Chapter 2: Water

ّ ‫"وجعلنا من الماء كل شيء حي‬ ّ 30 ‫أفل يؤمنون" النبياء‬ We made from water every living thing. Will they not then believe?
AL-ANBIYA 021. 030

Why is water important?

• Water is the most abundant compound found in living organisms (about 80%).
• Water provides suitable medium for biochemical reactions. • Macromolecular and supramoleclar structure components (i.e. proteins, phospholipid in biological membrane) assume there shapes in response to water.

Properties of water
1) Polarity Presence of a permanent dipole in the molecule as result of unequal sharing of electrons. • Covalent bonds (electron pair is shared) between oxygen and hydrogen atoms with a bond angle of 104.5o. • Oxygen atom is more electronegative than hydrogen atom --> electrons spend more time around oxygen atom than hydrogen atom --> result is a POLAR covalent bond. • Can determine relative solubility of molecules “like dissolves like”.

Water polarity

Electronegativity of most abundant elements Element • Oxygen • Nitrogen • Sulfur • Carbon • Phosphorus • Hydrogen Electronegativity 3.5 3.0 2.6 2.5 2.2 2.1

Hydrogen bonds
• Attraction between adjacent polar molecules, can occur between any electronegative atoms (N,O) with hydrogen atom attached to another electronegative atom. • Water hydrogen bonds = attraction of one slightly positive hydrogen atom of one water molecule and one slightly negative oxygen atom of another water molecule. • H-Bond is most stable when the H atom and the tow electronegative atoms (O) are aligned.

Hydrogen Bonding of Water
One H2O molecule can associate with 4 other H20 molecules

•Ice: 4 H-bonds per water molecule •Water: 2.3 Hbonds per water molecule

Hydrogen bonds and water physical properties
• Hydrogen bonds give water a high melting point. • Hydrogen bonds contribute to water’s high specific heat (amount of heat needed to raise the temperature of 1 gm of a substance 1oC). • Water has a high heat of vaporization - large amount of heat is needed to evaporate water because hydrogen bonds must be broken to change water from liquid to gaseous state.

Biological Hydrogen Bonds

Universal solvent
•Hydrophilic: Compounds interact (dissolve) with water  Polar compounds  Hydrogen bonds  Ionic compounds  Solvation spheres (shell of water molecules around each ion). •Hydrophobic: Compounds do not interact with water  Non polar compounds •Amphipathic: Compounds have both hydrophilic and hydrophobic portions to the molecule (detergents).

Hydrophilic compounds

Functional groups on molecules that confer solubility
 carboxylates  protonated amines  amino  hydroxyl  carbonyl *As the number of polar groups increases in a molecule, so does its solubility in water.

Hydrophobic compounds
• Water molecules tends to react with each other rather than nonpolar molecules (hydrophobic)  exclude nonpolar substance (oil droplets) forcing them to associat with each other. (Hydrophobic effect).

Amphipathics
Many lipids are amphipathic

How detergents work?

Noncovalent interactions in biomolecules
1) Charge-charge interactions (ionic bonds) • Occur between two oppositely charged particles (Electrostatic). • Strongest noncovalent force that occurs over greater distances (40

to 200 KJ/mol.
• Can be weakened significantly by water molecules (can interfere with bonding).

Noncovalent interactions in biomolecules 2) Hydrogen bonds  Stabilize structures such as proteins and nucleic acids. • Weaker than covalent bonds (about 2 – 20 KJ/mol).

Noncovalent interactions in biomolecules 2) Hydrophobic interactions: • Very weak (3-10 KJ/mol). • Important in protein shape and membrane structure.

4) Van der Waals forces • Occurs between neutral atoms. • Results from random movement of e around nucleus very small dipole • Can be attractive or repulsive ,depending upon the distance of the two atoms. • Much weaker than hydrogen bonds (0.4-4 KJ/mol. • The actual distance between atoms is the distance at which maximal attraction occurs.

Ionization of Water

Ionization of Water H20 + H20 H20
Keq= [H+] [OH-] [H2O] [H2O] Keq = [H+] [OH-]

H3O+ + OHH+ + OHKeq=1.8 X 10-16M [H2O] = w.t/(M.w x v) = 55.5 M

(1.8 X 10-16M)(55.5 M ) = [H+] [OH-] 1.0 X 10-14 M2 = [H+] [OH-] = Kw If [H+]=[OH-] then [H+] = 1.0 X 10-7 pH = -log [H+] = 7

pH Scale
 [H+] can range from 1M and 1 X 10-14M  using a log scale simplifies notation  pH = -log [H+] Neutral pH = 7.0 If [H+] > [OH-] , pH < 7, Acidic sol. If [H+] < [OH-] , pH > 7, Basic sol.

Weak Acids and Bases Equilibria
•Strong acids / bases – disassociate completely (HCl/ NaOH) •Weak acids / bases – disassociate only partially •Enzyme activity sensitive to pH • weak acid/bases play important role in protein structure/ function

Acid/conjugate base pairs
HA + H2O HA A- + H 3 O + A- + H+

HA = acid ( donates H+)(Bronstad Acid) A- = Conjugate base (accepts H+)(Bronstad Base) Ka & pKa value describe tendency to loose H+ large Ka = stronger acid small Ka = weaker acid

Ka = [H ][A ] [HA]
+ -

pKa = - log Ka

Buffers

• Buffers are aqueous systems that resist changes in pH when small amounts of a strong acid or base are added. • A buffered system consist of a weak acid (acetic acid) and its conjugate base (acetate). • Buffers are effective at pHs that are within +/-1 pH unit of the pKa. • The most effective buffering occurs at pKa and appear as the region of minimum slope (minimum change in pH value) on a titration curve.

How buffer resist changes of pH
HA A- + H+ + + H+ OH-

If OH-/H+ are added Not effect pH value

HA H2O

pKa values determined by titration

Henderson-Hasselbach Equation
HA A- + H+
HA = weak acid

1) Ka = [H+][A-] A- = Conjugate base [HA] 2) [H+] = Ka [HA] [A-] 3) –log [H+] = -log Ka -log [HA] * H-H equation describes [A ] the relationship between 4) -log[H+] = -log Ka +log [A-] [HA] 5) pH = pKa + log [A-] [HA]
pH, pKa and buffer concentration

Case where 10% acetate ion 90% acetic acid

• pH = pKa + log10

[0.1 ]
¯¯¯¯¯¯¯¯¯¯

[0.9]

• pH = 4.76 + (-0.95) • pH = 3.81

Case where 50% acetate ion 50% acetic acid

• pH = pKa + log10 • pH = 4.76 + 0 • pH = 4.76 = pKa

[0.5 ]
¯¯¯¯¯¯¯¯¯¯

[0.5]

Case where 90% acetate ion 10% acetic acid

• pH = pKa + log10

[0.9 ]
¯¯¯¯¯¯¯¯¯¯

[0.1]

• pH = 4.76 + 0.95 • pH = 5.71

Cases when buffering fails
• pH = pKa + log10 • pH = 4.76 + 2.00 • pH = 6.76 • pH = pKa + log10 • pH = 4.76 - 2.00 • pH = 2.76
[0.01 ]
¯¯¯¯¯¯¯¯¯

[0.99 ]
¯¯¯¯¯¯¯¯¯¯

[0.01]

[0.99]

Phosphate has three ionizable H+ and three pKas