An isolated system cannot exchange matter or energy with its surroundings.

A closed system can exchange only energy with its surroundings. A closed system inevitably reaches equilibrium. Open systems exchange both matter and energy with their surroundings and therefore cannot be at equilibrium. Living organisms must exchange both matter and energy with their surroundings and are thus open systems. Living organisms tend to maintain a constant flow of matter and energy, referred to as the steady state.

Lecture 2: Physical Properties of Water

Water is a polar molecule Hydrogen bonding Noncovalent interactions Solubility water of hydration Hydrophobic Effect Osmosis, Diffusion, Dialysis

Hydrogen Bond between water molecules O atom has partial charge of 0.66e H atom has partial + charge of +0.333e

Ice Structure Each water molecule interacts tetrahedrially with 4 other water molecules. H bonds are ~ 0.5 shorter than van der Waals distance between H bonded atoms. Ice has open structure water expands on chilling thus ice is less dense than water and floats

H bonding in liquid water Irregular structure with 3, 4 or 5 molecules arranged in ring structures.
Very hard to get precise structure for liquid water since molecules are constantly in motion

Noncovalent interactions between neutral molecules Collectively known as Van der Waals forces

Solvation of ions by water

Water dipoles orient according to ion charge

Uncharged polar molecules dissolve by H bonding of functional groups with solvent water molecules

Water molecules maximize H bonding by forming a cage around nonpolar solute

Aggregation of nonpolar molecules in water is entropy driven

(a) (b)

individual hydration of dispersed molecules decreases entropy of system (reduces H bonding possibilities of solvent water molecules aggregation increases entropy of system since fewer water molecules are needed to hydrate aggregate and more H bonding of water molecules is possible

Amphiphiles form micelles (a) and bilayers (b)

Osmosis is movement of solvent across membrane from high concentration (pure water) to lower concentration (water + solute molecules). Osmotic pressure is the pressure required to prevent inward flow of water

Diffusion is random movement of water & solute across membrane permeable to both from high concentrations to low concentrations thus water moves in and solute moves out of the dialysis bag.

Lecture 3: Chemical Properties of Water Ionization of Water Acids and Bases pH Buffers

Water is an important reactant in many biochemical reactions Condensation Reactions - loss of water Hydrolysis Reactions - addition of water

Condensation

Hydrolysis

O O O R O P OH R O P O P O-+ H2O O OOCondensation

Hydrolysis

O HO P OO-

ACIDS AND BASES I. Classical (Arrhenius) Definition Bases are compounds that yield OH- ions when dissolved in H2O Acids are compounds that yield H+ (H3O+) ions when dissolved in H2O However, often talk about acid-base reactions that involve neither H3O+ or OH- ions. 2 other common systems for describing acid-base Reactions II. Hydrogen-ion Transfer (Brnsted-Lowry System) Brnsted acid can give up a proton to another species Brnsted base can accept a proton from another species

III. Electron-pair Transfer

(more general system)

An acid-base Reaction consists of donation of a pair of electrons from the base to the acid

Brnsted-Lowry system most useful for typical biochemical reactions such as buffering.

WEAK ACIDS & BASES

BUFFERS

Of particular interest are reversible reactions involving hydrogen ions. These include weak acids & weak bases which have been defined by Brnsted as: HA Acid B + H+ Base H+ + Aconjugate base BH+ conjugate acid

A Brnsted acid can ionize to form a proton and its conjugate base

A Brnsted base can react with a proton to form its conjugate acid

CH3 COOH

H+ + CH3 COOConjugate acid-base pair

HOAc

H+ + OAc-

Incomplete dissociation of these acids and bases distinguish them from strong acids (HCl & HNO3) and from strong bases such as NaOH

Since most biochemical reactions take place in H2O, It is necessary to consider the ionization of water. Water acts as a weak acid: H2O H+ + OH-

At normal pressure & temperature the concentration of undissociated H2O is constant: 1000gL-1 / 18g mol-1 55.56 mol / L = 55.56 M
+ Keq = [H ][OH ] = 1.8 x 10 16 mole/L [H O] 2
constant

define a new equilibrium constant Kw which includes concentration of "solvent" H2O Kw = [H+] [OH-] = 1 x 10-14 mol2/L2 at 25C note the units This is the basis of the Sorensen pH scale which ranges from 0 14 (acidic to basic) Regardless of the concentration of H+ and OH- ions, which may be contributed by ionization of acids & bases in solution, the ion product of water Kw prevails: [H+] x [OH-] = 1.0 x 10-14
under normal conditions

Review: H2O H+ + OH-

[H+ ][OH ] K eq = = 1.8 10 16 mole liter 1 H2 O

55.56 M pure water (1) Kw = [H+] [OH-] = 55.56 M 1.8 X 10-16 M =1.0 X 10-14 mole2 / liter2 @ 25oC [H+] [OH-] = 1 X 10-14 mole2 / liter2 log [H+] + log [OH-] = -14 define
pH

pH = -log[H+] pOH = -log [OH-]

+ pOH = 14 Dissociation of weak acid

HA
K eq = [H ][A ] [HA]
weak acid +

H+ + Aconjugate base

dissociation constant Ka