Amherst College 2017-18 Catalog

  • Introduction
  • About Amherst College
  • Admission & Financial Aid
  • Regulations & Requirements
  • Amherst College Courses
  • Five College Programs & Certificates
  • Honors & Fellowships

Introduction

View Index

Biochemistry and Biophysics

Advisory Committee:  Professors Bishop, Goutte, Hansen, Loinaz (Chair), O'Hara, Poccia†, and Williamson; Associate Professor Jaswal; Assistant Professors Carter, Jeong, and Purdy. 

† On leave fall semester 2017-18.

Biochemistry and Biophysics is an interdisciplinary major that integrates the three disciplines of Biology, Chemistry, and Physics, using the principles of chemistry and  physics to explain and explore biological phenomena.

Major Program:  A student in the major takes six foundational courses in the three disciplines as well as three additional courses to develop a more advanced understanding along either a more biophysical or biochemical track.  Students develop their expertise by the election of two courses from a list of electives, at least one of which is a biology course with a lab.  One advanced course completes coursework for the major. 

The six foundational courses are CHEM 151/155, CHEM 161, BIOL 191, BIOL 251/291, PHYS 116/123, and PHYS 117/124.

The three additional courses depend on which track a student elects.  Students who are on the Biophysics Track will take MATH 140/272/STAT 235/PHYS 227; PHYS 225/CHEM 351; and PHYS 230/CHEM 361.  Students who are on the Biochemistry Track will take CHEM 221, BIOL 331, and PHYS 230/CHEM 361.

Two electives are then chosen, at least one of which must be a laboratory course in biology.  In the Biophysics Track, the electives include BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 331, BIOL 351, BIOL 381, BIOL 404, BIOL, 420, CHEM 221, CHEM 330, COSC 111, COSC 112, MATH 211, MATH 260, STAT 235, or PHYS 343.  In the Biochemistry Track, the electives include BIOL 220, BIOL 241, BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 351, BIOL 370, BIOL 381, BIOL 404, BIOL, 420, CHEM 231, COSC 111, MATH 140, MATH 272, or STAT 235.  Other courses not listed here may satisfy this elective upon approval by the Advisory Committee.

The required advanced course is BCBP 400/CHEM 400/PHYS 400/BIOL 400. 

Special Topics Course BCPB 490 may be elected for students who wish an intensive laboratory or research tutorial in Biochemistry and Biophysics with individual members of the faculty.

For completion of the major, a comprehensive requirement consists of attendance at 6 or more BCBP approved seminars during your senior year, and presentation of a paper to a committee of BCBP faculty. 

Departmental Honors Program: Some majors may elect to pursue an independent research project that enables them the opportunity to graduate with honors.  Candidates for the degree with honors should elect BCBP 498 and 499D.

240 The Physics and Biology of Ultrasound

(Offered as PHYS 240 and BCBP 240)  Why is ultrasound the most commonly used imaging technology used at clinics and hospitals? What happens at the biological level when ultrasound interacts with living matter? How can ultrasound be used for gentle imaging purposes, but also for disrupting cell membranes, bursting blood clots and breaking kidney stones? What other biological applications of ultrasound exist in modern research? We will answer these questions and more by first studying the theory and principles of acoustic waves at higher frequencies, including related phenomena such as acoustic streaming, acoustic radiation forces and cavitation, followed by a walk-through of modern biologically relevant applications of ultrasound. We will also introduce a novel research area called microscale acoustofluidics, where ultrasound is applied to microfluidic systems with applications in, for example, cellular separation, enrichment, isolation and tissue engineering.

Requisite: PHYS 116/123, PHYS 117/124, and MATH 111, or evidence of equivalent coverage in pre-collegiate courses. Fall semester. Stint Fellow Viklund.

2017-18: Offered in 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.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

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. Omitted 2017-18.  Professor Williamson.

2017-18: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017

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 Bishop and Jeong.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) 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 15 students. Open to juniors and seniors. Fall semester.  Professor Jeong.

2017-18: Offered in Fall 2017
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016

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 Carter.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017

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.  Omitted 2017-18.  Professor Williamson. 

2017-18: Not offered
Other years: Offered in Spring 2011, Fall 2016

490 Special Topics

Fall and spring semesters.

2017-18: Offered in Fall 2017 and Spring 2018
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 2016, Spring 2017

499D, 498 Senior Departmental Honors

A double course.  Spring semester.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

About Amherst College

View Index

Biochemistry and Biophysics

Advisory Committee:  Professors Bishop, Goutte, Hansen, Loinaz (Chair), O'Hara, Poccia†, and Williamson; Associate Professor Jaswal; Assistant Professors Carter, Jeong, and Purdy. 

† On leave fall semester 2017-18.

Biochemistry and Biophysics is an interdisciplinary major that integrates the three disciplines of Biology, Chemistry, and Physics, using the principles of chemistry and  physics to explain and explore biological phenomena.

Major Program:  A student in the major takes six foundational courses in the three disciplines as well as three additional courses to develop a more advanced understanding along either a more biophysical or biochemical track.  Students develop their expertise by the election of two courses from a list of electives, at least one of which is a biology course with a lab.  One advanced course completes coursework for the major. 

The six foundational courses are CHEM 151/155, CHEM 161, BIOL 191, BIOL 251/291, PHYS 116/123, and PHYS 117/124.

The three additional courses depend on which track a student elects.  Students who are on the Biophysics Track will take MATH 140/272/STAT 235/PHYS 227; PHYS 225/CHEM 351; and PHYS 230/CHEM 361.  Students who are on the Biochemistry Track will take CHEM 221, BIOL 331, and PHYS 230/CHEM 361.

Two electives are then chosen, at least one of which must be a laboratory course in biology.  In the Biophysics Track, the electives include BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 331, BIOL 351, BIOL 381, BIOL 404, BIOL, 420, CHEM 221, CHEM 330, COSC 111, COSC 112, MATH 211, MATH 260, STAT 235, or PHYS 343.  In the Biochemistry Track, the electives include BIOL 220, BIOL 241, BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 351, BIOL 370, BIOL 381, BIOL 404, BIOL, 420, CHEM 231, COSC 111, MATH 140, MATH 272, or STAT 235.  Other courses not listed here may satisfy this elective upon approval by the Advisory Committee.

The required advanced course is BCBP 400/CHEM 400/PHYS 400/BIOL 400. 

Special Topics Course BCPB 490 may be elected for students who wish an intensive laboratory or research tutorial in Biochemistry and Biophysics with individual members of the faculty.

For completion of the major, a comprehensive requirement consists of attendance at 6 or more BCBP approved seminars during your senior year, and presentation of a paper to a committee of BCBP faculty. 

Departmental Honors Program: Some majors may elect to pursue an independent research project that enables them the opportunity to graduate with honors.  Candidates for the degree with honors should elect BCBP 498 and 499D.

240 The Physics and Biology of Ultrasound

(Offered as PHYS 240 and BCBP 240)  Why is ultrasound the most commonly used imaging technology used at clinics and hospitals? What happens at the biological level when ultrasound interacts with living matter? How can ultrasound be used for gentle imaging purposes, but also for disrupting cell membranes, bursting blood clots and breaking kidney stones? What other biological applications of ultrasound exist in modern research? We will answer these questions and more by first studying the theory and principles of acoustic waves at higher frequencies, including related phenomena such as acoustic streaming, acoustic radiation forces and cavitation, followed by a walk-through of modern biologically relevant applications of ultrasound. We will also introduce a novel research area called microscale acoustofluidics, where ultrasound is applied to microfluidic systems with applications in, for example, cellular separation, enrichment, isolation and tissue engineering.

Requisite: PHYS 116/123, PHYS 117/124, and MATH 111, or evidence of equivalent coverage in pre-collegiate courses. Fall semester. Stint Fellow Viklund.

2017-18: Offered in 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.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

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. Omitted 2017-18.  Professor Williamson.

2017-18: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017

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 Bishop and Jeong.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) 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 15 students. Open to juniors and seniors. Fall semester.  Professor Jeong.

2017-18: Offered in Fall 2017
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016

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 Carter.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017

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.  Omitted 2017-18.  Professor Williamson. 

2017-18: Not offered
Other years: Offered in Spring 2011, Fall 2016

490 Special Topics

Fall and spring semesters.

2017-18: Offered in Fall 2017 and Spring 2018
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 2016, Spring 2017

499D, 498 Senior Departmental Honors

A double course.  Spring semester.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

Admission & Financial Aid

View Index

Biochemistry and Biophysics

Advisory Committee:  Professors Bishop, Goutte, Hansen, Loinaz (Chair), O'Hara, Poccia†, and Williamson; Associate Professor Jaswal; Assistant Professors Carter, Jeong, and Purdy. 

† On leave fall semester 2017-18.

Biochemistry and Biophysics is an interdisciplinary major that integrates the three disciplines of Biology, Chemistry, and Physics, using the principles of chemistry and  physics to explain and explore biological phenomena.

Major Program:  A student in the major takes six foundational courses in the three disciplines as well as three additional courses to develop a more advanced understanding along either a more biophysical or biochemical track.  Students develop their expertise by the election of two courses from a list of electives, at least one of which is a biology course with a lab.  One advanced course completes coursework for the major. 

The six foundational courses are CHEM 151/155, CHEM 161, BIOL 191, BIOL 251/291, PHYS 116/123, and PHYS 117/124.

The three additional courses depend on which track a student elects.  Students who are on the Biophysics Track will take MATH 140/272/STAT 235/PHYS 227; PHYS 225/CHEM 351; and PHYS 230/CHEM 361.  Students who are on the Biochemistry Track will take CHEM 221, BIOL 331, and PHYS 230/CHEM 361.

Two electives are then chosen, at least one of which must be a laboratory course in biology.  In the Biophysics Track, the electives include BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 331, BIOL 351, BIOL 381, BIOL 404, BIOL, 420, CHEM 221, CHEM 330, COSC 111, COSC 112, MATH 211, MATH 260, STAT 235, or PHYS 343.  In the Biochemistry Track, the electives include BIOL 220, BIOL 241, BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 351, BIOL 370, BIOL 381, BIOL 404, BIOL, 420, CHEM 231, COSC 111, MATH 140, MATH 272, or STAT 235.  Other courses not listed here may satisfy this elective upon approval by the Advisory Committee.

The required advanced course is BCBP 400/CHEM 400/PHYS 400/BIOL 400. 

Special Topics Course BCPB 490 may be elected for students who wish an intensive laboratory or research tutorial in Biochemistry and Biophysics with individual members of the faculty.

For completion of the major, a comprehensive requirement consists of attendance at 6 or more BCBP approved seminars during your senior year, and presentation of a paper to a committee of BCBP faculty. 

Departmental Honors Program: Some majors may elect to pursue an independent research project that enables them the opportunity to graduate with honors.  Candidates for the degree with honors should elect BCBP 498 and 499D.

240 The Physics and Biology of Ultrasound

(Offered as PHYS 240 and BCBP 240)  Why is ultrasound the most commonly used imaging technology used at clinics and hospitals? What happens at the biological level when ultrasound interacts with living matter? How can ultrasound be used for gentle imaging purposes, but also for disrupting cell membranes, bursting blood clots and breaking kidney stones? What other biological applications of ultrasound exist in modern research? We will answer these questions and more by first studying the theory and principles of acoustic waves at higher frequencies, including related phenomena such as acoustic streaming, acoustic radiation forces and cavitation, followed by a walk-through of modern biologically relevant applications of ultrasound. We will also introduce a novel research area called microscale acoustofluidics, where ultrasound is applied to microfluidic systems with applications in, for example, cellular separation, enrichment, isolation and tissue engineering.

Requisite: PHYS 116/123, PHYS 117/124, and MATH 111, or evidence of equivalent coverage in pre-collegiate courses. Fall semester. Stint Fellow Viklund.

2017-18: Offered in 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.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

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. Omitted 2017-18.  Professor Williamson.

2017-18: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017

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 Bishop and Jeong.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) 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 15 students. Open to juniors and seniors. Fall semester.  Professor Jeong.

2017-18: Offered in Fall 2017
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016

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 Carter.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017

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.  Omitted 2017-18.  Professor Williamson. 

2017-18: Not offered
Other years: Offered in Spring 2011, Fall 2016

490 Special Topics

Fall and spring semesters.

2017-18: Offered in Fall 2017 and Spring 2018
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 2016, Spring 2017

499D, 498 Senior Departmental Honors

A double course.  Spring semester.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

Regulations & Requirements

View Index

Biochemistry and Biophysics

Advisory Committee:  Professors Bishop, Goutte, Hansen, Loinaz (Chair), O'Hara, Poccia†, and Williamson; Associate Professor Jaswal; Assistant Professors Carter, Jeong, and Purdy. 

† On leave fall semester 2017-18.

Biochemistry and Biophysics is an interdisciplinary major that integrates the three disciplines of Biology, Chemistry, and Physics, using the principles of chemistry and  physics to explain and explore biological phenomena.

Major Program:  A student in the major takes six foundational courses in the three disciplines as well as three additional courses to develop a more advanced understanding along either a more biophysical or biochemical track.  Students develop their expertise by the election of two courses from a list of electives, at least one of which is a biology course with a lab.  One advanced course completes coursework for the major. 

The six foundational courses are CHEM 151/155, CHEM 161, BIOL 191, BIOL 251/291, PHYS 116/123, and PHYS 117/124.

The three additional courses depend on which track a student elects.  Students who are on the Biophysics Track will take MATH 140/272/STAT 235/PHYS 227; PHYS 225/CHEM 351; and PHYS 230/CHEM 361.  Students who are on the Biochemistry Track will take CHEM 221, BIOL 331, and PHYS 230/CHEM 361.

Two electives are then chosen, at least one of which must be a laboratory course in biology.  In the Biophysics Track, the electives include BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 331, BIOL 351, BIOL 381, BIOL 404, BIOL, 420, CHEM 221, CHEM 330, COSC 111, COSC 112, MATH 211, MATH 260, STAT 235, or PHYS 343.  In the Biochemistry Track, the electives include BIOL 220, BIOL 241, BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 351, BIOL 370, BIOL 381, BIOL 404, BIOL, 420, CHEM 231, COSC 111, MATH 140, MATH 272, or STAT 235.  Other courses not listed here may satisfy this elective upon approval by the Advisory Committee.

The required advanced course is BCBP 400/CHEM 400/PHYS 400/BIOL 400. 

Special Topics Course BCPB 490 may be elected for students who wish an intensive laboratory or research tutorial in Biochemistry and Biophysics with individual members of the faculty.

For completion of the major, a comprehensive requirement consists of attendance at 6 or more BCBP approved seminars during your senior year, and presentation of a paper to a committee of BCBP faculty. 

Departmental Honors Program: Some majors may elect to pursue an independent research project that enables them the opportunity to graduate with honors.  Candidates for the degree with honors should elect BCBP 498 and 499D.

240 The Physics and Biology of Ultrasound

(Offered as PHYS 240 and BCBP 240)  Why is ultrasound the most commonly used imaging technology used at clinics and hospitals? What happens at the biological level when ultrasound interacts with living matter? How can ultrasound be used for gentle imaging purposes, but also for disrupting cell membranes, bursting blood clots and breaking kidney stones? What other biological applications of ultrasound exist in modern research? We will answer these questions and more by first studying the theory and principles of acoustic waves at higher frequencies, including related phenomena such as acoustic streaming, acoustic radiation forces and cavitation, followed by a walk-through of modern biologically relevant applications of ultrasound. We will also introduce a novel research area called microscale acoustofluidics, where ultrasound is applied to microfluidic systems with applications in, for example, cellular separation, enrichment, isolation and tissue engineering.

Requisite: PHYS 116/123, PHYS 117/124, and MATH 111, or evidence of equivalent coverage in pre-collegiate courses. Fall semester. Stint Fellow Viklund.

2017-18: Offered in 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.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

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. Omitted 2017-18.  Professor Williamson.

2017-18: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017

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 Bishop and Jeong.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) 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 15 students. Open to juniors and seniors. Fall semester.  Professor Jeong.

2017-18: Offered in Fall 2017
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016

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 Carter.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017

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.  Omitted 2017-18.  Professor Williamson. 

2017-18: Not offered
Other years: Offered in Spring 2011, Fall 2016

490 Special Topics

Fall and spring semesters.

2017-18: Offered in Fall 2017 and Spring 2018
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 2016, Spring 2017

499D, 498 Senior Departmental Honors

A double course.  Spring semester.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

Amherst College Courses

View Index

Biochemistry and Biophysics

Advisory Committee:  Professors Bishop, Goutte, Hansen, Loinaz (Chair), O'Hara, Poccia†, and Williamson; Associate Professor Jaswal; Assistant Professors Carter, Jeong, and Purdy. 

† On leave fall semester 2017-18.

Biochemistry and Biophysics is an interdisciplinary major that integrates the three disciplines of Biology, Chemistry, and Physics, using the principles of chemistry and  physics to explain and explore biological phenomena.

Major Program:  A student in the major takes six foundational courses in the three disciplines as well as three additional courses to develop a more advanced understanding along either a more biophysical or biochemical track.  Students develop their expertise by the election of two courses from a list of electives, at least one of which is a biology course with a lab.  One advanced course completes coursework for the major. 

The six foundational courses are CHEM 151/155, CHEM 161, BIOL 191, BIOL 251/291, PHYS 116/123, and PHYS 117/124.

The three additional courses depend on which track a student elects.  Students who are on the Biophysics Track will take MATH 140/272/STAT 235/PHYS 227; PHYS 225/CHEM 351; and PHYS 230/CHEM 361.  Students who are on the Biochemistry Track will take CHEM 221, BIOL 331, and PHYS 230/CHEM 361.

Two electives are then chosen, at least one of which must be a laboratory course in biology.  In the Biophysics Track, the electives include BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 331, BIOL 351, BIOL 381, BIOL 404, BIOL, 420, CHEM 221, CHEM 330, COSC 111, COSC 112, MATH 211, MATH 260, STAT 235, or PHYS 343.  In the Biochemistry Track, the electives include BIOL 220, BIOL 241, BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 351, BIOL 370, BIOL 381, BIOL 404, BIOL, 420, CHEM 231, COSC 111, MATH 140, MATH 272, or STAT 235.  Other courses not listed here may satisfy this elective upon approval by the Advisory Committee.

The required advanced course is BCBP 400/CHEM 400/PHYS 400/BIOL 400. 

Special Topics Course BCPB 490 may be elected for students who wish an intensive laboratory or research tutorial in Biochemistry and Biophysics with individual members of the faculty.

For completion of the major, a comprehensive requirement consists of attendance at 6 or more BCBP approved seminars during your senior year, and presentation of a paper to a committee of BCBP faculty. 

Departmental Honors Program: Some majors may elect to pursue an independent research project that enables them the opportunity to graduate with honors.  Candidates for the degree with honors should elect BCBP 498 and 499D.

240 The Physics and Biology of Ultrasound

(Offered as PHYS 240 and BCBP 240)  Why is ultrasound the most commonly used imaging technology used at clinics and hospitals? What happens at the biological level when ultrasound interacts with living matter? How can ultrasound be used for gentle imaging purposes, but also for disrupting cell membranes, bursting blood clots and breaking kidney stones? What other biological applications of ultrasound exist in modern research? We will answer these questions and more by first studying the theory and principles of acoustic waves at higher frequencies, including related phenomena such as acoustic streaming, acoustic radiation forces and cavitation, followed by a walk-through of modern biologically relevant applications of ultrasound. We will also introduce a novel research area called microscale acoustofluidics, where ultrasound is applied to microfluidic systems with applications in, for example, cellular separation, enrichment, isolation and tissue engineering.

Requisite: PHYS 116/123, PHYS 117/124, and MATH 111, or evidence of equivalent coverage in pre-collegiate courses. Fall semester. Stint Fellow Viklund.

2017-18: Offered in 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.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

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. Omitted 2017-18.  Professor Williamson.

2017-18: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017

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 Bishop and Jeong.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) 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 15 students. Open to juniors and seniors. Fall semester.  Professor Jeong.

2017-18: Offered in Fall 2017
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016

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 Carter.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017

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.  Omitted 2017-18.  Professor Williamson. 

2017-18: Not offered
Other years: Offered in Spring 2011, Fall 2016

490 Special Topics

Fall and spring semesters.

2017-18: Offered in Fall 2017 and Spring 2018
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 2016, Spring 2017

499D, 498 Senior Departmental Honors

A double course.  Spring semester.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

Five College Programs & Certificates

View Index

Biochemistry and Biophysics

Advisory Committee:  Professors Bishop, Goutte, Hansen, Loinaz (Chair), O'Hara, Poccia†, and Williamson; Associate Professor Jaswal; Assistant Professors Carter, Jeong, and Purdy. 

† On leave fall semester 2017-18.

Biochemistry and Biophysics is an interdisciplinary major that integrates the three disciplines of Biology, Chemistry, and Physics, using the principles of chemistry and  physics to explain and explore biological phenomena.

Major Program:  A student in the major takes six foundational courses in the three disciplines as well as three additional courses to develop a more advanced understanding along either a more biophysical or biochemical track.  Students develop their expertise by the election of two courses from a list of electives, at least one of which is a biology course with a lab.  One advanced course completes coursework for the major. 

The six foundational courses are CHEM 151/155, CHEM 161, BIOL 191, BIOL 251/291, PHYS 116/123, and PHYS 117/124.

The three additional courses depend on which track a student elects.  Students who are on the Biophysics Track will take MATH 140/272/STAT 235/PHYS 227; PHYS 225/CHEM 351; and PHYS 230/CHEM 361.  Students who are on the Biochemistry Track will take CHEM 221, BIOL 331, and PHYS 230/CHEM 361.

Two electives are then chosen, at least one of which must be a laboratory course in biology.  In the Biophysics Track, the electives include BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 331, BIOL 351, BIOL 381, BIOL 404, BIOL, 420, CHEM 221, CHEM 330, COSC 111, COSC 112, MATH 211, MATH 260, STAT 235, or PHYS 343.  In the Biochemistry Track, the electives include BIOL 220, BIOL 241, BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 351, BIOL 370, BIOL 381, BIOL 404, BIOL, 420, CHEM 231, COSC 111, MATH 140, MATH 272, or STAT 235.  Other courses not listed here may satisfy this elective upon approval by the Advisory Committee.

The required advanced course is BCBP 400/CHEM 400/PHYS 400/BIOL 400. 

Special Topics Course BCPB 490 may be elected for students who wish an intensive laboratory or research tutorial in Biochemistry and Biophysics with individual members of the faculty.

For completion of the major, a comprehensive requirement consists of attendance at 6 or more BCBP approved seminars during your senior year, and presentation of a paper to a committee of BCBP faculty. 

Departmental Honors Program: Some majors may elect to pursue an independent research project that enables them the opportunity to graduate with honors.  Candidates for the degree with honors should elect BCBP 498 and 499D.

240 The Physics and Biology of Ultrasound

(Offered as PHYS 240 and BCBP 240)  Why is ultrasound the most commonly used imaging technology used at clinics and hospitals? What happens at the biological level when ultrasound interacts with living matter? How can ultrasound be used for gentle imaging purposes, but also for disrupting cell membranes, bursting blood clots and breaking kidney stones? What other biological applications of ultrasound exist in modern research? We will answer these questions and more by first studying the theory and principles of acoustic waves at higher frequencies, including related phenomena such as acoustic streaming, acoustic radiation forces and cavitation, followed by a walk-through of modern biologically relevant applications of ultrasound. We will also introduce a novel research area called microscale acoustofluidics, where ultrasound is applied to microfluidic systems with applications in, for example, cellular separation, enrichment, isolation and tissue engineering.

Requisite: PHYS 116/123, PHYS 117/124, and MATH 111, or evidence of equivalent coverage in pre-collegiate courses. Fall semester. Stint Fellow Viklund.

2017-18: Offered in 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.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

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. Omitted 2017-18.  Professor Williamson.

2017-18: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017

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 Bishop and Jeong.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) 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 15 students. Open to juniors and seniors. Fall semester.  Professor Jeong.

2017-18: Offered in Fall 2017
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016

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 Carter.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017

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.  Omitted 2017-18.  Professor Williamson. 

2017-18: Not offered
Other years: Offered in Spring 2011, Fall 2016

490 Special Topics

Fall and spring semesters.

2017-18: Offered in Fall 2017 and Spring 2018
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 2016, Spring 2017

499D, 498 Senior Departmental Honors

A double course.  Spring semester.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

Honors & Fellowships

View Index

Biochemistry and Biophysics

Advisory Committee:  Professors Bishop, Goutte, Hansen, Loinaz (Chair), O'Hara, Poccia†, and Williamson; Associate Professor Jaswal; Assistant Professors Carter, Jeong, and Purdy. 

† On leave fall semester 2017-18.

Biochemistry and Biophysics is an interdisciplinary major that integrates the three disciplines of Biology, Chemistry, and Physics, using the principles of chemistry and  physics to explain and explore biological phenomena.

Major Program:  A student in the major takes six foundational courses in the three disciplines as well as three additional courses to develop a more advanced understanding along either a more biophysical or biochemical track.  Students develop their expertise by the election of two courses from a list of electives, at least one of which is a biology course with a lab.  One advanced course completes coursework for the major. 

The six foundational courses are CHEM 151/155, CHEM 161, BIOL 191, BIOL 251/291, PHYS 116/123, and PHYS 117/124.

The three additional courses depend on which track a student elects.  Students who are on the Biophysics Track will take MATH 140/272/STAT 235/PHYS 227; PHYS 225/CHEM 351; and PHYS 230/CHEM 361.  Students who are on the Biochemistry Track will take CHEM 221, BIOL 331, and PHYS 230/CHEM 361.

Two electives are then chosen, at least one of which must be a laboratory course in biology.  In the Biophysics Track, the electives include BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 331, BIOL 351, BIOL 381, BIOL 404, BIOL, 420, CHEM 221, CHEM 330, COSC 111, COSC 112, MATH 211, MATH 260, STAT 235, or PHYS 343.  In the Biochemistry Track, the electives include BIOL 220, BIOL 241, BIOL 251, BIOL 271, BIOL 291, BIOL 301, BIOL 310, BIOL 321, BIOL 351, BIOL 370, BIOL 381, BIOL 404, BIOL, 420, CHEM 231, COSC 111, MATH 140, MATH 272, or STAT 235.  Other courses not listed here may satisfy this elective upon approval by the Advisory Committee.

The required advanced course is BCBP 400/CHEM 400/PHYS 400/BIOL 400. 

Special Topics Course BCPB 490 may be elected for students who wish an intensive laboratory or research tutorial in Biochemistry and Biophysics with individual members of the faculty.

For completion of the major, a comprehensive requirement consists of attendance at 6 or more BCBP approved seminars during your senior year, and presentation of a paper to a committee of BCBP faculty. 

Departmental Honors Program: Some majors may elect to pursue an independent research project that enables them the opportunity to graduate with honors.  Candidates for the degree with honors should elect BCBP 498 and 499D.

240 The Physics and Biology of Ultrasound

(Offered as PHYS 240 and BCBP 240)  Why is ultrasound the most commonly used imaging technology used at clinics and hospitals? What happens at the biological level when ultrasound interacts with living matter? How can ultrasound be used for gentle imaging purposes, but also for disrupting cell membranes, bursting blood clots and breaking kidney stones? What other biological applications of ultrasound exist in modern research? We will answer these questions and more by first studying the theory and principles of acoustic waves at higher frequencies, including related phenomena such as acoustic streaming, acoustic radiation forces and cavitation, followed by a walk-through of modern biologically relevant applications of ultrasound. We will also introduce a novel research area called microscale acoustofluidics, where ultrasound is applied to microfluidic systems with applications in, for example, cellular separation, enrichment, isolation and tissue engineering.

Requisite: PHYS 116/123, PHYS 117/124, and MATH 111, or evidence of equivalent coverage in pre-collegiate courses. Fall semester. Stint Fellow Viklund.

2017-18: Offered in 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.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

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. Omitted 2017-18.  Professor Williamson.

2017-18: Not offered
Other years: Offered in Fall 2007, Fall 2012, Spring 2017

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 Bishop and Jeong.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017

371 Molecular Genetics W/Lab

(Offered as BIOL 371 and BCBP 371) 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 15 students. Open to juniors and seniors. Fall semester.  Professor Jeong.

2017-18: Offered in Fall 2017
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015, Fall 2016

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 Carter.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016, Spring 2017

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.  Omitted 2017-18.  Professor Williamson. 

2017-18: Not offered
Other years: Offered in Spring 2011, Fall 2016

490 Special Topics

Fall and spring semesters.

2017-18: Offered in Fall 2017 and Spring 2018
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 2016, Spring 2017

499D, 498 Senior Departmental Honors

A double course.  Spring semester.

2017-18: Offered in Spring 2018
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016, Spring 2017