1. Bioenergetics Study of energy transformations in living organisms
Thermodynamics
1st Law: Conservation of E
Neither created nor destroyed
Can be transduced into different forms
2nd Law: Events proceed from higher to lower E states
Entropy (disorder) always increases
Universe = system + surrounds

2. Bioenergetics
(E content of system) H = (useful free E) G + (E lost to disorder) TS
Gibbs Free Energy: G = H - TS
If G = negative, then rxn is exergonic, spontaneous
If G = positive, then rxn is endergonic, not spontaneous
Standard conditions (ΔG°’): 25oC, 1M each component, pH 7, H2O at 55.6M

3. Bioenergetics A + B <--> C + D
Rate of reaction is directly proportional to concentration of reactants
At equilibrium, forward reaction = backward reaction
k1[A][B] = k2[C][D]
Rearrange:
k1/k2 = ([C][D])/([A][B]) = Keq
Relationship between ΔG°’ and K’eq is:
G°’ = * R * T * log K’eq
If Keq >1, G°’ is negative, rxn will go forward
If Keq <1, G°’ is positive, rxn will go backward

5. ΔG°’ is a fixed value at standard conditions
ΔG under actual cellular conditions can be different
e.g., for ATP hydrolysis inside a cell, can approach ΔG = -12 kcal/mol
We will work with ΔG°’ values

6. Coupling endergonic and exergonic rxns
Glutamic acid (Glu) + NH3 --> Glutamine (Gln) G°’=+3.4 kcal/mol
ATP --> ADP + Pi G°’=-7.3 kcal/mol
Glu + ATP + NH3 --> Gln + ADP + Pi G°’=-3.9 kcal/mol
Glutamyl phosphate is the common intermediate

7. ATP --> ADP + Pi ΔG°’= -7.3 kcal/mol
ADP + Pi --> ATP ΔG°’= +7.3 kcal/mol
C(diamond) + O2 --> CO2 ΔG°’= kcal/mol
PEP --> pyruvate + Pi ΔG°’= kcal/mol
C(graphite) + O2 --> CO2 ΔG°’= kcal/mol
P-creatine --> creatine + Pi ΔG°’= kcal/mol
G6-P --> glucose + Pi ΔG°’= -3.0 kcal/mol
1,3-BPG --> 3PG + Pi ΔG°’= kcal/mol
What is ΔG°’ of: PEP + ADP --> pyruvate + ATP ΔG°’= -7.5
What is ΔG°’ of: G6-P + ADP --> glucose + ATP
What is ΔG°’ of: P-creatine + ADP --> creatine + ATP
What is ΔG°’ of: C(s, diamond) --> C(s, graphite) ?

8. Equilibrium vs steady state
Cells are open systems, not closed systems
O2 enters, CO2 leaves
Allows maintenance of reactions at conditions far from equilibrium O2

9. Biological Catalysts Req’d in small amounts
Not altered/consumed in rxn
No effect on thermodynamics of rxn
Do not supply E
Do not determine [product]/[reactant] ratio (Keq)
Do accelerate rate of reaction (kinetics)
Highly specific for substrate/reactant
Very few side reactions (i.e. very “clean”)
Subject to regulation
No relationship between G and rate of a reaction (kinetics)
Why might a favorable rxn *not* occur rapidly?
Biological Catalysts

11. Overcoming the activation energy barrier (EA)
Bunsen burner: CH4 + 2O2 --> CO2 + 2H2O
The spark adds enough E to exceed EA (not a catalyst)
Metabolism ‘burning’ glucose
Enzyme lowers EA so that ambient fluctuations in E are sufficient

12. Overcoming the activation energy barrier (EA)
Bunsen burner: CH4 + 2O2 --> CO2 + 2H2O
The spark adds enough E to exceed EA
Metabolism ‘burning’ glucose
Enzyme lowers EA so that ambient fluctuations in E are sufficient
Catalyst shifts EA line to left <---

13. How to lower EA The curve peak is the transition state (TS)
Enzymes bind more tightly to TS than to either reactants or products

14. How to lower EA
Mechanism: form an Enzyme-Substrate (ES) complex at active site

15. How to lower EA
Mechanism: form an Enzyme-Substrate (ES) complex at active site
Orient substrates properly for reaction to occur
Increase local concentration
Decrease potential for unwanted side reactions

16. How to lower EA
Mechanism: form an Enzyme-Substrate (ES) complex at active site
Enhance substrate reactivity
Enhance polarity of bonds via interaction with amino acid functional groups
Possibly form covalent bonded intermediates with amino acid side chains

17. How to lower EA
Possibly form covalent bonded intermediates with amino acid side chains
Serine protease mechanism:

18. How to lower EA
Possibly form covalent bonded intermediates with amino acid side chains
Serine protease mechanism:

19. How to lower EA
Mechanism: form an Enzyme-Substrate (ES) complex at active site
Induce bond strain
Alter bonding angles within substrate upon binding
Alter positions of atoms in enzyme too: Induced fit

20. Induced fit

21. Induced fit

22. Enzyme kinetics: The Michaelis-Menten Equation
S <--> P
At low [S], rate/velocity is slow, idle time on the enzyme
At very high [S], rate/velocity is maximum (Vmax), enzyme is saturated
V = Vmax [S]/([S] + Km) Km = [S] at Vmax/2
A low Km indicates high enzyme affinity for S (0.1mM is typical)

23. Enzyme kinetics: pH and temperature dependence

24. Enzyme inhibitors Irreversible Example: penicillin penicillin
Form a covalent bond to an amino acid side chain of the enzyme active site
Block further participation in catalysis
Example: penicillin
Inhibits Transpeptidase enzyme required for bacterial cell wall synthesis
Weak cell wall = cell burst open
penicillin

25. Enzyme inhibitors Reversible Example: ritonavir Competitive
bind at active site
Steric block to substrate binding
Km increased
Vmax not affected (increase [S] can overcome)
Example: ritonavir
Inhibits HIV protease ability to process virus proteins to mature forms

26. Enzyme inhibitors Reversible
Noncompetitive
Do not bind at active site
Bind a distinct site and alter enzyme structure reducing catalysis
Km not affected
Vmax decreased, (increase [S] cannot overcome)
Example: anandamide (endogenous cannabinoid)
Inhibits 5-HT3 serotonin receptors that normally
increase anxiety
Competitive
Noncompetitive

28. Drug discovery Average cost to market ~ $1B
Average time to market ~13 years
Size of market ~ $289B per year in US (2006)
S. aureus infections are a problem in hospital settings
Drug targets
Metabolic rxns specific to bacteria
Sulfa drugs (folic acid biosynthesis)
Cell wall synthesis
Penicillin, methicillin, vancomycin
DNA replication, transcription, translation
Ciprofloxacin (DNA gyrase)
Tetracyclins (ribosome)
Zyvox (ribosome)
Introduced in 2000, resistance observed within 1 year of use