3/17/2016

Water: The Solvent for Biochemical

Reactions

Learning Objectives
Upon completion of this lecture, students
should be able to:
understand water and polarity
define hydrogen bonds
Describe covalent and non-covalent
bonds
understand acids and bases
know titration curves and buffers

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Water is essential to living organisms

No water = no life on earth
71% of earth is covered by water BUT 97.5% of it is salt
water i.e. ocean
2.5% fresh water: lakes, rivers and ice
60% of human body consist of water
Why is water important?
The principle component of most cells.
Geometry of water & its properties as a solvent.
Most biochemical processes essential for living
organism takes place in presence of water.
Water is the best solvent known universal solvent

Why is water the best solvent?

It is due to the polarity of water molecule.
What is polarity?
When 2 atoms with same electronegativity form a
bond, electrons are shared equally between the two
atoms. However, if atoms with differing
electronegativity form a bond, electrons are not
shared equally and more of negative charge is found
closer to one the atoms.

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Water and polarity

H2O is the main component in most cell
Electronegativity = tendency of an atom to attract electrons
to itself
Atoms of same element share electrons equally in a bond
equal electronegativity
Oxygen & nitrogen are both highly electronegativity than
carbon & hydrogen

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Electronegativity
If atom with different electronegativity form a bond,
electrons are not always shared equally
Eg: In H2O, the oxygen is more electronegative
than hydrogen - bonding of electrons are closer to
oxygen.
The different electronegativity oxygen and
hydrogen gives rise to partial positive and negative
charge (+ and -) = polar bonds
Nonpolar = the sharing of electrons in the bond is
very nearly equal. Ex. C-H in methane (CH4)
sharing electrons in bond is very nearly equal.

H2O

Vs. Methane

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Bonds in a molecule may be polar but molecule itself

is still nonpolar because of geometry. Ex. CO2, two
C=O bonds are polar but CO2 molecule is linear, the
attraction of oxygen for electrons in 1 bond is
cancelled out by the equal & opposite attraction for
the electron by oxygen on the other side. O=C=O
2+
- O=C=O -

Water is a bent molecule (bond angle: 104.3) and the

uneven sharing of the electrons in the two bonds is not
cancelled out as in CO2
The bonding electrons are more likely to be found at
the oxygen end of the molecule than at the
hydrogen end.
Bonds with positive and negative ends are called
dipoles.

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What does all that info means?

Because of the polarity of the molecules,
forms H-bonds.

water

Hydrogen bonds
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 Oxygen or Nitrogen, and
the negative end of the other dipole is an atom
with a lone pair of electrons, most commonly O or
N

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Even though hydrogen bonds are weaker than

covalent bonds, they have a significant effect on
the physical properties of hydrogen-bonded
compounds

Hydrogen Bonding
hydrogen
bond donor

hydrogen
bond acceptor
R
O

H
O

O C

H
R

Water and a
hydroxyl group
Water and the carbonyl group
of an aldehyde, ketone, carboxylic
acid, ester, or amide
An amino group and
a hydroxyl group

H
N

O C

An amino group and

a carbonyl group
An amino group and
another nitrogencontaining group

Important
in
proteins
and
nucleic
acids

Hydrogen bonding is important in stabilization of 3-D

structures of biological molecules such as: DNA, RNA,
proteins.

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Because of their polarity, water molecules are

strongly attracted to one another, which gives water
a high surface tension. The molecules at the surface
of the water "stick together" to form a type of "skin"
on the water, strong enough to support very light
objects.

But how do water work as solvent?

Three types of molecules characteristics when mixed
with water.
Hydrophilic water loving
Hydrophobic fear of water
Amphipatic part of the molecule is hydrophilic
while another part is hydrophobic.

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Water's polarity allows it to dissolve other polar

substances very easily.
Ionic compounds with full charges, potassium
chloride (KCl, K+ & Cl- in solution),
polar compound with partial charges (i.e. dipoles,
ethyl alcohol or acetone).
Principle : electrostatic attraction between unlike
charges.

Water's polarity allows it to dissolve other polar

substances very easily.
Negative end of water dipole attracts a positive ion or
positive end of other dipole. (vice versa).
Aggregation of unlike charges, held in proximity to one
another because of electrostatic attraction.
These ion-dipole and dipole-dipole attraction are
similar to interaction between water molecule
themselves.

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Solvent Properties of Water

The solvent properties of water is largely
determined by its polar nature.

Compounds with full charges

NaCl, KCl

Polar compounds with partial charges

Ethyl alcohol, acetone

These compounds are hydrophilic = waterloving

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Hydrocarbons (compounds made up of solely C and

H) are nonpolar.
Do not readily dissolve in water
Called hydrophobic = fear of water

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The favourable ion-dipole and dipole-dipole

interactions do not occur for nonpolar compound
so tend not to dissolve in water.
The interactions between nonpolar molecules and
water molecules are weaker than dipolar interactions
Do not readily dissolve in water
Called hydrophobic = fear of water

Some molecules are called amphipathic ie have

both polar and nonpolar portions in a single
molecule
Structure like this tends to form micelles in the
presence of water.

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Polar
carboxylic
acid group

Very polar : Contact

with aqueous
environment
Nonpolar :
sequestered from
water

Long
nonpolar
hydrocarbon

Interaction between nonpolar molecules is very

weak
The permanent dipole of the water molecule can
induce a temporary dipole in the nonpolar
molecule by distorting the spatial arrangement of
the electrons in its bonds.
Electrostatic attraction is possible between the
induced dipole of the nonpolar molecule and the
permanent dipole of the water molecule (a dipoleinduced dipole interaction), but it is not as strong
as that permanent dipoles.

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Interaction between nonpolar molecules is very

weak
depends on the attraction between temporary
induced dipole moments
called van der Waals interactions
this allow nonpolar molecules to either condense
to liquid or freeze to solids.

Why do oil and water mixed together

separate into layers?

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Why do oil and water mixed together

separate into layers?
Oil and water don't mix because oil is made up
of non-polar molecules while water molecules
are polar in nature.
Because water molecules are electrically
charged, they get attracted to other water
molecules and exclude the oil molecules.
This eventually causes the oil molecules, or
lipids, to clump together.

Acids, Bases and pH

What are acids and bases?
An acid is a molecule that acts as a proton donor
(hydrogen ion)
 Strong acid: an acid that is completely ionized
in aqueous solution
 HCl, HBr, HI, HNO3, and H2SO4
A base is a molecule that acts as proton acceptor
 Strong base: a base that is completely ionized
in aqueous solution
 LiOH, NaOH, KOH, Ca(OH)2, and Ba(OH)2

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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
CH3 COH
Acid

O
CH3 CO -

H2 O
Base

Conjugate base
of acetic acid

H3 O

Conjugate acid
of water

conjugate acid-base pair

*Acid-base reaction is a proton-transfer reaction, water acts as

base (i.e. solvent)

Degree of dissociation of acids in water

Complete dissociation strong acid
Incomplete to no dissociation weak acid
It is useful to derive a numerical measure of acid
strength.
Strength of acid is thus expressed as acid dissociation
constant (Ka)
Acid

Higher Ka
value =
stronger acid

Proton

Conjugate base

Bracket refer
to molar
concentration
= moles per
liter

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Acid-base reaction is actually a protontransfer reaction in which water acts solvent.

So more accurately,
acid

base

Conjugate acid

Conjugate
base

Note that the smaller the Ka, the larger the pKa.
Thus, stronger acids are represented by larger
Kavalues, but smaller pKa values.

pKa =-log10(Ka)

Also, whether an acid is strong of weak can be
readily identified by either its Ka or pKa:

Type
Ka
pKa

Strong acid
>1
< 0 (negative)

Weak acid
<1
> 0 (positive)

Acidic solutions are those where the [H3O+] is
greater than the [OH], and basic solutions are
those where the [OH] is greater than the [H3O+].

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*Hydrogen ion = hydroxide ion. At 23C in pure water = 10-7

This Kw equation is valid for any aqueous

solution whether neutral, acidic or basic.
The wide range of possible [H+] or [OH-] in aq
solution results in defining a quantity called
pH
Thus pH is defined as:
Important to
calculate pH of an
acid or base

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Calculate acid
Calculate pH of 1 x 10-3 M HCl
pH = -log [H+]
= - log (10-3)
=3

Calculate base

Calculate pH of 1 x 10-4 M NaOH
In 1 x 10-4 M NaOH, [OH-] = 10-4
Because Kw = [H][OH-]= 10-14
[H]=(10-14)/(10-4)
=10-10
pH = -log[H] = 10

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In biochemistry, most acid encountered are

weak acids. Thus to avoid using numbers with
large, negative exponents, pKa is used:

From this equation, Henderson-Hasselbalch

equation is derived

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Henderson-Hasselbalch
Henderson-Hasselbalch equation,
pH =

pK a + log [Conjugate base]

[Weak acid]

From this equation,

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

Importance for calculating pH of buffer

Calculate the pH of a buffer solution made from 0.20

M HC2H3O2 and 0.50 M C2H3O2- that has an acid
dissociation constant for HC2H3O2 of 1.8 x 10 -5 . Solve
this problem by plugging the values into the
Henderson-Hasselbalch equation for a weak acid and
its conjugate base.

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

pH = pKa + log ([C2H3O2-] / [HC2H3O2])
pH = -log (1.8 x 10-5) + log (0.50 M / 0.20 M)
pH = -log (1.8 x 10-5) + log (2.5)
pH = 4.7 + 0.40

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Exercise
Calculate the pH if you added 3 mL of 0.1
M HCl to 97 mL of pure water at pH 7.0.

Solution
3 mL = 0.003 L of 0.1 M HCl
0.003 L x 0.1 mol/L = 0.0003 moles H+
The 0.0003 moles H+ are in a final
volume of 100 mL or 0.1L
0.0003 moles/0.1 L = 0.003 M H+
pH = - log 0.003 = 2.52

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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)

Titration Curves

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Equivalence point
a monoprotic acid releases one H+ per mole
a diprotic acid releases two H+ per mole
a triprotic acid releases three H+ per mole

Inflection
point

Why are buffers important

Most biological processes are very sensitive to pH
e.g. enzyme activity
Buffers are needed to stabilize pH changes in
organism
Blood plasma is an example of a biological buffer

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All buffers are mixtures of weak acids and its

salt of conjugate base
Examples of acid-base buffers
containing
CH3COOH and CH3COONa
H2CO3 and NaHCO3
NaH2PO4 and Na2HPO4

are

solutions

We pick buffers by choosing pKa nearest to

the pH that we want.

Buffer Range
A buffer is effective in a range of about +/- 1 pH unit
of the pKa of the weak acid

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How does it work?

Buffers in the Body

H2PO4-/HPO42- (phosphate buffer system) is
the principal buffer in cells.
H2CO3/HCO3(carbonic acid-bicarbonate
buffer system) is an important (but not the
only) buffer in blood
E.g :
hyperventilation can result in increased blood pH
hypoventilation can result in decreased blood pH
CO2 dissolve  carbonic acids

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Exercise
1. Which has the larger numerical value?
a) The pKa of a strong acid or the pKa of a
weak acid?
b) The Ka of a strong acid or the Ka of a weak
acid?

Exercise
2. Which is the stronger acid:
a) Benzoic acid with a Ka of 6.5 x 10-5 or
hydrocyanic acid with a Ka of 4.9 x 10-10?
b) Boric acid with a pKa of 9.14 or carbonic
acid with a pKa of 6.37?

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Exercise
Ka for benzoic acid is 6.5 x 10-5.
What is the pKa of this acid?

Thank you

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