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What is Biochemistry?
Water is the medium for life on earth
What are the molecules in living cells?
Macromolecules
Amino acids------->
Nucleotides------->
Sugars--------->
Fatty acids-------->
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=
To convert kilocalories into
Covalent and Ionic Bonds kilojoules multiply by 4.184
H Cl
attraction
repulsion
Na Cl
Ionic (100-300 kcal/mol)
Hydrogen and hydrophobic interactions
Van der Waals
Polar and ionic molecules have positive and
negative charges and are therefore attracted
Nonpolar molecules are to water molecules because water molecules
hydrophobic (means "water are also polar. They are said to be
fearing"). They do not dissolve in hydrophilic because they interact with
water. (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
melting point
boiling point
osmolarity
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
Concentration of H+ in water is
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 =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 =
An acid is a substance that dissociates in aqueous solution, releasing H+ (a proton)
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.
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+log[A-]/[HA]
Titration of an acid
Buffers
O O
CH3C CH3C H+
OH O
Buffers
Weak acids or weak bases function as buffers because they do not fully dissociate
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
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).
Buffers
This time the situation is a bit more complicated because there are two processes which
can remove hydroxide ions.
Scenario1
Scenario2
Buffers and water
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
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