Make your Mutant - BSC 3466L
Course Syllabus – Spring 2023
U01: Friday 9AM – 12:50PM; U02: Friday 2PM – 5:50PM
Laboratory location: OE-304
Coordinator and Instructor:
Dr. Jaime Mayoral. Email - mayoralj@[Link]
Instructor:
Mr. Mario López. Email - mlopez618@[Link]
Section U01: Friday 9AM – 12:50PM
Section U02: Friday 2PM – 5:50PM
Office Hours:
Tuesdays: 1PM-2PM (Zoom)
Thursdays: 1PM-2PM (Zoom)
Goals of this course:
The objectives of this course are to provide students with hands-on experience performing
original research in molecular biology and biochemistry set ups and to contribute to a current and
relevant scientific problem in which different organizations are involved worldwide.
Co- and Pre-requisites:
Students taking this course MUST have completed OR be enrolled in Genetics (PCB3063) OR
General Biochemistry (BCH3033).
Course Description:
The Design to Data, or D2D, lab workflow has been developed with the goal of improving the
current predictive limitations of protein modeling software by functionally characterizing single
amino acid mutants in a robust model system. In this lab, students will have the opportunity to
engage in primary research by creating and functionally characterizing their own novel protein
mutant. Students will be expected to share the results of their work in a database that is shared by
a network of nationwide collaborators, thereby adding to the body of knowledge of protein
structure-function relationships. The tools used in this lab will provide students with a skill set of
techniques commonly used in medical, biopharmaceutical, and research fields.
If you take this course, you agree to:
● Think creatively.
● Work and collaborate with your lab mates.
● Create and deliver a team poster presentation.
Lab Routine:
• This lab will have four components: Design-Build-Test-Data. The first two weeks will
cover foundational principles of protein structure and function as well as basic bioinformatic
techniques that will enable students to Design their mutant protein. The Build phase will take
place over eight weeks, where students will use molecular biology and biochemistry tools to
create, purify, and express their mutant proteins. The following two weeks, students will Test the
functional consequences of their mutation. Students will spend the final two weeks summarizing
their Data, which they will present as a poster in class and write a formal report on.
Grading Policy:
• Each part of the course contributes to the final grade in the proportions shown below:
Surveys (pre and post)* 2.0%
Quizzes (9) 24%
Assignments (5) 24%
Attendance and participation 10%
Poster 25%
Mutant Report (max 2 pages) 15%
Total 100.0%
Extra credit – several tasks performed out of class along the semester (15-30 mins each) – 3%
*Credit for the surveys is only credited to students that completed BOTH surveys, the pre-
and post-survey, and strictly before the deadline assigned by the instructor.
Grade Scale for the course:
● A 90-100%; B+ 88-89.9%; B 80-87.9%; C+ 78-79.9%; C 70-77.9%; D 60-69.9%; F Less
than 60%
General Policies:
● There are no make-up quizzes.
● Students are to remain in the lab for the entire lab duration in order to receive quiz and
participation points.
● Assignments are due at the beginning of your lab session (i.e. 9AM or 2PM). Late
submissions are penalized 20% per day (including weekends).
● Attendance and being on time are mandatory. One excused absence is permitted (proper
documentation is needed); save it for a real emergency. Students will automatically
receive an "F" if they have more than 2 absences (any type).
● If you miss a lab session, points allocated to that lab session (quiz, attendance,
participation, poster session, etc.) will be deducted.
● Students who cheat or plagiarize from someone else or an internet source will be reported
to the Dean of Undergraduate Education as outlined under “Academic Misconduct” and
given an "F" for the course.
FIU COVID guidelines:
These are the guidelines stablished by FIU to keep students, faculty, and staff safe. FIU is
adhering to the last updated guidelines issued by the CDC on August 11, 2022. Please check
them at [Link] You can also
check the FIU website for the last updates [Link]
• Please note that the university community will no longer be using the P3 app to report
COVID symptoms or infections.
• If you do not feel well and/or have tested positive for COVID-19, please do not come to
class. Please contact your instructor by email or Canvas.
• Please take every precaution to keep yourself and others healthy. Per CDC guidelines,
you are encouraged to get vaccinated and strongly advised to wear a mask indoors and in
public including all FIU facilities.
• COVID related absences will be excused as per the policies outlines in the section
“General policies” above. Missing excessive days of lab due to COVID-19 (2 or more)
may lead to failing this class or a grade of incomplete.
Students with disabilities statement:
The Disability Resource Center collaborates with students, faculty, staff, and community
members to create diverse learning environments that are usable, equitable, inclusive and
sustainable. The DRC provides FIU students with disabilities the necessary support to
successfully complete their education and participate in activities available to all students.
Students that have a diagnosed disability and plan to utilize academic accommodations are asked
to please contact the Center at 305-348-3532 or visit the DRC, located at the Graham Center GC
190. Students are required to contact their instructor regarding their accommodations so the
proper arrangements with the DRC office can be made (preferably during the first week of lab).
Official written documentation from the DRC office must be provided to your instructor.
Required Course Materials:
● Laboratory coat (available for purchase at bookstore).
● Safety goggles (available for purchase at bookstore).
● Long pants and closed toe shoes.
● Computer with ability to run bioinformatics programs, generate graphs (e.g. Excel,
Quattro, various statistical packages), and to connect to internet.
● Before class: Students must print out and read the lab protocol and supplements for that
week.
● Students will print a poster at the end of the semester (one per team).
Disclosure Statement
Students are encouraged to employ critical thinking and to rely on data and verifiable sources to
interrogate all assigned readings and subject matter in this course as a way of determining
whether they agree with their classmates and/or their instructor. No lesson is intended to espouse,
promote, advance, inculcate, or compel a particular feeling, perception, viewpoint or belief
Schedule (subject to change): (see next page)
Date: Lab: See Canvas for Lab Handout Other activities/deadlines
Jan 13 ***** No class *****
Jan 20 Introduction to D2D course and project Learn how to use Foldit.
Homework BLAST & Jalview
Jan 27 Choose your mutant; and hypothesis Quiz Order Oligos.
Assignment 1 due
Feb 3 Pipetting ex. & phosphorylation of oligos Quiz
Hypothesis due
Feb 10 Oligo & plasmid annealing and polymerization Quiz
Feb 17 Cloning of your mutant# Quiz Extra credit opportunity
Intro assignment due
Feb 24 DNA Extraction and prep for sequencing Quiz
Mar 3 **No class: Spring Break**
Mar 10 Sequences analysis and Extra credit opportunity
cloning of mutants into expression system
Mar 17 Express your mutant Quiz
Methods Assignment due
Mar 24 Purify your mutant Quiz
Mar 31 Kinetics experiments & Thermal stability Quiz
heat challenge
Apr 7 SDS PAGE – purified protein? Quiz
Mutant comparison due
Apr 14 Discussing and preparing for the poster Upload data to network
Apr 21 Poster presentation sessions Mutant Report due
*Syllabus is subject to change at the discretion of the professor*
# Possible unofficial catch-up day: Sunday Feb 19th or Monday Feb 20st