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Summary Metabolism (WBBY058-05)
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Detailed summary of all lectures given in the Metabolism course
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Lecture 1 Introduction, Gibbs energy and glycolysisATP AND GIBBS ENERGY
ATP, carrier of Gibbs energy:
2 high-energy phosphate bonds
Gibbs energy is the driving force:
➢ Second law of thermodynamics: in all spontaneous process Gibbs energy is dissipated at constant
(environmental) temperature and pressure.
➢ Entropy: probability creates a net flow from left to right
➢ Energy: electrical force creates a flow from right to left
WHO WINS?
Who wins?
∆G = ∆U + p ∆V – T ∆S < 0
U = energy, p = pressure, V = volume, T = absolute temperature, S = entropy
Gibbs energy of a biochemical reaction:
Driving force of ATP hydrolysis (ATP → ADP + Pi):
1) Negative charges on phosphate repel each other.
2) Resonance stabilization of inorganic phosphate (Pi).
3) Two molecules are formed from one (entropy).
4) ADP and Pi are stabilized by bound water molecules.
However, it is difficult to calculate ∆G from first principles.
Computing reaction Gibbs energy:
A+BC+D
∆G = ∆G0’ + RT ln ([C]*[D])/([A]*[B])
∆G0’ can be related to the equilibrium constant of the reaction:
∆G0’ = -RT ln Keq
You can derive this equation, because at equilibrium:
∆G = 0 AND [C][D]/[A][B] = Keq
(or memorize it)
Why is ATP a good carrier of Gibbs energy?
ATP hydrolysis ∆G0’ = 30.5 kJ mol-1 (that’s a lot)
➢ ATP hydrolysis has a strong driving force, hence ATP is capable of driving uphill reactions.
➢ There are reactions with even more negative ∆G0’. These are required to recharge the carrier, i.e. drive the
synthesis of ATP from ADP.
➢ ATP is stable in the absence of enzymes.
,∆G and ∆G0’ are additive:
Hexokinase reaction:
ATP hydrolysis: a downhill reaction
Glucose-6P: an uphill reaction
Enzymes couple uphill and downhill reactions:
The production of glucose-6-P would be thermodynamically infeasible without an enzyme to couple it to ATP
hydrolysis.
So enzymes:
➢ Speed up reactions.
➢ Couple thermodynamically uphill and thermodynamically downhill reactions.
SO:
∆G = the real driving force, if this is negative, the reaction proceeds in the forward direction.
➢ If ∆G > 0 → reaction can’t proceed, only in reverse reaction
➢ If ∆G = 0 → reaction is an equilibrium
➢ If ∆G < 0 → reaction proceeds in forward direction
ENZYME KINETICS
Michaelis-Menten kinetics:
If [S] >> KM, then v = Vmax
If [S] = KM, then v = ½ Vmax
A high KM means a low affinity of substrate + enzyme
(v = rate of the enzyme, S = substrate)
Lineweaver-Burk plot:
,This way, you can directly read the Vmax
Competitive inhibitor:
➢ Vmax unchanged (only the rate is lower, eventually it will all reach the same Vmax)
➢ KM increased (= concentration required to reach the ½ Vmax)
GLYCOLYSIS
Glycolysis is a favorite fuel:
Net outcome: -2 ATP + 2*2 ATP = 2 ATP
Did you know that:
➢ Glycolytic enzymes were the first enzymes ever discovered.
➢ 1860: Pasteur proves that fermentation (glucose → ethanol) requires living cells.
➢ 1897: Eduard Buchner proves that fermentation takes place in yeast extracts without living cells (Nobel prize
1907).
➢ 1909-1942: Identification and purification of glycolytic enzymes.
➔ Major paradigm shifts
Glycolysis in cancer research:
PET scan: highly glycolytic tumor lesions.
, Glycolysis in movement science:
➢ Short and intense exercise depends primarily on glycolysis.
➢ Glycolysis can be upregulated 400-fold during a 100m sprint.
Glycolysis:
➢ Glycolysis is the first phase of glucose catabolism.
- Investment: 2 ATP
Gross yield: 4 ATP
Net yield: 2 ATP
➢ Microorganisms have many variants of the canonical Emden-Meyerhof-Parnas
pathway (= glycolysis)
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