Illustrated Biochemistry (Lange Medical Book)-

McGraw-Hill Medical; 31th edition (2018)
David L. Nelson, Michael M. Cox - Lehninger Principles of Biochemistry - Worth

Publishers Inc.,U.S.; 6th edition (2013)
Ferrier, Denise R. Lippincott Illustrated Reviews: Biochemistry. 7th ed.

Philadelphia, PA: Wolters Kluwer, 2017. MLA Citation. Ferrier, Denise R.

LifeScience I Week 1 Topic 2

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MEDICAL

1 M of water weights 18 g, then 1 L (1000g) contains 1000g/18g= 55,56 M/L.

Rearranging constant values in equation (1) leads to equation (2)

K[H2O] = [H+][OH¯] (2)

KW = K[H2O] = 1.8 x 10-16 x 55.56 = 1 x 10-14

pH = – log [H+] (3)

If pH < 7 acidic reaction

If pH > 7 basic reaction

If we know pH of any solution, we can calculate M of [H+] using equation (3)

Conjugate base / Conjugate acid

The Henderson-Hasselbalch equation also allows us to (1) calculate pKa, given

Titration is used to determine the amount

Almost every biological process is pH-dependent; a small change in pH produces a

• At the pH less than pI, the molecule is positively charged, whereas at pH

• As proteins are complex polyelectrolytes that contain many ionizable

• The removal of a proton makes a group more nucleophilic (necleophile is

• Nearly all enzymes involve general acid/base catalysis, and it is not

For example, some enzymes require a histidine imidazole in its

• Thus a change in pH has a dramatic effect on the enzyme's activity.

Robert K. Murray-Harper’s Illustrated Biochemistry (Lange Medical Book)-

David L. Nelson, Michael M. Cox - Lehninger Principles of Biochemistry - Worth

Ferrier, Denise R. Lippincott Illustrated Reviews: Biochemistry. 7th ed.

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