Biochemistry 103b - Advanced Biochemistry: Cellular Information Transfer Mechanisms

This syllabus is subject to change, please check back for updates (updated 01/03/18)

Biochemistry 103b - Advanced Biochemistry: Cellular Information Transfer
Mechanisms

Prof. Tijana Ivanovic, office Rosenstiel 450, ivanovic@brandeis.edu
Office hours by appointment on Friday (email to schedule by Thursday): 9-10am
Extra office hour with presenters on Friday (email to schedule a week ahead of time)

TA: Ingrid Marko
imarko@brandeis.edu
Office hours: TBD

Course meeting times: M, W 2-3:20pm (Block K)
Location: TBD

COURSE OVERVIEW:

The course will focus on fundamental principles underlying the faithful storage of genetic information
and its transfer into protein. Through in-depth analyses of primary literature, a special emphasis will
be placed on understanding experimental approaches and critically evaluating conclusions drawn
from experiments. We will sample historical papers describing seminal discoveries, such as the first
evidence for DNA as the genetic material, the elucidation of DNA structure, and the discovery of DNA
polymerase. These foundational discoveries have shaped much of biology over the past >65 years.
We will further explore select advanced concepts in nucleic acid-enzyme mechanisms and cutting-
edge approaches used in discovering them. Topics may include: DNA recombination and replication;;
transcription (DNA to RNA);; processing/maturation of precursor RNA transcripts;; and translation
(RNA to protein).

Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or equivalents. BIOL
14a or the equivalent is recommended.

COURSE MATERIALS:

Reading materials will be posted on LATTE about a week prior to their assigned date. You are
encouraged to read all posted materials prior to the lecture where they are discussed. Each week you
will be asked to read an assigned paper that deals with the topics discussed in class. You are
required to read the assigned papers in depth before they are discussed in class. The recommended
(not required) textbook for background reading is Biochemistry 4th edition by Voet and Voet.

PROBLEM SETS:

Problem sets will be based on assigned primary literature reading. They will be due at the beginning
of the class when a given paper is discussed.

EXAMS:

There will be no midterms. There will be a final exam. The final exam is cumulative and will cover all
topics treated throughout the course. It will be held during the last regular class period.

DISCUSSIONS/PRESENTATIONS:

You are strongly encouraged to come to every class prepared. This will help you participate in
lectures, either by answering questions (posed by me or other students), or by asking questions that
will help you understand concepts being covered. I welcome confusions from students. There is no
stupid question! The class is meant to challenge you to push the limits of your understanding of a
range of concepts, and the best way to accomplish that is if we all actively participate.

I will present the first couple of papers and lead the discussions based on them. After that, the
students will take up the role of presenters/discussion leaders. I will offer an additional office hour (by
appointment) on Fridays prior to the student presentations to meet with student presenters.

ATTENDANCE:

Attendance is required and class participation is a big part of your grade (however, if you are sick,
please stay home and get better). Even if you know that you will miss a class, you are still responsible
for turning in your problem sets in a timely fashion (in this context, I will allow electronic submissions
that are posted by the deadline).

EVALUATION:

Final grades will be determined by your performance on problem sets (25%), presentations (15%),
attendance/in-class discussions (35%), and the final exam (25%).

BACKGROUND EXPECTATION:

I expect that everyone will have familiarity with basic chemical structures of nucleotides and DNA,
base pairing and genetic code. I further expect that everyone will have a firm knowledge of basic
protein biochemistry.

Success in this 4 credit hour course is based on the expectation that students will spend a minimum
of 9 hours of study time per week in preparation for class (readings, papers, discussion sections,
preparation for exams, etc.).

POLICY ON ACADEMIC HONESTY:

Academic integrity is central to the mission of educational excellence at Brandeis University. You are
expected to be familiar with and to follow the University’s policies on academic integrity (see
http://www.brandeis.edu/studentaffairs/srcs/ai/). I will refer any suspected instances of dishonesty to
the Office of Student Development and Conduct. Violations of university policies on academic
integrity may result in failure in the course and could end in suspension from the university. All
homework must be your own work, except when assignments specifically authorize a collaborative
effort.

STUDENTS WITH DISABILITIES:

If you are a student with a documented disability on record at Brandeis University and wish to have a
reasonable accommodation made for you in this class, please see me immediately. Accommodations
cannot be made retroactively.

COURSE TOPICS BY WEEK:
Note: this may be subject to change

Week 1: Introduction, Basics of DNA
Week 2: Why nature chose phosphates
Week 3: DNA as the genetic material – historical perspective
Week 4: Discovery of DNA polymerase
Week 5: DNA replication
Week 6: Transcription, Transcriptional regulation
Week 7: RNA splicing/processing (Joerg Braun)
Week 8: Translation (Amy Lee)
Week 9: Viral mechanisms (I)
Week 10: Viral mechanisms (II)
Week 11: DNA repair, Genome editing
Week 11: DNA repair, Genome Editing
Week 12: Review
Week 13: Final exam

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This syllabus is subject to change, please check back for updates (updated 01/03/18)

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