585.746.81 - Biochemical and Cellular Engineering

Applied Biomedical Engineering
Spring 2024


This course provides a foundation of molecular and biochemical principles required for engineering cells accompanied by a survey of biomedical applications of biochemically engineered cells with a focus on medical uses. Class lectures provide an overview of molecular biology and biochemistry fundamentals that include protein/ligand binding, receptor/ligand trafficking, cell-cell interactions, cell-matrix interactions, and cell adhesion and migration at both theoretical and experimental levels. Lectures will also cover the effects of physical (e.g., shear stress, strain), biochemical (e.g., cytokines, growth factors), and other (e.g., electrical) stimuli on cell function, emphasizing gene regulation, signal transduction, metabolic engineering, polymeric biomaterials, and drug and gene delivery. Finally, lectures will cover biomedical applications of engineered cells ranging from viral-based systems, prokaryote manipulation (e.g., in the context of the microbiome), to cell-based therapies (e.g., CAR T cell and other immunotherapies). An ongoing emphasis in course lectures will be to provide illustrative examples of how “Nature” engineers cells and how these lessons can be applied by biomedical engineers for clinical translation applications. In addition to lectures provided by course instructors, students will work in teams on a course project on a topic of their choosing (subject to course instructor approval) that involves an oral presentation as well as a written report.Recommended prerequisites: Background in undergraduate level cell biology, biochemistry, and/or organic chemistry.


Profile photo of Kevin Yarema.

Kevin Yarema

Course Structure

The course materials are divided into modules which can be accessed by clicking Modules on the course menu. A module will have several sections including the overview, content, discussions, and assignments that include weekly quizzes, homework assignments due every second week, and the term project.  Each module is designed to be completed in seven (7) days (i.e., on a weekly basis); generally two modules will be available so that students can work ahead on the next week's assignments if they wish to. Students should regularly check the Calendar and Announcements for any updates or changes to assignment due dates.

Course Topics

Course Goals

The first main goal of this course is to provide students with basic knowledge of subcellular components and proficiency on how to manipulate these components to modulate cell (and higher level) biology. The second broad goal of this course is to enable students to use this knowledge and understanding of relevant experimental systems for practical biological, medical, and other applications with a particular focus on the clinical translation of biomedical technologies.

Course Learning Outcomes (CLOs)


Not required.

Student Coursework Requirements

Homework Assignments (25% of total grade)

Five homework assignments will be given that both cover course material and extend lecture concepts allowing for independent exploration of lecture topics based on a student’s interest. Each assignment will be worth 5% of the course grade and will be due at the ends of Modules 2, 4, 6, & 8 (note that the homework assignments are front-loaded into the class schedule to provide time for students to present, view, and peer-review other students’ Course Project presentations during the latter stages of the course).

Quizzes (30% of total grade)

This course will contain both ungraded and graded quizzes. Each module will contain a graded quizzes that will need to be completed (70% or better) before a student can move on to the next module. In addition, you will have access to an ungraded quiz that provides all the questions from the previous module’s graded quiz.

Discussion & Feedback (20% of total grade)

Asynchronous weekly discussions will be held for each module (1% each; 14% total) and peer-review feedback will be provided on students’ oral presentations (6%; which will be online / recorded for viewing by Week 10; the feedback will be due two weeks later at the end of Module 12 [feedback will be done in lieu of regular homework assignments during this time period])

Discussions and Feedback are evaluated by the following grading elements:

Discussion and Feedback is graded as follows:

Course Project (25% of total grade)

Students will work individually or with a partner to develop an “NIH R21 style” grant proposal. Project deliverables that will be graded in include selection of a topic (2% of the course grade); production of a Letter of Intent (LOI; 3%); submission of a Project Narrative, Project Summary, and Specific Aims (5%, combined), an oral presentation of the project (7.5%), and a finally a written report (7.5%).  In addition, "peer review" of your classmates projects will provide 6% of the course grade as part of the Disscussion & Feedback class component.  Refer to the Course Project Overview document for more information.

Grading Policy

Assignments are due according to the dates posted in your course site. You may check these due dates in the Calendar or the Assignments in the corresponding modules. I will post grades one week after assignment due dates.

I generally do not directly grade spelling and grammar. However, egregious violations of the rules of the English language will be noted without comment. Consistently poor performance in either spelling or grammar is taken as an indication of poor written communication ability that may detract from your grade.

A grade of A indicates achievement of consistent excellence and distinction throughout the course—that is, conspicuous excellence in all aspects of assignments and discussion in every week.

A grade of B indicates work that meets all course requirements on a level appropriate for graduate academic work. These criteria apply to both undergraduates and graduate students taking the course.

EP uses a +/- grading system (see “Grading System”, Graduate Programs catalog, p. 10).

Score RangeLetter Grade
100-97= A+
96-93= A
92-90= A−
89-87= B+
86-83= B
82-80= B−
79-77= C+
76-73= C
72-70= C−
69-67= D+
66-63= D
<63= F

Final grades will be determined by the following weighting:


% of Grade

Homework Assignments




Discussions & Feedback


Course Project


Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.