Begrippen PB
LES 1: Energy & equilibrium
Metabolism Cellular transformation of one
molecule into another
Glycolysis ATP synthesis out of glucose
Products: 2 ATP & 2 pyruvate
When O2 is present: 30 ATP’s
out of 1 glucose
ATP Adenosine trifosfaat; for energy
storage/transfer
NAD(P)H Nicotinamide adenine dinucleotide
(fosfaat); can transfer electrons to
reduce other molecules and these
can drive the process of liberating
energy
Transmembrane H+ gradients Movement of H+ (met
concentratiegradiënt mee)
produces energy because of
ATPase makes ATP
Precursor in metabolic reactions Intermediate molecules that can be
converted into final products
Precursor + E
Building blocks (bv amino
acids)
Macromolecules (bv protein)
Structures (bv flagella)
Brownian motion The random movement of particles
because of the surrounding
temperature
At nanometer scale:
deterministic forces (always
very dominant acting) have
same magnitude as thermal
forces they both work on
particles and this causes
stochastic motion
Without thermal forces (can
be neglected on macro scale)
only deterministic forces &
movement is deterministic
(not random)
Work Energy transfer that occurs when a
force is applied to an object
, causing it to move in the direction
of the force
Work-energy principle Work one by all the forces acting
on a system (resultant force) =
change in energy of the system
Potential E of a spring (with load) Sum of potential E of spring + that
of load (mgh)
Minimization E - Pot E: in mechanical
problems (T can be
neglected)
- Free E: where T is important
Energy function (bv ifv positie
x): can be minimized (afg = 0)
Near equilibrium: energy
function = quadratic function
(Taylor 2nd degree)
IN EQUILIBRIUM: 1e afgeleid = 0
Stress (spanning) = σ As result of force on an area
Strain (rek) = ε Hoe sterk het materiaal van lengte
verandert onder spanning
Young’s modulus Measure of material stiffness (how
resistant it is against
stretching/compressing)
Entropy Quantifies number of microscopic
configurations (different ways to
arrange particles) for 1 macrostate
More entropy = more
possible microstates
Minimizing free energy with When there are more possible
entropy microscopic states for one
microstate free energy is lower
You can have more entropy
(more possible
configurations) when:
- T increases (particles have
more energy and can travel
more and go to different
positions)
- Increase in volume/number
of particles: more different
ways of arranging them
Equilibrium <-> non equilibrium Systems first not in equilibrium
(free energy is not yet minimized),
then energy goes to minimum (&
entropy is maximized) and then in
equilibrium
Flux so that entropy
increases
Free energy Depends on the system’s energy &
, entropy
Energy minimizing
Entropy maximizing
Systems - Isolated: can’t exchange
energy/matter
- Closed: can exchange
energy, not matter
- Open: can exchange both
LES 2: Statistical mechanics
Boltzmann distribution Gives the probability of a certain
microstate based on its energy at a
certain T
Partition function Makes sure that when you sum up
all the possibilities you get 1
= sum of all microstate
possibilities
Statistical mechanics Using distributions to describe a
system of particles (in stead of
looking at each particle
individually)
Microstate 1 particular microscopic
arrangement of the particles (many
possibilities)
Microstate Observable state that occurs
because particles are arranged in a
certain microscopic state
1 macrostate can occur
because of multiple different
microstates
Two-state system System has only 2 possible
microstates (bv ion channels:
open/closed)
Each microstates leads to 1
macrostate
Multiplicity = 1
Multiplicity How many microstates lead to 1
macrostate amount of
microstates with the samen Ei
Specific energy Ei = energy of each individual
microstate (for every microstate
it’s different because all the
particles are arranged differently)
States & weights diagram - States: all possible
macrostates
- Weights: each microstate has
, a weight that represents its
probability (depends on
energy of the microstate & T)
= multiplicity*Boltzmann
factor (exponentiële term)
Average energy = expected value of total energy of
the system at T
Sum of all the energies
weighted by their
probabilities
Binomial coefficient (ligand- Number of ways in which L ligands
receptor) can be arranged in Ω space
elements
Chemical potential How the energy of a system
changes when particles are
added/removed (T & V stay
constant)
High chemical potential =
high energy cost per particle
adding another particle
would change the system’s
energy a lot
Particles move from higher
chemical potential to lower
so that chemical potentials
would eventually be in
equilibrium
Osmotic pressure in cell Concentration (chemical potential)
INSIDE cell is higher than OUTSIDE
of cell
Water will come into cell
Cellular components will go
out of the cell
= bad
Oplossing: pumping water out of
cell
Law of mass action Describes relationship between
rate of a chemical reaction and the
concentrations of the reactants &
products
Equilibrium constant =
product of concentrations of
all components of reaction all
to the power of their
stoichiometric coefficient
Missing information with Shannon Shannon entropy quantifies
entropy amount of information you don’t
LES 1: Energy & equilibrium
Metabolism Cellular transformation of one
molecule into another
Glycolysis ATP synthesis out of glucose
Products: 2 ATP & 2 pyruvate
When O2 is present: 30 ATP’s
out of 1 glucose
ATP Adenosine trifosfaat; for energy
storage/transfer
NAD(P)H Nicotinamide adenine dinucleotide
(fosfaat); can transfer electrons to
reduce other molecules and these
can drive the process of liberating
energy
Transmembrane H+ gradients Movement of H+ (met
concentratiegradiënt mee)
produces energy because of
ATPase makes ATP
Precursor in metabolic reactions Intermediate molecules that can be
converted into final products
Precursor + E
Building blocks (bv amino
acids)
Macromolecules (bv protein)
Structures (bv flagella)
Brownian motion The random movement of particles
because of the surrounding
temperature
At nanometer scale:
deterministic forces (always
very dominant acting) have
same magnitude as thermal
forces they both work on
particles and this causes
stochastic motion
Without thermal forces (can
be neglected on macro scale)
only deterministic forces &
movement is deterministic
(not random)
Work Energy transfer that occurs when a
force is applied to an object
, causing it to move in the direction
of the force
Work-energy principle Work one by all the forces acting
on a system (resultant force) =
change in energy of the system
Potential E of a spring (with load) Sum of potential E of spring + that
of load (mgh)
Minimization E - Pot E: in mechanical
problems (T can be
neglected)
- Free E: where T is important
Energy function (bv ifv positie
x): can be minimized (afg = 0)
Near equilibrium: energy
function = quadratic function
(Taylor 2nd degree)
IN EQUILIBRIUM: 1e afgeleid = 0
Stress (spanning) = σ As result of force on an area
Strain (rek) = ε Hoe sterk het materiaal van lengte
verandert onder spanning
Young’s modulus Measure of material stiffness (how
resistant it is against
stretching/compressing)
Entropy Quantifies number of microscopic
configurations (different ways to
arrange particles) for 1 macrostate
More entropy = more
possible microstates
Minimizing free energy with When there are more possible
entropy microscopic states for one
microstate free energy is lower
You can have more entropy
(more possible
configurations) when:
- T increases (particles have
more energy and can travel
more and go to different
positions)
- Increase in volume/number
of particles: more different
ways of arranging them
Equilibrium <-> non equilibrium Systems first not in equilibrium
(free energy is not yet minimized),
then energy goes to minimum (&
entropy is maximized) and then in
equilibrium
Flux so that entropy
increases
Free energy Depends on the system’s energy &
, entropy
Energy minimizing
Entropy maximizing
Systems - Isolated: can’t exchange
energy/matter
- Closed: can exchange
energy, not matter
- Open: can exchange both
LES 2: Statistical mechanics
Boltzmann distribution Gives the probability of a certain
microstate based on its energy at a
certain T
Partition function Makes sure that when you sum up
all the possibilities you get 1
= sum of all microstate
possibilities
Statistical mechanics Using distributions to describe a
system of particles (in stead of
looking at each particle
individually)
Microstate 1 particular microscopic
arrangement of the particles (many
possibilities)
Microstate Observable state that occurs
because particles are arranged in a
certain microscopic state
1 macrostate can occur
because of multiple different
microstates
Two-state system System has only 2 possible
microstates (bv ion channels:
open/closed)
Each microstates leads to 1
macrostate
Multiplicity = 1
Multiplicity How many microstates lead to 1
macrostate amount of
microstates with the samen Ei
Specific energy Ei = energy of each individual
microstate (for every microstate
it’s different because all the
particles are arranged differently)
States & weights diagram - States: all possible
macrostates
- Weights: each microstate has
, a weight that represents its
probability (depends on
energy of the microstate & T)
= multiplicity*Boltzmann
factor (exponentiële term)
Average energy = expected value of total energy of
the system at T
Sum of all the energies
weighted by their
probabilities
Binomial coefficient (ligand- Number of ways in which L ligands
receptor) can be arranged in Ω space
elements
Chemical potential How the energy of a system
changes when particles are
added/removed (T & V stay
constant)
High chemical potential =
high energy cost per particle
adding another particle
would change the system’s
energy a lot
Particles move from higher
chemical potential to lower
so that chemical potentials
would eventually be in
equilibrium
Osmotic pressure in cell Concentration (chemical potential)
INSIDE cell is higher than OUTSIDE
of cell
Water will come into cell
Cellular components will go
out of the cell
= bad
Oplossing: pumping water out of
cell
Law of mass action Describes relationship between
rate of a chemical reaction and the
concentrations of the reactants &
products
Equilibrium constant =
product of concentrations of
all components of reaction all
to the power of their
stoichiometric coefficient
Missing information with Shannon Shannon entropy quantifies
entropy amount of information you don’t
