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Chapter 1 2/5-2/6/07

Chapter 1 2/5-2/6/07. Overall important concept: D G = D H – T D S Toward lower enthalpy Forming bonds = good Toward higher entropy More degrees of freedom = good Toward lower energy ( D G < 0). Chapter 1. D G = D H – T D S “Manipulation” of this equation

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Chapter 1 2/5-2/6/07

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  1. Chapter 1 2/5-2/6/07 • Overall important concept: DG = DH – TDS • Toward lower enthalpy • Forming bonds = good • Toward higher entropy • More degrees of freedom = good • Toward lower energy (DG < 0)

  2. Chapter 1 • DG = DH – TDS • “Manipulation” of this equation • If entropy is bad (eg. ligand/substrate binding to a protein), improve enthalpy (ie. form bonds) • If overall DG is bad, “couple” the reaction to one with a very good DG

  3. Chapter 1 • Biological molecules • Small molecules • Amino acids • Nucleotides • Sugars • Macromolecules • Proteins • Nucleic acids • Lipids

  4. Chapter 2 2/7,12, 14, 16 • Weak interactions • Covalent bonds = strong interactions • Weak interactions • Ionic bonds • Hydrogen bonds • Hydrophobic forces • van der Waals interactions (induced dipole) • “Weak” is a relative term • eg. Ionic bonds >> Hydrogen bonds

  5. Chapter 2 • Hydrophobic interactions • Not a ‘normal’ interaction • Not so much an ‘attraction’ between two molecules/groups • Driven by avoidance of water (entropy)

  6. Chapter 2 • Osmosis • Requires semi-permeable membrane • System strives to reach equal osmolarity on both sides • Osmolarity = sum of all solutes • 100mM NaCl → 200 mOsm

  7. Chapter 2 • Acid/base • Acids: donate protons • Bases: accept protons (note: a base need not be negatively charged) • Autoionization of water • Kw = 10-14 H2O ↔ H+ + OH-

  8. Chapter 2 • Strong acids (and bases) • pH (and [H+] directly from the concentration of acid • HCl → H+ + Cl- • pH of 0.05 M HCl • [H+] = 5 x 10-2 M • pH = 1.3 (= -log(5x10-2))

  9. acid conjugate base • Weak acids dissociate incompletely HA ↔ H+ + A- final [H+] depends on acid concentration and equilibrium constant Ka = [H+][A-] [HA] • pKa = -log(Ka)

  10. Titration of acetic acid 0.1 M pKa = 4.76 “Buffering region” both acid and conjugate base are present in reasonable concentrations.

  11. Chapter 2 • Henderson-Hasselbalch equation • pH = pKa + log([base]/[acid])

  12. Chapter 3: 2/16, 19, 21, 23 • Amino acids • Names, abbreviations, general properties • Henderson-Hasselbalch/pI • Proteins • Structure/properties of a peptide bond • Techniques for separating proteins • Ion exchange • Gel filtration/Size exclusion • Affinity

  13. Ch. 3 • Be able to draw a polypeptide • Free amino acids vs. polymerized & pKa/pI • Side chains may have different pKas • pKa affected by charges on amino/carboxyl groups • pKa may be affected by interactions with other side chains in the larger molecule

  14. Ch.3 (and Ch.4) • Primary structure • Amino acids (can be enhanced by prosthetic groups) • Secondary structure • Alpha helices, beta strands/sheets, beta turns • What forces? • Tertiary structure • Quaternary structure • What forces?

  15. Ch.3 (and lab) • Protein purification • Exploit differences in physical/chemical characteristics (arising from…?) to separate proteins • Ion exchange • Gel filtration/Size exclusion • Affinity

  16. Ch. 4 (2/26, 27, 3/7) • Protein folding • Why do proteins fold? • Proteins are inherently flexible (breath) • Structural elements • Primary structure influences 2°, 3°, 4° • Proline: why not in alpha helices? • Structure/function • Fibrous proteins, eg. collagen • Globular proteins • How is 3D structure determined (X-ray crystallography, NMR) • Just a reminder, not on final

  17. Ch.4 • Proteins as ‘modular’ structures • Multi-domain proteins • Common, “evolutionarily”-conserved domains • The process of protein folding • Necessarily complex process • Determined by 1° structure (Anfinsen/RNase denaturation)

  18. Ch. 5 (3/9, 12, 14, 16) • Protein function: reversible ligand binding • Protein/protein • Protein/small molecule • Protein/DNA • Characteristics: • Specific but structurally adaptive • Equilibrium [P] + [L] ↔ [PL] (Ka) • Affinity often described with dissociation constant (ie. Kd)

  19. Kd • Assumption: [P]<<[L] • Theta (q) = % of binding sites occupied • When [L] = Kd, q = 0.5

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