Fundamentals of Experimental Molecular Biology

Syllabus

Course Format

Lecture and Faculty discussions: 1 session/week, 1.5 hours/session

Lab: 1 session/week; 3.5 hours/session

Students work in teams of two in the laboratory and are assigned to a bench station.

Prerequisites

None.

Course Description

7.002 is a laboratory course that teaches fundamental skills for performing biological research. Our focus is on helping you integrate factual knowledge with an understanding of experimental design and data analysis.

Throughout the semester, you will study an E. coli bacterial ATPase called ClpX. ClpX forms a hexameric ring that unfolds other proteins by pulling them through the pore of the ring using energy from ATP hydrolysis. Your specific experimental goal will be to characterize the ClpX residues that are important for ATP hydrolysis. You will mutate the clpX gene, express and purify mutant ClpX, and assess the ATPase activity of your mutant ClpX relative to wild-type ClpX. Through online recitations and daily lab questions, you will dive deeply into the concepts behind your laboratory experiments.

Please note: The on-campus version of 7.002 also involves meeting with guest professors each week during class. This component is not represented here.

Laboratory Notebooks

Maintaining an updated record of your daily lab work is an essential component of research. Each student must maintain an electronic laboratory notebook using the LabArchives platform. You will sign up for a notebook during the first class meeting.

Laboratory Manuals

Each student will need a lab manual for 7.002.  The manual contains instructions for the experiments and is required to perform the lab and prepare each day’s laboratory notebook entry.  A digital PDF copy of the Spring 2025 lab manual is available in the Lab Manual section.

Grading

A student’s final grade in 7.002 is determined based on their performance in six general areas:

Activities	Percentages
Pre-lab preparation via MITx (not represented in the OCW version): Students will complete the MITx unit scheduled for each week. Questions are graded. Some may be attempted two times.	20%
Post-lab analysis (lab notebooks): Maintaining a complete and accurate record of your experiments and results is crucial for when you (or others) need to repeat what you’ve done or troubleshoot experiments when things go wrong. In addition, lab notebooks serve as a record to support data that is published in scientific literature or used in a grant or patent. You will need to complete a post-lab for each lab day. The post-lab must be submitted via LabArchives by the following lab day. If students received 20% or more points from their first attempt, they may revise entries with the help of the instructors to obtain the full points.	25%
Discussion participation (not represented in the OCW version): Students will sign up on a Google Doc as the student panel for one of the faculty discussions. Students will take notes in the Monday faculty discussions and complete related questions on Canvas for participation scores. Contribution in the student panel will count toward discussion participation.	10%
Lab participation: You will be evaluated on your preparation and effort towards lab work and your safety in lab. Occasional pop quizzes may be given at the beginning of the lab days. In addition, you will be reviewing in-lab questions (ILQs) with the TAs during the labs. Participation in both lab activities and ILQ discussions are equally important for the lab participation grade.	25%
Presentation of lab results and analysis: You (and your lab partner) will be evaluated on your short presentation of the lab results and data analysis at the end of the semester. Detailed instructions will be provided.	5%
Final paper: Each student must submit a short summary of the experimental work they completed in 7.002 at the end of the semester. Detailed instructions will be provided.	15%

Attendance Policy

Learning in 7.002 is very active. Thus, most of these experiences cannot be replicated outside of the lab/classroom setting. For this reason, attendance at all laboratory meetings and classes is mandatory. Occasionally, an extraordinary circumstance may arise (illness, family emergency) that requires you to miss class. If you know that you will need to miss a lab session, you must contact an instructor to address any missed work. 

Lab sessions are scheduled to run from 1:00 PM to 4:30 PM. On most days, all lab experiments can be completed by 4:30 PM or earlier, provided that you are organized and work efficiently in the lab. Due to the unpredictable nature of lab work, however, experiments may often take longer than expected to complete. In addition, there are several busier lab days during the term that may last up till or slightly past 4:30 PM. Therefore, please plan on being present for the full lab session from 1:00 PM to 4:30 PM each day when scheduling your own personal travel plans and other activities during the semester, as there is no way to know for sure ahead of time whether a lab day may end early or not. Leaving lab early before the day’s experiments are completed will result in deductions from your participation grade.

Students who miss a faculty discussion or a lab session will receive zero points for that day’s participation grade (unless they have a Dean’s note to excuse their absence). Note that students with an excused absence are still responsible for completing and submitting any missed pre-lab work on the MITx site (prior to the original deadline) and post-lab notebook entries on LabArchives (on the original deadline). You may obtain data and observations from your instructors for any experiments you missed. A maximum of 3 absences are allowed to receive a passing grade due to the institute lab requirement.

Laboratory Safety

The teaching laboratories are regulated by the same local, state, and federal regulations as MIT’s research laboratories. Students will receive safety instruction throughout the semester and are expected to follow the instructions of the staff on matters of safety and waste disposal. In addition, students are responsible for knowing the standard operating procedures (SOPs) for hazardous chemicals used in the laboratory as part of the preparation for the laboratory each day. Students who have questions or concerns about laboratory safety should bring them to the attention of the lab instructors.

Acknowledgments

Dr. Chu and Dr. Cheung were the lab instructors and creators of the lab materials for the course. The faculty lecturer for the course was Prof. Thomas Schwartz.