Chapter 1 2/5-2/6/07

• Overall important concept: G = H – TS

– Toward lower enthalpy• Forming bonds = good

– Toward higher entropy• More degrees of freedom = good

– Toward lower energy (G < 0)

Chapter 1• G = H – TS

– “Manipulation” of this equation1. 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 = 10-14

H2O ↔ 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 10-2 MpH = 1.3 (= -log(5x10-

2))

• Weak acids dissociate incompletely

HA ↔ H+ + A-

final [H+] depends on acid concentration and equilibrium

constant

Ka = [H+][A-] [HA]

• pKa = -log(Ka)

acid conjugate base

Titration of acetic acid0.1 MpKa = 4.76

“Buffering region”both acid and conjugate baseare 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 pKas

• 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] (Ka)– Affinity often described with dissociation

constant (ie. Kd)

• Kd

– Assumption: [P]<<[L]– Theta () = % of binding sites occupied

– When [L] = Kd, = 0.5

dK

]L[

L