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BMB402 Syllabus

BMB402 is a hands-on laboratory course in Experimental Biochemistry and Molecular Biology, taught by Dr. Flavia Fontanesi, focusing on techniques such as spectrophotometry, protein purification, and PCR. The course includes assessments based on attendance, laboratory notebooks, tests, and group presentations, with a final laboratory report due in May. Students are expected to develop essential laboratory skills and maintain a detailed lab notebook throughout the semester.

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5 views

BMB402 Syllabus

BMB402 is a hands-on laboratory course in Experimental Biochemistry and Molecular Biology, taught by Dr. Flavia Fontanesi, focusing on techniques such as spectrophotometry, protein purification, and PCR. The course includes assessments based on attendance, laboratory notebooks, tests, and group presentations, with a final laboratory report due in May. Students are expected to develop essential laboratory skills and maintain a detailed lab notebook throughout the semester.

Uploaded by

khanali2902
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOCX, PDF, TXT or read online on Scribd
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BMB402

BMB402

Principals of Experimental Biochemistry and Molecular Biology

Basic Course Information

Instructor: Dr. Flavia Fontanesi


Department of Biochemistry and Molecular Biology
Office: UM Medical Campus 1600 NW 10th Avenue, RMSB #7094B
Phone: 305-2437215
E-mail: [email protected]
Office hours: By appointment

Class meeting time and location: Spring semester 2024


Tuesday and Thursday 9.00 am – 11.50 am
Cox Science Building room #261

Credits: 2 + Writing credit

Prerequisite: CHM202 or CHM221. Co-requisite: BMB401

Course Overview

The course provides students with a hands-on laboratory experience that introduces them to
several standard biochemical and molecular biology techniques, such as spectrophotometry,
protein purification, electrophoretic analysis, PCR, site-directed mutagenesis, etc. Emphasis is
placed on the analytic and quantitative aspects of experimental biochemistry, at the
experimental design, data collection and analysis levels. Moreover, the course is aimed at
promoting the interest of the students in pursuing a training experience in a
biochemical/biomedical research laboratory and at developing the basic skills and proper
laboratory habits instrumental for such experience.

Course Learning Outcomes

By the end of the course, you should be able to:


- Maintain a useful and appropriate laboratory notebook.
- Organize your lab bench space, material and work efficiently.
- Prepare common solutions, buffers and reagents used in a biochemistry lab.
- Be familiar with the principles of some basic techniques of experimental biochemistry
and molecular biology such as chromatography, spectrophotometry, electrophoresis
and PCR methods.
- Be able to follow several common laboratory protocols autonomously.
- Present your results in a clear, logic and critical manner.

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BMB402

Course Format and Safety Rules.

This is a lecture-lab course in which topics are presented by the instructor and experiments
are conducted by the students in small groups during lab hours. However, laboratory
notebooks and reports will be evaluated for each student individually.

Assessments and Evaluation

Your performance will be assessed though multiple activities, including classroom activities
and homework. You will receive regular feedback on your work to help you monitor and
improve your performance.

Class attendance is expected, and more than two absences will affect your final grade. If at
some point in the semester you cannot physically attend class sessions due to illness, you
must contact the instructor to access temporarily online course activities.

You will be asked to keep a laboratory notebook (one entry for each lab session), which will
be reviewed by the instructor midsemester to provide you with feedbacks. You will receive a
grade for your notebook at the end of the course.

Your final grade will be based on the following:

- Attendance and participation 20%


- Laboratory Notebook 20%
- Midterm test 20%
- Group paper presentation 20%
- Final Laboratory Report 20%

Tentative Course Schedule

Note: changes in the schedule may occur throughout the semester. You will be promptly
informed of any change.

(January 16-18, Preparation of materials. No classes.)

Tuesday January 23, Introduction to the course, lab safety, lab notebook, lab rudiments (use of
automatic pipette, preparation of reagents).

Thursday January 25, Solution preparation, Spectrophotometry, absorbance spectra, pKa and
extinction coefficient of p-nitrophenol - Part 1.

Tuesday January 30, Spectrophotometry, absorbance spectra, pKa and extinction coefficient of
p-nitrophenol - Part 2.

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Thursday February 1, Spectrophotometry, absorbance spectra, pKa and extinction coefficient


of p-nitrophenol - Part 3 and 4.

Tuesday February 6, Protein purification – Part 1, -galactosidase purification by affinity


chromatography.

Thursday February 8, Protein purification – Part 2, SDS-PAGE gel preparation.

Tuesday February 13, Protein purification – Part 3, SDS-PAGE and Coomassie blue staining
and Part 4, Protein quantification.

Thursday February 15, Measurements of enzymatic activity – Part 1, -galactosidase specific


enzymatic activity.

Tuesday February 20, Measurements of enzymatic activity – Part 2, -galactosidase enzymatic


activity, determination of KM and Vmax.

Thursday February 22, Measurements of enzymatic activity – Part 3, -galactosidase


enzymatic activity, effect of pH.

Tuesday February 27, Measurements of enzymatic activity – Part 4, inhibition of -


galactosidase enzymatic activity.

Thursday February 29, Review.

Tuesday March 5, Study day.

Thursday March 7, Midterm test.

Spring break (March 11-16)

Tuesday March 19, Introduction to the semester second half program (SOD1 and ALS). PCR
technology and its application to identify point mutations in genes - Part 1.

Thursday March 20, PCR technology and its application to identify point mutations in genes -
Part 2. Generation of a yeast model to analyze the effect of human disease-associated
mutations - Part 1, Bioinformatics analysis and primers design. Mutagenesis PCR.

Tuesday March 26, Generation of a yeast model to analyze the effect of human disease-
associated mutations - Part 2, E. coli transformation

Thursday March 28, Generation of a yeast model to analyze the effect of human disease-
associated mutations - Part 3, Plasmid extraction from E. coli (Minipreps).

Tuesday April 2, Generation of a yeast model to analyze the effect of human disease-
associated mutations – Part 4, Miniprep screening by endonuclease restriction analysis.

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Thursday April 4, Group presentation.

Tuesday April 9, Generation of a yeast model to analyze the effect of human disease-
associated mutations – Part 5, Yeast transformation.

Thursday April 11, Semi-quantitative analysis of enzymatic activity – Part 1, Preparation of


yeast cell extracts.

Tuesday April 16, Semi-quantitative analysis of enzymatic activity – Part 2, Electrophoresis


and SOD1 in gel activity.

Thursday April 18, Group presentation.

Tuesday April 23, Phenotypic analysis of yeast resistance to oxidative stress.

Thursday April 25, Review.

May 3 (final exam week), Final laboratory report due.

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