Molecular Biology and Biochemistry Courses

• This course will discuss state-of-the-art understanding of the biology of aging and longevity, considering what we know, what are particular challenges to tackling the problem, what are the controversies, what are the myths. Topics we will consider are genetics, diet, environment, chance, signaling pathways, epigenetics, late onset diseases.  Format will be lecture plus reading discussions, emphasis on molecular genetics of longevity and health span.
• Semester Offered: Fall
• Credits: 3
• Course URL: canvas

Prerequisites

Genetics (01:447:380 or 01:447:384/385) and Biochemistry (01:694:301, 01:694:395 or 01:694:407).  

Course Syllabus

 Spring 2024 (Fall 2025 syllabus will be updated soon)

Topics

• What is aging?
• Model systems in aging research
• Genetics of Longevity
• Longevity signaling pathways
• DNA damage and maintenance
• Telomere theories
• Stress responses and healthy aging
• Caloric restriction
• Free radical theory of aging
• Mitochondria
• Metabolism and Diabetes
• The aging brain
• Late-onset Neurodegenerative disease
• Epigenetics
• Stem Cells and regenerative biology
• Reproductive aging

Course Satisfies Learning Goals

1. Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.
2. Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
3. Students should demonstrate the ability to design experiments and critically analyze data.

 Exams, Assignments, and Grading Policy:

20% Quizzes 3-4, will announce dates, one week in advance 

25% Exam 1 midterm   

25% Exam 2 final           

20% Paper presentations 

10% Class participation (hw questions, discussion—you will need to attend class!) 

Course Materials

Assigned papers, weekly readings will be posted at the course Canvas site.

Course Closed?  

There is no wait list for this course. Please continue to monitor web-reg for openings.

Faculty

Prof. Monica Driscoll
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Nelson Biological Labs. Room A232

Yang Lyu
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.
Nelson Lab, Room A307A

Student Support Services

Student Success Essentials: https://success.rutgers.edu
Student Support Services: https://www.rutgers.edu/academics/student-support   
The Learning Centers: https://rlc.rutgers.edu/  
Rutgers Libraries: https://www.libraries.rutgers.edu/
Bias Incident Reporting: https://studentaffairs.rutgers.edu/bias-incident-reporting
Dean of Students – Student Support Office: https://success.rutgers.edu/resource/dean-students-student-support-office
Office of Veteran and Military Programs and Services: https://veterans.rutgers.edu  
Student Health Services: http://health.rutgers.edu/
Counseling, Alcohol and Other Drug Assistance Program & Psychiatric Services (CAPS):  http://health.rutgers.edu/medical-counseling-services/counseling/
UWill: free immediate access to teletherapy; you can choose a therapist based on your preferences including issue, gender, language, ethnicity. http://health.rutgers.edu/uwill/
Office for Violence Prevention and Victim Assistance: vpva.rutgers.edu/Office of Disability Services: https://ods.rutgers.edu/
Basic Needs Assistance (food, housing, and other   essentials):  https://ruoffcampus.rutgers.edu/basic-needs
Rutgers Student Food Pantry: https://ruoffcampus.rutgers.edu/food-pantry

** All information is subject to change at the discretion of the course coordinator.

• Course Description:  The aim of the course is to provide an introduction to chromatin dynamics, particularly the structural and biochemical modifications of chromatin that underlie epigenetic states and their effects on gene expression and development. The importance of epigenetic states is perhaps the major discovery of molecular biology in the past ten years. They are critical to understanding the control of gene expression in development, the programming and reprogramming that takes place in the differentiation of pluripotent stem cells and they provide an accounting for many of the genomic malfunctions that result in human disease. An acquaintance with the concepts of what has come to be known as Epigenomics is essential for a Molecular Biology major.
• Semester Offered: Fall
• Credits: 3

Prerequisites

One semester of Genetics (01:447:380 or 01:447:384) 

Course Syllabus:

Fall 2024 (subject to change)

Lesson Plan

1. Introduction [SG]
2. Nucleosome I [SG]
3. Nucleosome II [SG]
4. ATP-dependent nucleosome remodeling [SG]
5. Histone modification I [SG]
6. Histone modification II and histone variants [SG]
7. DNA methylation [SG]
8. Chromatin and cancer [SG] 
9. Review [SG]
10. Guest lecture by Dr. Simone Sidoli, “Proteomics for chromatin biology”
11. Techniques in Epigenomics [MZ]
12. Maintenance of epigenetic marks. [MZ]
13. Genome architecture [MZ]
14. Genomic programming and Imprinting [MZ]
15. Polycomb mechanisms [MZ]
16. Guest lecture by Dr. Marc Gartenberg (RWJMS), 
17. Dosage compensation [MZ]
18. Constitutive Heterochromatin [MZ]
19. RNAi as a heterochromatin signal [MZ]
20. Guest lecture by Dr. Mike Hampsey (RWJMS)
21. Guest lecture by Dr. Kevin Monahan (MBB)
22. Nuclear RNAi in C. elegans [SG]
23. piRNA [MZ]

Course Satisfies Learning Goals

• Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.
• Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.
• Students demonstrate the ability to communicate their research and findings orally through seminar and poster presentations and through written research papers.

Exams, Assignments, and Grading Policy

60% Exams (20% each)- Each exam will cover one of the sections, as well as the corresponding guest lecture. The format of the exams may vary between instructors. 

10% Participation- In lectures as well as other student presentations)

30% Student Presentation- Each group (2 students) will be assigned a research article at the beginning of the course. Both members of the team must participate in reading, analyzing and digesting the paper. They (as a team) will submit their written answers to a set of questions (see below) one month before the presentation.

Each group will make an appointment with a faculty member to rehearse their presentation 2 weeks before the scheduled presentation date.  At this meeting, the students will present written answers to a set of questions described below. The faculty member will provide feedback for the students to revise their presentation. The quality of the team preparation for this meeting, and how well the students incorporate faculty feedback into their presentation will become part of the grade for the student presentation section.

Each classroom presentation will consist of 20 minutes to present slides. The two team members will generally alternate in presenting the material. Additional 10 minutes after the presentation will be reserved for questions from the instructors and the other students. We encourage you to rehearse the final presentation to ensure a good time management.

Presentations should introduce the problem the paper is trying to address, give a brief overview of the techniques used (unless they are very common, like RT-PCR or Southern blotting), a rundown of the major results and conclusions, and present a critique of the paper’s strong and weak points. Do not attempt to discuss every single experiment but focus on the major issues. Remember that you only have 10 minutes each to present the paper, so be brief and to the point. The slides or transparencies should be free of superfluous clutter and clear enough to stand on their own. In order to fully understand the paper and the problem the students should be prepared to read and analyze the most important previous literature that the paper refers to. Questions from the audience and instructors may also refer to issues that the paper doesn’t cover directly but are pertinent to their conclusions, especially if they have been covered in class.

Questions (written answers are due three weeks one month before the presentation and should usually involve 4-5 pages):

Introduction:

• What are the main questions that the paper is trying to answer?
• What information is necessary to understand the main question addressed by the paper?
• What system is used by the study? Why?
• What are the specific discoveries made by the study? What is the most important finding?
• What is the significance to the field?

Methods:

• What techniques are used to address the questions?
• What are the advantages of the techniques?
• Can you think of an alternative technique?

Results:

• How do you describe the results that support the major conclusion? (For example: what do the bands in each lane of a gel represent? What are the controls? What are the axes of graphs?)
• Do you have any alternative interpretations?

Discussion:

• Do the experiments support the stated goals and conclusions?
• What models do the authors propose based on the finding?
• What are the new questions raised by the finding? 
• Are there any medical implications? 

Course Materials

All course materials will be posted on the Canvas site

Course Closed?  

If 694:413 is closed please contact This email address is being protected from spambots. You need JavaScript enabled to view it. or This email address is being protected from spambots. You need JavaScript enabled to view it.

Faculty

Co-Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.
                          Phone: 445-0824
                          Office: Nelson A123
                          Office hours: By Appointment

Co-Coordinator: This email address is being protected from spambots. You need JavaScript enabled to view it.
                           Phone: 445-1497
                          Office: Nelson A133
                          Office hours: By Appointment

** All information is subject to change at the discretion of the course coordinator.

• Semester Offered: Fall
• Credits: 3

Prerequisites

One semester of Genetics (01:447:380 or 01:447:384)

Co-requisite

Biochemistry (01:694:407 or 01:694:395 or 01:694:301 or 11:115:301 or 11:115:403)

Course Syllabus

Fall 2024 (Subject to change)

Course Description  

This is an upper level course, targeted at seniors. The purposes of the course are:

• to introduce students to several important research areas of advanced molecular biology and biochemistry, in particular topics related to molecular pathways and signal transduction (past topics include cell cycle regulation, proteomics and retrotransposon)
• to train students to think logically and independently through active participation in class discussion.

The course will present contemporary concepts and experimental techniques not covered in other classes

Topic 1.          Cell Cycle-regulation of mitosis (Dr. F. Matsumura)

1                      Cell division control, G2/M transition

2                      Maturation-Promoting Factor (MPF)

3                      Cyclin

4                      cdc2 Kinase

5                      Regulation of MPF- Proteolysis & Phosphorylation

6                      Exam 1 for the lectures (1-5) by Dr. F. Matsumura

7                      Downstream Events I (nuclear lamin)

8                      Downstream Events II (Chromosome segregation)

9                      Polo-like kinase1

10                    Current Topics: iPS

11                    Current Topics: iPS

12                    Exam 2 for the lectures (7-11) by Dr. F. Matsumura

Topic 2           Transposition  (Dr. A. Gabriel):

1                      Retrotransposon Replication Strategies

2                      Retrotransposon

3                      Reverse Transcription

4                      Transposon Integration I

5                      Transposon Integration II

6                      LINEs & SINEs & Processed Pseudogenes

7                      Exam 3 for the lectures by Dr. A. Gabriel

Topic 3.          Genomics, molecular pathways, and human evolution. (Dr. S. Anderson)

1                      Human genome, mutations, and evolution

2                      Meiosis, recombination, and haplotypes

3                      Genes that make us human, I

4                      Genes that make us human, II

5                      Aging, I

6                      Aging, II

7                      Review session

8                      Exam 4 for the lectures by Dr. S. Anderson

Course URL

Canvas

Course Satisfies Learning Goals

1. Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.

2. Students should demonstrate the ability to find and evaluate information about specific biological systems or problems.

Exams, Assignments, and Grading Policy

Grades will be assigned on the basis of four exams (90-95%), as well as the participation in class discussion (5-10%). The exams will consist of essay questions in which students are required to synthesize information from lectures and discussions.

Course Materials

There is no required textbook for this course. Rather papers from the current literature will be selected for lectures and discussion.

Students are required to participate in class discussion (believe me it is fun!).

Course Closed?

If this course is closed please contact Dr. Matsumura (This email address is being protected from spambots. You need JavaScript enabled to view it.)

Faculty

Dr. Fumio Matsumura
A323 Nelson Biology Labs
email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Dr. Stephen Anderson
CABM305
email: This email address is being protected from spambots. You need JavaScript enabled to view it.

** All information is subject to change at the discretion of the course coordinator.

• Semester Offered: Fall
• Credits: 3

Prerequisites

Organic Chemistry 01:160:209 or 01:160:307 or higher.  Credit not given for both 01:694:407 and 01:694:395, 01:694:301, 11:115:301 or 11:115:403.

Course Description

This course is a two-semester sequence offered as the primary foundation course for students interested in pursuing modern molecular biology. The first semester (01:694:407) presents a complete survey of Biochemistry topics, and the second semester (01:694:408) provides a thorough coverage of current ideas in Molecular Biology.

Topics include:

• Thermodynamics
• Enzyme Kinetics
• Protein Structure and Function
• Carbohydrates, Lipids and Membranes
• Gycolysis and the Citric Acid Cycle
• Electron Transport
• Membrane Transport
• Photosynthesis and Light Reactions
• Lipid Metabolism
• Protein Turnover and Signal Transduction
• Gluconeogenesis and Glycogen Metabolism
• Urea Cycle and Pentose Phosphate Pathway
• Amino Acid and Nucleotide Catabolism and Metabolism

Course Syllabus: 

Fall 2025

Course Satisfies Departmental Learning Goals:  

Students should demonstrate an understanding of the knowledge that is needed to begin biomedical research and that is required for post-graduate exams and studies.

Exams, Assignments, and Grading Policy:  

• Four Exams: 80%
• Weekly Homework: 10%
• Weekly Quizzes: 10%

The fourth hourly exam is given in the final exam time slot and there will be no cumulative final exam. The final grade is made up of the average of the exams and weekly assignments.

Course Materials

Required Texts:
Lehninger Principles of Biochemistry, Nelson and Cox, 8th edition
ISBN: 9781319230906 (Achieve Access Code)

Course Closed?  

Contact Course Coordinator

Course Coordinator

Dr. Kevin Monahan
Nelson Biological Labs, Room A317
Phone: (848) 445-9508

Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

Participating Faculty:

Dr. Tina Liu
CABM, 304
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Dr. Yang Lyu
Nelson Biological Labs, Room A307
Email: This email address is being protected from spambots. You need JavaScript enabled to view it.

** All information is subject to change at the discretion of the course coordinator.