Syllabus for Bio 105 – Molecular Biology
Spring 2016
Instructor:
Mitch McVey
Contact Info: Office: 200 Boston Avenue, Room 4741
Phone: (617) 627-4196
E-mail: mitch.mcvey@tufts.edu
Teaching
assistant:
Jenn Nguyen
Contact Info: Office: 200 Boston Avenue, Suite 4700
E-mail: jennifer.nguyen@tufts.edu
When will we meet? Tuesdays and Thursdays, 10:30-11:45 AM (block D+) in Eaton 206
Optional recitation on Mondays (9:30-10:20 AM) in Barnum 114
When can you talk to us outside of class?
Professor McVey:
Jenn Nguyen:
Mondays
10:30-11:30 AM
Barnum 211
Wednesdays 2-3 PM
200 Boston Avenue Room 4741
Tuesdays
12:30-1:30 PM
200 Boston Avenue Suite 4700
To arrange a different time, please send either of us an e-mail.
What materials are required for the course?
The required textbook is Molecular Biology: Principles and Practice, 2nd edition, by Cox et al. A
copy of the textbook is on 4-hour reserve in Tisch library. Additional handouts and papers will be
posted on the Bio105 Trunk site.
We will be using the Learning Catalytics student response system every day in class. In order to
participate, you will need to bring a web-enabled device (smartphone, tablet, or laptop) to class every
day. Please register for an account prior to the first day of class using the information provided at the
end of this syllabus and posted on Trunk.
What background knowledge will I need to succeed?
Bio 41 (Genetics) or the equivalent is highly recommended. We assume that you have a working
knowledge of basic molecular genetics. If your background in this is limited, you may want to find a
copy of a good genetics textbook for reference.
What will we discuss in this course?
Molecular biology deals with nucleic acids and proteins and how these molecules interact within the
cell to promote proper growth, division, and development. It is a large and ever-changing discipline.
This course will emphasize the molecular mechanisms of DNA replication, repair, transcription,
splicing, protein synthesis, and gene regulation in different organisms. We will study the techniques
and experiments used to discern these mechanisms, often referring to the original scientific literature.
In addition, we will take an in-depth look at some rapidly evolving fields, including chromatin
structure and function, genome editing techniques, backsplicing, and regulation of gene expression by
different types of RNAs.
What are our goals for this course? By the end of this semester, we would like you to:
1. Understand how molecular machines are constructed and regulated so that they can accurately
copy, repair, and interpret genomic information.
2. Appreciate that molecular biology is a dynamic and ever-changing experimental science.
3. Become comfortable with reading and critiquing primary research papers.
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What are the course objectives? By the end of the semester, you should be able to:
1. Explain and give examples of how ionic, hydrophobic, and hydrogen bonding interactions
determine the structure of nucleic acids and proteins and modulate the specificity of binding
between them.
2. Distinguish between different molecular biology techniques that are used to isolate, separate,
and probe for specific proteins, nucleic acids, and their interactions. Identify limitations of
these techniques.
3. Given a particular biological question, identify which experimental techniques are best used
to answer that question.
4. Compare and contrast the mechanisms of bacterial and eukaryotic DNA replication, DNA
repair, transcription, and translation.
5. Explain how DNA topology and chromatin structure affects the processes of DNA replication,
repair, and transcription.
6. Give examples of DNA and histone modifications and predict how they will affect gene
expression.
7. Describe mechanisms by which DNA can be damaged and describe the molecular
mechanisms by which protein complexes repair different forms of DNA damage.
8. Provide examples of how homologous recombination is used to ensure genome stability and
promote genetic diversity.
9. Explain how endogenous biological processes like site-specific recombination, transposition,
and the CRISPR-Cas9 system are being used to modify eukaryotic genomes.
10. Describe how pre-mRNA splicing occurs and explain how alternative splicing and
backsplicing can generate protein diversity.
11. Explain the molecular mechanisms behind different modes of gene regulation in bacteria and
eukaryotes at both pre- and post-transcriptional levels.
12. Compare and contrast various ways in which gene expression is regulated by small RNAs.
13. Interpret and critique data from primary research articles.
14. Write a perspective about a primary research article.
How will your progress be evaluated?
The final course grade will be determined based on the following point breakdown:
Exams, two highest scores
Exam, lowest score
Journal club perspective papers
Class participation
45%
15%
30%
10%
Exams: There will be three exams comprised of a combination of multiple choice, short answer, and
short essay questions. The questions will largely be drawn from annotated lecture slides, in-class
activities, and journal club discussions. Your lowest exam grade will count as 15% of your final
grade, and the other two exams will each count 22.5%.
No make-up exams will be given. If you know in advance that you will miss an exam, please notify
me at least one week ahead of time so that we can make alternate arrangements. If you miss an exam
due to a documented health or family-related emergency, your other two exams will each count 30%
of your total grade. Requests for re-grades must be made in to me writing within one week after the
day the exam is returned.
Exam #1
Exam #2
Exam #3
Tuesday, February 23
Thursday, March 17
Tuesday, April 26
Journal club perspective papers: Several of the class meetings are reserved for in-class discussion
of primary research papers. During these journal clubs, we will focus on the data presented in the
figures and tables, and small groups will be asked to present figures from the paper. In addition, for
each paper, you will be asked to write a short perspective describing the main findings of the paper
and evaluating the research. Instructions for these writing assignments will be posted on Trunk and
distributed in class.
Prior to the discussions, your perspectives should be submitted via Trunk. For journal club 1, you
will submit an individual paper. For journal clubs 2 and 3, you will submit a group paper. The groups
will be determined in class.
Journal Club #1
Journal Club #2
Journal Club #3
Tuesday, February 16
Tuesday, April 5
Monday, May 9 (7-9 PM)
Class participation: Your class participation grade will be determined by your attendance record,
level of involvement during in-class and out-of-class activities (including Learning Catalytics
questions), and by the quantity and quality of your contributions during journal club presentations
and discussions. In addition, you will have an opportunity to earn additional credit towards class
participation with the “Molecular Biology in the News” activities. These will be described in class.
What resources are available to you to help you succeed in this course?
Bio105 Trunk web site: Problem sets, journal club articles, handouts for class, and additional
resources will be posted on the course web site http://trunk.tufts.edu/.
Lecture Slides: Lecture slides will be posted on Trunk 1-2 days prior to the lecture. These will serve
as a guide to what you should focus on in the assigned readings. We will annotate these slides during
lecture. Because we frequently provide outlines, additional notes, and in-class activities during
lectures, the on-line slides by themselves will not adequately prepare you for exams.
Recitations: Yes, Monday morning at 9:30 is early, but recitations provide an opportunity for you to
clarify questions from the previous week’s lectures, try your hand at sample exam questions, and get
key insights into the next journal club paper. We make it worthwhile for anyone who attends.
Problem sets: Problem sets containing practice problems and questions representative of exam
material will be posted on the Trunk website. They are designed to highlight the important concepts
from lecture and to give you practice with the types of questions found on exams. Some of these
problems will be the focus of the recitations. We recommend that you first attempt these problems on
your own as the topics are addressed in lecture and then discuss your answers in the context of a
study group.
“Brain thaw” papers: Several times during the semester we will pose a “brain thaw” question in
class. These questions pertain to difficult concepts and are intended to mitigate the “brain freeze” that
often accompanies these types of questions. They also help you to prepare for the exams. These
papers are entirely optional, but for each answer that you submit, you may earn 1 percentage point of
extra credit towards your final grade.
How do I ensure that everyone has an equal opportunity to succeed in the class?
As your professor, I am responsible for ensuring that all students compete on a level playing field. A
student who is academically dishonest is claiming an advantage not available to other students. If you
ever have a question about the expectations concerning a particular assignment or project in this
course, be sure to ask Professor McVey or Jenn for clarification.
You are encouraged to work with your colleagues to do the problem sets and to discuss the journal
articles—science is a collaborative affair. However, your perspective papers and exams should be
your intellectual property only (or that of your group, if it is a group assignment). If you use
information from review papers or other articles, be sure to properly cite your sources. Any type of
plagiarism or cheating will be dealt with harshly, including a grade of ‘zero’ on the assignment and
possible other penalties as detailed in Tufts’ written policies.
As part of this course, we will utilize TurnItIn to help determine the originality of your work.
TurnItIn is an automated system which instructors can use to quickly and easily compare each
student's assignment with billions of websites, as well as an enormous database of student papers that
grows with each submission. When papers are submitted to TurnItIn, the service will retain a copy of
the submitted work in the TurnItIn database for the sole purpose of detecting plagiarism in future
submitted works. Students retain copyright on their original course work. In this class, you will be
given the opportunity to see the TurnItIn originality report for your papers submitted through Trunk.
Diversity Statement: Tufts University values the diversity of our students, staff, and faculty;
recognizing the important contribution each student makes to our unique community. Students with
disabilities are assured that the Student Accessibility Services (SAS) office will work with each
student individually to create access to all aspects of student life. Tufts is committed to providing
equal access and support to all qualified students through the provision of reasonable
accommodations so that each student may fully participate in the Tufts experience. If you have a
disability that requires reasonable accommodations, please contact the Student Accessibility Services
office at Accessibility@tufts.edu or 617-627-4539 to make an appointment with an SAS
representative to determine appropriate accommodations.
Please be aware that accommodations cannot be enacted retroactively, making timeliness a critical
aspect for their provision.
Student Learning Catalytics registration:
To access Learning Catalytics you will need to purchase a subscription ($12 for 6 months/ $20 for 12
months). Go to the Getting Started help page for a step-by-step walkthrough of the registration and
purchase process http://trunkuserguide.screenstepslive.com/s/8335/m/33860/l/480103-getting-startedwith-learning-catalytics-for-arts-science-engineering-students. You should complete this step before
the first day of class. Please use your Tufts email address as your Learning Catalytics username and
email address.
If you complete these steps you will be set to participate in class. Bring your web-enabled device
(smartphone, tablet, or laptop) to class and log in to https://learningcatalytics.com/. In the classroom
always connect your device to the "Tufts Secure” wireless network for a fast and secure
connection: https://it.tufts.edu/securewireless.
If you have any problems with your Learning Catalytics account contact your course team
or edtech@tufts.edu.
Tentative Schedule of Bio 105 Topics
Date
Topic
Unit 1
How do nucleic acids and proteins interact in a genomic context?
Th Jan 21
Hot topics in molecular biology
Enroll in Learning Catalytics
M Jan 25
T Jan 26
Th Jan 28
Recitation
Nucleic acids and tools for analysis
Genomic approaches to nucleic acid analysis
How to read a scientific paper
MBPP 6.1-6.4, pages 248-50
MBPP 7.1-7.2 (to pg 232)
M
T
Th
Th
Recitation
Proteins and tools for analysis
Last day to add classes
Interactions between nucleic acids and proteins
MBPP 5.1, pgs 241-43, 700-01
M Feb 8
T Feb 9
Th Feb 11
Recitation
DNA topology
Chromatin and its effects on DNA metabolism
MBPP 9.2-9.3
MBPP 10.1-10.3
M Feb 15
T Feb 16
Th Feb 18
No recitation (University holiday)
Journal Club #1, Perspective #1 due
Recitation (Tufts Monday schedule)
M Feb 22
T Feb 23
Recitation
Exam 1
Unit 2
How do organisms copy and protect their genomes?
Th Feb 25
Th Feb 25
Last day to withdraw without record of enrollment
DNA replication
MBPP 11.1-11.3
M Feb 29
T Mar 1
Th Mar 3
Recitation
Regulation of DNA replication
DNA damage and repair I
MBPP 11.4-11.5
MBPP 12.1-12.3
M Mar 7
T Mar 8
Th Mar 10
Recitation
DNA damage and repair II
Homologous recombination
MBPP 12.1-12.3, 13.4
MBPP 13.1-13.3
M Mar 14
T Mar 15
Recitation
Tools for genome editing (WebEx class)
MBPP 14.1-14.2, pgs 245-8, 477
Th Mar 17
Exam 2
Material 2/25 - 3/10
Feb 1
Feb 2
Feb 4
Feb 4
March 21-25 Spring Break
Assignment before class
MBPP 4.1-4.4, pgs 232-44, 275-6
Li et al., 2015
Material 1/21 – 2/16
Unit 3
What are different ways that organisms regulate gene expression?
Date
Topic
Assignment before class
M Mar 28
T Mar 29
Th Mar 31
No recitation
Mechanisms of transcription in bacteria
Mechanisms of transcription in eukaryotes
MBPP 15.1-15.2
MBPP 15.3, 16.1
M Apr 4
T Apr 5
Th Apr 7
Recitation
Journal Club #2 – Perspective #2 due
RNA splicing and processing
Lackner et al., 2015
MBPP 16.2-16.3
M Apr 11
T Apr 12
Th Apr 14
Recitation
The genetic code and translation initiation
Mechanisms and regulation of translation
MBPP 17.1, 18.1-18.3
MBPP 18.4-18.6, 22.2
M Apr 18
T Apr 19
Th Apr 21
No recitation – Patriot’s Day
Regulation of gene expression in bacteria
Regulation of gene expression in eukaryotes
MBPP 19.1, pgs 702-07
MBPP pgs 736-39, 22.4
M Apr 25
T Apr 26
Th Apr 28
Recitation
Exam 3
Course wrap-up
Material 3/15 – 4/21
Handouts
M May 2
M May 2
Recitation – prepare for Journal Club #3
Last day to withdraw with grade of ‘W’
M May 9
Journal Club #3, Perspective #3 due
Meeting time: 7-9 PM
Conn et al., 2015