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BSC 450

by: Jordana Baraad
Jordana Baraad
GPA 3.9

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Week 11 Notes, so Thurs 11/5 due to Tuesday's cancellation
Fundamentals of Biochemistry
Dr. Ramonell
Class Notes
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This 7 page Class Notes was uploaded by Jordana Baraad on Saturday November 7, 2015. The Class Notes belongs to BSC 450 at University of Alabama - Tuscaloosa taught by Dr. Ramonell in Summer 2015. Since its upload, it has received 30 views. For similar materials see Fundamentals of Biochemistry in Biological Sciences at University of Alabama - Tuscaloosa.

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Date Created: 11/07/15
11/5 Bioenergetics and ATP (13.1, 13.3) Overall goal of bioenergetics Obtain chemical energy from nutrients Turn nutrients into needed molecules:  breakdown of molecules = catabolism polymerize biomolecules building molecules = anabolism requires energy (major source = oxidation phosphorylation) provide energy for organization ATP = Energy currency (generated in oxidative phosphorylation) Cyclical process Biochemical Reactions must obey the laws of thermodynamics 1. Conservation of energy 2. Entropy of the universe always increases 3. Entropy is dependent on temperature a. Narrow physiological temperature range important to reactants All systems attempt to minimize ΔG to achieve stability Enzymes: looking @ ΔG  v.  Cell reactions: looking @ difference in energies between products and reactants (ΔG) Stability of products v. reactants Favorabiliy of a reaction also measures by its equilibrium constant (k ) eq Think about difference in energy between reactants and products ΔG & chemical equilibrium linked ΔG = ­RTln(k ) eq think about the difference in energy between reactants and products ΔG & chemical equilibrium linked  Standard free energy change is related to the k  oeqa reaction ΔG = ­RTln(k ) eq Standard conditions: 1 M products & reactants, 25 degrees Celsius, 1 atm pressure Not true in cell Concentration manipulated in cell  favorability 1 M H+: pH = 0 – NEVER the case in a cell SO… ΔG’  = biochemical standard conditions 25 degrees Celsius, 1 atm pressure, pH = 7.0 0   Calculations of ΔG’       from eq Isomerization reaction: moving functional groups Glucose 1 phosphate (G1P) ⇌ Glucose 6 phosphate (G6P) (1mM) (19 mM) higher concentration  favored products  favorable rxn keq = 19/1 = 19  0  ΔG’ = ­RTln(k ) =eq7.8 kJ/mol R = 8.315 J/mol Convert to kJ! Glycolysis: glucose (6C  2 3C molecules) Must have phosphate group to break bond Glucose  G3P + DHAP DHAP  G3P via isomerization G3P  pyruvate Lots of energy saved by having one pathway not 2 (no DHAP  pyruvate) Standard free energy changes some chemical reactions See Table 13­4 Acid anhydride hydrolysis reactions: double digit ΔG’ ‘s –VERY favorable Rearrangements = isomerizations G1P  G6P: single digit but still favorable Oxidation w/ molecular oxygen: LOTS of energy released Top: burning sugar: ­2840 kJ/mol Bottom: burning fat = more energy released : ­9770 kJ/mol But not all rxns favorable Cell gets around this by… 1. changing initial concentrations a. 1 M  Q (mass action ratio) 2. coupling rxns: unfavorable w/ favorable a. favorable ex. = hydrolysis of ATP b. ex. 3 steps of glycolysis power all 10 steps c.  net free energy (ΔG) Actual free­energy change is dependent on the mass­action ratio, Q 1. change initial concentrations Q = mass action ratio = [P] t [T] t Concentrations at SPECIFIC TIME in rxn 0  Actual ΔG = ΔG’ + RTlnQ Q substituted for k eq Modifying ΔG by using different concentrations of reactants and products The actual value of ΔG is based on the ratio of Q/k eq Practice problem to be completed next week Standard free­energy changes are additive Can add all ΔGs  complete ΔG 2. rxns can be coupled Glucose  G6P Step 1: add phosphate so glucose can’t be transported back out of the cell Unfavorable, so coupled w/ ATP hydrolysis Standard equilibrium constants are multiplicative ATP = most common molecule used for rxn coupling   “general energy currency of cell” but NOT the only one not always hydrolyzed sometimes transferring P  activation of another chemical group The free­energy change in ATP Hydrolysis is large and negative Lots of  charges close together DESTABILIZES reactant 2+ Ideally, we have 1 destabiilzed reactant Mg  stabilizes reactant; orients molecule correctly within active site **ATP can only be hydrolyzed by specific molecules – evolutionary selection ATP hydrolysis favored  ATP + H20 ⇌ ADP + P = ­30 kJ/ mol I “high­energy molecule”: large energy release high energy but VERY stable, kinetically (ΔG < 0) enzyme NECESSARY for rxn to proceed thermodynamically unstable  reaction favorability products more stable: ATP “wants” to hydrolyze The release of free­energy comes from the relative stability of the products Resonance  product stability  ionization Charges distributed around the molecule ADP + P : i nization – VERY stable Pi= inorganic phosphate Top left pic: ATP destabilized 3 main traits ATP rxn (contribute to favorability) 1. electrostatic strain 2. resonance 3. ADP ionization 2&3 concern products The mass action ration (Q) …  Save for Tuesday Other phosphoesters can be used as energy currency High­energy molecules generated in glycolysis So high­energy that can donate P to make ADP  ATP Direct donation: substrate­level phosphorylation v. proton gradient  oxidative phosphorylation PEP = phosphoenol pyruvate  pyruvate Step 10 (last): ATP synthesis ΔG’ = ­61.9 kJ/ mol Tautomerization  product stability Similar to resonance Thioesters also have a high free­energy of hydrolysis Acetyl­CoA: high energy Pantothenic acid portion= arm Sulfate at head = high­energy portion 1. ionization 2. resonance Why not use regular esters? SKIPPED Common chemical attributes of high­energy hydrolysis rxns 1. reactant: some bond strain; no resonance 2. products: ionize, resonance, and/or tautomerization ATP also provides energy though group transfer reactions Fig 13­18: pink = transferring phosphate group Phosphate­containing intermediate typically not shown Glutamate  glutamine is a 2­step rxn typically written as 1 Phosphate is a good leaving group bc of resonance Phosphate transfer activates bond  ATP works as an intermediate between higher and lower energy compounds Fig 13­19: can only “donate down”  Phosphate can be transferred from compounds with her ΔG’ 0 Rxns like PEP + ADP => Pyruvate + ATP Favorable, can be used for ATP synthesis Purpose of generating high energy molecules in phase 2 of glycolysis Need payoff of rxn Glucose  G3P took energy away ATP = perfect intermediate between high and low energy compounds


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