BIOCHEM 501 1st EditionExam # 2 StudyGuideLecture 12 SEPT 29Bioenergetics- Cells obtain most of their energy by "oxidation" of molecules; slow combustion occurs through a sequence of reactionsGlycolysis  citric acid cycle  ATP CO2 NADH + O22  H2O- In cells, some energy of oxidations "saved" as ATP- Net reactions "go" towards equilibrium- Conditions can be on "either side" of equilibrium Thermodynamics- G –Gibbs free energy (units of energy per mole, kJ/mle)1. how far from equilibrium2. how much energy will be released as reactions proceed towards equilibrium3. which direction a net chemical reaction will occur IF it does occur, which side is favorable or unfavorable- Standard conditions is indicated by the superscript - Has two components: enthalpy and entropy G=H-TS1. Enthalpy change D: H is the difference in bond energies - Exothermic: releases heat, negative H, more stable bonds formedo Candle burningo More "favorable" G- Endothermic: heat input/absorbed, positive H, less stable bonds formed2. Entropy change S = change in "randomness"- Increase in "'randomness" is a positive S which contributes to a "favorable" negative G- G and Keq relationship for standard conditions: G = -RT ln Keq- G large and negative, then Kew is large and negative  proportional - Actual G depends on reactant and product concentrations- Review: 1. Sign of G reveals direction2. Magnitude of G indicates how far from equilibrium/how much energy will be released as reaction proceeds to equilibrium--but thermodynamics do not predict how rapidly equilibrium is approached, the rate- Enzymes work by lowering the activation energy- They change the transition state, thus reaction rateATP—Universal Energy Carrier- Adenosine triphosphate- kinetically stable, little non-enzymatic breakdown- in vivo conditions of ATP hydrolysis –ATP + H2O  ADP = Pi- Actual G of hydrolysis is ~50kJ/mol, a good energy source- ATP usually provides energy by group transfers, not by direct hydrolysis-group transfers energizes recipient-unfavorable reactions can be driven by couple to favorable reactions by enzymesthrough common intermediates - Phosphate group transfer potentials: -much of metabolism involves the synthesis of high energy phosphate compounds-high-energy donate ~P, low energy receive ~P-ATP is in the middle, it must donate and receive ~PLecture 13 OCT 1Glycolysis- "Sugar breaking apart pathway"- ubiquitous: carbohydrates are an ancient method of energy storage and source of precursors for biosynthetic pathways- first pathway discovered: fermentation- Buchner, 1887 cell lysates fermented -Zymology: study of fermentationOverview1. Preparatory stage 1. Hexokinase reaction- 6C sugar, enzyme that adds phosphate group to a kinase- coupling a reaction to ATP breakdown makes it even more favorable2. Phosphohexose isomerase- substrate of 6C phosphate, rearranged double bond- converting glucose phosphate into fructose phosphate3. Phosphofructokinase (PFK-1)- rate limiting step- major control point: allosteric regulation- high ATP, fatty acids, citrate inhibits- high AMP, ADP stimulates4. Aldolase 5. Triose phosphate isomerase TPI2. Payoff stage- using the high energy compounds to make ATP6. Oxidation of glyceraldehydes-3-P- dehydrogenase reaction- only redox reaction in glycolysis- energy is preserved in 1. Phosphate bond and 2. NADHNAD: Nicotinamid- Adenine-Dinucleotide7. Phosphoglycerate kinase- first payoff; substrate level phosphorylation- higly favorable to form ATP from this reacion8. Phosphoglycerate mutase- to rearrange the molecule so phosphate is in a high energy state at this stage- redistribution of energy9. Formation of Phosphoenolpyruvate- same as above but at an even higher energy state10. ATP from PEP: pyruvate kinase- second payoff- lots of energy left over from all the energy in phosphate- Energy changesGlucose  2 pyruvate coupled to:2 ATP + 2 Pi  2 ATP; G = +61 kJ/mol2 NAD+  2 NADH G =+440 kJ/molOverall G is ~85 kJ/mol with about 500 kJ/mol retained for ATP and NADH- Glycolysis/metabolic pathway is irreversible under cellular conditions because there are irreversible steps such as the phosphofructokinase reaction- Starting and end products are interconvertible via "bypass" reactions of glyconeogenesis- Would require an extremely high ADP/ATP ratio, usually a healthy cell has a low ADP/ATP ratioLecture 14 OCT 3Entry into Citric Acid CycleFates of Pyruvate 1. Fermentation: anaerobic, no oxygen  2 lactate, 2 ethanol2. Aerobic respiration, with oxygen  2 acetyl-CoA + O2  4CO2 + 4 H2O (a full combustion)Pasteur effect: yeast glucose consumption much greater under anaerobic than aerobic conditions- must be anaerobically because yeast can only make ATP by glycolysis – 2 ATP/glucose- aerobic makes 30 ATPFermentations –ways too anaerobically regernate NAD+ from NADH to maintain high rate of glycolysis1. Pyruvate to lactate2. Pyruvate to ethanolDehydrogenase and energy content of molecules- more C-H and C-C bonds provide more energy when oxidizedMitochondia: site of oxidations- inner membrane: ATP synthase- matrix (soluble): citric acid cycle, fatty acid oxidation, pyruvate oxidationAerobic pathway –pyruvate  acetyl-CoAPyruvate dehydrogenase complex- huge, regulated enzyme complex- inhibited by NADH, ATP and Acetyl-CoA- stimulated by NAD+, AMP and CoA- 3 subunits and 5 cofactors- Lipoic Acid: Acyl- and Redox Carrier, long carbon chain/arm facilitates shuttling of substrate- Thiamine Pyrophosphate (TPP)1. Pyruvate DH Mechanism: E1 rxns—the "set up"- making C-C into C-H2. PDH Mech E2 rxns—the oxidation3. - making C-S bonds through oxidation4. PDH Mech E3 rxns—shuttling electrons to a carrier (NAD+) and enabling PDH to "go another round"- the overall reaction is overall very favorable - much of the energy of oxidation was preserved in NADH and thiolester in acetyl CoA- acetyl CoA can enter into the citric acid cycleCoupling does two things:1. Drive unfavorable reactions (hexokinase) via energy of ATp breakdown2. Preserve some of the energy of highly favorable reactions by coupling to ATP synthesis or the synthesis of other high energy compounds like NADH, acetyl CoA, etc. Lecture 15 OCT 6Citric Acid Cycle- final phase of aerobic path of glucose  pyruvate  acetate CO2- central energy-yielding path: point of