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Chapter 2

Chapter 2. 1.) Properties of water, hydrogen bonding and the hydrophobic effect 2.) Other important intramolecular interactions 3.) Acid/base chemistry. Liquid water. Ice. Hydrogen bonding D -H --- A. Water is a “ locally structured transient gel . ”.

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Chapter 2

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  1. Chapter 2 1.) Properties of water, hydrogen bonding and the hydrophobic effect 2.) Other important intramolecular interactions 3.) Acid/base chemistry

  2. Liquid water Ice

  3. Hydrogen bonding D-H---A

  4. Water is a “locally structured transient gel.”

  5. While the conformational entropy (# of possible arrangements) of the lipid is decreased by sequestering it, the overall system entropy increases due to the dramatically increased number of ways that the HOH molecules can be arranged. This is a direct result of the transient nature of HB networks…meaning, they are continuously fluctuating and any number of HOH molecules can occur within a given ‘location.’ time

  6. Diffusion is from high to low concentration!

  7. Chapter 2 1.) Properties of water, hydrogen bonding and the hydrophobic effect 2.) Other important intramolecular interactions 3.) Acid/base chemistry

  8. Intramolecular H-bonds

  9. Relative strength of the chemical interactions that we are interested in Note that the hydrophobic effect is NOT a direct force between nuclei. Rather, it is a bulk colligative property arising from the overall number of degrees of freedom within the system (as already discussed). Increasing strength Covalent bonds Salt bridges (aka ionic bonds) Hydrogen bonds Dipole-dipole interactions van der Waals interactions (aka, London forces)

  10. Notes Hooke’s law, U = 1/2k·l2 Hooke’s law, U = 1/2k·q2 We will ignore improper torsions Sinusoidal potential. Note the three minima, which depending on the local chemistry, may or may not be equally deep. U = q1q2 / (4pe·rij) Positive (destabilizing) values when ++ or --. Morse curve.

  11. Dissecting the force field

  12. What is a torsion angle? CH3-CH2-CH2-CH3

  13. While the hydrophobic effect is NOT a direct chemical interaction… Hydrophobic core Hydrophilic surface …it does contribute to increased propensity for chemical species of similar polarity to aggregate.

  14. Chapter 2 1.) Properties of water, hydrogen bonding and the hydrophobic effect 2.) Other important intramolecular interactions 3.) Acid/base chemistry

  15. (alkaline)

  16. Consider the halide diatomic acids (HF, HCl, etc.) Q: Which are “strong” acids? Which are not? Why?

  17. Nomenclature of common acid/conjugate base pairs

  18. Amino acid sidechain pKa values* Q: Why is there an asterisk here? Residue pKa values: CT: 3.8 (R-CO2H) Asp: 4.0 (R-CO2H) Glu: 4.4 (R-CO2H) His: 6.5 (imidazole) NT: 8.0 (R-NH3+) Cys: 8.5 (R-SH) Tyr: 10.0 (Ph-OH) Lys: 10.0 (R-NH3+) Arg: 12.0 (guanidinium) The answer is yes! You must know these values.

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