Download BIOC 4521 - College of Biological Sciences

BioC 4521
INTRODUCTION TO PHYSICAL BIOCHEMISTRY
GENERAL COURSE INFORMATION
Fall 2014 9:05A - 9:55A Monday, Wednesday, Friday
Lecture Room: MCB 2-120
INSTRUCTORS
Prof. Kevin Mayo (612-625-9968, [email protected])
Department of Biochemistry, Molecular Biology, and Biophysics
Office: 7-142 MCB, Minneapolis Campus
Office hours: After class or by appointment
Prof. Hideki Aihara (612-624-1491, [email protected])
Department of Biochemistry, Molecular Biology, and Biophysics
Office: 5-266 NHH, Minneapolis Campus
Office hours: After class or by appointment
TEACHING ASSISTANTS
Thomas Bohl ([email protected])
Department of Biochemistry, Molecular Biology, and Biophysics
Office hours: TBA
Soham Shah ([email protected])
Department of Biochemistry, Molecular Biology, and Biophysics
Office hours: TBA
COURSE WEBSITE
http://www.cbs.umn.edu/BMBB/about/courses/bioc4521
email Course Notices: Course information will be sent out by email. University of
Minnesota regulations require that this correspondence go to your assigned
“[email protected]” address. Please be sure to check your umn.edu mailbox frequently. Don’t
forward your umn.edu mail to another account (e.g. hotmail or yahoo), as these accounts
can fill up and reject important messages.
TEXTBOOKS
Physical Chemistry for the Life Science second edition, by Peter Atkins and Julio de
Paula, W. H. Freeman and Company, NY, 2011. ISBN: 978-1-4292-3114-5
The Solutions Manual will be available in the Bookstore and is recommended.
Not required, but may be helpful for certain sections:
Physical Chemistry: Principles and Applications in Biological Sciences,
4th ed. I. Tinoco, Jr., K. Sauer, J. C. Wang, and J. Puglisi. Prentice-Hall 2001.
PREREQUISITES
Chem 1022 Chemical Principles II
Math 1272 Calculus II
Phys 1202 Introductory Physics for Biology and Pre-medicine II
Bioc 4331 Biochemistry I
Also recommended: Chem 2301 & 2302 Organic Chemistry I & II
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COURSE OVERVIEW
The course objective is to introduce and develop physical concepts for the biochemist by
using ideas from physical chemistry (rather than pure mathematical formulations) to
exemplify biochemically relevant phenomena. The desired outcome is for students to
gain a basic understanding of how solution dynamics, thermodynamics, kinetics, and
spectroscopy can be applied to biochemical problems. In addition, the course aims to
provide a solid background in biophysical chemistry for those students who wish to
pursue further study in this field of science.
ATTENDANCE AND PARTICIPATION
Attendance at all of the class sessions is mandatory.
ASSIGNMENTS
Problems are available at the end of the chapter in the text book, and students should
use these problems to practice for in-class quizzes and exams. In addition, assigned
homework will comprise 20% of the final grade for the course.
PERFORMANCE EVALUATON
Grades will be determined by four 50 minute in-class exams, as well as by homework
and class participation. The exams will be closed book, and the questions on exams will
consist of calculations, short answers, and essay questions. Questions about exam
scores or requests for re-grading must be submitted in writing to one of the course
instructors within one week after any given exam is returned. Teaching Assistants
do not have authority to re-grade exams.
Letter grades may not necessarily follow a straight percentage breakdown and will be
determined based on a curve. Graduate and undergraduate students may be evaluated
separately if necessary.
Exam 1
Exam 2
Exam 3
Exam 4
Homework\class participation
20%
20%
20%
20%
20%
Make up Exams: You must contact the instructor either before the exam or in a timeframe
after the exam that is consistent with the reason for missing the exam. Vacations and
interviews are to be scheduled around your exams, not vice versa. The format of the
makeup exam is at the discretion of the instructor, and may include an oral or essay format.
The instructor may decide not to do make up exam and the grade will be prorated based on
the other exams.
Academic Misconduct: Cheating during an exam and altering an exam prior to
submission for regarding are examples of academic misconduct. Violations of
acceptable academic conduct will elicit penalties commensurate with the offense.
Penalties can include assignment of a failing grade for an examination or a failing grade
for the entire course, depending upon the nature and severity of the infraction. Although
collaboration during examinations is strictly forbidden, students may work together on
problem sets if the instructor gives explicit permission. See the “scholastic dishonesty”
section of the Student Conduct Code at
http://www1.umn.edu/regents/policies/academic/Student_Conduct_Code.html.
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Academic Integrity: The grade in a course is intended to be a reflection of what you have
learned in the course. Any instances of plagiarism (presenting someone else's work as your
own) will be dealt with through university procedures for academic dishonesty (see
http://www.policy.umn.edu/Policies/Education/Student/ACADEMICMISCONDUCT.html). If
you need assistance in distinguishing between plagiarism and legitimate use and citation of
someone else's work, please refer to http://writing.umn.edu/sws/index.htm.
Accommodations: Students with disabilities that might hinder their ability to participate in
the full range of class activities should contact the instructor as soon as possible. Additional
information on accommodation is also available from Disability Services in 230 Gateway
(V/TTY) 624-4037.
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Lecture, Homework, and Exam Schedule
9/3/14 W
9/5/14 F
9/8/14 M
9/10/14 W
9/12/14 F
9/15/14 M
9/17/14 W
9/19/14 F
9/22/14 M
9/24/14 W
Work and Heat
Energy and Heat Capacity
Entropy
Enthalpy and Phase
Gibbs Free Energy
Chemical potential
Equilibrium constants
Thermodynamics of protein folding
Proton Transfer Equilibria
Homework #1 due
Osmotic pressure, membrane potential
(KM)
(KM)
(KM)
(KM)
(KM)
(HA)
(HA)
(HA)
(HA)
(HA)
9/26/14 F
9/29/14 M
10/1/14 W
10/3/14 F
10/6/14 M
10/8/14 W
10/10/14 F
10/13/14 M
10/15/14 W
Exam #1 (covers 9/3 thru 9/22)
Passive transport, determining molecular weight
Reaction Rate law, Reaction order)
Second order reactions, kinetic data
Parallel & Series reactions, Equilibrium, Relaxation
Michaelis-Menten kinetics
Complex mechanisms of enzyme catalysis
Enzyme inhibition
Homework #2 due
Exam #2 (covers 9/24 thru 10/13)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
10/17/14 F
10/20/14 M
10/22/14 W
10/24/14 F
10/27/14 M
10/29/14 W
10/31/14 F
11/3/14 M
11/5/14 W
NMR spectroscopy
NMR spectroscopy
NMR spectroscopy
NMR spectroscopy
NMR spectroscopy
NMR spectroscopy
Mass spectrometry
Mass spectrometry
Homework #3 due
Exam #3 (covers 10/17 thru 11/3)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
(KM)
11/7/14 F
11/10/14 M
11/12/14 W
11/14/14 F
11/17/14 M
11/19/14 W
11/21/14 F
11/24/14 M
11/26/14 W
11/28/14 F
12/1/14 M
12/3/14 W
12/5/14 F
12/8/14 M
12/10/14 W
Intro to Optical Spectroscopy
Absorption and Emission of Radiation
IR and Raman
UV and VIS
Circular Dichroism
Fluorescence spectroscopy
Single-molecule techniques
Xray crystallography
Xray crystallography
Thanksgiving Break
Xray crystallography
Xray crystallography
Xray crystallography
Xray crystallography
Homework #4 due
Exam #4 (covers 11/7 thru 12/8)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
(HA)
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