(Brief) Mid-term review Paper Review assignment handed out/put on-line

Chapter 6 Catalysis in general –Activation energy (E A or  G ‡ ) 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  H or (and) better  S

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 –K m –V max /k cat –k cat /V max –K i Michaelis-Menten kinetics Lineweaver-Burk plots

Chapter 6 Enzyme regulation –Why? –How?

Chapter 1 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 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 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