BCH 341 Syllabus – Spring 2018

PDF VERSION: BCH341 Syllabus Spring 2018

BCH 341: General Information

• ASU Course Number: BCH 341 (Class # 22736 & 27899)
• ASU Course Dates: 1/8/18 – 2/27/18 (ASU Online and iCourse)
• Course Title: Physical Chemistry with a Biological Focus
• ASU Course Credits: 3 units
• Prerequisites: Introductory/General College Chemistry (ASU CHM 114, 116 or 118); Introductory/General College Physics (ASU PHY 101, 112 or 131); Organic Chemistry (ASU CHM 231, 233 or 333); Calculus (ASU MAT 251, 265 or 270)

ASU Catalog Description & Course Description

Thermodynamics, equilibrium, states of matter, solutions and chemical kinetics with a focus on biological systems. For students in biochemical, pre-medical, biomedical and educational curricula.

Instructor

Professor Jeffery L. Yarger

ASU Address: School of Molecular Sciences, Arizona State University, Interdisciplinary Science and Technology Building I (ISTB1), 550 E. Orange St., Tempe, AZ 85281.

ASU Office: Tempe Campus, Interdisciplinary Science and Technology Building I (ISTB1), Room 481H.

ASU Phone: 480-727-9824

Course Email Address: yarger@biopchem.education

Learning Outcomes

• Develop and understanding of the molecular and mathematical underpinnings of thermodynamics.
• Apply the principles of kinetics to biochemical processes and understand the molecular underpinnings of chemical kinetics.
• Develop the skills to apply a thermodynamic understanding to any biochemistry and/or life process.
• Use modern computer based computation and data analysis for understanding experimental measurements used to provide a thermodynamic and/or kinetic understanding of biochemical materials and systems.

Course Resources & Materials

Primary Website: ASU uses Blackboard as its online learning platform.  All information regarding this course will be posted to the ASU Blackboard website.  ASU Online Course info can be found generally at my.asu.edu and the direct link to Blackboard at ASU can be found at https://myasucourses.asu.edu  

Textbooks: There are numerous online freely available textbooks that cover physical chemistry, biophysical chemistry, thermodynamics and kinetics.  This course will make use of several freely available textbooks and does not require the students to purchase any textbook for this course.  That said, there are several excellent modern textbooks that can be purchased to better understand the material covered in this course.  The books most referenced in this course are provided below:

• J.P. Allen, BioPhysical Chemistry, Wiley-Blackwell, 2008. (free PDF version for ASU students)
• P. Atkins & J. De Paula, Physical Chemistry for the Life Sciences, 2nd Ed, Oxford Press.
• R.A. Alberty, Thermodynamics of Biochemical Reactions, Wiley, 2003.
• J. Kuriyan, B. Konforti & D. Wemmer, The Molecules of Life: Physical and Chemical Principles, Garland Science, 2013.
• R. Phillips et al., Physical Biology of the Cell, 2nd Ed., Garland Science, 2013.

Online Resources: All information and resources needed for the study and understanding of thermodynamics and kinetics can be found online.  The difficulty is searching out good information and websites.  Below are a few of my favorite regarding thermodynamics and kinetics.

• J.P. Allen, BioPhysical Chemistry, Wiley-Blackwell, 2008. (free PDF version for ASU students)
• W. Schartl, Basic Physical Chemistry: A Complete Introduction on Bachelor of Science Level, Bookboon, eBook, 2014. (freely available, ISBN 978-87-403-0669-9)
• L. Lue, Chemical Thermodynamics, Bookboon, eBook, 2009. (freely available)
• P. Klappa, Kinetics for Bioscientist, Bookboon, eBook, 2009. (freely available)

Computational: Computational chemistry is used extensively in biophysical chemistry and is often an important link between experiment and theory.  Useful computational chemistry programs and websites for biophysical chemistry are provided below.  Also, data analysis typically relies on plotting and fitting software and links are provided below for some useful data analysis packages and resources.

Course Evaluation

Homework: Suggested homework problems from J.P. Allen’s freely available book, BioPhysical Chemistry, Wiley-Blackwell, will be assigned along with suggested problems from the course instructor.  These problems will not be graded.

Quizzes: Quizzes will be posted on the course ASU BCH 341 Online Blackboard website.  These quizzes must be taken during the time period in which they are scheduled.  It is important to have a secure and stable internet connection.

Exams: Exams will be posted on the course ASU BCH 341 Online Blackboard website. There will be 3 midterm exams and one comprehensive final exam.  Exams should be submitted as a single PDF document on the ASU BCH 341 Online Blackboard website by the announced due date. The final exam is comprehensive and will contain similar problems as the three midterm exams.  The final exam can be used to replace a student’s total midterm exams score, if the score on the final exam is greater than the total of the 3 midterm exam scores.  

Below is a table that summarizes due dates and points assigned to each evaluation quiz and exam.  The final exam is comprehensive and factored separately for course evaluation.

Activities/Assignments	Points	Due Date
Week 1 & 2: Laws &/or Postulates of Equilibrium Thermodynamics (Jan 8-19)
Suggested Homework, Reading & Recommended Concept Videos	N/A	Jan 8-17, 2018
Quiz 1	25	Jan 11, 2018
Quiz 2	25	Jan 18, 2018
Exam 1	100	Jan 22, 2018
Week 3: Energy, Entropy & Temperature (Jan 22-28)
Suggested Homework, Reading & Recommended Concept Videos	N/A	Jan 23, 2018
Quiz 3	25	Jan 25, 2018
Week 4: Chemical, Biochemical & Physical Equilibria (Jan 29 – Feb 4)
Suggested Homework, Reading & Recommended Concept Videos	N/A	Jan 29-31, 2018
Quiz 4	25	Feb 1, 2018
Exam 2	100	Feb 5, 2018
Week 5: Bioenergetics & Electrochemistry (Feb 6-11)
Suggested Homework, Reading & Recommended Concept Videos	N/A	Feb 5-7, 2018
Quiz 5	25	Feb 8, 2018
Week 6: Kinetics & Enzymes (Feb 12-18)
Suggested Homework, Reading & Recommended Concept Videos	N/A	Feb 12-14, 2018
Quiz 6	25	Feb 15, 2018
Exam 3	100	Feb 19, 2018
Week 7: Introduction to Statistical Thermo & Non-Equilibrium Thermodynamics (Feb 20-25)
Suggested Homework, Reading & Recommended Concept Videos	N/A	Feb 19-21, 2018
Quiz 7	50	Feb 22, 2018
Comprehensive Final Exam (Feb 26)
Final Comprehensive Exam	300	Feb 26, 2018

Quizzes – 200 pts

Midterm Exams (3 midterm exams, 100 pts ea)

or Comprehensive Final Exam (300 pts) – 300 pts 

Course Total – 500 pts

Grades: Grades are designed to reflect a students performance on assignments and adherence to deadlines.  Graded assignments will be available within 48 hours of the due date via the gradebook in Blackboard.  The following grading system will be employed:

Grade	Points	Percentage
A	450-500	90-100%
B	400-449	80-89%
C	350-399	70-79%
D	250-349	50-69%
E	0-249	0-49%

Late Assignments & Exams: No exams or assignments will be accepted late. Plan to submit assignments in advance and anticipate the unexpected. In case of missing an exam, there are NO makeups and NO extensions. In case of a documented emergency, an oral or written make-up exam will be arranged.

Grade Appeals

Grade disputes must first be addressed by discussing the situation with the instructor. If the dispute is not resolved with the instructor, the student may appeal to the department chair per the University Policy for Student Appeal Procedures on Grades.

Submitting Assignments

All assignments, unless otherwise announced, MUST be submitted to the designated area of Blackboard. Do not submit an assignment via email.

Communication with Instructors

This course uses discussion forums for general questions about the course. Prior to posting a question, please check the syllabus, announcements, and existing posts. If you do not find an answer, post your question. Also, you are strongly encouraged to respond to the questions of your classmates. Students may earn extra credit for participation productively in discussion forums.

Email questions of a personal nature to jeff.yarger@asu.edu. Be sure to include “BCH341 online” in the subject line. You can expect a response within 48 hours.

ASU email is an official means of communication among students, faculty, and staff. Students are expected to read and act upon email in a timely fashion. Students bear the responsibility of missed messages and should check their ASU-assigned email regularly. All instructor correspondence will be sent to your ASU email account and/or will use ASU Blackboard.

Computer & Software Requirements

This course requires a modern pc, mac, chrome or linux computer with Internet access and the following:

Web browsers (Chrome, Internet Explorer, Mozilla Firefox, or Safari)

Adobe Acrobat Reader (free)

Adobe Flash Player (free)

Microphone (optional but strongly encouraged) and speakers

Drop and Add Dates/Withdrawals

This course adheres to a compressed schedule and may be part of a sequenced program, therefore, there is a limited timeline to drop or add the course. Consult with your advisor and notify your instructor to add or drop this course. If you are considering a withdrawal, review the following ASU policies: Withdrawal from Classes,  Medical/Compassionate Withdrawal, and a Grade of Incomplete.

Syllabus Disclaimer

The syllabus is a statement of intent and serves as an implicit agreement between the instructor and the student. Every effort will be made to avoid changing the course schedule but the possibility exists that unforeseen events will make syllabus changes necessary. Please remember to check your ASU email and the course site often.

Accessibility Statement

In compliance with the Rehabilitation Act of 1973, Section 504, and the Americans with Disabilities Act as amended (ADAAA) of 2008, professional disability specialists and support staff at the Disability Resource Center (DRC) facilitate a comprehensive range of academic support services and accommodations for qualified students with disabilities.

Qualified students with disabilities may be eligible to receive academic support services and accommodations. Eligibility is based on qualifying disability documentation and assessment of individual need. Students who believe they have a current and essential need for disability accommodations are responsible for requesting accommodations and providing qualifying documentation to the DRC. Every effort is made to provide reasonable accommodations for qualified students with disabilities.

Qualified students who wish to request an accommodation for a disability should contact the DRC by going to https://eoss.asu.edu/drc, calling (480) 965-1234 or emailing DRC@asu.edu. To speak with a specific office, please use the following information:

ASU Online and Downtown Phoenix Campus   University Center Building, Suite 160 602-496-4321 (Voice)	Polytechnic Campus 480-727-1165 (Voice)
West Campus University Center Building (UCB), Room 130 602-543-8145 (Voice)	Tempe Campus 480-965-1234 (Voice)

Student Conduct & Academic Integrity

Academic honesty is expected of all students in all examinations, papers, laboratory work, academic transactions and records. The possible sanctions include, but are not limited to, appropriate grade penalties, course failure (indicated on the transcript as a grade of E), course failure due to academic dishonesty (indicated on the transcript as a grade of XE), loss of registration privileges, disqualification and dismissal. For more information, see http://provost.asu.edu/academicintegrity. Additionally, required behavior standards are listed in the Student Code of Conduct and Student Disciplinary Procedures, Computer, Internet, and Electronic Communications policy, and outlined by the Office of Student Rights & Responsibilities. Anyone in violation of these policies is subject to sanctions.

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.

Appropriate online behavior (also known as netiquette) is defined by the instructor and includes keeping course discussion posts focused on the assigned topics. Students must maintain a cordial atmosphere and use tact in expressing differences of opinion. Inappropriate discussion board posts may be deleted by the instructor.

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.

Prohibition of Commercial Note Taking Services

In accordance with ACD 304-06 Commercial Note Taking Services, written permission must be secured from the official instructor of the class in order to sell the instructor’s oral communication in the form of notes.  Notes must have the notetaker’s name as well as the instructor’s name, the course number, and the date.

Course Evaluation

Students are expected to complete the course evaluation. The feedback provides valuable information to the instructor and the college and is used to improve student learning. Students are notified when the online evaluation form is available.

Student Success Tips

This is an online course. To be successful:

• check the course announcements/website daily
• read and respond to course email messages as needed
• complete assignments by the due dates specified
• communicate regularly with your teaching assistant, instructor and peers
• create a study and/or assignment schedule to stay on track

Technical Support

This course uses Blackboard to deliver content. It can be accessed through MyASU at http://my.asu.edu or the Blackboard home page at https://myasucourses.asu.edu.  To monitor the status of campus networks and services, visit the System Health Portal at http://syshealth.asu.edu/. To contact the help desk call toll-free at 1-855-278-5080.

Title iX – Discrimination or Harrassment

As a mandated reporter, I (Professor Jeff Yarger) am obligated to report any information I become aware of regarding alleged acts of sexual discrimination, including sexual violence and dating violence.  ASU Counseling Services, https://eoss.asu.edu/counseling, is available if you wish discuss any concerns confidentially and privately.

Title IX is a federal law that provides that no person be excluded on the basis of sex from participation in, be denied benefits of, or be subjected to discrimination under any education program or activity.  Both Title IX and university policy make clear that sexual violence and harassment based on sex is prohibited.  An individual who believes they have been subjected to sexual violence or harassed on the basis of sex can seek support, including counseling and academic support, from the university.  If you or someone you know has been harassed on the basis of sex or sexually assaulted, you can find information and resources at https://sexualviolenceprevention.asu.edu/faqs.