Chapter 2
Water
- Description of Physical & Chemical Properties of Water-
Noncovalent interactions in biomolecules
1. Hydrogen bonds
2. Ionic Interactions
3. Hydrophobic Interactions
4. van der Waals interactions
Hydrogen Bonding in Water
Hydrogen Bonding in Water
 Unusual properties of water
- High melting and boiling point, and heat of vaporization
 Hydrogen bond
 Weak bond dissociation energy

23 kJ/mol (c.f. O-H : 348 kJ/mol)

Average 3.4 hydrogen bonds /water molecule

4 hydrogen bonds /water molecule
 10% covalent and 90% electrostatic
 Liquid
 Ice
 Melting or evaporation at room temperature : DG<0
 Increase in enthalpy < increase in entropy
Hydrogen Bonding of Water with
Polar Solutes
 Common H bonds in biological systems
Directionality of H bond
Electrostatic Interaction of Water
with Charged Solutes
 Water solubility
 Hydrophilic : polar, water soluble
 Hydrophobic : nonpolar, water insoluble
Dissolving Salt in Water
 Hydration and stabilization of ions
 DG = DH – TDS
 Small positive DH, large positive DS 
negative DG
Dissolving Gas in Water
 CO2, O2, N2
 Poor solubility
 Nonpolar
 Decrease in entropy by dissolving in water
 Facilitating transport in organisms
 O2 carrier protein (hemoglobin, myoglobin)
 CO2 forms carbonic acid (H2CO3) in water
water soluble bicarbonate (HCO3-)
 NH3, H2S
 Polar and water soluble
Dissolving Nonpolar Compounds in
Water
 Poor solubility
 Small gain of enthalpy
 Decrease in entropy
 Highly ordered water molecules around nonpolar molecule
 Hydrophobic interactions
 Clustering of nonpolar molecules or regions in water
 Amphipathic molecules  form micelles
 Increase in entropy
Hydrophobic Interactions in Biological
Systems
 Many biomolecules are amphipathic
 Hydrophobic interactions
 Membrane structure (lipid-lipid & lipid-protein)
 Stabilization of 3D structure of protein
 Increase in entropy by increasing disordered water
 One of the driving force for enzyme-substrate
binding
Enzyme-substrate interaction
van der Waals Interactions
 van der Waals interactions (London forces)
 Weak interatomic interaction between transient
electric dipole
 van der Waals radius
 The point balancing van der Waals attraction and
repulsion
Weak Interactions in Macromolecular
Structure and Function
 Noncovalent interactions in biological system
 Hydrogen bonds, Ionic, hydrophobic,
and van der Waals interactions
 Weak but strong cumulative effect
Water in Biomolecules
 Structural water molecule
 Tightly bound to the proteins (not osmotically active)
 Biological function
 e.g. cytochrome f
Water chain in cyt f
Structural water in hemoglobin
Effect of Solutes on Colligative
Properties of Aqueous Solutions
 Colligative (tied together) properties of solvent
 Vapor pressure
 Boiling point
 Melting point
 Osmotic pressure
 Effect of Solutes on Colligative Properties
 Depending on the number of solute particles
 Lowering the effective concentration of water
Effect of Solutes on Colligative
Properties of Aqueous Solutions
 Osmotic pressure
 Pressure generated by diffusion of water from the
region of high water concentration to that of lower
water concentration
 van’t Hoff equation
 P = icRT
 ic: osmolarity
 c: solute’s molar concentration
 i: van’t Hoff factor
 e.g. NaCl: i =2
 Osmosis
 Movement of water across a semipermeable
membrane by osmotic pressure
Water Movement across Membrane
 Plasma membrane
 More permeable to water than other
small molecules
 Mechanisms to prevent osmotic lysis
 Bacteria, plant
 Rigid cell wall
 Fresh water protists
 Contractile vacuole pumping water out of
the cell
 Animals
 Maintain osmolarity of blood plasma and
interstitial fluid close to that of the cytosol
 Albumin in blood plasma
 Na+ pump
Inoization of Water
 H2O
H+ + OH Immediate hydration of
H+ to form hydronium ion
(H3O+)
 High ionic mobility of H+
and OH- than other ions
(Na+, K+, Cl-)
 Proton hopping
 Faster than diffusion of
individual proton
 Fast acid-base reaction in
water
Ionization of Water
 Keq for ionization of water at 25oC

Keq =
[H+] [OH-]
[H2O]
[H+] [OH-]
=
55.5M
 Kw : ion product of water

Kw = [H+] [OH-] = (55.5M)Keq
= (55.5M)(1.8 X 10-16 M)
= 1.0 X 10-14 M2
 pH = -log [H+]
 Neutral pH

[H+] = [OH-] = 1.0 X 10-7 M
Ionization of Weak Acids
 Ka: Dissociation constant (HA
H+ + A- )
 Equilibrium constant for ionization reactions
[H+] [A-]
pKa = -log Ka
Keq =
[HA]
= Ka
Titration Curve
 Titration curve of acetic acid



Gradual addition of 0.1M NaOH to
0.1M acetic acid
 Kw = [H+][OH-] = 1 X 10-14 M
[H+][Ac-]
Ka =
[HAc]
Removal of [H+] by addition of NaOH
 formation of H2O
 Dissociation of HAc to keep Ka
At midpoint of titration
 [Ac-] = [HAc]
 pH = pKa
Titration Curve
Buffers
 Aqueous systems that tend to
resist changes in pH when small
amount of acid or base are
added
 Consist of a weak base and its
conjugate base
 Maximum buffering power
 Midpoint of titration curve
 Buffering pH zone
 ~ pKa ± 1
 Hendeson-Hasselbalch equation
 pH = pKa + log [A-]/[HA]
Buffer System in Cells and Tissues
 Keeping pH is biological system
 pH 6.9 ~7.4
 Important for enzyme activity and
other structure and functions
 Weak acids and bases in biological
system
 Proteins (weak acids & base functional
groups of a.a)
 His :pKa of 6.0
 Nucleotides (phosphate of ATP)
 Low molecular weight metabolites
 Organic acids : vacuoles of plant cells
 Ammonia : urine
Important biological buffers
 Phosphate system : biological fluid
 H2PO4H+ + HPO42- : pKa of 6.86
 Bicarbonate system : blood plasma (pH 7.4)
 H2CO3
H+ + HCO3 CO2 (gas)  CO2 (dissolved) H2CO3
Water as Reactant
 Condensation reaction
 Elimination of water
 Endergonic
 Hydrolysis reaction
 Addition of water
 Exergonic
 Hydrolases
 Depolymerization of
proteins, carbohydrate,
nucleic acids
 Oxidation and reduction