Flashcards in Chapter 13 Bioenergetics and Biochemical Reaction Types Deck (63):
First Law of Thermodynamics
Conservation of energy: For any physical or chemical change, the total amount of energy in the universe remains constant; energy may change from one form or it may be transported from one region to another, but it cannot be created or destroyed.
Second Law of Thermodynamics
The universe always tends toward increasing disorder: in all natural processes, the entropy of the universe increases.
# 1) Explain how defining "System" and "Surroundings" allows living organisms to operate within the second law of thermodynamics
First, the second law of thermodynamics states that the universe is constantly moving towards disorder. Organisms (system) work within the 2nd law by exchanging matter and energy with the environment (surroundings) This exchange allows organisms to create order within themselves while also working within the 2nd law of thermodynamics.
Gibbs Free energy
G; expresses the amount of an energy capable of doing work during a reaction at constant temperature and pressure; -∆G spontaneous and exothermic; +∆G non spontaneous and endergonic.
H; the heat content of the reacting system. It reflects the number and kinds of chemical bonds in the reactants and products
S; a quantitative expression for the randomness or disorder in a system.
# 3. From where do cells acquire their necessary free energy? Why can't cells use heat as a free energy source?
Cells are isothermal. They work at constant, for the most part temperature. Heat cannot of itself pass from one body to a hotter body. Cells acquire their energy from nutrient molecules (heterotrophs), while others obtain energy from the sun (autotrophs)
#4. What exactly does "at equilibrium" mean in terms of (a) the rate of both the forward and reverse reactions and (b) the concentrations of the reactants and products?
(a) the rates of the forward and backwards reactions are equal (b) the concentration of the reactants and products are equal and there is no net change
#5. What reaction conditions are used to measure the standard free-energy change?
1M, 298˚K, 1 atm, pH 7.
# 6. If, at equilibrium, the concentration of products is greater than reactants is ∆G positive or negative? What can you say about the value of K'eq?
∆G is positive and K'eq
Energy required to break a bond
Energy released during bond formation
What determines the strength of a bond?
1) Relative electronegativity 2) distance from an elecrons nuclei 3) number of electrons shared 4) nuclear charge
Standard free energy change
∆G'˚ and K'eq. Physical constraints and constants for specific reactions. ∆G'˚ = - RTlnK'eq; this is simply an alternative mathematical way of expressing its equilibrium constant. The standard free energy change tells us in which direction and how far a reaction must go to reach equilibrium at the standard condtions
When K'eq is > 1.0
∆G'˚ is negative and the reaction proceeds forward
When K'eq = 1.0
∆G'˚ is zero and the reaction is at equilibrium
When K'eq is
∆G'˚ is positive and the reaction proceeds in the reverse direction.
Calculations of new version of ∆G to describe the energy of reactions performed at standard conditions: ∆G'˚
∆G = ∆G'˚ + RT ln[products/reactants**] This is the actual conditions. NOT the K'eq!
# 7. What effect does the presence of an enzyme have on the ∆G'˚ that is catalyzes?
Enzymes DO NOT have an effect on constants ∆G˚'. Enzymes do not alter the free energy of a reaction. Enzymes only lower the activation energy by providing an alternative reaction pathway with lower activation energy than the uncatalyzed reaction.
# 8. Under what circumstances can ∆G be negative if ∆G'˚ is positive? Could cells use this strategy to drive thermodynamically unfavorable reactions?
If the term RT ln (p/r) is negative and has a larger absolute value than ∆G˚'. This can occur if the ratio of products to reactants is low.
# 9. Does the value of ∆G˚' or ∆G tell you anything about (a) the rate at which a reaction occurs or (b) the pathway by which the final product is formed?
(a) ∆G˚' is a constant and tells us direction ∆G tells us the direction as well, but not specifically the rate. Neither tell the pathway
What is ∆G˚'?
∆G˚' is the difference between the free-energy content of the products and the free-energy of the reactants under standard conditions. When ∆G˚' is negative, the products contain less free energy than the reactants and the reaction will proceed spontaneously under standard conditions.
What is the difference between ∆G˚' and ∆G?
∆G˚' is a constant. It is unchanging for each reaction. ∆G is not a constant, and does not occur at standard conditions.
Q # 10 How can the coupling of a thermodynamically unfavorable reaction to a thermodynamically favorable reaction increase the K'eq of the overall equation?
∆G˚' are additive. An exergonic reaction can be added to an endergonic one to produce an energetically favorable reaction. K'eq (equilibrium constants) are multiplicative.
# 11 Explain why relatively small changes ∆G'˚ correspond to large changes in K'eq.
Because the relationship between K'eq and ∆G˚' are exponential.
# 12 Why might potentially relevant reactions fail to occur in living systems
1) Some reactions are too slow (high activation energies w/o enzymes to catalyze reactions) 2)
# 13 When will a carbon atom act as a nucleophile? As an electrophile?
Nucleophile - as carbanion ; electrophile as carbocation
# 14 List the five general categories of reactions that commonly occur in living cells, and include at least one example for each. Leave room for your list to add reactions as you encounter them in the following chapters
1) Reactions that make or break C-C bonds; 2) Internal rearrangements, isomerizations, and eliminations; 3) free-radical reactions; 4) group transfers; and 5) Oxidation-reductions
Reactions that make or break C-C bonds
1) Heterolytic Cleavage: Yields a carbanion and a carbocation. 2) Aldol Condensation 3) Claisen Ester Condensation 4) Decarboxylation of a b-keto acid
Internal Rearrangements, Isomerization, and Elimination
Rearrangement of the molecule without changing oxidation state. Arises as electrons redistribute themselves.
Arise from homolytic cleavage of covalent bonds.
Group transfer reactions
The transfer of acyl, glycosyl and phosphoryl groups from one nucleophile to another.
# 16 What physical and chemical factors contribute to the free-energy change of ATP hydrolysis?
ATP has a very repulsive bond due to the negative charges on each molecule. The release of pi relieves tension. Resonance structures in the ATP molecule cannot accommodate for the tension.
Phosphorylation potential. The actual free energy of hydrolysis of ATP under intracellular conditions
# 19 Why is the "single arrow" representation of the conversion of ATP to ADP and Pi deceiving?
The single arrow is deceiving, because it is actually a two step process. A phosphate group is typically transferred to the system, and then displaced.
# 21 What is the relative position of ATP in the hierarchy of compounds with phosphoryl group transfer potentials?
PEP (phosphoenolpyruvate) ranks #1 , ATP 2nd, glucose-6-phosphate is last.
# 30 Why are cell membranes critical to the generation of a proton-motive force in cells?
Cellular membranes house enzymes and proteins that utilize the movement of electrons from one species to another. Electron flow is coupled to proton pumps, ATP synthase, and other generative structures that ultimately do work for the cell. Cell membranes also create the barrier which allows for the difference in the concentration of molecules so that forces, like that generated in the proton motive force are possible.
EMF, force generated by the movement of electrons between two species with different affinities.
# 31 In the equation Fe2+ + Cu2+ (DA) Fe3+ + Cu+, which of the iron species is more oxidized? Which copper species is more reduced?
# 32 Why are there different oxidation states of carbon?
There are different oxidation states based on the difference in electronegativities between binding atoms.
In biological systems... Oxidation is synonymous with...
# 33 Besides the transfer of electrons in the form of hydrogen atoms, in what other ways does electron transfer occur?
1) directly as electrons 2) as a hydride ion H- 3) through direct combination w/ oxygen
# 35 Which has the higher (more positive) reduction potential, NADH or cytochrome b (Fe3+)? In which direction will electrons flow in a system that contains these two compounds?
Fe3+ electrons will flow from NADH to Fe 3+
Standard reduction potential
E˚ ; measured in volts; is the affinity of the electron acceptor of each redox pair for electrons
p.530 Go back and draw/explain a half cell
Electron flow in a Half cell
Electrons flow from the half cell with of lower E˚ to the higher E˚; the half cell that takes electrons is assigned a positive E˚; the greater E˚ will gain electrons (be reduced)
# 36 Why is it important to have a universal standard for measuring reduction potentials?
They are important because they allow us to understand the flow of electrons under certain conditions.
Free energy changes for oxidation-reduction reactions (∆G or ∆G'˚)
∆G = -nF∆E or ∆G'˚ = -nF∆E˚; where n = the number of electrons transferred in the reaction; also remember (∆G = ∆G'˚ + RT ln ([products])/([reactants)]
# 37 Calculate approximately how many molecules of ATP could be synthesized from the complete oxidation of glucose (∆G'˚ = -2840 Kj/mol)
Water soluble coenzymes
Undergo reversible oxidation and reduction; FAD; NAD; NADP; FMN
Lipid Soluble electron carriers
Quinones (ubiquinones, plastoquinone)
Peripheral/ Integral reduction/oxidation agents
Iron-sulfur proteins. cytochromes Serve as electron carriers in aqueous solutions
Reaction proceeds forward
Reaction proceeds in reverse
∆G'˚ = 0
Reaction at equilibrium
-∆G'˚ in relation to K'eq and products
When K'eq is greater than 1, (∆G'˚ is negative and the reaction proceeds forward) Products are greater than reactants.
∆G'˚ in relation to K'eq and products
K'eq is less than 1, ∆G'˚ is positive, and reactants are greater than products.
∆G'˚=0 in relation to K'eq and products
K'eq = 1, system is at equilibrium
What are the four types of redox reactions include:
1) Direct transfer e- (reduction); 2) Transfer of a hydrogen (H, or e- + H+) (Reduction; 3) Transfer of the hydride anion (H-) (reduction) 4) Direct combination with oxygen (O-x) Oxidation.
Measure the affinity for electrons; electrons travel from species with less electronegativity to higher electronegativity
E = RT/nF (faraday's constant) x ln [electron acceptor]/[electron donor]; ∆E = Eoxidant - Ereductant
∆G related to ∆E
∆G = -nF∆E