Spring 2018-2019

BCMB 272: Biochemistry 2

A comprehensive survey of carbohydrates, energy metabolism and metabolic biochemical pathways.  Topics to be covered will include Carbohydrate structure and function, Glycolysis, Gluconeogenesis, Pentose Phosphate Pathway, Glyogen Synthesis and Glycogenolysis, TCA cycle, catabolism, and anabolism.  The discussion section will involve in depth analyses of research articles from the scientific literature on recombinant DNA, inter- and intracellular signal transduction, enzymology, and other current topics in biochemistry. In the discussion section each student will assimilate and give a presentation on a scientific article by some of the leading researchers in Biochemistry.

By the end of the course, the successful student will:

1)    have command of carbohydrate structures and their chemical reactivity

2)    be able to follow and interrelate the major metabolic pathways

3)    know the detailed mechanisms of intermediary metabolic reactions

4)    have qualitative and quantitative understanding of the bioenergetics underlying biochemical reactions

5)    understand the principles and details of metabolic pathway regulation

6)    understand how enzymes catalyze individual metabolic reactions

7)    know cofactors involved in carrying electrons and chemical groups

8)    integrate the concepts of structure, function, and regulation

9)    understand and explain the logic underlying experimental approaches used in the scientific literature

10) be able to critically evaluate interpretations of experimental results in scientific articles

BCMB 276/376: Chemical Biology (Group A BCMB/CHEM, Capstone) (Undergraduate/Graduate course)

An in-depth discussion of tools and techniques of chemical biology and its applications in research, with a focus on cancer research. After discussion of the chemical tools, we shall study current research utilizing these tools to address biological problems. Some techniques that will be covered are chemical and biological library synthesis, library screening methods, quantitative techniques such as Fluorescence polarization, Surface Plasmon Resonance, Isothermal Calorimetry. Biological research problems such as kinase inhibition, modulation of protein protein interactions, targeted protein degradation in live cells and live cell imaging using bio-orthogonal reporters will be discussed.

Students will lead in-class literature discussions, understand and perform the processes of scientific literature critique and peer review and will develop an original research proposal.

To provide sufficient knowledge and understanding of utilizing chemical tools in solving biological problems, with a focus on cancer therapeutics.

By the end of the course, the successful student will:

1.    have an understanding of chemical and biological libraries.

2.    have an understanding of various methods of library screening such as Fragment based Drug Designs.

3. Be able to identify and describe various tools and assays for quantitative measurements such as Fluorescence polarization, Surface Plasmon Resonance, Isothermal Calorimetry.

4. Be able to identify and describe various qualitative assays such as ELISA and immunoprecipitation.

5. Understand how perturbation of cell signaling networks leads to cancer and describe important problems in cancer therapy.

6. understand and explain the logic underlying experimental approaches used in the scientific literature.

7. be able to critically evaluate interpretations of experimental results in scientific articles.

8. have an understanding and appreciation of the peer review process including writing, editing, and providing constructive criticism on others’ work.

Research Methods Instrumentation: Performing Fluorecence Polarization assays to measure binding of ligand to protein using Spectramax M5 Multimode Plate Reader

In this course, you will get acquainted with a gold standard instrument used in a majority of industrial and academic laboratories, the Spectramax M5 plate reader. This instrument can do measurements of luminescence, time-resolved fluorescence, fluorescence polarization, and Homogeneous Time Resolved Fluorescence, in addition to measuring standard absorbance. You will learn to operate the instrument and learn to use the software of the system. You will learn to use measure kinase activity using bioluminescence as a readout on the SpectraMax M5, and do an assay to measure the effect of an inhibitor on the kinase activity. This instrumentation course is recommended for graduate students, and for seniors and juniors who plan to work in an industrial biotech laboratory setting or pursue higher studies. 

By the end of the course, the student should be able to

1)    Develop an understanding of quantitative binding assays like fluorescence polarization.

2)    Be able to operate Spectramax M5 plate reader and use Softmax Pro software.

3)    Be able to design fluorescence polarization experiments.

4)    Be able to calculate reagent concentrations etc and make the reagents for  fluorescence polarization experiments.

5)    Be able to run binding experiments using fluorescence as readout and analyze the result of the experiment.

Fall 2018-2019

BCMB 271 -Biochemistry 1

A comprehensive survey of biochemistry and molecular biology including protein structure, enzyme kinetics, membrane structure, DNA structure, replication, transcription and translation. The laboratory introduces basic techniques including buffer preparation, protein isolation and identification, purification of enzymes, enzyme kinetics, gel electrophoresis, column chromatography and DNA isolation and characterization.


Spring 2017-2018

BCMB 276/376: Chemical Biology – techniques and applications in research

An in-depth discussion of tools and techniques of chemical biology and its applications in research, with a focus on cancer research. After discussion of the chemical tools, we shall study current research utilizing these tools to address biological problems. Some techniques that will be covered are chemical and biological library synthesis, library screening methods, quantitative techniques such as Fluorescence polarization, Surface Plasmon Resonance, Isothermal Calorimetry. Biological research problems such as kinase inhibition, modulation of protein protein interactions, targeted protein degradation in live cells and live cell imaging using bio-orthogonal reporters will be discussed.

Research Methods: Instrumentation: High Performance Liquid Chromatography

In this course, we shall learn the principles behind High Performance Liquid Chromatography (HPLC), learn to operate a High Performance Liquid Chromatography system, do sample separation using High Performance Liquid Chromatography, and analyze the results.

By the end of the course, the student will:

1)    Have an understanding of the theory behind High Performance Liquid Chromatography.

2)    Be able to operate Agilent HPLC system and use Agilent HPLC software

3)    Be able to  develop a  gradient for separation of peptide samples and make a customized method in the HPLC software.

4)    Be able to run peptide sample on the HPLC and analyze the result of the run.

5)    Be able to compare their run to other provided HPLC runs and be able to interpret the nature of their sample.