Lecture 1 Bioenergetics and Thermodynamics

Question 1

Bioenergetics

Answer 1

The quantitative study of the energy relationships and energy conversions in biological systems.

Question 2

Define system

Answer 2

Any part of the universe which is of interest to us. The rest is the surroundings.

• A system can exchange energy and matter with its surroundings. The following sections assume only energy is exchanged.

Question 3

1st law of thermodynamics

Answer 3

(conservation of energy)

For any physical or chemical change, the total amount of energy in the universe remains constant; energy may change form or it may be transported from one system to another, but it cannot be created or destroyed.

Question 4

Another formulation of the 1st law of thermodynamics

Answer 4

For any isolated system, the heat influx from the surroundings is equal to the change in internal energy of the system plus the work exerted by the system on its surroundings.

Question 5

2nd law of thermodynamics

Answer 5

Entropy (S) of isolated systems left to spontaneous evolution cannot decrease with time, as they always arrive at a state of thermodynamic equilibrium, where the entropy is highest. ΔS_universe​= ΔS_system​+ ΔS_surroundings ​> 0

formulations:

• Spontaneous processes evolve as a transition from order to disorder.
• The most probable arrangement of a system is one that maximizes disorder (W) which can be measured as the number of energetically equivalent ways of arranging the components of the system: S=k_BlnW.
  
  • A more useful formulation in biochemistry is: S≥Heat of reaction/T; Heat of reaction is known as a change in Enthalpy (∆S≥ ∆H/T) ⇒ ∆H−T∆S ≤ 0.

Question 6

What is Gibbs free energy

Answer 6

As per 2nd law → At constant temperature (T) and volume (V), biochemical systems can evolve (transform) spontaneously if as a consequence of their evolution (transformation)

Question 7

Gibbs free energy equation

Answer 7

∆G_{(products − reactants)} = ∆H−T∆S

Question 8

Difference between ∆G, ∆Gᴼ, and ∆Gᴼ’

Answer 8

• ∆G → The change in Gibbs free energy for a process under prevailing conditions; which is the difference between G_products - G_reactants
• ∆Gᴼ → compares the free energy of reactants and products at standard conditions
  
  • gases at 1 bar pressure
  • concentrations are 1 M
  • T = 25℃
• ∆G’ᴼ → compares the free energy of reactants and products at standard conditions in biochemistry

Question 9

Standard conditions of ∆Gº?

Answer 9

Change in free energy under ‘standard’ conditions. Standard conditions means:

• 1M concentrations of reactants and products
• T = 298 K
• P = 1 atmosphere
• ∆Gº is a constant because the standard conditions are fixed.

Note: the ‘standard’ conditions concentration of 1M rarely (if at all) occur in biological systems.

Question 10

How does a biochemical reaction proceed spontaneously?

Answer 10

A biochemical reaction will proceed spontaneously towards equilibrium if ∆G_{(products − reactants)} = ∆H−T∆S ≤ 0, so negative

• When this condition is met the reaction is said to be SPONTANEOUS and exergonic (energy releasing).
• In endergonic transformations (energy-consuming) this condition is NOT met.
• Once a system (reaction) reaches equilibrium then, ∆G=0.

Question 11

When is ∆G negative?

Answer 11

Question 12

What is used to make reaction systems occur faster?

Answer 12

enzymes

Question 13

What information does ∆G give about reaction rates?

Answer 13

∆G gives no information about reaction rates.

Question 14

What does the reaction rate depend on?

Answer 14

The rate depends on overcoming an activation barrier, which is what biological catalysts ‘enzymes’ do.

Question 15

What are K_eq and ∆Gº measures of?

Answer 15

measures of a reaction’s tendency to proceed spontaneously

• ∆G must be negative to proceed spontaneously

Question 16

What is K_eq in ∆Gº = -RTlnK_eq

Answer 16

Concentrations of reactants and products is a ratio to determine whether the reaction will occur or not.

Manipulating the concentrations A, B, C, D will change the ∆Gº

Question 17

Standard states of ∆G’ᴼ biochemistry

Answer 17

• pH = 7.0 meaning [H+] = 10^-7 M
• [H2O] = 55.5 M
• [Mg++] in solution is assumed to be constant at 1 mM.
• The concentrations of H2O, H+ and Mg++ are incorporated into K’_eq and ∆G’º.

Question 18

What do actual free energy changes depend on?

Answer 18

reactant and product concentrations, not just on ∆G’°

• Cellular conditions will determine whether a reaction will proceed.
• The reaction will proceed spontaneously if ∆G’ is negative even if ∆G’º is positive.
  
  • If you removed more product less likely to move forward
  • If you removed more reactants less likely to occur spontaneously

Question 19

What are coupled reactions?

Answer 19

Those in which an unfavorable (endergonic) process is coupled to and “pulled” by a favorable (exergonic) process involving a common intermediate.

• Free energy changes of reactions are additive.
• Energy released by an exergonic process can drive an endergonic process.

Question 20

How are coupled reactions carried out?

Answer 20

via 1 or more enzymes

Question 21

Direct coupling

Answer 21

In direct coupling , two consecutive reactions occur on the same enzyme (ex. hexokinase), whereby both reactions are linked by a common intermediate (ex. Pi).

Question 22

Indirect coupling

Answer 22

In indirect coupling, two consecutive reactions occur on two different enzymes, E1 and E2.