Biochemistry summary
1
,Thermodynamics 3
Interactions (Chapters 4+5) 4
Proteins (Chapters 6+7) 6
Ligand binding 8
Enzymes (Chapters 8+9) 9
Membranes 12
Transport 14
Redox reactions 14
Electron transport chain and oxidative phosphorylation 15
Metabolism 15
2
, Thermodynamics
- Thermodynamics: describes exchange of energy between the system (= what you investigate)
and its environment (= rest of universe)
> Theory that links various forms of energy, and how their conversion can be used to do
work
- State variables: describe state of system at given moment
> Independent of how system ended up in that state
> E.g. position, volume, temperature, pressure
> E.g. not work and heat
- Extensive state variables: add up if you combine 2 systems
> E.g. volume, energy
- Intensive state variables: do not add up if you combine 2 systems
> E.g. pressure, concentration, temperature
> There are pairs of state variables, where one is intensive and other extensive ->
di erence in intensive leads to exchange of extensive
> E.g. temperature-energy, pressure-volume
- Each system has certain amount of internal energy, U (sometimes E)
> Thermodynamics deals with changes in U: ∆U
- 1st law: energy is conserved (cannot disappear/be generated, only converted from one form
into another)
> Internal energy of system can be used:
1. To do work -> energy content of system decreases
2. To produce heat -> energy content of system decreases
> Positive ux of heat (q) means energy is added to system; -q means system produces
heat and loses internal energy
> Contributions of internal energy:
- Translation energy: rate of movement in space
- Rotation energy: molecules can rotate
- Vibration energy: movement of atoms within molecule
- Binding energy: energy in chemical bonds between atoms
- Potential energies caused by intermolecular interactions
- Electron energies: energies of electrons within atom
∆U = q - w
Growth: w = p × ∆V —> ∆U = q - p × ∆V
- Enthalpy change (∆H): heat added to or produced by the system at constant pressure
qp = ∆H = ∆U + p∆V
> ∆H = ∆U, except for volume changes (are negligible in many processes)
- Multiplicity (W or Ω): number of microscopic arrangements that have the same macroscopic
appearance
> We can only count/measure how many molecules/particles are in a compartment
> We cannot tell one molecule from another, but they are di erent ‘individuals’ that behave
independently
> Probability drive: when particles move randomly along compartments
- Equilibrium: particles are divided equally; individual particles still move, but there is no net
displacement
> Most probable state
- At level of atoms+molecules, energy occurs in quanta (= small packages) that can move
around atoms/molecules
> In combined system, the probabilities of each system are multiplied
- Exchange of energy: when 2 systems are brought in thermal contact, they will exchange
energy (heat) until they have the same temperature
> Driving force for exchange is probability drive
- More ways to distribute energy over 2 systems if they have equal temperature
- That makes iso-thermal state more likely
- For small systems (e.g. atoms), uneven distribution of energy (1 warm and 1 cold
end) occurs spontaneously from time to time
- The larger the systems, the less likely the uneven distribution becomes
3
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1
,Thermodynamics 3
Interactions (Chapters 4+5) 4
Proteins (Chapters 6+7) 6
Ligand binding 8
Enzymes (Chapters 8+9) 9
Membranes 12
Transport 14
Redox reactions 14
Electron transport chain and oxidative phosphorylation 15
Metabolism 15
2
, Thermodynamics
- Thermodynamics: describes exchange of energy between the system (= what you investigate)
and its environment (= rest of universe)
> Theory that links various forms of energy, and how their conversion can be used to do
work
- State variables: describe state of system at given moment
> Independent of how system ended up in that state
> E.g. position, volume, temperature, pressure
> E.g. not work and heat
- Extensive state variables: add up if you combine 2 systems
> E.g. volume, energy
- Intensive state variables: do not add up if you combine 2 systems
> E.g. pressure, concentration, temperature
> There are pairs of state variables, where one is intensive and other extensive ->
di erence in intensive leads to exchange of extensive
> E.g. temperature-energy, pressure-volume
- Each system has certain amount of internal energy, U (sometimes E)
> Thermodynamics deals with changes in U: ∆U
- 1st law: energy is conserved (cannot disappear/be generated, only converted from one form
into another)
> Internal energy of system can be used:
1. To do work -> energy content of system decreases
2. To produce heat -> energy content of system decreases
> Positive ux of heat (q) means energy is added to system; -q means system produces
heat and loses internal energy
> Contributions of internal energy:
- Translation energy: rate of movement in space
- Rotation energy: molecules can rotate
- Vibration energy: movement of atoms within molecule
- Binding energy: energy in chemical bonds between atoms
- Potential energies caused by intermolecular interactions
- Electron energies: energies of electrons within atom
∆U = q - w
Growth: w = p × ∆V —> ∆U = q - p × ∆V
- Enthalpy change (∆H): heat added to or produced by the system at constant pressure
qp = ∆H = ∆U + p∆V
> ∆H = ∆U, except for volume changes (are negligible in many processes)
- Multiplicity (W or Ω): number of microscopic arrangements that have the same macroscopic
appearance
> We can only count/measure how many molecules/particles are in a compartment
> We cannot tell one molecule from another, but they are di erent ‘individuals’ that behave
independently
> Probability drive: when particles move randomly along compartments
- Equilibrium: particles are divided equally; individual particles still move, but there is no net
displacement
> Most probable state
- At level of atoms+molecules, energy occurs in quanta (= small packages) that can move
around atoms/molecules
> In combined system, the probabilities of each system are multiplied
- Exchange of energy: when 2 systems are brought in thermal contact, they will exchange
energy (heat) until they have the same temperature
> Driving force for exchange is probability drive
- More ways to distribute energy over 2 systems if they have equal temperature
- That makes iso-thermal state more likely
- For small systems (e.g. atoms), uneven distribution of energy (1 warm and 1 cold
end) occurs spontaneously from time to time
- The larger the systems, the less likely the uneven distribution becomes
3
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