|
Week
|
Date
|
Topics
|
Summary
Note
|
|
Week 1
|
Aug. 25 -
Aug. 29
(ch. 1)
|
·
Introduction
to Biophysical Chemistry
Thermodynamics
·
Heat,
Energy, and Work
·
First Law
of Thermodynamics
|
L1
L2
L3
discussion_1
|
|
Week 2
|
Sept.3 -
Sept. 5
(ch. 1)
|
·
Enthalpy
·
Enthalpy
of phase change
·
Bond
enthalpy
·
Enthalpy
of reaction, Enthalpy of Formation
·
Hess’s
Law
|
L4
L5
discussion_2 key
|
|
Week 3
|
Sept. 8 -
12
(ch.1
& ch. 2)
|
·
Kirchoff’s
Law: Enthalpy vs. T
·
Entropy
and 2nd Law
·
Entropy
Measurements
·
Entropy
and hydrophobic interactions
·
Third Law
of Thermodynamics
|
L6
L7; L7
summary
L8
discussion_3; key
|
|
Week 4
|
Sept. 15
- 19
(ch.
2)
|
·
Entropy
of Substances and Chemical Reactions
·
Spontaneity
and Gibbs Free Energy
·
Calculating
DG
·
Protein structures
and interactions
·
Thermodynamics
of hydrogen-bonding and hydrophobic interaction
|
L9
L10
L11
discussion4
|
|
Week 5
|
Sept. 22
- 26
(ch.
3)
|
·
Temperature
and Pressure dependence of Free energy
·
Phase
diagrams
·
Application:
Thermodynamics of DNA duplex formation
·
Chemical potential; Ideal solutions
·
Osmosis
|
L12
L13
L14
|
|
Week 6
|
Sept. 29
– Oct. 3
(ch.
4)
|
·
Chemical
equilibrium
·
Calculating
DGorxn and temperature dependence
·
Equilibrium
constant & DGorxn
Exam 1, Wednesday, Oct. 1; in class
|
L15
L16
|
|
Week 7
|
Oct. 6 -
10
(ch.
4)
|
·
Temperature
Dependence of Equilibrium Constant
·
Acid Base
Equilibria
|
L17
L18
L19
Discussion 5: 4.49 (a) &
(b)
discussion5 key;
Excel plot
|
|
Week 8
|
Oct. 13 -
17
(ch.
4)
|
·
Buffers
·
Biochemical
standard state
·
Equilibrium
binding
|
L20
L21
L22
discussion6
key
|
|
Week 9
|
Oct. 20 -
24
(ch.
5)
|
·
Ions in
solution
·
Non-ideality
·
Ions
transport
·
Redox
Reactions
·
Nernst
Equation
Application:
Biological Electron Transfer
|
L23
L24
L25
discussion 7 & key
|
|
Week 10
|
Oct. 27 -
31
(ch.
6)
|
Chemical Kinetics
·
Reaction
Rates
·
Rate Laws
·
Temperature
Dependence
|
L26
L27
L28
|
|
Week 11
|
Nov. 3 -
7
(ch.
7)
|
·
Reaction
mechanisms
Exam 2, Wednesday Nov. 5; in class
|
L29
L30
|
|
Week 12
|
Nov. 10 -
14
(ch.
7, 8)
|
·
Reaction
dynamics
·
Kinetics
and Mechanisms of Enzymatic Reactions
·
Michaelis-Menten
Equation
|
L31
L32
supple_1; suppl_2
L33
|
|
Week 13
|
Nov. 17 -
21
(ch.
8)
|
·
Inhibition
·
Catalytic
efficiency
·
Energetics
of catalysis
·
Visualizing
Enzymes
|
L34
suppl_MM
L35
L36; pdb
note
Discussion: Tinoco 8.10; 8.21;
7.17
|
|
Week 14
|
Nov. 24 -
26
(ch.
9, 13)
|
Structure and Spectroscopy
·
Basic
quantum mechanics
·
Absorption
·
Beers law,
bio-chromophores
|
L37
L38
|
|
Week 15
|
Dec. 1 -
Dec. 5
(ch.13)
|
·
Emission
·
Fluorescence
Spectroscopy and FRET
|
L39
L40; suppl-note
L41
|
|
Dec. 8 -
10
|
Final Reviews:
Tue. Dec. 9, 3:00-4:00, SGM 226
|
review
|
|
Dec. 15
|
Final Exam, 8:00 – 10:00 am
|
|
