•  Based on physical principles
–  Physical principles (force, work/energy)
–  Examine biochemical changes
•  Applied to system of any size
–  e.g., a planet, or an atom.
•  Another tool to understand the complex
world of biochemistry.
Copyright © UC Regents Davis campus, 2005-14. All Rights Reserved.
d
f ( x)
dx
∫ f (x)dx
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Multivariable Differentiation!
Some functions have more than one variable. !
z = f (x, y)
Consider one variable at a time while fixing others!
€ Differentiation! (∂ )
!Partial
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Energy: the property of
matter and radiation that is
manifest as a capacity to
perform work
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States of Matter
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Kinetic Theory of Gases!
F
A
F = ( # molecules)(Δ - momentum/molecule)(collisions/sec)
p=
# molecules moving in one direction = N/3!
€
v2
Δ - momentum/molecule = mdv = m ∫ dv = m(v 2 − v1 )
v1
Δ - momentum = mv - (-mv) = 2mv (mass of atom in kg)
€
# collisions/sec =
v (velocity, meter/sec)
(units = sec -1 )
2l (twice the length, meter)
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€
N
v
( ) (2mv) ( )
Nmv 2
Nmv 2
3
2l
P =
=
=
l2
3l 3
3V
2
Nmv
PV =
= nRT
3
N = n • NA (NA = Avogadro's number, n = # moles)!
€
nN A mv 2
= nRT
3
N A mv 2
Mv 2
RT =
=
3
3
NAm = M (m = mass of atom, M = Molar Mass, in kg)!
€
3RT = Mv 2
3
1
RT = Mv 2 = Molar Kinetic Energy
2
2
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€
3
1
RT = Mv 2 = E trans
2
2
All Ideal gases have same Molar Kinetic Energy at same T!
€
Kinetic Theory of Gases derived from Pressure!
Pressure only measures kinetic energy!
i.e. translational motion, not rotation and!
vibration.!
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Molecular Kinetic Energy!
3 R
1 M 2
T =
v
2 NA
2 NA
3
1
kBT = mv 2
2
2
€
R
= kB = 1.381×10−23 J ⋅ K -1
NA
M = molar mass
m = molecular mass
Boltzmann’s Constant
€
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Energy is Conserved
m
Maximum Energy from generator = mgh
weight with
mass (m)
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Energy is Conserved
h2
w=
∫ F ⋅ dh
w=
∫ P ⋅ dV
2
€
2H2O(l) ! 2H2(g) + O2(g)
€
w=
∫ φ ⋅ dq
h1
€
w=
∫ m ⋅ g ⋅ dh
1
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€
(ΔG, E°)
Sample Problem:!
A hiker weighing 170 lbs hiked up from the Colorado River to the
rim of the Grand Canyon (4,620 ft). How energy does this
require? Convert this to how many Calories the hiker “burned”
from the vertical hike alone?!
Some Units!
1.00 kg = 2.20 lbs!
1.00 m = 3.28 ft!
1J = kg·m2·s-2 (= N·m)!
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Sample Problem:!
2.00 mole of Nitrogen at 1.00 atm, 25°C is allowed to!
Expand isothermally to final pressure of 0.132 atm.!
Calculate work done if the expansion is carried out!
!
!a.) against a vacuum!
!b.) against a constant external pressure of 0.132 atm!
!c.) reversibly!
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Isothermal gas expansion!
irreversible!
reversible!
Reversible process produces most work!
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State Function
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Endothermic / Exothermic Process!
Endothermic!
Surr. Syste
m
Exothermic!
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Sample Problem:!
100.0 g of nickel at 150.° C was placed in 1.00 L of water at 25.0°
C. What is the final temperature of the water after thermoequilibrium has been established. Assume this is an isolated
system and heat is only transferred between nickel and water (not
to surroundings). The specific heat capacity of nickel is 0.440
J·g-1·C-1.!
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How do we measure heat (q) transfer?!
Constant-volume adiabatic bomb calorimeter!
•  Measure heat of
combustion!
•  Tightly sealed!
–  Constant volume!
•  Adiabatic (no heat
exchange with lab, create
control “surroundings”)!
•  Calibrate by current!
•  q = IVt
(current•voltage•time)!
•  1 Amp•volt•sec = J!
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Constant Pressure and
Copyright © UC Regents Davis campus, 2005-14. All Rights Reserved.
U!
Sample Problem:!
0.5122g of Naphthalene (C10H8, MW=128.2 g/mol) was
“combusted” in a constant-volume calorimeter (CV = 5267.8
J·K-1), where the water temperature increased from 20.17° to
24.08°C.!
Calculate the molar ΔH and ΔU (@ 20.17°C) for the
combustion (oxidation) of Naphthalene (units: kJ·mole-1).!
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Boltzmann Distribution!
N2
= e−ΔE kT
N1
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P1V1
P2V2
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Copyright © UC Regents Davis campus, 2005-14. All Rights Reserved.
Sample Problem:
How much energy (in J) is required to melt an ice cube from
your -20°C freezer to a final temperature of 25° C?
(assume the ice cube is 5.0 x 3.0 x 3.0 cm in size)
Density of ice : 0.9167 g/cm³.
Enthalpy of fusion for water : 6.01 kJ/mol
Specific heat capacity of ice : 2.11 J•g-1•K-1
Copyright © UC Regents Davis campus, 2005-14. All Rights Reserved.
Sample Problem:
Using values in Appendix 2 in the back of the book, calculate the molar
heat of combustion for sucrose (table sugar) (C12H22O11) at 25.0° C. Use
this information to calculate how many dietary calories are in a teaspoon
of sugar (4.00 g), MW of sucrose is 342.3 g•mol-1.
Δ f H° C12 H 22O11 (s) = − 2221.7 kJ ⋅ mol -1
Δf
Δf
(
)
H° (CO (g)) = − 393.5 kJ ⋅ mol
H° ( H O(l)) = − 285.8 kJ ⋅ mol
-1
2
-1
2
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Sample Problem:
A hiker caught in a rainstorm might absorb 1 liter of water on his clothing.
It is windy so that the water evaporates quickly at 20°C.
a.) How much heat would be required for this process?
b.) If all the heat were removed from the 60kg hiker how much
would his body temperature drop.
The Heat of vaporization (ΔHvap) for water at 100°C is 40.66 kJ mol-1
and molar heat capacity of H2O(g) = 33.76 J K-1 mol-1 .
Assume CP is constant with temperature.
Since humans are made mostly of water, you can approximate the heat
capacity to be that of water.
Copyright © UC Regents Davis campus, 2005-14. All Rights Reserved.
Copyright © UC Regents Davis campus, 2005-14. All Rights Reserved.
Sample Problem:!
Using bond enthalpies, estimate the enthalpy of the !
decomposition of hydrogen peroxide (toxic in cells).!
2H2O2(l) ! 2H2O(l) + O2(g)!
Enthalpy of vaporization for hydrogen peroxide and water
are: 51.6 and 44.0 kJ•mol-1 respectively !
Copyright © UC Regents Davis campus, 2005-14. All Rights Reserved.
Hydrogen Bonds in Biochemistry
Hydrogen bonds stabilize DNA structure and specify base pair
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Hydrogen Bonds in Biochemistry
Hydrogen bonds stabilize protein secondary structure
α-helix
β-sheet
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Non-covalent bonds in Biochemistry
•  van der Waals Interaction
– Three type of interactions
• Between two permanent dipoles
• Between a permanent and an
induced dipole
• Between two mutually induced
dipoles
– London or dispersion forces
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Non-covalent bonds in Biochemistry
•  van der Waals Interaction
Between two mutually induced dipoles
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Increasing
Polarizability
Halogen
Radius (pm)
Boiling Point
F2
60
85K
Cl2
102
239K
Br2
120
332K
I2
139
457K (MP 386K)
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Increasing
Induced Dipole
Differential Scanning Calorimeter!
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