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1
Chapter 2: Water: The Solvent for Biochemical Reactions
o Induced dipole-induced dipole (London dispersion forces) – two molecules induce dipoles in each other
Weakest of the three forces
London dispersion force – Occur between nonpolar molecules as a result of small fluctuations in their
distribution of electrons that create a temporary separation of charge.
The attraction b/w transient induced dipoles; nonpolar groups such as methyl experience some
Know the relative strengths of biochemical bonds and which play the most vital role
o Weaker forces play a vital role in biological systems and structures
Covalent (C-H) > covalent (O-H) > ionic > ion-dipole > Hydrogen bonds > Van der Waal
o Alone they are weak; together they are strong as seen in drug molecules.
Weaker forces only act when the groups are very close together
o But if the groups approach too closely, van der Waal’s radii collide and a strong repulsive force overcomes the
attractive force.
Know how to rank melting or boiling points of compounds
o Based on nature and strength of intermolecular forces
Hydrophobic Effect
Know the difference between hydrophilic and hydrophobic tendencies
o Hydrophilic – tending to dissolve in water; ionic (or charged substances) and (un/charged) polar substances
o Hydrophobic – tending to not dissolve in water
Hydrophobic interactions – attractions b/w nonpolar molecules; examples include hexanes and alkanes.
Associate with each other – not with water
Understand the nature of amphipathic molecules
o Amphipathic – molecules that contain both hydrophilic and hydrophobic regions
EX: sodium palmitate is polar via the charged carboxyl group and nonpolar via its long hydrocarbon tail
Considered water insoluble b/c its mostly nonpolar
o There are degrees of both polarity and non-polarity
The greater the nonpolar surface area, the more nonpolar the compound
o How lipids can associate as micelles or membranes and what determines the nature of their association in an
aqueous environment
An amphipathic molecule that is mostly hydrophobic in surface area tends to aggregate together in various
ways depending on the molecule’s geometry
Fatty acids associate to form spherical arrangement via micelles – nonpolar tails aggregate and are
buried inside away from water while the polar head groups associate on the head surface in direct
contact w/ water’s solvent molecules.
o As a result, amphiphiles can form spherical micelle, a particle w/ solvated surface and
hydrophobic core.
o They may also form a sheet such as lipid bilayers- hydrophobic core sandwiched b/w
hydrated polar surfaces.
o One-tailed lipids tend to form micelles while two-tailed lipids form bilayers.
Formation shape depends on the attraction between temporary and induced dipoles
Nonpolar regions are involved in interactions due to induced dipoles
o The interaction of biomolecules is related highly to the hydrophobic effect.
o Benefits of lipid associations into membranes
Know how to recognize classes of molecules based on hydrophobicity (polarity)
Recognize that the hydrophobic effect is based mainly on changes in entropy – spontaneous associations
o In order to mix oil and water, free energy must be added to the system
The free energy barrier to the solvation process depends on the entropy term (∆𝑆) b/c when a hydrophobic
molecule is hydrated, it become surrounded by a layer of waters molecule that cannot participate in normal
hydrogen bonding. Instead, they must align themselves so that their polar heads are not oriented towards
the nonpolar solute.
This constraint on the structure of water represents a loss of entropy in the system b/c now the
highly mobile water molecules have lost some of their freedom to rapidly form, break, and reform
hydrogen bonds with other water molecules.
o The aggregation of nonpolar molecules in water –
The individual hydration of nonpolar molecules decreases the entropy b/c the hydrating water molecules
are not free to form hydrogen bonds
Aggregation of the nonpolar molecules increases the entropy of the (polar) water molecules b/c the # of
water molecules required to hydrate the aggregate solutes is less than the # of water molecules required to
hydrate the dispersed solute molecules.
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Chapter 2: Water: The Solvent for Biochemical Reactions
This increase in entropy accounts for the spontaneous aggregation of nonpolar substances in water.
The hydrophobic effect – the exclusion of nonpolar substances from an aqueous solution
o The nonpolar molecules do not experience any additional attractive force among themselves; they aggregate only b/c
they are driven out of the aqueous phase by the unfavorable entropy cost of individually hydrating them.
Hydrogen Bonding
Water has unique properties for a molecule its size such as a very high boiling point and melting point.
Understand the basic principles of hydrogen bonds
o Hydrogen bonds – result from noncovalent attractions between dipoles w/ one dipole as a donor & one as an
acceptor
The (+) dipole is a H atom covalently bonded to a highly electronegative donor (hydrogen bond donor)
The (-) end of the other dipole is also electronegative and contains a lone pair of electrons (hydrogen bond
acceptor)
o What contributes to a strong H-bond versus a weak one?
A linear alignment results in a greater overlap of Van der Waal’s radii = shorter bond length which is
stronger by definition
Nonlinear – weaker bond
o Electronegative element covalently bonded to H atom and electrostatically attracted to 2 nd H atom
Understand the molecular structure of water
o What makes it a polar molecule?
Polar solute (such as alcohol, carbonyl, amine) can serve as a donor or acceptor of H bonds
They can form H bonds with water and participate in nonspecific dipole-dipole ineractions
Acceptor to alcohol, donor to ketone, or an acceptor to an amine group.
o Hydrogen fluoride and ammonia can form hydrogen bonds
Each of their structures contains the required donor and acceptor atoms
HFl – one H donor (as a H bond) and 3 (lone pair) acceptors on fluorine
NH3 – three H donors (i.e. hydrogen bonds) and one acceptor (lone pair) on nitrogen
o Water is optimized for H bonding w/ 2 acceptors via the two lone pairs on Oxygen and 2 donors via the 2 H bonds
This optimum arrangement makes it the universal solvent
o The tetrahedral arrangement around Oxygen contributes to the unique bonding properties of water
Due to the two lone pairs around Oxygen, the bond angles are 104.3 degrees
Ice or solid water has a lower density as water as a liquid
Thus, the H bonding network is more restricted, leading to a more opened and less densely packed
arrangement of H bonds than liquid water
o Unique: water’s solid form is less dense than its liquid form letting ice float
Understand the formation of H-bonds in water in liquid and solid form
o What contributes to the surface tension of water?
o Why is solid water less dense than the liquid form?
Be able to recognize H-bond donors and acceptors
Know the significance of hydrogen bonds in biomolecules
o Hydrogen bonds are weaker than covalent bonds but still have strong effect on physical properties
Compared to molecules of similar size like CH4 or NH3, water has a super high boiling and melting point
o H bonding stabilizes 3D structures of molecules such as proteins, DNA, and RNA
Hydrogen bonds are usually bonded to electronegative elements – N, O, or S atoms – which function as hydrogen acceptors.
o Thus, water can form hydrogen bonds not just with other water molecules but with a wide variety of other
compounds that bear N-, O-, or S- containing functional groups.
These functional groups can form hydrogen bonds among themselves such as in base pairing DNA.
Review Exercises Recommended: 11, 13, 15, 17, 18
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Chapter 2: Water: The Solvent for Biochemical Reactions
KA describes the ratio of dissociated to undissociated forms
o As KA increases, acid strength increases; high K A = low pKa
This equation shows the participation of water – water accepts the proton to form hydronium ion
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Chapter 2: Water: The Solvent for Biochemical Reactions
At the start point (before base is added), the acid is present mainly in its CH 3COOH form. As small amounts of base are
added, protons dissociate until, at the midpoint of the titration (where pH 5 pK ), [CH3COOH] 5 [CH3COO2].
o The addition of more base causes more protons to dissociate until nearly all the acid is in the CH 3COO2 form (the
end point).
o Within one pH unit of the pK, additions of acid or base do not greatly perturb the pH of the solution
Groups of Acids
Understand the principles and properties of polyprotic acids
o Monoprotic acid – release 1 H+ ion and have 1 Ka and pKa
o Diprotic acids – release 2 H+ ion and have 2 Ka and pKa
o Polyprotic acids – release more than two H+ ion
Phosphoric acid is a polyprotic acid, with 3 protons to donate
o As each proton is released, the corresponding pKa
values increase because the ionized form becomes
more and more negative.
Thus, it becomes harder and harder to
stabilize the additional negative charges.
For each of the 3 pKa values, there is a corresponding acid and conjugate based pair.
Influence of pH on enzymatic activity –
o Each enzyme – pepsin, trypsin, lysozyme – have a pH range of activity
Protein activity can rapidly change as pH changes; pH range is critical in biological systems.
Know the general trend of pKa values for a polyprotic acid and why
Because of the stoichiometry, the moles of acid added will decrease the amount of conjugate base and increase the
amount of weak acid to the same extent
o New moles A- = 0.005 – 0.003 = 0.002
o New moles of HA = 0.005 + 0.003 = 0.008
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Chapter 2: Water: The Solvent for Biochemical Reactions
[A− ] 𝟎. 𝟎𝟎𝟐
pH = p𝑲a + 𝐥𝐨𝐠 = 𝟖. 𝟑 + 𝐥𝐨𝐠 ( ) = 𝟕. 𝟕
[HA] 𝟎. 𝟎𝟎𝟖
Review Exercises Recommended: 30, 31, 33, 35, 37, 41, 43, 44, 47, 51
Buffer Selection
Understand the principles of buffering capacity
o Effective buffering range – how much strong acid or base can be added without significantly altering pH
The midpoint – or inflection point – is reached when ½ of the acid had been titrated or converted to
conjugate base.
At the inflection point, the concentration of acid and conjugate base are equal: [HA]=[A --]
There is small pH changes in the vicinity of the inflection point of the titration curve.
Little change in relative abundance if the buffering capacity holds true for pH = pKa +/- 1
o Know that capacity increases with concentration of components
1 pH unit represents a 10-fold change in hydrogen ion concentration
If the pH changes by 2 units, the concentration changes by 100: 10 2 = 100
Know the criteria for buffer selection
o Find a buffer solution who’s pKa value is the closest match to the target pH
Buffer solutions maintain an about constant pH value at values near the pKa of the acid
o Buffer capacity = measure of the amount of acid or base that can be absorbed by a buffer w/ little changes in pH.
The buffering capacity increases with greater concentrations of weak acid and conjugate base.
o In summary, favorable criteria for selecting a buffer include –
Suitable pKa and suitable concentration of the buffer
No interference with reaction or with experimental assay
Suitable ionic strength of buffer
No precipitation of reactants or products
Nonbiological nature of buffer