Biophysics

of Macromolecules
BIOL 4596

Spring Semester 2013


Term:

January 14 May 4
Class Times:
MWF 9:30am 10:20am
Location:
201 Tureaud Hall

Instructor:
Michal Brylinski
E-mail:

michal@brylinski.org
Office/Lab:
407/401 Choppin Hall
Office Hours:
TTh 3pm 5pm or by appointment

Recommended Text: Molecular Biophysics: Structures in motion by Michael
Daune, Oxford University Press

Course Objectives: Understand the biophysical principles of structure, dynamics
and function of various biological molecules and their assemblies at the molecular
level. Students are expected to be able to apply key principles to their research and
to everyday life. Emphasis will be placed on principles and methods commonly used
in structure-based drug design. Progress will be assessed through homework
assignments, in-class discussions and quizzes, final presentation and exams.

Homework: Problems will be assigned from the textbook and other sources. These
will be collected and graded. You may discuss homework assignments with your
classmates or use online resources for help, but you must submit your own work.
Homework is due in no later than 5pm on the due date.

Grading Policy:
Homework 15%
Quizzes 15%
Presentation 20%
Midterm 20%
Final 30%

Tentative Schedule:

Week 1:

Conformation of biopolymers:
Geometry of a polymer chain
Intramolecular forces I

Week 2:

Conformation of biopolymers:
Intramolecular forces II
Calculation of conformations

Week 3:
HW1

Conformation of nucleic acids:

Primary structure
Structure of the nucleotide chain
The double-helix structure

Week 4:
Quiz1

Conformation of nucleic acids:

Polymorphism and flexibility of DNA
Structure of ribonucleic acid

Week 5:

Conformation of proteins:
Sequence
Conformational parameters of the peptide bond
Analysis of secondary structures

Week 6:
HW2

Conformation of proteins:
Prediction of secondary structures
Tertiary structure

Week 7:
Quiz2

Dynamics of biopolymers:
Brownian motion
Conformational changes
Experimental methods
Modeling of intramolecular dynamics
Hydration of biopolymers:
Properties of water
Hydrophobic and hydrophilic molecules
Hydration of proteins
Hydration of nucleic acids
Biopolymers as polyelectrolytes:
Charge distributions
Electrolytic solutions
Polyelectrolyte solutions

Week 8:

Week 9:
HW3

Week 10:
Quiz3

Week 11:
Week 12:
Week 13:
Week 14:

Associations between molecules:

A ligand and a macromolecule
Binding energy
Mechanisms and specificity of recognition
Formation of subcellular structures
Applications in drug discovery
Presentations
Presentations
Prep for Final Exam