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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)
Chapter 1
•
DG = DH – TDS
– “Manipulation” of this equation
1. If entropy is bad (eg. ligand/substrate binding to
a protein), improve enthalpy (ie. form bonds)
2. If overall DG is bad, “couple” the reaction to one
with a very good DG
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
H2O ↔ H+ + OH-
– Kw = 10-14
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))
• Weak acids dissociate incompletely
acid
conjugate base
HA ↔ H+ + Afinal [H+] depends on acid
concentration and equilibrium constant
Ka = [H+][A-]
[HA]
• pKa = -log(Ka)
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 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 (q) = % of binding sites occupied
 L
q 
[ L]  K d
– When [L] = Kd, q = 0.5