MCB 121 Syllabus

Molecular and Cellular Biology 121 (CRN 39810)

Fall 2016
ADVANCED MOLECULAR BIOLOGY

Lectures: Tues. Thurs., 6:10 – 7:30 PM, Giedt 1002

Instructor: Stacey Harmer, 2129 Life Sciences, Telephone: 752-8101

email: slharmer@ucdavis.edu
Office hours: Tuesdays, 11:30 am – 12:30 pm, 2064 Sciences Lab Bldg.
Fridays, 10:00 – 11:00 am, 2064 Sciences Lab Bldg.

Teaching Assistant: Krithi Bala, email: kibala@ucdavis.edu

Office hours: Mondays, 4:00 – 5:00 pm, 2064 Sciences Lab Bldg.
Tuesdays, 10:00 – 11:00 am, 2061 Sciences Lab Bldg.
Thursdays, 5:00 – 6:00 pm, 2064 Sciences Lab Bldg.

Exam Dates: Midterm I Tuesday, Oct. 18, in class

Midterm II Thursday, Nov. 10, in class
Final Exam Thursday, Dec. 8, 8:30 – 10:30 pm

Cheating: Don’t. We take cheating very seriously. Any form of cheating will result
in a grade of 0 for that exam and referral to Student Judicial Affairs.

Missed Exams: Accommodations will be arranged ONLY for students who miss a test
because of a doctor-excused illness or documented emergency. In either
case, I will require a signed document from a physician or other official.

Review Sessions: Review sessions will be scheduled prior to the first and second midterms
and the final exam.

Web Page: Reading assignments, handouts, problem sets, practice exams and midterm
solutions will be posted on SmartSite. Links to podcasts and other web
sites of interest will also be provided.

Prerequisite: You must have taken Biological Sciences 101 or a similar Genetics
course.

Text: Required - Molecular Biology: Principles and Practice by Cox, Doudna,

and O’Donnell, 1st or 2nd edition. W.H. Freeman & Co (2012 or 2015).
New versions can be purchased at the UC Davis bookstore; new or used
versions may be available online for less. In addition, note that a book
can be rented from various online retailers for the quarter for as little
as ~ $11! Whether you rent or buy, I strongly suggest you obtain a copy
of this book as it will help you understand the course material.

Copies of this book have been placed on reserve in Shields Library.

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MCB 121 Syllabus
Other required reading will be available for downloading through the
MCB 121 SmartSite page.

Lectures: Lectures will be digitally recorded and podcast; see web site for
downloads. However, keep in mind that important information will be
presented on the blackboard so use of podcast recordings should NOT be
considered a substitute for attending lectures.

Practice Problems: Problems will be assigned for each lecture and will be posted on the
course web site. Past exams will also be available on the course web site.

Grading: Final grades will be based on the results of two midterm exams (30%
each) and a final exam (40%). The class mean will fall in the B-/C+ range.
Exams will be a combination of multiple choice, matching, and short
answer questions. Practice exams will be available on the course web site.

Learning goals: At the end of this course, students should be able to:

1. Explain how the chemical and physical structures of DNA and RNA contribute to the
fidelity of template-directed replication.

2. Describe how DNA is organized in the nucleus through various levels of compaction and
through specific modifications of chromatin.

3. Explain how different levels of chromatin organization and modifications, along with the
cellular environment, influence processes underlying gene expression and genome
stability.

4. Compare and contrast the roles of functionally and structurally homologous enzymes in
maintaining genome structure and function in bacteria and eukaryotes.

5. Explain the relationship between an organism’s genotype and phenotype and how genetic
analyses are used to explore this relationship.

6. Explain how cells with the same genome can have very different phenotypes and
functions (e.g. neurons vs liver cells).

7. Describe how gene expression is regulated, at the levels of transcription, mRNA

processing, translation, and via small non-coding RNAs.

8. Understand modern molecular biological methods and evaluate the meaning of

experimental results produced using these methods.

9. Design and interpret experiments to derive and test specific scientific hypotheses, models
and theories.

10. Give examples of applications of technical and conceptual advances in molecular biology
to medicine, agriculture, and industry and discuss their potential impact on society.

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MCB 121 Syllabus

Tentative Lecture Schedule

Date Topic
1 Th Sept. 22 Genomes, genomics, and evolution
2 Tu Sept. 27 Structure of DNA, chromosomes, & genomes
3 Th Sept. 29 Molecular methods (hybridization, cloning, positional cloning, libraries and
PCR)
4 Tu Oct. 4 DNA replication (overview)
5 Th Oct. 6 DNA replication mechanisms
6 Tu Oct. 11 DNA repair and recombination
7 Th Oct. 13 Homologous recombination
8 Tu Oct. 18 1st Midterm (Topics up to and including DNA repair and recombination)
9 Th Oct. 20 Overview of gene expression
10 Tu Oct. 25 Basal transcription machinery
11 Th Oct. 27 Regulation of transcription I
12 Tu Nov. 1 Regulation of transcription II
13 Th Nov. 3 Integration of transcriptional regulation
14 Tu Nov. 8 RNA processing (Election Day – be sure to vote!)
15 Th Nov. 10 2nd Midterm (Homologous recombination – transcriptional regulation)
16 Tu Nov. 15 Splice regulation
17 Th Nov. 17 Translation
18 Tu Nov. 22 Small RNAs and gene regulation
Th Nov. 24 Thanksgiving – enjoy the holiday!
19 Tu Nov. 29 Epigenetics – molecular mechanisms
20 Th Dec. 1 Applications of molecular biology
Th Dec. 8 Final Exam, 8:30 – 10:30 pm (covers all course material)