Bio 404: Molecular Biology
Lecture:
MWF
Laboratory section 1: MTW
Laboratory section 2: MTW
Syllabus Fall 2015
10:00- 10:50 Thompson Hall - TH 297
12:00-16:00 Thompson Hall - TH 317
17:00-21:00 Thompson Hall - TH 317
Instructor:
Andreas Madlung
 253 879 2712
e-mail: amadlung@pugetsound.edu
Office: TH 223F
Office hours: to accommodate everyone’s schedule my office hours are
flexible by appointment. Just send me an email or talk to me after class or in
lab to set up a time to meet.
The best way to reach me for questions, appointments etc. is by email!
Molecular Biology is a wide term encompassing two often complementary fields of study: a)
laboratory and computer-based tools that can be used to study gene and genome identity
and function (“molecular tools”), and b) the underlying fundamental structure of DNA
and RNA.
In this class there will be about a 50:50 split between focus on molecular tools (techniques)
on the one hand, and the structure and function of DNA and RNA on the other hand. Proteins
are often the focus of Biochemistry classes, including the one here (Chem 460).
Molecular Biology (Bio 404) at Puget Sound requires Genetics (Bio 311) as a prerequisite for
enrollment. Since many of the same general topics are covered in Genetics as in Molecular
Biology the emphasis in Bio 404 is shifted in several ways:
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•
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Greater emphasis on structural details
Frequent use of current literature in class and in group discussions
Emphasis on molecular methods both in lecture and lab
Molecular Biology (Bio 404) stresses the application of advanced molecular tools in the lab,
and during analysis of scientific data presented in primary literature, in addition to covering
genetic topics in more detail than was done in previous classes.
Class expectations:
The major expectations of students in Bio 404 are :
• To be become familiar with molecular techniques.
• Understand the use of these techniques in the discovery of DNA and RNA
metabolism and function.
• Become more proficient at reading and critiquing primary literature.
• Become familiar with commonly used laboratory techniques in the lab.
• Emphasis is not on memorization of the details of the molecular machinery of the
cell. Instead, it is on developing skills to apply the learned techniques to the
understanding of scientific discovery (data interpretation), as well as to suggest ways
to study the function of molecules (experimental design).
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Molecular research is impossible to conduct in set 4-hour increments once a week. While I
will try my best to contain lab activities to the scheduled times there will be cases where the
nature of the experiment requires you to come to lab outside normal lab times.
Textbook/Readings:
• Burton Tropp: Molecular Biology, 4th edition, 2012
I will use parts of some chapters of this book in lecture and it will be a good resource for
looking up details, and reading ahead or after class. I will not require any of the online
exercises etc. It is therefore not essential that you purchase a copy with a valid online access
code. Some short excerpts of this book will be provided on Moodle under fair use copyright
rules. Book purchase is recommended but not required. Student feed-back in the past has
often indicated that students found class notes and Powerpoints more useful and/or sufficient
than the book, but learning styles vary and you should decide for yourself if you might be
better off with the text book.
• Other readings (required, will be provided as PDF files on the Moodle site)
• Lab manual (required, will be provided as PDF files on the Moodle site)
• Primary literature as needed (provided as PDFs on Moodle site)
Schedule:
To maintain flexibility and accommodate specific class interests, the schedule is tentative and
might be adjusted somewhat during the semester. Please check the Moodle site for updates.
Main pedagogical class goals:
1. Learn facts about molecular biology. (Lecture + lab material)
2. Improve ability to interpret scientific literature and data sets. (Literature discussions,
data interpretation in class and on exams.)
3. Understand specifically the use of molecular methods and their application to
biological research. (Lectures, paper discussions, lab)
Class policies:
Attendance is mandatory for all laboratories and paper discussions. Laboratory research, and
your participation in the discussion of student contributions are part of your grade. Labs are a
vital part of the class as they illustrate techniques discussed in class. I understand that there
might be a time when you are unable to come to lab and cannot make up the lab, either. I will
allow one such absence. After that, 25 points for each unattended lab may be deducted from
your total score. Please talk to me if circumstances beyond your control (sickness or family
emergencies) prevent you from coming to lab. Should you have to miss a lecture I ask you to
inform me before your absence. If you have to miss a lab period please also inform your lab
partner. You are responsible for obtaining information on any schedule changes as well as
on class materials you may miss during absence from class. Missed exams or quizzes
cannot be made up and assignments can be made up only if you missed them for medical
reasons or family emergencies. To be fair to everyone in class and to follow departmental and
university policies, documentation for such emergencies will be required.
Grading: (small changes in point distributions may be made)
2 Midterm exams (each 70 points)
140 points
5 Quizzes (4x10 points each, quiz 5 =20 points)
60 points
1 Research paper (lab write-up)
40 points
2
Lecture participation
Carefulness in lab and preparation for labs
Lab prelabs/postlabs
Paper discussion prep (5x10 points)
and participation (5x10 points)
Total
20 points
20 points
~50 points
100 points
410 points
Letter Grade Assignments:
Generally, the following table applies to assign a letter grade at Puget Sound:
Percentage of all possible points
Letter Grade
91-100
A
81-90
B
71-80
C
60-70
D
below 60
F
It may be necessary to adjust this table slightly to account for unforeseen events (e.g. if an
exam was harder than I thought, etc.). In that case a curve is applied. This should help you
earn a better grade.
What is my current grade in the class?
I often get asked this question. To help you track your progress in class I encourage you to
use the following table to calculate your current grades.
Below is an example with fictitious numbers to illustrate how to calculate a current grade:
Quizzes (100)
Mid terms (300) Final (150)
Lab work (200) Total (750)
add points from add points from
add final points add points from total all your
all quizzes
all midterms
labs, papers etc. points
Divide the total points you have by the total number of points available so far. Then multiply
by 100 and you have your current percentage. For example:
Let’s assume you have a total of 400 points but two quizzes, the second midterm and the final
paper have not been added yet as well as 40 points worth of lab work. Therefore let’s assume
the current total possible at the time of your calculation is 480 points.
(400/480) *100 = 83.3%. So currently you are somewhere in the B or B- range.
Exams, pre- and post-labs, paper discussions
Assignments and quizzes are designed to keep you and me aware of gaps in your basic
understanding that need attention. Questions on quizzes will include fill-in-the-blanks,
multiple choice, short answer, and short essay. Quizzes test fundamental knowledge but are
short and their topics are well-defined. As the course progresses test questions will become
more and more “application-based”.
There will be two take-home mid-terms. The take-home exams will be in part based
on a primary literature paper that you will receive ahead of time. Questions will then focus on
interpretation of the figures and experiments and apply concepts from class discussions. They
might also ask you to design an experiment to test a hypothesis. Conceptual and some
practical information from the lab may also be covered on the exams. Take-home exams are
open-book and open-notes but have to be completed on your own.
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For the take home exams you will receive any data sets or primary literature required
for the exam ahead of time. The literature can be discussed with other students, the questions
on the take home exam must not be discussed with anyone.
Paper discussions require you to prepare answers to questions about the paper to be
discussed ahead of time. There are between 5-8 questions to be answered for each paper. I
will read and grade only one or two randomly chosen questions (the same for every student)
on each of these pre-discussion questions. You will need the answers for all questions for
participation in class during the discussion, so it is imperative that you prepare well for both
types of assignments (questions and discussion).
Lab
It is important to keep a neat and bound notebook for the lab, but you do not need to buy an
expensive lab notebook. At the end of the semester you will be required to turn in a research
paper describing the work you did on the lab project and put it in context of a greater
scientific question. Only one lab report/paper will be handed in for the semester. This report
reflects multiple weeks of work. Therefore make sure to collect gel photos, instrument
readings, microarray and qPCR data analyses, so that you have all the files you need for
your final paper. While all class and lab assignments have to be written individually unless
specified differently, the final lab report can be written collaboratively with your lab partner,
or individually if you prefer.
Preparation for labs: Labs in this class are very expensive and it is of great importance that
you come prepared to lab. In the past I have simply relied on suggesting that everyone read
the manual before lab. However, it only takes one un- or underprepared person to make an
experiment fail – often for more students than just that one person. So I have decided that
some form of enforcement of the preparation requirement is needed and have reverted to prelab assignments, which test your level of preparedness. In addition there is now a grade for
“carefelness in lab”. This grade is based on whether you are prepared for lab or excessively
ask unnecessary questions that you could have answered yourself by reading the manual. I do
encourage asking questions, but I also encourage self reliance and careful attention to detail.
Not every experimental failure is due to operator error. Such failed experiments are common
and will not influence your lab grade negatively.
Late assignments
In order to be fair to all course participants, assignments that are turned in late will, if
accepted at all, be subtracted 10% of your score per started 24 hours that the assignment is
late. Take home exams cannot be handed in late. If take-home exams are not turned in on
time the resulting grade is 0 points. No assignments due before the last day of classes are
accepted after the last day of class.
Participation
Participation in class discussions is expected. I will try to encourage discussions in class that
challenge you to present your opinions, your questions, and your current understanding of
topics. In a large class this may be a challenge but I will try to call on those of you not
participating frequently to bring everyone into the discussion of the material. If you do not
like to be called upon I urge you you prepare questions before class that you might ask
to boost your participation rate and prevent me from calling on you more frequently.
For the regular paper discussions I will ask you to answer assigned pre-discussion questions
and turn them in before the class discussion. Make a second copy for yourself so that you
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have your answers handy during the class period as well. These questions are intended to
guide your reading while preparing for the discussions. Participation is graded as outlined.
Assignments should only be handed in to me in person, usually electronically. Some
papers, slipped under my office door or my mailbox, have been lost in the past. You may
place assignments in my department mailbox in the Biology office after obtaining an official
time stamp from the secretary or another faculty member. If you hand in assignments this
way, please send me a follow-up email immediately so I can check that I received your
work. Note that most of the larger assignments are due as attachment by email.
Please read the following notes provided by the University Administration
Disability Services
If you have a physical, psychological, medical or learning disability that may impact your course work,
please contact Peggy Perno, Director of the Office of Accessibility and Accommodation, 105 Howarth,
253.879.3395. She will determine with you what accommodations are necessary and appropriate. All
information and documentation is confidential.
Student Bereavement Policy
Upon approval from the Dean of Students’ Office, students who experience a death in the family, including
parent, grandparent, sibling, or persons living in the same household, are allowed three consecutive
weekdays of excused absences, as negotiated with the Dean of Students’. For more information, please see
the Academic Handbook
Classroom Emergency Response Guidance
! Please review university emergency preparedness, response procedures and a training video posted at
www.pugetsound.edu/emergency/. There is a link on the university home page. Familiarize yourself
with hall exit doors and the designated gathering area for your class and laboratory buildings.
If building evacuation becomes necessary (e.g. earthquake), meet your instructor at the designated
gathering area so she/he can account for your presence. Then wait for further instructions. Do not
return to the building or classroom until advised by a university emergency response representative.
If confronted by an act of violence, be prepared to make quick decisions to protect your safety. Flee
the area by running away from the source of danger if you can safely do so. If this is not possible,
shelter in place by securing classroom or lab doors and windows, closing blinds, and turning off room
lights. Lie on the floor out of sight and away from windows and doors. Place cell phones or pagers on
vibrate so that you can receive messages quietly. Wait for further instructions.
Next Emergency Drill: The Fall 2015 emergency drill will be conducted on Wednesday, September 16,
at 12:40 – 12:50 p.m. This will be a shelter-in-place/lockdown drill. More information will be coming;
today’s message is simply to make you aware of the date and time of the drill so that, if you teach during
the Wednesday noon hour, you can adjust (e.g., not schedule a test that day).
Many campuses have experienced high impact emergencies and disasters. Preparedness is vital for
facilitating effective response to potential adverse events. If you have any questions, please contact
Associate Vice President for Business Services John Hickey, Director of Security Services Todd
Badham, or Associate Dean Sunil Kukreja.
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Biology 404: Molecular Biology
Student Contract
Please sign and return this contract to me in order to receive a grade for the course by Friday
of week 1. On-time return of this signed form results in 1 bonus point.
I have read and I understand the syllabys and the university’s emergency response
procedures, and I am aware of the following:
•
Exam dates and times. I understand that in fairness to all class participants and
according to departmental policies make-up quizzes and exams are generally not
given, nor can participation points be earned if the student is absent during paper
discussions. Exceptions can only be arranged in documented cases of sickness and
emergency circumstances.
•
Assignment schedule: I understand that all assignments are due at the date and time
stated and that points will be subtracted for late assignments.
I have read and I understand the statement on academic honesty and scientific misconduct
and the University policy on academic honesty (which can be found in the University of
Puget Sound Bulletin and on the website). I understand these policies associated with
violations of the guidelines. I pledge to refrain from any act of academic dishonesty or
scientific misconduct, including:
•
cheating on exams, quizzes, or other assignments
•
any form of plagiarism, including copying or paraphrasing any part of another
student’s or researcher’s work (including textbooks and papers), and using the ideas
or wording of another person without proper citation.
•
fabrication or falsification of data or research results, including lab exercises.
I am aware that even though data might be collected collaboratively, all written assignments
must be prepared by each individual independently, unless clearly stated otherwise.
I understand that papers and assignments should only be handed in to the instructor in person
or by email. I take responsibility for lost assignments (for example those slipped under the
door or into the mail box) or those without an official time stamp by the department secretary
or another faculty member.
Name (please print)___________________________________________________
Signature:__________________________________ Date:___________________
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Biology 404 (Molecular Biology Fall 2015): Estimated Schedule of Topics
Week
Date
Topic
Tentative Lab Schedule
Things due/ suggested readings
1
8/31
Nucleic acid structure
Lab1a: Microarray analysis
Tropp 109-119
9/2
Nucleic acid structure, Genome organization
RNA extraction 1
Miesfield (Cot curves)
Madlung Ch 2: 51-53 and 56 – 61 (for lab)
Tropp 153 (top), 160-162, 174-177, 201205
9/4
RNA techniques (hybridization, reporters)
Tropp: 185-194
Madlung Ch 2: 73 - 74
2
9/7
Labor Day: No class
No labs this week
9/9
RNA techniques (qPCR),
9/11
NO LECTURE TODAY
Tropp, p 187
On your own, review the DNA sequencing method by Sanger
(“Chain termination method”)
Fill out homework form and turn in by
email (due 9/11, 3 pm)
https://www.youtube.com/watch?v=nudG0r9zL2M
https://www.youtube.com/watch?v=vK-HlMaitnE
https://www.youtube.com/watch?v=bEFLBf5W
or other websites or books
3
9/14
DNA sequencing methods (whole genome approach)
9/16
QUIZ 1: RNA techniques/Nucleic acids
Lab1b: Microarray analysis
c-DNA production
Metzker, 2010 (Nature Reviews, focus on
Illumina sequencing)
DNA sequencing methods (whole genome approach)
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9/18
Gene mapping
9/21
Gene mapping
9/23
Lab1c: Microarray analysis
Strachnan: Ch 14
Slide hybridization
Craig: 797-804
QUIZ 2: Sequencing
Gene mapping
9/25
Paper Discussion 1: (Li et al., 2008, Human genome
variation).
Answers to questions due before class.
Listen to RadioLab on Race and the Human
Genome; read Keita, 2004
http://www.radiolab.org/2008/dec/15/
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9/28
Statistics for microarray analysis
Lab1d: Microarray analysis
Reading: Microarray analysis (on Moodle)
9/30
QUIZ 3: Mapping/cloning
Slide analysis: first part in lab.
Tropp: 448-466
DNA damage
Finish slide analysis/statistics on your
own time after all slides are pre-analyzed
after Monday night’s lab.
Tropp: 468-505
10/2
DNA repair
Gene list of significantly changed genes in
array analysis due 10/04, 5:00 pm.
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10/5
DNA repair, Technique: EMSA (for paper 2)
10/7
Paper Discussion 2 (Moolenar et al., 1995 DNA repair)
10/9
DNA repair
Lab 2a: Bioinformatics (Intro to Unix)
Answers to questions due before class.
TAKE HOME EXAM #1 due Thursday (10/15) at 10:00 am
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10/12
Recombination
Lab 2b: Bioinformatics (RNAseq)
Tropp: 512-540
Madlung: Ch 2: 54-56 (meiosis review)
8
10
10/14
Recombination
10/16
Recombination/
Tropp: 574-579
Discussion of Li et al 2004 (SPO11, RAD51) (no need to
read this paper before coming to class)
(Craig: 681-686)
10/19
FALL BREAK: NO CLASS
10/21
NO LECTURE: Prepare paper for Friday’s discussion
10/23
Paper Discussion 3 (Anderson and Kowalczykowski, 1997
Recombination)
10/26
Transposons
10/28
Transposons
10/30
The transcription unit
Madlung Ch 2: 53-54
FALL BREAK: NO LAB
Answers to questions due before class.
Lab 2c: Bioinformatics (RNAseq)
Madlung Ch 2: 62-67
Smale 2003 (background reading)
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11/2
Eukaryotic transcriptional regulation
11/4
Eukaryotic transcriptional regulation
Prokaryotic transcription: initiation, elongation, termination
11/6
Transcriptional regulation/Epigenetics
Lab 2d: Bioinformatics (RNAseq)
12
11/9
11/11
13
Epigenetics
Lab 3a: q-PCR
Tropp: 231-236, 810-816
Madlung Ch. 2: 65-67
QUIZ 4: The transcription unit
- Primer design for qPCR, primer
dilution, and qPCR machine software
introduction.
Epigenetics (technique: Immunoprecipitation)/RNAi
- cDNA production
11/13
Paper Discussion 4 (Epigenetics, Hsia et al., 2010 )
11/16
RNAi
TAKE HOME EXAM #2 due Monday (11/23), 10:00 am
14
15
16
Quantitative PCR lab 3b: annealing
temperature optimization
Watson: Ch. 9
Madlung Ch. 2: 67-71
- Analysis of annealing temperature data
11/18
RNAi
11/20
RNAi
11/23
CRISPR/Cas9
Quantitative PCR lab 3c:
11/25
THANKSGIVING: NO CLASS
- Set up of Standard curve
11/27
THANKSGIVING: NO CLASS
- Analysis of Standard curve
11/30
Splicing
Quantitative PCR lab 3d:
12/2
Splicing
- Set up of experimental plate (first try)
12/4
Paper Discussion 5 (Paper TBA)
- Analysis of experimental plate
Answers to questions due before class.
12/7
Agrobacterium and gene transformation
Quantitative PCR lab 3e:
Madlung Ch. 2: 75-76
12/9
QUIZ 5: Molecular techniques
12/18
Final Exam Date: 8-10 am (lab report due, no exam)
- Set up of second experimental plate (if
needed)
- Preparing Results section of lab report
- Using Zotero reference manager
Tropp: 847-849, 851-861, 863-864, 868-870
Lab report due at 10 am