Chemistry
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Amherst College Chemistry for 2013-14

100 Molecular Gastronomy and Food Science: from Test Tubes to Taste Buds

Living organisms require resources to fuel the processes necessary for staying alive. We require a certain number of calories to fuel metabolic processes and to provide building blocks to replace old cells and build new ones.  Our food should provide a balance of proteins, carbohydrates, fats, vitamins and minerals that we need to consume regularly for a healthy existence. Yet humans have developed another relationship with food that can be either enriching or pathological.  Sharing meals with others, developing the skills to enjoy the sensory pleasures of food, learning about other cultures through their gastronomic habits, and eating moderately while consciously are all examples of a deeper productive relationship with food.  On the darker side, food can be a palliative to relieve our stress or satiate our addictions to sugar, fats, or salt.  Modern humans can be so far removed from our food sources that we lose the connection between animal and meat and do not know if the food on our plates contains added hormones, pesticides, or genetically modified products. This course will examine our core requirements for food as we eat to live, and some of the cultural, social, historical, and culinary dimensions as we live to eat.  Readings will include Barbara Kingsolver’s Animal, Vegetable, Miracle, Michael Pollan’s The Omnivore’s Dilemma, and selections from Modernist Cuisine: The Art and Science of Cooking by Nathan Myhrvold, Chris Young and Maxime Billet.

The two sections will meet together for 80-minute lecture/demos twice a week and each section will meet separately for a culinary lab every other week for two hours.  

Limited to 30 students. Spring semester.  Professor O'Hara.

2013-14: Offered in Spring 2014

131 Chemical Basis of Biological Processes

(Offered as CHEM 131 and BIOL 131.) What are the natural laws that describe how biological processes actually work?  This course will use examples from biology such as human physiology or cellular signaling to illustrate the interplay between fundamental chemical principles and biological function.  We will explore how bonding plays a central role in assembling simple biological building blocks such as sugars, amino acids, and fatty acids to form complex carbohydrates, proteins, and membranes.  What underlying thermodynamic and kinetic principles guide systems to biological homeostasis or reactivity?  What is pH, and how are proton gradients used to generate or change an organism's response?  Emphasis is on using mathematics and physical sciences to understand biological functions. Three classroom hours and three hours of laboratory per week.

Enrollment is limited to 15 first-year students who are interested in science or premedical study, who are recommended to begin with either MATH 105 or MATH 111 (Intensive), and who are enrolled in a Mathematics course but not in CHEM 151.  Admission with consent of the instructor.  Fall semester.  Visiting Lecturer Hebda.

2013-14: Offered in Fall 2013
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012

151 Introductory Chemistry

This course examines the structure of matter from both a microscopic and macroscopic viewpoint. We begin with a detailed discussion of the physical structure of atoms, followed by an analysis of how the interactions between atoms lead to the formation of molecules. The relationship between the structures of molecular compounds and their properties is then described. Experiments in the laboratory provide experience in conducting quantitative chemical measurements and illustrate principles discussed in the lectures.

Although this course has no prerequisites, students with a limited background in secondary school science should confer with one of the CHEM 151 instructors before registration. Each laboratory section is limited to 24 students.  In the fall, sufficient sections will be added to meet total enrollment.  The spring semester is limited to two laboratory sections.  Four class hours and three hours of laboratory per week.

Fall semester: Professors Burkett and Kushick. Spring semester: Professor Jaswal.

2013-14: Offered in Fall 2013 and Spring 2014
Other years: Offered in Fall 2007, Spring 2008, Fall 2008, Spring 2009, Fall 2009, Spring 2010, Fall 2010, Spring 2011, Fall 2011, Spring 2012, Fall 2012, Spring 2013, Fall 2014, Spring 2015

155 Fundamental Principles of Chemistry

A study of the basic concepts of chemistry for students particularly interested in natural science. Topics to be covered include atomic and molecular structure, spectroscopy, states of matter, and stoichiometry. These physical principles are applied to a variety of inorganic, organic, and biochemical systems. Both individual and bulk properties of atoms and molecules are considered with an emphasis on the conceptual foundations and the quantitative chemical relationships which form the basis of chemical science. This course is designed to utilize the background of those students with strong preparation in secondary school chemistry and to provide both breadth in subject matter and depth in coverage. Four hours of lecture and discussion and three hours of laboratory per week.

Limited to 40 students. Fall semester. Professor Marshall.

2013-14: Offered in Fall 2013
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2014

161 Chemical Principles

The concepts of thermodynamic equilibrium and kinetic stability are studied. Beginning with the laws of thermodynamics, we will develop a quantitative understanding of the factors which determine the extent to which chemical reactions can occur before reaching equilibrium. Chemical kinetics is the study of the factors, such as temperature, concentrations, and catalysts, which determine the speeds at which chemical reactions occur. Appropriate laboratory experiments supplement the lecture material. Each laboratory section is limited to 24 students.  In the spring, sufficient sections will be added to meet total enrollment.  The fall semester is limited to two laboratory sections.  Four class hours and three hours of laboratory work per week.

Requisite: CHEM 151 or 155 (this requirement may be waived for exceptionally well-prepared students; consent of the instructor is required); and MATH 111 or placement by the Mathematics department into MATH 121 or higher.  Fall semester: Professor Young. Spring semester: Professors Leung. 

2013-14: Offered in Fall 2013 and Spring 2014
Other years: Offered in Fall 2007, Spring 2008, Fall 2008, Spring 2009, Fall 2009, Spring 2010, Fall 2010, Spring 2011, Fall 2011, Spring 2012, Fall 2012, Spring 2013, Fall 2014, Spring 2015

191 Bridging Macroscopic and Molecular: Experimental Design for Teaching and Learning in Chemistry

There is a tremendous gap between the length scale of the molecular world and the macroscopic dimensions of our experience, but macroscopic observation and physical manipulations nonetheless lie at the heart of the experiments that gave rise to atomic theory and modern chemistry. Although sophisticated instrumentation has been developed to “image” atoms and molecules, macroscopic observation through laboratory experimentation remains an essential component of teaching and learning chemistry at the elementary school, secondary school, and undergraduate level. This course focuses on the question of what makes an experiment effective as a tool for understanding chemistry. Types of laboratory experiments to be discussed include expository, discovery, guided inquiry, and problem-based (open inquiry). Students will evaluate existing experiments and design original experiments and demonstrations for a variety of audiences, from elementary school students through undergraduates, with emphases on conceptual content, pedagogical style, and safety and environmental considerations. Two 80-minute discussion-based classes and one 3-hour lab per week.

Requisite: CHEM 151 or CHEM 155. Limited to 12 students.  Spring Semester. Associate Professor Burkett.

2013-14: Not offered
Other years: Offered in Spring 2015

221 Organic Chemistry I

A study of the structure of organic compounds and of the influence of structure upon the chemical and physical properties of these substances. The following topics are emphasized: hybridization, resonance theory, spectroscopy, stereochemistry, acid-base properties and nucleophilic substitution reactions. Periodically, examples will be chosen from recent articles in the chemical, biochemical, and biomedical literature. Laboratory work introduces the student to basic laboratory techniques and methods of instrumental analysis. Four hours of class and four hours of laboratory per week.

Requisite: CHEM 161 or equivalent.  Fall semester. Professors Bishop and Collins.

2013-14: Offered in Fall 2013
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2014

231 Organic Chemistry II

A continuation of CHEM 221. The second semester of the organic chemistry course first examines in considerable detail the chemistry of the carbonyl group and some classic methods of organic synthesis. The latter section of the course is devoted to a deeper exploration of a few topics, among which are the following: sugars, amino acids and proteins, advanced synthesis, and acid-base catalysis in nonenzymatic and enzymatic systems. The laboratory experiments illustrate both fundamental synthetic procedures and some elementary mechanistic investigations. Four hours of class and four hours of laboratory per week.

Requisite: CHEM 221.  Spring semester. Professor Ball and Visiting Professor Collins. 

2013-14: Offered in Spring 2014
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2015

290, 290H, 390, 390H, 490, 490H Special Topics

A full course. 

Admission with consent of the instructor. Fall and spring semesters. The Department.

2013-14: Offered in Fall 2013 and Spring 2014
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Spring 2012, Fall 2012, Spring 2013, Fall 2014, Spring 2015

330 Biochemical Principles of Life at the Molecular Level

(Offered as BIOL 330 and CHEM 330) What are the molecular underpinnings of processes central to life?  We will explore the chemical and structural properties of biological molecules and learn the logic used by the cell to build complex structures from a few basic raw materials. Some of these complex structures have evolved to catalyze chemical reactions with enormous degree of selectivity and specificity, and we seek to discover these enzymatic strategies. We will consider the detailed balance sheet that shows how living things harvest energy from their environment to fuel metabolic processes and to reproduce and grow.  Examples of the exquisite control that permits a cell to be responsive and adapt its responses based on input from the environment will be considered.  We will also consider some of the means by which cells respond to change and to stress.  A student may not receive credit for both CHEM 330 and BCBP/BIOL/CHEM 331.

Requisite:  BIOL 191 and CHEM  221.  Limited to 30 students.  Fall semester.  Professor Jaswal.

2013-14: Offered in Fall 2013
Other years: Offered in Fall 2011, Fall 2012, Fall 2014

331 Biochemistry

(Offered as BIOL 331, BCBP 331, and CHEM 331.) Structure and function of biologically important molecules and their role(s) in life processes. Protein conformation, enzymatic mechanisms and selected metabolic pathways will be analyzed. Additional topics may include: nucleic acid conformation, DNA/protein interactions, signal transduction and transport phenomena. Four classroom hours and four hours of laboratory work per week. Offered jointly by the Departments of Biology and Chemistry. A student may not receive credit for both BCBP/BIOL/CHEM 331 and CHEM 330. 

Requisite: CHEM 221 and BIOL 191; or consent of the instructor. CHEM 231 is a co-requisite. Spring semester. Limited to 45 students. Professor Bishop (Chemistry) and Professor Qi (Biology).

2013-14: Offered in Spring 2014
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2015

351 Quantum Chemistry and Spectroscopy

The theory of quantum mechanics is developed and applied to spectroscopic experiments. Topics include the basic principles of quantum mechanics; the structure of atoms, molecules, and solids; and the interpretation of infrared, visible, fluorescence, and NMR spectra.  Appropriate laboratory work will be arranged. Three hours of class and four hours of laboratory per week.

Requisite: CHEM 161, MATH 121, PHYS 116 or 123.  Limited to 24 students. Fall semester. Professor Leung.

2013-14: Offered in Fall 2013
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2014

361 Physical Chemistry

The thermodynamic principles and the concepts of energy, entropy, and equilibrium introduced in CHEM 161 will be expanded. Statistical mechanics, which connects molecular properties to thermodynamics, will be introduced. Typical applications are non-ideal gases, phase transitions, heat engines and perpetual motion, phase equilibria in multicomponent systems, properties of solutions (including those containing electrolytes or macromolecules), and transport across biological membranes. Appropriate laboratory work is provided. Four hours of class and four hours of laboratory per week.

Requisite: CHEM 161, PHYS 116 or 123, and MATH 121. MATH 211 is recommended.  Limited to 24 students. Spring semester.  Professor Marshall.

2013-14: Offered in Spring 2014
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2012, Spring 2013, Spring 2015

371 Inorganic Chemistry

The structure, bonding, and symmetry of transition metal-containing molecules and inorganic solids are discussed. Structure and bonding in transition metal complexes are examined through molecular orbital and ligand field theories, with an emphasis on the magnetic, spectral, and thermodynamic properties of transition metal complexes. Reactions of transition metal complexes, including the unique chemistry of organometallic compounds, will be examined. The laboratory experiments complement lecture material and include a final independent project. Four hours of class and four hours of laboratory per week.

Requisite: CHEM 221 or consent of the instructor. Limited to 24 students. Fall semester.  Professor Ball.

2013-14: Offered in Fall 2013
Other years: Offered in Spring 2009, Fall 2009, Fall 2010, Fall 2011, Spring 2013, Fall 2014

400 Molecular and Cellular Biophysics

(Offered as PHYS 400, BIOL 400, BCBP 400, and CHEM 400.) How do the physical laws that dominate our lives change at the small length and energy scales of individual molecules? What design principles break down at the sub-cellular level and what new chemistry and physics becomes important? We will answer these questions by looking at bio-molecules, cellular substructures, and control mechanisms that work effectively in the microscopic world. How can we understand both the static and dynamic shape of proteins using the laws of thermodynamics and kinetics? How has the basic understanding of the smallest molecular motor in the world, ATP synthase, changed our understanding of friction and torque? We will explore new technologies, such as atomic force and single molecule microscopy that have allowed research into these areas. This course will address topics in each of the three major divisions of Biophysics: bio-molecular structure, biophysical techniques, and biological mechanisms.

Requisite: CHEM 161, PHYS 116/123, PHYS 117/124, BIOL 191 or evidence of equivalent coverage in pre-collegiate courses.  Fall semester. Professors Carter and O'Hara.

2013-14: Offered in Fall 2013
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Spring 2015

408 Seminar in Chemical Biology: The Chemistry/Biology Interface

(Offered as CHEM 408 and BCBP 408.) This advanced seminar will focus on the ways in which chemical approaches have been used to study and engineer biological systems. We will explore a series of case studies in which the tools of chemistry have been brought to bear on biological questions and seek to answer the following: Did the application of small molecules that were designed and synthesized by chemists allow the researchers to elucidate biological phenomena that would have remained opaque using genetic and biochemical approaches? Do the findings suggest further experiments? If so, could follow-up experiments be carried out with known techniques, or would development of further chemical tools be required? Topics will include: the design and synthesis of chemical modulators of gene expression, signal transduction, and protein-protein interactions; chemical approaches to protein engineering and drug-target validation; activity-based proteomics; and chemical tagging of biomolecular targets. Readings will draw heavily from the primary scientific literature. Students will be expected to participate actively in class discussions, to write, and to present their work to the class. This course can be used to fulfill either the elective requirement for the CHEM major or the seminar requirement for the BCBP major. Two eighty-minute classes per week.

Requisite: CHEM 231.  Recommended requisite:  CHEM 330 or 331.  Spring semester.  Professor Bishop. 

2013-14: Offered in Fall 2013 and Spring 2014
Other years: Offered in Fall 2012

420 Medicinal Chemistry and Drug Design

This course will focus on the fundamentals of medicinal chemistry, an organic-chemistry-based discipline that interfaces strongly with the biological and pharmaceutical sciences. Broadly, the field of medicinal chemistry is concerned with the discovery and preparation of biologically active compounds; the study of their metabolism; the interpretation of their mode of action at the molecular level; and the construction of structure-activity relationships. We will center our attention on the science of drug design, with an emphasis on the organic synthesis of viable drug candidates. The structure and function of macromolecular drug “targets” (e.g., receptors, enzymes, nucleic acids), as well as the mechanisms by which drugs interact with their targets, will also be considered. Furthermore, we will take into account the complexity of human physiology as we study the ways in which the physical and chemical properties of a drug candidate can influence its absorption, distribution, and metabolism in a human patient. Readings will be drawn from the primary scientific literature and case studies.  Students will be expected to participate actively in class discussions, to write, and to present their work to the class.

Requisite: CHEM 231. Fall semester.  STINT Fellow Sandström.

2013-14: Offered in Fall 2013

498, 498D, 499, 499D Senior Departmental Honors

A full course.

Open to Senior Honors candidates, and others with consent of the Department. Fall semester. The Department.

2013-14: Offered in Fall 2013
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2014
 

Merrill Hall