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Amherst College Biochemistry-Biophysics for 2016-17

251 Molecular Genetics

(Offered as BIOL 251 and BCBP 251) 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.

Requisite: BIOL 191 or equivalent. Limited to 30 students. Not open to first-year students.  Fall semester. Professor Jeong


2016-17: Offered in Fall 2016
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2017

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.

2016-17: Offered in Spring 2017
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2018

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 for addressing how specific biological problems are solved at the atomic level. Three classroom hours per week plus one hour discussion.

Requisite: BIOL 191 and CHEM 161; CHEM 221 would be helpful but is not required. Spring semester.  Professor Williamson.

2016-17: Offered in Spring 2017
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. Limited to 45 students. Spring semester. Professors Jeong and O'Hara.

2016-17: Offered in Spring 2017
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2018

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.  Spring semester.  Professor Loinaz.

2016-17: Offered in Spring 2017
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2018

404 Seminar in Biochemistry

(Offered as BIOL 404 and BCBP 404) 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 18 students.  Fall semester.  Professor Williamson. 

2016-17: Offered in Fall 2016
Other years: Offered in Spring 2011

420 Seminar in Molecular Genetics: DNA Makes RNA

(Offered as BIOL420 and BCBP 420.) If the basic tenants of eukaryotic molecular biology have followed the prokaryotic paradigm-- DNA makes RNA makes protein--established decades ago, the importance of eukaryotic RNA that is not translated into protein is only now becoming appreciated. While barely more than 1% of the human genome encodes protein, there is evidence that as much as 98% of our genome is transcribed! What function, if any, do all those RNA species serve? Incorporating articles from the recent scientific literature, this course will focus on topics such as: the diverse roles of micro RNAs in regulating gene expression; the use of piwi RNAs in genome defense; and the role of long non-coding RNAs in gene regulation, X chromosome inactivation, and other epigenetic phenomena. Riboswitches and CRISPR count, too. Three classroom hours per week.

Requisite: BIOL 251; alternatively, any two of the following courses: BIOL 220, 241, 291, 330/1, and 380/1. Limited to 15 students. Spring semester. Professor Ratner.

2016-17: Offered in Spring 2017
Other years: Offered in Fall 2009, Spring 2015

490 Special Topics

Fall and spring semesters.

2016-17: Offered in Fall 2016 and Spring 2017
Other years: Offered in Fall 2011, Spring 2012, Fall 2012, Spring 2013, Fall 2013, Spring 2014, Fall 2014, Spring 2015, Fall 2015, Spring 2016, Fall 2017, Spring 2018

498, 499D Senior Departmental Honors

Fall semester.

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2011, Fall 2012, Fall 2013, Fall 2014, Fall 2015, Fall 2017