Fundamentals of BioEngineering

ChE 338 Spring 2021

Class T/Th 9:30 am – 10:45 am #15030, 15031

zoom at least through spring break
ECJ 1.202
Instructor
JENNIFER MAYNARD (SHE/HER) [email protected]
Office hours T 11-12:00 pm zoom (links on canvas)

TA
YUTONG LIU (SHE/HER) [email protected]
Office hours Th 11-12:00 pm zoom (links on canvas)

Tutors & Graders

Natalie Ling (she/her) [email protected] zoom, 3 hrs/ week (TBD)
Matthew Dulaney (he/his) [email protected] zoom, 1 hr/ wk (TBD)

Textbook
• The HW, quiz and exam materials will be based primarily on lectures. To supplement this, readings
will be available for the textbooks below and other handouts posted on canvas. When these readings
are considered very important, they may be accompanied by a reading quiz (you will know this in
advance).
• Biochemistry, TA Brown (Scion) - $42 paperback OR Essential Biochemistry, by Pratt & Cornely
(BCH369 text; $64; used in UT Biochemistry classes)
• OPTIONAL: Quantitative Fundamentals of Molecular and Cellular Bioengineering by Wittrup, Tidor,
Hackel and Sarkar ($75 on Amazon).

Overview
Introduction to basic biological processes including transcription, translation, protein/enzyme function,
cellular energetics, protein secretion and modifications. Application of quantitative engineering principles
to the analysis of biological processes, including thermodynamics, kinetics and stoichiometry.

This course is designed for students with an engineering background to learn the biological
fundamentals of biotechnology using chemical engineering analyses. The course emphasizes conceptual
appreciation of the molecular interplays which are the basis of “chemical processes” in living systems.
The objective of the course is to provide students with a comprehensive and concise overview of
biochemical science with emphases on quantitative, especially stoichiometric, thermodynamic and
kinetic, perspectives.

Course goals
To provide chemical engineering students with a basic understanding of fundamental biological principles
and a working vocabulary that would enable them to expand their knowledge base during their academic
and professional careers. To convey to students an appreciation of the wide variety of engineering
applications that are related to the fields of biochemistry, cell biology, genetics, general microbiology, and
environmental microbiology.

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Objectives
• Apply material balances to biological processes such as transcription and translation and cellular
growth
• Apply mass action chemical kinetics to DNA annealing, protein aggregation, antibody-antigen and
ligand-cellular receptor binding
• Apply thermodynamics to protein-ligand binding and protein aggregation processes. Calculate free
energies of DNA annealing.
• Understand structural basis of molecular recognition in biological systems

Knowledge, abilities and skills students should have

Prerequisites: completion of ChE 317. Material balances, thermodynamics and kinetics will be employed,
but will also be reviewed before first used.
• You should have a working knowledge of algebra and simple ordinary differential equations, i.e.,
M408C/D at UT or the equivalent with a grade of at least C.
• This course is ultimately intended to replace Bio311C in the ChE curriculum.

Chemical engineering program outcomes achieved

• An ability to identify, formulate, and solve complex engineering problems by applying principles of
engineering, science, and mathematics

Course procedure
• Canvas will be used to post homework assignments, assignment grades, reading material and any
announcements.
• Gradescope will used to submit and grade most assignments.
• Lecture will be on zoom at least through spring break. The general format will be: an exciting advance
in biochemical engineering, then the biology background needed to understand this and the associated
engineering analyses to design/ optimize with an example problem and solution.
• Office hours will be held on zoom. We will aim to provide additional office hours on weeks with
assignments or other assessments due. If these become crowded, we will include 15 min sign-ups for
a total of ~5 students to help ensure everyone has an opportunity to ask questions.
• Quizzes: weekly lecture/ comprehension checks, typically on Tuesdays after class. The lowest two
quiz scores will be dropped; if you need to miss a quiz for any reason, this will be one of your dropped
quizzes.
• Homework: will be due roughly every other Friday throughout the semester (~6 total).
• Two midterm exams will include problems similar to those worked in class and on homework.
• Project (in lieu of final exam): Students (in small groups) will prepare a presentation about a “feat of
bioengineering” – a technology or therapeutic related to the class, including the basic biology and
engineering approaches to either understand or assist with design of the technology. The presentation
(~10 min) will include an overview of the project goals, approach and key data, as well as commentary
of the project’s significance, weaknesses and whether the data fully supports the conclusions. Topics
may be selected from a suggested list or selected by the students. To manage the class size, we’ll pre-
record these and everyone will watch 5, ask a written question and answer a related quiz problem.
• Participation: this will be evaluated via Insta-polls conducted during lecture, approximately one per
lecture. These will include lecture comprehension and simple problem solving. For some in-class
problems, you will be placed into small, pre-assigned breakout rooms (~4 students) to work together
to determine a response. Breakout room groups will be changed approximately once a month. You will
receive 1/3 credit for an incorrect attempt and full credit for a correct response; your lowest four insta-
poll scores will be dropped. Five people per class assigned to answer questions. You will also be
expected to ask questions (electronically) of the projects you review.

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Grading
Final grades will be based on the following weighted percentages and will include +/- grades according to
the standard cut-offs below. Due to the flexible grading scheme described above, I do not expect to further
revise these, nor provide any extra credit options.

Quizzes (weekly) 20% (cover lecture content & short problems; 2 drops)
Homework (~bi-weekly) 20%
Project presentation (1) 10%
Midterm exam 1 15% (solve several short problems)
Midterm exam 2 15% (solve several short problems)
Class participation 20% (daily insta-poll, 4 drops; ask questions on presentations)
Total 100%

< 59 60-63 64-66 67-69 70-73 74-76 77-79 80-83 84-86 87-89 90-93 94-100
F D D+ D C- C C+ B- B B+ A- A

Exam dates
Exam 1: Th, March 25, 2021
Exam 2: T, May 4, 2021

Presentation dates
Group 1: March 23-25, 2020 (we’ll start planning ~Feb 23, record by March 11)
Group 2: May 6-8, 2020 (we’ll plan ~ Apr 13, record by Apr 29)

Course organization
1. Overview of basic cell and molecular biology concepts (Weeks 1-2)
1a. Biological building blocks
1b. Cellular structure & organization
1c. Cell replication, communication and signaling

2. Cell growth and energetics (Weeks 3-5)

2a. Cell growth models
Case study: stem cells and cancer growth
Case study: model for infection spread
2b. Cell material balance and carbon sources
2c. Cellular energetics and electron sources
Case study: minimal cells; bacterial batteries, environmental remediation
2d. Cellular metabolism and engineering
Case study: enhanced penicillin production
Case study: flux balances analyses

3. Nucleic acids and related technologies (Weeks 6-8)

3a. Nucleic acids: structures, annealing thermodynamics and kinetics
Case study: diagnostics sensitivity with PCR material balance
3b. Transcription: mRNA material balance and basic regulation
Case study: siRNA therapeutic Onpattro
3c. Translation: protein material balance, control features
Case study: gene therapy (mRNA vax, factor VIII)

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Midterm 1 and first set of presentations

4. Protein folding and function (Weeks 10-13)

4a. Protein folding & thermodynamics
Case study: engineering the COVID vaccine
4b. Protein aggregation & kinetics
Case study: beta-amyloid aggregation in Alzheimer’s
Case study: accelerated aggregation of pharmaceuticals
4c. Molecular recognition: binding kinetics & Michaelis-Menton kinetics
Case study: Antibody therapies for targeting breast cancer

5. Infection, immunity & therapeutics (Weeks 13-14)

5a. Pharmacokinetics and toxicity: macro- and microscopic compartment models
Case study: controlled release and PK
5b. Immunology: arms of the immune system, generation of antibody diversity
Case study: Cellular therapy (eg, CAR T cells)
5c. Infectious diseases: viruses & anti-virals; bacteria & antibiotic functions
Case study: Vaccines, including cancer vaccines

Midterm 2 and second set of presentations

Official notes
Classroom policies
• Our physical and virtual classrooms are safe places for sharing opinions and thoughts in which we will
all show our respect for each other by engaging without judgement, regardless of race, culture,
ethnicity, religion, politics, gender or gender variance and nationality. This year more than ever is a
time for us all to practice patience and kindness with ourselves and with others.
• My goal is to have you all learn and see the relevance of the selected topics to your own lives and your
chosen profession. If there are aspects of this course that prevent you from learning or exclude you,
please let me know as soon as possible so we can jointly identify strategies that meet your needs and
the requirements of the course. A number of resources which may be helpful are noted in the following
sections.
• This year has been particularly challenging, which is reflected in the flexibility built into the grading
schemes. If you experience any specific additional hardships, such as illness, accident or family crisis
please know that these policies may be amended. In this situation, please communicate with me or Dr.
Kelly McQueary as soon as you feel comfortable doing so. If you do not feel comfortable discussing
with us, please visit Student Emergency Services.
• Absences are accounted for in your 4 dropped insta-poll quizzes. Class periods will be automatically
recorded and available through canvas.

COVID-related information
• This course may be offered in a format to which you are unaccustomed. If you are looking for ideas
and strategies to help you feel more comfortable participating in our class, please explore the resources
available here: https://onestop.utexas.edu/keep-learning/ .
• For the most up to date information on learning during COVID-19, including guidance about safety,
cloth masks in classrooms, and classroom guidelines, see https://protect.utexas.edu/learning/ .
• While we will post information related to the contemporary situation on campus, you are encouraged
to stay up-to-date on the latest news as related to the student experience. https://protect.utexas.edu/

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Academic integrity Each student in the course is expected to abide by the University of Texas Honor
Code: “As a student of the University of Texas at Austin, I shall abide by the core values of the University
and uphold academic integrity.” Plagiarism is taken very seriously at UT. You are responsible for
understanding UT’s Academic Honesty and the University Honor Code which can be found at the following
web address: https://deanofstudents.utexas.edu/conduct/standardsofconduct.php

Dropping the course An engineering student must have the Dean’s approval to add or drop a class after
the 4th class day of the semester. Adds or drops are not approved after the fourth class day except for
good cause. “Good cause” is determined to be documented evidence of an extenuating circumstance
(such as health or personal problems) that did not exist before the 4th day of class. Applications for approval
to drop a course after the 4th day should be made in the Office of Student Affairs, ECJ 2.200.

If you want to drop a class after the 12th class day, you’ll need to execute a Q-drop before the Q-drop
deadline, which typically occurs near the middle of the semester. Under Texas law, you are only allowed
six Q drops while you are in college at any public Texas institution. For more information, see:
http://www.utexas.edu/ugs/csacc/academic/adddrop/qdrop

Pass/Fail or Credit/No Credit Grading Policy. For the spring 2021 semester, undergraduate students
may choose to have a total of three (3) classes graded on a Pass/Fail or Credit/No Credit basis without
penalty. These exceptions are new and apply only to the fall 2020 and spring 2021 semesters. For more
information please visit UT's policy on the Extended deadline for Q-drops and P/F Flexibility.

Religious holidays By UT Austin policy, you must notify the instructor of your pending absence at least
fourteen days prior to the date of observance of a religious holy day. If you must miss a class, an
examination, a work assignment, or a project in order to observe a religious holy day, you will be given an
opportunity to complete the missed work within a reasonable time after the absence.”)



Emergency evacuations The following recommendations regarding emergency evacuation from the
Office of Campus Safety and Security, 512-471-5767, http://www.utexas.edu/safety/.

Students with disabilities The university is committed to creating an accessible and inclusive learning
environment consistent with university policy and federal and state law. Please let me know if you
experience any barriers to learning so I can work with you to ensure you have equal opportunity to
participate fully in this course. For more information, contact the Office of the Dean of Students at 471-
6259, 471-4641 TTY or the College of Engineering Director of Students with Disabilities at 471-4321.
Division of Diversity and Community Engagement, Services for Students with Disabilities, 512-471-6259,
https://diversity.utexas.edu/disability/

Counseling and Mental Health Center The Counseling and Mental Health Center at
https://cmhc.utexas.edu/index.html being, academic and life goals. To learn more about your counseling
and mental health options, call CMHC at (512) 471-3515. If you are experiencing a mental health crisis,
call the CMHC Crisis Line 24/7 at (512) 471-2255.

The Sanger Learning Center Did you know that more than one-third of UT undergraduate students use
the Sanger Learning Center each year to improve their academic performance? All students are
welcome to take advantage of the Sanger Center’s workshops, private learning specialist appointments,
peer academic coaching, and tutoring for more than 70 courses in 15 different subject areas. For more
information, please visit http://www.utexas.edu/ugs/slc or call 512-471-3614 (JES A332).

BeVocal is a university-wide initiative to promote the idea that individual Longhorns have the power to
prevent high-risk behavior and harm. At UT Austin all Longhorns have the power to intervene and reduce
harm. To learn more about BeVocal and how you can help to build a culture of care on campus, go to:
https://wellnessnetwork.utexas.edu/BeVocal.

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If you have concerns about the safety or behavior of fellow students, TAs or Professors, call BCAL (the
Behavior Concerns and COVID-19 Advice Line): 512-232-5050. Your call can be anonymous. If
something doesn’t feel right – it probably isn’t. Trust your instincts and share your concerns.