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

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

Chapter 1 Biological molecules –Small molecules Amino acids Nucleotides Sugars –Macromolecules Proteins Nucleic acids Lipids

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

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

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

Chapter 2 Acid/base –Acids: donate protons –Bases: accept protons (note: a base need not be negatively charged) –Autoionization of water –Kw = H 2 O ↔ H + + OH -

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 M pH = 1.3 (= -log(5x10 -2 ))

Weak acids dissociate incompletely HA ↔ H + + A - final [H + ] depends on acid concentration and equilibrium constant K a = [H + ][A - ] [HA] pK a = -log(K a ) acidconjugate base

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

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

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

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

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?

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

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

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)

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] (K a ) –Affinity often described with dissociation constant (ie. K d )

K d –Assumption: [P]<<[L] –Theta (  ) = % of binding sites occupied –When [L] = K d,  = 0.5