L03 thermodynamics
law of thermodynamics
1. The first law of thermodynamics
Energy is conserved
Enthalpy（H）
To descript the total energy of a thermodynamic system.
$$
H = U+pV
$$
For a biochemical reaction (under constant pressure of 1 bar), ΔH = the amount of heat produced in system between the initial and final states
2. The second law of thermodynamics
Energy spontaneously disperses from being localized to becoming spread out if it is not hindered from doing so
Equilibrium
Reversible processes，正向与反向的反应速度相等
Far from equilibrium
Irreversible processes (spontaneous processes)
Entropy（S）
Entropy measures the spontaneous dispersal of energy: how much energy is spread out in a process, or how widely spread out it becomes — at a specific temperature
The degree of randomness
The entropy of an isolated system will tend to increase to a maximum value
Gibbs Free Energy（G）
In closed system，entropy is dominant，but biological systems are open system
$$
G = H-TS \ \Delta G = \Delta H-T\Delta S
$$
$$
\Delta G = \Delta G °+RT lnQ
$$
R = the gas constant = 8.314 J/mol$\cdot$k
Q = reaction quotient = [productes]/[reactants]
在平衡时，$\Delta G = 0,\ \Delta G° = -RTlnQ$
#### The favored process in thermodynamics
+ In the direction Gibbs Free Energy minimum
+ $\Delta$ G is negative (A description of second law in open systems)
3. Cell Drive unfavorable reactions
使得 Q < K，从而使得unfavorable reactions 得以进行
通过Coupling an unfavorable reaction to a highly favorable reaction 实现
Biological organisms develop from disorder
- Entropy in an open system can decrease
- Non-equilibrium thermodynamics
Philosophy of life
- Life is an irreversible process
- Equilibrium with environment = DEATH
- Living organisms costs dying of the universe (Entropic)
The applications of free energy in biological systems
1. Biological dynamics
- ATP hydrolysis
- Protein dynamics (protein folding)
- Ligand binding
- Membrane diffusion
- Enzyme kinetics
2. Cell metabolism
- Photosynthesis
- Cell respiration
Enzyme kinetics
The kinetics determine the reaction rate, and the dynamics determine weather the reaction will happen
favorable reactions可能反应速率并不快，Lower energy barrier, and thereby increase reaction rate. 而降低energy barrier 就是酶的工作。