Syllabus MCDB 3135 (2012F) - MCD Biology

MCDB 3135 – Molecular Cell Biology I
Fall 2012 Syllabus
Professor: Greg Odorizzi, odorizzi@colorado.edu, 303-735-0179
Office hours: Tuesday 12:00 – 2:00 PM, Room A420C MCD Biology, or by appointment
Lab Coordinator: Joy Power, Joy.Power@colorado.edu, 303-735-2723
Teaching Assistants: Kati Buchtel, Christine Crotzer, Roni Denglar, Eli Gendron, April Griffin
Course web site: learn.colorado.edu
Lecture hours: Tuesdays & Thursdays, 9:30 – 10:45 AM in HUMN 1B50
Important dates:
Wednesday, September 12 (5:00 PM): deadline to drop the course without penalty
Thursday, September 20, 2011: Midterm Exam I (9:30 – 10:45 AM in HUMN 1B50)
Wednesday, October 10 (5:00 PM): deadline to drop the course without petitioning the dean
Thursday, October 18, 2011: Midterm Exam II (9:30 – 10:45 AM in HUMN 1B50)
Thursday, November 15, 2011: Midterm Exam III (9:30 – 10:45 AM in HUMN 1B50)
Monday, December 17, 2011: Final Exam (7:30 – 10:00 PM in HUMN 1B50)
Course requisites: MCDB 2150 or EBIO 2070 (prerequisite); CHEM 1133 (pre-requisite or corequisite);
MCDB 3140 is recommended with either MCDB 3135 or MCDB 3145.
Course description: examines the central dogma of biology by discussing DNA, RNA, and
protein, and how their synthesis (DNA replication, transcription, RNA processing, and translation)
is regulated. Incorporated into the discussion is how recombinant DNA techniques are used to
discover and dissect cellular processes, how to design and interpret experiments, and
understanding the limits of experiments to draw conclusions. These principles are the foundation
for subsequent examination of intracellular mechanisms in MCDB 3145.
Learning objectives: After taking this class, you should know the key concepts of the central
dogma of molecular biology, including the composition of genomes and the basic mechanisms of
replication, transcription, RNA processing, translation and RNA turnover, and how the complexes
that perform these activities identify their targets, carry out their function and can be regulated to
meet cellular needs. In addition, you should have a basic understanding of the experimental
approaches and deductions that have shaped, and continues to shape, our understanding of these
concepts. Doing well in this class requires solid prior understanding of genetics, biochemistry
and organic chemistry. For more details about the learning objectives, see the ‘Learning Goals’
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MCDB 3135 – Molecular Cell Biology I! Fall 2012 Syllabus
COURSE STRUCTURE
Textbook: The recommended textbook for this course is Molecular Biology by Cox et al., 1 st
edition (2012), Freeman Publishing, ISBN-13: 978-0-7167-7998-8. Copies of this text are on
reserve at Norlin library.
Lectures: The lectures will follow the general order of the central dogma of biology
(DNA→RNA→Protein). We will, therefore, first discuss the composition and structure of DNA,
the composition of genomes, the use of recombinant DNA in research, DNA replication and
repair, transcription, RNA processing, mRNA translation, and regulation of gene expression. Key
experiments and deductions that underlie the understanding of the different processes will be
discussed.
A pdf of the lecture slides will be provided on the course website preceding each lecture. The
slides comprise a skeletal record of what happens in the lecture. However, you may find the
lecture slides unintelligible without your own written notes. Therefore, do not think of them as a
second, independent “book” you can read but instead as a collaborative record of the lecture that
you will create.
Clickers: To obtain extra credit, you will need an i-clicker (not a different system such as H-ITT
or PRS). See http://oit.colorado.edu/cuclickers-faq/general-questions/where-can-iclicker-remotesbe-purchased.
Clickers will be used for rapid feedback to foster interactive learning in a large
classroom setting. Clicker questions will be used during class to make you think about and
discuss with your peers how the newly discussed material fit within the bigger picture of
molecular biology and how experimental observation and experimental design can address
questions in molecular biology. Register your i-clicker ASAP.
COURSE SCHEDULE:
Dates Topic Text
Aug 28 – Sep 18 Genes & Genomes Chapters 6-10
Sep 20 Midterm Exam I
Sep 25 – Oct 16 DNA Replication and Repair Chapter 11-14
Oct 18 Midterm Exam II
Oct 23 – Nov 13 Transcription and Translation Chapter 15-18
Nov 15 Midterm Exam III
Nov 27 – Dec 13 Regulation of Gene Expression Chapter 19-22
Dec 17 Final Exam
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MCDB 3135 – Molecular Cell Biology I! Fall 2012 Syllabus
EXAMS and GRADING
Your grade in MCDB 3135 will be derived from your final score calculated as follows:
Midterm Exam I 22.5%
Midterm Exam II 22.5%
Midterm Exam III 22.5%
Final Exam 22.5%
Problem Sets 10%
Total 100%
Midterm Exams: Three midterm exams will be given during class time. Each exam will count
toward your final grade. See the ‘Course Schedule’ for exam dates.
Final Exam: The final exam will focus on the material discussed after Midterm Exam 3.
Weekly Problem Sets: Weekly problem sets will be administered through the course web site; no
new problem set assigned the week of an exam. Failure to complete a problem set will result in a
zero for that set. The average of the ten highest problem set scores will count for 10% of your
final grade. The lowest two problem set scores will be dropped.
Exam policies:
1. The Midterm and Final exams must be completed in ink. Using a pencil on any part of an
exam will void the entire exam’s eligibility for a re-grade (see below).
2. Pens and ID are the only personal items you may have with you during an exam. Any other
items you bring (backpacks, phones turned OFF, etc.) must be placed entirely under your seat and
are subject to being moved at the TAs' and professor's discretion.
3. Requests to reconsider grading must be submitted in writing with your original exam to Joy
Power within one week of the exam return date. Answering any part of an exam in pencil will
void the entire exam’s eligibility for a re-grade. If anything on the exam submitted for regrading is
found to be altered from its original state, it will be considered a breach of the honor code and
will be grounds for failure in the course and additional disciplinary action.
Extra credit: Extra credit will be based on clicker use (regardless of whether you get the answers
right) and on input from Joy Power and TAs. To get credit for the whole semester, register your
clicker at the beginning of the semester. The amount of extra credit awarded is at the discretion
of the professor. Cheating with clickers by having someone other than yourself use your clicker
during class is considered a breach of the honor code and will result in the loss of all clicker
points for the semester for both yourself and the person bringing your clicker, as well as any
additional disciplinary action as indicated by the honor code. Correct clicker use will be
monitored by the professor and TAs during class.
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MCDB 3135 – Molecular Cell Biology I! Fall 2012 Syllabus
CLASS POLICIES:
Attendance: Attendance in class is optional but strongly encouraged.
Etiquette: Please refrain from doing anything that might distract you or others (eating, reading
newspapers, surfing the web, texting, and engaging in conversations). Please shut off cell
phones. If you must leave class early, please exit with the least amount of disruption.
Academic integrity: Cheating will not be tolerated and will be subjected to disciplinary action as
discussed above under exams and clickers and as indicated by the honor code. All cheating will
be reported to the University. Please review the University honor code: http://
www.colorado.edu/policies/student-honor-code-policy. It is easier to pass this course by putting
the energy into understanding the material rather than cheating.
Letters of recommendation requirements: Acceptance into programs to further your education
can be very competitive. Thus, you should carefully choose letter writers who know you well and
who can honestly state that you achieved one of the top scores in their class and that your
demonstrated enthusiasm, diligence, and hard work makes the writer confident that you will be
an excellent candidate for the school of application. For me to write a letter of recommendation,
you must have done very well in the class, and you must have been an active participant.
Lecturer’s of smaller classes will usually know you much better, and their letters of
recommendation will, therefore, usually carry much more weight.
Disabilities: If you qualify for accommodations because of a disability, please submit to me a
letter from Disability Services in a timely manner so that your needs may be addressed.
Disability Services determines accommodations based on documented disabilities. Please see
guidelines at: http://www.colorado.edu/disabilityservices/.
Responsibilities: In a class of 200 or more students, it is impossible to teach directly to
everyone’s needs. It is my (and the TAs) responsibility to come to class well prepared and to
provide students with multiple pathways to learning the topics. It is your responsibility to make a
significant effort by reading the text and coming to class prepared for the material.
TIPS ON HOW TO DO WELL:
The most important point is to keep up. The pace is unrelenting because the field of molecular
biology is a rapidly expanding due to intense research. The following practices will help:
1. Print out slides before each lecture.
2. Take good notes during lectures.
3. Actively participate in clicker questions.
4. Read the textbook before and after class.
Your grade will be decided entirely from your final score, not on how you do compared to other
students, so it will never hurt you to help fellow students. In fact, research on learning has shown
that whether you are on top of the material or are having a hard time understanding the concepts,
you will improve your learning by discussing the material with other students. Memorizing slides
and texts is not an efficient method of learning. While some memorization is required to become
literate in molecular biology, the primary goal of the course, and what you will be tested on, is
understanding the key concepts of molecular biology and how to interpret simple experimental
observations.
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MCDB 3135 – Molecular Cell Biology I! Fall 2012 Syllabus
LEARNING GOALS FOR MCDB 3135:
After completing this course, students should be able to:
1. Compare the structures of DNA and RNA.
a) Describe how the building blocks of DNA and RNA are similar and how they are different.
b) Describe the 3-D structure of DNA.
c) Describe the nature of DNA supercoiling, its advantages/disadvantages, and how it is relieved.
d) Describe denaturation and renaturation of double-stranded nucleic acids, methods to measure
the degree of double-strandedness, and practical applications of these techniques.
e) Describe how dideoxynucleotides are used to determine DNA sequences.
f) Explain the difference between a gene and a genome.
g) Describe the mechanistic basis for gene duplication and gene transposition and the role both
have in evolution.
2. Describe techniques for manipulating and characterizing cloned DNA.
a) Describe the role of restriction endonucleases in gene cloning.
b) Explain the procedures by which DNA fragments can be ligated into plasmid vectors,
introduced into recipient cells, and their presence selected in the cell population.
c) Describe the key elements required for a plasmid to be useful as a cloning vector.
d) Describe how PCR works and how it can used to generate enough starting material for
cloning.
e) Describe how DNA sequencing works and its practical applications.
f) Compare the procedures for making clone libraries from genomic DNA versus cDNA as
starting material, and cite examples where each would be useful.
g) Explain how to screen clones and/or entire libraries for a DNA segment of interest.
h) Compare the methods for determining gene function in vitro and in vivo.
i) Compare different types of cloning vectors in terms of their applications for cDNA versus
genomic DNA cloning and for production of proteins.
3. Explain the process of DNA replication.
a) Interpret results of the experiments that distinguished proposed models of DNA replication.
b) Explain the semidiscontinuous nature of DNA replication.
c) Explain the utility of temperature-sensitive mutations in the study of DNA replication.
d) Compare the events of replication on the leading and lagging strands (the trombone model).
e) Explain the processivity of DNA polymerase III.
f) Compare the events that occur at replication origins during the initiation of DNA synthesis in
bacteria and eukaryotes.
g) Describe the properties of a DNA molecule that allow it to serve as a template for replication.
h) Describe the roles of DNA helicase, SSBs, the β clamp, DNA gyrase, and DNA ligase.
i) Describe how termination of replication in bacteria differ.
j) Explain the importance of telomeres with respect to germ cells and cancer.
k) Describe the factors that contribute to the high fidelity of DNA replication.
l) Contrast the events of nucleotide excision repair and base excision repair.
m) Explain how parental and newly synthesized strands are distinguished in mismatch repair.
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MCDB 3135 – Molecular Cell Biology I! Fall 2012 Syllabus
4. Describe the key steps in transcription and translation.
a) Explain the role of a promoter in transcription.
b) Describe the steps during initiation of transcription in bacteria versus eukaryotes.
c) Explain the relationship between a pre-RNA and a mature RNA.
d) Describe the differences in transcription of rRNAs, tRNAs, and mRNAs and explain their
functional relationship.
e) Diagram the structure of a typical eukaryotic gene, showing locations of the transcriptional
start site, 5’-untranslated region (UTR), exons, introns, donor and acceptor splice sites,
translational start site, translational stop site, 3’UTR, and poly-A addition sequence.
f) Explain the steps in processing of an hnRNP into a mature mRNA, and describe the role of
snRNAs and the spliceosome.
g) Describe the triplet nature of the genetic code and how the identities of individual codons
were established.
h) Distinguish between synonymous and nonsynonymous mutations in the genetic code.
i) Explain how tRNAs function as adaptor molecules.
j) Compare the initiation of translation versus elongation.
k) Explain how the effect of a nonsense mutation differs from that of a frameshift mutation.
l) Explain how polysome formation differs in bacteria versus eukaryotes.
m) Explain how bacterial translation is inhibited by certain antibiotics.
5. Describe how gene expression is regulated.
a) Describe the relationship between histones and and DNA in a nucleosome core particle.
b) Explain how nucleosomes are organized into higher levels of chromatin.
c) Describe the structural and functional difference between heterochromatin and euchromatin.
d) Describe the histone code and explain how it determines the state of a chromatin region.
e) Diagram a typical bacterial operon.
f) Describe the mechanistic nature of inducible and repressible operons in bacteria.
g) Describe the mechanistic function riboswitches.
h) Explain the difference between a transcriptional activators and a transcriptional repressor;
between a coactivator and a corepressor.
i) Explain the difference between a general transcription factor and a gene-specific transcription
factor.
j) Describe how the domain structure of transcription factors relate to their function.
k) Describe mechanisms by which transcription factors are converted between active and
inactive forms.
l) Explain the concept of epigenetics in the control of gene expression.
m) Describe how alternative splicing can effectively increase the number of genes in the genome.
n) Describe 3 different mechanisms of translational-level control of gene expression.
o) Describe ways in which mRNA stability is maintained or destroyed.
p) Describe how ubiquitination causes proteins to be unstable.
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