Syllabus-Molecular Cell Biology

SYLLABUS-MOLECULAR CELL BIOLOGY 351 FALL 2008

Instructors: Dr. Betsy Read Dr. Matt Escobar SHII 125 SHII 123 Phone: 750-4129 Phone: 750-8083 [email protected] [email protected] Office Hours: 11:15-2:00 Tuesday Office Hours: 3:45-5:00 Wed., Thurs. and/or by appointment

Course Description An introduction to the molecular biology of the cell. Includes studies of the nature of the organization of the cell, bioenergetics and enzyme function, membrane structure and function, cell metabolism, basic genetic mechanisms, the flow of information within and between cells, cellular development, and specialized functioning of cells.

Learning Outcomes At the end of the course students should:

1. have acquired appreciation of the dynamics of the cell as a basic unit of life and understanding of the major concepts in cell and molecular biology, including protein function, genome structure and organization, DNA replication, transcription, translation, gene regulation, membrane structure and function, and protein trafficking

2. be able to write clear and well-argued descriptions of these topics, based on the course material and textbook articles

3. be able to design, perform and analyze simple experiments in cell and molecular biology

4. acquired basic skills in bioinformatics and computational biology including how to perform, BLAST searches, sequence alignments, restriction mapping, phylogenetic analysis, genome annotation

5. be able to critically read and engage in discussion of scientific papers relating to the field of molecular cell biology 6. appreciate how technology and different research methods have been used to address major concepts in molecular cell biology

7. have acquired stronger critical thinking, reasoning, and problem-solving skills, scientific attitudes and values

8. be able to make responsible decisions about social issues that relate to science, technology, the environment and health, such as aging, cancer, drugs, energy, genetic engineering, heredity, and nutrition.

9. be familiar with employment opportunities in the biological sciences and contributions of biology to modern society.

Text: The Molecular Biology of the Cell, 5th Edition, Alberts, B. et al., 2008.

Make-up Work If you miss class or a lab for any reason, it is up to you to get the information, announcements, assignments, etc. you missed. Contact me immediately if you are going to or have missed a test. Make-up tests will not necessarily be the same test the rest of the class took. Expect a make-up test to be more difficult and/or to have 10% automatically deducted from the score.

Grading Grading will be based on a total accumulation of points (850 possible). 400 points for exams midterm 100 pts take home exam 100 points final exam of 200 points 300 points for lab write-ups (3 at 100 points each) 100 points in class article presentation 50 points for lab participation Grades will be assigned on a straight percentage basis whereby: 90-100 A 80-89 B 70-79 C 60-69 D < 60 F No extra credit

Lab Write-ups You are required to come to each laboratory with a flow-sheet outlining that laboratory experiment; you will not be allowed into the lab without your flow-sheet! Each laboratory write- up will include: 1) Title, 2) an Abstract that summarizes what was done and what the major findings were 3) an Introduction, which spells out the exact purpose(s) and objective(s) of the experiment and the theoretical background; what was done, to what, why, and how 4) a Flow sheet of experimental details, 5) a Results section to include all the raw data generated and all calculations (data may be presented in the form of tables, graphs, formulas, etc., ), and 6) a Discussion section which states your findings and includes any interpretations, conclusions, or suggestions regarding the results obtained. Write-ups will be collected one week following the completion of that exercise and will be collected at the beginning of the laboratory period. One laboratory write-up should be turned in for each team of two.

Outside Readings Each team of 2 students will be required to read and critique a journal article which pertains to Cell and Molecular Biology. The paper will be assigned to you and your partner in lab and you will be responsible for presenting the paper orally to the class. The oral presentation should be informal, 20-30 minutes long, and should be accompanied by brief (2-3 pages) written summary of the paper. These topics will be presented on the afternoon of your respective laboratory session, and all students should be prepared to participate. These sessions are meant to be discussions, rather that formal oral reports, covering current techniques and advances in research that are particularly relevant to material be covered in lecture and/or laboratory exercises. I have selected papers from the current literature and will provide relevant reviews and background reading for each topic. A schedule will be set up during our 2nd class meeting. Please come to see me or Dr. Esobar prior to presenting your article so that we might help you to better understand the article.

Course Outline

Week Topic Lab 8/25 Chapter 3: Proteins 1: Making Solutions The shape and Structure of Proteins Protein Function 9/1 Chapter 4: DNA and Chromosomes No Lab The Structure and Function of DNA Chromosomal DNA and its Packaging in the Chromatin Fiber The Global Structure of Chromosomes 9/8 Chapter 5: DNA Replication, Repair and Recombination 2: Preparing Competent The Maintenance of DNA Sequences Cells/Transformation DNA Replication Mechanisms The Initiation and Completion of DNA Replication in Chromosomes DNA Repair General Recombination Site-Specific Recombination 9/15 Chapter 6: How Cells Read the Genome 3: Plasmid Miniprep From DNA to RNA DNA Quantification From RNA to Protein Restriction Digest The RNA World and the Origin of Life 9/22 Chapter 6: How Cells Read the Genome (cont) 4: Agarose Gel/DNA Seq 9/29 Chapter 7: Control of Gene Expression 5: DNA Sequence Analysis The Molecular Genetic Mechanisms that Create Cell Types An Overview of Gene Control DNA Binding Motifs in Gene Regulatory Proteins How Genetic Switches Work 10/6 Chapter 7: Control of Gene Expression 6: Isolation Genomic DNA The Molecular Genetic Mechanisms that Create Cell Types DNA Quantification Posttranscriptional Control How Genomes Evolve 10/13 Chapter 7: Gene Expression (Cont) 7. Agarose Gel/Southern 10/20 Mid Term Exam 8: DIG Probe Synthesis 10/27 Chapter 10: Membrane Structure 9: Hybridization/Detection The Lipid Bilayer Membrane Proteins 11/3 Chapter 11: Membrane Transport 10: RNA Isolation Principles of Membrane Transport RNA Quantitation Carrier Proteins and Active Transport Ion Channels and Electrical Properties 11/10 Chapter 12: Intracellular Compartments No Lab Compartmentalization of Cells Transport of Molecules Between the Nucleus and the Cytosol Transport of Proteins into the Mitochondria and Chloroplast Peroxisomes The Endoplsmic Reticulum 11/17 Chapter 12 : Intracellular Compartments 11. RNA Gel/cDNA Syn 11/24 Chapter 13: Intracellular Vesicular Trafficking 12. Real Time PCR The Molecular Mechanisms of Membrane Transport and And the Maintenance of Compartmental Diversity Transport from the ER Through the Golgi Apparatus Transport from the Trans Golgi Network to Lysosomes Transport into Cells from the Plasma Membrane Endoctytosis Transport from the Trans Golgi Network to the Cell Exterior 12/1 Catch-Up and Review 13: RT PCR Data Analysis

12/11 Final Exam (7:00-9:00)

Labs Reports Include: Report # 1 will Cover Labs 2-5 = 100 points, Due in lab 10/6 Preparation of Competent Cells/Transformation Plasmid Miniprep Agarose Gel/Restriction Digest DNA Sequence Analysis

Report #2 will Cover Labs 6-9= 100 points, Due in lab 11/3 Genomic DNA Isolation Quantitating DNA/Restriction Digest Agarose Gel/Southern Transfer Making and Using Non-Radioactive Probes Probing the Nylon Membrane/Washes/Detection

Report #3 will Cover Labs 10-14= 100 points, Due in lab 12/5

Tips on How To Succeed In this Class: 1. Read material BEFORE coming to class. 2. Re-read material and notes after attending lecture. 3. Take organized, clear notes. 4. Attend SI sessions 5. Be an active participant in the learning process—ask questions in class and seek clarification when the material is unclear. 6. Demonstrate that you are responsible for your own learning. Search for your own answers first and then ask questions when information is not clear. Many have the same questions but are afraid to ask. 7. Start lab reports early 8. Work Collaboratively/Form Study Groups- 9. Make time to exercise and get 6-8 hours of sleep! 10. Keep a positive attitude. You education is a gift to yourself!

Techniques: Teach someone else or pretend to; study with a partner; re-do drawings; write memory songs/poems; link with applications; go to SI; draw it; symbolize it; write it out; speak the words out loud; explain in sequence a list of events; make a story out of the information; make flash cards for terms or symbols. Imagine what questions you would ask if you were the professor. Learn the new terms and symbols. Relate the information to what you already know or to experiences you have had. Find the techniques for study that work best for you and make time to focus on those.