Molecular Systems Biology
Course Objectives: This
four-credit course will present a quantitative description of the
molecular networks that underlie the myriad phenotypes of living cells,
from yeast to human. Topics covered include various high-throughput
genomics technologies (genome sequencing, DNA microarrays, proteomics),
quantitative modeling of transcriptional and post-transcriptional
regulatory networks, synthetic biology, and the world of RNA structure,
dynamics, and function. Lectures on these topics will be integrated
with introductory lectures on molecular and structural biology,
thermodynamics, statistics, and machine learning. The course is
intended for advanced undergraduates as well as beginning graduate
students in Biology, Chemistry, Physics, Engineering, and Computer
Science. Taught by research scientists active in various of systems
biology, the course is highly interdisciplinary and rooted in recent
research, with a soft focus on cancer. [syllabus]
Biochemistry I: Structures and Metabolism (C3501/W4501)
Course Objectives: In this course, we will cover subject matter in biochemistry, organic chemistry and structural biology. We will discuss the structure and function of both proteins and small molecules in biological systems. Proteins are the primary class of biological macromolecules and serve to carry out most cellular functions. Small organic molecules function in energy production and creating building blocks for the components of cells and can also be used to perturb the functions of proteins directly.
The first half of the course will cover protein structure and enzyme kinetics. The second half of the course will explore how small molecules are used endogenously by living systems in metabolic and catabolic pathways; this course will focus on the mechanistic organic chemistry involved in metabolic pathways. The course is intended to provide a foundation of structural biology, bio-organic chemistry and biochemistry and to expose students to some emerging areas of research. [syllabus]
Biotechnology (BIOL W4034x)
Prerequisites: genetics or molecular biology.
The course covers techniques currently used to explore and manipulate gene function and their applications in medicine and the environment. Part I covers key laboratory manipulations, including DNA cloning, gene characterization, association of genes with disease, and methods for studying gene regulation and activities of gene products. Part II covers commercial application, including animal cell culture, production of recombinant proteins, novel diagnostics, high throughput screening, and environmental biosensors. [syllabus]
Introduction to Biophyiscal Modeling (E4400)
Chemical Biology (W4312)
Course Objectives: In this course, we will cover subject matter in chemical biology. We will discuss approaches for discovering and optimizing chemical tools for measuring and perturbing biological systems. Topics covered will include high-throughput assay development, screening, chemical library creation, high-throughput chemistry, affinity purification of target proteins and target validation, protein microarrays, molecular evolution, protein engineering and synthetic biology.
The course is intended to provide a foundation needed for advanced chemical biology research, i.e. the creation and use of chemical probes of biological processes and macromolecular function. The course will be of interest to students at the interface between chemistry and biology, and students interested in medicine, academic chemical biology and drug discovery efforts.
Signal Transduction (G4600)
This course contains mainly molecular biology, biochemistry & genetic content, is based on reading research articles and requires writing a research proposal.
Biophysical Chemistry (G4170)
Course Objectives: This four and a half-credit course will present an introduction to the Biophysical Chemistry and Structural Biology of proteins and nucleic acids. Topics covered include introductions to biomolecular structure, physico-chemical tools used to probe biomolecular structure and dynamics, intermolecular forces that govern these structures and dynamics, and experimental and computational approaches for studies of biomolecular folding and function. The course includes a series of biophysical research-related topics including practical introductions to the software tools available for the visualization and modeling of biomolecular structures and the bioinformatic analysis of biomolecular sequence and structural homology.
Seminar in Epigenetics (G4035)
Course description: This is a combined lecture/seminar course designed for advanced undergraduates and graduate students. The focus is on understanding the mechanisms underlying epigenetic phenomena: the heritable inheritance of genetic states without change in DNA sequence. Epigenetic mechanisms play important roles during normal animal development and oncogenesis. It is an area under intensive scientific investigation and the course will focus on recent advances in understanding these phenomena. In each class, students will present and discuss in detail recent papers and background material concerning each individual topic, followed by an introductory lecture on the following week's topic. This course will emphasize critical analysis of the scientific literature and help students understand how to identify important biological problems and how to address them experimentally.
Protein Engineering (CHEN E4800)
Prerequisites: CHEN E4230, may be taken concurrently, or the instructor's permission.
Course description: Fundamental tools and techniques currently used to engineer protein molecules. Methods used to analyze the impact of these alterations on different protein functions with specific emphasis on enzymatic catalysis. Case studies reinforce concepts covered, and demonstrate the wide impact of protein engineering research. Application of basic concepts in the chemical engineering curriculum (reaction kinetics, mathematical modeling, thermodynamics) to specific approaches utilized in protein engineering.