Energy Metabolism and Thermodynamics in Living Systems

1. Quiz • Please expand to alternate seats • 5 points • 10 minutes (starting on the hour) • #2 pencils

3. Energy Metabolism • Metabolism (meta=after; Bol=to throw) • Greek : Metabole = change) • Catabolism (kata=down; Bol=to throw) • Anabolism (ana=upward; Bol=to throw)

4. Thermodynamics • First Law: Energy cannot be created or destroyed. • Second Law: • Heat will flow only from hot to cold • Entropy of a closed system always increases • The second law, in its most general form, states that the world acts spontaneously to minimize potentials • All reactions proceed in an “energetically favorable” direction until they reach equilibrium • Intrinsic properties of reactants and products • Relative concentrations of reactants and products • Temperature

5. A+B C+D Gibbs Free Energy • G (Gibbs free energy) H(heat)+S(entropy) • ∆G=∆H-T∆S (releasing heat or increasing entropy makes ∆G negative) • Change(∆) in (Gibbs)free energy= ∆G = ∆Gº +RTlnK • Convention • If ∆G is negative A and B continues to get made into C and D • If ∆G is positive C and D continues to get made into A and B • Therefore if nothing is happening any more (ie equilibrium is reached), then ∆G is ZERO • When ∆G =0 then ∆Gº=-RTlnK • The standard free energy ∆Gº is different that the free energy ∆G • The standard free energy at 37ºC in water is ∆Gº’

6. A+B C+D 99 99 1 1 A+B C+D 1 1 99 99 A+B C+D [C][D] K 50 50 50 50 = [A][B] Reaction Equilibrium Thought Experiment:Mix 100 As with 100 Bs K =0.0001 No reaction K =10000 Complete Reaction K =1 Partial Reaction

8. Which way do reactions go?Two paradoxes • Reactions that break bonds are generally thermodynamically favorable (catabolism) • They release heat • They increase entropy • Reactions that make bonds are generally thermodynamically unfavorable(anabolism) • they create more order, therefore lower entropy

9. Why doesn’t everything break down?Resolution to the catabolism paradox • Thermodynamics vs. Kinetics • Activation Energy

10. Why does anything build up?Resolution to anabolism paradox • Coupling of reactions ∆Gº’=-7.3kcal/mol A-P-P-P A-P-P Glucose Glucose-6-P ∆Gº’=+3.3kcal/mol

11. H C S1 O H H H C C S2 O H S2 O H H Oxidation /ReductionA. Passing H- around C S1 O H Reduced Oxidized NAD+ Oxidized 2e- Reduced NAD-H H+ Reduced Oxidized

12. Carbon Oxidation

13. O C S1 O H O O C O O Oxidation /ReductionB. Reducing Oxygen Reduced Oxidized NAD+ Oxidized 2e- Reduced NAD-H H+ Reduced Oxidized H O H +3ATP

14. Metabolism • Catabolism • Breaks bonds to yield energy in ATP currency • Results in smaller carbon skeletons -Cells prefer to use glucose for energy generation (catabolite repression) • Anabolism • Uses ATP to make bonds and increase the size of carbon skeletons

15. Where does the glucose come from? • Sun emits photons of light • Photons excite chlorophyll • Excited chlorophyll converts water to oxygen, protons, and electrons • Electrons are coupled to ATP generation and NADP+ reduction • ATP and NADPH are used to generate glucose (Calvin cycle Fig. 2.39) • Glucose is eaten by animals Light reactions Dark reactions

16. Where did the glucose come from? • Sun emits photons of light • Reducing atmosphere and sparks created amino acids • Amino acids were assembled into glucose?

17. BiosynthesisCarbohydrates, Lipids • Gluconeogenesis • lactate, amino acids, glycerol to pyruvate • pyruvate to glucose • Polysacharide synthesis (Fig.2.40) • glucose to UDP-Glucose to chain • Lipid synthesis • Pyruvate to Acetyl-CoA to chain

18. BiosynthesisAmino acids

19. BiosynthesisNucleotides

20. Catalytic Mechanisms

21. Active Sites

22. Feedback Regulation • Thermostat • Toilet

23. Allosteric Control • Allo (other ,different); Stere (solid, three dimensional) • Non-covalent: O2 in hemoglobin, metabolites in feedback control • Covalent: Phosphorylation, methylation,acetylation, etc..

24. Genetics • Mendelian • independent segregation of traits; 1865 • Traits determined by pairs of inherited factors (alleles) • Chromosomes • Exist as pairs • Linkage • dependent segregation of traits; early 1900s • Incomplete Linkage • Recombination during Meiosis • One gene-one enzyme • multiple mutations in one gene • George Beadle; Edward Tatum; 1941

25. Discovery of the Genetic Substance • Chromosomes have both DNA and Protein • Activation of Inactive Pneumococcus • Oswald Avery; ColinMcleod; Maclyn McCarty; 1944 • Ratios of A:T and G:C are 1 • Erwin Chargaff • DNA is helical • Maurice Wilkins; Rosalind Franklin; 1952 • Model Building • James Watson; Francis Crick; 1953 • Semiconservative Replication • Mathew Meselson; Frank Stahl; 1958

26. Readout of DNA • Colinearity of genes and proteins • Charles Yanovsky • tryptophan synthetase • Discovery of mRNA • Sidney Brenner, Francois Jacob; Mathew Meselson • E. Coli; T4 phage • Genetic Code; triplet code • In vitro translation • tRNA adapters • Mathew Meselson; Frank Stahl; 1958

27. Recombinant DNA Technology • Restriction Enzymes • Restriction Maps • Gel Electrophoresis • Vectors • Libraries • cDNA vs Genomic • Sequencing • PCR • Southern; Northern • Antibodies • Western Blots • Immunoprecipitations

28. Recombinant DNA Technology • Reverse Genetics • Use yeast to illustrate • Gene Transfer • Selectable markers • Controlled mutagenesis

29. Molecular Biology Methods