Water and pH

What is Biochemistry?

Water is the medium for life on earth

What are the molecules in living cells?

 Macromolecules

All macromolecules comprise multiple carbons joined together in some way.

Two important properties of macromolecules:

Polymers are made from monomeric units

Amino acids------->

Nucleotides------->

Sugars--------->

Fatty acids-------->

 Condensation and Hydrolysis

Two types of reactions affect bonds- condensation and hydrolysis

If you have two monomers. One has a hydroxyl group and the other has a hydrogen group. And
these two react with one another and, with the use of energy, water is released (dehydration), and
the two monomers are joined.

The converse of that is hydrolysis where you add water and use energy to break up a polymer and
release a monomer.

 Interactions

Electronegativity=

Valance=

Integral to understanding macromolecules is the notion of chemical bonds

 To convert kilocalories into
Covalent and Ionic Bonds kilojoules multiply by 4.184

Covalent (100-400 kcal/mol)

H Cl

attraction

repulsion

Na Cl
Ionic (100-300 kcal/mol)

Hydrogen and hydrophobic interactions

H2 (12-16 kcal/mol) Hydrophobic Interactions

attraction between a hydrogen
atom in one molecule and a atom of
high electronegativity in another
molecule. It is an intermolecular
force, not an intramolecular force.

To convert kilocalories into kilojoules multiply by 4.184

Van der Waals


Nonpolar molecules are
hydrophobic (means "water
fearing"). They do not dissolve in
water.
Polar and ionic molecules have positive and
negative charges and are therefore attracted
to water molecules because water molecules
are also polar. They are said to be
hydrophilic because they interact with
(dissolve in) water by forming hydrogen
bonds.
 Structure of Water

 Structure of Water

Hydrogen bonds in water

Common Hydrogen bonds

Important hydrogen bonds

 Strong and weak hydrogen bonds

Polar, Non-polar and amphipathic molecules

Water and NaCl- water as a solvent

Water cages and amphipathic molecules

Water and Lipid micelles

Enzyme-substrate
interactions and
water

 Colligative properties

Some properties of a solution do not depend on the chemical properties of the

dissolved substance but does depend upon the NUMBER of solute molecules in a
unit of water

melting point

boiling point

osmolarity

Osmotic pressure and water in cells

Water moves from high water conc to low water conc.

A solute separated from Osmosis
water by a semi-permeable
membrane.

Water and cell membranes

 xxxxxxx

 Ionization of water

H20 H+ + OH

Kw(equilibriumconstant)

Kw=[H+][OH]
[H2O]
Kw=[H+][OH]
[55.5]

MeasuredKw=1.8x1016M

[1.8x1016][55.5]=1x1014=[H+][OH]

 Concentration of water

Weight of 1 liter of water at 1 atmosphere is

Molecular weight of water in g is

Therefore concentration of water is

Water spontaneously dissociates into H+ and OH-

(Water molecules can function as both acids and bases)

H2O is in equilibrium with H+ and OH-

The dissociation constant for water is 1.8x10-16

Concentration of H+ in water is

pH is negative logarithm (base 10) of the molar concentration of hydrogen ions

(H+)

i.e. pH of water is 7 at a particular temperature (~25C)

 pH scale

LowpH=

HighpH=

pH+pOH=14

pH Scale

An Acid gives rise to excess of H+ in aqueous solution - a proton donor is defined as an acid

Strong acids and bases - are completely ionized in water in pH range 0-14
Weak acids and bases - defined as incompletely ionized in water in pH range 0-14

Ka is a value used to describe the tendency of compounds to dissociate (the dissociation

constant)

HA----> H + A (A is the conjugate base of the acid HA)

Ka=

Ka =equilibrium constant
Ka is the dissociation value for a compound in water;
A stronger acid dissociates completely and will have a large [H+] concentration and hence a
large Ka.
Due to the many orders of magnitude spanned by Ka values, a logarithmic measure of the
constant is more commonly used

The value of the pKa changes with temperature. pKa values are temperature dependent in a
non-linear way.

 Acid dissociation

Aceticacid
Ka=1.74x105M
pKa=4.76

HCl
Ka=
pKa=4

Ka = dissociation constant

pKa =

(strong acid----->large Ka----->small pKa)

(pKa measures acidity)

An acid is a substance that dissociates in aqueous solution, releasing H+ (a proton)

The liberated proton combines with a water molecule to give a hydronium

HA(acid) + H2O(base) <----> A-(conjugate base) + H3O+(conjugate acid)

The designation of an acid or base as "conjugate" depends on the context.

H2O (acid)+B (Base) <---- OH- (conjugate base)+ BH+ (conjugate acid)

Acids and bases are thus regarded simply as donors and acceptors of protons
respectively.

You can measure pKa of an acid by performing a titration curve.

Take and acid, measure pH--- say 1.0

Add a strong base such as NaOH and after each addition of NaOH, you measure pH

The pH at mid-point of the titration is the pKa for that acid at that temperature

pH=pKa=50% ionized acid

It is possible to calculate the equilibrium concentration of acids and bases in solution

when the pH is known.

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

Titration of an acid

 Buffers

Buffers are mixtures of weak acids and their anions

Buffers resist change in pH

At pH = pKa, there is a 50:50 mixture of acid and anion forms of the

compound

Buffering capacity of acid/anion system is greatest at pH = pKa

O O

CH3C CH3C H+

OH O

 Buffers

Weak acids or weak bases function as buffers because they do not fully dissociate

They end up being a mixture of weak acid and its salt

Weak acids (HA) are a reserve of protons that can neutralize any OH- added into the
reaction

The salt of a weak acid (A-) acts as a base and can neutralize any H+ added into the
reaction

Buffers can both bind or release protons and in so doing prevents the pH from changing
rapidly.

The pH that a buffer can maintain varies and is determined by its pKa

A buffer is at optimal strength when there is equal amount of HA and A. This occurs
when pH=pKa

 Buffers

Acetic acid + sodium acetate buffer (pKa=4.76)

CH3COOH ---> CH3COO- + H+

<------------

Since this is a weak acid, very little dissociates and most of the CH3COOH is
undissociated.

A buffer is a mixture of a weak acid (CH3COOH) and its conjugate base (CH3COONa)
dissolved in water.
(Water and sodium ions which are present aren't important to the argument).

Lets add acid (H+) to this buffer.

 Buffers

CH3COOH ---> CH3COO- + H+

<------------

Now lets add a base (OH-) to this buffer.

This time the situation is a bit more complicated because there are two processes which
can remove hydroxide ions.

Scenario1

Scenario2

Acetate has a pKa of 4.76. It is a good buffer around 4.76

Buffers and water

Acetic acid + acetate buffer: absorbs H+ or OH-

 Henderson Hasselbalch Equation

ItdescribestitrationcurvesbyrelatingpH,pKaandbufferconcentration

pH=pKa+log[A]
[HA]

Usefulforbiochemists:
1) YoucancalculatepKafrompHandconcentrationofprotonacceptorand
donor

2) YoucancalculatepHfrompKaandconcentrationofprotonacceptorand
donor

3) YoucancalculatetheratioofprotondonorandacceptorbasedonpHand
pKa

 Acid-base pairs
Aceticacid
Ka=1.74x105M O O
pKa=4.76
CH3C CH3C H+

OH O

Ammonium(urine) (Also
phosphateincytosol
Ka=5.62x1010 NH4+ NH3 H+ Bicarbonateinblood)
pKa=9.25

NH3+ NH3+ GlycineCarboxyl

O O Ka=4.57x103M
pKa=2.34
CH2 C CH2 C H+

OH O
NH3+ NH2
O O
GlycineAmino
Ka=2.51x1010M CH2 C CH2 C H+
pKa=9.60
O
O
Titration curves

Amino acid titration curves

Histidine side chain is a weak acid