Bio 441A Exam 3 Study Guide With Complete Solution.

BIO 441A EXAM 3 STUDY GUIDE WITH COMPLETE SOLUTION. LECTURE ONE - METABOLISM INTRODUCTION ● Autotrophs synthesize all their own cellular constituents from simple molecules ● Heterotrophs obtain energy through oxidation of organic compounds and therefore rely on autotrophs ● Metabolism involves many reactions such as ○ Glycolysis/gluconeogenesis ○ The citric acid cycle ○ Oxidative phosphorylation ● Catabolism is the degradation of biomolecules ○ Energy rich nutrients are converted such as carbs, fats, proteins are converted into energy-deprived simple molecules such as water, carbon dioxide, and ammonia ● Anabolism is the build-up of biomolecules ○ Polymers to monomers ● In a cell, oxidation of chemical energy fuels H+ pumping out of the cell and H+ flow back into the cell reduces oxidation products back into chemical energy molecules → cyclic between oxidation and reduction ● Enzymes catalyze many different rxn types of catabolism via nucleophiles and electrophiles within them ○ Oxidation-reduction ○ Group-transfer ○ Elimination/isomerization/rearrangement ○ Breaking or forming C-C bonds ● Dehydrogenase enzymes catalyze proton removal in oxidation/reduction rxns and have a Rossman fold specific for NAD+ binding ● Catabolism via rxns involving breaking/forming C-C bonds involve either homolytic or heterolytic cleavage ○ Homolytic- the cleavage has the same effect on both ends of the bond broken ■ ex) R3C-H → ← R3C● + ●H ■ ex) R3C-CR3 → ← R3C● + ●CR3 ○ Heterolytic- the cleavage has a different effect on either end of the bond broken ■ ex) R3C-H → ← R3C:- + H+ ■ ex) R3C-H → ← R3C + + H- ■ ex) R3C-CR3 → ← R3C:- + +CR3 ● Know the different examples of catabolism, what type of reaction it is, mechanism, etc. ○ Glucose 6-phosphate → ← fructose 6-phosphate ■ Isomerization rxn ■ Catalyzed by phosphohexose isomerase ○ Glucose → glucose 6-phosphate ■ Group transfer ■ Coupled with ATP hydrolysis to ADP + Pi ○ Lactate → pyruvate ■ Catalyzed by lactate dehydrogenase ■ Oxidation-reduction reaction ■ Lactate is reduced, gets oxidized into pyruvate ○ PEP3- → pyruvate ■ Hydrolysis then tautomerization ■ Gives enol first but favors keto ○ 1,3-biphosphoglycerate4- → 3-phosphoglycerate3- ■ Hydrolysis then isomerization ■ 3-phosphoglycerate3- stabilized by resonance ○ Acetyl CoA → acetic acid → acetate ■ First step is hydrolysis, second is isomerization ■ Acetate is stabilized by resonance ○ Succinate + FAD → ← fumarate + FADH2 ■ Oxidation of succinate ■ Reduction of FAD ○ Malate + NAD+ → ← oxaloacetate + NADH + H+ ■ Oxidation of malate ■ Reduction of NAD+ ● NAD is the common electron carrier ○ NAD+ reduced to NADH (and NADP+ reduced to NADPH) when electrons bind ○ NADH/NADPH reduced forms occur in two stereoisomers at the stereocenter where the proton added ● FAD is the electron carrier in the CAC and in FA oxidation ○ Reduction of FAD has an intermediate radical step FADH● called semiquinone before reaching its fully reduced FADH2 state ● ATP is composed of adenosine inside of AMP inside of ADP inside of ATP ○ -P-O-P- (X2) phosphoanhydride bonds ○ -P-O-CH2- phosphodiester bond ● ATP hydrolysis (know mechanism for attack on ɣ phosphate) for ATP4- + H2O → ADP3- + HPO4 2- + H+ ○ Pi2- is short for HPO4 2- ○ Pi2- is stabilized by resonance ○ Attack on the ɣ phosphate is called phosphoryl transfer → ADP + HPO4 2- ● Attack on the β phosphate is called pyrophosphoryl transfer → RO-PO2 - -PO3 2- + AMP ● Attack on the α phosphate is called adenylyl transfer → RO-PO3 - -ribose-adenine + PPi ● “Low-energy” phosphate compounds have ΔG’0 between -30 and 0 ○ Glucose → glucose 6-phosphate hydrolysis/isomerization ○ No different resonance stabilization or charge separation of the substrate or the hydrolysis product ○ α-D-glucose-6-phosphate and L-glycerol-3-phosphate are “low-energy” hydrolysis products of glucose/glycerol ● “High-energy” phosphate compounds have ΔG’0 less than -30 ● Acetyl CoA has a thioester bond -S-C=O ● Studying oxidation/reduction rxns in an electrochemical cell measures the voltage difference to obtain free energy change ○ Separate the half reactions, one half being reduction and one half being oxidation, and measure the voltage change between them ● Thermodynamics of rxns dictate the direction and regulatory capacity of a metabolic pathway (given A+B→C+D) ○ ΔG depends on the nature of the reactants (ΔG’0 ) and reactant/product concentrations (Keq) ○ Keq represents the equilibrium constant for the rxn ○ ΔG0 and ΔG’0 represent the standard free energy change of a reaction ○ ΔH represents change in enthalpy ○ ΔS represents change in entropy ○ In cells, when ΔG is about zero, changes in K can move the rxn in either direction ○ When K1 and ΔG’00 rxn proceeds forward ○ When K=1 and ΔG’0=0 rxn is at equilibrium ○ When K1 and ΔG’00 rxn proceeds in reverse ○ When the mol ratios for the rxn are all 1, Keq= [C][D]/[A][B] ■ When the mol ratios aren’t one, Keq = [C]c [D]d /[A]a [B]b ○ ΔG = ΔH - TΔS ○ ΔG = ΔG’0 + RT ln (Keq) ■ At equilibrium → ΔG’0 = -RT ln (Keq) ○ For oxidation-reduction reactions ΔG’0 = -n ƑΔE’0 ■ ΔE’0 = E’0 reduction - E’0 oxidation ■ Ƒ = 96.485 J/(V x mol) ○ For oxidation-reduction rxns, more energy is more reduced since reduced compounds have ΔG0 that’s more negative and oxidized compounds have ΔG0 closer to zero ■ CH4 CH3OH HCOH HCOOH CO2 in terms of ΔG0 approaching zero and reaching complete oxidation state ■ For example, FAs are more reduced than glucose → oxidization of FAs yields more ATP .