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 BYNCSA
This plot of velocity vs. substrate concentration is based on the MichaelisMenten equation. The MichaelisMenten 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.
Syllabus
Subject Description
Our objective in this subject is to have you successfully learn the following:

What are fundamental principles concerning kinetic and dynamic behavior of biological molecules, biomolecular networks, cells, and cellular systems.

How to understand molecular, network, cell, and tissue behavior in terms of mathematical analysis applied to quantitative experimental measurement methods.

How to design molecular and cellular biotechnologies based on this understanding.

How higherlevel 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.
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, 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.
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

LigandReceptor 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 Cellcell 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)


