351 FALL 2008
Dr. Betsy Read
SHII 125
Phone: 750-4129
Office Hours: 11:15-2:00 Tuesday
and/or by appointment
Dr. Matt Escobar
SHII 123
Phone: 750-8083
Office Hours: 3:45-5:00 Wed., Thurs.
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
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.
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
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:
< 60
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 writeup 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
Chapter 3: Proteins
The shape and Structure of Proteins
Protein Function
Chapter 4: DNA and Chromosomes
The Structure and Function of DNA
Chromosomal DNA and its Packaging in the Chromatin Fiber
The Global Structure of Chromosomes
Chapter 5: DNA Replication, Repair and Recombination
The Maintenance of DNA Sequences
DNA Replication Mechanisms
The Initiation and Completion of DNA Replication in Chromosomes
DNA Repair
General Recombination
Site-Specific Recombination
Chapter 6: How Cells Read the Genome
From DNA to RNA
From RNA to Protein
The RNA World and the Origin of Life
Chapter 6: How Cells Read the Genome (cont)
Chapter 7: Control of Gene Expression
The Molecular Genetic Mechanisms that Create Cell Types
An Overview of Gene Control
DNA Binding Motifs in Gene Regulatory Proteins
How Genetic Switches Work
Chapter 7: Control of Gene Expression
The Molecular Genetic Mechanisms that Create Cell Types
Posttranscriptional Control
How Genomes Evolve
Chapter 7: Gene Expression (Cont)
Mid Term Exam
Chapter 10: Membrane Structure
The Lipid Bilayer
Membrane Proteins
Chapter 11: Membrane Transport
Principles of Membrane Transport
Carrier Proteins and Active Transport
Ion Channels and Electrical Properties
Chapter 12: Intracellular Compartments
Compartmentalization of Cells
Transport of Molecules Between the Nucleus and the Cytosol
Transport of Proteins into the Mitochondria and Chloroplast
The Endoplsmic Reticulum
Chapter 12 : Intracellular Compartments
Chapter 13: Intracellular Vesicular Trafficking
The Molecular Mechanisms of Membrane Transport and
And the Maintenance of Compartmental Diversity
1: Making Solutions
No Lab
2: Preparing Competent
3: Plasmid Miniprep
DNA Quantification
Restriction Digest
4: Agarose Gel/DNA Seq
5: DNA Sequence Analysis
6: Isolation Genomic DNA
DNA Quantification
7. Agarose Gel/Southern
8: DIG Probe Synthesis
9: Hybridization/Detection
10: RNA Isolation
RNA Quantitation
No Lab
11. RNA Gel/cDNA Syn
12. Real Time PCR
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
Catch-Up and Review
Final Exam (7:00-9:00)
13: RT PCR Data Analysis
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 Groups9. 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.
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