Chapter 1 2/5-2/6/07
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Transcript of Chapter 1 2/5-2/6/07
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