*****
Physical Methods of Biochemistry - Fall 2009 *****
Instructor: David W.
Hoffman,
Associate Professor, Dept of Chemistry
& Biochemistry
Office: Room 3.422FA MBB (at
the north end of 3.422)
Office hours: Mon & Thurs
noon - 1 pm, or by appointment.
Email:
dhoffman@mail.utexas.edu
Class meeting: Tuesday &
Thursday 9:30 AM, in Welch 2.256
Class unique number:
54230
Textbook: Mostly, the
course will be based on class notes. If you want to buy a book, a
course text "Principles of Physical Biochemistry" by K.E. van Holde,
W.C. Johnson & P.S. Ho, 2nd edition (2005) ISBN # 0130464279 is
available for those who want. The textbook is optional, not
required.
Schedule for Fall 2009
Thur Aug 27 Course organization;
amino acids & proteins. HW #1 (2
pages, PDF file)
some notes
Tues Sept 1 Similarity among
proteins, multiple sequence alignment and structure.
slides from 2nd class
Thur Sept 3 Nucleic acids - common
motifs, stability, hypochromism. some notes
Tues Sept 8 Electrophoresis, IEF. some notes
Thur Sept 10 Analytical ultracentrifugation,
sedimentation. some notes
Tues Sept 15 Separation of proteins, protein
purification. some notes
Thur Sept 17 Mass
spectrometry.
** hw # 1 due ** some notes
Tues Sept 22 Fluorescence. some notes
Thur Sept 24 Ligand binding. some notes
Tues Sept 29 Isothermal
titration
calorimetry
(ITC) some notes
Thur Oct 1 Surface plasmon
resonance
(SPR) some notes
Tues Oct 6 ***
Midterm exam #1 *** ** hw
# 2 due **
Thur Oct 8 Structure determination;
X-ray
crystallography some notes
Tues Oct 13 Structure determination,
continued class notes
Thur Oct 15 Structure determination,
continued class notes
Tues Oct 20 Structure determination,
continued class notes
Thur Oct 22 Structure determination,
continued class notes
Tues Oct 27 last day of x-ray
crystallography class notes
Thur Oct 29 Small angle x-ray
scattering (SAXS) class
notes
Tues Nov 3 IR and Raman spectroscopy, and
CD. class notes
hw #3 **
hw
# 3 due **
Thur Nov 5 Single molecule
methods. class notes
Tues Nov 10 ***
Midterm exam #2
***
Thur Nov 12 NMR spectroscopy class notes
Tues Nov 17 NMR spectroscopy (continued) class notes
wuthrich nobel lecture
Thur Nov 19 NMR spectroscopy (continued) class notes
Tues Nov 24 NMR for studying molecular motions
Thur Nov 26 Thanksgiving holiday.
Tues Dec 1 Cryo-EM *** hw #
4
due
*** hw #4
Thur Dec 3 topic to be
determined.
Final exam: Date and time
is set by the university registrar.
According to the registrar's web page, the final is Friday Dec. 11, 9
am - noon.
Grading: Midterm exam #1,
midterm exam #2: about 100
pts each; final exam: about 200 pts.
Homeworks,
about 50 pts each.
Course grades will be based on total points earned. Grades will
likely be as follows:
A 93 % of possible points ; A- 90%
of possible points
B+ 87% to 90% ; B 83% to 87% ; B- 80 to
83 %
C+ 77% to 80% ; C 73% to 77% ; C- 70 to
73 %
D+ 67% to 70% ; D 63% to 67% ; D- 60 to
63 %
F < 60 % of possible points
There will not be make up exams, except under
extraordinary circumstances. There is no excuse for over-sleeping
- use two alarms
to wake
up if necessary.
Homework: There will be four
graded
homework assignments. Homework will not be accepted late, except under
truly extraordinary circumstances, such as a documented medical
emergency. I intend to be strict with this, so plan ahead,
and start working on your homework early.
Note regarding homework assignments:
You may discuss
your homework with the instructor, TAs, and other students in the
class. But the work that you
turn in must be your own. Do
not copy another person's work.
Homework may be typed or handwritten, or some combination of
these. But the homework that you turn in should be neat and well
organized.
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