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Thermodynamics of Protein Folding
Protein Dynamics
MD Simulations
Energy minima and energy landscape
Keq and folding fraction
Statistical View of Entropy of Folding
S = R ln W
Proton Transfer Equilibria
pgs. 174-193
Auto-protolysis equilibrium
P
Lecture 1
- Background
- Work & Heat
Textbook: pgs. 1 - 29
Quiz
Calculate the concentration of 10 milligrams of
lactose (360 Da) in 0.5 milliliters.
How many molecules of lactose are in this solution?
Quiz - Answers
Calculate the concentration of 10 milli
Gibbs Free Energy
Chemical Potential
pgs. 91102
& 120-129
DG = DH - TDS
DG = nGm(2) - nGm(1) = ncfw_Gm(2) - Gm(1)
Partial molar Gibbs energy is called chemical potential
G n A A n B B
Chemical potentials will tend to their minima, from which
they will not
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Second and Third Laws of Thermodynamics
Basically, Entropy in the universe is always increasing.
Carnot Cycle
qtotal
V2
V4
= nRThot ln + 0 + nRTcold ln + 0
V1
V3
dqrev
=0
T
S =
dS =
dqrev
T
Entropy: function of Volume, Pressure, Temperature, M
Gibbs Free Energy
Chemical Potential
pgs. 91 - 102
Gibbs Free Energy,
a new variable of state
G = H - TS
H, T, S are state functions, therefore so is G
At constant temperature:
G = H - TS
At constant temperature and pressure: rSsur = - rH / T
So rH = - TS
Lecture 2
- Energy
- Heat Capacity
Textbook: pgs. 32 - 49
Absolute zero: the ground state
Quantum mechanically there is a lowest energy state for any
given system.
This state is called the ground state.
T(K) = 0 system in its ground state
As we will see l
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First law of thermodynamics
Heat Capacity
Entropy
pgs. 77-90
Second Law of Thermodynamics
The Entropy of a system tends to increase.
Third Law of Thermodynamics
The Entropy of any pure, prefect crystal is zero at 0 K,
or at 0 K, the number of m
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Reaction Quotient, Q
Equilibrium Constant, Keq
DG = -RT ln K
DG = DH TDS
freactant = 1/(1+K)
fproduct = K/(1+K)
Effect of temperature
D r G D r H TD r S
Neither the reaction enthalpy nor the reaction entropy
varies much with temperature.
D r G
D
Zero & First Order Reactions
Rate of reaction: n = dc/dt
A + 2B3C + D
d[D]/dt = 1/3d[C]/dt = - d[A]/dt = -1/2d[B]/dt
general equation for rate of reaction:
n = 1/uj d[J]/dt
Rate law: n = k (CA)m (CB)n (CP)q
k : rate constant, and overall order = m + n + q
BioC 4521
INTRODUCTION TO PHYSICAL BIOCHEMISTRY
GENERAL COURSE INFORMATION
Spring 2014 9:05A - 9:55A Monday, Wednesday, Friday
Lecture Room: MCB 2-120
INSTRUCTORS
Prof. Kevin Mayo (612-625-9968, [email protected])
Department of Biochemistry, Molecular Biol
Chemical Kinetics
pgs. 238 - 250
Rate law
The rate of reaction can be written as a function of
concentration of reactants or products.
n = f(c)
n: rate of reaction
f(): function
c : concentration
If concentration changes with time:
n = dc/dt (units of mol
Flux: J = n/(At)
dc
J D
dx
Ficks first law of diffusion
D kBT / f
d 2Dt1/2
k T
1/ 3
B
6 r
s
Rmin
3M2
4N 0
Rtotal
1/
0 3
Rmin
1 1 1
2
Rhyd ~ 3
dc
J D
dx
Ficks first law of diffusion
Flux, J = n/(At)
D kBT / f
d 2Dt1/2
k T
1/ 3
B
6 r
s
Rmin
3M2
Osmotic pressure and
Membrane potential
pgs. 134-146
200-206
Osmosis/osmotic pressure:
why cells burst in pure water
Concentration gradients
Membrane potential
Cellular transport processes
Osmosis:from the Greek word push
Osmosis: passage of a pure solven
Membrane Potential
Passive & Active Transport
pgs. 200-206
296-306
Transport through a Membrane
Passive transport: spontaneous movement of species down
concentration and membrane potential gradients
Active transport: non-spontaneous movement, driven by AT