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Course Syllabus

UN3501/GU4501 — Biochemistry: Structure and Metabolism

Fall 2018
Professor Brent Stockwell, 1208 Northwest Corner Building
bstockwell@columbia.edu, 212-854-2948
Class room: TBD, Class time: Tuesday and Thursday 2:40-3:55 pm

Recitation Section
This course has a required recitation section; please register for a recitation section when you register.

The recitation times are:


Mon 5:40-6:40 PM (Section 001, TA: Hengrui Liu)
Tue 4:20-5:20 PM (Section 002, TA: Niki von Krusenstiern)
Wed 4:30-5:30 PM (Section 003, TA: Carla Bezjian)
Thu 5:40-6:40 PM (Section 005, TA: Hui Tan)
Fri 11:00-12:00 PM (Section 004, TA: Auste Kanapeckaite)

Course Description
In this course, we will study the chemistry of living systems. We will discuss how living systems convert
environmental resources into energy, and how they use this energy and these materials to build the
molecules required for the diverse functions of life. Finally, we will discuss the applications of such
biochemical knowledge to mechanisms of disease and to drug discovery.

Learning Goals
At a high level, we expect that at the conclusion of the course, you should be able to explain:
• the basic mechanisms by which living systems harness energy from their environment
• how living systems construct the molecules necessary for the functions of life
• how these processes go awry in a variety of disease, including cancers
• how drugs can be discovered to treat such diseases

Using this knowledge, you should be able to diagram the major metabolic pathways and compare how
these pathways are dysregulated in normal tissues in and disease states. In addition, you should know what
techniques are used to uncover this knowledge and how to design and interpret experiments that will
address these questions. You should also be capable of collaborating with other people in the analysis and
interpretation of biochemical data, and be able to communicate, defend and refute interpretations of data.
More specific learning objectives related to each class session are described in the table below.

Pre-requisites
In this course, we assume familiarity with basic concepts of modern biology, so having completed one year
of college-level biology is essential. In addition, we explore the reaction mechanisms governing a variety of
transformations in metabolism. It will be difficult to learn this material without the foundation provided by
having completed one year of organic chemistry.

Homework
The homework will consist of video tutorials, readings, and self-administered quizzes on Courseworks. You
may refer to any materials you like (textbooks, readings, videos) while answering the homework questions.
If you choose to work with someone else on the homework, please indicate the person with whom you
worked when you submit the homework.
Class Participation
You are required to attend every class (but see below). In class, we will discuss, in small teams, problems
and questions related to the material. It is critical to the learning process that you participate in these
activities, and that you come to class prepared to be actively engaged in the course material. This means
doing the assigned homework before you come to class, asking and answering questions in class, and
participating enthusiastically in all of the activities we do in class. You may request to be on the same team
as one other person. If you would like to make this request, email Auste Kanapeckaite at
ak4094@columbia.edu.

Learning Catalytics: We will be using the student response system at Learning Catalytics. You will need to
bring a smartphone, tablet or laptop to class to submit your answers to the posted questions. You will need
to register at www.learningcatalytics.com to use the system, which you can also access through the link in
Courseworks. You click on the “Register” link in the upper right-hand corner, then click “I am a student” and
you can purchase 6 month access to Learning Catalytics (you can also purchase access for 12 months for if
you know you will be using it for another course in the Spring). If you have a Mastering code from another
course, you already have access to Learning Catalytics—in that case, just use your Pearson login to access
Learning Catalytics.
You must use your Columbia email address with your UNI before the @ symbol (e.g.
aa1111@columbia.edu) as your email address when you register with Learning Catalytics. This is how we
will able to associate your grades in Learning Catalytics with your grades in Courseworks. There is an
instructional video on the Learning Catalytics site that you may find useful. See Appendix 1 below for more
information using Learning Catalytics.

Team Problems: Everyone will be divided into teams of four students for classroom activities. Each team
will work together on problems posed in class, but each individual will need to submit their own answer
using the Courseworks Quiz function, so everyone will need a laptop, tablet or smartphone to answer these
questions in class. We will have a few extra iPad minis in case you don’t have one.

Office hours
Professor Stockwell will hold two types of meetings with students in his office. To see Professor Stockwell
for office hours, you can access the 12th floor of the NWC building by using your Columbia ID card to swipe
at the glass doors, which will give you access to the bank of three elevators. Please note that you cannot
use the freight elevator outside of the glass doors.

Sign up for each of these using the Signup feature on Courseworks.

Group student discussions: Professor Stockwell will host student discussions in which any student is
welcome to bring questions to be discussed with other students who attend the session. The goal of these
meetings is to learn together, so you may come even if you don’t have specific questions, as you may be
able to help other students understand issues that are not clear for them. There is a maximum of 6 students
per group, so you must sign up in advance.

One-on-one meetings: If you need to discuss sensitive information with Professor Stockwell, you may sign
up for a private meeting with him. Please do not use this option for questions about the course material, as
it is more productive to share your questions and answers in the student discussions group above, given
that many students might have the same questions as you, and might be able to explain it in a way that
makes more sense to you, given that they themselves have only recently learned the material.

In addition, each of the TAs has office hours each week to enable you to ask questions with in the presence
of a smaller group.
Piazza: We will also be using the Piazza feature of Courseworks, which allows you to post and respond to
questions from other students. Please do not email questions to Professor Stockwell or the TAs, as they will
ask you to post them on Piazza so everyone can benefit from the question and discussion around it. This
tool is most effective if a large number of students participate in both posting questions and responding to
questions. The instructors will also monitor this site and respond to questions that students struggle to
answer satisfactorily. Please be respectful in your language in class and online.

In addition, if you have any specific questions about these topics, please discuss with the designated
person:

Team Assignments Auste Kanapeckaite


Piazza: Niki von Krusenstiern, Hui Tan
Team Problems: Carla Bezjian
Homework Questions: Hengrui Liu
Lecture recordings: Hui Tan
Learning Catalytics: Auste Kanapeckaite
ODS matters: Elise Jiang (ej2288@columbia.edu)

Recitations
All students in the course are required to register for a recitation. In recitation, you will be able to review the
material covered in class and the homeworks, and ask additional questions.

Additional Reading Material


These books have been placed on reserve in the Science Library, in the Northwest Corner Building. None
of these readings are required for the course—they are simply suggested as additional resources you may
find helpful.

Dean R. Appling, Spencer J. Anthony-Cahill and Christopher K. Mathews. Biochemistry Concepts


and Connections. Pearson, Hoboken, NJ, 2016.
• This is a comprehensive biochemistry text that has detailed information about large areas of
biochemistry, some of which we cover in the course and some of which we don’t. Reading
parts of this textbook may be useful if you find yourself confused about some topics or
seeking a more nuanced understanding of some of the material.

John McMurry and Tadhg Begley. The Organic Chemistry of Biological Pathways. Roberts and
Company, Englewood, Colorado, 2005.
• This textbook describes the organic chemistry of the core energy metabolism and
biosynthesis pathways in biochemistry, most of which we discuss in the course. It also
provides some foundational material on the types of organic chemistry that commonly is
seen in biological systems. If you are rusty with your organic chemistry, or just looking to
understand biochemistry better from an organic chemistry standpoint, this book will be
useful.

Brent Stockwell. The Quest for the Cure. The Science and Stories Behind the Next Generation of
Medicines. Columbia University Press, New York, 2011.
• This is an overview of the history and future of drug discovery written for a general reader. It
is most relevant to the last few classes in the course.

Navdeep Chandel. Navigating Metabolism. Cold Spring Harbor Laboratory Press, Cold Spring
Harbor, 2015.
• This is an integrative look at metabolism, and how it relates to disease. It describes recent
modern advances in understanding metabolism, and how different pathways are integrated.
Douglas R. Green. Means to an End. Apoptosis and Other Cell Death Mechanisms. Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, 2011.
• This book provides an overview of apoptosis and other cell death mechanisms.

There will also be a number of animations and papers on Courseworks related to the course
material that may help you understand some of the processes we discuss. These can be found in
Files and Resources in Courseworks.

Calculation of grades
Grades will be determined based on:
• Recitation attendance and participation (3%)
• In class polling problems using Learning Catalytics (15%)
o 90% credit for each question will be assigned for responding with any answer and 10%
credit for responding with a correct answer.
• In class quizzes solved with your team (15%)
o These will be automatically graded by Courseworks
• Homework submitted via Courseworks before class (17%)
o These will be automatically graded by Courseworks
• Scores from four exams (32% total, 8% each)
• Comprehensive final exam (18%)

Please be aware that no makeup exams are offered.

Homework quiz answers need to be submitted by 2:40 PM (the start of class) the day they are due.
Learning Catalytics responses must be submitted during class. Team problems must be submitted by 3:55
PM (the end of class). Please be aware that no credit is awarded for late submissions.

There is no curve in the course. Your cumulative course grade is not rounded up or down in Courseworks.
98.00 – 100 = A+
93.00 – 97.99 = A
90.00 – 92.99 = A-
87.00 – 89.99 = B+
83.00 – 86.99 = B
80.00 – 82.99 = B-
77.00 – 79.99 = C+
73.00 – 76.99 = C
70.00 – 72.99 = C-
60.00 – 69.99 = D
<60.00 =F

The philosophy of the course is that what matters is your absolute level of knowledge and skills relative to
the course content, not your standing relative to other students in the course. Thus, we hope that everyone
will work together to maximize the understanding and performance of all students.

Please note that the final exam will be Thursday, December 20th from 1:10-4:00 PM.
No makeup exam is offered. You must take the final exam to receive a passing grade in the course.

The first exam will cover classes 1-5, the second exam will cover material in classes 6-10, the third
exam will cover material in classes 11-14, the fourth exam will cover classes 15-19 and the final
exam will be cumulative and cover all of the material in the course, but with an extra emphasis on
classes 20-21, which will not be covered in the first four exams.

The first exam will be given as a do-at-home exam in Courseworks, available starting at 2:40pm on
Sept 25th, due at 3PM on Sept 26th.
You may submit two LC and two in-class problem sets up to 48 hours late without penalty. Thus, if
you miss a class due to a religious holiday, outside activity, or illness, you should still complete the
LC and in class problems within 48 hours, and review the material covered in the missed class.
However, your grade will not be affected by these late submission, for up to two classes.

Minireview Requirement for Students Enrolled in GU4501


Students enrolled in 4501 are required to write a minireview on a topic related to biochemistry
(students in 3501 are not permitted to write a minireview). The minireview should be less than 3,000
words (5-10 pages, not including references, double spaced). Figures are not required but can be
used. Key, current references should be cited. All of the text must be in your own words. The style
and content should be similar to that found in Annual Reviews in Biochemistry, but there must not
be an existing review on your topic within the last 3 years. A good approach is to identify several
recently published primary research papers around a specific topic and describe the main findings,
background text and future directions of the research area. The grade on the paper will adjust your
course grade up or down by one increment or decrement (i.e. B to B+, or B to a B-). The minimum
margin size is 0.5 inch and the font is 11 point Arial. It must be submitted electronically. The due
date is the last day of class—email it to Professor Stockwell by 2:40 PM on December 4th.

We will use the 3501 Courseworks site for all course materials. If you are a student in 4501, you will
be given access to the 3501 site to access the course materials.
Outline
Date Class Assignment Topic Learning Goals
#
9/4 1 Syllabus Course overview • Describe the goals and structure of the course and
expected roles and activities for students
• Explain the general concepts involved in metabolism
9/6 2 V1: Amino Amino acids, • Be able to predict which amino acid is used in a
acids and peptides and specific context based on the reactivity and
proteins proteins properties of amino acids
• Be able to design an experiment to separate and
purify proteins
• Be able to design an experiment to determine the
structure and/or sequence of a protein
9/11 - Rosh No class
Hashannah
9/13 3 Courseworks Discussion of • Be able to read a primary research article and identify
paper protein structure the main assertions, the evidence supporting those
paper assertions and how the evidence was obtained
experimentally
• Describe how protein misfolding causes disease
• Be able to design and interpret experiments to test
the mechanism of aggregation
9/18 4 V2: Protein Enzyme and • Draw the reaction mechanism for an enzyme-
function protein function catalyzed reaction
• Describe how enzymes are characterized kinetically
• Predict the effect of mutations or changes in
substrate on enzyme-catalyzed reactions
• Design experiments to characterize an enzyme’s
reaction mechanism and kinetic parameters
9/20 5 Courseworks Discussion of • Describe how mutations in IDH1 change its
paper enzyme and enzymatic mechanism and contribute to cancer
protein function formation
paper • Read and understand research papers involving
enzyme mechanisms
• Design experiments to test the functional effects of
mutations in an enzyme
9/25 EXAM Covering Exam taken at home on Courseworks during the
1 classes 1 - 5 period of time from 2:40 pm on Sept 25th to 3 pm on
Sept 26th
9/27 6 V3: Bioenergetics and • Predict whether a reaction is energetically favorable
Bioenergetics reaction classes • Explain how coupling of reaction energetics drives
unfavorable reactions
• Categorize a specific reaction within the major
classes of chemical mechanisms founds in
biochemistry
• Draw the reaction mechanisms for common
biochemical transformations
10/2 7 V4: Glucose • Diagram the mechanism for converting glucose into
Gluconeogenes metabolism pyruvate (glycolysis)
is and the PPP • Diagram how and where ATP and NADH are
consumed and produced during glycolysis
• Draw reaction mechanisms for each step of
glycolysis
• Predict when and how specific cofactors are needed
for chemical transformations
• Predict how alternative substrates would be
processed through the glycolysis pathway
10/4 8 review Practice problems
on glycolysis and
review of material
10/9 9 Courseworks Discussion of • Explain how HK2 was shown to be important for
paper glycolysis paper tumorigenesis
• Be able to design experiments testing the role of a
gene in tumor formation
• Be able to interpret, defend and critique figures in the
assigned paper, as well as related experiments

10/11 10 V5: The TCA The TCA cycle • Understand how the TCA cycle, glycolysis and the
cycle) ETC are linked
• Draw mechanisms for each step of the TCA cycle
and related processes
• Predict the reactions of intermediated and alternative
substrates for the TCA cycle
• Predict how changes in the TCA cycle cause disease
10/16 EXAM Covering
2 classes 6-10
10/18 11 Courseworks Oxidative • Understand how mitochondria convert electron flow
paper phosphorylation I into ATP
• Explain and diagram the mechanisms governing the
ETC and ATP synthesis
• Design experiments to test the effects of functional
changes to the OXPHOS system
10/23 12 Oxidative • Be able to diagram mechanisms for production of
phosphorylation II ROS
• Be able to predict the mechanism of action of toxins
that act through the OXPHOS pathway or through
ROS production
• Understand and explain the how caloric
restriction affects aging

10/25 13 Courseworks Discussion of • Understand and explain how catalase affects murine
paper reactive oxygen lifespan
species paper • Interpret, defend and critique figures in the assigned
paper
• Design experiments testing the role of ROS in
specific diseases
10/30 14 V6: Protein and Amino acid • Be able to draw mechanisms involved in amino acid
amino acid catabolism catabolism, ubiquitin activation and conjugation, and
catabolism protein degradation
• Be able to predict the products of specific catabolic
reactions, such as deamination
• Be able to predict which cofactors are used in
specific catabolic reactions
• Be able to predict where and how proteins will be
conjugated to ubiquitin
11/1 EXAM Covering
3 classes 11-14
11/6 Election Day No class •
11/8 15 V7: Biological Lipid metabolism I • Be able to diagram the mechanisms involved in
membranes triacylglycerol, fatty acid and terpene metabolism
• Be able to predict how labeled carbon will proceed
through lipid metabolism
• Be able to predict the relative energy yield of
molecules when they are metabolized
• Be able to compare metabolic pathways to identify
when common reactions are used
11/13 16 V8: Lipid Lipid metabolism II • Be able to diagram the mechanisms involved in lipid
biosynthesis biosynthesis
• Be able to predict the effects of novel substrates and
cofactors related to those involved in lipid
biosynthesis
11/15 17 V9: cell death Cell death • Be able to describe the molecular mechanisms
introduction underlying phenotypic changes during cell death
• Be able to predict the cell death mechanisms that
occurs in specific cell contexts
Be able to draw the mechanisms underlying enzymatic
processes occurring during cell death, such as
proteolysis
11/20 18 Courseworks Discussion of cell • Be able to understand, critique and defend data in
paper death paper papers similar to the assigned paper
• Be able to design an experiment or project involving
purifying proteins involved in cell death processes
Be able to predict the outcome of experiments similar
to those used in the assigned paper
11/27 19 Review session
11/29 - Covering Exam #4
classes 14-18
12/4 20 Lipid Discussion of lipid
metabolism metabolism paper
12/6 21 Courseworks Protein • Critique and defend data in drug discovery papers
paper druggability and similar to the one assigned
protein-protein • Design experiments to test the target selectivity of
interactions compounds
• Prioritize different compounds based on a variety of
properties
Design, interpret, critique and defend experiments
that predict mechanism of action of compounds
12/20 FINAL Cumulative 1:10 – 4:00 PM in
EXAM 417 IAB
Appendix I: Learning styles and study tips

Learning style
While there is limited direct evidence that learning via your preferred learning style is more effective,
knowing how you prefer to learn may enhance your enjoyment and stamina when studying. See the
attached self-administered quiz below to provide some insight into your learning style.

Study tips
Here are some methods that have been demonstrated to improve learning and performance on
exams (from Marilla Svinicki, December 2014 issue, Volume 24, Number 1, of the National
Teaching and Learning Forum):

1. Spacing Effect. Spaced schedules of studying and self-testing produce better long-term
retention than a single study session or test. This means you should study regularly (e.g., weekly)
and not just before each exam. This is why we have a quiz due before each class and four exams
throughout the semester, to assist you in realizing this goal.

2. Generation Effect. Learning is enhanced when learners produce answers, rather than simply
recognizing answers. This means that rather than simply reading problems and their solutions, you
need to try to solve the problem and only look at the solution after you have generated your own
answer. This is also why we solve problems during class, to give you a chance to answer before
seeing the solution.

3. Feedback Effect. Learners benefit from feedback on their performance in a learning task. This
means that after each quiz, exam and class, you should review your performance and determine
what you understood and what you did not understand. You can then evaluate which study
strategies were effective and which were not, and adapt your strategies to be more effective in the
future. We provide as much feedback as possible via the grading, and in office hours, but please
come and ask for more feedback if you are not sure about what you need to do to perform well and
learn maximally in this course.
Appendix 2. Getting Started on Learning Catalytics- Student Registration
1) Go to
www.learningcatalytics.com and
click Create student account.

2) Click Purchase 6 (or 12)


months of access.

3) Read through the Pearson


Privacy Policy and License
Agreement, and then click I
Accept.
4) Enter your login name, choose
a password, and click Next.

5) Enter you name, email address.


Enter you School country, and
zip/ postal code, then click Next.

6) You can click Print this page to


have a copy for your records on
the Confirmation and Summary
page, and click Log in Now to log
into Learning Catalytics.