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CHEM524: Biochemistry II (Spring 2018)

Course Specifics:

Instructor:          Dr. Jason C. Hurlbert
                          Office:  Sims 301B
                          Office hours:  MWF 1:00 - 2:00 PM and by appointment
                          Phone:  323-4928

Meeting Times: Mondays and Wednesday: 5:00 - 6:15 PM
Location: Sims 113C

Textbook: Fundamentals of Biochemistry, 4th edition by Voet, Voet and Prattt (required). The text may be rented, but if you are considering attending graduate or professional school after graduation, I would highly recommend purchasing and keeping the book.

Course Outline:

Biochemistry is the branch of science focused on studying the structure, function and interactions of the molecules found in living systems. Its very name tells you that it is a hybrid discipline incorporating biology, organic chemistry, physical chemistry and even physics into the study of the chemical reactions and interactions that allow life to exist. This course builds upon the vocabulary and concepts that were learned in the first course of the biochemistry series (CHEM523).

During the semester, we will cover:  1) The chemistries of the various enzyme-catalyzed reactions involved in cellular metabolism, 2) The chemistries of the Central Dogma of Molecular Biology, 3) Cellular pathways and reactions involved in the metabolism of glucose, 4) Oxidative phosphorylation, 5) Lipid metabolism and 6) Fatty acid biosynthesis.

A large portion of your grade in the course will be based upon your synthesis of information learned in this and in previous courses as you write a review article on a protein of your choosing.  For this review article, you will be expected to perform a complete literature search, perform a thorough phylogenetic analysis of your protein, completely describe the binding site(s) and reaction mechanism and elucidate the role of the protein in the physiology of the host organism.  Details for the protein assignment are found on the course website, as are the grading rubrics for the written and oral components of the assignment.

This is a 500 level course, which means that the concepts we will discuss are advanced and will require you to spend a lot of time and work outside of the classroom to fully understand and apply them. This class is meant to prepare students for admission to graduate, dental, medical or other professional schools and, as such, everyone taking it will be held to the highest possible standards.  Since this class is not required for participating students to earn a degree from the university, it is assumed that you are enrolled in the course because you want to take it and, more importantly, you want to use the information discussed in the next stage of you academic careers.  This means several things, but first and foremost:  you will be accountable for your actions in all aspects of the course.

Week Date Topic  

9 Jan

Course Introduction

Core Concept Review: Intermolecular forces, Amino Acids, Water, Protein Folding and Protein Dynamics

11 Jan

Core Concept Review: Substrate Binding and Enzymatic Catalysis


16 Jan

Martin Luther King, Jr Day - No Scheduled Class Meeting

18 Jan

Core Concept Review: Transcriptional Control


23 Jan

Enzymes: Oxidoreductases

25 Jan

Enzymes: Transferases and Hydrolases


30 Jan

Enzymes: Isomerases

1 Feb

Principles of Drug Design


6 Feb

Small Molecule Docking

8 Feb

Phylogenetic Analysis and Paleobiochemistry


13 Feb

Test 1

15 Feb

Chapter 14: Metabolism - Overview

20 Feb

Chapter 15: Glucose Catabolism

22 Feb


27 Feb

1 Mar

Test 2

6 Mar

Chapter 17: The Citric Acid Cycle

8 Mar

10 13 Mar - 17 Mar
Spring Break

20 Mar

Chapter 18: Electron transport and Oxidative Phosphorylation

22 Mar



27 Mar

29 Mar

Test 3


3 Apr

Chapter 16: Glycogen metabolism and Gluconeogenesis

5 Apr



10 Apr

Chapter 20: Lipid Metabolism

12 Apr


17 Apr

Chapter 20: Fatty acid Biosynthesis

19 Apr

16 24 Apr No Class Meeting
Final Paper Due in Course Dropbox folder at start of class
Final Exam: Saturday, 29 Aoril, 2016, 3:00 PM

Grading for the Course

In-class quizzes
Throughout the semster we will have a 10 minute quiz covering the highlights of the material from the previous week. These quizzes will be picked up promtply at 5:10, so if you show up late to class, you will have that much less time to complete the quiz.

Approximately every 2 weeks throughout the semester, students will complete a problem set due on the date specified on the course website.

Four tests will be administered during the semester.  Each exam will be worth 100 points.

Protein Project
In the first month of the semester, each student will choose a protein. Students will be responsible for working with this protein during the semester. As we learn different bioinformatic, computational and visualization techniques, students will apply them to help understand and explore their assigned protein. The grade for the protein project is derived from two unique components:

At the end of the semester, students will write a 10-page review article about their protein. This article will be due on the last day of the semester. Grading rubrics for the paper will be available on the course website.

Final Exam
A cumulative final exam will be given on the date and time specified by the University Final Exam schedule.

Extra Credit Opportunities
Throughout the semester you may be given several opportunities to earn extra credit points. These opportunities will be challenging and are meant to be extremely difficult. Failure to complete the assignment exactly as instructed will result in no points being awarded. Extra credit assignments are always non-negotiable:  You do the assignment completely, you do the assignment well and you do the assignment in the manner it was intended to be done or you do not get any bonus points.

Final Grade
Homework Assignments: = 6 x 50 points = 300 points
In class quizzes:  10 exams x 10 points = 100 points
Tests: 4 x 100 points = 400 points
Protein Assignment: 50 points
Final Exam: 150 points

Total Number of Points for Course: 1000 points

Grading Scale:

A: >93% of the total Points
A-: 90.0 - 92.9% of the total points
B+: 87 - 89.9% of the total Points
B: 83 - 86% of the total Points
B-: 80 - 82.9% of the total points
C+: 77 - 79.9% of the total Points
C: 70 - 76.9% of the total Points
D: 60 - 69.9% of the total Points
F: <60% of the total Points

Technology in the Classroom

No cellular phones may be used when class is meeting. Once class starts, all cellular telephones must be turned to silent mode for the duration of class. Should your cellular telephone ring while the class is meeting, you will be asked only once to silence it. A second violation of this policy will result in immediate removal from that class session. Anyone caught using these devices during class without prior permission will immediately be asked to leave the class. Anyone caught texting, using Facebook or other forms of social media during class will be immediately ejected from class. This policy is non-negotiable and will be enforced without exception. ANY and ALL violations of these rules will result in forfeiture of all earned bonus points and violators will also be ineligible for future extra credit opportunities.

Student Code of Conduct

As noted in the Student Conduct Code: “Responsibility for good conduct rests with students as adult individuals.” The policy on student academic misconduct is outlined in the “Student Conduct Code Academic Misconduct Policy” in the online Student Handbook.

Time Management and Your Role as a Student

As members of the Winthrop community of life-long learners, you are expected to treat your role as a student with the utmost respect and seriousness. Properly mangaging your time and effort is a big part of that and I urge you to begin working on assignments as early and often as possible. Not only will your life be a lot less stressful because you aren't trying to cram everything in at the last minute, but you can also identify things that you are having trouble understanding with enough time to ask me for help. If you know that you have a scheduling conflict with an assignment due in this course, please come talk to me about it as soon as possible. I will do everything I can to work with you, but I expect you to shoulder your responsibilities as part of the partnership.

Students with Disabilities

Students with Disabilities

Winthrop University is dedicated to providing access to education.  If you have a disability and require specific accommodations to complete this course, contact the Office of Disability Services (ODS) at 323-3290.  Once you have your official notice of accommodations from the Office of Disability Services, please inform me as early as possible in the semester.