Biochemistry, Biophysics, and Molecular Biology

The application of concepts and approaches from physics and mathematics (e.g. mechanics, thermodynamics, electromagnetism, quantum physics, probability) to deepen understanding of molecular and cell biology. We will focus on simplified models that capture the salient features of biological systems. Example topics include diffusion, hydrodynamics and cellular locomotion, free energy transduction, ligand binding, entropic forces,  molecular motors, macromolecular conformation, signal propagation in neurons, gene expression, and vision. Includes exercises in computation; no prior coding experience assumed. Three one-hour lectures per week; weekly problem sets; exams. May be elected as Physics 324.

This course provides students with a detailed examination of protein structure and function, focusing on the role of proteins in molecular recognition and catalysis. Topics include: techniques used to characterize proteins; enzyme kinetics and mechanisms; signal transduction across membranes; bioenergetics; catabolism of proteins, fats, and carbohydrates; and integration of metabolism and disease. Students will actively participate in group problem-solving, and gain experience reading and critiquing scientific journal articles. Applies to the Molecular/Cell requirement for the Biology major.  

Examination of nucleic acid structure and function, focusing on gene expression and mechanisms of gene regulation. Other topics include molecular biology of viruses, mobile genetic elements, the genetic basis of cancer, and aspects of genomics. Required for BBMB majors. Applies to the Molecular/Cell requirement for Biology majors. Open to non-BBMB majors only with consent of instructor.

Laboratory exercises on a range of biophysical top­ics. Experimental testing of models developed in BBMB 324. Study of macromolecules using techniques that may include absorption spectroscopy, fluorescence spectroscopy, circular dichroism, NMR, crystallization and structure determination via X-ray diffraction. One three- to four- hour laboratory per week. May be elected as Physics 334. Open to non-BBMB majors only with consent of instructor.

A semester-long team project introducing students to the core laboratory techniques and methods in protein biochemistry for characterizing a catalytic protein.  Students will engage in biochemical reagent preparation, enzyme isolation and purification, enzyme and protein assays, gel electrophoresis, and immunodetection methods. Applies to the Molecular/Cell requirement for the Biology major. Open to non-BBMB majors only with consent of instructor.

Laboratory exercises in nucleic acid biochemistry, including molecular cloning, PCR, and DNA and RNA isolation and analysis techniques. One three-hour laboratory per week. Applies to the Molecular/Cell requirement for the Biology major. Open to non-BBMB majors only with consent of instructor.

The human immune system possesses a remarkable ability to distinguish among a wide array of molecular structures. This evolutionary adaptation enables the recognition and response to microbial pathogens as well as host cancer cells, while tolerating normal host cells, commensal microbes, and harmless environmental exposures.  This course will explore the molecular and cellular basis of immune system function (hematopoiesis, innate immunity, molecular diversity of antigen recognition and presentation, and T- and B-cell adaptive immunity),  perturbations of the immune response (allergies, autoimmunity, and tissue transplantation) and the use of immunotherapies to manipulate the immune system (vaccines, monoclonal antibodies, T-cell therapies).   Coursework will involve instructor- and student-led presentations, the reading and discussion of peer-reviewed research articles, and case-studies that highlight host-pathogen interactions, evolutionary pressures, immune modulation, and the development of diagnostics and therapeutics. Applies to the Molecular/Cell requirement for the Biology major.

The 20th century made great strides in identifying protein structure and function, creating the field of structural biology. At the turn of the century, research began focusing on proteins without structure. Referred to as "intrinsically disordered," these proteins were linked to the physical phenomenon of liquid-liquid phase separation and biomolecular condensates. Like oil in water, they form dense liquid droplets of protein designed to carry out cellular functions. In this course we will focus on the nature of disorder, the science driving phase separation, and the roles of these proteins in relation to both disease and synthetic life. Course work will involve lectures to provide background information, reading and discussion of peer-reviewed research articles, collaborative learning activities, experimental design, and some hands-on lab activities. Applies to the Molecular/Cell requirement for the Biology major. Prerequisites: Biology 205 and Chemistry 245; or Biology 111 and Chemistry 246.

The senior seminar will serve as the capstone of the major by providing a forum for all seniors to make a full-length oral presentation. Each student will describe the background, methodologies, and experimental results of the senior research project and respond to questions and critiques from his or her peers. Open to non-BBMB majors only with consent of instructors.

This course will use the practices of public health to explore the role of infectious disease on human mortality and morbidity from biomedical, social, and economic perspectives. Readings, discussion, and journal writing will focus on: epidemiology and burden of disease, the immune system and the host response to viruses, bacteria, and parasites; antimicrobial agents and drug resistance; and vaccine development and policy. Each student will work in a team to present a week-long Case Study on a disease of global importance such as COVID, influenza, dengue, HIV, malaria, or tuberculosis.

Research projects or independent studies arranged with individual students. The students must consult with a faculty member prior to the semester of the anticipated project to determine if the project is suitable, and the project must be done with the supervision of a Whitman faculty member.

Each student will take part in a research project involving the collection and analysis of data, and write a thesis on that research in accepted scientific style. One or more drafts of the thesis will be required before the final version is due in the last week of classes. Each student also will publicly present his/her research results in the BBMB 400 Senior Seminar or a similar presentation venue. A total of three credits are required in the senior year; credits may be taken in the Fall and/or Spring. 

Research and writing of the senior honors thesis. Students register for BBMB 490, not for BBMB 498. The registration will be changed from BBMB 490 to 498 for those students who attain honors in BBMB. Open only to senior BBMB majors.