biophysics Flashcards
water characteristics
dipolar (H-bonding) > high bp
hydration cell of interactions
solubility of larger biological molecules
more polar / charged side groups = higher solubility
charged side groups
amino
carboxyl
phosphate
polar side groups
alcohol
thiol
carbonyl
ester
amide
hydrophibicity
apolar groups disrupt H-bonding
drives protein folding
ampiphatic
both polar and non-polar end
brownian motion
thermal energy moving molecules in solution
diffusion
net flux of molecules down a concentration gradient due to random thermal motion
what drives passive transport across membranes
steady state diffusion
flux equation
J = P (C1-C2)
J= flux
P= permeability
time scale to transverse distance R with diffusion coefficient D
T=R^2/6D
U/ internal energy
capacity of a system to do work
chemical potential
determined by:
chemical bonds within
intermolecular bonding
1st law of thermodynamics
change in H = change in U + p (change in V)
enthalpy change = energy released by a reaction - work
ammonium nitrate solution
favourable but has positive enthalpy change
entropy
measure of system disorder
2nd law of thermodynamics
entropy of an isolated system will either increase or remain the same
entropy vs enthalpy
large change in entropy can drive a reaction despite enthalpic favourability
positive change in enthalpy
order to disorder
high to low enthalpy
negative change in enthalpy of system
Boltzmann formula
entropy = boltzmann constant *ln(number of accessible microstates)
Boltzmann constant
1.3*10^-23 J/K
minimum entropy
0
entropy relation to microstates
less entropy = less translational microstates accessible
KE relation to accessible microstates
as KE decreases so does number of accessible microstates
entropies of perfectly crystalline substances at 0K
0
Gibbs free energy function
determines whether reaction is favourable
Gibbs free energy equation
free energy change = enthalpy change - temperature*entropy change
Gibbs free energy change at constant temp and pressure
- temperature * change in total entropy
when is a reaction feasible?
when free energy change is negative
when is a reaction not feasible?
when free energy change is positive?
G in relation to useful work
what’s left from internal energy and entropy changes in system after taking away wasted work
ATP synthesis favourability
unfavourable as gibbs energy change is +
couple to H+ transport
when do molecules react in a collision
if KE > Ea
what does most probable speed depend on?
mass/ temp
kinetic energy formula
1/2 m v^2
Kinetic energy average formula
3/2KbT
what does RoR depend on?
temp
enzymatic catalysis
concentration
first order reactions
single atom or molecule determines rate
e.g decomposition
rate of decomposition
k[A]
2nd order reactions
when 2 molecules collide to determine rate
rate of 2nd order reactions
k[A]^2
rate of bimolecular reaction
k[A][B]
how are orders of reaction found?
experimentally or by full knowledge of the kinetic pathway
what’s order of a reaction controlled by?
the slowest, rate-limiting step of a reaction
Kc
[AB]/[A][B]
Kc effect on product yield
Kc»_space; 1 (mostly product)
Kc «_space;1 (mostly reactant)
Kc = 1 (mixture)
Le Chatelier’s principle
“when a system at eq is disturbed, system composition adjusts to minimise the disturbance”
equilibrium formula for gibbs free energy change
-RTlnKeq
R= gas constant
exponential effect on equilibrium constant
makes v sensitive to small changes in gibbs free energy
pH formula
-log10[H+]
pH effects
affects protein solvation
enzyme activity
pH effect on cells
6-7 death
7-7.35 acidosis
7.45-7.8 alkalosis
7.8-9 death
2H2O dissociation
H3O+ + OH-
hydroxonium doesn’t exist in water
equilibrium constant of water
([H+][OH-])/[H2O]^2
H2O doesn’t change in aq solutions so
Kw = [H+][OH-]
Kw at 25 degrees celcius
110^-14
therefore [H+]=[OH-]=110^-7
free energy
weighted sum of partial molar Gibb’s energy
entropic effect of mixing A with other components
RTln[A]
conc difference enthalpy balancing reverse
electrical potential difference
Nernst potential
electrical potential difference required to stop flow of ions arising from conc difference
change in potential energy
q*change in v
chemical potential difference
zFchange inV
F
Faraday’s constant
impermeable macromolecule charge density
125mM conc of e-=
Donnan equilibrium
equilibrium internal concentration of each ion and membrane potential difference
sodium anomaly
Nernst potential of Na is far more + than membrane potential
cellular osmolytes required so cell doesn’t burst
how does pH imbalance store free energy
chemical contribution (concentration gradient)
electrostatic contribution (potential difference)
combination of chemical and electrostatic contribution
proton motive force
-200mV
rotary motors powered by proton flux
ATP synthase and bacterial flagellar motor
