Chapter 1 Outline

Biochemistry

• Biochemistry and life HERE
• Evolution Timeline HERE, Tree of Life HERE
• DNA's Bases HERE, Covalent Structure HERE, Double Helix HERE
• Base pairs HERE, HERE

Charges and Interactions

• Covalent Bonds
• Hydrogen Bonds HERE / in biomolecules HERE
• van der Waals Interactions HERE
• Ice Structure HERE
• Hydrophobic Effect HERE
• Protein Folding HERE

Thermodynamics

• First Law
• Second Law
• Free Energy
  • G = H - TS

Acid-Base Reactions

• pH = -log [H⁺]
• pOH = -log [OH^-]
• pH + pOH = 14
• pKa = -log Ka
• For acetic acid(HAc), HAc <=> H+ + Ac-
• So the acid dissociation constant for acetic acid is Ka = [H⁺][Ac^-]/[HAc]
• The lower the pKa for an acid is, the stronger the acid will be
• The larger the pKa for an acid is, the weaker the acid will be
• pKa is a constant for a given acid
• Strong acids, like HCl completely dissociate in water to H⁺ and Cl^-
• Strong bases, like NaOH completely dissociate in water to Na⁺ and OH^-
• Weak acids, like HAc DO NOT COMPLETELY DISSOCIATE in water, meaning that some HAc will be left undissociated. The amount of dissociation will be related to the pH of the solution it is in.
• Addition of protons to a solution containing sodium acetate will favor formation of HAc (called the undissociated acid form) - see HERE and HERE
• Addition of hydroxides to a solution containing acetic acid will favor formation of Ac- (called the salt form)
• Thus, for HAc <=> H⁺ + Ac^-, the extent of the dissociation will be a function of pH
• We can determine the amount of the dissociation from the Henderson-Hasselbalch equation - pH = pKa + log[Ac-]/[HAc]
• Knowing the extent of dissociation of weak acids at any pH is essential for understanding the role of charge in biochemistry
• Weak acids and weak bases act as buffers. Buffers RESIST changes in pH when protons or hydroxides are added IF the buffer is in its buffering region
• The buffering region for a buffer is within one pH unit above or below the pKa of the weak acid composing it.
• A buffer has its maximum buffering capacity (maximum ability to resist pH change) when the pH of the solution equals the pKa of the buffer. A buffer will be efffective only when the pH is within on pH unit (above or below) the pKa.
• It is useful for the purpose of estimating charge (and only for that) to make the following assumptions - if the pH of a solution is more than one pH unit below the pKa of a particular group, the proton is ON the group. If the pH of a solution is more than one pH unit above the pKa of a particular group, the proton is OFF the group.
• The pI of a molecule is the pH at which the charge is exactly zero. Note that to get the pI, one must calculate it - you cannot use the above assumption to get it.
• Buffer plot HERE