Transcript Slide 1

(Brief) Mid-term review
Paper Review assignment handed out/put on-line
Chapter 6
• Catalysis in general
– Activation energy (EA or DG‡ ) is a kinetic
barrier to reaction
– Enzymes lower this barrier (don’t change DG
or the equilibrium constant)
• Create a new reaction pathway with better DH or
(and) better DS
Chapter 6
• General types of catalysis (how do
enzymes change the reaction pathway?)
– General acid/base
• Donate/accept protons from a substrate
(substrates)
– Many times water (activation of water)
– Covalent catalysis
– Metal ion catalysis
• Stabilize (slightly) negatively charged
intermediates (ie. lower H of transition state)
• Oxidation/reduction
Chapter 6
• Quantification of catalysis
– Km
– Vmax/kcat
– kcat/Vmax
– Ki
• Michaelis-Menten kinetics
• Lineweaver-Burk plots
Chapter 6
• Enzyme regulation
– Why?
– How?
Chapter 1
• 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
• Weak interactions
– Covalent bonds = strong interactions
– Weak interactions
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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
• 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