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Lahore University of Management Sciences

BIO 413/513 – Biophysical Methods/ Biophysical Techniques


Fall 2018
Instructor
Dr Syed Shahzad ul Hussan
Room No. 9-313A
Office Hours Thursday, 3-5pm
Email Shahzad.hussan@lums.edu.pk

Telephone 423-560-8351
Secretary/TA
TA Office
Hours

Course Basics
Credit Hours 3
Lecture(s) Nbr of Lec(s) 2 Duration 75 minutes each
Per Week

Course Distribution
Core Elective
Elective
Open for Student Students having taken Chem101 or Bio212 courses and graduate
Category students of Biology and Chemistry majors
Closed for Student
Category

COURSE DESCRIPTION

The Biophysical methods course is designed to provide undergraduate and graduate students an
understanding of detailed concepts of state of the art techniques involved in biological and
biochemical research. Students will learn the fundamental principles of these techniques and
details of experimental application in biological research. This course will particularly be helpful for
the students who are aiming to pursue Ph.D and perform scientific research. The topics such as
UV/IR spectroscopy, Mass spectrometry in proteomics, NMR spectroscopy in protein structures,
protein-ligand complexes & drug-receptor interactions, chromatography and calorimetry will be
covered with the aim to answer biological questions at sub-molecular level.

COURSE PREREQUISITE(S)

• Bio212 or Chem101

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COURSE OBJECTIVES

• Introduction to modern techniques involved in molecular and sub-molecular level investigation


of biological processes
• To understand the basic concepts and principles of these techniques
• To understand how these biophysical tools are applied to answer a biological question.

Grading Breakup and Policy

Assignment(s): 1 (5 %)
Quiz(s): 4 (5 % each)
Class Participation and attendance: 5 %
Midterm Examination: 35 %
Final Examination: 35 %

Examination Detail

Yes/No: Yes
Midterm Combine/Separate: Separate
Exam Duration: 2.5 Hrs
Preferred Date:
Exam Specifications: multiple choice, true and false and short descriptive questions
Yes/No:
Final Combine/Separate: Separate
Exam Duration: 2.5 Hrs
Exam Specifications: multiple choice, true and false and short descriptive questions

Instruct Recommended Book,


Lecture Topics
or chapter
Methods of macromolecule production and
Lecture 1 purification SSH

An overview and basic concepts, Introduction to


Lecture 2
UV/visible spectroscopy and its application in biology SSH Spectroscopy by
Pavia, chapter 10
Basic concepts of infrared spectroscopy and its Introduction to
Lecture 3
application in biology particularly in protein study SSH Spectroscopy by
Pavia, chapter 2
Proteomics: basic concepts of mass spectrometry Introduction to
Lecture 4
and its application in structural biology and SSH Spectroscopy by
proteomics Pavia, chapter 4
Lecture 5 Nuclear Magnetic Resonance (NMR) spectroscopy: SSH
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basic concepts

High Resoultion NMR


Lecture 6 Quantum mechanical aspects of NMR Technique, 2nd
SSH Edition, chapter 2
Quantum mechanical aspects of NMR High Resoultion NMR
Lecture 7
SSH Technique, 2nd
Edition, chapter 2
Structural Biology: Introduction to high resolution High Resoultion NMR
Lecture 8
NMR SSH Technique, 2nd
Edition, chapter 1
How to study the internal mobility of a molecule: High Resoultion NMR
Lecture 9
Concepts of spin relaxations SSH Technique, 2nd
Edition, chapter 2
Practical aspects of Biomolecular NMR: Dealing with High Resoultion NMR
Lecture 10
the instrument SSH Technique, 2nd
Edition, chapter 3
Practical aspects of high resolution NMR: sample High Resoultion NMR
Lecture 11 preparation, data acquisition, processing and Technique, 2nd
SSH
analysis Edition, chapter 3

Structural study of a bio-macromolecules: correlation High Resoultion NMR


Lecture 12
through chemical bonds, homonuclear correlations SSH Technique, 2nd
Edition, chapter 5
Structural study of a bio-macromolecules: correlation High Resoultion NMR
Lecture 13
through chemical bonds, heteronuclear correlations SSH Technique, 2nd
Edition, chapter 6
Lecture 14 Correlation through space: concepts of Nuclear High Resoultion NMR
Overhauser Effect (NOE) SSH Technique, 2nd
Edition, chapter 7

Midterm Exam

Lecture 15 Conformational analysis of flexible biomolecules: High Resoultion NMR


application of NOE SSH Technique, 2nd
Edition, chapter 7
Bioactive conformation of ligands when bound by Review, by Thomas
Lecture 16 biomacromoleucles: concept of transferred NOE Peters and B. Meyer
SSH
(trNOE)

Drug-target interactions by NMR: determining the Review by Carole


binding epitope of a ligand by Saturation Transfer Bewley and Shahzad-
Lecture 17
Difference (STD) NMR and quantitative analysis of SSH ul-Hussan
recognition phenomenon
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Drug-target interactions by NMR: identifying the High Resoultion NMR
Lecture 18 target-binding ligand and its kinetics by diffusion Technique, 2nd
SSH
NMR spectroscopy Edition, chapter 9

NMR at the surface of a virus: characterizing the Review by Christoph


Lecture 19
ligand binding directly to a virus. SSH Radamacher

Structure of proteins: concepts of triple resonance Fundamental of


NMR spectroscopy protein NMR
Lecture 20
SSH spectroscopy, Gordon
S Rule and T Kevin
Hitchens
Structure of proteins: experimental estimation of Fundamental of
inter-proton distances, 15N-edited and 13C-edited protein NMR
Lecture 21
3-dimensional NOE experiments SSH spectroscopy, Gordon
S Rule and T Kevin
Hitchens
Structure of proteins: experimental estimation of Fundamental of
dihedral angles in proteins protein NMR
Lecture 22
SSH spectroscopy, Gordon
S Rule and T Kevin
Hitchens
Structure of protein-protein and ligand-protein Fundamental of
complexes by NMR protein NMR
Lecture 23
SSH spectroscopy, Gordon
S Rule and T Kevin
Hitchens
Circular Dichroism (CD) and its application to study Biophysical tools,
Lecture 24 biomolecules Methods in Cell Biol,
SSH
Volume 84, chapter
10
Experimental aspects of thermodynamics: SSH Biophysical tools,
Isothermal Calorimetry Titration (ITC) and its Methods in Cell Biol,
Lecture 25
application to study the bio-macromolecule/ligand Volume 84, chapter 4
interactions

Experimental aspects of Kinetics: Surface Plasmon SSH Biophysical tools,


Lecture 26 Resonance (SPR) and its application to study the Methods in Cell Biol,
bio- macromolecule/ligand interactions Volume 84, chapter 3

Analytical Ultra Centrifugation: Determining the SSH Biophysical tools,


Lecture 27 conjugation of bio-macromolecules by sedimentation Methods in Cell Biol,
phenomenon Volume 84, chapter 6

Lecture 28 Overview of crystallization and X-ray crystallography SSH Biophysical tools,


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Methods in Cell Biol,
Volume 84, chapter
13

Recommended reading:
1. Introduction to spectroscopy by Pavia,
2. Introduction to modern liquid chromatography by Snyder and Kirkland
3. Mass spectrometry by Watson and Sparkman
5. Biophysical Tools for Biologists, Volume 1 (Methods in Cell Biology volume 84)
Author: John J. Correia, H William Detrich III
6. Physical Chemistry for the Biological Sciences, by Gordon G Hemmes
7. Introduction to Proteomics: From concepts to sample preparation, mass spectrometry data
analysis.
Author: Josiph Lovric
8. High resolution NMR spectroscopy
Author: Timothy Claridge
9. Fundamental of protein NMR spectroscopy
Author: Gordon S Rule and T Kevin Hitchens