MCDB 4550/5550 Syllabus: Cells, Molecules and Tissues: A Biophysical Approach

Crosslisted as: MCEN 4228/5228; CHEM 4751/5751; PHYS 7810-004/4810-001
Instructor: Thomas Perkins,

Straightforward application of classical Newtonian physics does a poor job of providing insight into biological processes. This course will develop a simple description of the biophysics governing the motion of molecules inside of cells. This course starts with an overview of the physics that governs molecular motors, the cytoskeleton and, more generally, proteins inside of the cell as well as a review of single molecule techniques. Topics covered will include diffusion, entropy, chemical energy, polymers, intermolecular forces, cytoskeleton, molecular motors, and single-molecule techniques. Each student will give two oral presentations on journal articles. Problem sets will provide a quantitative understanding of the topics discussed. A final paper will be required that addresses a critical question in biophysics and/or outlines a proposed experimental approach to answer the question, or a design project to address a biomedical application.

Prereq, CHEM 1131 or 1171, physics 2010, 2020, MCDB 3120, or instructor consent. 
Recommended prereq., Math 1300 and/or CHEM 3311. Same as MCDB 5550.

Grade determination:

15%    Participation in class discussion
30%    Oral presentation
25%    Problem sets
30%    Final paper


Each student will give two oral presentations, in teams if necessary, on the primary literature reading assignments. These presentations will be followed by a discussion led by the presenting student(s) to critically analyze the reading material and to review what students have learned from the presentation and the reading material.


Each student will write a 6-8 page paper (10-12 for graduate students) that either proposes (i) an experiment using biophysical techniques with quantitative estimates, (ii) a critique of a set of papers, (iii) a design project (upon approval by an instructor) or (iv) a topic mutually agreed upon between the student and an instructor. Paper is due April 28th by 5 PM. 

Texts (required for course):

Mechanics of Motor Proteins and the Cytoskeleton by Jonathon Howard, 2001

Texts (supplementary information):

  • Molecular Biology of the Cell  54th Edition, silver cover),  By Alberts, et al.,  (any addition)
    --A good, encyclopedic biology text book. Very good for learning vocabulary but a little dry
  • Biochemistry  (7th Edition, grey cover), By Berg, Tymoczko,  Stryer, &, 2010 or equivalent 
  • Physical Biology of the Cell, 2nd Edition, Phillips et al. (Excellent but more advanced)

Office Hours

Time: Wednesday 2-3 pm 

Office: JILA A503 or zoom (Meeting ID: 942 0224 5122; Passcode distributed by email, same as class zoom.





1: 1/11-13

Reading: Chapter 1

Random walks & mechanical forces
Reading: Chapter 2 (HW #1 due 1/20/2022)

2: 1/18-20

Mass, stiffness & damping of a protein
Reading: Chapter 3

Single Molecule Techniques: Optical Traps and applications to molecular motors (Perkins, 2009, & Perkins, 2014) (HW#2 due 1/27/2022)

3: 1/25-27

Cytoskeletal filaments

Reading: Chapter 7

Motor proteins

Reading: Chapters 12-13

4:  2/1-3

Thermal forces & diffusion
Reading: Chapter 4

Chemical forces
Reading: Chapter 5 (HW#3 due 2/10/2022)

5:  2/8-10

Points on presenting a scientific paper

Presentation example: Hua et al., Distinguishing inchworm and hand-over-hand processive kinesin movement by neck rotation measurements (HW#4 due 2/17/2022)

6:   2/15-17

Single Molecule Techniques: Fluorescence

Group 1 Presentation: Asbury et al, Kinesin moves by an asymmetry is hand over hand mechanism (HW #5 due 2/24/2022)

7:   2/22-24

Single molecule techniques: Atomic Force microscopy

(Neuman et al, 2008),

Group 2 Presentation: Yildiz et al Kinesin walks hand over hand

8: 3/1-3

Single molecule techniques: Magnetic tweezers (Neuman et al, 2008),

Cytoskeletal filament mechanics and polymerization

Reading: Chapters 8-9

9: 3/8-10

Guest lecture: Erik Schaeffer. High resolution stepping of kinesin

(HW #6 due March 15)

Nanomechanics DNA and nucleic acid hairpins

(Chapter 6) (HW #7 due March 17)

10: 3/15-17

Group 3 Presentation: Group 3: Wang & Ha, Defining single molecular forces required to activate integrin and notch signaling

Group 4 Presentation: Zhang, et al., DNA-based digital tension probes reveal integrin forces during early cell adhesion  (HW #8 due 3/31/2022)


Spring Break

Spring Break

11:  3/29-31


Reading: Chapters 9-10

Group 1 Presentation: Kerssemakers et al, Assembly dynamics of microtubules at molecular resolution (HW #9 due 4/7/2022)

12: 4/5-7

Active polymerization

Reading: Chapters 11

Group 2 Presentation: Asbury et al., Dam1 kinetochore complex harnesses microtubule dynamics to produce force and movement (HW #10 due 4/14/2022)

13:  4/12-14

ATP Hydrolysis

Reading Chap 14

Group 3 Presentation: LeBlanc et al., Type III secretion system effector proteins are mechanically labile(HW #11 due 4/21/2022)

14:  4/19-21

Steps, forces, and motility models

Reading: Chapter 15-16

Group 4 Presentation: Zhao & Woodside, Mechanical strength of RNA know in Zika virus protects against cellular defenses


15:  4/26-28

Guest Lecture: Dick McIntosh





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