102: BIBC Metabolic Biochemistry (Prof. Scheffler) TA: Edward Chen [e-mail] OH: Mondays 4-5pm @ CLICS
Handout #1
I.
Enzyme
a. Function Enzyme is a catalyst that speeds up rate of reaction by lowering activation energy. b. Classification (LNC p. 192) c. Specificity Enzymes are very selective. Two models for formation of enzyme-substrate complex: 1. Lock and key model (lock = enzyme, key = substrate) 2. Induced fit (conformation change at active site where the enzyme changes) d. Thermodynamics General Reaction: E + S ES EP E+P a. Enzymes do nothing to G. They only affect G b. Enzymes alter the activation energy by stabilizing the transition state. Reaction Rates: aA + bB cC + dD Keq = [P]/[S] = [C]c[D]d / [A]a[B]b and G`o = -RT ln Keq (if k > 1, G < 0 rxn forward) (if k < 1, G > 0 rxn backwards) When k = 0 equilibrium
e. Kinetics 1st order rxns: [A] = [Ao]e-kt or ln [A] = ln [Ao] x -kt
ln [Ao]
m = -k
BIBC 102: Metabolic Biochemistry (Prof. Scheffler) TA: Edward Chen [e-mail] OH: Mondays 4-5pm @ CLICS
2nd order rxns: 1/[A] = 1/ [Ao] + kt
1/[A]
Regulation of Enzyme Activity At the level of gene expression and protein turnover o Ex: By covalent modifications of side chains o Ex: By binding of small molecules (ligands) that are not substrates o Ex:
II.
General Reaction:
E+S
k k 1 ES E + P k 1 k
2 2
Two Assumptions of MichaelisMenten:
Michaelis-Menten Equation:
Vo =
d [ ES ] V max[ S ] k2 k ; where Km = dt Km [ S ] k1
1
BIBC 102: Metabolic Biochemistry (Prof. Scheffler) TA: Edward Chen [e-mail] OH: Mondays 4-5pm @ CLICS
Lineweaver-Burk (AKA equation: double reciprocal plot)
1 V max
1 Km = Vo V max
1 1 + [ S ] V max
Reactions with more than one substrate and enzyme inhibition: (a) Enzyme reaction involving a ternary complex
BIBC 102: Metabolic Biochemistry (Prof. Scheffler) TA: Edward Chen [e-mail] OH: Mondays 4-5pm @ CLICS
(b)
Enzyme reaction in which no ternary complex is formed
III.
Enzyme Inhibitors:
Competitive Inhibition:
BIBC 102: Metabolic Biochemistry (Prof. Scheffler) TA: Edward Chen [e-mail] OH: Mondays 4-5pm @ CLICS
Non-competitive Inhibition:
Mixed Inhibition: Equation: Graph:
IV.
Regulation
Allosteric Regulation Allosteric inhibitor (-) = binds to site and decreases activity of the enzyme. Allosteric activator (+) = blah blah and increases blah blah =p Inhibition o Feedback o Reversible inhibition o Irreversible inhibition o Allosteric enzyme conformation change
V.
Types of Organic Reactions
1) Group transfer 2) Oxidation-reduction reactions 3) Eliminations, isomerizations, rearrangements 4) making or breaking of C-C bonds See slide 3-39 for details
BIBC 102: Metabolic Biochemistry (Prof. Scheffler) TA: Edward Chen [e-mail] OH: Mondays 4-5pm @ CLICS
VI.
Bioenergetics
Gibbs Free Energy: (1) (2) (3)
G = H - TS
Gibbs Free Energy (G) the change in energy between the product and the substrate. Enthalpy (H) the change of heat content in a reacting system. Entropy (S) measurement of disorder.
Coupling Reactions (1) endergonic: need energy (2) exergonic: release energy (3) Use coupling to drive reactions
WHAT'S THIS? SOMETHING TO MEMORIZE! (ATP)