PHYS 307 -- Introduction to Biophysics -- Spring 2006

Location: MP408         Time: MWF 10:40am - 11:30am
Prerequisites: BIOL 191, CHEM 112, MATH 170, PHYS 112 or 212 with labs.

Text:   "Biophysics An Introduction" by Rodney Cotterill
URL:   http://www.boisestate.ed/physics/kim/phys307
Instructor:    Dr. Byung Kim       ByungKim@boisestate.edu    (208) 426-3659      MP-425
Office Hours:    MWF 9:30am - 10:30am

Week Mon date Topics
 

Part 1; Bonds, Reactions, Transport, and Techniques
Exam 1 over Chapters 1 to 6 on Wed Mar 1

1. 1/16 (Holiday); Introduction; QM and Exclusion Principle, Chemical Bonding
reading:  (No Class);  1; 2.1-2.3;
2. 1/23 Electronegativity and Secondary Bonds; Potentials and Forces; Bond Energies and Spring Const.
reading:       2.4,2.5; 3.1-3.3; 3.4,3.5 
due 1/30 : HW set 1
3. 1/30 Thermal & Stat. Mech.; Acid, Base and Reaction; Diffusion
reading: 4.1-4.3; 4.4-4.6; 5.1
due 2/6 : HW set 2
4. 2/6 Viscosity and Thermal Conduction; XRD; NMR
reading: 5.2, 5.3; 6.1; 6.2
due 2/13 : HW set 3
5. 2/13 AFM;  Optical Tweezers ; Patch Clamps
reading:    6.3 6.4; 6.5;6.6
due 2/22 : HW set 4
6. 2/20 (Holiday); Molecular dynamics  Energy Contours
reading:    (No Class); 6.7;   6.8
due 2/27 : HW set 5
  Part 2: Biological Polymers and Membranes
(Exam 2 over Chapter 7 to 8 on Wed Apr 5)
7. 2/27 Nucleic Acids; Exam 1  ; DNA
reading: 7.1; Chap. 1-6;   7.2
due 3/6 : HW set 6
8. 3/6 RNA; Proteins ; Proteins
reading:      7.3;   7.4; 7.4
due 3/13:   HW set 7
9. 3/13 Protein Folding;  Membranes; Membranes
reading:    7.5; 8.1; 8.1,8.2
due 3/20:   HW set 8
10. 3/20 Membrane Chemistry; Membrane Structure; Membrane Physics
reading:      8.2;  8.2; 8.3
due 4/3:   HW set 9
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SPRING BREAK 3/27-3/13
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  Part 3:    Biological Energy and Muscular Movement
(Exam 3 over Chapters 9 to 10 on Wed Apr 26)
11 4/3 Respiration;   Exam 2; Photosynthesis
reading:    9.1, 9.2; Chap. 7-8; 9.3
due 4/10:    HW set 10
12 4/10 Photo- and ATP- synthesis; ATP Synthesis;  Bacterial Motion
reading:  9.3-9.4; 9.4; 10.1
due 4/17:    HW set 11
13 4/17 Bacterial Motion; Chemical Memory; Muscular Movement  
reading:    10.1; 10.2,10.3; 10.3,10.4 
due 4/24:  HW set 12
  Part 4:    Excitable Membranes and Nerve Signals
(Final Exam over Comprehensive Text)
14 4/24 Diffusion and Mobility of Ions; Exam 3; Resting Potential
reading:  11.1;Chap. 9-10;11.2
due 5/1: HW set 13
15 5/1 Passive Response; Nerve Impulse; Nervous System 
reading:    12.1 ; 12.2; 12.3
due 5/8:  HW set 14
16 5/8 Optional Review;   Final Exam
reading:    comprehensive text, notes, problems, exams 
 

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


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.

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 three in-class exams (worth 10% each) and a comprehensive two-hour final exam (worth 20%.) 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 beginning of next 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 = 87.5 - 100,    B = 75 - 87.5,   C = 60 - 75,   D = 45 - 60