nucleic acid and bioenergetics Flashcards
Define Entropy
deltaS, measure of microscopic disorder in a system
Define Enthalpy
deltaH, measure of energy of a thermodynamic system
Define Gibbs Free Energy
deltaG, Amount of work that can extracted from a system, deltaG =deltaG0 + RT ln [PRODUCTS]/[REACTANTS]
Define high energy componds
Compounds that store chemical energy in their bonds, which can be accessed for work on other compounds with rela.ve ease.
Name some high energy compounds
ATP, Glucose, NADH
Define free energy
The change in Gibbs free energy is the maximum work that a process can perform under constant pressure. A nega.ve Gibbs free energy suggests a reac.on or process is thermodynamically favorable and will occur spontaneously since the products are stable_
What is a Redox reaction?
A chemical reaction in which atoms have their oxidation state changes (i.e. the exchange of electrons between atoms or compounds) deltaG’o = -nF deltaE’o where deltaE’o = E’o electron acceptor - E’o electron donor in volts, n is number of electrons transferred, Positive deltaE’o corresponds to negative deltaG’o
How to convert from cal to joules
1 cal = 4.184 joules.
Define redox potential
Reduction potential E is a measure of the readiness with which an atom or molecule accepts an electron relative to H+. The
more positive the value of E, the more a molecule likes to accept electrons. The more negative the value of E the more it likes to donate electrons. Reduction potential E is measured in volts (V).
Electron flow in biological systems
In cells, glucose is a major source of electrons and O2 is the final electron acceptor. As electrons pass from compounds with low to high E free energy is released The resulting electromotive force (emf) is used to make high energy compounds ATP, NADH, and NADPH that are used to do biological work.
Define First Law of Thermodynamics
Energy is always conserved (i.e. energy cannot be created or destroyed)
Define Second Law of Thermodynamics
The entropy of the universe if always increasing (i.e. it takes energy to put things in an orderly fashion)
Define kinetic energy
Radiant (carried by photons from the sun), thermal mechanical, and electric energy (charged particles down gradients of electric potential)
Define potential energy
Stored in chemical bonds, concentration gradients, electric fields from charge separation, and redox pairs
What are the four ways that potential energy is stored?
Chemical bonds, concentration gradients, in redox pairs, in electric fields from charge separation
What are the three basic thermodynamic equations?
deltaG =deltaG0 + RT ln [PRODUCTS]/[REACTANTS] or deltaG = 2.3RT log [C2] / [C1], deltaG0 = - RT lnKeq, deltaG = deltaH – T deltaS
Define standad state free energy
deltaG0 = - RT lnKeq , the free energy change of a reac.on under standard condi.ons (298 K, 1atm, 1M, and pH=7), Keq= {[C][D]/[A][B]}
If _G is negative which way does the reaction proceed?
Forward (i.e. the forward reaction is spontaneous), a nega.ve G is synonymous with a posi.ve Keq and both demonstrate that a reac.on at equilibrium favors the forma.on of products more than the reversion back to reactants.
What does it mean when _G is zero?What does K equal at this point?
The reaction is at equilibrium K=1
What is K when _G0 is positive?
K is less than 1, Keq = 10(-deltaG0/2.3RT)
What equation does one use to relate Gibbs Free Energy to Redox potential
deltaG = -nFdeltaE Where n = number of electrons transferred, F = Faraday’s constant (96,500 C/Mol of e-), deltaE = difference in reduction potential in (volts), n= no. electrons transferred
What might the system be doing if it is moving electrons?
Creating energy
How might one make a reaction with a +_G move in the forward direction?
Couple it with a spontaneous reaction, deltaG3 =deltaG1 +deltaG2<0
What are some high energy compounds used in biological systems?
Lipids and Carbohydrates
What are the two main classes of high energy bonds?
Thioester (Sulfur - Carbon eg acetyl-Coa )High energy phosphate bonds (including phosphoanhydride e.g. ATP, phosphocreatine eg P-N, and phosphoenolpyruvate eg C-O-P)
Examples of work done by cells
synthesis of molecules or other constitutes, cellular movements, transport of molecules against concentration gradient, generation of electric potential, and heat generation
What are the major high energy compounds used to store energy
NADH, ATP, NADPH, and FADH2
Which nitrogenous bases are purines? Pyrimidines?
Purines: AG Pyrimidines: CTU
