Please have a backup plan in place in case your computer or your internet go down during the semester as make-ups will not be given due to technical difficulties. I would especially suggest taking any online exams during our OIT helpdesk normal business hours.  You may wish to

check on the hours and locations of the Rutgers computer labs and/or have a backup plan with a friend or family member to safeguard against missing due dates because of a lack of available or availability to resources.  If you are in an online section or if the in-person section goes

online, then the exams will be proctored by Respondus Monitor, an online proctoring service

who will record the audio and visuals of your session. You will need an uninterrupted internet connection (I highly suggest a cat6 cable plugged directly into your router).  The proctoring

service may require software to run on your computer.   If you have an issue with this, you need to raise it to me before the end of add/drop period.

Prerequisites

Elementary Organic Chemistry or Equivalent

• 01:160:209 or

• 01:160:307 or

• 01:160:315 or

• 21:160:335

Course Learning Objectives

By the end of this course, students should successfully be able to:

•   explain and apply core concepts of matter and energy transformation,

including thermodynamic calculations, enzyme catalysis and the coupling of exergonic and endergonic reactions in biochemical systems.

•   explain and examine core concepts of homeostasis, the organization of

chemical processes, and the regulation of biological molecules in the cell.

•   describe and analyze macromolecular structure and function, including the nature of biological macromolecules, their interaction with water, the relationship

between structure and function, and mechanisms for regulating their function.

•   explain and apply core concepts of biological information focusing on the manner in which information is encoded, transcribed and translated, and the mechanisms by which information is transmitted and maintained across generations.

•   analyze and evaluate peer-reviewed literature in order to formulate hypotheses that will further biochemical research required for post-graduate exams and studies.

Course Materials

Required Subscription(s)

•   A subscription to Modified Mastering Chemistry/Biochemistry from Pearson or

Rutgers bookstore is available if you opted out of the First Day program. If you didn’t opt out and First Day is apart of your term bill you should have access to Pearson

Mastering Chemistry on the first day of classes.  Mastering Chemistry codes from

sources other than this have a high probability of not working for this class and I

wouldn’t suggest buying them from anywhere except Pearson or the Rutgers

bookstore. There will bean integrated button in the Canvas LMS that you will be able to pushto get the Mastering Course once the class starts (see module zero in Canvas  for instructions).  You don’t need a course ID or anything, the button will take you

right to the course.  If you prefer a printed version of the text, you can get that as

well. You can get ane-text, 3-hole punched pages for a binder, or a hardcover book. The book is on reserve at many of the Rutgers Libraries. If you have a problem with  the Mastering Chemistry code, please contact Pearson directly.   I will also have a

Pearson representative available during one of the scheduled class meeting times (I will announce which meeting prior to the meeting if you have questions).

https://www.pearsonmylabandmastering.com/northamerica/

Textbook

• Biochemistry: Concepts and Connections Dean R. Appling, Spencer J. Anthony-Cahill and Christopher K. Mathews, offered in hardcover, 3 ring hole-punched (a-la carte) ore-text text (part of your Mastering subscription) can be purchased with or without Modified  Mastering Chemistry. Please see the Rutgers bookstore orPearson’sstorefor a bundle

package that includes the textbook material and a subscription to Mastering

Chemistry/Biochemistry and then you don’t need to buy the hardcover text on its own. Reading assignments will be provided out of this textbook.  I also have one copy of this   text on reserve at various Rutgers libraries.

•     A potential useful reference, but not required text for the course is, Biochemistry: The Molecular Basis of Life by McKee and McKee updated fifth edition or newer.  I have

this book on reserve at a couple of the Rutgers libraries if you would like to read a

topic from another author’s perspective.  This book and newer editions have a great review of some relevant gen chem and organic chemistry principle in it too.

Required Videos and/or Website Materials

•   All the Canvas video lectures and any

suggested videos contained in the course.

(https://tlt.rutgers.edu/canvas)

Technology Requirements

Baseline technical skills necessary for online courses

•    Basic computer and web-browsing skills

•    Navigating Canvas

Technology skills necessary for this specific course

•    Live web conferencing using Zoom, Webex or Canvas for office hours and any required meetings.

•    Use of the Respondus Monitor and Lockdown Browser software system. See the first Canvas Module for more details.

•    Use of our learning management system, Canvas.

Required Equipment

•    Computer: current Mac (OS X) or PC (Windows 7+) with a reliable high-speed internet connection

•    Webcam: built-in or external webcam, fully installed

•    Microphone: built-in laptop or tablet mic or external microphone

•    A pair of headphones for listening to videos and office hours

•    A non-memory calculator like a TI-30X or equivalent (no graphing/programmable calculators)

•    If you will betaking online exams,a well-lighted room that you can be alone in for the duration of the exam.

Required Software

•    Microsoft Word or equivalent

•    Microsoft PowerPoint or equivalent

•    Google Chrome web browser ONLY for course materials.

•    The use of online proctoring tool extensions or other items related to online proctoring.

Assessments and Scheduling

Important Dates (see schedule below assignment deadlines)

Please check the Rutgers registrar’s office for details and official dates and times of the course. All exams will be given according to the schedule below.

Course Schedule and Deadlines

Mastering Chemistry Assignments for a specific module and an End of Module Quiz for a specific module will be due at the same date and time and the dates will be posted on Canvas and in the

below grid.  Mastering Chemistry and End of Module Quizzes are open book/open notes and

working ahead is highly advised since no makeup work or extensions will be provided after the   due date. Exams are closed book/closed resources. Your lowest Mastering Chemistry grade and

End of Module quiz grade will be dropped. There will bean optional cumulative exam offered

during finals period that can replace your lowest exam grade. There are no makeup exams

offered. As a student, you should copy these due dates down into your phone’scalendar and

set reminders and work ahead of the due dates and times.

Assignment Overviews

Exam 1

•     This exam will contain a total of 43 multiple-choice questions.  The exam will be broken into three parts. Part 1 will consist of 30 questions worth 2 points each   and should not require much work to arrive at an answer (math, graphing,

extrapolation, etc.). Part 2 will contain 5 questions worth 2 points each from the first paper assigned to you (see Enzymology Paper assignment description

below). Part 3 will have 8 questions worth 3.75 points each and will involve you

performing tasks. The exam will have multiple choice, provide a numerical

answer, matching and/or multiple select question types. You will be given 1 hour    to complete the exam. If you are in the in-person course, we will intend to have exams during the published lecture time on the Rutgers schedule of classes. If you are in a fully online or hybrid class or we go remote for any reason, exams will be given through Respondus Monitor given during the class meeting time listed above. If a student is taking an online proctored exam,a slow and

complete view of the student’s desk surface must be provided during the start of the exam and the student’s face must remain clearly in view of the camera for the full duration of the exam. A point penalty on the exam maybe applied if these rules are not followed.

Exam 2

•     This exam will contain a total of 43 multiple-choice questions.  The exam will be broken into three parts. Part 1 will consist of 30 questions worth 2 points each   and should not require much work to arrive at an answer (math, graphing,

extrapolation, etc.). Part 2 will contain 5 questions worth 2 points each from the second paper based on the group you joined (see Interest Topic assignment

description below). Part 3 will have 8 questions worth 3.75 points each and will

involve you performing tasks. The exam will have multiple choice, provide a

numerical answer, matching and/or multiple select question types. You will be

given 1 hour to complete the exam. If you are in the in-person course, we will

intend to have exams during the published lecture time on the Rutgers schedule of classes. If you are in a fully online or hybrid class or we go remote for any

reason,  exams will be given through Respondus Monitor given during the class meeting time listed above. If a student is taking an online proctored exam, a

slow and complete view of the student’s desk surface must be provided during the start of the exam and the student’s face must remain clearly in view of the camera for the full duration of the exam. A point penalty on the exam maybe applied if these rules are not followed.

Exam 3

•     This exam will contain a total of 43 multiple-choice questions.  The exam will be   broken into two parts. Part 1 will consist of 35 questions worth 2 points each and should not require much work to arrive at an answer (math, graphing, extrapolation,  etc.). Part 2 will have 8 questions worth 3.75 points each and will involve you

performing tasks. The exam will have multiple choice, provide a numerical

answer, matching and/or multiple select question types. You will be given 1 hour   to complete the exam. If you are in the in-person course, we will intend to have

exams during the published lecture time on the Rutgers schedule of classes. If you are in a fully online or hybrid class or we go remote for any reason, exams will be given through Respondus Monitor given during the class meeting time listed above. If a student is taking an online proctored exam,a slow and

complete view of the student’s desk surface must be provided during the start of the exam and the student’s face must remain clearly in view of the camera for the full duration of the exam. A point penalty on the exam maybe applied if these rules are not followed.

Optional Cumulative Exam

•   This optional cumulative exam will coverall material taught and contain a total

of 86 multiple-choice questions.  The exam will be broken into two parts. Part 1 will consist of 70 questions worth 2 points each and should not require much

work to arrive at an answer (math, graphing, extrapolation, etc.). Part 2 will have 16   questions worth 3.75 points each and will involve you performing tasks. The exam will have multiple choice, provide a numerical answer, matching and/or multiple     select question types. You will be given 2 hours to complete the exam.  This exam  will be offered in an online format only with video proctoring. If the result of this  exam is higher than either any single grade you have for exam 1, 2 or 3, the

optional cumulative final grade will replace one of them.  If it is lower than all of   them, it will not replace any of them This exam will be administered online only using Respondus Monitor. The exam window will be for 24hrs on a date

specified for final exams asynchronous courses. A student taking this exam is expected to show a slow and complete view of the student’sdesk surface

during the start of the exam and the student’s face must remain clearly in view of the camera for the full duration of the exam. A point penalty on the exam

maybe applied if these rules are not followed.

Enzymology paper and Interest Topic paper

•     The enzymology paper will be assigned to you during module 2 and you will have the option to use the forum posts to collaborate with other students and discuss the

paper.  Five, two point questions regarding the findings, how fundamental principles taught in lecture are applied to this paper, and/or the significance of this paper will

appear on exam 1.  A set of papers that you will pick from will be provided for Exam 2. Announcements will be made regarding how to do this when the assignment is given.

End of Module Quizzes in Canvas

•   There will be a quiz at the end of each module and a link to this quiz will be found in the    final lesson page of each module.  You can locate these lessons by clicking on the Home    button in Canvas, then the proper module and finally the lesson you would like to be in.    You are responsible for keeping up with the due dates for these quizzes.  There will be a    due date for these quizzes and extensions will not be given.  These quizzes are open book and open notes.

Mastering Chemistry Online Homework

•    Unless you opted out of it, Mastering Chemistry and a copy of the online textbook is available to you by entering the Canvas LMS site and clicking on Frist Day Course

Materials button and after that, clicking on the Access Pearson button.  Our class will  automatically be available to you and should be included in your tuition payment as a part of the First Day system from Pearson.

At Home Reading Assignments from the Textbook and Canvas Pre-recorded Lectures

•   You are expected to be reading the sections of the chapters covered during lecture after watching each lecture.  This is apart of the expectation of the course.  The lecture will    highlight what I feel are important topics in biochemistry and illustrate and/or interpret the material so that it can be comprehended better by a student when they read the

textbook later.  The reading should further your understanding and allow you to hear   the content presented to you by another voice (the author of the book), but also allow you to spend time reflecting on concepts presented in lecture.

Summary Paper (for Basic Biochemistry Only 16:682:531)

•   Graduate students will be expected to write a 3-5 page mini-review (single spaced, 12pt Times New Roman font).  I’m including 3 papers for you to write a minireview of a topic   on. In your syllabus this is entitled “Summary Paper to be assigned”. You will find that

these papers relate to a molecule called CD44 and I would like you to write a 3-5 page mini-review of the topic with citations. You should use primary sources in your review

and may need to go outside of these paper for the purpose of citing further background articles or newer things published after these papers have been out. I do advise you to  look up a current review article published by JBC to get an idea of what they look like

and use that as a guide to the layout of what your paper should look like and attempt to do. https://www.jbc.org/ I would like the review handed-in (uploaded as a PDF in

Canvas) by the due date in the syllabus. If you need an idea of what a minireview would look like you can see some here.  The paper titles are below and can be looked up

through Rutgers libraries and downloaded.

Paper 1

Targeting CD44 by CRISPR-Cas9 in Multi-Drug Resistant Osteosarcoma Cells   Xiao Z.a,b · Wan J.a · Nur A.A.c · Dou P.a · Mankin H.c · Liu T.a,c · Ouyang Z.a Cell Physiol Biochem 2018;51:1879– 1893

Paper 2

CD44 promotes multi-drug resistance by protecting P-glycoprotein from FBXO21- mediated ubiquitination

Abhilash K. Ravindranath,1 Swayamjot Kaur,1 Roman P. Wernyj,1 Muthu N. Kumaran,1 Karl E. Miletti-Gonzalez,1,4Rigel Chan,1 Elaine Lim,1 Kiran Madura,1,2 and Lorna

Rodriguez-Rodriguez1,3 Oncotarget. 2015 Sep 22; 6(28): 26308–26321.

Published online 2015 Jul 3. doi: 10.18632/oncotarget.4763

Paper 3

Doxorubicin induces drug resistance and expression of the novel CD44st via NF- κB in  human breast cancer MCF-7 cells XIN JIAN FANG1,2, HUA JIANG2 , YA QUN ZHU1 , LI YUAN ZHANG1 , QIU HONG FAN1 and YE TIAN1 1 Department of Radiotherapy

and Oncology, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu

215004; 2 Department of Medical Oncology, The Second People's Hospital of Lianyungang (Lianyungang Hospital Affiliated to Bengbu Medical College),

Lianyungang, Jiangsu 222000, P.R. China Received January 17, 2014; Accepted February 24, 2014

Please seeyour grading scheme above for how much this assignment is weighted in your final grade for the course.

GUIDELINES BASIC BIOCHEMISTRY REVIEW ARTICLE

We are using the JBC guidelines listed below.

The Journal of Biological Chemistry (JBC) publishes timely reviews that highlight new

insights and paradigm shifts in our understanding of the molecular and cellular basis of life processes.

All JBC Reviews should be written for a broad interdisciplinary readership and highlight

the opportunities, challenges and wider implications of the work. We welcome a spectrum of reviews that may: critically review and provide new insight into the state of a field; focus on advances in methods, tools, techniques and resources that are of broad interest to the  biological chemistry community; and/or address forward looking, multidisciplinary and

cross-cutting themes.

The JBC Reviews Committee will work with authors and associate editors during the

preparation of reviews to assist in refining the focus and scope by providing feedback on outlines or early drafts to help identify missing elements, comment on figures, and make suggestions on the global organization. JBC will give editorial input on the overall

organization and presentation of the first submission. JBC will provide artistic support for critical figures that can be used for educational purposes and capture the central

message(s) of the review to create a consistent style for the JBC Reviews section. Please note that this step will only occur once it is clear the review is on track to publication; the    initially submitted figures must be sufficiently developed to facilitate the peer review

process.See more information regarding this part of the process.

Additional considerations

•     JBC Reviews are normally invited. However, authors may submit brief outlines for consideration by the Committee.

•     Where the focus is more on a particular field, authors should discuss open questions, controversies in that field and the broader implications of new findings.

•     Discussion of advances in methodologies/tools/resources should articulate

opportunities, describe new developments and insights, and provide critical assessment of the benefits and pitfalls of new approaches.

•     Works highlighting opportunities that are forward-looking and have a broader and multi- disciplinary approach that provide new insight to multiple themes and fields are

particularly welcome.

•     Please avoid lengthy details about specific experiments, unless they are directly relevant to the central advances you want to highlight.

•     New analysis of publicly available data (such as extracting mutations from gene

databases or overlaying biomolecule structures) will be allowed at the editor’s

discretion; the inclusion of new primary data is not allowed. Unpublished data are not generally allowed.

Formatting guidelines

•     Titles should be accessible to a broad readership and not exceed 150 characters (including spaces).

•     Abstracts should not exceed 250 words.

•     The overall length is at the author’s discretion, pending input from the Committee and  referees. JBC welcomes short reviews (comparable to previous JBC Mini-reviews, i.e. 28000 characters) but longer monographs are fine where a more comprehensive

approach is justified.

•     The figures and tables should illustrate the main points of the Review and/or provide  useful resources; authors should generally aim for 6 or fewer images to make optimal use of artistic support. Ideally at least one image summarizing the overall

system/process/biomolecule featured in the review will be included to assist interested non-experts.

•     The number of references is not restricted. References should be cited by number.

Citation of original research for the majority of the references is preferred, although

providing a clear statement of the relationship of this review to any previous reviews is recommended.

•     For the initial submission, it is not necessary to adopt specific formatting. For

subsequent submissions, please refer to theInstructions for Authorspage for guidance on JBC’s preferred formatting style (e.g., running title, keywords etc.).

•     Supplementary information is not permitted in review articles.