580 likes | 837 Views
Part II and Chapter 13. Bioenergetics and Metabolism. Bioenergetics and Reactions. Key topics : Learning Goals. Thermodynamics applies to biochemistry Organic chemistry principles at work Some biomolecules are “high energy” with respect to their hydrolysis and group transfers
E N D
Part II and Chapter 13 Bioenergetics and Metabolism
Bioenergetics and Reactions Key topics: Learning Goals • Thermodynamics applies to biochemistry • Organic chemistry principles at work • Some biomolecules are “high energy” with respect to their hydrolysis and group transfers • Energy stored in reduced organic compounds can be used to reduce cofactors such as NAD+ and FAD, which serve as universal electron carriers
Metabolic Pathways Cooperate To: • Obtain Chemical Energy by: • a. Capturing Solar Energy, or • b. Oxidizing Energy Rich Chemicals from the Environment. • Convert Nutrient Molecules to metabolic intermediates, then monomers or waste products. • Polymerize monomers to polymers (proteins, carbohydrates, nucleic acids, lipids). • Synthesize and Degrade (turnover) biomolelcules.
Pathways Arranged as Multi-Protein Modules Flagella LPS Outer Membrane Peptidoglycan Cytoplasmic Membrane Glycolysis ATPase RNA
5 Main Classes of Metabolic Reactions • Oxidation-Reduction Reactions • Reactions that Make or Break Carbon-Carbon Bonds • Internal Rearrangements, Isomerizations, Eliminations. • Group Transfer Reactions. • Free Radical Reactions.
Showed that Respiration Was Oxidation of Carbon and Hydrogen…thus began Thermodynamics
Laws of Thermodynamics • First Law – for any change, the energy of the universe remains constant; energy may change form or it may be transported, but can not be created or destroyed. • Second Law – The Entropy Law can be stated 3 ways: • 1. Systems tend from ordered to disordered. • 2. Entropy can remain the same for reversible processes but increases from irreversible processes. • 3. All processes tend towards equilibrium. • Everything Equilibrium = Death. • Third Law – Entropy goes to zero when ordered substances approach absolute zero = 0oK
Thermodynamics Gibbs Free EnergyG and ΔG EnthalpyH and ΔH EntropyS and ΔS ΔG = ΔH - TΔS
Biochemistry Uses ΔGo’ Not ΔGo Standard Conditions (all reactants and products at 1M, gases at 1 atm, Temp = 25C) are Not Biological Conditions So, ΔGo’ takes out water (55.5M), and [H+] is set at pH 7 (not 1M which would be pH=0) and for humans ΔGo’ uses 37oC (310 K), but for bacteria ΔGo’ uses 25oC (298 K)….or the temperature of the environment. ΔGo’ = - RT lnKeq You should be able to do EOC Problems 2 and 3 easily EOC Problem 6: the difference between ΔGo’ and ΔG.
Free energy, or the equilibrium constant, measure the direction of processes
ΔGo’s Are Additive Hexokinase Rxn: Glucose + ATP Glucose-6-P + ADP Glucose + Pi Glucose-P + H2O ΔGo’ = 13.8 kJ/mole ATP + H2O ADP + Pi ΔGo’ = -30.5 kJ/mole Overall = ΔGo’ = -16.7 kJ/mole Exergonic ! So: K’eq = 7.8 x 102 EOC Problems 9 and 12: the ΔGo’ for 2 coupled reactions.
Biochemical Pathways Have Evolved To: • Use reactions that are relevant to metabolic systems: • Makes use of available substrates – with reaction rates that are NOT slow (have too high activation energies even with enzymes!) to produce useful products (which are themselves substrates). And, • Maximize Rates • Evolution’s Toolbox: reactions that work. • : circumvent “impossible” reactions. • : most reactions in organic chemistry occur in biology, except one, the Diels Alder Rxn…but we will see about that.
You be a radical ! You be inonic !
Rich in electrons donate electrons Electron poor suck up electrons from donors
The Importance of Carbonyls Nucleophile Electrophile Imines are like carbonyls Here the carbonyl is an electrophile
Energy Charge [ATP] + ½ [ADP] [ATP] + [ADP] + [AMP] Energy Charge =
Energy Charge Why the ½ [ADP] ??? It is because of Adenyl Kinase: ADP + ADP ATP + AMP
NucleotideConc, μMNucleotideConc, μM ATP 3,000 GTP 923 ADP 250 GDP 128 AMP 105 GMP 20 dATP 175 dGTP 122 dTTP 77 dCTP 65 UTP 894 CTP 515 cAMP 6 cGMP nd ppGpp 31 NAD+ 790 NADP 54 NADH 16 NADPH 146 FAD 51 FMN 88 AcCoA 231 SuccCoA 15 Nucleotide Intracellular Concentrations* in Salmonella enterica subsp Typhimurium from Bochner and Ames, 1982, J. Biol. Chem 257:9759-9769
Magnesium Stabilizes Tri- and Di-phosphates EOC Problem 19: How much ATP is used in a human/day. EOC Problem 20: About turn over of the α and β phosphates (can you located them above?).
What About Actual ΔG ? ΔG = ΔG’o + RT ln([products]/[substrates]) This is the real, biological ΔG in a cell !! At 25oC RT = 2.48 kJ/mole (2.5 kJ/mole) At 37oC RT = 2.58 kJ/mole (2.6 kJ/mole) We will be doing this a lot later on !
Doing Worked Example 13-2 Using E. coli ΔG = ΔGo’ + RT ln [ADP][Pi]/[ATP] ΔG = -30.5 kJ/mole + [ (8.315 J/mole.K)(310K) ln(1.04mM)(7.9mM)/7.9 mM] ΔG = -30.5 kJ/mole + 2.58 kJ/mole (-6.8) ΔG = -30.5 kJ/mole + (-17.6) ΔG = -48.1 kJ/mole Note: Calculate mM such as 1.04mM = 1.04 x 10-3M In the text for the Human Erythrocyte it works out to ΔG = -52 kJ/mole
Acetyl-CoA (Thiol-ester) Has the Energy of ATP! EOC Problem 21: Cleavage of ATP to AMP + PPi…..why is this different (see Table 13-6 above). (What DNA enzyme did the same? It’s in Chapter 8)
Enzyme Reaction Phosphorylation Intermediates Used to form C-N Bonds
Phosphates: Ranking by the Standard Free Energy of Hydrolysis Phosphate can be transferred from compounds with higherΔG’ to those with lowerΔG’. Reactions such as PEP + ADP => Pyruvate + ATP are favorable, and can be used to synthesize ATP.
Nucleoside Diphosphate Kinase makes NTP’s from ATP and NDP’s
EOC Problem 24: Respiratory chain thermodynamics (we will do this in Chapter 19)…learn it well now!
Calculations Differences between half cells…Example of electron transfer from NADH to cytochrome-b: NADH Eo’ = -.32 v Cyt-b Eo’ = 0.077 v ΔEo’ =Eo’oxidized – Eo’ reduced = 0.077v – (-0.32v) ΔEo’ = 0.397v
Further Calculations What is the ΔG’o for oxidation of NADH by cytochrome-b ΔG’o = - nℱΔEo’ Faraday Constant = 96,480 J/v.mole ℱ = 96.5 kJ/v.mole ΔG’o = - (2) 96.5 kJ/v.mole (0.397v) = - 77 kJ/mole What about the real ΔE ?...and then ΔG ! ΔE = ΔE’o + (RT/nℱ) ln ([products]/[substrates]) EOC Problem 25 and 26 are all about this.
Lactic Acid Dehydrogenase = LDH Rossmann fold, a structural motif in Dehydrogenases
Vitamin Niacin is Made from W and Needs to be Amidated for NAD+