REGARDING THE BIO 466 BIOPHYSICS COURSE

SPRING 2009-2010

BIO 466 BIOPHYSICS

Instructor: Deniz Sezer

Office: FENS G021

Email: dsezer@sabanciuniv.edu

Phone: 483-9881

Office Hours:

            Wednesday    15:00 – 17:00            FENS G021

 

Lecture Hours:

Wednesday    12:40 – 13:30                       FASS G056     (in class quiz)

Thursday       12:40 –
13:30                        FASS G056     (homework due)

 

Course Description: The objective of this course is to introduce
the students to concepts and techniques in theoretical biophysics. To this end,
a selection of basic molecular processes encountered in courses on molecular
and cell biology will be examined from a quantitative perspective. Throughout,
the non-equilibrium and single-molecule (stochastic) aspects of these processes
will be emphasized. In addition to weekly quizzes and homework, students will
be expected to write a concise report introducing a biophysical problem of
their choice and summarizing the status of its current scientific
understanding.

 

Course Content:

1.     Biology and Numeracy

·        Cells and organisms

·        Molecular strategies

2.     Statistical Thermodynamics and Models

·        Mechanical and chemical equilibrium in the cell

·        Ideal gases, ideal solutions and lattice models

·        The random walk model and protein folding

3.     Enzymes and Signals

·        Thermodynamics and kinetics of ligand binding

·        Allosteric cooperativity and regulatory domains
on a leash

·        Fluctuating enzymes and dynamic cooperativity

·        Error reduction through kinetic proofreading

4.     Cell Shape and Motility

·        Diffusion, flow and chemoreception

·        Why don’t bacteria swim like fish?

·        The dynamic cytoskeleton

·        Molecular motors and diffusion under force

5.     Biological Electricity

·        Electrostatics of solutions

·        Membrane permeability and ion channels

·        Action potential and nerve impulses

6.     Quantum Mechanics in Biology

·        Electron and proton transfer in biomolecules

·        Photosynthesis and respiration

 

Textbooks:

1.     Physical
Biology of the Cell, Rob Phillips, Jane Kondev, Julie Theriot. Our main
textbook.

2.     Molecular
Driving Forces, Ken Dill, Sarina Bromberg. Supplementary textbook.

3.     Biological
Physics, Philip Nelson. Supplementary textbook.

All textbooks are available on library reserve.

 

Evaluation:

·        Weekly Homework:  10
%

·        Weekly Quizzes:        15
%

·        Term Report:             20
%

·        Midterm Exam:          25
%

·        Final Exam:                30
%