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Lauffenburger, Douglas, and Forest White, 20.320 Biomolecular Kinetics and Cell Dynamics, Spring 2006. (Massachusetts Institute of Technology: MIT OpenCourseWare), http://ocw.mit.edu (Accessed 07 Jul, 2010). License: Creative Commons BY-NC-SA
This plot of velocity vs. substrate concentration is based on the Michaelis-Menten equation. The Michaelis-Menten constant, KM, 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.
Syllabus
Subject Description
Our objective in this subject is to have you successfully learn the following:
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What are fundamental principles concerning kinetic and dynamic behavior of biological molecules, biomolecular networks, cells, and cellular systems.
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How to understand molecular, network, cell, and tissue behavior in terms of mathematical analysis applied to quantitative experimental measurement methods.
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How to design molecular and cellular biotechnologies based on this understanding.
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How higher-level physiological function in populations, tissues, and devices can be influenced by genetic, biochemical, and biophysical manipulations at the molecular level.
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:
Grading criteria.
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ACTIVITIES
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PERCENTAGES
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Exam 1
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20%
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Exam 2
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20%
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Exam 3
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20%
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Homework
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40%
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Textbooks
Lauffenburger, Douglas A., and Jennifer Linderman. Models for Binding, Trafficking, and Signaling. New York, NY: Oxford University Press, 1996. ISBN: 0195106636.
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
Course calendar.
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SES #
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INSTRUCTORS
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TOPICS
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KEY DATES
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L1
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FMW
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Introduction - 20, 20.320, Biology, Mechanisms, and Modeling Protein Interactions
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R1
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KA/SW/CR
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Recitation 1
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L2
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FMW
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Protein Interactions II
Thermodynamics of Monovalent Interactions
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Problem set 1 assigned
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L3
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FMW
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Monovalent Interactions
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R2
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Recitation 2
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L4
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FMW
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Fractional Saturation
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Problem set 1 due
Problem set 2 assigned
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L5
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FMW
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Measurement Techniques for Kd
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R3
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KA/SW/CR
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Recitation 3
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L6
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FMW
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Perturbations to Monovalent Interactions
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Problem set 2 due
Problem set 3 assigned
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L7
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FMW
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Perturbations II - Solution Effects
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R4
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Recitation 4
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L8
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FMW
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Multivalent Binding
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Problem set 3 due
Problem set 4 assigned
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L9
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FMW
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Cooperativity
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R5
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Recitation 5
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L10
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FMW
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Avidity and Effective Concentration
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Problem set 4 due
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R6
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CR/SW
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Recitation 6
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FMW
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Exam 1 - Monovalent Binding, Measurement, Perturbations, Multivalent Binding, Cooperativity
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L11
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FMW
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Enzyme Kinetics I
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L12
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FMW
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Enzyme Kinetics II
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R7
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Recitation 7
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R8
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Recitation 8
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L13
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DAL
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Enzyme Inhibitors
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Problem set 5 assigned
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L14
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DAL
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Integrating Pathways Into Networks
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R9
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Recitation 9
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L15
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DAL
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Ligand-Receptor Interactions
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Problem set 5 due
Problem set 6 assigned
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L16
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DAL
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Endocytic Trafficking I
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R10
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Recitation 10
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R11
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CR/SW
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Recitation 11
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Problem set 6 due
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DAL/FMW
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Exam 2 - Avidity, Enzymes, and Networks
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L17
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DAL
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Endocytic Trafficking II
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Problem set 7 assigned
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L18
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DAL
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Biomolecular Reactions in Context of Transport
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R12
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Recitation 12
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L19
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DAL
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Fundamentals of Molecular Transport
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Problem set 7 due
Problem set 8 assigned
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L20
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DAL
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Reaction Terms and Approximations
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R13
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Recitation 13
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L21
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DAL
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Macroscopic and Microscopic Effects of Diffusion
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Problem set 8 due
Problem set 9 assigned (ungraded)
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L22
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DAL
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Autocrine/Paracrine Cell-cell Communication
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R14
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Recitation 14
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L23
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DAL
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Cell Population Dynamics I: Cell Growth, Death, Differentiation, and Product Synthesis
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L24
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DAL
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Cell Population Dynamics II: Application to Tissues and Bioreactors
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DAL
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Exam 3 - Test Accumulated Knowledge (Emphasis on Mechanisms Underlying Biomolecular Systems)
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