1. Chapter Two Water: The Solvent for Biochemical Reactions

2. What makes water polar What is a polar bond:
• Electrons are unequally shared,more negative charge found closer to one atom.
• Due to difference in electronegativity of atoms involved in bond.

3. Electronegativity
Electronegativity: a measure of the force of an atom’s attraction for electrons it shares in a chemical bond with another atom
Oxygen and Nitrogen, more electronegative than carbon and hydrogen
Fluorine is most electronegative (4)

4. Solvent Properties of H2O
Ionic compounds (e.g.,KCl) and low-molecular- weight polar covalent compounds (e.g., C2H5OH and CH3COCH3) tend to dissolve in water
The underlying principle is electrostatic attraction of unlike charges; the positive dipole of water for the negative dipole of another molecule, etc.
ion-dipole interaction: e.g., KCl dissolved in H2O
dipole-dipole interactions: e.g., ethanol or acetone dissolved in H2O
dipole induced-dipole interactions: weak and generally do not lead to solubility in water

5. Hydration Shells Surrounding Ions in Water

6. Ion-dipole and Dipole-dipole Interactions
• Ion-dipole and dipole-dipole interactions help ionic and polar compounds dissolve in water

7. Solvent Properties of H2O
Hydrophilic: water-loving
tend to dissolve in water
Hydrophobic: water-fearing
tend not to dissolve in water
Amphipathic: has characteristics of both properties
molecules that contain one or more hydrophobic and one or more hydrophilic regions, e.g., sodium palmitate

8. Amphipathic molecules
• both polar and nonpolar character
Interaction between nonpolar molecules is very weak
called van der Waals interactions

9. Micelle formation by amphipathic molecules
Micelle: a spherical arrangement of organic molecules in water solution clustered so that
their hydrophobic parts are buried inside the sphere
their hydrophilic parts are on the surface of the sphere and in contact with the water environment
formation depends on the attraction between temporary induced dipoles

10. Examples of Hydrophobic and Hydrophilic Substances

11. Hydrogen Bonds
Hydrogen bond: the attractive interaction between dipoles when:
positive end of one dipole is a hydrogen atom bonded to an atom of high electronegativity, most commonly O or N, and
the negative end of the other dipole is an atom with a lone pair of electrons, most commonly O or N
Hydrogen bond is non-covalent

12. Interesting and Unique Properties of Water
• Each water molecule can be involved in 4 hydrogen bonds: 2 as donor, and 2 as acceptor
• Due to the tetrahedral arrangement of the water molecule (Refer to Figure 2.1).

13. Hydrogen Bonding
Even though hydrogen bonds are weaker than covalent bonds, they have a significant effect on the physical properties of hydrogen-bonded compounds

14. Other Biologically Important Hydrogen bonds
• Hydrogen bonding is important in stabilization of 3-D structures of biological molecules such as: DNA, RNA, proteins.

15. Acids, Bases and pH Acid: a molecule that behaves as a proton donor
Strong base: a molecule that behaves as a proton acceptor

16. Ionization of H2O and pH
Lets quantitatively examine the dissociation of water:
• Molar concentration of water (55M)
• Kw is called the ion product constant for water.
• Must define a quantity to express hydrogen ion concentrations…pH

17. Acid Strength
One can derive a numerical value for the strength of an acid (amount of hydrogen ion released when a given amount of acid is dissolved in water).
Describe by Ka: 
Written correctly,

18. Henderson-Hasselbalch
Equation to connect Ka to pH of solution containing both acid and base.
We can calculate the ratio of weak acid, HA, to its conjugate base, A-, in the following way

19. Henderson-Hasselbalch (Cont’d)
Henderson-Hasselbalch equation
From this equation, we see that
when the concentrations of weak acid and its conjugate base are equal, the pH of the solution equals the pKa of the weak acid
when pH < pKa, the weak acid predominates
when pH > pKa, the conjugate base predominates

20. Titration Curves a monoprotic acid releases one H+ per mole
Titration: an experiment in which measured amounts of acid (or base) are added to measured amounts of base (or acid)
Equivalence point: the point in an acid-base titration at which enough acid has been added to exactly neutralize the base (or vice versa)
a monoprotic acid releases one H+ per mole
a diprotic acid releases two H+ per mole
a triprotic acid releases three H+ per mole

21. Buffers
buffer: a solution whose pH resists change upon addition of small to moderate amounts of a strong acid or base
consists of a weak acid and its conjugate base
Examples of acid-base buffers are solutions containing
CH3COOH and CH3COONa
H2CO3 and NaHCO3
NaH2PO4 and Na2HPO4

22. Buffers

23. Buffer Capacity
Buffering capacity is related to the concentrations of the weak acid and its conjugate base
the greater the concentration of the weak acid and its conjugate base, the greater the buffer capacity

24. Naturally Occurring Buffers
H2PO4-/HPO42- is the principal buffer in cells
H2CO3/HCO3- is an important (but not the only) buffer in blood
hyperventilation can result in increased blood pH
hypoventilation can result in decreased blood pH

25. Selecting a Buffer The following criteria are typical suitable pKa
no interference with the reaction or detection of the assay
suitable ionic strength
suitable solubility
its non-biological nature

26. Laboratory Buffers

27. Problem set
3, 11, 12, 14, 32