2. Chapter 1 Foundations of biochemistry –Biological –Chemical –Physical –Genetic –Evolutionary Focus on chemical and physical –Need to know biological!

3. Hierarchy of biology Ecosystem Organism Organ systems Organs Tissues Cells Organelles Molecules Biosphere Physical and chemical properties that define their function

4. Cells are transducers of energy First law of thermodynamics SOLAR CHEMICAL (C-C Bonds) CHEMICAL (ATP)

5. Cells are transducers of energy Synthesis of macromolecules Mechanical work Osmotic/electrical/chemical gradients Light production Genetic information: transfer/maintenance Heat

6. Second law of thermodynamics Disorder always tends to increase –ENTROPY Life requires order Creating/maintaining order requires work, therefore energy

7. Gibbs free energy (G) Amount of energy in a system available to do work “Force” that drives chemical reactions A system always strives to achieve minimum free energy

8. System strives to reach lowest energy

9. G = H - TS T = temperature –In vivo ~constant –Becomes important in vitro H = enthalpy –Heat/thermal energy –Chemical bonds Break bonds: add heat Form bonds: release heat

10. G = H - TS S = entropy –Disorder –Randomness –Freedom –More degrees of freedom: higher entropy

11. Which has more entropy? vs.

12. Which has higher entropy? vs. Liquid waterSolid water

13. G = H - TS Chemical reaction: Reactants and products have different Gs Change of free energy:  G  G =  H – T  S Negative  G: exergonic Positive  G: endergonic

14. A + B ↔ C + D Lower free energy is ‘better’  G < 0 (-  G) -reaction is spontaneous (no energy input necessary) -proceeds from L to R  G > 0 (+  G) -reaction isn’t spontaneous -proceeds from R to L  G = 0 -both reactions are spontaneous -reaction at equilibrium

15. Two ways to “manipulate”  G Energy payoff:  H vs.  S Cooperation: couple unfavorable and favorable reactions

16. The energy ‘payoff’ Decreased enthalpy (  H < 0) favored Increased entropy (  S > 0) favored But, overall  G has to be negative –If  H is positive, reaction can be ‘driven’ by entropy

17. Energetic coupling Unfavorable reactions can be coupled to favorable reactions to make an overall favorable reaction

18. Glucose + phosphate → glucose-6-phosphate  G > 0 ATP → ADP + phosphate  G << 0 Glucose + ATP → glucose-6-phosphate + ADP  G < 0

19. Chemical equilibrium 1. Start with all reactants (Initial conditions) 2. Reactants become products (  G < 0) 3.Products become reactants exactly as fast as reactants become products Equilibrium – “Steady State” At steady state:  G = 0

20. Equilibrium is related to  G° aA + bB ⇌ cC + dD High K eq, neg  G: reaction ‘favors’ products Low K eq (<1): reaction ‘favors’ reactants

21. ENERGY (G°) REACTION PROGRESS  G < 0 Reaction should be spontaneous Equil should favor products Biological reaction: sugar + oxygen ↔ CO 2 + water Reactants (R) Activation energy E A Kinetic barrier to reaction High energy “Transition state” Intermediate between R & P Products (P)