Complete summary of the Biochemistry course (AB_1137) from the 1st year of biomedical sciences, VU Amsterdam. This summary contains all information needed for the exam, and includes all the material from the lectures and the book that was required for this course. This summary was made during my fi...
Module 1 of Biochemistry (Thermodynamics + Interactions)
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Vrije Universiteit Amsterdam (VU)
Biomedical Sciences
Biochemistry (AB_1137)
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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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