Stryer Short Course Chapter 2 Water and Weak Bonds Stryer Short Course Chapter 2

Water Polarity Medium for Brownian motion Solvent

Intermolecular Forces Electrostatic: Ionic Permanent dipole H-bonding Van der Walls Not true categories…

H-bonding 1/10 the strength of some covalent bonds Donor/acceptor ~2.3 H-bonds/ water molecule

Transient Interactions Intermediate strength of H-bonds key to function Changes in structure, association

Solvation Of Ions Dielectric constant Solvation shell Solvent/solute

Hydrophobic Effect Exclusion of nonpolar substances from aqueous solution DG = DH – TDS Cage-like structure of water minimized upon aggregation Powerful structural determination

Structure of Biomolecules Increased order in protein Decreased order overall How?

Amphipathic Compounds Structures determined by hydrophobic effect Micelles Bilayer Vesicle

Functional Groups

Functional Groups

Autoionization of Water Proton jumping: faster than diffusion limit

Kw, The Ion Product of Water

Reciprocal Relationship

pH of Neutral Water

pH of Solutions If acid is added to water, the concentration of hydronium increases and pH decreases If base is added to water, the concentration of hydronium decreases (ion product of water) and the pH increases Addition of MORE acid vs. addition of a STRONGER acid

Strong Acid Complete dissociation What is the pH of a 0.01 M HCl solution? You add a drop of HCl to make a 1 x 10-8 M solution. What is the pH? What is your assumption?

Weak Acids Strong Weak

Weak Acid Dissociation Constants Weak acids have low [pdts], therefore low Ka Low Ka = high pKa Weaker acids have __________ Ka values and __________ pKas

Henderson-Hasselbalch Proton Acceptor Proton Donor

Qualitative Understanding Relationship of Solution pH Strength of acid Ratio of CB to CA Solve quantitatively, but understand qualitatively

Quantitative Understanding What percent of molecules in an imidazole buffer are protonated at pH 7.2?

Understand Figures Be able to explain what is happening as you trace the line from left to right in this figure. Key Tool in biochemistry: Buffer

Buffers

Buffer Capacity Depends on pKa of CA/CB mix Depends on concentration of CA/CB

Polyprotic Acids Must be able to match the pKa with the appropriate proton Assumptions are legitimate if the pKa values are more than ~3 units from each other

What is/are the major ionization state(s) for succinic acid at pH 3 What is/are the major ionization state(s) for succinic acid at pH 3.2, 4.2, 5.2, and 6.2?

Blood Buffer Physiological pH 7.4 Closed vs. Open systems Acidosis

Kidney Function Kidneys fight acidosis caused by common metabolic processes Reclaims excreted bicarbonate by excreting acid Forms new bicarb by CO2 producing metabolism