Chemistry & Biochemistry

Undergraduate Courses

BB 4170. Experimental Genetic Engineering

Cat I (offered at least 1x per Year).
This laboratory course focuses on modern DNA technologies and general applications of gene manipulation. Topics include gene amplification and recombination, promoter and plasmid engineering, gene expression and analysis, model systems, CRISPR, genomics and transgenics. Experiments in this course are integrated into an overall genetic engineering project throughout the term that will involve techniques such as electrophoresis, quantitative spectro-fluorimetry, and real-time quantitative PCR. Methods of data analysis, common statistical approaches and technical writing will be emphasized throughout the course.

BB 4190. Regulation of Gene Expression

Cat I (offered at least 1x per Year).
Through lectures, problem sets, reading and discussion, and presentations this course will help elucidate for students the processes that allow regulated gene expression, mechanisms used in each type of regulation, and methods and techniques used for investigation of regulatory mechanisms. Readings from the current original research literature will explore the growing use of model systems and omics level approaches to enhance our ever expanding understanding of the gene regulatory mechanisms. The development of cell-based therapeutics and genetic engineering as they relate to gene regulation will be introduced.

CH 1010. Chemical Properties, Bonding, and Forces

Cat I (offered at least 1x per Year).
The CH 1010 course is an introduction to chemistry using the fundamental structures of atoms as a starting point. Emphasis is placed on discussing how all properties of matter as well as bonding mechanisms arise from atomic structure. Lewis structures and molecular orbitals are used to understand bonding, and the intermolecular forces present in chemicals systems are used as a prelude to reactivity patterns covered in future courses.

CH 1020. Chemical Reactions

Cat I (offered at least 1x per Year).
Bonding theories introduced earlier in the sequence are applied to chemical reactions, including reduction/oxidation reactions, to demonstrate patterns in reactivity. Solution thermodynamics, concentration scales, and colligative properties are discussed in the context of balanced chemical reactions both in aqueous solution and in the gas phase.

CH 1030. Kinetics, Equilibrium and Thermodynamics

Cat I (offered at least 1x per Year).
This course will examine the dynamic nature of solutions at the molecular level, and will develop an understanding of the mathematical aspects of molecular dynamics and equilibrium. Reaction kinetics will be outlined in detail leading into exploration of various fundamentals and examples of equilibrium processes in the gas phase as well as in solution, including acid-base chemistry and precipitation. Principles of thermodynamics will be introduced (entropy, free energy), and relationships with equilibrium will be explored. Case studies in current topics will be emphasized throughout the course.

CH 1040. Spectroscopy in Organic and Polymer Chemistry

Cat I (offered at least 1x per Year).
We will examine the nature of molecular motions and their interaction with electromagnetic radiation, which provides us with all of our structural information about molecules. In addition, students will be introduced to the fundamentals of mass spectrometry and electrochemistry. The concepts of these techniques will be discussed in the context of structural organic chemistry and polymer characterization

CH 2310. Organic Chemistry I

Cat I (offered at least 1x per Year).
A systematic survey of the major reaction types and functional groups in organic chemistry. The course will provide a representative collection of characteristic reactions and transformations of a variety of types of organic molecules. Most of the examples will be drawn from aliphatic chemistry. Some theoretical models will be introduced with a view toward establishing a general overview of the material. The course is intended for chemists, chemical engineers, pre-medical students and all those interested in the biosciences. A familiarity with the material presented in the general chemistry courses is assumed.

CH 2320. Organic Chemistry II

Cat I (offered at least 1x per Year).
Modern theories of aromaticity, including a general assessment of delocalized bonding. The chemistry of some significant functional groups not surveyed in Organic Chemistry I, and the meaning of acidity and basicity in organic chemistry, will be more fully explored. The course will provide an introduction to the systematic synthesis of polyfunctional organic compounds.

CH 2330. Organic Chemistry III

Cat I (offered at least 1x per Year).
This course fully explores three most important analytical methods in organic chemistry: infrared spectroscopy, mass spectrometry, and nuclear magnetic resonance spectroscopy. It will continue the coverage of aromatic chemistry. New topics to be introduced include structures, properties, and reactivities of aldehydes and ketones, carboxylic acids and their derivatives, amines, and the interaction among polyfunctional compounds. It reinforces the retrosynthetic analysis and multistep synthesis of organic compounds and revisits reaction mechanisms and stereochemistry of all the new functional groups studied.

CH 2360. Organic Laboratory

Cat I (offered at least 1x per Year).
Laboratory experience in standard methods for the preparation and purification of organic compounds. The course will provide sufficient training in laboratory technique so that no previous laboratory experience beyond that of general chemistry is required. This course may be taken concurrently or following lecture courses in organic chemistry. Recommended for pre-medical students and students majoring in disciplines outside of chemistry and biochemistry that desire laboratory experience in basic methods of organic synthesis.

CH 2640. Experimental Chemistry I: Instrumental Analysis

Cat I (offered at least 1x per Year).
This laboratory course focuses on the application of modern instrumental methods of analysis to chemical, biochemical and environmental problems. Practical experience is gained in quantitative electrochemistry, ultraviolet-visible spectrophotometry, fluorometry and bioluminescence, high performance liquid chromatography, and capillary electrophoresis. Principles of experimental design and execution are developed as student teams select a chemical, biochemical or environmental problem, formulate an approach, conduct the analysis, and present findings to the class. Methods of data analysis and common statistical approaches are emphasized throughout the course.

CH 2650. Modern Physical Chemistry Methods

Cat I (offered at least 1x per Year).
This laboratory course emphasizes principles, techniques, and instrumentation employed in modern physical chemistry with a view towards applications throughout the molecular sciences. Investigations include chemical thermodynamics and phase equilibria; gas-phase, solution-phase, and interfacial reaction kinetics and dynamics; and molecular modeling of small molecules. Emphasis includes data collection, interpretation, error analysis, and write-up.

CH 2660. Organic Synthesis and Analysis Laboratory

Cat I (offered at least 1x per Year).
The emphasis in CH 2660 is on fundamental techniques essential for the synthesis, purification, and characterization of organic compounds. These techniques include setting up, running and monitoring reactions, isolation and purification by solvent extraction, crystallization, distillation, and chromatographic techniques, followed by determination of physical properties and characterization by infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy Micro-synthetic methods and multi-step synthesis are introduced. This course differs from CH 2360 by providing in-depth experience with spectroscopic characterization of molecular structure and hands-on training operating core instruments in addition to methods of organic synthesis. This course is required for students majoring in chemistry, and is recommended for students majoring in biochemistry and disciplines outside of chemistry that desire a strong background in methods of organic synthesis and characterization.

CH 2670. Investigation of Coordination Complexes Through Inquiry

Cat I (offered at least 1x per Year).
The synthesis, isolation, and characterization of inorganic compounds are emphasized. Syntheses of main group compounds, classical transition metal complexes, and organotransition metal compounds are included. In addition to reinforcing and building on standard techniques of synthesis and characterization, several new techniques are introduced: synthesis under inert atmosphere, measurement of magnetic susceptibility by NMR, and cyclic voltammetry. Some exposure to 13C NMR is also provided. The final experiment of the course requires the student to design a synthesis for a compound selected from a list provided, based on strategies learned in the course.

CH 3310. Advanced Organic Chemistry

Cat II (offered at least every other Year).
This course will review and further develop concepts introduced in CH 2310, CH 2320, and CH 2330. These concepts will include oxidation states of organic compounds, acidity and basicity, and stereochemistry and conformational analysis. Chemical reactivity will be emphasized and will include functional group interconversion and ionic and free radical carbon-carbon bond formation. This course will be offered in 2022-23, and in alternating years thereafter.

CH 3410. Structure, Bonding, and Reactivity in Inorganic Chemistry

Cat I (offered at least 1x per Year).
This course provides the fundamental understanding of atomic, molecular and solid state structures and properties. Orbital structures of atoms, symmetry of molecules and point groups are used to understand chemical bonding and reactions. Various acid-base concepts are explored to analyze the acidity of cations and basicity of anions, solubility and precipitations of inorganic compounds, and metal-ligand binding affinities. Redox properties are discussed using Pourbaix diagrams. Thermodynamic stabilities of inorganic species are discussed using acid-base and redox concepts and thermochemical analyses are used to analyze chemical reactivity at atomic, molecular, and solid state level.

CH 3510. Chemical Thermodynamics

Cat I (offered at least 1x per Year).
The content of this course will be the development of the principles of classical thermodynamics. The laws of thermodynamics will be developed by using a series of increasingly complex model systems and a universal equation of state is formulated which incorporates the relationships illustrated by these model systems. Using this equation it will be possible to appreciate that thermodynamic laws are applicable to all systems of matter, regardless of their complexity. Finally, the principles developed are applied to problems of a chemical nature, focusing on predicting the spontaneity of chemical reactions. The material in this course will be of greatest interest to those students enrolled in the basic sciences including biology, chemistry, and physics, and in applied fields such as chemical engineering, materials science and biotechnology.


In this course, selected mathematical methods (such as group theory, Fourier transform, and integration techniques) are used to solve problems in chemistry and biochemistry. The emphasis is not on complete coverage of any specific traditional teaching subject, but rather on the ways each technique can be applied in more than one direction. The main focus is placed on problems relevant in such generally important areas as kinetics and spectroscopy.

Recommended background: Chemical Thermodynamics and Calculus I – IV or equivalent courses.

CH 3530. Quantum Chemistry

Cat I (offered at least 1x per Year).
An introduction to quantum mechanics with applications to atomic and molecular species. The course will be developed systematically beginning with the postulates of quantum mechanics. The Schroedinger equation will be applied to systems such as the particle in a box, the rigid rotor, the harmonic oscillator and the hydrogen atom. Emphasis will be given to a quantum mechanical description of multielectron atoms, molecular bonding and spectroscopy. This course is normally for students in their third year.

CH 3550. Chemical Dynamics

Cat I (offered at least 1x per Year).
This course deals in a general way with the interactions between energy and molecules, and considers how energetic and structural considerations affect the outcome of molecular interactions. The manipulation of kinetic data and results is stressed. Selected topics from both organic and inorganic chemistry are analyzed in terms of reaction thermodynamics, rates and mechanisms. Students are expected to be familiar with thermodynamics, equilibria, reaction rates and the Periodic Table of the elements.

CH 4110. Protein Structure and Function

Cat I (offered at least 1x per Year).
The fundamental concepts of protein architecture and dynamics are presented with an emphasis on the functional outcomes of chemistry coordinated in three dimensional space. Catalytic mechanics and enzyme function are outlined in detail. Current methods in the determination of enzyme structure and function will be discussed, and students will use common tools in macromolecular analysis and structural modeling. Case studies in enzyme dysfunction, disease, and current research will be used throughout the course.The following three courses, CH 4110, CH 4120, and CH 4130, are a three-term sequence intended to provide a strong emphasis in biochemistry.

CH 4120. Lipids and Biomembrane Functions

Cat I (offered at least 1x per Year).
Oriented around biological membranes, this course begins with a description of lipids and proteins forming biomembranes. Permeability and the mechanism of transmembrane mass transport are presented. Transport of electrons and redox equivalents is explained within the context of aerobic production of ATP and plant photosynthesis. Finally the transport of information across biomembranes in signal transduction and neurotransmission are discussed.The following three courses, CH 4110, CH 4120, and CH 4130, are a three-term sequence intended to provide a strong emphasis in biochemistry.

CH 4130. Nucleic Acids and Bioinformation

Cat I (offered at least 1x per Year).
This course presents the structure and function of DNA. Precursors and biomolecules that give rise to DNA, the mechanism of DNA replication, RNA synthesis, and protein synthesis are described in detail. In addition to mechanistic studies, regulation of these processes is covered as well as those of genetic mutation, DNA repair, and epigenetics.The following three courses, CH 4110, CH 4120, and CH 4130, are a three-term sequence intended to provide a strong emphasis in biochemistry.

CH 4150. Enzymology and Protein Characterization Laboratory

Cat I (offered at least 1x per Year).
The experiments in this laboratory course have been designed to acquaint the students with the basic skills necessary to perform biochemical studies. The course will cover, for instance, protein purification, subcellular fractionation, enzyme kinetics (Km, Vmax, specific activity, effector-protein interaction, etc.), exclusion and ion exchange chromatography, and electrophoresis.


This course has been designed to familiarize students with the theoretical and practical aspects of advanced biophotonic techniques, including FRET, fluorescence lifetime and fluorescence anisotropy measurements. In the synthetic part of the lab course, students will learn to link molecular structures with fluorescent properties. Cell based experiments will be used to study labeling of subcellular compartments using fluorescent probe molecules.
Recommended background: experimental organic chemistry (CH2360 or CH2660) instrumental analysis (CH2640), and biochemistry (CH4110).

CH 4160. Membrane Biophysics

Cat II (offered at least every other Year).
This course will focus on different areas of biophysics with special emphasis on membrane phenomena. The biomedical-biological importance of biophysical phenomena will be stressed. The course will begin with the introduction of the molecular forces relevant in biological media and subsequently develop the following topics: Membrane Structure and Function; Channels, Carriers and Pumps; Nerve Excitation and related topics; and Molecular Biophysics of Motility. This course will be offered in 2021-22, and in alternating years thereafter.

CH 4420. Principles and Applications of Group Theory in Chemistry

Cat I (offered at least 1x per Year).
The principles and applications of group theory as a tool in chemistry are presented with an emphasis on systems in inorganic chemistry. Topics covered include the development of symmetry group representations and character tables, applications of group theory in quantum-mechanical wavefunctions, molecular vibrations, ligand field theory, and molecular orbital theory. Particular emphasis will be placed on transition metal complexes, including classical coordination complexes, metal carbonyl complexes, and organotransition metal complexes.

CH 538. Medicinal Chemistry

This course will focus on the medicinal chemistry aspects of drug discovery from an industrial pharmaceutical Research and Development perspective. Topics will include Chemotherapeutic Agents (such as antibacterial, antiviral and antitumor agents) and Pharmacodynamic Agents (such as antihypertensive, antiallergic, antiulcer and CNS agents).For details about this Graduate Course, Click Here.

CHE 554. Molecular Modeling

This course trains students in the area of molecular modeling using a variety of quantum mechanical and force field methods. The approach will be toward practical applications, for researchers who want to answer specific questions about molecular geometry, transition states, reaction paths and photoexcited states. No experience in programming is necessary; however, a background at the introductory level in quantum mechanics is highly desirable. Methods to be explored include density functional theory, ab initio methods, semiempirical molecular orbital theory, and visualization software for the graphical display of molecules.

Graduate Courses

CH 4110. Biochemistry I

The principles of protean structure are presented. Mechanisms of enzymatic catalysis, including those requiring coenzymes, are outlined in detail. The structures and biochemical properties of carbohydrates are reviewed. Bioenergetics, the role of ATP, and its production through glycolysis and the TCA cycle are fully considered.

CH 4120. Biochemistry II

Oriented around biological membranes, this term begins with a discussion of electron transport and the aerobic production of ATP, followed by a study of photosynthesis. The study of the biosynthesis of lipids and steroids leads to a discussion of the structure and function of biological membranes. Finally, the membrane processes in neurotransmission are discussed.

CH 4130. Biochemistry III

This course presents a thorough analysis of the biosynthesis of DNA (replication), RNA (transcription) and proteins (translation), and of their biochemical precursors. Proteins and RNAs have distinct lifetimes within the living cell; thus the destruction of these molecules is an important biochemical process that is also discussed. In addition to mechanistic studies, regulation of these processes is covered.

CH 4140. Metabolism and Disease

Cat I.
This course presents a thorough analysis of the most relevant metabolic processes in cells. The catabolism of sugars and lipids will be presented in the context of energy generation and storage. Nucleotide and amino acid metabolism will discussed as building blocks for large biomolecules. Throughout the course the links between metabolism, hereditary pathologies, as well as risk of metabolic imbalances such as diabetes and obesity will be presented.Specific concepts that we will discuss are: Glucose and glycogen metabolism; Gluconeogenesis; Citric Acid Cycle; Lipid, amino acid and nucleotide metabolisms; Mammalian Fuel Metabolism: Integration and Regulation.

CH 4330. Organic Synthesis

Modern synthetic methods as applied to the construction of societally relevant target molecules will be the focus of this course. Discussions may emphasize the logic and strategy in synthetic approaches toward active pharmaceutical ingredients, agrochemicals, fine chemicals, materials, and other targets of interest. The analysis of current examples from the primary literature will draw attention to the most state-of-the-art synthetic tactics. Recommended for graduate students and undergraduates who have a basic understanding of the principles governing organic reactions, such as those covered in CH2310, CH2320, and CH2330.

CH 4420. Inorganic Chemistry II

Complexes of the transition metals are discussed. Covered are the electronic structures of transition metal atoms and ions, and the topological and electronic structures of their complexes. Symmetry concepts are developed early in the course and used throughout to simplify treatments of electronic structure. The molecular orbital approach to bonding is emphasized. The pivotal area of organotransition metal chemistry is introduced, with focus on complexes of carbon monoxide, metal-metal interactions in clusters, and catalysis by metal complexes.

CH 4520. Chemical Statistical Mechanics

This course deals with how the electronic, translational, rotational and vibrational energy levels of individual molecules, or of macromolecular systems are statistically related to the energy, entropy and free energy of macroscopic systems, taking into account the quantum mechanical properties of the component particles. Ensembles, partition functions, and Boltzmann, Fermi/Dirac and Bose-Einstein statistics are used. A wealth of physical chemical phenomena, including material related to solids, liquids, gases, spectroscopy and chemical reactions are made understandable by the concepts learned in this course.

CH 516. Chemical Spectroscopy

The emphasis is on using a variety of spectroscopic data to arrive at molecular structures, particularly of organic molecules. Major emphasis is on inland C-NMR, IR and MS. There is relatively little emphasis on theory or on sampling handling techniques.

CH 520. Cell Signaling

Cell signaling defines the way cells respond to changes in their environment including, heat, nutrients, drugs, hormones, and other factors. These external factors allow cells to grow, divide, migrate and proliferate depending on the stimulus, and inappropriate responses lead to cancer and other diseases. This course is directed for advanced undergraduates and graduate level course that is a combination of on-line lectures, discussions, and review of recent literature. Students who previously took the CH 555 version of this course cannot take CH 520 for credit.

CH 536. Theory and Applications of NMR Spectroscopy

This course emphasizes the fundamental aspects of 1D and 2D nuclear magnetic resonance spectroscopy (NMR). The theory of pulsed Fourier transform NMR is presented through the use of vector diagrams. A conceptual nonmathematical approach is employed in discussion of NMR theory. The course is geared toward an audience which seeks an understanding of NMR theory and an appreciation of the practical applications of NMR in chemical analysis. Students are exposed to hands-on NMR operation. Detailed instructions are provided and each student is expected to carry out his or her own NMR experiments.

CH 540. Regulation of Gene Expression

This course covers the biochemical mechanisms involved in regulation of gene expression: modifications of DNA structures that influence transcription rates, transcriptional regulation, post-transcriptional processing of RNA including splicing and editing, nuclear/cytoplasmic transport, regulation of translation, and factors that control the half-lives of both mRNA and protein. During the course, common experimental methods are explored, including a discussion of the information available from each method.

CH 541. Membrane Biophysics

This course will focus on different areas of biophysics with special emphasis on membrane phenomena. The biomedical-biological importance of biophysical phenomena will be stressed. The course will begin with an introduction to the molecular forces relevant in biological media and subsequently develop the following topics: membrane structure and function; channels, carriers and pumps; nerve excitation and related topics; and molecular biophysics of motility. Topics will be developed assuming a good understanding of protein and lipid chemistry, enzyme kinetics, cell biology, and electricity.

CH 542. Drugs in the Brain

This class will introduce the concepts of basic neuropharmacology and the action of major neurotransmitter families in the brain. The mechanisms of action of the major psychoactive drugs families including cannabis, opioids, and psychedelics will be covered. The effects of pharmaceutical treatments for anxiety and depression on brain chemistry will be discussed as well.

CH 543. Organometallic Chemistry and Catalysis

Organometallic chemistry and catalytic reactions have fundamentally changed the way drugs and polymeric materials are made today. Furthermore, they have enabled the synthesis and application of new electronic materials (e.g. in OLEDs and molecular wires) and materials mimicking natural processes (e.g. self-healing and anti-bacterial coatings). This course will establish principles to understand the reactivity of organometallic compounds of transition and main groups metals. Furthermore, metal-free catalysis will be introduced. Pulling on influences from both inorganic and organic chemistry, the class will provide insight into catalysis approaches that have revolutionized synthetic chemistry, enabling highly efficient, sustainable production of compounds that are used in such different areas as drug discovery, protein analysis, and performance plastics. Case studies will be drawn from the current literature and applications that are widely used in industrial and academic settings and will include work that has led to recent Nobel prizes in the area. Recommended preparation includes the organic chemistry sequence (CH2310, CH2320, and CH2330) and CH3410. The course is recommended for both graduate and advanced undergraduate students.

CH 544. Elucidation of Organic Reaction Mechanisms

In this advanced course, students will develop skill sets to independently understand, explain, and predict reactions of organic molecules. Principles of modern physical organic chemistry, such as bonding, hybridization, molecular orbital theory, non-covalent interactions, stereochemistry, and conformational analysis, will be introduced alongside experimental techniques related to thermodynamics and kinetics to provide scientists with tools to understand existing reaction pathways and study new reactions. The interplay between mechanistic hypotheses and experimental observations will be demonstrated using case studies from the primary literature. Recommended for graduate students and undergraduates who have completed the sequence in organic chemistry (CH2310, CH2320, and CH2330).

CH 545. Plant Natural Products

This class will cover the chemistry of a number of families of plant-derived natural products, including, terpenoids, phenolic compounds, and alkaloids. The coverage of aspects of the chemistry involving these natural products may include biosynthesis, chemical synthesis, and medicinal chemistry applications. The historical and current roles of select natural products, such as tetrahydrocannabinol, taxol, heroin, and quinine, in society may also be discussed. This class will be offered in 2020-2021 and alternating years thereafter.

CH 546. Natural Product Isolation and Analysis

In this laboratory class, students will learn strategies to isolate and characterize natural products. Techniques used during this course may include solvent extraction, supercritical fluid extraction, NMR spectroscopy, IR spectroscopy, mass spectrometry, gas chromatography, and liquid chromatography. This class will be offered in 2021-2022 and alternating years thereafter.

CH 554. Molecular Modeling

This course trains students in the area of molecular modeling using a variety of quantum mechanical and force field methods. The approach will be toward practical applications, for researchers who want to answer specific questions about molecular geometry, transition states, reaction paths and photoexcited states. No experience in programming is necessary; however, a background at the introductory level in quantum mechanics is highly desirable. Methods to be explored include density functional theory, ab initio methods, semiempirical molecular orbital theory, and visualization software for the graphical display of molecules.

CH 555. Advanced Topics

A course of advanced study in selected areas whose content and format varies to suit the interest and needs of faculty and students. This course may be repeated for different topics covered.This course is 1-3 credits as arranged.

CH 560. Current Topics in Biochemistry

In this seminar course, a different topic is selected each semester. Current articles are read and analyzed.

CH 561. Functional Genomics

In this seminar course, students will present and critically analyze selected, recent publications in functional genomics. The course will conclude with a written project, either a mini-grant proposal or an analysis of publicly available data in a research manuscript format. The course will be offered in alternate years, and is offered by special arrangement only based on expressed student interest.

CH 571. Seminar

Reports on current advances in the various branches of chemistry.

CH 598. Directed Research

CH 599. M.S. Thesis

CH 699. Ph.D. Dissertation