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Syllabus

BCMB 515
Fall 2014
MWF 10:10-11:00
Place*: WLS M415, M313
Instructors; Drs. Das, Maitreyi Emmanuel; Guo, Hong; Wright, Edward
Dr. Das (August 20th-29th)
1.
Yeast as a model system for cell biology studies (3 lectures)
a.
Lecture 1- Yeast techniques-molecular biology tools. In this lecture we will learn about
yeast molecular biology and understand what makes it an excellent model system. We will also
look into some historical and transformative studies using the yeast system.
b.
Lecture 2- Yeast as genetic model system. In this lecture we will see how yeast genomics
have changed the way we do science. We will learn about genetic screens and understand how
these screens have helped identify entire functional pathways.
c.
Lecture 3- Yeast for proteomic studies. Here we will study how protein-protein
interactions can be studied in yeast at the proteomic level.
2.
Live cell imaging approaches (2 lectures)
a.
Lecture 1- Here we will discuss different types of imaging approaches to study live cells.
We will look at the limitations and advantages of each approach.
b.
Lecture 2- Here we will learn about some basic image analysis techniques using the
ImageJ software. For this lecture students are advised to bring in their computers if possible.
Please download the free ImageJ software from the NIH website or the link here.
http://imagej.nih.gov/ij/download.html
For this section students will be graded on the basis of take home assignments which constitute
1/6th of the total grade. The details of which will be provided later.

Dr. Guo* (Sept 3-October 3) (* Dr. Guos lectures will be held in the BCMB computer
laboratory (WLS M313))
Computational and informatics aspects of biological research
Overview of different databases, including, but not limited to, PubMed, PDB, GenBank, EMBL
and Swiss-Prot.
BLAST/Psi-BLAST and some other tools. Application of these tools in biological research (e.g.,
identifying genes in certain diseases and amino-acid resides important for protein function) and

for compare biological sequences and structure through use of a number of examples and
tutorials.
Introduction of conserved domains and PubChem databases and application of such databases in
biomedical research. Use of NCBI Map Viewer, for instance, to view and search an organism's
complete genome, display chromosome maps, and zoom into progressively greater levels of
detail, down to the sequence data for a region of interest.
There will be one take-home exam/project (for about one week) constitutes 1/3rd of the total
grade.

Dr. Edward Wright (October 6- December 1)


1. Cloning, expression and purification of recombinant proteins
Sequence identification and analysis
Experimental approaches to cloning including gene synthesis, primer design, PCR and DNA
sequencing
Properties of expression vectors and host strains including inducible promoters, ribosome
binding sites, affinity tags, fusion proteins, folding enhancers and rare codons
Factors influencing expression and strategies for optimization
Other expression systems including cell-free and eukaryotic systems
Techniques used in protein purification including cell lysis, centrifugation and
chromatography.
Criteria for monitoring quality of purification strategy including electrophoresis,
spectroscopy and functional assays.
2. Biochemical and biophysical characterization of proteins and other biomolecules.
Methods to study folding, stability, dynamics and structure including fluorescence
spectroscopy, circular dichroism, differential scanning calorimetry, electron paramagnetic
resonance, mass spectrometry, analytical ultracentrifugation, NMR and x-ray
crystallography.
Methods to quantify interactions of proteins with small molecules, nucleic acids, lipids and
other proteins including radiolabel and antibody based assays, isothermal titration
calorimetry and surface plasmon resonance.
Data analysis and interpretation including error analysis and effective presentation
There will be two take-home exams/projects and one presentation/assignment. These three
activities will constitute 1/2 the total course grade.

Letter grading will be determined by the total grade and curving the class average. The class
average receives the grade B. Tests are to be submitted electronically to either the instructor or
to dropbox on the Blackboard course site. Late submissions will be penalized by 10% reduction
of the grade per half hour of being late.
Make up exams can be given only in case of sickness and family emergencies in documented
cases.
Attendance to lectures is required. Exceptions are sickness, conference attendance and family
emergencies with documentation. Being late by more than 5 minutes will be considered as
absence from the class. Missing more than 4 classes (10%) during the semester will result in
10% grade reduction for each additional 4 missed classes.
Plagiarism will result in a failing grade. Description and examples of plagiarism can be seen at :
http://www.indiana.edu/~wts/pamphlets/plagiarism.shtml or
http://plagiarism.org/. These links are posted on the course Blackboard site.
Additional policies on UTK academic honesty and disabilities restricting learning can be found
at:
http://tenntlc-utk-edu.wpengine.netdna-cdn.com/files/2012/11/CAMPUS-SYLLABUS1.pdf