Chapter 2:

Water

‫ي‬
ّ ‫ح‬ ‫شيء‬ ّ
‫ل‬ ‫"وجعلنا من الماء ك‬
30 ‫أفل يؤمنون" النبياء‬

We made from water every living

thing. Will they not then believe?
AL-ANBIYA 021. 030
 Why is water important?

• Water is the most abundant compound found in

living organisms (about 80%).
• Water provides suitable medium for biochemical
reactions.
• Macromolecular and supramoleclar structure
components (i.e. proteins, phospholipid in
biological membrane) assume there shapes in
response to water.
 Properties of water
1) Polarity
Presence of a permanent dipole in the molecule as result of
unequal sharing of electrons.
• Covalent bonds (electron pair is shared) between oxygen
and hydrogen atoms with a bond angle of 104.5o.
• Oxygen atom is more electronegative than hydrogen
atom --> electrons spend more time around oxygen atom
than hydrogen atom --> result is a POLAR covalent
bond.
• Can determine relative solubility of molecules “like
dissolves like”.
Water polarity
 Electronegativity of most abundant
elements
Element Electronegativity
• Oxygen 3.5
• Nitrogen 3.0
• Sulfur 2.6
• Carbon 2.5
• Phosphorus 2.2
• Hydrogen 2.1
 Hydrogen bonds
• Attraction between adjacent polar molecules, can occur
between any electronegative atoms (N,O) with hydrogen
atom attached to another electronegative atom.
• Water hydrogen bonds = attraction of one slightly
positive hydrogen atom of one water molecule and one
slightly negative oxygen atom of another water molecule.
• H-Bond is most stable when the H atom and the tow
electronegative atoms (O) are aligned.
Hydrogen Bonding of Water
One H2O molecule can
associate with 4
other H20 molecules

•Ice: 4 H-bonds
per water molecule
•Water: 2.3 H-
bonds per water
molecule
 Hydrogen bonds and water physical
properties
• Hydrogen bonds give water a high melting point.
• Hydrogen bonds contribute to water’s high specific heat
(amount of heat needed to raise the temperature of 1 gm of a
substance 1oC).
• Water has a high heat of vaporization - large amount of
heat is needed to evaporate water because hydrogen bonds
must be broken to change water from liquid to gaseous
state.
Biological
Hydrogen
Bonds
 Universal solvent

•Hydrophilic: Compounds interact (dissolve) with water

 Polar compounds  Hydrogen bonds
 Ionic compounds  Solvation spheres (shell of water
molecules around each ion).

•Hydrophobic: Compounds do not interact with water

 Non polar compounds

•Amphipathic: Compounds have both hydrophilic and

hydrophobic portions to the molecule (detergents).
Hydrophilic compounds
Functional groups on molecules that confer solubility
 carboxylates
 protonated amines
 amino
 hydroxyl
 carbonyl
*As the number of polar groups increases in a molecule, so
does its solubility in water.
 Hydrophobic compounds
• Water molecules tends to react with each other
rather than nonpolar molecules (hydrophobic) 
exclude nonpolar substance (oil droplets) forcing
them to associat with each other. (Hydrophobic
effect).
 Amphipathics
Many lipids are amphipathic
How detergents work?
 Noncovalent interactions in biomolecules

1) Charge-charge interactions (ionic bonds)

• Occur between two oppositely charged particles (Electrostatic).
• Strongest noncovalent force that occurs over greater distances (40
to 200 KJ/mol.
• Can be weakened significantly by water molecules (can interfere
with bonding).
 Noncovalent interactions in biomolecules
2) Hydrogen bonds  Stabilize structures such as
proteins and nucleic acids.
• Weaker than covalent bonds (about 2 – 20 KJ/mol).
 Noncovalent interactions in biomolecules
2) Hydrophobic interactions:
• Very weak (3-10 KJ/mol).
• Important in protein shape and membrane structure.
4) Van der Waals forces
• Occurs between neutral atoms.
• Results from random movement of e
around nucleus very small dipole
• Can be attractive or repulsive ,depending
upon the distance of the two atoms.
• Much weaker than hydrogen bonds (0.4-4
KJ/mol.
• The actual distance between atoms is the
distance at which maximal attraction
occurs.
Ionization of Water
 Ionization of Water
H20 + H20 H3O+ + OH-
H20 H+ + OH-
Keq= [H+] [OH-] Keq=1.8 X 10-16M

[H2O] [H2O] = w.t/(M.w x v)

[H2O] Keq = [H+] [OH-] = 55.5 M

(1.8 X 10-16M)(55.5 M ) = [H+] [OH-]

1.0 X 10-14 M2 = [H+] [OH-] = Kw
If [H+]=[OH-] then [H+] = 1.0 X 10-7
pH = -log [H+] = 7
 pH Scale
 [H+] can range from 1M and
1 X 10-14M
 using a log scale simplifies
notation
 pH = -log [H+]
Neutral pH = 7.0
If [H+] > [OH-] , pH < 7, Acidic sol.
If [H+] < [OH-] , pH > 7, Basic sol.
 Weak Acids and Bases Equilibria
•Strong acids / bases – disassociate completely (HCl/ NaOH)
•Weak acids / bases – disassociate only partially
•Enzyme activity sensitive to pH
• weak acid/bases play important role in protein structure/

function
 Acid/conjugate base pairs
HA + H2O A- + H 3 O +
HA A- + H+
HA = acid ( donates H+)(Bronstad Acid)
A- = Conjugate base (accepts H+)(Bronstad Base)
Ka & pKa value describe tendency to
Ka = [H ][A ]
+ -
loose H+
[HA]
large Ka = stronger acid
small Ka = weaker acid
pKa = - log Ka
 Buffers
• Buffers are aqueous systems that resist changes in
pH when small amounts of a strong acid or base are
added.
• A buffered system consist of a weak acid (acetic
acid) and its conjugate base (acetate).
• Buffers are effective at pHs that are within +/-1 pH
unit of the pKa.
• The most effective buffering occurs at pKa and
appear as the region of minimum slope (minimum
change in pH value) on a titration curve.
How buffer resist changes of pH

HA A- + H+
+ +
H+ OH- If OH-/H+ are added

HA H2O Not effect pH value

pKa values determined by titration
 Henderson-Hasselbach Equation
HA A- + H+
HA = weak acid
1) Ka = [H+][A-]
[HA] A -
= Conjugate base
2) [H+] = Ka [HA]
[A-]
3) –log [H+] = -log Ka -log [HA]
* H-H equation describes
[A ]
-
the relationship between
pH, pKa and buffer
4) -log[H+] = -log Ka +log [A-] concentration
[HA]
5) pH = pKa + log [A-]
[HA]
Case where 10% acetate ion 90% acetic acid

• pH = pKa + log10 [0.1 ]

¯¯¯¯¯¯¯¯¯¯

[0.9]

• pH = 4.76 + (-0.95)
• pH = 3.81
Case where 50% acetate ion 50% acetic acid

• pH = pKa + log10 [0.5 ]

¯¯¯¯¯¯¯¯¯¯

[0.5]

• pH = 4.76 + 0
• pH = 4.76 = pKa
Case where 90% acetate ion 10% acetic acid

• pH = pKa + log10 [0.9 ]

¯¯¯¯¯¯¯¯¯¯

[0.1]

• pH = 4.76 + 0.95
• pH = 5.71
 Cases when buffering fails

• pH = pKa + log10 [0.99 ]

¯¯¯¯¯¯¯¯¯¯

[0.01]

• pH = 4.76 + 2.00
• pH = 6.76

• pH = pKa + log10 [0.01 ]

¯¯¯¯¯¯¯¯¯

[0.99]

• pH = 4.76 - 2.00
• pH = 2.76
Phosphate has three ionizable H+ and three pKas