Chemistry & Biochemistry

Todd Smith

The fundamental goal of the chemistry program at Marlboro is to teach students a powerful way of thinking about the natural world. Atomic structure accounts for atomic properties, as well as the periodic trends in these properties, and this understanding can be used to predict the physical and chemical behavior of atoms and molecules. We then apply this core concept as we explore topics that range from the history of chemistry to the many ways that chemistry is employed in, for example: the natural environment and human interaction with our environment, medicine, electronics and advanced materials technology.

Chemistry is sometimes referred to as the central science—chemists apply underlying principles of physics to their study of matter, and the principles of chemistry have applications in all aspects of biology. Chemistry therefore requires an understanding of physics, and is essential preparation for study in biology.

There are five traditional subdivisions of chemistry: organic chemistry, biochemistry, physical chemistry, inorganic chemistry and analytical chemistry. Students may pursue advanced work in organic and biochemistry and many related topics. Analytical chemistry is woven into many courses and tutorials. Tutorials in physical and inorganic chemistry are offered for advanced students as needed.

Areas of Interest for Plan-level Work:

  • Protein biochemistry  
  • Environmental chemistry, green chemistry, phytoremediaton
  • Cell physiology  
  • Endocrinology
  • Molecular biology
  • Immunology  
  • Neuroscience
  • Biogenesis  
  • Human physiology  
  • Cell biology

Starting Points (Basic and Introductory Courses)

CHEMISTRY IN THE KITCHEN (NSC596)
Ever wonder why bread dough rises? Or what makes a chocolate bar melt when it’s heated? When we cook, we see food change. Chemistry explains these changes. Harold McGee, author of On Food and Cooking: the Science and Lore of the Kitchen, agrees: “Science can make cooking more interesting by connecting it with the basic workings of the natural world.” In this course, we will explore food and cooking through experiments that ask questions such as: How does heat change food? How do bacteria perform fermentation? Why is the fermented food acidic? What is an acid, anyway? Through these explorations we will build an understanding of how chemistry explains cooking. This is a chemistry course with the kitchen as our laboratory. The course will meet twice a week: once in the classroom, and once in the kitchen. Each week we will discuss a new topic in chemistry and then use our laboratory time in the kitchen to address our questions. Prerequisite: None     Introductory | Credits: 3

GENETIC ENGINEERING:  WHO’S DRIVING THE TRAIN? (NSC601)
In 1953 scientists James Watson and Francis Crick first deduced the structure of DNA, and since then the advances in molecular biology have been staggering. Scientists can make plants resistant to pesticides. Doctors can cure children born with no immune system. Genome sequencing and stem cell technology may someday lead to personalized medical advice and replacement organs grown from your own skin cells. But DNA science also raises serious ethical questions. For example, what risks do we take when we release genetically engineered organisms into the environment, and do pest-resistant GM crops really reduce the use of pesticides? In this course we will explore advances in human understanding of DNA, and the promises and perils associated with scientists’ ability to manipulate genetic material. We will examine the personalities driving DNA research, as well as the politics and financial incentives involved. This course will provide a general introduction to the nature and function of DNA, RNA and protein, both in the classroom and in the laboratory. Students with prior experience in these topics are welcome although the course is intended as a general introduction to non-specialists. This course is therefore not considered a foundation course that prepares students for advanced study in the field. Prerequisite: None     Introductory | Credits: 4

GENERAL CHEMISTRY I (NSC158)
Chemistry has a rich history, including ancient theories on the nature of matter and recipes for converting lead into gold. Modern research and applications are equally exciting, and include topics such as creating more efficient solar collectors and the reactions of natural and human-made chemicals in the environment. In this course, we will study topics such as atomic structure and the periodic table, reaction stoichiometry, chemical bonds and molecular structure. Many topics are related to current health and environmental issues. For example, discussions of pH and reduction-oxidation reactions include research on the natural chemistry of surface waters and the effects of acid rain on natural systems. Prerequisite: None     Introductory | Credits: 4

GENERAL CHEMISTRY I LAB - EXPLORATION OF BIOFUELS (NSC444)
Science is a process, not a collection of facts. In this laboratory we will combine the study of chemistry with the process of science by exploring the production of biofuels. We will begin by developing some basic quantitative skills and familiarity with laboratory techniques. The activities for these early parts of the lab will be fairly structured. As you develop your ability to approach a problem scientifically the activities will be less structured and you will have more responsibility for designing and conducting your own experiments on the production and analysis of biofuels. Students will work on projects in groups but each student will keep their own laboratory notebook and write their own laboratory reports. Prerequisite: Concurrent enrollment in General Chemistry I     Introductory | Credits: 2

GENERAL CHEMISTRY II (NSC505)
The central focus of general chemistry is the composition of matter and transformations of matter. In the second half of this course we will examine in detail models of chemical bonds, reaction kinetics, acid-base equilibria and electrochemistry. We will also explore some aspects of organic chemistry, nuclear chemistry and analytical chemistry. Environmental chemistry will continue to be a secondary theme of the course as we relate all of these topics to the effects of human activity on our environment. Prerequisite: General Chemistry I (NSC158)     Intermediate | Credits: 4

GENERAL CHEMISTRY II LAB (NSC506)
The laboratory sessions will continue to be an opportunity for students to hone their lab skills and to explore topics and ideas discussed in class. We will use primary literature to provide some context for our experiments, and students will work in teams to devise, conduct and analyze experiments. Also, this semester there will be a greater focus on employing the principles of green chemistry in our lab experiments. Prerequisite: Concurrent enrollment in General Chemistry II    Intermediate | Credits: 2

Pursuing Interests (Intermediate and Thematic Courses)

ORGANIC CHEMISTRY I (NSC12)
Carbon can form bonds with itself and almost all of the other elements, giving rise to an enormous variety of carbon-containing molecules. Early organic chemists struggled with the structure of one—benzene—until Friedrich Kekulé solved the puzzle in a dream: he saw the carbon atoms “twisting in a snake-like motion. But look! What was this? One of the snakes had seized hold of its own tale, and the form whirled mockingly before my eyes.” In this course we study the chemistry of these carbon-based compounds—their structures, properties and reactions. Many examples include descriptions and mechanisms of biological reactions. This is an intermediate chemistry course and provides essential background for biology, chemistry, pre-med and pre-vet students. Prerequisite: General Chemistry I (NSC158)     Intermediate | Credits: 4

ORGANIC CHEMISTRY I LAB (NSC17)
In the laboratory you will apply the same concepts and analytical skills we use in the classroom. You will continue to hone problem-solving skills and become familiar with organic chemistry laboratory equipment and procedures. Laboratory sessions will be designed to allow you to explore ideas discussed in class through structured protocols and through more open-ended inquiry. Initial labs will guide you through the isolation and identification of various compounds of interest, preparing you for your own more in-depth research. By using these techniques you will become comfortable working in a laboratory and
familiar with techniques commonly used by organic chemists. Prerequisite: Concurrent enrollment in Organic Chemistry I (NSC12)    Intermediate | Credits: 2

ORGANIC CHEMISTRY II (NSC22)
Organic chemistry takes its name from the ancient idea that certain molecules—organic molecules—could only be made by living organisms. In second semester organic chemistry we will continue our study of different classes of organic compounds and their reactions. The first part of the semester will include material on important analytical techniques such as IR spectroscopy and nuclear magnetic resonance. In the latter part of the semester we will turn to the original realm of organic chemistry—living systems. For example, we will examine properties and reactions of amines, carboxylic acids, carbohydrates, nucleic acids, amino acids, peptides and proteins and lipids. This semester will also include a special focus on the process of olfaction in humans. Prerequisite: Organic Chemistry I (NSC12)     Intermediate | Credits: 4

ORGANIC CHEMISTRY II LAB (NSC23)
The laboratory sessions will continue to be an opportunity for students to hone their lab skills and to explore topics and ideas discussed in class. We will use primary literature to provide some context for our experiments, and students will devise, conduct and analyze experiments. Also, this semester there will be a greater focus on self-designed laboratory investigations. Through this approach, and by using these laboratory techniques students will become comfortable working in a laboratory, and they will become familiar with techniques commonly used by organic chemists. Prerequisite: Organic Chemistry I (NSC12); Concurrent enrollment in Organic Chemistry II (NSC22)     Intermediate | Credits: 2

BIOCHEMISTRY OF THE CELL (NSC13)
Biochemists used to debate the nature of proteins: their composition, structure and function. Now we know many extraordinary details of the shapes of proteins and how they function. For example, how they help our bodies acquire nutrients from food, use those nutrients for fuel and carry oxygen to our tissues. In particular, researchers have revealed the intricacies of how a protein’s structure is related to its function. In this course we will employ an evolutionary perspective as we discuss major topics such as amino acids, proteins and protein structure, bioenergetics, enzymes and enzyme function. We will also study major metabolic pathways and their key control points. Our goals are for you to develop a thorough understanding of how enzymes work and to be familiar with key metabolic pathways and how they are controlled. The course will include class discussions and presentations based on the text and primary literature, homework assignments, a five-page paper and exams (including a final exam). Prerequisite: General Chemistry I and II, or instructor’s permission     Intermediate | Credits: 4

BIOCHEMISTRY OF THE CELL LABORATORY (NSC587)
This laboratory will be an introduction to techniques commonly used by biochemists, and must be taken in conjunction with Biochemistry of the Cell. Your work in the laboratory will focus on a semester-long investigation of an enzyme. This project will allow you to perform your own biochemistry research project in which you will employ the principles of chemistry and biochemistry that we study in the classroom. The protein you will investigate is already well-characterized. That is, previous research has described in detail the properties of the enzyme. Your goal is to determine if the enzyme you isolate is the same as that described in the primary literature. To answer this question we will begin with basic laboratory procedures such as preparing reagents, chromatography, and performing a protein assay. We will then explore techniques for studying the activity of enzymes, and methods for separating proteins, such as one and two-dimensional electrophoresis. Finally we will employ methods for the identification of specific proteins using immuno-staining, and a phenomenally sensitive technique for quantifying a specific protein in solution, the enzyme-linked immuno-sorbent assay (ELISA). Throughout this semester-long project you will also learn about the procedures for data acquisition and analysis that will allow you to draw meaningful conclusions from your results. Prerequisite: General Chemistry I & II  Corequisite: Biochemistry of the Cell     Intermediate | Credits: 2

LABORATORY IN BIOCHEMICAL TECHNIQUES (NSC425)
This laboratory will be an introduction to techniques commonly used by biochemists, and must be taken in conjunction with Biochemistry of the Cell. Your work in the laboratory will focus on a semester-long investigation of an enzyme. This project will allow you to perform your own biochemistry research project in which you will employ the principles of chemistry and biochemistry that we study in the classroom.
The protein you will investigate is already well-characterized. That is, previous research has described in detail the properties of the enzyme. Your goal is to determine if the enzyme you isolate is the same as that described in the primary literature. To answer this question we will begin with basic laboratory procedures such as preparing reagents, conducting chromatography and performing a protein assay. We will then explore techniques for studying the activity of enzymes, and methods for separating proteins, such as one- and two-dimensional electrophoresis. Finally we will employ methods for the identification of specific proteins using immuno-staining, and a phenomenally sensitive technique for quantifying a specific protein in solution, the enzyme-linked immuno-sorbent assay (ELISA). Throughout this semester-long project you will also learn about the procedures for data acquisition and analysis that will allow you to draw meaningful conclusions from your results. Prerequisite: Past or current enrollment in Biochemistry of the Cell (NSC13)     Intermediate | Credits: 2

FUNDAMENTALS OF MOLECULAR BIOLOGY (NSC415)
Scientists’ ability to explore, understand and manipulate DNA has increased dramatically in the past 20 years. In this course we will explore the structure of nucleic acids, and the organization of genes and chromosomes. We will also examine DNA replication, the roles of DNA and RNA in protein synthesis and the control of gene expression. A major theme of this course will be how experimental evidence supports our current understanding of the structure and function of genes. This course will include discussions of how these processes can be manipulated to yield powerful laboratory techniques for the study of the organization and function of genes and gene products. The central structure of the course will be weekly lectures and discussions of selected readings, including journal articles. We will also discuss homework assignments, and all of these discussions will be informed by readings from the text. Prerequisite: Biochemistry of the Cell (NSC13)     Intermediate | Credits: 4

FUNDAMENTALS OF MOLECULAR BIOLOGY LAB (NSC420)
This course will explore, through experiments and demonstrations, a variety of fundamental laboratory techniques used by molecular biologists. Over the course of the semester we will pursue several different projects. Students will be involved in all aspects of each project, from designing experiments to ordering lab supplies. Some lab sessions will involve only computer-based bioinformatics research and discussions of experimental design. We will begin with safety and basic laboratory techniques, and then move on to projects based on the following topics: DNA packaging, nucleosomes and nucleases; satellite DNA, genetic polymorphisms and PCR; DNA extraction from bone and organism identification; RT-PCR, virus mutation and virus variation with in a single host. Students will develop detailed strategies for pursuing these projects as part of this lab course, and therefore the time devoted to each project may vary. Prerequisite: Biochemistry of the Cell (NSC13); concurrent enrollment in Fundamentals of Molecular Biology (NSC415)     Intermediate | Credits: 2

Good Foundation for Plan

Foundations for Plan must start with introductory course work. In chemistry and biology the place to begin is the two-semester sequence of General Chemistry and General Chemistry Laboratory. These courses serve as a valuable foundation for more advanced study in all aspects of chemistry, biology, and environmental studies. For more advanced study in chemistry students should take the two-semester Organic Chemistry (with lab) sequence, followed by the one-semester course Biochemistry of the Cell (with lab). This sequence opens up the possibility of Plan work in many areas. For example, students may pursue advanced work through tutorials in neuroscience, cell biology, immunology and physiology. Students interested in applying the tools of molecular genetics should first follow Biochemistry of the Cell (fall semester) by taking Fundamentals of Molecular Biology (spring semester, and the accompanying laboratory class. Organic Chemistry I & II and the Biochemistry/Molecular Biology sequence are offered in alternate years, so students should consider this rotation when planning their course of study. Plan students are required to take at least two semesters of the laboratory classes that accompany the classroom chemistry and biochemistry courses.

Although students should study broadly at Marlboro, the study of chemistry also requires a foundation in mathematics and physics. Chemistry Plan students should therefore also study differential and integral calculus, as well as General Physics. Linear algebra and statistics are also excellent companion courses for advanced study, as are physics courses in quantum mechanics, thermodynamics and statistical mechanics. For advanced work in chemistry and biochemistry, students and I discuss and design tutorials as their interest in specific chemistry or biochemistry topics begins to develop (see “Guidelines for Tutorial Work”).

Many Plan students elect to conduct an experiment as part of their work. I heartily endorse and support such efforts, and I especially encourage students to pursue summer internships after their junior year as a way to conduct their own research.

Guidelines for Tutorial Work

When a student expresses interest in an exploratory tutorial, I ask the student to write a draft of a tutorial description and to present some of their ideas for a semester-long syllabus. Since the tutorial may be the first time the student is exploring this topic in some detail, I expect that together we will evaluate materials for the syllabus and then agree on a reading list. I encourage a tutorial format where the student and I review foundational material on the selected topic in the first part of the semester, for example, by reading chapters from textbooks. Next, the student would read primary scientific literature, usually articles that the student tracks down. For the last part of the semester, the student focuses on writing a paper based on the material they read over the course of the term, but with the goal of relying more heavily on the primary literature.

When several students express an interest in the same topic, I take the opportunity to offer a group tutorial. For example, I recently had a number of juniors each ask for tutorials in very similar topics. I was able to meet all of their interests by offering a group tutorial in Cell Physiology. In this instance the students and I relied on a cell physiology textbook for most of the semester’s material. For their final papers each student delved more deeply into some topic that he/she had already discussed to see if it would make an exciting subject for a Plan of Concentration.

In the fall semester, seniors and I use Plan tutorials as a way for the students to finish collecting and reading a set of reference materials (primary and secondary literature) and sharpen their focus on a topic. They also finalize an outline that will serve as a road map for the completion of their Plan, and make the transition from planning for writing, to actually writing Plan papers. Plan tutorials in the spring semester are a time for students to finish writing their Plan papers and for the student and I to discuss the organization and editing of those papers.

Sample Tutorial Topics

  • Immunology of HIV/AIDS
  • Biochemistry of Parasitic Infections  
  • Advanced Topics in Human Physiology
  • Exploring the Polymerase Chain Reaction  
  • Neuroscience: Introduction to the Structure and Function of the Nervous System
  • Molecular Biology of Genetic Diseases