2. Water, pH, Buffers

Why is water more than just a neutral medium?

(1) is essential to maintain

the 3D structure and proper functioning of biochemical

molecules, and

(2) is an active participant in

biochemical reactions

Example, H2O molecules are bound to DNA strands

to maintain the structure of the DNA double helix

Properties of Water

polar molecule

Hydrogen bonds

% Mass of water in hydrated DNA

35-50%

% Mass of water in hydrated Protein

~20%

% Ionic character of O-H bond in H2O

33%

How quickly do hydrogen bonds shift?

Matter of PICOseconds (psec)

Av. Hydrogen bonds per water molecule

3.4 Bonds/molecule

Two opposing forces of water

Kinetic energy (disperse)

Hydrogen Bonding (Stay together)

Structure of Ice

Fixed, three-dimensional network

Open lattice structure

Low density (more open than liquid water) (ice floats on wtaer)

Water as a solvent

Form hydration shells around ions

• Participate in hydrophobic interactions

• Form H-bonds with polar solutes

• Produce micelles with amphiphilic molecules

Hydration shells

Water molecules form hydration shells around ions in solution.

clathrate structures

“Cage-like” structures

Water forms bonds around oil (non-polar solute)

Surface of oil allows water to slow down enough to encourage hydrogen bonding

Micelles

These spherical structures are formed by amphiphilic molecules such as fatty acids in water.

Nonpolar tail comprised of single Carbon chain

Lipid Bilayers

Lipids such as glycerophospholipids form lipid bilayers in water instead of

micelles.

Nonpolar tail comprised of 2 carbon chains

Effect of lipid bilayer on ion concentrations

Varying levels on intra- and extraceulluar levels of ions