Chemistry & Biochemistry

Todd Smith

The chemistry program at Marlboro College has the same fundamental goal shared by all chemistry programs: to teach students how atomic structure accounts for atomic properties, the periodic trends in these properties, and how this understanding can be used to predict the physical and chemical behavior of atoms and molecules.

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. Advanced work is available in organic and biochemistry. Analytical chemistry is woven into courses and tutorials in the other areas. Tutorials in physical and inorganic chemistry are offered for advanced students as needed.

Students should begin their studies in chemistry with General Chemistry, followed by Organic Chemistry and then Biochemistry. These last two courses are offered in alternate years, so students should consider this rotation when selecting their courses. I also require students to take at least one of the laboratory classes that accompany the classroom chemistry courses. For advanced work students and I discuss and design tutorials as their interest in specific topics begins to develop.

For the study of chemistry a suitable foundation in mathematics includes an understanding of differential and integral calculus. Linear algebra and statistics are also excellent preparation for advanced study.

COURSES OFFERED ON A ROTATING OR PERIODIC BASIS

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. (Introductory, every fall semester)

General Chemistry I Laboratory (NSC444)
In the laboratory, we will apply the same concepts, information and analytical approach we use in the classroom. You will continue to hone problem-solving skills and become familiar with laboratory equipment and procedures. Laboratory sessions will be designed to allow you to explore ideas discussed in class through field and lab work in environmental chemistry. Also, we will try to apply concepts from the field of ‘green chemistry’ to make our investigations more environmentally sustainable. (Introductory, every all semester)

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. (Introductory)

General Chemistry II Laboratory (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. (Introductory)

Human Physiology (NSC295)
Physiology is the study of a difficult balancing act: our bodies must coordinate needs such as the acquisition of food and energy, the elimination of waste, and the maintenance of body temperature. Claude Bernard (1813-1878) is famous for noting that this balancing act demonstrates that "the constancy of the internal environment" is a necessary condition for life. In this course we will explore how individual organ systems work, and how all of our organs together work to maintain a constant internal environment. Central topics will include the respiratory, circulatory, digestive, excretory, nervous and endocrine systems and how they are controlled. Discussions of the relationship between anatomy of particular organs and their function will also be included. (Introductory)

Genetic Engineering: Who’s Driving the Train? (CDS534), team-taught with Stevenson
In 1953 scientists James Watson and Francis Crick first deduced the structure of DNA, and since then the advances in molecular genetics have been staggering. Scientists can make plants resistant to pesticides. Doctors can cure children born with no immune system. Stem cell technology may someday lead to permanent cures for a variety of diseases. But DNA science also raises serious ethical questions. For example, should we release genetically engineered organisms into the environment, and should researchers use human embryos as a source of stem cells? 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. (Introductory)

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 Kekule 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 tail, and the form whirled mockingly before my eyes." In this course we study the chemistry of these carbon-based compounds. This is an introductory chemistry course and is essential for all biologists, chemists, pre-meds, and pre-vets. Minimal use of mathematics. Many examples include descriptions and mechanisms of biological reactions. (Intermediate)

Organic Chemistry I Laboratory (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. (Intermediate)

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. In the latter part of the semester we will turn to the original realm of organic chemistry – living systems. Several topics are included that cover organic chemistry in biological systems. For example, we will examine reactions of amines, carboxylic acids, carbohydrates, nucleic acids, amino acids, peptides and proteins, and lipids. (Intermediate)

Organic Chemistry II Laboratory (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 work in teams to devise, conduct and analyze experiments. Also, this semester there will be a greater focus on self-designed laboratory investigations. (Intermediate)

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 how proteins 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, research has 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. (Intermediate)

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. We will begin with basic laboratory procedures such as preparing reagents, chromatography, and performing a protein assay. We will then explore techniques for separating proteins such as one and two-dimensional electrophoresis, and the identification of specific proteins using immunostaining. Finally, we will explore a technique for quantifying proteins in solution, the enzyme-linked immuno-sorbent assay (ELISA). (Intermediate)

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. (Intermediate)

Laboratory in Fundamentals of Molecular Biology (NSC420)
This course will explore a variety of fundamental laboratory techniques used by molecular biologists. We will begin with safety and basic laboratory techniques before learning bacterial culture and transformation of bacteria with foreign (plasmid) DNA. This course will also cover DNA and RNA purification, restriction digests for DNA, electrophoresis, the polymerase chain reaction (PCR), and northern blotting. We will emphasize how these techniques would be used in the course of a research project, and students will be asked to demonstrate their understanding in these processes through written laboratory reports. (Intermediate)


COURSES OFFERED OCCASIONALLY OR AS NEEDED


Immunology (NSC301)
A study of the immune system, with an emphasis on humans.

Enzymology (NSC257)
The study of biological reactions, including mechanisms, kinetics, nomenclature, allosterism, and control.

Physical Chemistry (NSC24)
A study of quantitation in chemistry, including topics in kinetics, thermodynamics, spectroscopy, etc. Biological examples are stressed where possible.


AREAS OF INTEREST FOR PLAN-LEVEL WORK

SAMPLE TUTORIAL TOPICS

Guidelines for Tutorial Work

When a student expresses interest in an exploratory tutorial, Todd asks 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, Todd expects that together he and the student will evaluate materials for the syllabus and then agree on a reading list. Todd encourages a tutorial format where he and the student review basic information on the selected topic in the first part of the semester, for example, by reading chapters from textbooks. Next, they 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 Todd takes the opportunity to offer a group tutorial. For example, he recently had a number of juniors each ask for tutorials in very similar topics. He was able to meet all of their interests by offering a group tutorial in Cell Physiology. In this instance he and the students relied on a cell physiology textbook for most of the semester’s material. For their final papers the students delved more deeply into some topic they had already discussed to see if it would make an exciting subject for their Plan of Concentration.

In the fall semester seniors and Todd use Plan tutorials as a way for them 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 roadmap for the completion of their Plan and make the transition from planning for writing to actually writing Plan papers. Plan tutorial in the spring semester is a time for students to finish writing their Plan papers and for the student and Todd to discuss the organization and editing of those papers.