Transcript Prof. Kamakaka`s Lecture 1 Notes

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
kilojoules multiply by 4.184
Covalent and Ionic Bonds
Covalent (100-400 kcal/mol)
H
Cl
attraction
Na
Ionic (100-300 kcal/mol)
Cl
repulsion
Hydrogen and hydrophobic interactions
H2 (12-16 kcal/mol)
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.
Hydrophobic Interactions
To convert kilocalories into kilojoules multiply by 4.184
Van der Waals
Polar and ionic molecules have positive and
Nonpolar molecules are
hydrophobic (means "water
fearing"). They do not dissolve in
water.
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
water by a semi-permeable
membrane.
Osmosis
Water and cell membranes
xxxxxxx
Ionization of water
H20
Kw (equilibrium constant)
Kw= [H+][OH-]
[H2O]
Kw= [H+][OH-]
[55.5]
Measured Kw= 1.8x10-16M
[1.8x10-16][55.5]= 1x10-14= [H+][OH-]
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 OHThe 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
Low pH=
High pH=
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
Acetic acid
Ka= 1.74x10-5 M
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
CH3C
O
CH3C
OH
H+
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
It describes titration curves by relating pH, pKa and buffer concentration
pH = pKa + log [A-]
[HA]
Useful for biochemists:
1) You can calculate pKa from pH and concentration of proton acceptor and
donor
2)
You can calculate pH from pKa and concentration of proton acceptor and
donor
3)
You can calculate the ratio of proton donor and acceptor based on pH and
pKa
Acid-base pairs
Acetic acid
Ka= 1.74x10-5 M
pKa = 4.76
O
O
CH3C
CH3C
H+
OH
Ammonium (urine)
Ka=5.62x10-10
pKa= 9.25
NH3+
NH4+
O
CH2
O-
CH2
C
Glycine-Carboxyl
Ka= 4.57x10-3 M
pKa= 2.34
O
H+
C
O-
OH
NH3+
Glycine-Amino
Ka= 2.51x10-10 M
pKa= 9.60
H+
NH3
NH3+
(Also
phosphate in cytosol
Bicarbonate in blood)
CH2
O
NH2
CH2
C
O-
O
H+
C
O-
Titration curves
Amino acid titration curves
Histidine side chain is a weak acid