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Protein Biochemistry

Angelo Corti Tumor Biology and Vascular Targeting Unit, Division of Molecular Oncology San Raffaele Scientic Institute, Milan corti.angelo@hsr.it (0226434802)

Protein Biochemistry Weak interactions in water solutions Aminoacids, Peptides and Proteins Protein Purication and Characterization Protein Structure Protein Function - Oxygen Binding Proteins - Enzymes - Antibodies

Molecular interactions in acqueous solutions


Hydrogen bonds Hydrophobic interactions Van der Waals interactions Ionic interactions

The dipolar structure of water and the formation of hydrogen bonds

Partial charges

Unequal sharing

Electrostatic attraction

1.77 A Longer and weaker than O-H Half life: 10-9 sec Dissociation energy: 20 kJ/mole Dissociation energy for O-H: 461 kJ/mole 0.965 A +

Bond energy
amount of energy necessary to break the bond (or the energy released in the environment when the bond is formed) (1 cal = 4.184 J)

Endothermic and esothermic reactions


- Endothermic reactions absorb energy from the surroundings in the form of heat (H>0)

- Exothermic reactions release energy in the form of heat (H<0)


The Change in Enthalpy (H) accounts for the type and number of bonds broken and formed in a reaction
(Enthalpy is a measure of the total energy of a thermodynamic system. Under constant pressure, H is the heat absorbed (or released) by a chemical reaction).

Endoergonic and esoergonic reactions


Reactions can be esoergonic (spontaneous) or endoergonic (non spontaneous) depending on the change in the Gibbs Free Energy (G). G depends on H, T e S

G = H-TS
Esoergonic (spontaneous): G<0 Endoergonic (non-spontaneous): G>0

Ice melting is an esoergonic and endothermic process


Hydrogen bonds in the ice: n=4 Hydrogen bonds in liquid water: n=3.4

Ice melting (spontaneous at r.t, G <0 ) is made possible by the increase of entropy (breaking of hydrogen bonds needs energy H>0).

G = H - TS G <0; H>0

Hydrogen bonds in biological systems

C-H does not form hydrogen bonds

The hydrogen bond is directional

Water is a polar solvent (dissolves polar compounds)

Non polar compounds are insoluble (or poorly soluble) in water

Non Polar (poorly soluble)

Polar (soluble)

Amphipathic compounds
Contain both polar and non polar regions example:

O || HO-C
Polar (hydrophilic head group)

Fatty acids

Non polar (hydrophobic alkyl chain)

Amphipatic compounds in water

Hydrophobic interactions and formation of micelles by fatty acids and detergents

Highly ordered water

micelles

Less ordered water (free to form hydrogen bonds) Thermodynamically favored (higher entropy)

Van der Waals interactions (4 kJ/mole)


Van der Waals interactions are the sum of the attractive or repulsive forces between molecules (or between parts of the same molecule) They include: forces between two permanent dipoles forces between a permanent dipole and a corresponding induced dipole forces between two instantaneously induced dipoles

Weak interactions are important for the structure of macromolecules and for their function

The cumulative effect of many weak interactions can generate strong interactions

Water ionization and buffers

Self-ionization of water
H20 = H+ + OH[H+][OH-] Keq = [H2O] [H2O] = 55.5 M = 1.8 x 10-16 M

Ionization constant (ion product of water) Kw = [H+][OH- ] = 55.5 x Keq = 10-14 M2 [H+] = [OH- ]

pH
pH = - log [H+]

Example: 0.01 M = 10-2 M

pH = 2

Acid dissociation constant


CH3COOH = CH3COO + H+

[CH3COO] [ H+] Ka = [CH3COOH] [CH3COOH] [CH3COO-] pKa = -log Ka pH = pKa + log [CH3COO-] [CH3COOH]
Henderson-Hasselbalch equation

(1.74 x 10-5 M)

[ H+] =

Ka

(4.76)

Henderson-Hasselbalch equation

pKa of monoprotic, diprotic and triprotic acids


pH = pKa + log [A-] [AH]
Eq. of Henderson-Hasselbalch

Titration curve of acetic acid and buffering region

pH = pKa

Burette (NaOH)

pHmeter

CH3COOH

Buffering regions of acids with different pKa

Buffering regions