PHYS 307 -- Introduction to Biophysics -- Spring 2008

GOALS: To obtain a basic understanding of the key concepts of biophysics, especially molecular biophysics, by applying physical principles, methods, and techniques to the study of biological phenomena. Lectures stress the elementary behavior of ions, proteins, and nucleic acids in the biological membranes, biopolymers, muscular movement, and nervous systems. The course objectives will be accomplished through lecture and discussion of selected topics in class, through laboratory studies, through group exercises, and by students working through the assigned parts of text, including all assigned homework problems. Assessment will come from the tests (which will be based on the assigned parts of the text, the assigned homework problems, and the lectures), the lab-reports, and the assigned homework.

Location: MP408     Time: Tu Th 4:40 pm - 5:55 am     MP-408
Prerequisites:    BIOL 191, CHEM 112, MATH 170, PHYS 112 or 212 with labs

Text:    "Biophysics, An Introduction" by Rodney Cotterill
Supplemental text: “Molecular Biology of the Cell”, 4th Edition by Alberts et. al.
“Principles of Physical Biochemistry,” by K. E. van Holde, W. C. Johnson, P. S. Ho.
URL:    http://www.boisestate.edu/physics/kim/phys307
Instructor:    Dr. Byung Kim     ByungKim@boisestate.edu     (208) 426-3659     MP-425
Office Hours:   Tu 1:30pm – 4:30 pm or by appointment

 Week  Tue Date  Topics
 
Part 1:   Bonds, Reactions, Transport, and Techniques
(Exam 1 over Chapters 1 to 6 on Thursday Mar 6)

1. 1/22 Introduction,  QM and Exclusion Principle;  Chemical Bonding, Electronegativity and Secondary Bonds
reading:  1, 2.1-2.2;  2.3, 2.4, 2.5
2. 1/29 Potentials and Forces;  Bond Energies and Spring Const.
reading:   3.1-3.3;  3.4,3.5
due 2/5:  HW set 1
3. 2/5 Thermal & Stat. Mech.;  Acid, Base and Reaction
reading:   4.1-4.3;  4.4-4.6
due 2/12:  HW set 2
4. 2/12 Diffusion, Viscosity and Thermal Conduction; XRD
reading:   5.1-5.3;  6.1
due 2/19:  HW set 3
5. 2/19 NMR;  STM and AFM
reading:   6.2;  6.3-6.4
due 2/26:  HW set 4
6. 2/26 Optical Tweezers and Patch Clamps;  Molecular dynamics and Energy Contours
reading:   6.5-6.6;  6.7-6.8
due 3/4:  HW set 5
 
Part 2:   Biological Polymers and Membranes
(Exam 2 over Chapters 7 to 8 on Thursday Apr 3)

7. 3/4 Nucleic Acids and DNA Topology;  Exam 1
reading:   7.1,7.2;  Chap. 1-6;
due 3/11:  HW set 6
8. 3/11 RNA; Protein Structures
reading:   7.3;  7.4
due 3/18:  HW set 7
9. 3/18 Protein Folding;  Membranes Chemistry and Structure
reading:   7.5;  8.1-8.2
due 4/1:  HW set 8
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SPRING BREAK 3/24 - 3/28
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10. 4/1 Membrane Physics;   Exam 2
reading:   8.3;  Chap. 7-8
due 4/8:  HW set 9
 
Part 3:   Biological Energy and Muscular Movement

11. 4/8 Energy and Photosyntheis;  ATP Synthesis;
reading:   9.1-9.3;  9.4
due 4/15:  HW set 10
12. 4/15 Bacterial Motion and Chemical Memory;  Muscular Movement
reading:   10.1-10.2;  10.3
due 4/22:  HW set 11
13. 4/22 Muscular Movement;  Diffusion and Mobility of Ions;
reading:   10.3-10.4;  11.1
due 4/29:  HW set 12

Part 4:   Excitable Membranes and Nerve Signals

14. 4/29 Resting Potential;  Passive Response
reading:   11.2,  12.1
due 5/6:  HW set 13
15. 5/6 Action Potentials;  Nervous System
reading:   12.2;  12.3
due 5/13:  HW set 14
16 5/13 Optional Review;  Final Exam
reading: comprehensive text, notes, problems, exams

****** FINAL EXAM (Comprehensive) on the date TBA ****************


EXAMS: 50% of your grade is based on the exams. ALL EXAMS WILL BE COUNTED, AND NO MAKE-UP EXAMS WILL BE GIVEN. There will be twi in-class exams (worth 12.5 % each) and a comprehensive two-hour final exam (worth 25%.) You may bring one 8.5" by 11" sheet of formulas for each one-hour exam, along with your formula sheets from your previous PHYS 307 exams. All formula sheets must be labeled at the top by exam number, be signed and handwritten by you, and be turned in with your exam. Your formula sheet should contain only numbered formulas from those sections of the chapters that are covered on the exam, and you must write the textbook equation number next to each formula. No other comments, drawing, or other information are allowed on the formula sheet. It is your responsibility to know the meaning of every symbol on your formula sheet, and to understand the meaning, applicability, and use of every equation you include on your formula sheet.

HOMEWORK: 25% of your grade is based on the homework. Hand in what you have on the due date, at the beginning of class. NO LATE HOMEWORK ACCEPTED. Homework problems will form the basis for many of the exam problems. Look over your graded homeworks carefully and make sure you can work and understand every assigned homework problem. You are strongly encouraged to talk to the instructor about homework problems that you do not understand.

LABORATORY: 25% of your grade is based on the lab reports. Turn in what you have at the end of the laboratory class. NO LATE REPORT ACCEPTED.

READING: Consult the syllabus and read the assigned sections before the material is covered in class. As you read, write down any questions you have and bring them to class. Ask questions in class.

ACADEMIC HONESTY: Although you are encouraged to discuss the class lectures, readings, and assignments with your classmates, all the work that you turn in must be your own. No cheating or plagiarism (presenting other people's work as if it were your own) will be tolerated, including any use of homework solutions found on the web. If you make use of sources besides the class lectures or textbooks, you must provide explicit written references to the sources you used. Failure to follow this rule or any others listed in the Academic Handbook could have drastic consequences, including (but not limited to) ejection from the course with a failing grade.

GRADING:

A+ = 92.5 -100,  A = 90 – 92.5,  A- = 87.5 - 90,

B+ = 87.5 - 83,  B = 79 - 83,  B- = 75 - 79,

C+ = 70 - 75,  C= 65 - 70,  C- = 60 – 65,

D+= 55-60,  D=50-55,  D- = 45 -50