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20.320 Biomolecular Kinetics and Cell Dynamics
Spring 2006
This plot of velocity vs. substrate concentration is based on the Michaelis-Menten equation. The Michaelis-Menten constant, K_{M}, is the substrate concentration at which the enzyme reaction proceeds at half the maximum velocity. (Figure by MIT OCW.)
Course Highlights
This course features a full set of assignments.
Course Description
This class covers analysis of kinetics and dynamics of molecular and cellular processes across a hierarchy of scales, including intracellular, extracellular, and cell population levels; a spectrum of biotechnology applications are also taken into consideration. Topics include gene regulation networks; nucleic acid hybridization; signal transduction pathways; and cell populations in tissues and bioreactors. Emphasis is placed on experimental methods, quantitative analysis, and computational modeling.
Technical Requirements
Special software is required to use some of the files in this course: .m.
Syllabus
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Subject Description
Our objective in this subject is to have you successfully learn the following:
Background
You will be most effectively prepared to take this subject if you have previously taken the following subjects:
- 5.07 (Biological Chemistry I) or 7.05 (General Biochemistry);
- 18.03 (Differential Equations);
- 20.011J (Statistical Mechanics of Biological Systems).
Homework, Exams, and Grading
Homework sets will be assigned on a weekly basis and must be turned in on the due date to the designated box. No late homeworks will be accepted, no exceptions. The lowest homework grade will be dropped at the end of the term. Working together on problem sets is acceptable, but each student is expected to turn in his/her own work. Names of people working together must be written on each assignment.
There will be 3 exams, each covering approximately 1/3 of the subject material periodically across the Semester. Final grades will be based on the following distribution:
ACTIVITIES | PERCENTAGES |
---|---|
Exam 1 | 20% |
Exam 2 | 20% |
Exam 3 | 20% |
Homework | 40% |
Textbooks
Lauffenburger, Douglas A., and Jennifer Linderman. Models for Binding, Trafficking, and Signaling. New York, NY: Oxford University Press, 1995. ISBN: 9780195106633.
Tidor, Bruce, and K. Dane Wittrup. Biological Kinetics.
Calendar
The calendar below provides information on the course's lecture (L) and recitation (R) sessions.
DAL: Prof. Douglas Lauffenburger
FMW: Prof. Forest White
KA: Kathyryn Armstrong
SW: Shan Wu
CR: Craig Rothman
SES # | INSTRUCTORS | TOPICS | KEY DATES |
---|---|---|---|
L1 | FMW | Introduction - 20, 20.320, Biology, Mechanisms, and Modeling Protein Interactions | |
R1 | KA/SW/CR | Recitation 1 | |
L2 | FMW | Protein Interactions II Thermodynamics of Monovalent Interactions | Problem set 1 assigned |
L3 | FMW | Monovalent Interactions | |
R2 | Recitation 2 | ||
L4 | FMW | Fractional Saturation | Problem set 1 due Problem set 2 assigned |
L5 | FMW | Measurement Techniques for Kd | |
R3 | KA/SW/CR | Recitation 3 | |
L6 | FMW | Perturbations to Monovalent Interactions | Problem set 2 due Problem set 3 assigned |
L7 | FMW | Perturbations II - Solution Effects | |
R4 | Recitation 4 | ||
L8 | FMW | Multivalent Binding | Problem set 3 due Problem set 4 assigned |
L9 | FMW | Cooperativity | |
R5 | Recitation 5 | ||
L10 | FMW | Avidity and Effective Concentration | Problem set 4 due |
R6 | CR/SW | Recitation 6 | |
FMW | Exam 1 - Monovalent Binding, Measurement, Perturbations, Multivalent Binding, Cooperativity | ||
L11 | FMW | Enzyme Kinetics I | |
L12 | FMW | Enzyme Kinetics II | |
R7 | Recitation 7 | ||
R8 | Recitation 8 | ||
L13 | DAL | Enzyme Inhibitors | Problem set 5 assigned |
L14 | DAL | Integrating Pathways Into Networks | |
R9 | Recitation 9 | ||
L15 | DAL | Ligand-Receptor Interactions | Problem set 5 due Problem set 6 assigned |
L16 | DAL | Endocytic Trafficking I | |
R10 | Recitation 10 | ||
R11 | CR/SW | Recitation 11 | Problem set 6 due |
DAL/FMW | Exam 2 - Avidity, Enzymes, and Networks | ||
L17 | DAL | Endocytic Trafficking II | Problem set 7 assigned |
L18 | DAL | Biomolecular Reactions in Context of Transport | |
R12 | Recitation 12 | ||
L19 | DAL | Fundamentals of Molecular Transport | Problem set 7 due Problem set 8 assigned |
L20 | DAL | Reaction Terms and Approximations | |
R13 | Recitation 13 | ||
L21 | DAL | Macroscopic and Microscopic Effects of Diffusion | Problem set 8 due Problem set 9 assigned (ungraded) |
L22 | DAL | Autocrine/Paracrine Cell-cell Communication | |
R14 | Recitation 14 | ||
L23 | DAL | Cell Population Dynamics I: Cell Growth, Death, Differentiation, and Product Synthesis | |
L24 | DAL | Cell Population Dynamics II: Application to Tissues and Bioreactors | |
DAL | Exam 3 - Test Accumulated Knowledge (Emphasis on Mechanisms Underlying Biomolecular Systems) |
Readings
Help support MIT OpenCourseWare by shopping at Amazon.com! MIT OpenCourseWare offers direct links to Amazon.com to purchase the books cited in this course. Click on the Amazon logo to the left of any citation and purchase the book from Amazon.com, and MIT OpenCourseWare will receive up to 10% of all purchases you make. Your support will enable MIT to continue offering open access to MIT courses. |
Instructors
DAL: Prof. Douglas Lauffenburger
FMW: Prof. Forest White
KA: Kathyryn Armstrong
SW: Shan Wu
CR: Craig Rothman
Textbooks
[W&T] Tidor, Bruce, and K. Dane Wittrup. Biological Kinetics.
[L&L] Lauffenburger, Douglas A., and Jennifer Linderman. Models for Binding, Trafficking, and Signaling. New York, NY: Oxford University Press, 1996. ISBN: 9780195106633.
SES # | INSTRUCTORS | TOPICS | READINGS |
---|---|---|---|
L1 | FMW | Introduction - 20, 20.320, Biology, Mechanisms, and Modeling Protein Interactions | W&T. Chapter 2. |
R1 | KA/SW/CR | Recitation 1 | |
L2 | FMW | Protein Interactions II Thermodynamics of Monovalent Interactions | W&T. Chapter 2, 2.5.2. |
L3 | FMW | Monovalent Interactions | W&T. Chapter 3. |
R2 | Recitation 2 | ||
L4 | FMW | Fractional Saturation | W&T. Chapter 3.1-3.2. |
L5 | FMW | Measurement Techniques for Kd | |
R3 | KA/SW/CR | Recitation 3 | |
L6 | FMW | Perturbations to Monovalent Interactions | |
L7 | FMW | Perturbations II - Solution Effects | |
R4 | Recitation 4 | ||
L8 | FMW | Multivalent Binding | W&T. Chapter 3.3. |
L9 | FMW | Cooperativity | W&T. Chapter 3.3.2. |
R5 | Recitation 5 | ||
L10 | FMW | Avidity and Effective Concentration | W&T. Chapter 3.3.2. |
R6 | CR/SW | Recitation 6 | |
FMW | Exam 1 - Monovalent Binding, Measurement, Perturbations, Multivalent Binding, Cooperativity | ||
L11 | FMW | Enzyme Kinetics I | |
L12 | FMW | Enzyme Kinetics II | |
R7 | Recitation 7 | ||
R8 | Recitation 8 | ||
L13 | DAL | Enzyme Inhibitors | |
L14 | DAL | Integrating Pathways Into Networks | |
R9 | Recitation 9 | ||
L15 | DAL | Ligand-Receptor Interactions | |
L16 | DAL | Endocytic Trafficking I | L&L. Chapter 3. |
R10 | Recitation 10 | ||
R11 | CR/SW | Recitation 11 | |
DAL/FMW | Exam 2 - Avidity, Enzymes, and Networks | ||
L17 | DAL | Endocytic Trafficking II | L&L. Chapter 6.1.3b. |
L18 | DAL | Biomolecular Reactions in Context of Transport | |
R12 | Recitation 12 | ||
L19 | DAL | Fundamentals of Molecular Transport | |
L20 | DAL | Reaction Terms and Approximations | |
R13 | Recitation 13 | ||
L21 | DAL | Macroscopic and Microscopic Effects of Diffusion | |
L22 | DAL | Autocrine/Paracrine Cell-cell Communication | L&L. Chapter 6.1.3c. |
R14 | Recitation 14 | ||
L23 | DAL | Cell Population Dynamics I: Cell Growth, Death, Differentiation, and Product Synthesis | |
L24 | DAL | Cell Population Dynamics II: Application to Tissues and Bioreactors | |
DAL | Exam 3 - Test Accumulated Knowledge (Emphasis on Mechanisms Underlying Biomolecular Systems) |
Recitations
This section contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.
SES # | HANDOUTS |
---|---|
R1 | Ligand Activated Signaling Cascades (PDF)^{#} |
R2 | General Concepts (PDF) |
R4 | Problems (PDF)^{#}, Solutions (PDF)^{#} |
R5 | Problems (PDF)^{#}, Solutions (PDF)^{#} |
R12 | Problems (PDF), Solutions (PDF) |
Assignments
Special software is required to use some of the files in this section: .m. This section contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.
ASSIGNMENTS | SOLUTIONS | SUPPORTING FILES |
---|---|---|
Problem Set 1 (PDF) | (PDF)^{#} | |
Problem Set 2 (PDF) | (PDF)^{#} | pset2_data.htm (HTM) |
Problem Set 3 (PDF) | (PDF)^{#} | hw3.m (M) C_function.m (M) |
Problem Set 4 (PDF) | (PDF)^{#} | pset4_data.htm (HTM) |
Problem Set 5 (PDF) | (PDF)^{#} | |
Problem Set 6 (PDF) | (PDF) | pset6_matlab.m (M) KinaseCascade.m (M) Ferrell, J. E., Jr. "Tripping the switch fantastic: how a protein kinase cascade can convert graded inputs into switch-like outputs." Trends Biochem Sci 21, no. 12 (December 1996): 460-6. Kuhl, P. R., and L. G. Griffith-Cima. "Tethered epidermal growth factor as a paradigm for growth factor-induced stimulation from the solid phase." Nat Med 2, no. 9 (September 1996): 1022-7. |
Problem Set 7 (PDF) | (PDF) | gross_lodish.m (M) pset7_matlab.m (M) Gross, A. W., and H. F. Lodish. "Cellular trafficking and degradation of erythropoietin and novel erythropoiesis stimulating protein (NESP)." J Biol Chem 281, no. 4 (January 27, 2006): 2024-32. Epub (November 11, 2005). |
Problem Set 8 (PDF) | (PDF)^{#} | myfun.m (M) demo_fsolve.m (M) pset8_matlab.m (M) |
Problem Set 9 (PDF) | (PDF) | Sarkar, C. A., and D. A. Lauffenburger. "Cell-level pharmacokinetic model of granulocyte colony-stimulating factor: implications for ligand lifetime and potency in vivo." Mol Pharmacol 63, no. 1 (January 2003): 147-58. |
Exams
This section contains documents created from scanned original files and other documents that could not be made accessible to screen reader software. A "#" symbol is used to denote such documents.
PRACTICE PROBLEMS | SOLUTIONS |
---|---|
Practice for Exam 1 (PDF) | |
Practice for Exam 2 (PDF) | (PDF) |
Practice for Exam 3 (PDF) | (PDF)^{#} |
Exam Solutions
Exam 1 Solution (PDF)^{#}
Exam 2 Solution (PDF)^{#}
Exam 3 Solution (PDF)^{#}
Study Materials
Special software is required to use some of the files in this section: .m. This section contains documents created from scanned original files, which are inaccessible to screen reader software. A "#" symbol is used to denote such documents.
MATLAB® Basics
MATLAB® Reference Sheet (PDF)
MATLAB® Tutorial: Basics (PDF)
MATLAB® Tutorial: Basics - Solutions (PDF)
Code for Additional Exercise 1, add_ex1.m (M)
Code for Additional Exercise 2, add_ex2.m (M)
Code for Additional Exercise 3, add_ex3.m (M)
MATLAB®: ODE Solving and Nlinfit
MATLAB® Tutorial 2: Slides and Notes (PDF)^{#}
Code for 2nd MATLAB® Tutorial, ODEexample.m (M)
Function Code for ODEexample.m, ODEexample_equations.m (M)
Code from 2nd MATLAB® Tutorial for Nlinfit, SPR_leastSquares.m (M)
SPR_function.m (M)
The Parameters and ICs you Need to do Exercise 1, ex1.m (M)
Solution to Exercise 1, ex1_solution.m (M)
Function File for Exercise 1 (Part of the Solution), ex1_equations.m (M)
The Data you Need to do Exercise 2, ex2.m (M)
Solution to Exercise 2, ex2_solution.m (M)
Function File for Nlinfit in Exercise 2, with PFOA (Part of the Solution Function file, ex2_function_PFOA.m (M)
Function File for for Nlinfit in Exercise 2, without PFOA (Part of the Solution), ex2_function.m (M)
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