2

Water: The
Solvent for
Biochemical
Reactions
2003 Thomson Learning, Inc.
All rights reserved
2-1
2 The Polar Nature of Water
Given the difference in electronegativity between
oxygen and hydrogen (3.5 - 2.1 = 1.4) and its
shape, water is a polar molecule with a dipole
moment of 1.85D
the net charge on oxygen is -0.66 and that on each
hydrogen is +0.33
-0.66
-
+ O +
H H
+0.33 +0.33

2003 Thomson Learning, Inc.

All rights reserved
2-2
2

- an irregular, slightly
skewed tetrahedron
2003 Thomson Learning, Inc.
All rights reserved
2-3
2 Electronegativity
Electronegativity: a measure of the force of an
atoms attraction for electrons it shares in a
chemical bond with another atom
on Paulings scale, fluorine, the most electronegative
element, is assigned a value of 4.0

H
2.1
1A 2A 3A 4A 5A 6A 7A
Li Be B C N O F
1.0 1.5 2.0 2.5 3.0 3.5 4.0
Na Mg Al Si P S Cl
0.9 1.2 1.5 1.8 2.2 2.6 3.0

2003 Thomson Learning, Inc.

All rights reserved
2-4
2

2003 Thomson Learning, Inc.

All rights reserved
2-5
 2 Water, pH and Biological Molecules

Whats so special about

water?

Its a great solvent.

It holds tons of heat.

It has high surface

tension.
Its less dense as a solid
than a liquid.

2003 Thomson Learning, Inc.

All rights reserved
2-6
2 Water Chemistry
Water is the most abundant chemical in
A. ________
the body.
B. Water has many characteristics that make it
vital to our bodies.
1. Size
_____ - water is a very small molecule, so it moves
fast and can squeeze into tiny crevasses between other
molecules.

2003 Thomson Learning, Inc.

All rights reserved
2-7
2 Water Chemistry
B. Water has many
characteristics that make it
vital to our bodies.
Polarity - Hydrogen
2. _________
has a slightly positive
charge while oxygen has
a slightly negative
charge. This makes it
easy for water to pry
apart other charged
molecules, dissolving
them. Called a Universal Solvent
2003 Thomson Learning, Inc.
__________________.
All rights reserved
2-8
2 Water Chemistry
B. Water has many characteristics that make it
vital to our bodies.
3. Crystal structure Due to polarity, water
_____________________-
forms a crystal structure that is less dense than liquid
water.

2003 Thomson Learning, Inc.

All rights reserved
2-9
2 II. Water Chemistry
B. Water has many characteristics that make it
vital to our bodies.
Heat capacity - water absorbs and releases
4. __________________
heat energy slowly, and can hold a great deal of heat
energy. This helps organisms maintain their body
temperature in the safe range.

2003 Thomson Learning, Inc.

All rights reserved
2-10
2 II. Water Chemistry
B. Water has many
characteristics that make it
vital to our bodies.
5. Cohesion & Adhesion
__________________________
-- Polarity allows water to stick
to itself (cohesion) and to any
charged material (adhesion).
Water can glue materials
together.

2003 Thomson Learning, Inc.

All rights reserved
2-11
2 Water Chemistry
B. Water has many
characteristics that make
it vital to our bodies.
Buffer -- Water can
6. _________
act as either an acid or a
base, maintaining a stable
pH in our bodies.

2003 Thomson Learning, Inc.

All rights reserved
2-12
2 Polar Bonds & Molecules
Molecules such as CO2 have polar bonds but,
given their geometry, are nonpolar molecules;
that is, they have a zero dipole moments
- + - -0.21 +0.42 -0.21

O= C= O

2003 Thomson Learning, Inc.

All rights reserved
2-13
2 Solvent Properties of H2O
Ionic compounds (e.g.,KCl) and low-molecular-
weight polar covalent compounds (e.g., C2H5OH
and CH3COCH3) tend to dissolve in water
The underlying principle is electrostatic
attraction of unlike charges; the positive dipole
of water for the negative dipole of another
molecule, etc.
ion-dipole interaction: e.g., KCl dissolved in H2O
dipole-dipole interactions: e.g., ethanol or acetone
dissolved in H2O
dipole induced-dipole interactions: weak and
generally do not lead to solubility in water
2003 Thomson Learning, Inc.
All rights reserved
2-14
2

2003 Thomson Learning, Inc.

All rights reserved
2-15
2 Bond Energies
Table 2.3 Some Bond Energies

Type of Energy
Bond Example kJmol -1 kcalmol -1

Covalent O-H 460 110

H- H 416 100
C-H 413 105

Non- Hydrogen bond (H 2O) 20 5

covalent Ion-dipole bond 20 5
Hydrophobic interaction 4-12 1-3
van der Waals bond 4 1

2003 Thomson Learning, Inc.

All rights reserved
2-16
2 Solvent Properties of H2O
Hydrophilic: water-loving
tend to dissolve in water
Hydrophobic: water-fearing
tend not to dissolve in water
Amphipathic: loving on both ends
molecules that contain one or more hydrophobic and
one or more hydrophilic regions, e.g., sodium palmitate

2003 Thomson Learning, Inc.

All rights reserved
2-17
2

2003 Thomson Learning, Inc.

All rights reserved
2-18
2 Solvent Properties of H2O
Table 2.2 Examples of Hydrophobic and Hydrophilic
Substances

Hydrophilic
Polar covalent compounds
such as low-molecular-weight
alcohols (e.g., ethanol) and
ketones (e.g., acetone)
Hydrophobic
Nonpolar covalent compounds
such as hydrocarbons (e.g.,
hexane and toluene)

Sugars (e.g., glucose, sucrose) Fatty acids (e.g., palmitic

and stearic acids) and
choles terol
Ionic compounds (e.g., KCl)
Amino acids and phosphate
esters

2003 Thomson Learning, Inc.

All rights reserved
2-19
2 Solvent Properties of H2O
Micelle: a spherical arrangement of organic
molecules in water solution clustered so that
their hydrophobic parts are buried inside the sphere
and
their hydrophilic parts are on the surface of the sphere
and in contact with the water environment
Example: a sodium oleate micelle
Interaction between nonpolar molecules is very
weak
depends on the attraction between temporary induced
dipole moments
called van der Waals interactions
2003 Thomson Learning, Inc.
All rights reserved
2-20
2

2003 Thomson Learning, Inc.

All rights reserved
2-21
2 Hydrogen Bonding
Hydrogen bond: the attractive interaction
between dipoles when the
positive end of one dipole is a hydrogen atom bonded
to an atom of high electronegativity, most commonly O
or N, and
the negative end of the other dipole is an atom with a
lone pair of electrons, most commonly O or N
The strength of hydrogen bonding is about 2-5
kcalmol -1
for water, it is 5 kcalmol-1

2003 Thomson Learning, Inc.

All rights reserved
2-22
2 Hydrogen Bonding
Even though hydrogen bonds are weaker than
covalent bonds, they have a significant effect on
the physical properties of hydrogen-bonded
compounds
Table 2.4 Comparison of the physical properties of water,
ammonia, and methane

Molecular Melting Point Boiling Point

Compound Weight (C) (C)

H2 O 18.02 0.0 100.0

N H3 17.03 -77.7 -33.4
CH4 16.04 -182.5 -161.5

2003 Thomson Learning, Inc.

All rights reserved
2-23
2

2003 Thomson Learning, Inc.

All rights reserved
2-24
2

2003 Thomson Learning, Inc.

All rights reserved
2-25
2

2003 Thomson Learning, Inc.

All rights reserved
2-26
2

2003 Thomson Learning, Inc.

All rights reserved
2-27
2 Hydrogen Bonding
hydrogen hydrogen
bond donor bond acceptor
R
O H O Water and a
hydroxyl group
H H
Water and the carbonyl group
O H O C of an aldehyde, ketone, carboxylic
H acid, ester, or amide
R
An amino group and
N H O a hydroxyl group
H Important
in
An amino group and
proteins
N H O C a carbonyl group
and
nucleic
An amino group and acids
N H N another nitrogen-
containing group

2003 Thomson Learning, Inc.

All rights reserved
2-28
2

2003 Thomson Learning, Inc.

All rights reserved
2-29
2

2003 Thomson Learning, Inc.

All rights reserved
2-30
2

2003 Thomson Learning, Inc.

All rights reserved
2-31
2

2003 Thomson Learning, Inc.

All rights reserved
2-32
2

2003 Thomson Learning, Inc.

All rights reserved
2-33
2

2003 Thomson Learning, Inc.

All rights reserved
2-34
2

2003 Thomson Learning, Inc.

All rights reserved
2-35
2 Hydrophobic Interactions
- refers to the tendency of non-polar
compounds to self-associate in an aqueous
environment

- this self-association is driven neither by

mutual attraction nor by what are sometimes
incorrectly referred to as hydrophobic bonds

- the interaction between non-polar groups

2003 Thomson Learning, Inc.

All rights reserved
2-36
2 Electrostatic Interactions
- interactions between charged groups help
shape biomolecular structures

- electrostatic interactions between oppositely

charged groups within or between biomolecules
are termed salt bridges

- they thus often facilitate the binding of charged

molecules and ions to proteins and nucleic acids

2003 Thomson Learning, Inc.

All rights reserved
2-37
2 Van der Waals Forces
- Van der Waals forces arise from attraction
between transient dipoles generated by the rapid
movement of electrons on all neutral atoms

- they are significantly weaker than hydrogen

bonds but potentially extremely numerous

- they act over very short distances, typically

24
2003 Thomson Learning, Inc.
All rights reserved
2-38
2 Acids and Bases
Strong acid: an acid that is completely ionized in
aqueous solution
HCl, HBr, HI, HNO3, HClO4, and H2SO4
Strong base: a base that is completely ionized in
aqueous solution
LiOH, NaOH, KOH, Ca(OH)2, and Ba(OH)2

2003 Thomson Learning, Inc.

All rights reserved
2-39
2 pH
- the term pH was introduced in 1909 by Srensen,
who defined pH as the negative log of the hydrogen ion
concentration
pH = - log [H+]
- to calculate the pH of a solution
a. Calculate the hydrogen ion concentration [H+]
b. Calculate the base 10 logarithm of [H+]
c. pH is the negative of the value found in step b

2003 Thomson Learning, Inc.

All rights reserved
2-40
2 What is the pH of a solution whose
hydrogen ion concentration is
3.2 X 10-4 mol/L

pH = - log [H+]

= - log [3.2 x 10-4]

= 3.5

2003 Thomson Learning, Inc.

All rights reserved
2-41
2 Weak Acids and Bases
An acid or base that is incompletely ionized in
aqueous solution
carboxylic acids, such as acetic acid, are weak acids

conjugate acid-base pair

O O
+
CH3 COH + H2 O CH3 CO - + H3 O
Acid Base Conjugate base Conjugate acid
of acetic acid of water

conjugate acid-base pair

2003 Thomson Learning, Inc.

All rights reserved
2-42
2 Ionization of H2O and pH
Kw is called the ion product constant for water

-
H2 O OH + H+
+ - + -
Ka = [ H ] [ OH ] = [ H ] [ OH ]
[ H 2 O] 55.5

Kw = Ka x 5 5 . 5 = [ H + ] [ OH - ]

Kw = 10 -14

2003 Thomson Learning, Inc.

All rights reserved
2-43
2 Weak Acids and Bases
The equation for the ionization of a weak acid,
HA, in water and the acid ionization constant, Ka,
for this equilibrium are
- +
HA + H2 O A + H3 O
+ -
[ H3O ] [ A ]
Ka = Ke q [ H2 O] =
[ H A]

pKa = - log K a

2003 Thomson Learning, Inc.

All rights reserved
2-44
2 Table 2.6 Dissociation cons tants of some acids
Acid Formula pK a Conjugate Bas e
pyruvic CH3 COCOOH 2.50 CH3 COCOO -
lactic CH3 CH( OH) COOH 3.86 CH3 CH( OH) COO -
acetic acid CH3 COOH 4.76 CH3 COO-
ammonium ion N H4 + 9.25 N H3
malonic (1) HOOCCH2 COOH 2.83 HOOCCH2 COO -
malonic (2) HOOCCH2 COO - 10.20
-
OOCCH2 COO -
succinic (1) HOOC( CH2 ) 2 COOH 4.21 HOOC( CH2 ) 2 COO -
succinic (2) HOOC( CH2 ) 2 COO - 5.63 -
OOC( CH2 ) 2 COO -
carbonic (1) H2 CO 3 6.37 HCO 3 -
carbonic (2) HCO 3 - 10.20 CO 3 2 -
phosphoric (1) H3 PO 4 2.14 H2 PO 4 -
phosphoric (2) H2 PO 4 - 7.20 HPO 4 2 -
phosphoric (3) HPO 4 2 - 12.40 PO 4 3 -
2003 Thomson Learning, Inc.
All rights reserved
2-45
2
We can calculate the ratio of weak acid, HA, to its
conjugate base, A-, in the following way
H2 O A-
HA + H+
Weak Conjugate
acid b ase
the acid dissociation constant for the weak acid is
+
[Conjugate base][H ]
Ka =
[Weak acid]

2003 Thomson Learning, Inc.

All rights reserved
2-46
2 Henderson-Hasselbalch
taking the logarithm of this equation and rearranging
terms gives

This term, by This term, by

definition, is pH definition, is pK a

[Conjugate base]
-log [H + ] = -log K a + log
[Weak acid]

pH = pK a + log [Conjugate base]

[Weak acid]

2003 Thomson Learning, Inc.

All rights reserved
2-47
2 Henderson-Hasselbalch
Henderson-Hasselbalch equation
[Conjugate base]
pH = pK a + log
[Weak acid]

From this equation, we see that

when the concentrations of weak acid and its
conjugate base are equal, the pH of the solution equals
the pKa of the weak acid
when pH < pKa, the weak acid predominates
when pH > pKa, the conjugate base predominates

2003 Thomson Learning, Inc.

All rights reserved
2-48
2 Titration Curves
Titration: an experiment in which measured
amounts of acid (or base) are added to measured
amounts of base (or acid)
Equivalence point: the point in an acid-base
titration at which enough acid has been added to
exactly neutralize the base (or vice versa)
a monoprotic acid releases one H+ per mole
a diprotic acid releases two H+ per mole
a triprotic acid releases three H+ per mole

2003 Thomson Learning, Inc.

All rights reserved
2-49
2 pH

HPO 4 2 -
Buffer
region

pH = pK a + 1
7.2 = pK a

pH = pK a - 1
[ H 2 PO 4 - ] = [ HPO 4 2 - ]

H2 PO 4 -

% H2 PO 4 - 100 90 50 10 0
% HPO 4 2 - 0 10 50 90 100

2003 Thomson Learning, Inc.

All rights reserved
2-50
2

Titration
Curve for
Acetic acid

2003 Thomson Learning, Inc.

All rights reserved
2-51
2

2003 Thomson Learning, Inc.

All rights reserved
2-52
2 When 0.1 mol of NaOH is added, 0.1 mol of acetic acid
reacts with it to form 0.1 mol of the acetate ion, leaving
0.9 mol acetic acid. The composition is 90% acetic
acid and 10% acetate ion.
pH = pKa + log [ acetate ion]
[acetic acid]
pH = pKa + log 0.1
0.9
= 4.76 + log 0.1
0.9
= 4.76 0.95
= 3.81
2003 Thomson Learning, Inc.
All rights reserved
2-53
2 When 0.3 mol of NaOH is added, 0.3 mol of acetic acid
reacts with it to form 0.3 mol of acetate ion, leaving
0.7 mol acetic acid. The composition is 70% acetic
acid and 30% acetate ion.

pH = pKa + log [acetate ion]

[acetic acid]

pH = pKa + log 0.3

0.7
= 4.76 - 0.37
= 4.39

2003 Thomson Learning, Inc.

All rights reserved
2-54
2 Acid-Base Buffers
Acid-base buffer: a solution whose pH resists
change upon addition of either more acid or more
base
consists of a weak acid and its conjugate base
Examples of acid-base buffers are solutions
containing
CH3COOH and CH3COONa
H2CO3 and NaHCO3
NaH2PO4 and Na2HPO4

2003 Thomson Learning, Inc.

All rights reserved
2-55
2

2003 Thomson Learning, Inc.

All rights reserved
2-56
2

2003 Thomson Learning, Inc.

All rights reserved
2-57
2

2003 Thomson Learning, Inc.

All rights reserved
2-58
2

2003 Thomson Learning, Inc.

All rights reserved
2-59
2

2003 Thomson Learning, Inc.

All rights reserved
2-60
2 Practice Session
Calculate the pH of the solution obtained when
1.0 mL of 0.10 M HCl is added to 99.0 mL of pure water
1.0 mL of 0.10 M NaOH is added to 99.0 mL of pure
water

2003 Thomson Learning, Inc.

All rights reserved
2-61
2 On dilution, we have 100 mL of 0.001M HCl and
100 mL of 0.001M NaOH.

Acid added, [H3O+] = 10-3 M

therefore, pH = 3

Base added, [OH-] = 10-3 M

Since [OH-] [H3O+] = 1 x 10-14 M
[H3O+] = 10-11 M
therefore, pH = 11

2003 Thomson Learning, Inc.

All rights reserved
2-62
2 Buffer Range
A buffer is effective in a range of about 2 pH units
relative to the pKa of the weak acid
Table 2.7 pH values and base/acid ratios for buffers

pH [Base]/[Conjugate Acid]
pK a -3 1/1000
pK a -2 1/100
pK a -1 1/10
effective
pK a 1/1 buffer
pK a +1 10/1 range
pK a +2 100/1
pK a +3 1000/1
2003 Thomson Learning, Inc.
All rights reserved
2-63
2
Buffer Capacity
Buffer capacity is related to the concentrations of
the weak acid and its conjugate base
the greater the concentration of the weak acid and its
conjugate base, the greater the buffer capacity

2003 Thomson Learning, Inc.

All rights reserved
2-64
2 Buffers in the Body
H2PO4-/HPO42- is the principal buffer in cells
H2CO3/HCO3- is an important (but not the only)
buffer in blood
CO 2 ( g) CO 2 ( aq )

CO 2 ( aq ) + H2 O( l) H2 CO 3 ( a q)

H2 CO 3 ( a q) H+ ( a q) + HCO 3 - ( a q)

CO 2 ( g) + H2 O( l) H+ ( a q) + HCO 3 - ( a q)

hyperventilation can result in increased blood pH

hypoventilation can result in decreased blood pH

2003 Thomson Learning, Inc.

All rights reserved
2-65
2
Selecting a Buffer
The following criteria are typical
suitable pKa
no interference with the reaction or detection of the
assay
suitable ionic strength
suitable solubility
its non-biological nature

2003 Thomson Learning, Inc.

All rights reserved
2-66
2 Laboratory Buffers
N-2-hydroxyethylpiperazine-N-2-ethane sulfonate (HEPES)
HOCH2 CH 2
+ N N CH2 CH 2 SO 3 -
H

HOCH 2 CH2 N N CH2 CH 2 SO 3 - + H+ pK a = 7.55

3-(N-morpholino)propanesulfonic acid (MOPS)

CH 2 CH2 CH 2 SO 3 -
O N+
H
O N CH 2 CH2 CH 2 SO 3 - + H+ pK a = 7.2

Piperazine-N,N'-bis(2-ethanesulfonic acid) (PIPES)

CH2 CH 2 SO 3 -
-
O 3 SCH2 CH 2 -N N+
H
-
2003 Thomson Learning, Inc. O 3 SCH2 CH 2 -N N CH2 CH 2 SO 3 - + H+ pK a = 6.8
All rights reserved
2-67
2

2003 Thomson Learning, Inc.

All rights reserved
2-68