Bioenergetics

Question 1

What information does ΔG^o’ tell you about a reaction?

Answer 1

The spontaneity and direction of a reaction under standard biochemical conditions, where all liquids are at 1 M solutions, the temperatue is 310 K, the pH is 7, and the concentration of H⁺ is 1 x 10^-7 M and Mg²⁺ is I mM

Question 2

Under biological standard conditions, what is the concentration of H⁺?

Answer 2

1 x 10^-7 M

Question 3

Under biological standard conditions, what is the concentration of Mg²⁺?

Answer 3

1 mM

Question 4

What information does ΔG’ tell you about a reaction?

Answer 4

The spontaneity and direction of a reaction under real or actual conditions

Question 5

What is the relationship between these two thermodynamic parameters ΔG^o’ and ΔG^’?

Answer 5

ΔG’ = ΔG^o’ + RT lnQ

ΔG’ = -RT lnk + RT lnQ

Question 6

What is the relationship between Q and K? How do these parameters provide us with similar information about a biochemical reaction?

Answer 6

Q = K reaction at equilibrium

Q < K reaction moves toward products (spontaneous)

Q > K reaction moves toward reactants (nonspontaneous)

Question 7

What does the value of K tell us about ΔG^o’?

Answer 7

If K > 1, then ΔG^o’ < 0 (spontaneous)

If K < 1, then ΔG^o’ > 0 (non-spontaneous)

Question 8

What does the value of Q tell us about ΔG’?

Answer 8

If Q > 1, then ΔG’ < 0 (spontaneous)

If Q < 1, then ΔG’ > 0 (nonspontaneous)

Question 9

What is the equation for determining Q using standard Gibbs free energy?

Answer 9

K = e^{-ΔGo’​/RT}

Question 10

The cell cannot let reactions with large equilibrium constants to reach equilibrium. Why?

Answer 10

1. Osmotic pressure
2. Solubility

At very high concentrations of a metabolite, the osmotic pressure of the cell becomes very high and the solubility of the metabolite decreases

Question 11

What does it mean for a reaction to operate “far from equilibrium”?

Answer 11

If Q and K are within 1 to 2 orders of magnitude, the reaction is near equilibrium; if Q and K are outside of this range, then the reaction is considered to be “far from equilibrium”

Question 12

If Q = 1, what do we know about the standard Gibbs Free energy and the actual Gibbs Free energy?

Answer 12

If Q = 1, then ΔG^o’ = ΔG^’

Question 13

Not all reactions with a ΔG^o’ are non-spontaneous. List two different ways to drive a reaction towards the products even if it has a ΔG^o’

Answer 13

1. The concentration of products is very, very, very small
2. Coupling

Question 14

The hydrolysis of ATP is what type of reaction?

Answer 14

A nucleophilic substitution reaction

Question 15

What is the mechanism of the hydrolysis of ATP?

Answer 15

Question 16

What type of mechanism does the active site of the enzyme that catalyzes the hydrolysis of ATP use?

Answer 16

General acid-base catalysis

Question 17

Why are phosphocreatine and ATP considered “high-energy” compounds?

Answer 17

Because upon hydrolysis of the compounds, large amounts of energy are released

Question 18

Other high-energy compounds include ADP, phosphoenolpyruvate, and acetyl coenzyme A. Why is the hydrolysis of these compounds so thermodynamically favorable?

Answer 18

Because their immediate products can be stabilized via resonance, tautomerization, and/or ionization relative to the products

Question 19

Why is ADP considered a “high energy” compound?

Answer 19

Because upon its hydrolysis, it produces the immediate product protonated AMP, which can undergo ionization not present in the reactants (in addition to resonance via the phosphate ion)

Question 20

Why is phosphoenolpyruvate considered a “high energy” compound?

Answer 20

Because upon its hydrolysis, its immediate product is an enol, which can then tautomerize to a keto (AKA pyruvate), a far more stable compound that the reactant

Question 21

Why is acetyl-coenzyme A considered a “high energy” compound?

Answer 21

Because upon hydrolysis, acetyl-CoA is converted to acetic acid, which can undergo ionization and further resonance thereby increasing the stability of the products relative to the reactants

Question 22

What is the driving force for ATP hydrolysis?

Answer 22

The stabilization of products relative to the reactants

Question 23

What are things to look for when considering why product stabilization drives ATP hydrolysis? Three things were discussed in class.

Answer 23

1. Less electrostatic repulsion in products (ATP^4- –> ADP^2-)
2. Resonance stabilization of the products
3. Ionization of the products (HPO₄^2- –> H+ + PO₄^2-)

Question 24

Why is AMP not considered “high energy”?

Answer 24

Because upon its hydrolysis, it produces inorganic phosphate and a non-ionizable product

Question 25

Why is glucose-6-phosphate not considered a high energy compound?

Answer 25

Because upon its hydrolysis, glucose is formed, which can not undergo ionization, resonance, or tautomerization not already present in the reactants

Question 26

Whyat is the significance of high-energy containing phosphoryl compounds?

Answer 26

Phosphoryl groups can be transferred from ADP to form ATP via substrate-level phosphorylation

Question 27

In phosphoryl transfer reactions where the phosphoryl group is transferred to an alcohol moiety, what acts as the nulceophile? What does it attack?

Answer 27

The oxygen of the hydroxyl acts as the nucleophile and attacks the gamma phosphate of ATP, leaving ADP behind

Question 28

What dictates which phosphate group of ATP will be attacked in a phosphoryl transfer?

Answer 28

The enzyme

Question 29

What is the name of the reaction that attacks the beta-phosphate of ATP, adding two phosphate groups to the attacking molecule?

Answer 29

Pyrophosphorylation

Question 30

What is the name of the reaction that occurs via attack of the alpha-phosphate of ATP by an alcohol, attaching “AMP” to the alcohol and releasing pyrophosphate?

Answer 30

Adenylylation