Proposal to Make BCHM 465 and BCHM 485
Required Courses for the Biochemistry Major
Introduction: The Department of Chemistry and Biochemistry is
submitting a request to make BCHM 465 (biochemistry III) and the
new BCHM 485 (physical biochemistry; proposed) required courses
for biochemistry majors. The present status of 465 is that of
an elective; 485 will replace CHEM 482 (physical chemistry II)
as a required course. The science and math courses required for
the major are outlined below.
Present Courses
CHEM 143
CHEM 153
CHEM 227
CHEM 237
CHEM 247
BCHM 461
BCHM 462
BCHM 464
CHEM 395
CHEM 481
CHEM 482
CHEM 483
CHEM 425
Capstone
(5 cr)
(3)
(4)
(4)
(4)
(3)
(3)
(3)
(1)
(3)
(3)
(2)
(4)
Total 45 cr
Supporting
Courses
MATH 140 (4)
MATH 141 (4)
BCSI 105 (4)
PHYS 141 (4)
PHYS 142 (4)
BSCI 2xx (3-4)
BSCI 4xx (3)
Total 26-27 cr
New Program
(proposed)
CHEM 143 (5 cr)
CHEM 153 (3)
CHEM 227 (4)
CHEM 237 (4)
CHEM 247 (4)
BCHM 461 (3)
BCHM 462 (3)
BCHM 464 (3)
BCHM 465 (3)
CHEM 395 (1)
CHEM 481 (3)
BCHM 485 (3)
CHEM 483 (2)
CHEM 425 (4)
Capstone
Total 45-8 cr*
*BCHM 465 is an approved capstone. If BCHM 465 is
used to satisfy this requirement the total credits
would remain at 45
BCHM 465: Although, the addition of BCHM 465 to the major
requirements adds three additional credits, there is, in
practice, no net increase since the course can be used to
satisfy the capstone requirement. Many biochemistry majors take
three or more credits of CHEM 399 (undergraduate research, also
a capstone) in addition to BCHM 465. Over the last two
semesters, spring and fall 2003, the enrollment in BCHM 465 was
46 students.
Timing: The BCHM 465 requirement will go into effect for students
entering the biochemistry major in Jan. 2004 and after.
Rationale: Molecular biology (genomics, proteomics,
bioinformatics, and systems biology) is likely to be one of the
major areas of scientific and technological innovation in the
coming century. In particular, the Maryland biotechnology
corridor (Human Genome Sciences, Celera, TIGR, MedImmune, NIH,
NCI, EPA, FDA, IGEN, EntreMed, Gene Logic, Oncor, hundreds of
others) is vital to the continuing economic health of the State.
Our biochemistry graduates are employed throughout this area and
need a strong foundation in biological information processing.
Currently biochemistry majors are exposed to this material bit
by bit, over and over, in patchy and qualitative ways in lowerdivision biology courses. For example, biochemistry majors know
what a DNA polymerase is, that ribosomes make proteins, but not
how, and perhaps that DNA is continually damaged and repaired. It
is essential the majors take a cohesive advanced course that
covers this material (and more) from a rigorous bio/chemical
perspective. BCHM 465 is that course, but to date it has not been
a graduation requirement. It is estimated that about half of the
biochemistry majors take 465, and up to half of the 465
enrollment comes from other majors, including chemistry.
A typical BCHM 465 syllabus is attached.
BCHM 485: The proposal to establish BCHM 485, physical
biochemistry, has been submitted (VPAC log # 0313090). 485 will
replace CHEM 482 (physical chemistry II) as a degree requirement
for biochemistry majors starting in the Fall 2004 semester. It
is hoped that the initial offering of 485 will take place in the
spring 2004 semester. In the event a biochemistry major has
already taken CHEM 482, it will be used as the major requirement
in lieu of 485.
____________________
Department PCC Chair
Chemistry & Biochemistry
___________________
Dean
College of Life Sciences
_____________________
Department Chair
Chemistry and Biochemistry
Biochemistry 465 (Biochemistry III: Molecular Genetics) — Spring, 2002
TuTh, 9:30-10:45 a.m., Chemistry 0128
Assoc. Prof. Jason D. Kahn, Dept. of Chemistry and Biochemistry, UMCP
Office:
Chemistry 2505 (in Biochemistry, Wing 5 of the Chemistry
complex)
Office hours:
Weds. 2-3 p.m., Thurs. 1-2 p.m., Chemistry 2505; there is no
TA for the course
Contacting me: kahn@adnadn.umd.edu much preferred to 405-0058. Please do not
drop in to my office or lab, but I will be happy to set up
Class web site:
appointments outside of office hours if necessary.
http://www.biochem.umd.edu/biochem/kahn/bchm465; there will also be an e-mail reflector.
Course Description:
This course concerns the structure and function of nucleic acids and the mechanisms of nucleic acid
transactions: a biochemical approach to molecular genetics. We will generally cover both prokaryotic
and eukaryotic systems, emphasizing common logic and mechanisms. Topics are as follows:
•
Chemistry and structure of DNA and RNA, from nucleotides to chromosomes,
and some methods for studying, sequencing and manipulating nucleic acids.
Simple bioinformatics.
•
Interactions between nucleic acids and proteins.
•
Selected aspects of the biochemistry and regulation of DNA replication,
transcription, recombination, and repair, and how these processes interact
with each other.
•
Translation, RNA splicing, and general RNA catalysis.
Texts (note that the course is primarily lecture-based):
Required: Weaver, R. F. (2002). Molecular Biology. 2nd ed., WCB/McGraw-Hill,
Boston. Excellent source for historical and modern experiments. Also see
http://www.mhhe.com/biosci/cellmicro/weaver2/.
Occasional required reading from the primary or review literature may be
provided.
Recommended: Any of the standard Biochemistry texts you have used for BCHM
461, 462, or 463.
Other recommended sources,
Chemistry Library:
available
on
reserve
in
the
White
Memorial
Bates, A. D. and Maxwell, A. (1993). DNA Topology. Oxford: IRL Press at
Oxford University Press. Excellent short monograph on this difficult
topic.
Bloomfield, V.A., Tinoco, I., Jr. and Crothers, D.M. (2000). Nucleic Acids:
Structure, Properties and Functions. University Science Books, Sausalito
CA. Nucleic acid structure, biophysical chemistry.
Kornberg, A. and Baker, T. A. (1992). DNA Replication. 2nd ed. New York: W.H.
Freeman and Co. Great source for historical background, good breadth.
Ptashne, M. (1992). A Genetic Switch: Phage λ and Higher Organisms. 2nd ed.
Cambridge, MA: Cell Press and Blackwell Scientific. Heuristics of gene
regulation.
Schleif, R. (1993). Genetics and Molecular Biology. 2nd ed. Baltimore: The
Johns Hopkins University Press. Eclectic, emphasizing experiments leading
to conclusions.
Travers, A. (1993). DNA-Protein Interactions. London: Chapman & Hall. Focuses
on DNA structure.
Wolffe, A. (1999). Chromatin: Structure and Function. 3rd ed. San Diego:
Academic Press, Inc. Covers from structure to biology.
Requirements, Grading and Academic Honesty Policies:
There will be two 75-minute midterm exams (100 pts each), group class
projects in lieu of a third exam (75 pts), and a two hour final (150 pts).
Exams will be about 50% short-answer questions, testing your comprehension of
lecture material, and about 50% essay or computational questions, testing
your ability to apply and extend this basic knowledge. The final will
explicitly cover only the latter part of the course but will inevitably draw
on older material. There will be a review session before each exam (typically
Tuesday evening before a Thursday exam, or to be determined). Past years’
exams will be on the web site and the answers will be on reserve in the White
Memorial Chemistry Library.
The class projects, to be conducted by small groups, are intended to give you and others an understanding of
the sources of our knowledge of molecular machines. Each group of 4-5 students will study a type of
DNA/RNA transaction (e.g. replication, transcription, repair, RNA splicing, recombination, translation).
The panoply of components involved in the process will be schematized in web page form, with links to
pages on the experiments in which they were first identified, their essential functions identified, and their
structures if available. Last year’s class did similar projects, with generally excellent results. This year,
some groups will refresh previous web pages with more current information, while other groups will do
similar work on new topics. The goal is that at the end of this class we will all be proud to make the work
generally accessible as a teaching resource useful to the world at large. More information will be
provided on the projects.
Your final letter grade will be based on your performance relative to the
class as a whole and to my expectations (i.e. it’s curved, but I draw the
lines between grade levels depending on how I felt the class as a whole
performed). Midterm letter grades will not be assigned. Final grades, with
plus/minus, will be given out only through the MARS system. The exams are
quite difficult, but in the past I have had few complaints about final
grades.
I
encourage
questions
and
discussion
in
class,
but
class
participation does not affect grading.
If you absolutely must miss a midterm exam, you must call me in advance or
within 24 hours after the exam, and you must also present a valid University
excuse, in order to be eligible for the assignment of a grade based on the
remaining course work. If you miss the final, do not turn in a project, or
miss both hour exams, you will receive a failing grade.
The University has an active Student Honor Council, which administers an
Honor Code. The Honor Council sets high standards for academic integrity, and
I support its efforts. Please note in this regard the University Honor
Pledge. The Student Honor Council proposed and the University Senate approved
this Pledge: “I pledge on my honor that I have not given or received any
unauthorized assistance on this assignment/examination.” The Pledge statement
should be handwritten and signed on the front page of all examinations and
the group project. Students who fail to write and sign the Pledge will be
asked
to
confer
with
me.
(Adapted
from
http://www.inform.umd.edu/CampusInfo/Departments/JPO/AI/honorpledge/.)
Furthermore, I otherwise expect and enforce adherence to the University’s Code of Academic Integrity,
found at http://www.inform.umd.edu/CampusInfo/Departments/JPO/code_acinteg.html. Specifically,
“plagiarism” will be interpreted in its broadest sense: ideas from others must be referenced; words from
others must be in quotation marks and referenced (from Phil DeShong). Paraphrasing without
referencing will be considered plagiarism. Extensive paraphrasing from a single source is unacceptable,
referenced or not. You are hereby specifically directed to read my personal statement on plagiarism as a
condition of taking this course, at http://www.biochem.umd.edu/biochem/kahn/plagiarism.html. Please
do not test me on this. Plagiarism is surprisingly easy to detect and I will pull the trigger without
hesitation.
Lecture Schedule (approximate):
READING
ASSIGNMENTS ARE FOR REFERENCE, NOT REQUIRED UNLESS EXPLICITLY STATED.
ALL
I.
1.
ASSIGNMENTS REFER TO
WEAVER, MOLECULAR BIOLOGY.
Nucleic Acid Structure and Chemistry, Protein-Nucleic Acid Interaction (12 lectures)
Introduction; nucleic acid building blocks
Chapters 1, 2, 3
1/29/02
Central dogma, nucleotide structure, primary structure, chemical stability, nomenclature
2.
Structures of double helices
A, B, and Z form helices, base pairing and hydrogen bonding
Chapter 2
3.
DNA and RNA hybridization and thermodynamics
Chapters 2, 5
Base-pair stability rules, melting, hypochromism, hybridization, gene chips
2/5/02
4.
RNA structure and triple helices
Chapters 2, 19
Tertiary structure and tRNA, prediction of RNA folding, antisense and modified DNA
2/7/02
5.
DNA bending, twisting, and supercoiling; topoisomerases
Chapters 6, 7, 20
Persistence length, linking number, superhelix structure, topo reaction mechanisms
2/12/02
6.
Enzymatic manipulation of nucleic acids
Chapters 4, 5
Restriction enzymes, nucleases, radiolabeling, basic genetic engineering, polymerases, PCR
2/14/02
7.
Sequencing and synthesis of DNA and RNA
Maxam-Gilbert and Sanger sequencing, genomics, bioinformatics
2/19/02
8.
Catch-up day on nucleic acid sequence and structure
2/21/02
9.
Methods for studying protein-nucleic acid complexes
Chapters 5, 9
Binding curves, mobility shifts, footprinting, in vitro and in vivo crosslinking, structural methods
2/26/02
10.
Protein structural motifs for nucleic acid binding
Helix-turn-helix, zinc fingers, bZIP proteins, TBP, hnRNP, etc.
2/28/02
11.
Recognition of nucleic acids
Chapters 9, 12
Major groove vs. minor groove, hydrogen bonding, direct vs. indirect readout, deformability
Chapters 5, 24
Chapters 9, 12
—> EXAM I <— Covers through lecture 10
12.
II.
1/31/02
3/5/02
3/7/02
Chromosome structure
Chapter 13
Nucleosomes, chromatin, higher-order structure, telomeres, effects on transcription
3/12/02
DNA Transactions (10 lectures)
13.
DNA replication: fundamental mechanisms
Polymerization reaction mechanisms, fidelity, structure
Chapters 3, 20, 21
3/14/02
14.
Genome replication
Chapters 20, 21
Origin recognition and polymerase holoenzyme in E. coli; the cell cycle
3/19/02
15.
Transcription: fundamental mechanisms
Chapters 6, 8, 10, 11
RNA polymerases, transcription cycle, transcription bubble, supercoiling
3/21/02
Spring Break March 25-29
16.
Regulation of transcription in prokaryotes
Chapters 7, 8
Repression and activation paradigms: lac operon, araC, ntrC; searching mechanisms
4/2/02
17.
Transcription in eukaryotes
Chapters 10, 11, 12, 13
Holoenzyme vs. initiation complex assembly, activators, chromatin, recruitment
4/4/02
18.
Catch-up day
—> PROJECT OUTLINES DUE <—
4/9/02
19.
Homologous recombination
Holliday junctions, recABCD
Chapter 22
4/11/02
20.
Site-specific recombination
λ phage integration/excision, HIV integrase
Chapter 23
4/16/02
—> EXAM II <— Covers through Lecture 19
4/18/02
21.
DNA repair
BER, NER, mismatch repair, cancer
Chapter 20
22.
“Interprocess communication”
Review of regulatory and biochemical connections among replication, transcription, repair
4/23/02
4/25/02
III. RNA Transactions (5 lectures)
23.
Translation: fundamental chemistry, fidelity
tRNA synthetases, peptidyl transferase chemistry, proofreading
Chapters 18, 19
4/30/02
24.
Translation: mechanism and regulation
Ribosome structure, elongation cycle, mRNA degradation
Chapters 18, 19
5/2/02
25.
Catalytic RNA
Self-splicing RNA, ribozymes, origin of life
Chapter 14
5/7/02
26.
RNA splicing
mRNA splicing mechanisms
—> PROJECTS DUE <—
Chapters 14, 16
5/9/02
27.
Review
FINAL EXAM: Covers Lectures 20-27
5/14/02
Tuesday, 5/21/02, 1:30-3:30 p.m., Chem. 0128
A proposal for a new course, Physical Biochemistry (BCHM 485), to replace
CHEM 482 as a requirement for the Biochemistry major
BCHM 485, Physical Chemistry for Biochemists
Rationale
Biochemistry 485? Why change physical chemistry for biochemists? There are several excellent
reasons. First, even our best biochemistry students do not understand the applicability of physical
chemistry to their interests in biology and biochemistry. A course tailored more to the application of
physical chemistry to biological systems will be much more interesting, useful, and attractive to them.
Second, there is far too much physical chemistry to be taught in a year, and inevitably some topics are
emphasized more than others. The physical chemistry most useful for biomolecular science, versus a
traditional physical chemistry course, concentrates more on statistical mechanics, on modeling and
simulation, on the liquid phase, and on polymer dynamics. Finally, biochemistry is becoming a more
and more physical science. The recent revolutions in single-molecule methods, in the structural
determination of macromolecular complexes like the ribosome, in quantitative simulation methods,
and in the understanding of genetic and metabolic networks are all based on physical chemistry
techniques and principles. A working knowledge of biophysical chemistry is essential to tomorrow’s
biochemist. We are attempting to send our graduates out with rigorous yet practical training in the
ideas that will help them bring biology into the 21st century.
History and Scheduling
The biochemistry and physical chemistry divisions met in December to discuss these issues, and
agreed in outline to the plans below. A committee (Kahn, Fushman, Muñoz, Walker, Weeks) was
formed to hash out the details of articulation between 481 and 482 and reasonable syllabi. The goal is
to have BCHM 485 in place for the spring, 2004 semester. Drs. Fushman and Muñoz will teach the
course initially, with Dr. Fushman as the first instructor. Other faculty who might be suitable include
Beckett, English, Hu, Kahn, Lorimer, Thirumalai and future hires in the areas of physical and
biochemistry. We anticipate enrollment of about 30-40 students per year. The course is a core
requirement for biochemistry majors and will offered both fall and spring semesters. The number of
CHEM 482 sections (physical chemistry II for chemistry and chemical engineering majors) will be
reduced from 3 to 2 per year.
Details of the Proposal
1. Biochemistry majors will continue to take CHEM 481 as before. 481 is slatted to become more
molecules-oriented and less formalism-oriented. As part of this process, it is suggested covering
more statistical mechanics in CHEM 481 and reducing some coverage of classical
thermodynamics. Rob Walker’s previous and revised 481 syllabi are appended below. In addition,
more examples and problems drawn from biochemistry will be used in 481.
2. The physical chemistry track will bifurcate in the second semester. Chemistry majors will take
CHEM 482 as before. Biochemistry majors will take BCHM 485 or may opt to take CHEM 482
as before. Credit will not be given for both CHEM 482 and BCHM 485. BCHM 485 will have the
same prerequisites as CHEM 482 and will not be a prerequisite for any other course. Many
students will have had BCHM 461 and 462 first and these will be useful but not necessary.
3. Biochemistry 485 will be a rigorous, mathematically demanding physical chemistry course
emphasizing the principles and applications most relevant to biochemistry. It will focus on three
main areas: (1) statistical mechanics with applications to biochemistry, (2) kinetics from
Maxwell-Boltzmann to physical-organic and enzymes, and (3) quantum mechanics with
applications to spectroscopy and structure determination. See the attached proposed syllabus by
Fushman, Kahn, and Muñoz, which has benefited substantially from commentary by the physical
chemistry division. A CHEM 482 syllabus from spring 2003 is included for comparison. The
BCHM 485 syllabus is feasible, although ambitious, for a one-semester course. It is similar to
courses taught at Madison (offered as a one-semester physical chemistry replacement), UNC
(optional course in addition to 2 semesters of physical chemistry), Harvard (one-semester physical
chemistry replacement), and Berkeley (two-semester physical chemistry for biologists).
ATTACHED: Syllabi for BCHM 485 (proposed), CHEM 481, fall 2003, CHEM 482, spring 2003.
PHYSICAL BIOCHEMISTRY
(PHYSICAL CHEMISTRY FOR BIOCHEMISTS)
BCHM 485
One-semester course, two 75 min or three 50 min lectures per week
Pre-requisite: CHEM 481
Credit will not be granted for both CHEM 482 and BCHM 485
PROPOSED SYLLABUS
Week
1
2
3
4
5
General area
Statistical
thermodynamics
Statistical
thermodynamics
Statistical
thermodynamics
Statistical
thermodynamics
Kinetics
6
Kinetics
7
Kinetics
8
Quantum
9
Quantum
10
Quantum
11
Quantum
Specific topics, description
Review the concept of partition functions. Applications to
binding equilibria, single- and multicomponent systems,
phase transitions. Crystallization.
Statistical mechanics of biomolecules as polymer chains:
helix-coil transition, protein folding, lattice models,
wormlike chain.
Review of solutions (non-ionic and ionic) and
polyelectrolytes. Applications in biochemistry: dialysis,
equilibrium sedimentation, liquid chromatography.
Transport phenomena, channels, diffusion equation,
Brownian motion. Applications in biochemistry:
sedimentation and electrophoresis.
Kinetic theory of gases. Maxwell-Boltzmann. General
kinetics. Differential and integrated rate laws.
Transition state theory. Statistical mechanical treatment.
Physical organic chemistry: mechanisms of chemical
reactions.
Liquid phase kinetics. Diffusion limited processes.
Kinetics methods in biochemistry: relaxation methods.
Enzyme kinetics.
Postulates of quantum mechanics. Observables and
operators (+operator algebra), the uncertainty principle,
wave functions and eigenvalues, Schrödinger equation.
Postulates of quantum mechanics. Quantization of energy,
particle-in-a-box, harmonic oscillator, rigid rotor,
separation of variables. Quantization of angular
momentum.
Postulates of quantum mechanics. Hydrogen atom.
Electron spin, Pauli principle. Atomic states.
Spectroscopy. Selection rules.
Molecules, rotation and vibration, Born-Oppenheimer
approximation. Electronic spectra. Optical spectroscopy.
Applications to biomolecules: absorption, circular
dichroism, vibrational spectroscopy.
Reading
B: 166201
EC: 649686
EC: 271358
EC:700739
B: 651696
B: 702725
EC: 212258
B:273287
B: 288306,316347
B: 352365,371382.
B: 403405, 481516. EC:
593-604
12
Quantum
Fluorescence. Techniques, applications to biomolecules
13
Quantum
Magnetic resonance spectroscopy (ESR, NMR).
Applications to biomolecules.
14
Diffraction
Scattering. X-ray, electron, neutron diffraction, crystal
structures, space symmetry groups. Methods for
biomolecular structure determination.
EC: 582589
B:560582; EC:
605-636
EC: 798841
Exams and assignments:
3 hour exams (lowest dropped, 40%)
final exam (30%)
graded homework assignments every 2 weeks (30%)
This syllabus is designed to cover topics that are particularly relevant to problems and applications of
physical methods to modern biochemistry. Therefore the course is focused on the physical properties
of the liquid state, polyelectrolytes, kinetic theory, and statistical mechanics of polymer chains. There
is significant emphasis on various experimental techniques: sedimentation, chromatography,
electrophoresis, relaxation kinetics, a broad range of spectroscopies applied to biomolecules, and on
methods for structure determination. These techniques are used in the everyday work of the
biochemistry lab, and a student graduating with a degree in biochemistry must be familiar with their
physical background.
Mathematical level required: biophysical chemistry is a quantitative discipline. Many of the problems
and techniques discussed throughout the course require familiarity with the following mathematical
methods: basic vector analysis, derivation and integration techniques, methods to solve differential
equations, determinant and matrix calculus. Additional elements of linear algebra will be introduced
in the quantum part of the course as required.
Textbooks:
B : David Ball, Physical Chemistry. Brooks/Cole –Thomson Learning. (Same textbook as CHEM
481)
EC : David Eisenberg, Donald Crothers, Physical Chemistry with Applications to the Life Sciences.
Benjamin/Cummings Publishing Co. (available in softcover for $69.).
Physical Chemistry I
Chemistry 481
FALL 2003
SYLLABUS
General info
instructor:
office:
email:
phone:
office hours:
Dr. Rob Walker
2224D Chemistry
rw158@umail.umd.edu
301-405-8667
Th. 2 p.m. – 3:30 p.m. or by appointment
Lecture: MWF
8:00 am – 8:50 am
1402 Chemistry
Instructional Materials
Physical Chemistry by D. Ball (1st edition)
Additional reading in Engines, Energy and Entropy (J. Fenn)
Class Format
Attendance is important and expected. The lectures will supplement the text, define goals, and hopefully stimulate
thought and questions. Please try to keep ahead of the lectures in your reading of the assigned text. If a session is missed,
it is the student’s sole responsibility to make up any work missed.
Expectations of Students
Material Covered in Lecture and Assigned Reading:
Students are responsible for all material covered in lecture and in the assigned reading materials that includes
supplemental handouts. All attempts will be made by your instructor to adhere to the outline as indicated below.
However, the presentation may vary somewhat from that of the textbook.
Academic Honor Principle:
Students are expected to observe the University’s Code of Student Conduct. Cheating on examinations and/or problem
sets is not acceptable and will be met with zero tolerance!
Problem Sets:
There will be no quizzes in Chemistry 481. Instead, problem sets will be handed out weekly or bi-weekly. Often these
will consist of assigned problems from the text and several supplemental questions. You are expected to work the
problems and hand in the results in discussion. The TA will grade your answers and solution sets will be provided. You
are encouraged to discuss these problems with each other. However, it is important for you to learn to work these
problems independently, since they mimic typical exam questions and (we hope) the kinds of problem solving skills used
by practicing scientists. You may drop your lowest score provided that it comes on a problem set that was handed in.
(You will not be able to drop a 0 if you fail to hand in a problem set.)
Exams:
You will take three 1-hour exams during the semester in addition to the Final Exam. The hour exams will cover primarily
material discussed since the last exam but may include earlier material as well. As you probably have realized by now,
chemistry is a subject that builds upon what is already known. Accordingly questions on exams (and problem sets) will
frequently require that you use knowledge learned earlier in the semester. The exams themselves will focus on applying
problem solving skills developed in class to new, chemically significant situations. The best way to prepare for exams is
to be completely familiar with the problem sets and to relax.
Grading
Exam 1 (The laws of thermodynamics & free energy)
Exam 2 (chemical equilibrium & phase transitions)
Exam 3 (ionic solutions & electrochemistry)
Final Exam (Cumulative)
Problem Sets
20%
20%
10%
25%
25%
Tentative dates for Exams 1-3 are as follows: October 6 (Hour Exam 1); November 14 (Hour Exam 2); December 3 (Hour
Exam 3). Different weightings of the hour exams approximately reflects the amount of material covered. The Final Exam
is Scheduled for Monday, 15 December from 10:30 am – 12:30 pm and will be cumulative.
Course Outline
Week
topics
Reading
3 Sept
Equations of state, math review
1.1-1.5
8 Sept
Non-ideality (virial, vdW), intro to energy
15 Sept
First Law, Enthalpy, Thermochemistry
2.5-2.12
22 Sept
Entropy – 2 definitions & Second Law
3.1-3.7
PS2
29 Sept
Fund. Eqn., Gibbs Energy
4.1-4.7
PS3
6 Oct
Chem potential, fugacities
4.8-4.9, 4.10
HE1
13 Oct
Equilibrium: an introduction
5.1-5.6
20 Oct
Equilibrium: phanse transitions
6.1-6.7
27 Oct
Equilibrium: multiple components
7.1-7.5
3 Nov
Excess functions, activities
7.5-7.9
PS5
10 Nov
Ionic solutions (& Debye-Hückel)
8.2, 8.6-8.8
HE2
17 Nov
Equilibrium: electrochemical (Nernst Eqn)
24 Nov
Chem 481 challenge?, T’giving
Assignment
1.6-1.8, 2.1-2.4
PS1
PS4
8.3-8.5
PS6
1 Dec
Elements of statistical thermodynamics
17.1-17.5
8 Dec
State functions from stat. thermo.
15 Dec.
Final Exam! (Monday, 15 December, 10:30 am – 12:30 pm)
b
17.6-17.8, 18.8
HE3
PS7
PHYSICAL CHEMISTRY II
CHEM 482, SECTION 0101, MWF 8
SPRING 2003
CHE-2108
PROFESSOR: Dr. J. H. Moore
CHM-2216A
tel: 405-1867; e-mail: jm89@umail.umd.edu
office hours M 9, W3, and by appointment
TEXT: Physical Chemistry by John S. Winn
Week
Topics
Read
29 Jan
the calculation of average properties
molecular velocities
the Maxwell-Boltzmann distribution
mean free path
pressure from gas molecule dynamics
899-915
transport phenomena
diffusion
thermal conductivity
viscosity
952-982
Planck relation
de Broglie relation
postulates of quantum mechanics
operators and operator algebra
uncertainty principle
wave functions and eigen values
Schrödinger Equation
349-371
particle-in-a-box
harmonic oscillator
separation of variables
rigid rotor
388-415
hydrogen atom
angular momentum
electron spin
415-440
3 Feb
10 Feb
17 Feb
24 Feb
EXAM 1 (28 Feb)
3 Mar
10 Mar
helium atom
orbital approximation
antisymmetrization
term symbols
H2+
molecular orbitals (MO's)
H2
451-459, 468-475, 479-488
17 Mar
BREAK
31 Mar
FEMO
498-516, 519-527
molecular electronic configurations
molecular term symbols
536-553
molecules
rotation and vibration
Born-Oppenheimer approximation
691-717
EXAM 2 (4 Apr)
7 Apr
14 Apr
21 Apr
28 Apr
spectroscopy
selection rules
rotation-vibration spectra
electronic spectra
665-682, 720-732
reaction kinetics
rate law
reaction mechanisms
997-1016
temperature dependence
collision theory
1018-1022, 1039-1058
transition state theory
catalysis
1058-1063, 1081-1089
EXAM 3 (2 May)
5 May
a brief introduction to statistical mechanics
thermodynamic variables from statistical mechanics
transition-state theory from statistical mechanics 819-826, 830-833,
852-859, 864-865, 1063-1067
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PREPARATION: Physical chemistry is a fairly rigorous and mathematical topic. It is important to keep abreast
of the reading and lectures. With reading, homework problems and exam preparation, you
may anticipate a minimum of six hours/week of work outside class. The reading assignment
for each week should be read before coming to lecture Monday morning. Take notes as you
read. Pay particular attention to the "Practice with Equations" at the end of each chapter. The
professor for this course is notoriously lazy and can be expected to crib from this section when
writing exams.
QUIZZES:
A brief quiz on the reading assignment each Monday morning. Reading notes may be used
when taking the quiz.
HOMEWORK: Homework will be assigned each Friday and will be due the following Friday. Late homework
will not be accepted.
GRADING:
Homework--20%
Quizzes--20%
Hour Exams--20% each, one exam grade will be dropped, no makeups
Final--20%
FINAL EXAM: 10:30 AM-12:30 PM, Friday, 16 May in CHE-2108.