BIOL101 Fall2015
Updated Aug 21, 2015
Biol 101a: Molecular Biotechnology, Fall 2015
Class Meeting Time: Tuesdays and Fridays 9:30-10:50 a.m.
Room: TBA
Instructor: Dr. Rachel Woodruff
woodruff@brandeis.edu
Office Hours: drop-in to Bassine 251 12-1pm Wednesdays, or make an appointment (see LATTE)
TA: Lisa Weingarten
Office Hours: see LATTE
Summary:
Biol 101 is a course designed for beginning graduate students and advanced undergraduates. This course will focus on the theoretical application
of the tools and processes used to manipulate nucleic acids and proteins in molecular biology.
Course Goals: An overarching goal of this course is to give you the knowledge and skills to research, choose, and interpret the best experimental
approaches for answering research questions in molecular biology. More detailed goals are listed in the table on the last page of this syllabus.
Course Format: Class meetings will involve a mixture of lecture, discussion, group work, and problem-solving. Many challenging in-class
activities will be graded for effort, to give you a safe place to “fail” on your way to learning and success. You will also need to be an active
participant outside of class: reading, working practice problems, and developing your own research proposal. Readings will include research
articles, reviews, and proposals, as well as excerpts from the textbook. The research proposal project is an important part of this course: you will
need to commit substantial amounts of time to this project both during and outside of class time. The course is intended to be more “experiential”
than a traditional lecture class would be (see description of experiential learning on LATTE for more on the rationale for this).
Time commitment: You are expected to attend class meetings. This class should take you, on average, about 12 hours per week, including class
time, and assignments are distributed throughout the semester. You should therefore expect to spend, on average, 4-5 hours on work for this class
between each class meeting (Tuesday or Friday) and the next (Friday or Tuesday).
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BIOL101 Fall2015
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Homework assignments: You should read the assigned readings, which will be a mix of textbook readings and research articles, before the class
for which they are assigned. In addition, there will be a writing assignment or problem set for each class meeting. Some of these will be due in
class; others will be due the day before the class meets (giving me time to read them before class).
Exams: To help you assess your learning, there will three midterm exams. The latter two will be cumulative. Note the scheduled exam dates and
do not miss an exam! There will be no written make-up exams: in the event that you miss a midterm exam, you will be given an oral exam
instead.
Project: Research Proposal! A key component of your learning experience will be writing your own research proposal. The research proposal
will involve choosing a scientific question of interest to you, finding high-quality sources of information in the scientific literature relating to your
question, self-directed reading of the scientific literature on this topic, writing, and oral presentation. You will begin developing your proposal
early in the semester, and your final paper will be due at the end of the semester; a schedule of the stages of this project is posted on LATTE. I
want to see each of you challenge yourself and make improvements in your proposal over the course of the semester.
To avoid plagiarism in your writing, please speak with Dr. Woodruff if you have any questions about how to deal with your sources. (Also see
section on Academic Integrity below.)
Late work policy: Deadlines are set early in the semester. I encourage you to plan your time ahead so that you can keep these deadlines. Should
you foresee having difficulties in meeting a deadline, you should ask for an extension at least 48 hours before the assignment is due; in some cases
it may be possible for me to grant you an extension if you ask in advance. Unless I have given you specific written permission for a deadline
extension, points will be deducted for late work.
LATTE: The course website on LATTE is the central point of distribution for lecture slides/notes, practice problems, assignments, schedule
updates etc. It is important that you check this site regularly.
Textbook:
From Genes to Genomes, By Jeremy Dale and Malcolm von Schantz ISBN 9780470683859
Additional readings: Assigned research articles and reviews will be available through LATTE. A few additional assigned readings (also posted
on LATTE) will be excerpts from other textbooks, including Strachan’s Genetics and Genomics in Medicine, which you may also have for another
class. In addition, you will also be responsible for finding research articles to read for your own research proposal.
Disabilities: If you are a student with a documented disability on record at Brandeis University and wish to have a reasonable accommodation made for
you in this class, please contact me during the first week of class.
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BIOL101 Fall2015
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Cell phones and laptops: Use common sense. If I or any of your classmates suspect that you are distracting yourself or anyone else by using these tools
in class, you will need to put them away. To state the obvious: No texting or tweeting or skyping in class.
Academic Integrity: You are expected to be familiar with and to follow the University’s policies on academic integrity (see
http://www.brandeis.edu/studentlife/sdc/ai ). Faculty may refer any suspected instances of alleged dishonesty to the Office of Student Development and
Conduct. Instances of academic dishonesty may result in sanctions including but not limited to failing grades being issued.
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BIOL101 Fall2015
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Course Plan: Actual course schedule will differ somewhat from this projected course schedule.
Date
Class Meeting Agenda
Readings and Homework
*Note that a written response is due by 11:59pm every night
before a class day except when noted.
1 Friday,
Introduction
Dale Chapter 1, all
Aug. 28
Bring your laptop to class if you
Optional: Strachan Chapter 1 if you have this book
have one.
No written response
Recommended: Introduce yourselves through the questionnaire on
LATTE
2
Challenges in Research Activity
Firestein TED talk video (on LATTE)
Tuesday,
Research article: Pauling and Corey
Sept 1
Check meeting location
Complete miniquiz(zes)
3
DNA Structure and Replication
Readings: Watson and Crick; Meselson and Stahl
Friday,
Optional reading: Crick’s letter to his son
Sept 4
If you have additional time, I recommend you read ahead, as we have
a lot of readings assigned for Sept 11.
4
Research and Biological Molecules I Research Article TBA (will be posted on LATTE)
Tues, Sept
8
5
Quiz
Readings:
Friday,
-Strachan, pp65-70
Sept 11
-Dale pp29-36 and 308-315
Introduction to Research
-Research Proposal Examples (on LATTE)
Proposals
DNA Features and Behavior
Sept 15
No class
6
Scientific Literature Workshop
Optional readings: Strachan chapter 3; NIH grant proposal checklist
Strachan Chapter 2
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BIOL101 Fall2015
Friday,
Sept 18
DNA and RNA mechanisms
Updated Aug 21, 2015
Research article relating to your topic of interest due instead of
normal written response.
Bring your laptop to class if you
have one
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Tuesday,
Sept 22
8
Friday,
Sept 25
DNA, RNA and gene function
Strachan Chapter 2
PCR and its applications
Dale Chapter 4, all
Rough statement of question and Annotated bibliography for your
proposal due instead of normal written response
Sept 29
9
Friday,
Oct 2
10
Tuesday,
Oct 6
No class
Exam 1
Study and Review readings, activities, and practice problems
PCR and its applications, II
Read PCR review article (on LATTE)
11
Friday, Oct
9
Gene Regulation Analysis:
Overview, gel electrophoresis,
Hybridization assays, Western
blotting
Dale Chapter 6, pp169-171 and 174-87
12
Tuesday,O
ct 13
13
Friday,
Oct 16
Developing Research Questions
Manipulation and analysis of gene
expression: antisense and RNAi
Specific Aims Discussion
Sanger and Next-generation
sequencing technologies, I
Research article on LATTE
Reading: Specific aims examples (on LATTE)
Strachan pp70-75
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BIOL101 Fall2015
14
Tuesday,
Oct 20
15
Friday,
Oct 23
16
Tuesday,
Oct 27
17
Friday,
Oct 30
18
Tuesday,
Nov 3
19
Friday,
Nov 6
Various
(Nov 6Dec4)
20
Tuesday,
Nov 10
Updated Aug 21, 2015
DNA Sequencing Technologies
Workshop
GWA Review Article (on LATTE)
Chapter 8: 8.2, pp229-263
GWAS and Genome Analysis
Analysis of Proteins, protein-protein
interactions
DNA sequencing research: written response due in class today.
Dale pp320-323
Research article on LATTE
Gene Cloning, Expression, and
Mutagenesis
Paragraph describing your research question due by 11:59pm
Oct 22 instead of normal written response.
Dale Chapter 2, pp36-61
Dale Chapter 7 pp195-204 and 215-224
Experimental Plans Workshop I
Transgenic organisms: knock-outs,
knock-downs, knock-ins
Dale Chapter 11 pp327-353
Dale Chapter 8, pp271-274
CRISPR and how it relates to
transgenics
Articles posted on LATTE
Experimental plans workshop II
Exam 2
Individual short meetings with
Dr. Woodruff to get feedback on
drafts.
Genetic Variation and analysis
Full draft of your research proposal paper due: You will sign up
for a specific duedate and meeting date. Due dates fall between
Nov 8 and 28. Meeting dates fall between Nov 9 and Dec 4.
Dale Chapter 9, pp275-298
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BIOL101 Fall2015
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Friday,
Nov 13
22
Tuesday,
Nov 17
23
Friday,
Nov 20
24
Tuesday,
Nov 24
Nov 27
25
Tuesday,D
ec 1
Various
(Nov 24Dec4)
26
Friday,
Dec 4
27
Tuesday,
Dec 8
Dec 10
Updated Aug 21, 2015
Genetic Variation and analysis
Dale Chapter 9, pp275-298
Clinical Trials, Study Design, and
Gene Therapy
Strachan 336-346 (gene therapy)
Epigenetics and Data Analysis
Reading: article on LATTE
Research Activity
Reflection on draft of research proposal due today
No Class. Happy Thanksgiving!
Student presentations
Prepare your presentation and/or revise your proposal
Additional Student Presentations
Each student should plan to attend one of these 50-minute
sessions outside of class time
Student presentations
Prepare your presentation and/or revise your proposal
Exam 3
no class, but...
Final research proposal papers due 8am
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BIOL101 Fall2015
Grading:
Description
Homework assignments (including proposal-related
assignments not listed below)
In-class Activities (including proposal-related activities)
Exams and Quizzes
Research proposal project: Sum of the following:
- Annotated bibliography (3 %)
- Research Question Paragraph (2 %)
- Full Draft of Proposal (effort) (6 %)
- Oral Presentation (9 %)
- Final written proposal (20 %)
Updated Aug 21, 2015
Percentage of Final Grade
10%
10%
45 %
40 %
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BIOL101 Fall2015
BIOL101 2015 Course Goal
By the end of the course, students should:
1. Understand how to critically read and evaluate
scientific literature
2. Understand the relationships between the
molecules and processes central to molecular
biology (DNA, RNA, protein, DNA replication,
transcription, translation, RNA splicing, gene
expression, etc)
3. Understand the implications of the physical and
chemical qualities of DNA and RNA
4. Understand the use of important molecular
biological techniques (for example: PCR, cloning,
Sanger sequencing, CRISPR, Western blots,
Southerns and Northerns, microarrays, GWAS,
transgenic organisms, gene therapy, RNAi
knockdown, nextgen sequencing)
Updated Aug 21, 2015
Objective
By the end of the course, students should be able to:
1-1 Identify the key question(s) addressed by a research article
1-2 Identify experiments supporting conclusions in a paper
1-3 Analyze data presented in paper
1-4 Critique authors’ analysis of their results
1-5 Critique study design and/or choice of experiments
1-6 Differentiate between high-quality and low-quality sources of information
2-1 Identify class of molecule by chemical structure
2-2 Explain in detail the relationships between biological molecules and processes
2-3 Understand gene structures
2-4 Explain the significance of multiple levels of regulation of gene expression
3-1 Describe how physical features of DNA molecules relate to “behavior” of DNA in
natural processes (eg,replication, transcription) and in molecular assays or
techniques
3-3 Outline the steps of DNA replication
3-4 Diagram a replication bubble
3-5 Interpret hybridization/melting data
3-6 Use your knowledge and research skills to explain novel DNA/RNA techniques
3-7 Diagram phosphodiester backbone of DNA
3-8 Recognize the chemical structures of the nitrogenous bases of DNA and RNA
4-1 Explain which feature(s) of DNA each technique is dependent upon
4-2 Analyze data resulting from each technique
4-3 Explain what question(s) each technique can be used to address
4-4 Design experiments to determine the level(s) at which a gene’s expression is
regulated
4-5 Design DNA oligomers for specific applications
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BIOL101 Fall2015
5. Understand the process and challenges of
developing a molecular biology research
proposal
Updated Aug 21, 2015
5-1 Identify high quality biological questions that can answered by
experiment/observation
5-2 Develop novel research questions that could answered by observation and
experiment
5-3 Select appropriate molecular techniques to address particular biological
questions
5-4 Critique the experimental choices of research studies (proposed or completed)
5-5 Differentiate between designs, goals, and outcomes of genome-wide vs.
targeted studies
5-6 Understand the purpose and qualities of a good research proposal
5-7 Write your own research proposal (using all the skills listed above)
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