BCH 361: Principles of Biochemistry Fall 2018, Liu

Class number: 76763 Class time: T, Th 1:30-2:45 pm Location: PSH152

Dates: 08/16/18-11/29/18 (Note: 4th exam is on 12/6/18 at 12:10-2:00 pm, PSH152)

Instructor: Prof. Yan Liu

Phone: 480-727-0397 (office)
Email: yan_liu@asu.edu (please always include BCH 361 Fall 2018 in the
subject line) Please note that email is not a substitute for office hours.
If your email requires an answer of more than a few lines, you need to
see me in my office hours.
Office: Biodesign Institute, Building A, 114A.
Office hour M T W Th 9:30-11 am, Biodesign Institute. (Note: Please bring your
photo ID to any of the Biodesign reception desk. I will be called to
meet you at the entrance to A110. This is because even though you
are allowed to walk into the hallway by yourself, the entrance to the
office area is always locked.) I am also available by appointment.
Please email me your intended time to meet.

Teaching assistant: Miss Yueming Hu. yuemingh@asu.edu.

Office Hour: T and Th 12:20-1:20 pm, LRC (PSH137)

Textbook
Biochemistry, a short course, 2nd Ed. by Tymoczko,
Berg and Stryer (2012) Publisher: Freeman.
Minimum requirement: The paper book. Plenty of
used books are available from Amazon. The
textbook is required. Access card is not
required.
The ASU bookstore has the ASU edition of the textbook,
which only has ~ 20 chapters that are covered in
the lectures. (not necessary the best deal)
You may also purchase the access card to have the E-
book on the publisher site. (not required if you already have the paper
book, only your personal preference)
E-book with LaunchPad access card: ISBN-10: 1-4641-6731-1
http://www.macmillanhighered.com/launchpad/tymoczko2e/3675421
There are plenty of exercises at the Launchpad site (Learning curve, etc.). But
this is not required.

Expectations:
• Read your textbook.
• Do your practice (problem sets after the chapters). There are plenty of
questions after the chapters in the textbook for your own practice that will help
to check your understanding and mastery of the material.
• Do your homework on Sapling site on time (you need to sign up at Sapling,
instruction details in below), be prepared to class.
• Arrive the class on time and remain quiet and attentive.
• Come to every class and participate in class Q&A sessions.
• Have a notebook to write down important points.
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• Please download the powerpoint slides from Blackboard (in the Content
folder) and study.
• You are welcome to ask questions after the class, but preferably not before the
class unless it is a question that can be answered in a few words.
• Check your ASU email regularly everyday for announcements and read our
emails carefully. To save everybody’s time, I will not repeat myself in class if I
have made an announcement on Blackboard and have sent it to everyone
through email.
• Join the class Facebook group and be active in asking and answering
questions related to the content of the course.
• Visit your instructor or TA office hour if you have questions that require long
answers.

Grading policies:

A. Exams: We will have four in class exams. Tentative dates for the exams are
9/6 (Th), 10/4 (Th), 11/1 (Th) (the first three exams are at 1:30-2:45 pm), and
12/6 (Th, at 12:10-1:25 pm). The instructor reserves the right to change the
dates of the exams. Each exam will be approximately 200 points and counts for
~20% of the final score (the points in each exam will vary depending on the
contents covered). There will be no cumulative final exam. Together with the
homework and class quiz/participation points, there will be a total of 1000 points
possible in the course. Although exams will not be overtly cumulative, this is a
course where topics presented later in the semester require you to use concepts
and information covered earlier in the semester.

B. Homework points: We will have Sapling online homework system for

questions and quizzes that you are required to finish on time.
• These homework assignments will be automatically graded based on
correctness and completeness.
• Homework submitted late (within 10 days) will still be graded, but will have
10% deduction of score per day late.
• You are allowed to try multiple times until you get the correct
answer. Each additional attempt will have 5% deduction of the
points. Please try to limit your number of attempts to less than 3
(stop, study and come back to the question again).
• The homework points will be finally rescaled and topped to 200 points
at the end of the semester and will represent 20% of the final score.
• You are allowed to miss up to one HW without penalty on your score.

C. Class quiz: We will have class Question and Answer sessions randomly in the
lectures. Your answers will not be graded. The questions will be in the similar
format as those in the exams.

D. Final Grades will be assigned as follows:

A+: 970-1000, A: 900-969, A-: 880-899, B+: 850-879, B: 800-849,

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B-: 770-799, C+: 730-769, C: 650-729, D: 600-649, E: <599

We reserve the right to adjust the score requirements for each letter grade depending
upon the overall performance of the class. We will not raise the boundary scores. It is
your responsibility to keep track of how many points you have [updated on blackboard
(exams) and on Sapling (Homework)] to dispute any discrepancies.

Instruction for access Sapling online homework:

Please follow the instructions in the following webpage on how to enroll in the course
site:

Please go to www.saplinglearning.com/login to log in or create an account. Please each

student only register once using one email account! The following link includes detailed
instructions on how to register for your
course: https://community.macmillan.com/docs/DOC-5972-sapling-learning-registering-
for-courses.

You need to do three things: 1. Create a student account.

2. Find and register to the correct course.
3. Pay for the access.

GENERAL STUDENT INSTRUCTIONS

1. Go to
https://www.macmillanlearning.com/Catalog/elearningbrowsebymediatype/SaplingLearni
ng choose “Students Login or Create Account”. click “US Higher Ed”. follow the prompt
to fill in the information (Username, password, email, first name, last name, institution,
time zone.)
2. Under Enroll in a new course, Look for “Arizona State University- Tempe - BCH361 - Fall
2018 – LIU.” You should see Courses at [Your College]. Click to expand this list and see
courses arranged by subject. Click on a subject to see the terms that courses are
available.

Click on the term to expand the menu further (note that Semester 1 refers to the first
course in a sequence and not necessarily the first term of the school year).

Once the menus are fully expanded, you’ll see a link to a specific course. If this is indeed
the course you’d like to register for, click the link.

Need Help? The technical support team can be reached by phone, chat, or by email via
the Student Support Community. To contact support please open a service request by
filling out the webform: https://macmillan.force.com/macmillanlearning/s/contactsupport.

3. The cost is $42. You may pay by Paypal or credit card.

Sapling Learning offers a grace period on payment; for most courses, 14 days from the first day
of the semester. But if you forgot to pay, you will lose the access and may lose the completed
homework points. Please do not take that risk!

During sign up or throughout the term, if you have any technical problems or grading issues,

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please direct them by sending an email to support@saplinglearning.com to explain the issue.

Review the system requirements and confirm that Flash is updated and enabled in your
browser. Please read this the following webpage if you encounter an error message like this:

https://macmillan.force.com/macmillanlearning/s/article/Enable-Adobe-Flash-player

The technical support can also be reached by phone or by webform via the Student
Support Community. The following link contains detailed hours and information.
https://community.macmillan.com/docs/DOC-6915-students-still-need-help

Video for students: https://www.youtube.com/watch?v=VPqfaR68RQE

Please bookmark this page to make it easy to return to.

http://www.saplinglearning.com/ibiscms/course/view.php?id=83771

Please sign in to access the Sapling course as soon as possible. The homework
assignments will generally be available on the sapling course site the day before the
chapter will be discussed in the classroom. The due time for each assignment is
generally set before midnight (11:59 pm, Arizona time) after the content of one chapter
has been completely discussed, the due dates may generally fall on a Monday or a
Wednesday night (please refer to the tentative course schedule at the end of the
document). Please make sure the time setting on your computer is Arizona time,
otherwise it may automatically mark you a late submission if you are in the last
hour. Be proactive.

Ways of Communications:

A. Blackboard: ASU Blackboard will be used to post lecture notes, related

files and send announcements to all the students. Grades for the exams will
be posted here and the grades for the homework assignments will be updated
after each exam.

Please login to the ASU blackboard everyday for updates and anouncements.
I also send emails to all users from blackboard every time I have made an
update. Please read my emails.

B. Facebook Group: I have created a Facebook group for our class named
“BCH361 Fall 2018 (ASU, section 76763 Prof. Yan Liu)”. Search the bold
keyword you will find this group. Or copy and paste the weblink into your web
browser: https://www.facebook.com/groups/2195272777426413/

This is a closed group within ASU. ASU student may find this page, but only
registered users can see the contents and post. You are welcome to join the

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group as soon as possible. This facebook group is created to facilitate

discussions among the students, the TA and the instructor on course-related
topics. Questions and answers posted here will be visible to all registered group
members. Everyone in this course is welcome and strongly recommended to join
the group and post questions related to the lectures, quiz, homework, exams,
and reviews. Everyone is also welcome to answer questions that are posted
here. We intend to help each other to have an excellent learning experience.
Please do not post anything that is not related to the course.

Webpage: https://www.facebook.com/groups/2195272777426413/

Email contact: We welcome email contact; however, please keep the following items
in mind.

• Please use email only if the expected response is brief. If the topic in question
requires a discussion, please see the instructor or TA in person.
• You must include “BCH361 Fall 2018” in the subject line.
• Due to the number of students in the course, our time to answer emails will be
limited. If your email asks a question that is answered in the syllabus or
announcement by email or on blackboard, you will probably not get a separate
response.
• It is your responsibility to read the syllabus, read emails from the instructor and
TAs, and read the announcements in blackboard!
• Correct spelling, capitalization and punctuation is required. If we cannot
understand your email, we will not be able to respond.

Exams:

A. Format of Exams: All exams will contain a combination of fill in space,

match up, true/false, multiple choice, short answer, and/or essay
questions. Exams will take materials both from the lecture and textbook.
This includes the suggested problems after each chapter from the textbook.
In the event of a classroom disturbance during an exam, the method of
evaluation will be modified by the instructor. Scantron will be provided.

B. Make up exam: In the event of an anticipated missed exam, you must speak
with the instructor ahead of time to schedule a make up exam. If a make up
exam is administered, the format will be decided by the instructor.

C. Re-grade of exams: Any requests for re-grade on exams must be

accompanied by a Re-grade Request Form and turned to the instructor
before the announced deadline. The re-grading form is available in the
blackboard contents folder.

D. Academic integrity: You will be bound by the ASU academic integrity

policy: https://provost.asu.edu/academicintegrity

E. Conduct during exams:

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• Be quiet so that all students have the opportunity to take exams with minimal
distractions.
• Turn off or silence any electronic devices and put them away in your backpack.
• Be on time for exams. If you are late to an exam, please enter the room as
quietly as possible (this includes making sure the door does not slam shut behind
you).
• If you have a question during the exam, please raise your hand and wait for the
instructor or TA to come to you. Do not leave your seat to ask questions.
• When you are finished, quietly turn in your exam, show your student ID, sign
your name in the sheet provided and leave the room.
• Use of any unauthorized electronic device during the exam will result in a score
of zero on the exam and confiscation of the device for evidence.

Reading: We strongly suggest that you do the textbook reading (minimum

requirement) before class! The lectures will serve primarily to stress important
aspects of the reading and to clarify difficult concepts presented in the text. The
problems in the textbook will not be assigned or graded but you may see very similar
questions on the exams. Do not get behind with the material! You are encouraged
to go ahead of the schedule on your study.

Cell phone and computer use: Cell phones or other communication devices may be
used during the lecture, however they must be silenced. Computers may be used if they
are being used in conjunction with the lecture material (taking notes or viewing the
lecture notes). If you are using these for purposes other than a lecture aid and
distracting those around you, you may lose your computer use privileges for the
remainder of the term. Please respect the other members of your class and refrain from
using your computer in any way that detracts you or others from the time spent in
lecture. During exams, computers and/or cell phones cannot be used. The only
electronic device allowed for exams is a stand-alone calculator if the instructor allows
one to be used.

Eating and drinking during class: Due to the length of the class period, we realize
that students might get hungry and want to eat. If you are going to eat or drink during
class, please be respectful to others and bring your food and beverages in a package
that can be opened silently.

Academic Integrity And Student Conduct:

Academic Integrity
Please review the following obligations as set forth in the ASU Student Academic Integrity
Policy (https://provost.asu.edu/academicintegrity). All BCH 361 students are expected to abide
by these rules and your TA and Instructor will be following a zero tolerance policy. Failure to
comply will result in appropriate sanctions up to and including a grade of XE (failure through
academic dishonesty).

Student Obligations
Each student must act with honesty and integrity, and must respect the rights of others in
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carrying out all academic assignments. A student may be found to have engaged in academic
dishonesty if, in connection with any Academic Evaluation or academic assignment, he or she:

A. Engages in any form of academic deceit

B. Refers to materials or sources or uses devices (e.g., computer disks, audio recorders,
camera phones, text messages, crib sheets, calculators, solution manuals, materials from
previous classes, or commercial research services) not authorized by the instructor for use
during the Academic Evaluation or assignment

C. Possesses, reviews, buys, sells, obtains, or uses, without appropriate authorization, any
materials intended to be used for an Academic Evaluation or assignment in advance of its
administration;

D. Acts as a substitute for another person in any Academic Evaluation or assignment

E. Uses a substitute in any Academic Evaluation or assignment

F. Depends on the aid of others, including other students or tutors, in connection with any
Academic Evaluation or assignment to the extent that the work is not representative of the
student's abilities;

G. Provides inappropriate aid to another person in connection with any Academic Evaluation or
assignment, including the unauthorized use of camera phones, text messages, photocopies,
notes or other means to copy or photograph materials used or intended for Academic
Evaluation

H. Engages in Plagiarism

I. Uses materials from the Internet or any other source without full and appropriate attribution

J. Permits his or her work to be submitted by another person in connection with any Academic
Evaluation or assignment, without authorization

K. Claims credit for or submits work done by another

L. Signs an attendance sheet for another student, allows another student to sign on the
student's behalf, or otherwise participates in gaining credit for attendance for oneself or another
without actually attending

M. Attempts to influence or change any Academic Evaluation, assignment or academic record

for reasons having no relevance to academic achievement.

“Students are entitled to receive instruction free from interference by other members of the
class. An instructor may withdraw a student from the course when the student's behavior
disrupts the educational process per Instructor Withdrawal of a Student for Disruptive
Classroom Behavior.
The Office of Student Rights and Responsibilities accepts incident reports from students,
faculty, staff, or other persons who believe that a student or a student organization may have
violated the Student Code of Conduct.”
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Tentative class schedule:

Changes might be made depending on circumstances in class.

Dates Monday Tuesday Wednesday Thursday

First day of Fall
Semester:
August Introduction of the course
16
Chapter 1: Biochemistry
and the Unity of Life
Course
August Chapter 1: Chapter 2: Water, week
related quiz
20-25 Biochemistry and the bonds and generation of
on Sapling
Unity of Life cont’ order out of chaos
due
August Chapter 1 Chapter 2
Chapter 3: Amino Chapter 4: Protein three-
27- homework homework
acids dimensional structure
31 due due
Labor Day
No school
Chapter 4: Protein Chapter 4
Sept 3-7 three-dimensional homework Exam 1 (Ch. 1-4)
Chapter 3
structure cont’ due
homework
due
Chapter 6: Basic Chapter 6
Sept 10- Chapter 7: Enzyme:
concepts of enzyme homework
14 Kinetics and Regulation
action due
Chapter 8: Enzymes: Chapter 7 Chapter 8: Enzymes:
Sept 17-
Mechanisms and homework Mechanisms and
21
Inhibitors due Inhibitors cont’

Chapter 8 Chapter 9: Chapter 9

Sept 24-
homework Hemoglobin, an homework Chapter 33 Nucleic acids
28
due allosteric protein due

Chapter 33 Chapter 10
Chapter 10:
Oct 1-5 homework homework Exam 2 (Ch. 6-10, 33)
Carbohydrates
due due

Oct 9-13 Fall Break Fall Break Chapter 11: Lipids

Chapter 12:
Chapter 11 Chapter 12 Chapter 14: Digestion:
Oct 15- Membrane
homework homework turning a meal into
19 structures and
due due cellular biochemicals
functions

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Chapter 14 Chapter 15: Chapter 15

Oct 22-
homework Metabolism: basic homework Chapter 16: Glycolysis
26
due concepts and Design due
Chapter 16
Oct 29- Chapter 16: Exam 3 (Ch. 11-16, no
homework
Nov 2 Glycolysis cont’ 13)
due
Chapter 17
Chapter 17: Chapter 18: Preparation
Nov 5-9 homework
Gluconeogenesis for the cycle
due
Chapter 19: Harvesting
Chapter 18 Chapter 19:
Nov 12- electrons from the cycle
homework Harvesting electrons
16 Cont’
due from the cycle

Chapter 19 Chapter 20: The Chapter 20

Nov 19- Thanks-giving
homework Electron transport homework
23 No school
due chain due
Chapter 21
Nov 26- Chapter 21 The
homework Review
30 proton motive force
due
Exam 4 at 12:10-1:30
Dec 3-7 No class
pm (Ch. 17-21)