Physics 451-076, 452-076, & 581A-001 Biophysics II

This is a three-credit course with undergraduate tracks [451-076(CR/NC) & 452-076(graded)] and a graduate track [581A-001(graded)].

    Biophysics a.k.a. Biological Physics a.k.a. Physical Biology

    The textbook for this course is the book Biological Physics by Philip Nelson published by Freeman and available at the UNM bookstore as well as from Amazon and other web stores. It will be on reserve at the CSEL library when the library acquires a copy.

    The book Molecular Biology of the Cell, Fourth Edition by Bruce Alberts, Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walter is a wonderful source of background material for any course on biophysics. But it is 1463 pages long and amounts to an undergraduate curriculum in molecular and cell biology. So it is not required for this course.

    The course will meet during the fall of 2006 on Tuesdays and Thursdays from 3:00 to 4:15 pm in room 5 of the Department of Physics & Astronomy on Lomas at Yale.

    There are no prerequisites for this course, but first-year physics and elementary calculus would be helpful, as would a vague memory of high-school chemistry and biology.

    The course will begin with a review of Biophysics I. The web pages for that course lie below.

    In the first lecture, I discussed some basic biochemistry: chemical bonds and groups of biological molecules; water, hydrogen bonds, and molecules that are hydrophilic or hydrophobic; acids, bases, and the pH; hydrogen bonds and van der Waals bonds; hydrophobic forces and ionic bonds; monosaccharides.

    In the second lecture, I shall discuss a little more biochemistry: disaccharides and oligosaccharides; fatty acids, lipids, and phospholipids; micelles and bilayers; nucleotides; nucleic acids; thermodynamics; entropy and free energy. This table of relative cancer rates shows that diet, exercise, and environment play an enormous role in determining who gets what cancer.

    Here are my notes for chapter one.

    Here are my notes for chapter two.

    Here and there and there are my notes for chapter three.

    Here and here and here and here and here and here and here and here and here are my notes for chapter four.

    Here, and here, and there are my notes for chapter five.

    Here is a video of a demo of laminar flow at low Reynolds number, R = 0.2.

    First homework problem: Find the scale height in air (or vacuum) for a molecule whose molecular weight is 400. The scale height kT/mg is defined in chapter five. Take T = 295 K. Due 10/5.

    Here, and here, and there are my notes for chapter six.

    Here and there and there are my notes for chapter seven.

    Homework problems: Students in 451 or 452 (undergraduates) should do two of the four problems 7.2, 7.3, 7.5, and 7.6; students in 581 should do all four problems. I will do 7.1 and 7.4 in class. In problem 7.3, you should assume that in the 1 mM salt solution, the osmotic pressure inside a cell just balances the osmotic pressure outside the cell. Let's say that these problems are due on 31 October, Halloween.

    Here and here and here and here and here and here are my notes on chapter 8. Homework problems: Students in 451 or 452 (undergraduates) should do two of the five problems 8.2, 8.3, 8.4, 8.5, and 8.6; students in 581 should do all five problems. I will do 8.1 and 8.7 in class. These problems are due on Tuesday, 21 November, but students with emergencies, such as huge exams on Monday or Tuesday, may turn in their solutions late.

    Here is a cartoon about disulfide bonds, which can form in oxidizing environments when two cysteine side chains are near each other.  Disulfide bonds are broken in reducing environments, like that of the cytosol.  Here (in the jargon of chemists) reduce means "reduce the electric charge, not counting protons."  The cytosol reduces a disulfide bond, breaking it, by adding two neutral hydrogen atoms, which consist of two electrons if one neglects the protons.  The oxidizing environment outside cells can remove the two neutral hydrogen atoms, which consist of two electrons if one neglects the protons, increasing the charge by two units and refroming the disulfide bond.

    Disulfide bonds


    Here and here and here are my notes on chapter 11. A cartoon of ATP synthase and a ribbon diagram of most of its structure. An electron micrograph of a mitochondrion of a liver cell. A cartoon of a mitochondrion. An explanation of this cartoon. A cartoon of oxidative phosphorylation. An electron micrograph of the inner surface of an inner mitochondrial membrane showing ATP-synthases and the molecular machines of the electron-transport chain. A summary of how a mitochondrion makes ATP from oxygen, pyruvate, and fatty acids. Homework problems: Students in 451 or 452 (undergraduates) should do two of the four problems 11.1, 11.2, 11.3, and problem C.11.9; students in 581 should do all four problems. These problems are due on Tuesday, 5 December, but students with emergencies, such as huge exams on Monday or Tuesday, may turn in their solutions late.

    Here is an html file of my notes on Chapter 12.

    Here is a pdf file of a recent talk of mine on vitamin D and prostate cancer.

    The purpose of this course is to teach students of biology and medicine some of the basic physics of cells and to teach students of physics some of the biological applications of physics. Some of the topics of the course are:

  1. Basic physical concepts
  2. Cells
  3. Elementary ideas about probability
  4. Random walks, friction, diffusion
  5. Viscous fluids and Reynolds numbers
  6. Entropy, temperature, and free energy
  7. Entropic forces
  8. Chemical forces and self-assembly
  9. Cooperative transitions in macromolecules
  10. Enzymes and molecular devices
  11. Machines in membranes
  12. Nerve impulses

    13. Known typos and errors in the first, second, and third printings of the textbook Biological Physics are listed here.

    The educational resources of the Biophysical Society are worth looking at.

    The instructor is Kevin Cahill cahill@unm.edu, 277-5318, room 176 of physics department.
    The grader is Douglas Bradshaw bradshaw@unm.edu.

    List of demonstrations:
    1. Sulfuric acid sucks water out of damp sugar, leaving behind carbon. Shows that sugars are of the form n*(CH2O). Done on patio.
    2. The enzyme catalase in liver and kidney cells catalyzes the transfer of two hydrogen atoms from a toxic molecule H2R to H2O2 forming 2H2O + R. In the demo, R was O2, and so catalase catalyzed 2H2O2 -> 2H2O + O2. Lots of fizz.
    3. Ideal-gas demo: a vacuum pump was connected to a gallon metal can. When the pump was turned on, the air in the can left it at the rate of about five liters per second. With no air molecules banging against the insides of the walls of the can, the air molecules bouncing against the outsides of the walls of the can collapsed the can.
    4. Osmosis: A sugar-in-water solution dyed with red food color rose in a thistle tube that was upside-down in a beaker of water and sealed with a semi-permeable membrane (a Naturalamb condom). The water molecules moved across the membrane until their concentrations were the same on both sides.
    5. Electrolysis: A 5-Volt DC power supply was applied to two copper wires immersed in tap water. There were small bubbles and a current of about 5 mA -- oxygen bubbles at the positive wire, and hydrogen bubbles at the negative wire. Then a pinch of cupric bromide CuBr2 was added to the water, and the current jumped to between 20 and 80 mA depending on the distance between the wires and the amount of stirring. Bromine bubbled up from the positive wire, and a dark brown copper compound formed on the negative wire.
    6. Laminar flow at low Reynolds number: I put two quarts of corn syrup (Smith's) into a very wide beaker and placed a much narrower beaker in the center of the corn syrup. I used a big pipette to blow a drop of corn syrup, dyed dark-red with food coloring, into the middle of the syrup, which itself was red from previous demos:
    After I rotated the inner beaker one-half turn clockwise, the drop smeared out:
    After a full clockwise rotation of the inner beaker, the drop smeared out further, front view:
    and side view:

    Then I rotated the inner beaker counter-clockwise one-half turn, and the drop began to reform:

    A full counter-clockwise rotation of the inner beaker nearly reformed the drop:

    Flow of a fluid of viscosity v and density d at speed s about an object of length L has Reynolds number R = s L d /v .

    For the first homework assignment, students in 452-009 should do problems 1.3, 1.4, and 1.5, which are at the end of the first chapter. Students in section 552-008 should do problems 1.3, 1.4, 1.5, 1.6, and 1.7. The homework is due on Wednesday, February 1st. For the convenience of students who don't yet have a copy of the textbook, here is a pdf file of the problems.

    Here are my notes for chapter one. Here are the solutions to problems of chapter 1.

    Here is a pdf file of some highlights of chapters 2-6 of MBoC4.

    Here are links to the figures,the panels and tables, and the powerpoint files of the book Molecular Biology of the Cell.

    For the second homework assignment, do problems 2.1, 2.2, 2.3, 2.4, and 2.5 by Wednesday, February 15th.

    Here are my notes for chapter two. Here are the solutions to problems of chapter 2.

    For the third homework assignment, graduate students should do all the problems of chapter three; undergraduates should do problems 3.1, 3.2, 3.3, & 3.4. This assignment is due on Monday 20 March.

    Here and there and there are my notes for chapter three. Here are two figures that illustrate mitosis and meiosis. In the meiosis cartoon, one of the black chromosomes is missing its red spot in the last line of the first figure. Here are the solutions to problems of chapter 3.

    For the fourth homework assignment, graduate students should do all the problems of chapter four; undergraduates should do problems 4.1a&b, 4.2, 4.3, 4.4, 4.5a, 4.6, 4.7, and 4.8. Problem 4.3 has an error in it; here is the corrected problem. Here and there are partial solutions of problems that are similar to these homework problems.

    This assignment is due on Monday, 10 April.

    Here and here and here and here and here and here are my notes for chapter four.

    Fifth homework assignment: undergraduates should do problems 5.2, 5.4, and 5.5; graduate students should do all the problems of chapter 5, except for 5.1, 5.2, 5.8, & 5.9. But students who wish to do 5.8 and/or 5.9 may turn them in as extra-credit problems. The due date is May 1st. Here are the problems.

    Here, there, and elsewhere are my notes for chapter five.

    Last homework assignment: Undergraduates should do two of the following five problems: 6.2, 6.4, 6.5, 6.6, & 6.7; graduate students should do three of these five problems. This homework is due at the time of the final examination, Wednesday, May 10th, at 5:30, in room 5. (There will be a lecture, no test.) Here are the problems.

    Here, there, and elsewhere are my notes for chapter six.

    Here are my notes for chapter seven.

    Here are my very sketchy notes for chapter eleven.