IB 270: Evolution of Molecules and Cells
Fall 2013
This class will cover basic molecular and cellular topics necessary to understand questions of
fundamental importance and public interest in biology. Where did life come from? What is Mad
Cow Disease and why is cannibalism a bad idea? How much did the Human Genome Project cost
and was it worth it? What is a stem cell? Lecture topics have been loosely grouped into three
organizing themes: 1) Information, 2) Energy and 3) Evolution. The first deals with inheritance,
system regulation (transcriptional and post-transcriptional) and genomes. The second deals with
the question, how do organisms make a living on earth? (heterotrophy, autotrophy, enzymatics,
metabolism). The third integrates these concepts into an understanding of the major milestones in
evolution: the origin of the prokaryotic cell, the origin of the eukaryotic cell, and the origin of
multicellularity.
Most Mondays and Wednesdays will include lectures or other learning activities. Most Fridays will
include “journal club”, where we discus a primary literature paper.
Course Intro
8/26 Course introduction
(week 1)
Inheritance
(week 1-2)
8/28 Mendelian genetics, genetic linkage (Biol. Ch. 14.1-2)
8/30 Complex inheritance: epistasis, GxE, pleiotropy (Biol. Ch. 14.3)
9/2 Holiday
9/4 Discovery of DNA as the genetic substrate (Biol. Ch. 15, 16.1)
9/6 Journal club: Breaking the dogma – what is the genetic substrate in Scrapie?
Precursors and Complex Biomolecules
(week 3)
9/9 Survey of important precursors: nucleotides, amino acids, lipids (Biol. Ch. 4)
9/11 Complex biomolecules: fats, polysaccharides, nucleic acids and proteins (Biol. Ch. 5)
9/13 Journal Club: Origin of the precursors
DNA, RNA and the Origin of Life
(week 4)
9/16 DNA structure, replication and recombination (Biol. Ch. 16.2)
9/18 Transcription, translation and the genetic code (Biol. 17)
9/20 Journal Club: “RNA World” and the origin of life
How to make a living on earth?
(week 5)
9/23 Metabolism: respiration, fermentation and photosynthesis (Biol. Ch. 8-9)
9/25 How to make a living: autotrophy, heterotrophy (what is a photoheterotroph?)
9/27 Journal Club: Microbial extremophiles
Prokaryote Diversification
(week 6)
9/30 Introduction to molecular systematics
Discovery project (Lab III) preliminary proposal due
10/2 Diversity, introduction to genomes, genetic recombination in prokaryotes
Midterm Exam I
10/4 Covers weeks 1 – 6.
Evolution of the Eukaryote
A. Organelles with genomes and without genomes
(week 7)
10/7 Mitochondria and chloroplasts, Eukaryote as a symbiotic association (Biol. 6.5, 28.1,2)
10/9 ER & Golgi; cytoskeleton (Biol. 6)
10/11 Plasma membrane, fluidity and permiability. Cell polarity (Biol. 7)
Discovery project (Lab III) formal proposal due
B. Cell division and genetic recombination
(week 8-9)
10/14 Cell division; Mitosis (Biol. 12)
10/16 Meiosis and recombination in detail (Biol. 13, 18.3)
10/18 Journal Club
10/21 Other forms of genetic exchange (viruses, bacteria, transposons) (Biol. 18.1-3)
System regulation
A. Cell communication and gene regulation
(week 9-10)
10/23 Cell communication (Biol. 11)
10/25 Journal Club
10/28 Chromatin, transcriptional & post-trans. regulation (Biol. 19)
10/30 Communication gone wrong: cancer
11/1 Journal Club
B. Advanced topics: RNA interference (RNAi) and microarrays (week 11)
11/4 RNAi (review by Hannon, 2002)
11/6 Introduction to microarrays (Biol. pp 400-402)
11/8 Journal Club: 1st microarray paper - auxotrophic shift in yeast (DeRisi et al. 1997)
Midterm Exam II
11/11 Covers weeks 7 – 11.
Evolution of Multicellularity and Development
A. Evolution
11/13 Origin of multicellularity, cell identity (Biol. 26.5)
11/15 Development (Biol. 21)
(week 12)
B. Development
11/18 Patterning in the fly embryo (MBG, pp. 590-609)
11/20 Evo-devo (comparative evolutionary development)
11/22 Journal Club
(week 13)
-- vacation -Genomics
A. Genomes
12/2 Genome sequencing
12/4 Comparative genomics – survey of sequenced genomes
12/6 Journal Club
(week 14)
(week 15)
B. Genome methods
(week 16)
12/9 Human genome scans
12/11 Special Topic: Genetic “profiling”: promises, ethical dilemmas
Final Exam
12/20 (Friday) 8:00-11:00 AM in 407 Morrill Hall; roughly ½ comprehensive, ½ later
material. May include concepts or methods from lab.
Laboratory schedule (Wednesdays, 1 – 5 pm; 283 Morrill Hall):
8/28 Organizational Meeting in 283 Morrill Hall
Lab I: Mendelian Inheritance & Linkage with Caenorhabditis elegans
9/4 – 9/25 approximate run time for lab
10/3 Individual Lab Report due
Lab II: DNA – Building a Plasmid Restriction Map
10/2 – 10/23 approximate run time for lab
10/31 Individual Lab Report due
Lab III: Discovery Project – Testing YFG* Function in C. elegans (*Your Favorite Gene)
Work on this throughout semester…
9/30 Preliminary proposal due (your group’s gene hypothesis; justification; rough method)
10/11 Formal proposal due
12/11 Group Lab Report due; Poster Presentation (during lab time)
Instructor / TA / Helper
Charlie Whitfield (cww@illinois.edu; 244-2889). Office Hours: M, 1 – 2 or by arrangement.
TA: Marsha Wheeler (marsha.wheeler@gmail.com)
Helper (TA in training): Laura Steele (steele11@illinois.edu)
Lecture / Discussions
Class will be held in 407 Morrill Hall, MWF 11:00 – 11:50. Mondays and Wednesdays will usually
include lecture or other learning activities. Most Fridays will include “journal club” where we cover
a primary literature paper. These papers are not easy (even for me) but will introduce you to
important historical developments (as they were originally published) or new science at the
“cutting edge” that is not yet in textbooks. Power Point lectures and primary literature papers will
be posted at http://www.life.illinois.edu/ib/270/ (login: ib270; password: honeybee). I will also hand
out copies of papers for Friday discussion one week in advance.
Readings
There will be required reading before each class from a variety of sources. There is no required
textbook, although much of the required reading for the first half of the class is from Biology (we
have several copies in the class common space). Required reading also will include online
sources and handouts. I will provide a handout each week that covers reading & objectives for the
next week. This syllabus, weekly reading & objectives sheets, and papers for journal club will be
available at http://www.life.illinois.edu/ib/270/ (login: ib270; password: honeybee). You should do
assigned reading and/or investigate the listed concepts before class. This will make
Monday/Wednesday lectures more useful, but it is especially important on Fridays when we
discuss papers without a formal lecture (it’s a small class so it will be obvious if you haven’t made
a good effort to read the paper). To ensure reading is done before class, or that you have
reviewed concepts, I will often give short (5 minute) quizzes at the beginning of class (see below).
Textbooks:
Biology, 7th or 8th ed. Cambell, Reece
Molecular Biology of the Gene, Watson et al.
Other reading:
The Major Transitions in Evolution, Smith, Szathmary
Lab related:
Molecular Cloning: a Laboratory Manual, Sambrook, Russell
C. elegans and C. elegans II, Riddle et al.
Exams
There will be two midterm exams given during the course of the semester. The dates and classes
covered are indicated on the course syllabus above. The exams will be short-answer format and
worth 20% of your final grade (10% each).
The final exam will cover the last few weeks of the class (about half) and also will be cumulative
(about half). It will be worth 20% of your final grade.
Exams cover both lecture and paper discussion material. Important working skills from lab (like
how to make and use a Punnett square) may also be tested.
For midterms and final exam, there will be make-up exams for anyone having a legitimate exam
conflict. The University has an established definition of exam conflict. If you think you have a
conflict, discuss this with me. If you are absent from the exam without a legitimate conflict and
without prior notification you will receive zero credit.
Quizzes
I will give “pop quizzes” at the beginning of many classes. These will count
towards 10% of your grade. Generally, these will include 3 questions and take
about 5 minutes. The first two should be easy if you did the assigned reading; the
3rd question may be more challenging. The purpose is to encourage both
preparation and attendance.
Laboratory
Laboratory will be covered in detail in separate handouts. The orientation meeting on
8/28 will cover use of the lab and Honors common space and issues related to safety
and conduct. After this, there will be three laboratory exercises, each spanning multiple
weeks, covering I: Mendelian Inheritance & Linkage using Caenorhabditis elegans,
II: DNA – Building a Plasmid Restriction Map, and III: Discovery Project – Testing
YFG* Function in C. elegans (*Your Favorite Gene). Because these are “real”
experiments that take their own time, it will be necessary to conduct certain steps
outside of the regularly scheduled lab period, sometimes on weekends. It will be your
group’s responsibility to ensure that these steps are performed. If no one is in town for a
critical step, you can ask the TA or me to do it for you, but it is your responsibility to
ensure that it happens. An Online Laboratory Notebook will be maintained by your
group using Moodle (I will provide template). This notebook will include objectives and
detailed methods before you actually start the experiment. You will also use it to record
all steps taken during the course of the experiment at the time you do it. The TAs and I
will frequently inspect this book so that we know how your experiment is progressing.
For Lab I and II, each student will turn in an individual Lab Report which includes
introduction, methods, results and conclusion. For Lab III, you will turn in a Lab Report
as a group, and also present your project in a Poster Session during the last laboratory
period (12/11, 1 – 5 pm).
Overall, laboratory will account for 40% of your grade. 20% is based on your
group and individual conduct of experiments (which includes maintenance of your
group’s Laboratory Notebook), 5% for each written lab report (3 total), and 5% for
the final presentation of Lab III during the poster session.
Discovery Research Project (Lab III)
Preparation for this lab begins early in the semester (before we have even
finished Lab I). For this project, your group will make a hypothesis about a
particular gene’s function – and then test it. Your hypothesis should be 1) welljustified, 2) novel, 3) important, and 4) testable using the model organism
Caenorhabditis elegans (with which you will become very familiar during the
course of Lab I). Gene function can be “knocked down” via RNA interference or
using existing strains that have mutations in your gene. Within reason, we will
make every effort to obtain material or resources necessary to conduct your
experiment.
The “novel” requirement is that there should be no proven relationship between
the particular gene in C. elegans and the particular function (or phenotype) that
you hypothesize. However, that does not mean you should just “make it up.”
Instead, you need to be smart and creative! This means doing some library and
computer research on a particular molecular/cellular process to be able to present
a “gene  function” hypothesis that is supported by a plausible justification,
based on other known functions described in literature and/or on-line databases.
The effort here should be towards reading, assimilating a connection, generating
a testable hypothesis, performing the test in the laboratory, and interpreting
results. You must also indicate why this hypothesis is “important”. Perhaps it will
provide insight into general mechanisms of cell proliferation and cancer. Or
perhaps it will say something specific about C. elegans evolution or ecology. This
is meant to be a creative assignment.
There are four dates to keep in mind for Lab III:
1) Preliminary “feasibility” proposal (1 page maximum)
2) Formal proposal (including detailed methods)
3) Group lab report (written) and poster presentation
9/30
10/11
12/11
I will provide more detailed instructions on each of these items as they approach.
You will be graded on the quality of the hypothesis (see four listed criteria above)
and experimental plan, the conduct of the experiment, and the interpretation of
results (what do they say about the original hypothesis?).
Grades
Your grade will be calculated as:
Lab Conduct (notebook & quality of work)
Lab Reports & Lab III Oral presentation
Quizes
Midterm Exam I
Midterm Exam II
Final Exam
Extra credit:
Discussion participation
10%
20%
20%
10%
10%
10%
20%
100%
(This is one whole letter grade, so speak up!)
The course grade will be derived from the numerical average (indicated below)
≥100%* = A+
93-99% = A
90-92% = A88-89% = B+
83-87% = B
80-82% = B-
78-79% = C+
73-77% = C
70-72% = C68-69% = D+
63-67% = D
60-62% = D-
<55% = F, definitely
56-59% F or D-; depending on
any possible extenuating
circumstances
*And excellent participation in paper discussions
Special needs
If you need accommodations for any sort of physical or learning disability, please
speak to me after class, make an appointment to see me, or see me during my
office hours.