Course Outline

Biophysics 354, Fall 2000

Meeting: 423, Natural History Building, 2.00 - 3.30 p.m., Tuesdays and Thursdays

Instructor: A. R. Crofts, 149 Davenport Hall (

Course assistance: Dr. Vlad Shinkarev, (
Office hours: Friday, 2-4:00 pm, 144 Davenport Hall

Lecture schedule

Date Topic Physical chemistry discussed Hours
8/24 Introduction Biological energy conversion, 
overview and global perspective.
8/29 8/31 Cellular Metabolism 

Review of glycolysis; 
anaerobic metabolism
; role of AYP in cell

Thermodynamic functions; equilibrium constant, 
pH, pK, enthalpy, entropy and free energy
9/5 9/7 Review of aerobic metabolism
Review of TCC; substrate 
level phosphorylation
Coupling between reactions; DGo' for ATP 
hydrolysis; redox reactions; electrode 
potential and relation to free energy.
9/12 9/14 Aerobic Bioenergetics 

Electron transport chains; 

Effects of ligands, H+, on redox 
potential. Redox potentiometry.
9/19 9/21 Electron transport chains 
as proton pump
Chemical potential; electrochemical 
potential; membrane potential; coupling 
between electron and proton transport
9/26 9/28 ATP synthesis The proton circuit, surface potential, 
local proton activity; mechanisms.
10/2 10/5 Proton conduction, stoichiometry Methodology; spectrophotometry; selective electrodes. 
Work, power, and potential.
10/10 10/12 Transport and Motility 

Transport of metabolites; bacterial transport

Kinetics and thermodynamics of transport. 3
10/17 10/19 Motility, muscle and 
related systems
Chemical and mechanical work. 3
10/24 10/26 Electron transfer; kinetic aspects 1st and 2nd order kinetics, relation to equilibrium constant; 
activation energy, theory of electron transfer.
10/31 11/2 Solar Energy Conversion 

Light harvesting

Energetics of exciton transfer; 
fluorescence; Forster theory.
11/7 MID TERM EXAM (Take home exam, no class this day) 1.5
11/9 11/14 Photochemical reaction centers,
structures: bacterial RC, photosystem II
Phototrapping; kinetics and 
thermodynamics; mechanism
11/16 11/21 Photosystem II; oxygen evolution; two-electron gates O2 evolution, detailed discussion of mechanism 3
11/23 Thanksgiving break (No class this day)
11/28 11/30 Photosystem I, and electron transfer between and around the photosystems Photosynthetic electron transfer
Intermediate chains
bc1 complex; and b6f complex
Couping to metabolism
12/5 12/7 Coupling to the proton gradient:
Membrane voltmeters; delayed fluorescence; protolytic reactions
Electrochromism; rapid pH changes. Coupling in the steady state 3
12/9 Reading day (No class this day) 1.5
12/14 FINAL EXAM DUE, 6.30 p.m. (TAKE HOME EXAM replaces scheduled exam, 7:00-10:00 PM, Thur, Dec 14)  


The WWW material for this course is fairly comprehensive. If you feel you need a textbook, the following is recommended:

Authors: W.A. Cramer and D.B. Knaff

Title: Energy Transduction in Biological Membranes: A Textbook of Bioenergetics

Publisher: Springer-Verlag New York/Berlin/London


(You should have a Physical Chemistry textbook available for reference, but any good text will be sufficient).

Authors: Tinoco, Sauer and Wang

Title: Physical Chemistry, Principles and Applications in the Biological Sciences

Publishers: Prentice Hall

Author: David Walker

Title: Energy, Plants and Man

Publishers: University Science Books, Mill Valley, CA 94941