Principles Of Biochemistry

• BIOC 3(3-0)
• Learning Aims
(1) Understanding of physiological phenomena.
(2) Understanding of chemical basis of working
of bio molecules.
(3) Understanding of major metabolic activities in
livings.

•
Ionic Product Of Water And Its
relationship With pH

2
 Hydrogen Ion Concentration &
pH
• Water is most abundant substance in the human
body making up to 60% to 70% of the body mass.
• Water is dipolar molecule, Hydrogen bonds exists
between water molecules making it a liquid at
room temperature and give solvent properties.
Pure water is very slightly dissociated.At25 C
1out of10 million molecules in pure water is
ionized.

3
 Ionic Product of Water & pH

H2O H+ + OH-

[H+] [OH-]
Keq = = 1.8x10-16 M
[H2O]

Concentration of “water in water” ([H2O]) is 55.6 M [next slide], thus

Kw = [H+] [OH-] = 10-14 M2 Constant ion product!

Pure water has equal quantities of H+ and OH- ions, or, put differently,
pure water has equal [H+] and [OH-].

[H+] = [OH-] = 10-7 M = 0.1 M

 Molarity Of Water

Concentration is measured in moles per liter (mol/l) or simply M.

1 l = 1,000 ml of water has a mass of 1,000 gr.

1 mole of water has a mass of 18 gr (hydrogen 1 Da, oxygen 16 Da).

Thus 1 liter of water (1,000 gr) contains 1,000 gr / 18 gr moles of water.

[H2O] = (1,000 gr / 18 gr) M = 55.6 M.

 pH
• pH is commonly expressed as –log[H+]
• Pure water has [H+]=10-7 and thus pH=7.
• Acids have a high [H+] and thus a low pH.
• Bases have a low [H+] and thus a high pH.
Bases contribute –OH ions when they dissociate. These bind to the H+ ions produced when water dissociates. Thus, these OH ions

“suck up” the H+ ions in solution, reducing their concentration.

NaOH with a pH of 12.0 contributes so many –OH ions that almost all the H+ ions are bound into water molecules, reducing the free
-12
H+ (and hydronium) ion concentration to 1 x 10 (1,000,000,000,000 = 1/trillion)
 Acids and bases

• Acids have a lot of Hydrogen ions (H+) and bases have a lot of Hydroxide
ions (-OH).

• A solution is neutral if its pH equals seven.

More acidic More basic

+ + + H+ Neutral - -
H + H - + - + OH -OH-
+ H+ H + OH H + + OH H - OH
H + H H H OH - - OH
+ H+ H + - - - OH OH -
H +H + + (H ) + ( OH) = OH OH - OH
H + H+H +
H +
- OH -
OH -
H + H - H + OH OH
OH H
 pH scale is logarithmic

Change in
just one unit
of scale
= tenfold
change in H+
concentration
.

Image: pH & hydronium ion concentration, UBC Wiki

From the Virtual Cell Biology Classroom on ScienceProfOnline.com
The pH Scale…
 Why is pH important in biology?
• pH affects solubility of many substances.
• pH affects structure and function of most proteins -
including enzymes.
• Many cells and organisms (esp. plants and aquatic
animals) can only survive in a specific pH environment.
• Important point -
– pH is dependent upon temperature
 pH of Some Biological Fluids

Body Fluids PH Body Fluids pH

Blood Plasma 7.35----7.45 Milk 6.6---6.9

Gastric juice 1.0-----3.0 Saliva 6.35----6.85

Intestinal juice 7.0-----8.2 Tears 7.4

Pancreatic juice 7.5-----8.0 Urine 4.5----8.0

8
pH profiles of enzymatic reactions

Amylase

Pepsin

UCI Bio199 Independent Research

 Strong acids and bases
pH = -log [H+]

HCl H+ + Cl-
HCl is a strong acid that completely dissociates in
water. 1 M HCl will thus yield 1 M [H+] and the pH will be
pH = -log [H+] = -log(1) = 0

NaOH is a strong base that completely dissociates in

water. 1 M NaOH will thus yield 1 M [OH-]. Since
[H+] [OH-] = 10-14 M and must remain constant
[H+] = 10-14 M and the pH will be
pH = -log [H+] = -log(10-14) = 14

Life is compatible only in a narrow pH range around pH 7.

 (L3) BUFFER
SOLUTION
An aqueous solution system which
tends to maintain the pH of the
solution when small amount of acid
or base is added to it .
 Buffers
Buffers
• resist changes in pH from the addition of acid or
base
• in the body absorb H3O+ or OH from foods and
cellular processes to maintain pH
• are important in the proper functioning of cells and
blood
• in blood maintain a pH close to 7.4; a change in the
pH of the blood affects the uptake of oxygen and
cellular processes
16
 Buffers (continued)
When an acid or base
is added
• to water, the pH
changes drastically
• to a buffer solution,
the pH does not
change very much;
pH is maintained

17
 BIOLOGICAL BUFFER
SYSTEMS
• Bicarbonate buffer (53%)
• Hemoglobin (35%)
• Plasma proteins (7%)
• Phosphate (5%)
 L4 How does a buffer work?

At the pKa, [HAc] = [Ac-] so the system is able to absorb the addition of HO-
or H+. If we add HO- near the pH where [Hac] = [Ac-] (ie pH ~= pKa) then
HAc can release H+ to offset the HO- added but the ratio of HAc to Ac- does
not change much. If we add H+ then Ac- can absorb H+ to form HAc.
Hence, the pH does not change much.
Titration curves
[H+] [Ac-]
Ka =
[HAc]

pH = pKa + log [Ac-

]
[HAc]

Start at low pH and begin to add HO-.

2
The product of [H+] [HO-] must
remain constant, so adding HO-
means [H+] must decrease and thus
pH increases. At the pKa, [Ac-] and
[HAc] are equal, so adding more HO-
does not change the ratio of [Ac-] to
[HAc] very much and thus the pH
does not change very much (shallow
slope of titration curve from ~1 pH
unit below pKa to ~1 pH unit above).
Buffers are vitally important in biochemical systems
since pH needs to be controlled. Living systems must
be “buffered” to resist large variations in pH.

Phosphate
H3PO4 H+ + H2PO4- pKa1 = 2.2
H2PO4- H+ + HPO42- pKa2 = 6.86
HPO42- H+ + PO43- pKa3 = 12.7

Carbonate
CO2 + H2O H2CO3
H2CO3 H+ + HCO3- pKa1 = 6.4
HCO3- H+ + CO32- pKa2 = 10.2
Phosphate buffering
Measuring pKa values

NH4+ H+ + NH3

[H+] [NH3]
Ka =
[NH4+ ]

pKa = pH when [NH4+] = [NH3]

 The Henderson-Hasselbalch Equation
[H+] [Ac-]
HAc H+ + Ac- Ka =
[HAc]

[Ac-]
take the -log on both sides -log Ka = -log [H ] -log
+
[HAc]

pKa = pH -log [Ac-

]
apply p(x) = -log(x)
[HAc]

and finally solve for pH…

pH = pK + log [Ac-] [Proton acceptor]

= pKa + log
a
[HAc] [Proton donor]
Acid-base Balance
 The importance of pH control
• The pH of the ECF remains between 7.35 and
7.45
– If plasma levels fall below 7.35 (acidemia), acidosis
results
– If plasma levels rise above 7.45 (alkalemia), alkalosis
results
– Alteration outside these boundaries affects all body
systems
 Types of acids in the body
• Volatile acid
– Can leave solution and enter the atmosphere (e.g.
carbonic acid)
• Fixed acids
– Acids that do not leave solution (e.g. sulfuric and
phosphoric acids)
• Organic acids
– Participants in or by-products of aerobic metabolism
• Carbonic acidCommon Acids
is most important factor affecting
pH of ECF
– CO2 reacts with water to form carbonic acid
– Inverse relationship between pH and concentration of
CO2
• Sulfuric acid and phosphoric acid
– Generated during catabolism of amino acids
• Organic acids
– Metabolic byproducts such as lactic acid, ketone
bodies
 Physiologic Buffer Systems
• Lungs/respiratory
– Quickest way to respond, takes minutes to hours to
correct pH
– Eliminate volatile respiratory acids such as CO2
– Doesn’t affect fixed acids like lactic acid
– Body pH can be adjusted by changing rate and depth
of breathing “blowing off”
– Provide O2 to cells and remove CO2
Carbon dioxide-carbonic acid-bicarbonate buffer

If blood pH drops due to metabolic

production of H+ then [H2CO3] increases
by protonation of HCO3-, H2CO3 rapidly
loses water to form CO2(aq), which is
expelled as CO2(g).

If the blood pH rises, [HCO3-] increases

by deprotonation of H2CO3, then
breathing rate changes and CO 2(g) is
converted to CO2(aq) and then to H2CO3
in the capillaries in the lungs.

What happens to blood pH when you hyperventilate?

What happens to blood pH when you hypoventilate?