New College’s Biochemistry AOC is an interdisciplinary program designed to let you explore the interface between all four areas of the natural sciences, especially chemistry and biology. While the classes and labs are quite challenging, you’ll take them in a flexible, non-competitive environment with guidance from faculty members who have earned doctorates from some of the nation’s premier research institutions, including University of Wisconsin, MIT, Berkeley, Cornell, University of Arizona and Florida State University.
Like our Chemistry program at New College, our Biochemistry AOC encourages and develops independence, scientific judgment and a high level of performance. As a Biochemistry student, you will work closely with faculty trained at leading universities and conducting engaging and relevant research. With their guidance, you will develop the skills needed for scientific research in academia and industry.
You will also work with state-of-the-art, research-grade instruments, including our real-time PCR instrument, fluorimeter, UV-visible spectrophotometers, electrophoresis equipment, visible and fluorescent microscopes, and more.
As a student in Biochemistry, you will complete three independent study projects, two in any subject and one in Chemistry or Biochemistry, and a Biochemistry senior thesis, a project in which you will do graduate-level work. You will receive extensive mentoring from faculty members, from formulating your project to performing bench work in the laboratory to examining the results.
You will also have access to state-of-the-art equipment so you can delve deeply into the world of biochemistry. In 2006, New College received a grant to help three professors further their research into animal and plant development and gene expression. Through the grant, New College became one of only a small number of undergraduate institutions in the country to have a real-time PCR (polymerase chain reaction) instrument to measure DNA and RNA levels in tissue samples taken from organisms.
Our Biochemistry and Chemistry students also have a long tradition of being awarded prestigious undergraduate research grants. In the past five years, nine New College students have received highly prized National Science Foundation Research Experience for Undergraduates (REU) grants for the summer. The programs are sponsored by the National Science Foundation and are hosted in various universities. They are among the most prestigious summer programs in which an undergraduate can participate. Through this program, New College students conducted:
• Biochemistry research at the University of Arizona.
• Molecular genetics and proteomics research at the University of Minnesota.
• Chemistry research at the University of Minnesota.
• Chemistry research at Columbia University.
These experiences, resources and training will complement your senior thesis project, a level of research that most students do not attempt until graduate school. That explains why our Biochemistry and Chemistry students have very high acceptance rates to top graduate schools. In the last three years, New College students have been admitted into Ph.D. programs in chemistry at MIT, Berkeley, Caltech, Johns Hopkins, Brown and Emory University. During that same period, students have also been admitted to medical school programs at the University of Florida, University of Wisconsin, University of Illinois, and New York University.
And you can expect your professors to provide the counseling and recommendations you need as you move on from New College, either to the high-level graduate programs our students consistently attain or to a career in industry, medicine, or other professional fields.
Our students must complete seven contracts, three Independent Study Projects and a senior thesis project to graduate. Contracts consist of three to five academic activities — courses, tutorials, internships, independent reading projects, etc. — that will develop your personal educational goals during a semester.
Here’s a list of recent course offerings in Biochemistry:
Biochemistry I, Protein Structure and Function
This course will be an in-depth study of protein and nucleic acid structure, function, and regulation. The focus of the class will be on molecular mechanisms of protein function. Mechanisms of human diseases will also be discussed. The last two weeks of the course will include advanced topics chosen by the students themselves.
Biochemistry II, Metabolism and Advanced Topics
This course will be a continuation of Biochemistry I. We will cover advanced topics including sugar, amino acid, lipid, and nucleotide metabolism as well as eukaryotic mechanisms for transcription regulation. The last two weeks of the course will include advanced topics chosen by the students themselves.
This class will allow students to get experience using a variety of modern techniques in biochemistry and molecular biology. Experimental design, laboratory methods, and data analysis will be emphasized. Students will learn to do protein purifications, enzyme essays, the polymerase chain reaction (PCR), restriction enzyme digestions, DNA ligation and transformation of E. coli. Students will do a research project during the course.
The functions of inorganic centers in biological systems will be examined. Why certain metals are involved in specific functions, mechanisms of metalloenzyme-catalyzed reactions, synthetic structural and functional models, and physical methods used to study bioinorganic systems, are some of the topics we will discuss. Additionally, we will examine in some depth several specific problems in bioinorganic chemistry. Using this approach, course participants will gain substantial practice in reading the primary literature, and will experience the way in which research on a particular problem unfolds. Some choices of topics will be determined by student interest.
Cell Biology Lecture
This course will focus on the structure and function of eukaryotic cells. Topics will include bioenergetics, the structure and function of membranes, organelles and the cytoskeleton, cellular metabolism, macromolecular transport and cellular organization, the cell cycle, cell signaling, and the extracellular matrix. The cellular bases of diseases and of extracellular signal perception will be emphasized.
Cell Biology Laboratory
This laboratory course is designed to compliment the Cell Biology Lecture course. Students will develop laboratory technique and data analysis skills while learning several different approaches used to study cells. Some independent inquiry will be required. Such cell biological techniques as microscopy (various types), tissue preparation for microscopy, sub cellular separation, protein and nucleic acid extraction, gel electrophoresis, immunoblotting, and real time RT-PCR will be emphasized.
Chemical Structure Elucidation
The use of instrumentation to determine chemical structures is an essential skill for anyone continuing in the field of chemistry. This course will cover the the theory and use of NMR, IR, MS, UV-VIS and other common research instrumentation needed to determine the identity of a chemical compound. There will be additional class time scheduled for use of the instruments.
Chemistry Inquiry Laboratory
This laboratory focuses on purification of compounds and the determination of chemical structure by spectroscopic methods. The lab emphasizes group work and collaboration. In one lab, students must first determine who else in the lab has the same material as they do, then form a group to determine the compound’s structure. Substitution and elimination reactions are explored.
Enzyme Reaction Mechanisms
This course will cover the chemical strategies used by a wide variety of enzymes to catalyze biochemical reactions. We will cover general mechanisms including group transfer, oxidation reduction, substitution, carboxylation, decarboxylation, isomerization, and aldol reactions. Topics will also include methods to elucidate reaction mechanisms, the three-dimensional structure of enzyme active sites, and methods of enzyme regulation.
General Chemistry I
This is the first course in a two-semester general chemistry sequence that is intended for first-year students and designed for all science students interested in chemistry-related fields. Students are expected to complete General Chemistry I and II and Organic Chemistry I and II and their respective labs to satisfy the two years of chemistry required by many graduate and medical school programs.
General Chemistry II
This course is a continuation of General Chemistry I. Topics this semester will include thermodynamics, chemical kinetics, equilibrium, acid-base chemistry and electrochemistry.
General Chemistry Laboratory
This is a rigorous laboratory course to accompany General Chemistry. Development of laboratory technique, problem-solving skills, quantitative data analysis and communication skills will be stressed. Experimental work will include calorimetry, chemical equilibrium, acid-base chemistry, spectroscopy, and kinetics.
Introduction to Genetics
Genetics is a comprehensive course encompassing classical Mendelian hypotheses, biochemical genetics, cytoplasmic heredity, population applications and new concepts in DNA technology. We will explore these areas using simulations, small observational experiments in class in addition to interactive lectures.
The genetics lab is a full term endeavor. It is divided into two parts emphasizing the major areas of genetic experimentation.
Genetics Laboratory Part I – Classical Genetics Techniques Laboratory
Part One (Module 1)
Goals are to acquaint the student with laboratory instruments, to instill lab safety and to begin building lab poise. Experiments will center around classical Mendelian genetics. Thus, little knowledge of chemistry is required to complete this course successfully.
Genetics Laboratory Part II – Fundamentals of Applied Genetics
Part Two (Module 2)
Laboratory skills gained in the Module 1 Lab will be extended and amplified in this course. Students will be required to do a series of experiments using a variety of organisms. Development of micro techniques in this course is essential.
This course will cover various advanced topics in molecular biology. The focus will be on transcription regulation and on methods used in molecular biology. We will discuss methods such as in vitro transcription, reverse transcription, PCR, site-directed mutagenesis, and cloning.
Organic I, Structure & Reactivity
This is the first course of a two-semester sequence in Organic Chemistry and covers the core of how the chemical structure of organic compounds relates to chemical reactivity. We review fundamental chemistry concepts and then use basic principles to predict the reactivity of organic compounds. Our purpose is to understand how and why reactions occur rather than memorizing a large vocabulary of reactions. We will emphasize recognition of structural similarities and grouping by like processes so that the student achieves a coherent understanding of the basis of chemical reactivity. The course covers substitution, elimination and electrophilic addition processes.
Organic II, Structure & Reactivity
This course continues the theme of how chemical structure relates to reactivity of organic compounds. The first part is the reactions of carbonyl compounds and carboxylic acid derivatives. The second part comers aromatic compounds, radical reactions, sugars, amino acids, and macromolecular chemistry.
Organic Chemistry Laboratory
This laboratory explores the preparation and characterization of organic compounds. We will also study a reaction in detail to explore the reaction mechanism. All students will have direct access to most research instrumentation.
Internships, ISPs and Tutorials
In addition to traditional classes, students in Biochemistry at New College augment their coursework with an assortment of internship opportunities, ISPs (Independent Study Projects) and individual and group tutorials. Below are examples of some of the recent internships, ISPs and tutorials completed by our students.
ISPs (Independent Study Projects)
• C. elegans Strain Construction and Molecular Biology Lab
• Plastic Surgeon Observation
• Protein Purification and Enzyme Kinetics
• Shadowing A Doctor
• Brain Health Center Shadowing at Cleveland Clinic
• Enzyme Assay Analysis of Sistrurus barbouri Venom
• Enzyme Kinetics of C. elegans GPD-3
• Medicinal Chemistry
• Purification and Characterization of AChE from D. suzukii
• Quantification of Male rha-1 C. elegans Mutant mRNA Thesis Lab
• Measuring Small RNA Expression with RT-PCR
• Protein Purification Research Lab
Carly Summers is a Ph.D. student at Cornell University in the Department of Plant Pathology and Plant-Microbe Biology. Her research is focused on identifying fungal and oomycete pathogens infecting plants grown in a variety of cover crop mixtures with the goal of determining if certain mixtures of cover crops foster soils suppressive to pathogens. After graduating from New College of Florida in 2005, she spent two years as a Peace Corps volunteer in agroforestry in El Salvador. There she conducted community- and school-based work focused on sustainability of environmental and health education. Back in the U.S., she worked as a chemistry research associate at Archer Pharmaceuticals in Sarasota, looking into organic chemistry molecule synthesis and process optimization in the research and development of potential Alzheimer’s drugs. She has also worked as a laboratory technician in the Department of Plant Pathology at University of Florida in Wimauma and at Sarasota’s Selby Botanical Gardens in the Gesneriad Research Center.
New College is proud of the many Biochemistry graduates who have contributed to the field. Here’s a sampling of some of our graduates:
• Brent Gardner has continued his research into virology at the University of Florida’s Department of Pathology, Immunology and Laboratory Medicine. He is a published co-author on several studies on HIV and HPV virulogy.
• Amanda Hughes is a graduate student at the University of Massachusetts.
• Chris Bauer is a postdoctoral researcher at New York University in the Siegel Lab, which aims to understand phenotypic evolution by studying the processes by which the genetic networks underlying development diverge.
• Amy Nath is the corporate responsibility coordinator for BayCare Health System, where she was previously associate counsel.
• Hannah Weber recently graduated and is currently enrolled in medical school at NYU.
• Justin Spengler is attending graduate school at the University of Montana in environmental engineering.
• Andrew Schuster is attending graduate school in biochemistry at the University of Reno.
• Fermin Guerra is attending graduate school in biochemistry at the University of Montana.
• Andrew Carothers is attending the University of Florida Dental School.
• Lindsey Young worked as a lab tech at the University of New Mexico and is now attending graduate school in biochemistry at the University of California at Berkeley.
• Alice Abernathy received a Fulbright Scholarship to Spain and is currently in medical school at the University of Florida.
• Matt Felsen worked at Apple before entering the MFA program in Design and Technology at Parsons the New School for Design.
• Shelley Batts earned her Ph.D. from the University of Michigan and is currently a postdoc at Stanford. She served as an adjunct professor at New College in spring 2013.
• Cindy Griffin earned her J.D. from the University of Georgia.
• Sara Bondi is currently enrolled in the Ph.D. program in biochemistry at the University of Michigan.
• Maame Nketsiah earned a master’s in public health from Harvard.
• Vijay Sivaraman received his Ph.D. in biochemstry from the University of North Carolina at Chapel Hill. He recently joined the faculty at North Carolina Central University.
• Angus Jameson received his M.D. from SUNY Albany.
• Danny Gonzalez earned his M.S. in biochemistry from Florida International University and is currently enrolled in the Ph.D. program in biochemistry at the University of Florida.
• Ira Do received his Ph.D. in pharmacology from the University of Michigan and currently works in the pharmaceutical industry.
• David Dayan is currently enrolled in graduate school at the University of Miami.
• Emma Cassidy works with homeless youth in Vermont.
Sample of Graduate and Medical Schools Attended by NCF Students in Biochemistry
• Cornell University
• University of California – Berkeley
• Duke University
• University of Michigan
• University of Wisconsin – Madison
• Emory University
• New York University Medical School
• SUNY Albany
• University of Arizona
• University of California – Irvine
• University of Chicago
• University of Florida Medical School
• University of Georgia
• University of Illinois Medical School
• University of Massachusetts
• University of Miami Medical School
• University of South Florida Medical School
Each academic experience builds toward your senior thesis project. It’s required for graduation, and our students tell us that while it’s demanding, it’s also one of the most rewarding experiences of their lives. Here are some thesis projects in Biochemistry:
“The Possible Role of rha-1 in the piRNA Gene Regulatory Pathways in the Germline of Caenorhabditis elegans” by Megan Gautier
“Quantification of Male rha-1 Mutant Germline Gene Expression Regulated by Small RNA Pathways of Caenorhabditis elegans” by Penelope Lindsay
“Purification and Characterization of Acetylcholinesterase from Drosophila Suzukii” by Valeria Valbuena
“Kinetic Characterization of Caenorhabditis elegans Postembryonic Glyceraldehyde-3-Phosphate Dehydrogenase” by Ruth Silimon
“Examination of RNA Helicase A Function in Small Regulatory RNA Pathways of the Caenorhabditis elegans Germline” by Sarah K. O’Connor
“Expression, Purification, and Analysis of Caenorhabditis elegans Mitochondrial Malate Dehydrogenase” by Devin S. Robinson
“Ch-Ch-Ch-Changes! Measuring the Differential Expression of Small Noncoding Rna in Influenza A H1n1 Infected Epithelial Cells Using Q-Pcr” by Andrew Schuster
“Subcloning and Characterization of C. Elegans Glyceraldehyde-3-Phosphate Dehydrogenase-3” by Justin Spengler
“Myeloid-Derived Suppressor Cell Acquisition of Antigen from Dendritic Cells and Induction of Antigen-Specific T Cell” by Hannah Weber
“Determining the Rate and Activation Energy of rRNA Degradation under Prebiotic Earth Conditions” by Alice Abernathy
“Purification and Characterization of C. elegans Mitochondrial Malate Dehydrogenase” by Emma Cassidy
“Synthesis and Biological Evaluation of (Hydroxethyl) Urea Peptidomimetic Transition-State Analogs for Use in a Click Chemistry Approach to Studying the Gamma-Secretase Complex” by Eric Gars
“Detecting Protein-Protein Interactions with RNA Helicase A (RHA-1) in Caenorhabditis elegans: A Yeast Two-Hybrid Screen Assay” by Brent Gardner
“Sensitivity to dsRNA feeding, fertility, and X-Linked gene expression in wild type, rha-1(tm329), rde-2(ne211, rde-2;rha-1, and mut-7;rha-1 mutant worms” by Amanda Hughes
“X-Linked Gene Expression in Wild-Type, rha-1(tm329), and rde-2(ne221) C. elegans Using Realt-Time Reverse Transcription Polymerase Chain Reaction” by Justin White
“Analysis of the Expression of RNA Helicase A in C. elegans using Real-Time Reverse Transcription Polymerase Chain Reaction” by Christopher R. Bauer
“Investigation of Caenorhabditis elegans RNA Helicase A Protein Binding with a Yeast 2-Hybrid Assay” by Carly Summers
“The Relevance of a Conserved ATPase Domain to the Overall Function of Caenorhabditis elgans RNA Helicase A” by Amy Rani Nath
The 34,000-square-foot Heiser Natural Sciences Complex includes teaching and research labs for chemistry, biochemistry, biology, bioinformatics, computational science, mathematics and physics. A new state-of-the-art Optical Spectroscopy and Nano-Materials laboratory and a research greenhouse are part of the complex. Special equipment includes a scanning electron microscope, fluorescent microscopes, and many visible microscopes in biology and biochemistry and a 24-station chemistry teaching lab with transparent fume hoods. The Heiser Natural Sciences Complex is also home to Soo Bong Chae Auditorium, a tiered lecture hall for the natural sciences named after the longtime New College mathematician.
Biochemistry laboratories include research grade equipment for performing real-time PCR, gel imaging, centrifugation, agarose and acrylamide gel electrophoresis, protein purification, and other molecular biology procedures. Traditional and ultra cold refrigerators and freezers are available for long-term storage of samples. Kinetics can be studied using computer-controlled ultraviolet-visible spectrophotometers. Our PTI fluorescence research instrument is the most sensitive bench-top fluorometer available and is used in the biochemistry laboratory for protein studies. Cell culture procedures can be performed in the laminar flow hood.
Other equipment available in the chemistry laboratories is listed on the Resources in Chemistry page.
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