Water and Weak Bonds
Stryer Short Course
Chapter 2
Water
• Polarity
• Medium for Brownian
motion
• Solvent
Intermolecular Forces
• Electrostatic: Ionic
– Permanent dipole
• H-bonding
• Van der Walls
Not true categories…
H-bonding
• 1/10 the
strength of
some covalent
bonds
• Donor/acceptor
• ~2.3 H-bonds/
water molecule
Transient Interactions
• Intermediate strength of H-bonds key to
function
• Changes in structure, association
Solvation Of Ions
• Dielectric
constant
• Solvation shell
• Solvent/solute
Hydrophobic Effect
• Exclusion of nonpolar substances from aqueous solution
• DG = DH – TDS
• Cage-like structure of water minimized upon aggregation
• Powerful structural determination
Structure of Biomolecules
• Increased order in protein
• Decreased order overall
• How?
Amphipathic Compounds
• Structures determined
by hydrophobic effect
– Micelles
– Bilayer
– Vesicle
Functional Groups
Functional Groups
Autoionization of Water
Proton jumping:
faster than
diffusion limit
Kw, The Ion Product of Water
Reciprocal Relationship
pH of Neutral Water
pH of Solutions
• If acid is added to water, the
concentration of hydronium
increases and pH decreases
• If base is added to water, the
concentration of hydronium
decreases (ion product of
water) and the pH increases
• Addition of MORE acid vs.
addition of a STRONGER acid
Strong Acid
• Complete
dissociation
• What is the pH of a
0.01 M HCl
solution?
• You add a drop of
HCl to make a 1 x
10-8 M solution.
What is the pH?
• What is your
assumption?
Weak Acids
Strong
Weak
Weak Acid Dissociation Constants
• Weak acids have
low [pdts],
therefore low Ka
• Low Ka = high pKa
• Weaker acids
have __________
Ka values and
__________ pKas
Henderson-Hasselbalch
Proton Acceptor
Proton Donor
Qualitative Understanding
• Relationship of
– Solution pH
– Strength of acid
– Ratio of CB to CA
• Solve quantitatively,
but understand
qualitatively
• What is/are the
major ionization
state(s) for succinic
acid at pH 3.2, 4.2,
5.2, and 6.2?
Understand Figures
Be able to explain what is happening as you trace
the line from left to right in this figure.
Key Tool in biochemistry:
Buffer
Buffers
Cl-
H
N
H
N
H
N
H
N
NH
NH
H+
NH
+
H
N
H
NH
H
N
NH
H
N
H
HCl
N
HCl
H
N
+
H
N
HCl
NH
H
N
NH
N
H
N
H
N
N
H
N
HCl
NH
HCl
Cl
H
N
H
N
NH
Cl-
-
H
N
NH
NH
H
N
N
NH
H+
H
N
Cl
N
-
N
H
N
NH
H+
H
N
NH
Cl-
Buffer Capacity
• Depends on pKa
of CA/CB mix
• Depends on
concentration of
CA/CB
Polyprotic Acids
• Must be able to
match the pKa with
the appropriate
proton
• Assumptions are
legitimate if the pKa
values are more than
~3 units from each
other
Blood Buffer
• Physiologic
al pH 7.4
• Closed vs.
Open
systems
• Acidosis
Kidney Function
• Kidneys fight
acidosis caused by
common metabolic
processes
• Reclaims excreted
bicarbonate by
excreting acid
• Forms new bicarb
by CO2 producing
metabolism