Biochemistry and Biophysics
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Amherst College Biochemistry-Biophysics for 2012-13

281 Molecular Genetics

(Offered as BIOL 251 and BCBP 281) A study of the molecular mechanisms underlying the transmission and expression of genes. DNA replication and recombination, RNA synthesis and processing, and protein synthesis and modification will be examined. Both prokaryotic and eukaryotic systems will be analyzed, with an emphasis upon the regulation of gene expression. Application of modern molecular methods to biomedical and agricultural problems will also be considered. The laboratory component will focus upon recombinant DNA methodology. Four classroom hours and four hours of laboratory per week; some laboratory exercises may require irregular hours.

Requisite: BIOL 191 or equivalent. Limited to 30 students. Not open to first-year students.  Omitted 2012-13. Professor Ratner.

2015-16: Not offered

291 Cell Structure and Function

(Offered  as BIOL 291 and BCBP 291)  An analysis of the structure and function of cells in plants, animals, and bacteria. Topics to be discussed include the cell surface and membranes, cytoskeletal elements and motility, cytoplasmic organelles and bioenergetics, the interphase nucleus and chromosomes, mitosis, meiosis, and cell cycle regulation. Four classroom hours and three hours of laboratory per week.

Requisite: BIOL 191 and completion of, or concurrent registration in, CHEM 161.  Limited to 24 students. Spring semester. Professor Poccia.

2015-16: Offered in Spring 2016
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015

310 Structural Biochemistry

(Offered as BIOL 310 and BCBP 310.) This course will concentrate on the structure of proteins at the atomic level. It will include an introduction to methods of structure determination, to databases of structural information, and to publicly available visualization software. These tools will be used to study some class of specific structures, (such as membrane, nucleic acid binding, regulatory, structural, or metabolic proteins). These proteins will provide the framework for discussion of such concepts as domains, motifs, molecular motion, structural homology, etc., as well as addressing how specific biological problems are solved at the atomic level. Four classroom hours per week plus one hour discussion .

Requisite: BIOL 191 and CHEM 161; CHEM 221 would be helpful but is not required. Limited to 20 students. Fall semester.  Professor Williamson.

2015-16: Not offered
Other years: Offered in Fall 2007, Fall 2012

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. Professors Williamson (Biology) and Bishop (Chemistry).

2015-16: Offered in Spring 2016
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015

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 Williamson.

2015-16: Offered in Spring 2016
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015

405 Seminar in Biochemistry

(Offered as BIOL 404 and BCBP 405) The topic of this advanced seminar will be cholesterol.  It has been said that more Nobel prizes have been awarded for the study of cholesterol than any other biological topic, yet it is astonishing how much we have learned only in the last few years, and how much we still don't understand.  The topics in this course will include biosynthesis, transport, regulation, physiology, and biophysics of cholesterol.  In many cases, these subjects illuminate or are illuminated by cholesterol-related diseases, so the biochemical bases for high cholesterol medications and for a genetic propensity for getting heart disease from eating broccoli are likely to come up.  The course will be based on the scientific literature, and will include writing and presentation assignments.

Requisite:  BIOL 191 and 291 or 331 or equivalent.  Limited to 15 students.  Omitted 2012-13.  Professor Williamson.

2015-16: Not offered

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.  Fall semester.  Professor Bishop. 

2015-16: Not offered
Other years: Offered in Fall 2012, Fall 2013, Spring 2014

490 Special Topics

Fall and spring semesters.

2015-16: Offered in Fall 2015 and Spring 2016
Other years: Offered in Fall 2011, Spring 2012, Fall 2012, Spring 2013, Fall 2013, Spring 2014, Fall 2014, Spring 2015

498, 499D Senior Departmental Honors

Fall semester.

2015-16: Offered in Fall 2015
Other years: Offered in Fall 2011, Fall 2012, Fall 2013, Fall 2014