Chemistry, Water, and Buffers

Biochemistry Free For All

Basic Chemistry
Geometry of Carbon
Tetrahedral
Handedness & Stereochemistry
Basic Chemistry

Electronegativity
Relative “pull” of nuclei for outer shell electrons
Hydrogen Bonds
Partial Negative & Partial Positive Charges
Arise From Different Electronegativities
Reduction / Oxidation

Reduction - Gain of electrons

Oxidation - Loss of electrons

H3CHC=O + NADH + H+<=> H3CH2COH + NAD+

Gibbs Free Energy

ΔG = ΔH - TΔS
aA + bB <=> cC + dD
Keq = {[C]ceq[D]deq]} / {[A]aeq[B]beq}

{[C] c [D]d ]} / {[A]a [B]b }

ΔG = ΔG°’ + RTln eq eq eq eq

ΔG°’ = -RTlnKeq
Water & Buffers

Uneven Charge Distribution

Dipolar
Hydrogen Bonds
Hydrophilic vs Hydrophobic
Amphiphilic
Other Amphiphilic Substances

Membrane Lipids
Glycerophospholipids
Sphingolipids
Other Amphiphilic Substances

Membrane Lipids
Glycerophospholipids
Sphingolipids
Lipid Bilayers
Protein Folding
Hydrophilic
Hydrophobic Outside
Inside

UNFOLDED FOLDED

Water’s Chemistry Affects Molecules

Hydrogen Bonding Between Water Molecules
Hydrogen Bonding Between Water and Other Molecules
Hydrogen Bonding Between Water and Other Molecules
Hydrogen Bonding in the Cell
Bond Strength
Ionization and Acid Strength
Acid Measurement

pH = -Log[H+]
pOH = -Log[OH-]
pKevinAhern = -Log[KevinAhern]
pH + pOH = 14
Weak Acid Dissociation
Weak Acid Dissociation
Henderson Hasselbalch Equation

pH = pKa + log ([HCO3-]/[H2CO3])

pH = pKa + log ([Ac-]/[HAc])

In General,

pH = pKa + Log([Salt]/[Acid])
pKa and Acid Strength

Strong Acids, like HCl, essentially have no pKa value

Low pKa - Stronger Weak Acid
High pKa - Weaker Weak Acid
Formic Acid (pKa = 3.75) vs Acetic Acid (pKa = 4.76)
 Buffers
Rapid pH Change
Resist Changes in pH
Limited pH Change
Weak Acid Systems

Buffering Capacity

Rapid pH Change
Acids With Multiple pKa Values
Estimating Weak Acid Charge

1. If pH > pKa by one or more pH units - Proton OFF

2. If pH < pKa by one or more pH units - Proton ON

-COOH vs -COO-
-NH3+ vs -NH2