605.205.8VL - Molecular Biology for Computer Scientists

Course Structure

The course materials are divided into modules which can be accessed by clicking Course Modules on the course menu. A module will have several sections including the overview, content, readings, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates.

Course Topics

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

• Identify and describe the parts, functions, and organization of the cell, as well as cellular energetics, metabolism, and signaling.
• Recognize, examine, and summarize foundational concepts in developmental, oncogenic (cancer), neurobiological, and immunological biology.
• Evaluate, summarize, and lecture over a bioinformatics research topic through a team-based paper and presentation project.

Module Topics:

• Cells and Genomes
• Cells: Organization and Function
• Macromolecules: Structure and Function
  
• Gene Expression: Transcription
• Gene Expression: Translation
• Controlling Gene Expression: Regulation
• Biological Membranes and Transmembrane Transport
• Metabolism and Cellular Energetics
• Cell Signaling and Signal Transduction
• Foundational Concepts: Development Biology
• Foundational Concepts: Cancer Biology
• Foundational Concepts: Neurobiology
• Foundational Concepts: Immunology

Course Goals

 Identify and describe foundational concepts, characteristics, organization, and function of cells and their component parts. Explain and illustrate concepts related to cellular energetics and membrane transport mechanisms. Collect, analyze, and interpret differences between and within gene expression. Explore research areas in bioinformatics and computational biology.

Course Learning Outcomes (CLOs)

• Module 1 CLOs: Introduction to DNA and RNA; Major features of eukaryotic cells
• Module 2 CLOs: The role of the endoplasmic reticulum; Compartments comprised of the cell and the relationships between them; Introduction to mitochondria
• Module 3 CLOs: DNA synthesis; The effect of chromatin structure on DNA function; The role of genetic mutations in evolution
• Module 4 CLOs: Maintaining DNA fidelity; How DNA replicates in chromosomes; Basic description of viral lifecycle
• Module 5 CLOs: Synthesis of RNA from DNA; Principal types of RNA and their functions
• Module 6 CLOs: Molecular mechanisms for specialized cell type differentiation; Post transcriptional modifications; Small non-coding RNA transcripts
• Module 7 CLOs: Membrane structure and proteins; Intra and extra-cellular small molecule transport; Electrical properties of membranes; Endocytosis
• Module 8 CLOS: Glycolysis; Citric acid cycle; ATP production and mitochondria
• Module 9 CLOs: Major classes of cell surface receptor proteins; Alternative signaling routes in gene regulation
• Module 10 CLOs: Early stages of embryogenesis; Cerebral cortex development; The role of cell polarity in morphogenesis
• Module 11 CLOs: The role of genetic mutations in the development of cancer; Epigenetic markers; Viruses and cancer
• Module 12 CLOs: Molecular mechanisms associated with neural tube formation; Associated diseases and conditions
• Module 13 CLOs: Components and roles of the innate immune system; Vaccines and antibody responses; T-cells, B-cells, and MHC proteins
• Module 14 CLOs: Application of course learning objectives

Textbooks

Alberts, B., Heald, R., Johnson, A., Morgan, D., Raff, Martin, Roberts, K., Walter, P., Wilson, J., Hunt, T.  (2022). Molecular Biology of the Cell (7th ed.). New York: W. W. Norton & Company.

ISBN-10: 0393884821
ISBN-13: 978-0393884821

Other Materials & Online Resources

Smartwork Assignments from the course textbook are required.

Student Coursework Requirements

It is expected that each module will take approximately 7–10 hours per week to complete. Here is an approximate breakdown: reading the assigned sections of the texts (approximately 3–4 hours per week) as well as some outside reading, attending weekly virtual lecture at the scheduled time, participating in group work, and writing assignments and quizzes (approximately 2–3 hours per week).

This course will consist of the following basic student requirements:

Preparation and Participation (10% of Final Grade Calculation)

You are responsible for carefully reading all assigned material and being prepared for discussion. The majority of readings are from the course text. Additional reading may be assigned to supplement text readings.

Part one of your grade will be attendance during synchronous lecture and group project time. This is determined by being present within the first 10 minutes of synchronous class each week, and also returning after each scheduled break during the weekly lecture. Please use your first and last name on Zoom so attendance is appropriately recorded.

Part two of your grade is your active participation during lectures and group breakouts (i.e., responding to classmate postings with thoughtful responses). Feel free to agree or disagree with your classmates. Please ensure that your interactions are civil and constructive.

Preparation and participation are evaluated by the following grading elements:

Attendance (50%)

Active Participation (50%)

Preparation and participation are graded as follows:

• 100–90 = A: Attendance [regular and timely to all classes]; Active Participation [rich in content; full of thoughts, insight, and analysis].
• 89–80 = B: Attendance [frequently attends classes]; Active Participation [substantial information; thought, insight, and analysis has taken place].
• 79–70 = C: Attendance [infrequently attends classes]; Active Participation [generally competent; information is thin and commonplace].
• <70 = F: Attendance [rarely attends classes]; Active Participation [rudimentary and superficial; no analysis or insight is displayed].

Assignments (30% of Final Grade Calculation)

Assignments will include a mix of qualitative assignments (e.g. literature reviews) and quantitative problem sets (e.g., quizzes, Smartwork). Include a cover sheet with your name and assignment identifier for qualitative assignments. Also include your name and a page number indicator (i.e., page x of y) on each page of your submissions. Each problem should have the problem statement, assumptions, computations, and conclusions/discussion delineated. All Figures and Tables should be captioned and labeled appropriately.

All assignments are due according to the dates in the Calendar.

Late submissions will be reduced by one letter grade for each week late (no exceptions without prior written coordination with the instructors).

If, after submitting a written assignment you are not satisfied with the grade received, you are encouraged to contact the instructors and request permission to redo the assignment and resubmit it within two (2) weeks of receiving the grade. If the resubmission results in a better grade, that grade will be substituted for the previous grade. Any resubmission received after the two-week period has lapsed will be subject to the same late submissions penalty as stated above.

Qualitative assignments are evaluated by the following grading elements:

1. Each part of question is answered (20%)
2. Writing quality and technical accuracy (30%) (Writing is expected to meet or exceed accepted graduate-level English and scholarship standards. That is, all assignments will be graded on grammar and style as well as content.)
3. Rationale for answer is provided (20%)
4. Examples are included to illustrate rationale (15%) (If you do not have direct experience related to a particular question, then you are to provide analogies versus examples.)
5. Outside references are included and properly cited (15%)

Qualitative assignments are graded as follows:

• 100–90 = A—All parts of question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rich in content; full of thought, insight, and analysis].
• 89–80 = B—All parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [substantial information; thought, insight, and analysis has taken place].
• 79–70=C—Majority of parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [generally competent; information is thin and commonplace].
• <70=F—Some parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rudimentary and superficial; no analysis or insight displayed].

Quantitative assignments are evaluated by the following grading elements:

1. Smartwork assignments and course quizzes are automatically graded based on accurate and precise answers for multiple choice and matching-style questions.

1. Short answer questions that require critical thinking may be included in digital problem sets or course quizzes. When they are graded, the same evaluation criteria for Qualitative Assignments will apply.

Quantitative assignments are graded as follows:

• 100–90 = A—All parts of question are addressed; All assumptions are clearly stated; All intermediate derivations and calculations are provided; Answer is technically correct and is clearly indicated; Answer precision and units are appropriate.
• 89–80 = B—All parts of question are addressed; All assumptions are clearly stated; Some intermediate derivations and calculations are provided; Answer is technically correct and is indicated; Answer precision and units are appropriate.
• 79–70=C—Most parts of question are addressed; Assumptions are partially stated; Few intermediate derivations and calculations are provided; Answer is not technically correct but is indicated; Answer precision and units are indicated but inappropriate.
• <70=F—Some parts of the question are addressed; Assumptions are not stated; Intermediate derivations and calculations are not provided; The answer is incorrect or missing; The answer precision and units are inappropriate or missing.

Course Project (30% of Final Grade Calculation)

A team-based course project will be assigned several weeks into the course. The next-to-the-last week of the course will be devoted to finalizing the course project. The parts of the project are as follows:

1. Topic approval (10%)
2. Outlined paper (10%)
3. Annotated bibliography (20%)
4. Final paper (30%)
5. Final Presentation (30%)

Topics will come from Frontiers in Nature

https://www.frontiersin.org/journals/bioinformatics/research-topics?submission=2

The course project is evaluated by the following grading elements:

1. Student preparation and participation (as described in Course Project Description) (40%)
2. Student technical understanding of the course project topic (as defined in the Course Project Description) (20%)
3. Team preparation and participation (as described in Course Project Description) (20%)
4. Team technical understanding of the course project topic (as defined in the Course Project Description) (20%)

Course Project is graded as follows:

• 100–90 = A—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities well defined and understood; individual/ team well versed in use of Adobe Connect; individual/ team work product(s) agreed to, well prepared and available to all team members/ instructors]; Student Understanding/ Team Understanding [rich in content; full of thought, insight, and analysis].
• 89–80 = B—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities well defined and understood; individual/ team well versed in use of Adobe Connect; individual/ team work product(s) agreed to and prepared]; Student Understanding/ Team Understanding [substantial information; thought, insight, and analysis has taken place].
• 79–70 = C—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities agreed to; individual/ team well versed in use of Adobe Connect; individual/ team work product(s) prepared]; Student Understanding/ Team Understanding [generally competent; information is thin and commonplace].
• <70 = F—Student Preparation and Participation/ Team Preparation and Participation [individual/ team roles and responsibilities not well understood; individual/ team has difficult with use of Adobe Connect; individual/ team work product(s) partially prepared]; Student Understanding/ Team Understanding [rudimentary and superficial; no analysis or insight displayed].

Exams (30% of Final Grade Calculation, each exam worth 10%. Three total exams, final exam is COMPREHENSIVE)

The 1st Exam will be available in Module 6, and the 2nd and Comprehensive Final Exam will be available in the next-to-last Module.

You will have one week to complete both parts of the exams, and they will be due by 5PM exactly one week from their release. You may use the course text and notes to complete the exams, as well as the Internet. If you use the Internet, you MUST cite your sources using APA 7th edition citation style. You are prohibited from working together, with each other or anyone else, to complete the exams.

The exams will be timed. They will be composed of short-answer and essay style questions. They will open the first day of that module week, and closes at 5PM the last day of the module. They will be evaluated by the following grading elements:

1. Each part of question is answered (20%)
2. Writing quality and technical accuracy (30%) (Writing is expected to meet or exceed accepted graduate-level English and scholarship standards. That is, all assignments will be graded on grammar and style as well as content.)
3. Rationale for answer is provided (20%)
4. Examples are included to illustrate rationale (15%) (If a student does not have direct experience related to a particular question, then the student is to provide analogies versus examples.)
5. Outside references are included and cited using APA 7th edition format (15%)

All exams are graded as follows:

• 100–90 = A—All parts of question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rich in content; full of thought, insight, and analysis].
• 89–80 = B—All parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [substantial information; thought, insight, and analysis has taken place].
• 79–70 = C—Majority of parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [generally competent; information is thin and commonplace].
• <70 = F—Some parts of the question are addressed; Writing Quality/ Rationale/ Examples/ Outside References [rudimentary and superficial; no analysis or insight displayed].

Grading Policy

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

We 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 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).

100-98 = A+ 97-94 = A 93-90 = A− 89-87 = B+ 86-83 = B 82-80 = B− 79-77 = C+ 76-73 = C 72-70 = C− <70 = F

Final grades will be determined by the following weighting:

Item	% of Grade
Preparation and Participation	10%
Assignments (Smartwork + Quizzes)	30%
Course Project	30%
Exams (1st, 2nd, Comprehensive Final)	30% (10% + 10% + 10%)

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. 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. Our courses are designed with a proactive approach to accessibility to minimize the need for disability disclosure and accommodation requests, but we recognize that you may need additional support. 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 EP Student Disability Services at 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 Student Conduct Code website.

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.