CHE 316: Biochemistry II

Department of Chemistry and Physical Sciences

Quinnipiac University
Spring 2020

Instructor: Robert E. Collins, Ph.D.

Office: BC 122A
Email: Robert.Collins@quinnipiac.edu
Phone: (203) 582-6407
Office Hours*: https://quinnipiac.zoom.us/my/recollins
Monday 4:00-5:00 ; Tuesday 11:00-12:30 ; Thursday 2:00-3:00, or by appointment

*I encourage you to use my booking website: professorcollins.youcanbook.me as I might otherwise be engaged

with a student, research mentee or advisee. It is helpful if you include a brief note about what you need
assistance with. Meetings with study groups are encouraged.

Class meeting location and time:

Monday/Wednesday 5:00-6:15, Center for Comm.& Engineering 118

Course Description:
Students examine the key metabolic pathways of carbohydrates, fatty acids, amino acids and nucleotides with a
focus on the structural biology, thermodynamics and regulation of key enzymes. Nucleic acids, DNA and RNA
are investigated to understand the chemical principles that govern the flow of genetic information. Students
apply key concepts toward an understanding of the molecular basis of disease (e.g., type II diabetes/metabolic
syndrome).

Prerequisites: CHE 315 and CHE 315L (minimum grade of C).

Course Goals and Learning Objectives:

Upon completion of this course, students should be able to apply key chemical concepts (kinetics,
thermodynamics, bond types and energetics) to macromolecular systems (metabolism, transcriptional
regulation) and biological processes.

University Essential Learning Outcomes:

Quinnipiac graduates demonstrate a number of key outcomes essential to the life and practice of a responsible,
educated citizen, consciously and decisively. Graduates acquire these Essential Learning Outcomes (ELOs)
through a purposeful integration of the University Curriculum, requirements within one’s major, and co-
curricular experiences.

This course emphasizes the development of oral communication skills within your major field of study.

It requires the development of a number of important skills, and some are listed below:

Disciplinary Knowledge
Higher-Order Thinking
Creative Thinking
Inquiry and Analysis

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Required Textbook, Equipment, and Supplies:
Please bring a laptop and scientific calculator to each class session.
We will use open-source texts. Links to readings will be posted to Blackboard.

Class Attendance
This is an on-ground synchronous class. Students are expected to attend in-person each day. If you are ill or
have an excused absence and notify me in advance, I will allow attendance by Zoom, and/or provide class
recordings. I will take attendance regularly. Your advisor will be notified if you consistently miss class. You are
responsible for all announcements and material covered in class regardless.
Students are expected to take scheduled exams on the date/time as announced either in the syllabus and class.
If you have a university approved absence that you know will occur on the exam date (athletic competition,
religious observance, etc.) you must notify your instructor a minimum of one week in advance, provide the
associated documentation, and schedule a make-up date/time to take the exam.  
If you are ill on the day of an exam, you are required to send an email to me either before or within 24 hours of
the class meeting date/time and indicate the reason for your absence.  Any failure to do so will result in a zero
for the exam.
Class sessions may be recorded by instructors in whole or in part for use by enrolled students in this class,
including those who are unable to attend live. These recordings are the intellectual property of the instructors,
and they may not be shared or reproduced without the explicit, written consent of the faculty member. Further,
students may not share these sessions with those not in the class or upload or distribute them via or to any other
online environment. Doing so would be a breach of the Academic Integrity Policy and, in some cases, a
violation of the Family Educational Rights and Privacy Act (FERPA), a federal law governing privacy and
students’ academic records.

Suggested Learning process:

1) Before class: There is a readings and study guide folder on Blackboard. Read the assigned reading
before class, understand the key concepts, and come to class prepared to ask about material and
problems you haven’t mastered.
2) In-class: I use short lectures to clarify difficult points. In class exercises (paper discussions, group
problem solving, data interpretation) will serve to reinforce key concepts. I will periodically collect
and grade these assignments.
3) After Class: review. Make constant progress on class projects. Practice exam questions will be
posted.

Evaluation and Grading:

Midterm exam 15%
Final exam (comprehensive) 20%
Problem sets/other assignments 15%
Preparedness/ Class participation 10%
Class Project 1 (Drug design) 25%
Class Project 2 (Bioinformatics) 15%
Total 100%
Mid-term Exam: March 9th in class. It will emphasize key concepts and the application of the methods we
learn this semester to new problems. Practice problems will be posted to Blackboard.

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Final Exam: 6:00-8:00 PM on May 11th. As per Quinnipiac policy, a comprehensive two-hour final exam will
be given during the finals week and must be taken (i.e., will not be dropped). Our exam time is set by the
Registrar; you should plan accordingly. It will emphasize application of the methods we learn this semester to
new problems. Practice problems will be posted to Blackboard.
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Class Projects: You will use in-silico techniques to (1) redesign a drug and (2) to discover a new enzyme with
beneficial activities. These processes are used by pharma and biotech companies, as well as academic scientists.
You will write a formal report for each. Details and rubrics will be posted.
Participation: A variety of methods will be used for in-class work: homework discussion, group problem
solving and other active learning exercises. I will evaluate your preparedness and participation.

Grading Scale:
93 – 100 A 77 – 79 C+
90 – 92 A- 73 – 76 C
87 – 89 B+ 70 – 72 C-
83 – 86 B 60 – 69 D
80 – 82 B- 0 – 59 F

Academic Integrity:
Academic integrity is a core value of Quinnipiac University. QU courses follow the University Academic
Integrity Policy as found in the Quinnipiac University Catalog: Academic Integrity Policy.

As a member of the Quinnipiac University community, you are expected to understand and observe the
university policy. All students must adhere to the QU Academic Integrity Policy as found in the QU Student
Handbook. Refer to the policy for details. Failure to follow this policy could lead to an “F” in the course,
suspension, and even expulsion from the University. By taking the course and by attending Quinnipiac
University you agree to these conditions. Please see your research mentor at any time with questions.

Therefore, students are expected to be honest with the instructor in all conversations and discussions and to treat
them and their fellow students with respect. You are expected to do your own work, and you may never
plagiarize or cheat on tests or papers. Written assignments may be discussed generally with other students, but
all written work must be done individually. All work you submit must be completed by you for this specific
class. In all written work and exams, you may paraphrase or cite your class notes, but do not copy sentences or
fragments of sentences word for word from any textbook, journal, newspaper, magazine, book, or on-line
source. You are expected to properly acknowledge others’ work when you use it to inform your own work. I
will apply plagiarism-detecting software to written assignments. If you are unclear what constitutes plagiarism,
please discuss your concerns with me.

By taking the course and by attending Quinnipiac University, you agree to these conditions. The consequences
and procedures for academic misconduct are detailed in the Handbook. Please see me at any time with
questions.

Note regarding online study “resources”: Sites encouraging students to upload course materials are
proliferating. You should realize uploading course assignments that are the intellectual property, and often
copyrighted materials, of your instructor, other instructors or publishing companies could be subject to civil and
criminal penalties. Additionally, procuring unauthorized assistance and facilitating the academic misconduct of
others are specifically identified as misconduct in the Quinnipiac University Academic Integrity Policy.

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Classroom policies: Professional behavior is a requirement in this course. Students are expected to treat one
another and the professor with respect. Respect is conveyed in many forms, not all of which will be discussed
herein. We want to build a classroom climate that is comfortable for everyone. To do so, it is especially
important that we (1) display respect for all members of the classroom, including the professor and students; (2)
pay attention to and participate in all class sessions and activities- plan on staying the entire class session until
the class is released when coming to class; (3) avoid unnecessary disruption during class time (e.g., having
private conversations, reading non-course related materials, sleeping, doing work for other classes,
making/receiving cell phone calls, text messaging, instant messaging, using social media, etc.); and (4) avoid
racist, sexist, homophobic, or other negative language that may unnecessarily exclude members of our campus
and classroom. This is not an exhaustive list of behaviors; rather, they represent the minimal standards expected
in the classroom and profession. Cyber-bullying or cyber-harassment involves the posting of hate speech,
personal information, rumors, sexual remarks, or threats online. Cyber-bullying or cyber-harassment is not
tolerated at Quinnipiac University. Students who are concerned they may have been cyber-harassed should
contact the Dean of Students Office: 203-582-8753

Students Requesting Special Accommodations: QU is committed to creating a learning environment that

meets the needs of its diverse student body. If you anticipate or experience any barriers to learning in this
course, please feel welcome to discuss your concerns with the instructor. If you have a disability, or think you
may have a disability, plan to meet with the Office of Student Accessibility, to begin this conversation or to
request reasonable accommodations. Quinnipiac University complies with the Americans with Disabilities Act
and Section 504 of the Rehabilitation Act of 1973. Please contact the Office of Student Accessibility by
emailing access@qu.edu or by calling (203) 582–7600. If you have already been approved for accommodations
through the Office of Student Accessibility, please be sure to send approval to and meet with your instructor to
develop an implementation plan together.
Disabilities Policy

Title IX Policy: QU is dedicated to fostering a healthy and safe environment that is free from all forms of sex
discrimination and sexual misconduct. The University complies with Title IX of the Education Amendments of
1972. Title IX prohibits discrimination on the basis of sex in educational programs or activities that receive
federal financial assistance. If you believe that you have been subjected to discrimination on the basis of sex or
gender, you are encouraged to file a complaint with the University’s Title IX Coordinator, Dennis Kwarteng.
The Title IX Coordinator can be contacted by phone at (203) 582-7327, or by email at
dennis.kwarteng@qu.edu. Faculty members and other University staff are designated as “Responsible
Employees.” This means that faculty and staff are required to report any allegations of sexual misconduct
directly reported to us, or of which we are made aware, to the University’s Title IX coordinator or deputy
coordinator. On-campus resources are available that can provide confidentiality, sharing options and advice
without any obligation to inform other University staff members unless requested. Such on campus confidential
resources include Counseling Services, Student Health Services and/or Campus Ministry. Additionally,
community members can seek out assistance from an off-campus crisis center, which can maintain
confidentiality.

CARE Policy: Quinnipiac is dedicated to supporting our students through high-touch practices from CARE
(Community, Assessment, Response and Evaluation). The CARE team employs a caring, preventive, early
intervention approach with students who exhibit concerning or disruptive behaviors. The CARE team works to
promote student well-being and success in the context of community safety. CARE referrals are submitted by
faculty, staff, students, and community members. Referrals range from topics including helping a student during
difficult times such as the passing of a loved one; when a student needs support for their physical, emotional,
mental, spiritual, financial health; and/or when experiencing social challenges with roommates, friends, and/or
peers. More information about the CARE team, behaviors of concern, how to make a referral, and answers to
frequently asked questions can be found on the CARE page on MyQ. If you are concerned about a peer, or
yourself, please submit a referral CARE and Conduct Incident Reporting Form.
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COVID-19 Compliance Protocols
For the latest information, consult the Back to Bobcat Nation page:
https://www.qu.edu/back-to-bobcat-nation.html

CHE 316: Biochemistry II

Department of Chemistry and Physical Sciences
Quinnipiac University
Spring 2022

TENTATIVE Schedule
Changes will be announced in class and on Blackboard

Key Dates

Project 1 due: March 1st

Midterm Exam: In-class, March 9th
Spring Break: March 14, 2022 - March 19, 2022
Last day to withdraw with a grade of W: April 1, 2022
Project 2 due: April 25th
Final Exam: 6:00-8:00 PM on May 11th

Other assignments and deliverables will have their due dates posted to Blackboard.

The course is organized into 5 ~3 week modules.

Dates Topic Key Methods

1/24-2/9 Neurotransmitters/Pharmacology Structural Biology / ADME / In
silico drug development
2/14-3/2 Photosynthesis/Nitrogen Fixation Electrochemistry / Inorganic
and oxidoreductases biochemistry
3/21-3/30 Protein Evolution Bioinformatics/Homology
Modelling
4/4-4/14 Biofuels/Biotechnology Synthetic Biology Recombinant
protein expression
4/18-5/4 Histone Code Hypothesis Quantification of protein-
protein interactions
Quantitative analysis of
transcription / ChIP