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7.002 | Spring 2025 | Undergraduate

# Fundamentals of Experimental Molecular Biology

#### Week 1:

Lecture: Class logistics, overview of ClpX, MITx enrollment, electronic notebook exercise, and complete MITx Start of Semester units.

Lab: Computer lab, described in active learning module publication:

Chu, E.W.K. “Database Query to Prove Your Intuitions on Gene Predictions and Genetic Mutations.” Advances in Biology Laboratory Education, 2025, Volume 45.

#### Week 2:

Lecture: Faculty discussion

Lab Day 0: Lab walk-through, basic lab skills (pipetting, sterile technique, gels)

#### Week 3:

Lecture: Faculty discussion

Lab Day 1: Design primers for RTH mutagenesis of ClpX plasmid, prepare sterile media

#### Week 4:

Lecture: 7.002 & Enzyme Engineering

Lab Day 2: Set up round-the-horn PCR with mutagenic primers, prepare buffers and agarose gel

#### Week 5:

Lecture: Faculty discussion

Lab Day 3: Run PCRs on gel to verify amplification, purify PCR products, set up DpnI/PNK/Ligase reactions with PCR products, pouring LB+Amp Agar Plates

#### Week 6:

Lecture: Faculty discussion

Lab Day 4: Transform DpnI/Ligase reactions into DH5α bacteria

#### Week 7:

Lecture: Faculty discussion

Lab Day 5: Miniprep mutated ClpX plasmids from DH5α bacteria, send ClpX plasmid minipreps out for sequencing

#### Week 8:

Data Analysis Lab: Lab Day 6 Part 3.1 sequencing analysis

Lab Day 6: Analyze mutant ClpX plasmid sequence, transform mutated ClpX plasmid into expression strain, prepare purification buffer

Lab Day 6.5: Express mutant ClpX protein, collect cell pellet

#### Week 9:

Lecture: Faculty discussion

Lab Day 7: Analyze E. coli LOBSTR BL21(DE3) transformations, purify mutant ClpX protein, determine mutant ClpX protein concentration

#### Week 10:

Lecture: Faculty discussion

Lab Day 8: Run purification samples on two SDS-polyacrylamide gels, transfer one gel to PVDF membrane (western blot), incubate one gel in Coomassie stain

#### Week 11:

Lecture: Faculty discussion

Lab Day 9: Rehydrate, block, probe, and develop western blot, destain Coomassie-stained gel

#### Week 12:

Lecture: Faculty discussion

Lab Day 10: In vitro ATPase assay to test mutant ClpX activity, lab cleanup

#### Week 13:

Lecture: Group discussion

Lab: Student presentations: report group analysis and discuss class results

#### Week 14:

Class wrap up, final paper due by the following day

## Course Info

##### Instructors

- Dr. Eric Chu
- Dr. Vanessa Cheung

##### Departments

- Biology

##### As Taught In

Spring 2025

##### Level

Undergraduate

##### Topics

- Science
  - Biology
    - Cell Biology
    - Genetics
    - Molecular Biology

##### Learning Resource Types

assignment Activity Assignments
assignment Laboratory Assignments
assignment Written Assignments

Browse Resources

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